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{"href": "https://publications-affiliated.scilifelab.se/account/arian.lundberg%40scilifelab.se.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/account/arian.lundberg%40scilifelab.se"}}, "email": "arian.lundberg@scilifelab.se", "name": "Arian Lundberg", "orcid": "0000-0002-6630-2787", "role": "curator", "status": "enabled", "login": "2026-09-17T08:55:26.199Z", "created": "2025-03-20T07:29:52.075Z", "modified": "2026-09-17T08:55:26.199Z"}, {"entity": "account", "iuid": "d43c3178d34e4f2eb4d55e4b9b6b7144", "timestamp": "2026-10-16T12:22:06.642Z", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/account/clemensw%40chalmers.se.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/account/clemensw%40chalmers.se"}}, "email": "clemensw@chalmers.se", "name": "Clemens Wittenbecher", "orcid": "0000-0001-7792-877X", "role": "curator", "status": "enabled", "login": "2025-11-28T07:15:18.925Z", "created": "2022-11-07T15:25:22.426Z", "modified": "2025-11-28T07:15:18.925Z"}, {"entity": "account", "iuid": "d5c7b132522e4bfba385982822c43477", "timestamp": "2026-10-16T12:22:06.642Z", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/account/fredrik.edfors%40scilifelab.se.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/account/fredrik.edfors%40scilifelab.se"}}, "email": "fredrik.edfors@scilifelab.se", "name": "Fredrik Edfors", "orcid": "", "role": "curator", "status": "enabled", "login": null, "created": "2022-11-07T15:26:37.289Z", "modified": "2022-11-07T15:26:37.306Z"}, {"entity": "account", "iuid": "df19b491db304ca1a5570f77986eca44", "timestamp": "2026-10-16T12:22:06.642Z", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/account/nicholas.pearce%40liu.se.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/account/nicholas.pearce%40liu.se"}}, "email": "nicholas.pearce@liu.se", "name": "Nicholas Pearce", "orcid": "", "role": "curator", "status": "disabled", "login": "2022-12-05T18:55:54.441Z", "created": "2022-11-07T15:28:38.705Z", "modified": "2026-09-22T10:48:35.677Z"}, {"entity": "account", "iuid": "f8ad39af2bcc490081b2ce813e28e68e", "timestamp": "2026-10-16T12:22:06.642Z", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/account/bjorn.forsberg%40liu.se.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/account/bjorn.forsberg%40liu.se"}}, "email": "bjorn.forsberg@liu.se", "name": "Bj\u00f6rn Forsberg", "orcid": "0000-0002-6247-4063", "role": "curator", "status": "enabled", "login": "2024-10-17T11:16:18.341Z", "created": "2024-10-17T11:15:32.999Z", "modified": "2025-09-29T13:35:12.624Z"}], "publications_count": 1013, "publications": [{"entity": "publication", "iuid": "cc5365ff98814141a42cbc2c55c1b6ff", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/cc5365ff98814141a42cbc2c55c1b6ff.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/cc5365ff98814141a42cbc2c55c1b6ff"}}, "title": "A novel multiomics machine learning signature identifies rapid progression in clinically low risk prostate cancer", "authors": [{"family": "Rafeletou", "given": "Alexandra", "initials": "A"}, {"family": "Fathi", "given": "Faezeh", "initials": "F"}, {"family": "Kise\u013cova", "given": "Tatjana", "initials": "T"}, {"family": "Taheri", "given": "Golnaz", "initials": "G", "orcid": "0000-0002-2741-0355", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/014c217121d346b2b371bbc1c2fede57.json"}}, {"family": "Lundberg", "given": "Arian", "initials": "A", "orcid": "0000-0002-6630-2787", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/baa2c7c8963840bfb6a22d7c5cfe35f9.json"}}], "type": "journal-article", "published": "2026-09-14", "journal": {"title": "NPJ Digit Med", "issn": "2398-6352", "issn-l": null, "volume": "9", "issue": "1", "pages": null}, "abstract": "Risk stratification in primary prostate cancer remains heavily reliant on clinicopathological criteria that frequently miss the heterogeneity underlying early aggressive disease. We present a novel machine learning non-linear prognostic framework encoding somatic copy-number alterations and biological information associated with gene products, along with an integrative multi-omics approach including epigenomics and transcriptomics into a patient-specific biological network. Applied to the TCGA-PRAD (n = 498), our weighted graph-based feature selection and LASSO-Cox model identified ZNF268 as a master regulator gene, in which the hypermethylation of its promoter region is linked to a distinct oncogenic transition exclusive to Low/Intermediate-risk disease. Post-hoc analysis of Low-ZNF268 tumors showed a distinct somatic landscape enriched for driver mutations and predicted sensitivity to MAPK, ATR, and PI3K/mTOR inhibitors, providing potential therapeutic vulnerabilities alongside the prognostic signal. Topological network analysis further revealed that ZNF268 loss impacts a co-expression rewiring gene network, quantified as a Rewiring Score: associated with Progression-Free Survival in the TCGA-PRAD (HR: 2.79, 95% CI: 1.36-5.71, p = 0.0049) and Biochemical Recurrence in two external cohorts. By capturing tumors at an active molecular transition state preceding systemic progression, this framework offers a prognostic tool to identify biologically aggressive prostate cancer disease within patients currently undertreated by standard risk criteria.", "doi": "10.1038/s41746-026-03254-5", "pmid": "42736338", "labels": {"Arian Lundberg": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC13575102"}, {"db": "pii", "key": "10.1038/s41746-026-03254-5"}], "notes": [], "created": "2026-09-17T08:55:54.574Z", "modified": "2026-10-07T06:26:29.703Z"}, {"entity": "publication", "iuid": "b18a8d3139574233b6caaae6a511053a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b18a8d3139574233b6caaae6a511053a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b18a8d3139574233b6caaae6a511053a"}}, "title": "Biologically informed neural network models are robust to spurious interactions via self-pruning.", "authors": [{"family": "Nordenstorm", "given": "Olof", "initials": "O"}, {"family": "Baghdassarian", "given": "Hratch", "initials": "H"}, {"family": "Xu", "given": "Xuechun", "initials": "X", "orcid": "0000-0003-1850-0946", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2d02b83768c24f5396b85938a9590b7f.json"}}, {"family": "Lauffenburger", "given": "Douglas A", "initials": "DA", "orcid": "0000-0002-0050-989X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ac0a09cb7c9c49de95b660756a4e5464.json"}}, {"family": "Nilsson", "given": "Avlant", "initials": "A", "orcid": "0000-0002-9476-4516", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f2e21dbc1c624f6a841c59e959e948e4.json"}}], "type": "journal article", "published": "2026-08-03", "journal": {"title": "Bioinformatics", "issn": "1367-4811", "volume": "42", "issue": "8", "issn-l": "1367-4803"}, "abstract": "Computational models of cellular networks hold promise to uncover disease mechanisms and guide therapeutic strategies. Biology-informed neural networks (BINNs) is an emerging approach to create such models by combining the predictive power of deep learning with prior knowledge, a vital aspect of biological research. The architectures of BINN's enforces a network structure from which mechanism can ideally be inferred. However, a key challenge is to evaluate the reliability of these models, as cells are inherently complex, involving intricate and sometimes unknown interactions. Currently, analysis mainly focuses on selected pathways rather than a more comprehensive perspective.\n\nIn this work we demonstrate an alternative holistic approach: we measure to which extent purposefully introduced spurious interactions are down-weighted by a BINN during training (self-pruning). The metric suggested RRA (Relative Residual Area) allows for direct distribution comparison with perfect self-pruning achieved at zero and a failure to self-prune if above one. To enable rapid testing, we updated LEMBAS (Large-scale knowledge-EMBedded Artificial Signaling-networks), our recurrent neural network framework for intracellular signaling dynamics, with full GPU acceleration. Our implementation achieves a > 7-fold speedup compared to the original while preserving predictive accuracy. We evaluated self-pruning in 3 different datasets and found that when spurious interactions are introduced at random, the model prunes these to a larger extent than those from the prior knowledge network (PKN), provided the model is regularized with a sufficiently large L2 norm. This suggests that BINNs can be robust to uncertainty in the PKN.\n\nOur implementation of LEMBAS is freely available under a MIT license at https://github.com/AvlantNilssonLab/LEMBAS_GPU. The models and results to generate the figures can be downloaded through https://zenodo.org/records/17425598.", "doi": "10.1093/bioinformatics/btag556", "pmid": "42502984", "labels": {"Avlant Nilsson": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC13457084"}, {"db": "pii", "key": "8742075"}], "notes": [], "created": "2026-08-17T11:11:10.279Z", "modified": "2026-08-17T11:13:01.812Z"}, {"entity": "publication", "iuid": "5427edeae7e84dbe87a61cb6fd64fb4d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5427edeae7e84dbe87a61cb6fd64fb4d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5427edeae7e84dbe87a61cb6fd64fb4d"}}, "title": "AllTheBacteria: a community resource empowers biology and discovers novel peptide antibiotics.", "authors": [{"family": "Hunt", "given": "Martin", "initials": "M", "orcid": "0000-0002-8060-4335", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/72842646f10542de943a31e46b93bbd1.json"}}, {"family": "Torres", "given": "Marcelo D T", "initials": "MDT"}, {"family": "Alikhan", "given": "Nabil-Fareed", "initials": "NF", "orcid": "0000-0002-1243-0767", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ede08d0818d74854adf8987007f128d3.json"}}, {"family": "Anderson", "given": "Daniel", "initials": "D", "orcid": "0000-0003-4422-9520", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c82d2c74338b4ee1b8b96bbc44e14110.json"}}, {"family": "Andreani", "given": "Maria Luiza", "initials": "ML", "orcid": "0000-0002-1308-865X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e44d67cad3c64f46996131dd643a754d.json"}}, {"family": "Blom", "given": "Josefin", "initials": "J", "orcid": "0009-0000-9910-7374", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/361785c07fb04b5497ce209141d2c337.json"}}, {"family": "Bouras", "given": "George", "initials": "G", "orcid": "0000-0002-5885-4186", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5cc91f0fe9424fe8bc108d997eaeb269.json"}}, {"family": "Brinkman", "given": "Fiona S L", "initials": "FSL", "orcid": "0000-0002-0584-4099", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/64718ed4c3554342a75a8aa510e9db8a.json"}}, {"family": "Carroll", "given": "Laura M", "initials": "LM", "orcid": "0000-0002-3677-0192", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02112eccb0664819af916a3c3dc79daa.json"}}, {"family": "Croxen", "given": "Matthew A", "initials": "MA", "orcid": "0000-0002-9564-7952", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/922716b7aca5471e8961679ae2090cda.json"}}, {"family": "Floto", "given": "R Andres", "initials": "RA", "orcid": "0000-0002-2188-5659", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f02671adb32947bfac84bc6612b5bad2.json"}}, {"family": "Hall", "given": "Michael B", "initials": "MB", "orcid": "0000-0003-3683-6208", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/39d8e11a39f54685bb73e8af739c1a6e.json"}}, {"family": "Hawkey", "given": "Jane", "initials": "J"}, {"family": "Horsfield", "given": "Samuel T", "initials": "ST", "orcid": "0000-0002-3859-4073", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b7d5c04b6b25449fa8ade3cee3dd8bb5.json"}}, {"family": "Jia", "given": "Baofeng", "initials": "B", "orcid": "0000-0002-4735-4709", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/733048a036094f31888c4bf56fc33737.json"}}, {"family": "Lacey", "given": "Jake A", "initials": "JA"}, {"family": "Lee", "given": "Hyun-Su", "initials": "HS"}, {"family": "Lima", "given": "Leandro", "initials": "L"}, {"family": "MacAlasdair", "given": "Neil", "initials": "N"}, {"family": "Mallawaarachchi", "given": "Sudaraka", "initials": "S", "orcid": "0000-0001-8899-3323", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a5f1f09ecc474ab98b8d68714086b623.json"}}, {"family": "Matlock", "given": "William", "initials": "W", "orcid": "0000-0001-5608-0423", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d080532109064f0a9540ea89396f32b7.json"}}, {"family": "Moustafa", "given": "Ahmed M", "initials": "AM", "orcid": "0000-0002-9949-6936", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/abddffbcc13b4551917cf44a3c575a56.json"}}, {"family": "Petit", "given": "Robert", "initials": "R"}, {"family": "Ramnath", "given": "Vignesh", "initials": "V", "orcid": "0009-0005-8315-5343", "researcher": {"href": 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"https://publications-affiliated.scilifelab.se/researcher/df167518f3df4d3187a779d777ec561a.json"}}, {"family": "Seemann", "given": "Torsten", "initials": "T", "orcid": "0000-0001-6046-610X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/425664c47a6b42028fd2ff409dc357f2.json"}}, {"family": "Shaw", "given": "Liam P", "initials": "LP"}, {"family": "Shen", "given": "Wei", "initials": "W", "orcid": "0000-0002-8099-8258", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f31dc07519254f8b8cbac8b5e3b1c67e.json"}}, {"family": "Thomson", "given": "Nicholas", "initials": "N"}, {"family": "Tonkin-Hill", "given": "Gerry", "initials": "G", "orcid": "0000-0003-4397-2224", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/026c81af4e234af1af1ac54770446a0a.json"}}, {"family": "Toussaint", "given": "Jackie", "initials": "J", "orcid": "0000-0002-3305-2320", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b9369549140746199a653b7f178ae325.json"}}, {"family": "Viet", "given": "Thanh Le", "initials": "TL", "orcid": "0000-0002-2106-8130", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2dc6acbcd7b34953ac0c6daf88e22316.json"}}, {"family": "von Wachsmann", "given": "Johanna", "initials": "J"}, {"family": "Wan", "given": "Fangping", "initials": "F"}, {"family": "Weimann", "given": "Aaron", "initials": "A", "orcid": "0000-0003-4597-2471", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/89cdef1c076b49cab71c89ef5c279cb2.json"}}, {"family": "Wheatley", "given": "Rachel M", "initials": "RM", "orcid": "0000-0003-1212-2286", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b2c3f58742064158a2296769222d2837.json"}}, {"family": "Wiatrak", "given": "Maciej", "initials": "M"}, {"family": "Xie", "given": "Ouli", "initials": "O", "orcid": "0000-0002-5032-1932", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b04d0924e7504edebe68fcd92cb201e6.json"}}, {"family": "de la Fuente-Nunez", "given": "Cesar", "initials": "C"}, {"family": "Lees", "given": "John A", "initials": "JA", "orcid": "0000-0001-5360-1254", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ea89090f7dbe4b10a007fe8bde5f6a3e.json"}}, {"family": "Iqbal", "given": "Zamin", "initials": "Z", "orcid": "0000-0001-8466-7547", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/346273c9c94f4d27b5ba17e608600148.json"}}], "type": "journal article", "published": "2026-07-07", "journal": {"title": "bioRxiv", "issn": "2692-8205", "issn-l": null}, "abstract": "Public microbial genomes encode an immense record of biological diversity, evolution and molecular function, but much of this information remains difficult to reuse because raw sequencing data are not uniformly assembled, quality controlled, annotated or searchable at scale. Here we present AllTheBacteria, an open, community-built resource that transforms public bacterial short-read whole-genome sequencing reads into a uniformly processed discovery platform. The current analysed release contains 2,440,377 high-quality bacterial and archaeal genomes from 11,273 species, together with standardized taxonomic assignments, genome annotations, antimicrobial resistance calls, antiphage-defence annotations, protein structure predictions and AI-ready sequence tables. We show that this infrastructure enables applications that would otherwise be impractical, from global sequence search and outbreak contextualization to pangenome method development, antimicrobial resistance reservoir mapping and antiphage-defence ecology. As a stringent experimental demonstration, we mined 3,919,096 encrypted peptide fragments from AllTheBacteria proteomes using our deep learning model APEX 1.1, identifying 1,867 candidates with predicted antimicrobial activity. We synthesized 24 representative peptides and tested them against 20 clinically relevant bacterial strains, including antibiotic-resistant pathogens. Multiple peptides showed low-micromolar activity, membrane-responsive conformational transitions and selective envelope perturbation. A lead molecule, ATB20, reduced Acinetobacter baumannii burden in a murine skin abscess model with efficacy comparable to polymyxin B and no overt toxicity. Together, these results establish AllTheBacteria as both a foundational community resource for microbiology and a renewable engine for AI-guided antimicrobial discovery.", "doi": "10.1101/2024.03.08.584059", "pmid": "42465405", "labels": {"Laura Carroll": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC13370402"}, {"db": "pii", "key": "2024.03.08.584059"}], "notes": [], "created": "2026-09-23T13:41:39.749Z", "modified": "2026-09-23T13:41:40.812Z"}, {"entity": "publication", "iuid": "97f780e691d94d8ba772515784f4d06e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/97f780e691d94d8ba772515784f4d06e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/97f780e691d94d8ba772515784f4d06e"}}, "title": "Clonal haematopoiesis and risk of incident rheumatoid arthritis: results from the UK Biobank.", "authors": [{"family": "Cui", "given": "Jing", "initials": "J"}, {"family": "Yu", "given": "Zhi", "initials": "Z"}, {"family": "Oakes", "given": "Emily G", "initials": "EG"}, {"family": "Truong", "given": "Buu", "initials": "B"}, {"family": "Uddin", "given": "Mesbah", "initials": "M"}, {"family": "Bick", "given": "Alexander", "initials": "A"}, {"family": "Niroula", "given": "Abhishek", "initials": "A"}, {"family": "Solomon", "given": "Daniel H", "initials": "DH"}, {"family": "Natarajan", "given": "Pradeep", "initials": "P"}, {"family": "Costenbader", "given": "Karen H", "initials": "KH"}], "type": "journal article", "published": "2026-07-00", "journal": {"title": "Clin. Exp. Rheumatol.", "issn": "0392-856X", "volume": "44", "issue": "7", "pages": "1403-1409", "issn-l": null}, "abstract": "Clonal haematopoiesis of indeterminate potential (CH), somatic genetic mutations conferring stem cells selective advantage, are associated with increased inflammatory cytokine production, cardiovascular disease (CVD), and malignancy. We investigated whether CH was related to risk of rheumatoid arthritis (RA), an inflammatory autoimmune disease.\n\nWithin the UK Biobank, we studied 186,577 unrelated individuals with baseline data collection, genome-wide genotyping, whole exome sequencing (WES) read for CHIP, and linked general practice (GP) data for identification of incident RA in follow-up. We excluded those with prevalent RA or taking RA medications at baseline. We tested for associations between variant allele fraction (VAF) >2% and >10% for the 8 most common CHIP mutations in the general population, and incident RA, identified by billing code algorithms. Cox regression models estimated hazard ratios (HR, 95% confidence interval) for incident RA.\n\n594 participants developed incident RA over median follow-up 7.1 years (IQR 6.4-8.0); median time to RA was 3.9 years (IQR 2.0-5.6). Incident RA cases were slightly older at enrolment, more likely to be female, have smoked, have higher body mass index (BMI), and have prevalent CVD, and hypercholesterolaemia at baseline. However, there was no difference in the presence of CHIP mutations at baseline; 6.3% vs. 6.4% of those who did and did not develop incident RA in follow-up had any CHIP mutation at >2% VAF.\n\nCommon CHIP mutations, including TET2, TP53, and SF3B1 mutations, were not associated with risk of incident RA when restricted to those with most complete general outpatient and hospital record follow-up in the UK Biobank.", "doi": "10.55563/clinexprheumatol/23hcbl", "pmid": "41779596", "labels": {"Abhishek Niroula": "", "DDLS Fellow": ""}, "xrefs": [{"db": "mid", "key": "NIHMS2134214"}, {"db": "pmc", "key": "PMC12962563"}, {"db": "pii", "key": "23086"}], "notes": [], "created": "2026-10-01T08:37:02.590Z", "modified": "2026-10-01T08:37:02.630Z"}, {"entity": "publication", "iuid": "263f70dfd2e941b4b0f072b5f9fe5fae", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/263f70dfd2e941b4b0f072b5f9fe5fae.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/263f70dfd2e941b4b0f072b5f9fe5fae"}}, "title": "Seeking knowledge or efficiency: Profiling students\u2019 AI-use through survey-based latent class analysis", "authors": [{"family": "Hugerth", "given": "Mattias W", "initials": "MW", "orcid": "0009-0006-2406-5214", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eb42b13600614f78bcf7fad7734277bc.json"}}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW", "orcid": "0000-0001-5432-1764", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/246ed7b405dd4c3f9ec5e7ff9f1d3ade.json"}}], "type": "journal-article", "published": "2026-06-00", "journal": {"title": "Computers and Education: Artificial Intelligence", "issn": "2666-920X", "volume": "10", "pages": "100531", "issn-l": null}, "abstract": null, "doi": "10.1016/j.caeai.2025.100531", "pmid": null, "labels": {"DDLS Fellow": "", "Luisa Hugerth": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T06:49:34.208Z", "modified": "2026-09-24T18:34:22.770Z"}, {"entity": "publication", "iuid": "22f6e10d4d60441a86a092b4ca737121", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/22f6e10d4d60441a86a092b4ca737121.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/22f6e10d4d60441a86a092b4ca737121"}}, "title": "Convergent evolution of complex structural variants drives therapy resistance in metastatic prostate cancer", "authors": [{"family": "Moreno-Rodriguez", "given": "Thaidy", "initials": "T", "orcid": "0000-0003-3588-3889", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/be9adfae1d354f85a76d66de8bc08cba.json"}}, {"family": "Zhang", "given": "Meng", "initials": "M"}, {"family": "Lundberg", "given": "Arian", "initials": "A", "orcid": "0000-0002-6630-2787", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/baa2c7c8963840bfb6a22d7c5cfe35f9.json"}}, {"family": "Shrestha", "given": "Raunak", "initials": "R", "orcid": "0000-0002-1144-1413", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1ee8056667cd46ecbec79e2789ae8029.json"}}, {"family": "Sj\u00f6str\u00f6m", "given": "Martin", "initials": "M", "orcid": "0000-0002-2629-9966", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b42d7aeedc844018bbe28980b73cb6c6.json"}}, {"family": "Pasam", "given": "Anupama", "initials": "A"}, {"family": "Chan", "given": "Joanna", "initials": "J"}, {"family": "Devereux", "given": "Lisa", "initials": "L"}, {"family": "Foye", "given": "Adam", "initials": "A", "orcid": "0000-0002-9910-9836", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/74c8c402b4a243ab95b9d20ecc43d4b9.json"}}, {"family": "Zhu", "given": "Xiaolin", "initials": "X", "orcid": "0000-0002-3221-595X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/30d1c66f02ef4b5abc414a110705ccf9.json"}}, {"family": "Weinstein", "given": "Alana S", "initials": "AS", "orcid": "0000-0002-1563-9072", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e16ba4d459704a96adc34a85197bab05.json"}}, {"family": "Trigos", "given": "Anna S", "initials": "AS"}, {"family": "Wyatt", "given": "Alexander W", "initials": "AW", "orcid": "0000-0003-2399-0329", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/41e8ef800a344c68be341f0691438260.json"}}, {"family": "Alumkal", "given": "Joshi J", "initials": "JJ", "orcid": "0000-0003-1278-0166", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/92169d39d28f4819959b032eff1b1b80.json"}}, {"family": "Small", "given": "Eric J", "initials": "EJ", "orcid": "0000-0003-3191-6268", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a5a6d3bacede42059d6bf0f2cbfe0fec.json"}}, {"family": "Aggarwal", "given": "Rahul", "initials": "R", "orcid": "0000-0001-7003-7982", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dc6eb510bedd42bbb6f57e03e724efba.json"}}, {"family": "Dehm", "given": "Scott M", "initials": "SM", "orcid": "0000-0002-7827-5579", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eb947d721b424bb190ddf41a808a2cb0.json"}}, {"family": "Bootsma", "given": "Matthew L", "initials": "ML"}, {"family": "Zhao", "given": "Shuang G", "initials": "SG", "orcid": "0000-0002-9166-6507", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c7d9e7e456be4376adb63a3e5ab895a7.json"}}, {"family": "Lupien", "given": "Mathieu", "initials": "M", "orcid": "0000-0003-0929-9478", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1967a3e4d1ff43998c93ea10d874cd01.json"}}, {"family": "Feng", "given": "Felix Y", "initials": "FY", "orcid": "0000-0002-0963-7687", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c5af5c0e774941ac97890f17640a339e.json"}}, {"family": "Sandhu", "given": "Shahneen", "initials": "S"}, {"family": "Quigley", "given": "David A", "initials": "DA", "orcid": "0000-0002-4726-1473", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a7672a24a905407c8b5f9d1e28deea02.json"}}], "type": "journal-article", "published": "2026-04-15", "journal": {"title": "Genome Biol.", "issn": "1474-760X", "issn-l": "1474-7596", "volume": "27", "issue": "1", "pages": null}, "abstract": "Targeted therapy prolongs the lives of men with metastatic castration-resistant prostate cancer (mCRPC) but mCRPC is ultimately lethal. DNA copy gains that amplify the Androgen Receptor (AR) gene locus are a key driver of resistance to targeted therapy in mCRPC. Our group has recently shown that extra-chromosomal DNA (ecDNA) frequently drives this amplification. We hypothesized that ecDNA and other complex structural variants (cSVs) also affect other established drivers of therapy resistance in mCRPC and continue to evolve over time. To test this hypothesis, we reconstructed cSV profiles in 193 mCRPC tumors using whole genome and transcriptome sequencing, with matched Hi-C data for 77 tumors.\n\nWe identify ecDNA in more than half of mCRPC biopsies and show it frequently amplifies driver genes such as AR and MYC and their non-coding enhancers. The presence of ecDNA is significantly associated with whole genome doubling, chromothripsis, and inactivating TP53 alterations. Deep sequencing analysis of 53 rapid autopsy samples shows cSVs amplifying AR can arise independently within distinct tumors in a single patient. Phylogenetic analysis of tumor evolution implicates this cSV as an early event during metastatic spread. Additionally, a paired analysis of mCRPC samples as patients developed resistance to AR pathway inhibitor (ARPI) therapy demonstrates cSVs evolve in response to ARPI and can be detected in both tumor tissue and circulating tumor DNA.\n\nWe conclude that cSVs, particularly ecDNA, are a pervasive contributor to intra-patient heterogeneity in late-stage mCRPC and a key driver of targeted therapy resistance.", "doi": "10.1186/s13059-026-04074-2", "pmid": "41987223", "labels": {"DDLS Fellow": null, "Arian Lundberg": null}, "xrefs": [{"db": "pmc", "key": "PMC13191960"}, {"db": "pii", "key": "10.1186/s13059-026-04074-2"}], "notes": [], "created": "2026-04-15T19:30:46.855Z", "modified": "2026-07-06T20:08:37.710Z"}, {"entity": "publication", "iuid": "cb64d786281d480d984052947db110c2", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/cb64d786281d480d984052947db110c2.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/cb64d786281d480d984052947db110c2"}}, "title": "Androgen receptor splice variant 7 expression levels distinguish AR-mutated from nonmutated metastatic castration-resistant prostate cancers", "authors": [{"family": "Paschalis", "given": "Alec", "initials": "A", "orcid": "0000-0001-9566-5096", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/de1cf8539acd4ec3a8cad39b966ccaa1.json"}}, {"family": "Figueiredo", "given": "Ines", "initials": "I"}, {"family": "Bogdan", "given": "Denisa", "initials": "D", "orcid": "0000-0002-3017-4832", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/960fd8ea3ce143559ebaff1149a59ea3.json"}}, {"family": "Lundberg", "given": "Arian", "initials": "A", "orcid": "0000-0002-6630-2787", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/baa2c7c8963840bfb6a22d7c5cfe35f9.json"}}, {"family": "Santos", "given": "Rita", "initials": "R"}, {"family": "Gurel", "given": "Bora", "initials": "B", "orcid": "0000-0002-5018-8078", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c0ed82612d614c16b45a528515cfba94.json"}}, {"family": "Taha", "given": "Tarek", "initials": "T"}, {"family": "Longoria", "given": "Ossian", "initials": "O"}, {"family": "Ferreira", "given": "Ana", "initials": "A"}, {"family": "Bertan", "given": "Claudia", "initials": "C"}, {"family": "Brittain", "given": "Nicholas", "initials": "N"}, {"family": "Nelson", "given": "Ryan", "initials": "R"}, {"family": "Walker", "given": "Laura", "initials": "L"}, {"family": "Neeb", "given": "Antje", "initials": "A", "orcid": "0000-0002-6516-2938", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6529e261d8be4c33878b9cf8d399632d.json"}}, {"family": "Welti", "given": "Jonathan", "initials": "J"}, {"family": "Yuan", "given": "Wei", "initials": "W"}, {"family": "Mitsopoulos", "given": "Costas", "initials": "C"}, {"family": "Plymate", "given": "Stephen R", "initials": "SR"}, {"family": "Haffner", "given": "Michael C", "initials": "MC", "orcid": "0000-0003-0809-6425", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cce395fe9a8b4fcdaec08d5d1cb37dde.json"}}, {"family": "Sowalsky", "given": "Adam G", "initials": "AG", "orcid": "0000-0003-2760-1853", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3692960b43fa4971b3b05958abeb12ce.json"}}, {"family": "Carreira", "given": "Suzanne", "initials": "S", "orcid": "0000-0002-5077-5379", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9a1f9e675b844e93928caec267794b80.json"}}, {"family": "Sharp", "given": "Adam", "initials": "A", "orcid": "0000-0002-3740-1612", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/25a4df1796a54c66ace14e632a239cd7.json"}}, {"family": "Gaughan", "given": "Luke", "initials": "L"}, {"family": "de Bono", "given": "Johann", "initials": "J", "orcid": "0000-0002-2034-595X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/22ac727724ef47b591c0f0bc2285adcc.json"}}], "type": "journal-article", "published": "2026-04-01", "journal": {"title": "J. Clin. Invest.", "issn": "1558-8238", "issn-l": "0021-9738", "volume": "136", "issue": "7", "pages": null}, "abstract": "New androgen receptor (AR) pathway inhibitors (ARPIs) in clinical development, including AR degraders and CYP11A inhibitors, largely target ligand-dependent AR activation and have reported antitumor activity in metastatic castration-resistant prostate cancer (mCRPC) resistant to established ARPIs, predominately against tumors with AR mutations. We hypothesized that AR-mutated mCRPC exhibits lower AR splice variant 7 (AR-V7) expression and remains full-length-AR (FL-AR) driven, explaining, in part, the antitumor activity of these AR ligand-binding domain (LBD) targeting drugs. The data herein demonstrate that mCRPC tissue biopsies with detectable AR mutations express significantly lower levels of AR-V7 protein and associate with better overall survival and enhanced sensitivity to ARPIs. This is independent of differences in the total number of global splicing events but may be related to differences in splicing factor expression between AR-mutated and nonmutated mCRPC. In conclusion, AR-mutated mCRPC frequently exhibits low AR-V7 expression, arguably explaining the enhanced sensitivity to ARPIs observed in these cancers. Consequently, AR mutation status may serve as a biomarker to predict response to AR-directed therapies.", "doi": "10.1172/jci198193", "pmid": "41919503", "labels": {"DDLS Fellow": null, "Arian Lundberg": null}, "xrefs": [{"db": "pmc", "key": "PMC13038193"}, {"db": "pii", "key": "198193"}], "notes": "Authorship note: AP, IF, DB, and AL are co\u2013first authors.", "created": "2026-04-02T07:53:43.865Z", "modified": "2026-07-10T08:28:48.410Z"}, {"entity": "publication", "iuid": "4fb1dd6f5f864787baae2144e261cca4", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4fb1dd6f5f864787baae2144e261cca4.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4fb1dd6f5f864787baae2144e261cca4"}}, "title": "A tissue-specific atlas of protein-protein associations enables prioritization of candidate disease genes.", "authors": [{"family": "Laman Trip", "given": "Diederik S", "initials": "DS", "orcid": "0000-0001-6635-0626", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a30f1c008f82468c8ae1d8964d997067.json"}}, {"family": "van Oostrum", "given": "Marc", "initials": "M", "orcid": "0000-0001-8747-9787", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/141897b2c0e748a9abb86cdea8bd8614.json"}}, {"family": "Memon", "given": "Danish", "initials": "D"}, {"family": "Frommelt", "given": "Fabian", "initials": "F", "orcid": "0000-0003-3666-8005", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e71a93da1624a17bcbace26ba50c5a5.json"}}, {"family": "Baptista", "given": "Delora", "initials": "D"}, {"family": "Panneerselvam", "given": "Kalpana", "initials": "K", "orcid": "0000-0003-2534-198X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e2cfb623f9d74273a76b9d5ddc894129.json"}}, {"family": "Bradley", "given": "Glyn", "initials": "G"}, {"family": "Licata", "given": "Luana", "initials": "L", "orcid": "0000-0001-5084-9000", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dbfb64fa4d6a4c61b68d808a13e173b7.json"}}, {"family": "Hermjakob", "given": "Henning", "initials": "H", "orcid": "0000-0001-8479-0262", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7ef7fa5ba29447fba798a69b305c0228.json"}}, {"family": "Orchard", "given": "Sandra", "initials": "S", "orcid": "0000-0002-8878-3972", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/869478a873ea4465ab43ecef5aee865c.json"}}, {"family": "Trynka", "given": "Gosia", "initials": "G", "orcid": "0000-0002-6955-9529", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/22558d9cbf844bf6bd0063c2dde6f513.json"}}, {"family": "McDonagh", "given": "Ellen M", "initials": "EM"}, {"family": "Fossati", "given": "Andrea", "initials": "A"}, {"family": "Aebersold", "given": "Ruedi", "initials": "R", "orcid": "0000-0002-9576-3267", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4aa50db862e94831b8cac04c4426daf1.json"}}, {"family": "Gstaiger", "given": "Matthias", "initials": "M", "orcid": "0000-0002-3245-3253", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8370f12358274bb2a5a4cd524ae4f465.json"}}, {"family": "Wollscheid", "given": "Bernd", "initials": "B"}, {"family": "Beltrao", "given": "Pedro", "initials": "P", "orcid": "0000-0002-2724-7703", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/952eba119d2e4d4b89e14b294c5c6885.json"}}], "type": "journal article", "published": "2026-04-00", "journal": {"title": "Nat. Biotechnol.", "issn": "1546-1696", "volume": "44", "issue": "4", "pages": "654-667", "issn-l": "1087-0156"}, "abstract": "Despite progress in mapping protein-protein interactions, their tissue specificity is understudied. Here, given that protein coabundance is predictive of functional association, we compiled and analyzed protein abundance data of 7,811 proteomic samples from 11 human tissues to produce an atlas of tissue-specific protein associations. We find that this method recapitulates known protein complexes and the larger structural organization of the cell. Interactions of stable protein complexes are well preserved across tissues, while cell-type-specific cellular structures, such as synaptic components, are found to represent a substantial driver of differences between tissues. Over 25% of associations are tissue specific, of which <7% are because of differences in gene expression. We validate protein associations for the brain through cofractionation experiments in synaptosomes, curation of brain-derived pulldown data and AlphaFold2 modeling. We also construct a network of brain interactions for schizophrenia-related genes, indicating that our approach can functionally prioritize candidate disease genes in loci linked to brain disorders.", "doi": "10.1038/s41587-025-02659-z", "pmid": "40316700", "labels": {"DDLS Fellow": "", "Andrea Fossati": ""}, "xrefs": [{"db": "pmc", "key": "PMC13090126"}, {"db": "pii", "key": "10.1038/s41587-025-02659-z"}], "notes": [], "created": "2026-08-20T08:59:34.792Z", "modified": "2026-09-23T09:05:32.445Z"}, {"entity": "publication", "iuid": "53deef8658d14591b6b08382650120d7", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/53deef8658d14591b6b08382650120d7.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/53deef8658d14591b6b08382650120d7"}}, "title": "Zero-shot prediction of drug responses using biologically informed neural networks trained on phosphoproteomic timeseries.", "authors": [{"family": "Antonopoulos", "given": "Konstantinos", "initials": "K", "orcid": "0000-0003-2781-3872", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/04cb0389161647d888b443050b719c05.json"}}, {"family": "Nordenstorm", "given": "Olof", "initials": "O", "orcid": "0009-0003-5711-376X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/54552421d6f448f9bc2b6bdf93931dfa.json"}}, {"family": "Nilsson", "given": "Avlant", "initials": "A", "orcid": "0000-0002-9476-4516", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f2e21dbc1c624f6a841c59e959e948e4.json"}}], "type": "journal article", "published": "2026-03-00", "journal": {"title": "PLoS Comput Biol", "issn": "1553-7358", "volume": "22", "issue": "3", "pages": "e1014100", "issn-l": "1553-734X"}, "abstract": "Cellular signaling is driven by complex, dynamic phosphorylation networks that control growth and survival, and their dysregulation underlies diseases such as cancer. Although modern mass spectrometry enables large-scale quantification of phosphoproteomic responses over time, these measurements remain descriptive and cannot by themselves predict how signaling will evolve under perturbations. Here, we extend a biologically informed recurrent neural network framework (LEMBAS), to learn time-resolved phosphoproteomic trajectories. We introduce two interpretable modules; a phosphosite mapping that links signaling nodes to measured phosphorylation sites and a monotonic time mapping that aligns continuous experimental times to discrete signaling steps. Using synthetic benchmarks and an EGF-stimulation dataset with inhibitor treatments, the model accurately interpolates unseen time points and predicts drug-induced phosphoproteomic responses in a zero-shot setting, outperforming na\u00efve and fully connected baselines. Importantly, the model identifies both canonical and non-canonical signaling effects, including modulation of the transcription factor FOXO3:S7 (from the PI3K/AKT pathway) by drugs affecting PTPN11 (from the RAS/ERK pathway). By combining mechanistic priors with deep learning, our framework provides a scalable approach to interpret and predict dynamic drug responses from phosphoproteomic data.", "doi": "10.1371/journal.pcbi.1014100", "pmid": "41849361", "labels": {"Avlant Nilsson": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC13035234"}, {"db": "pii", "key": "PCOMPBIOL-D-25-02219"}], "notes": [], "created": "2026-08-17T11:12:39.491Z", "modified": "2026-08-17T11:12:39.736Z"}, {"entity": "publication", "iuid": "fe5a284dda5743fb91cbc7646fe5afd1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/fe5a284dda5743fb91cbc7646fe5afd1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/fe5a284dda5743fb91cbc7646fe5afd1"}}, "title": "Proteome-scale autoantibody profiling in PSC: Associations with clinical phenotypes and evidence for neuroendocrine deregulations.", "authors": [{"family": "Cornillet", "given": "Martin", "initials": "M", "orcid": "0000-0001-7981-0927", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8f2b2dde303f445e8c47f726a9dbf6ae.json"}}, {"family": "B\u00e5ve", "given": "Aiva Lundberg", "initials": "AL"}, {"family": "Sun", "given": "Dan", "initials": "D"}, {"family": "Nouairia", "given": "Ghada", "initials": "G"}, {"family": "Villard", "given": "Christina", "initials": "C"}, {"family": "Grigoriadis", "given": "Aristeidis", "initials": "A"}, {"family": "von Seth", "given": "Erik", "initials": "E"}, {"family": "Jansson", "given": "Hannes", "initials": "H"}, {"family": "\u00c1lvez", "given": "Mar\u00eda Bueno", "initials": "MB", "orcid": "0000-0002-2669-7796", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a7d09e4780a445b9b432d494c76d07e8.json"}}, {"family": "Bergstr\u00f6m", "given": "Sofia", "initials": "S", "orcid": "0000-0003-2910-4754", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/552414173f564ce4b813e107812f446d.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3db33fa3edb94febb8be7927a16838d0.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ea446aa574042a295d5f69437402f76.json"}}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e213b04f8984c8eb00c68f5bc2f6a36.json"}}, {"family": "St\u00e5l", "given": "Per", "initials": "P"}, {"family": "SweHep consortium", "given": "", "initials": ""}, {"family": "Sparrelid", "given": "Ernesto", "initials": "E"}, {"family": "Bj\u00f6rkstr\u00f6m", "given": "Niklas K", "initials": "NK", "orcid": "0000-0002-0967-076X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ded8cd7038b4c42ac16f62f89b9229c.json"}}, {"family": "Halfvarson", "given": "Jonas", "initials": "J", "orcid": "0000-0003-0122-7234", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e4dfcde6a8f74a179e0bb0f37dee1f4b.json"}}, {"family": "Bergquist", "given": "Annika", "initials": "A"}], "type": "journal article", "published": "2026-03-00", "journal": {"title": "JHEP Rep", "issn": "2589-5559", "volume": "8", "issue": "3", "pages": "101719", "issn-l": null}, "abstract": "Primary sclerosing cholangitis (PSC) is a rare cholestatic liver disease with heterogeneous phenotypes and progression. Autoimmune traits, such as the presence of autoantibodies, are suspected to drive its heterogeneity.\n\nWe performed a proteome-scale autoantibody screen of IgG and IgA isotypes using >42,100 protein fragments. This was followed by a validation of 1,153 selected autoantibodies, in serum samples from 466 patients with PSC in a longitudinal setting using the SUPRIM cohort and 214 controls.\n\nWe identified autoantibodies associated with clinical phenotypes, biochemical and clinical severity, comorbidities, and disease progression (e.g. alkaline phosphatase and albumin level p 107 chemical fragments in silico against Neisseria gonorrhoeae or Staphylococcus aureus, subsequently expanding promising fragments, and an unconstrained de novo compound generation, each using genetic algorithms and variational autoencoders. Of 24 synthesized compounds, seven demonstrated selective antibacterial activity. Two lead compounds exhibited bactericidal efficacy against multidrug-resistant isolates with distinct mechanisms of action and reduced bacterial burden in vivo in mouse models of N. gonorrhoeae vaginal infection and methicillin-resistant S. aureus skin infection. We further validated structural analogs for both compound classes as antibacterial. Our approach enables the generative deep-learning-guided design of de novo antibiotics, providing a platform for mapping uncharted regions of chemical space.", "doi": "10.1016/j.cell.2025.07.033", "pmid": "40816267", "labels": {"Andreas Luttens": "", "DDLS Fellow": ""}, "xrefs": [{"db": "mid", "key": "NIHMS2127187"}, {"db": "pmc", "key": "PMC12790861"}, {"db": "pii", "key": "S0092-8674(25)00855-4"}], "notes": [], "created": "2026-09-23T07:46:32.473Z", "modified": "2026-09-23T07:46:32.512Z"}, {"entity": "publication", "iuid": "fb29b512feb245c88b3146865fab9555", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/fb29b512feb245c88b3146865fab9555.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/fb29b512feb245c88b3146865fab9555"}}, "title": "Reference genome bias in light of species-specific chromosomal reorganization and translocations.", "authors": [{"family": "Maurstad", "given": "Marius F", "initials": "MF", "orcid": "0000-0001-7894-1693", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/958ec319e3674f9683957590400c48e2.json"}}, {"family": "Hoff", "given": "Siv Nam Khang", "initials": "SNK", "orcid": "0000-0001-8113-338X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/db76a491cfab4d5c9227443701eaed37.json"}}, {"family": "Cerca", "given": "Jos\u00e9", "initials": "J", "orcid": "0000-0001-7788-4367", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b9119ffe17f1400ea74e0eaf43c105fc.json"}}, {"family": "Ravinet", "given": "Mark", "initials": "M", "orcid": "0000-0002-2841-1798", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/01b9b7c21953456e8c12a46803d6ab78.json"}}, {"family": "Bradbury", "given": "Ian", "initials": "I"}, {"family": "Jakobsen", "given": "Kjetill S", "initials": "KS", "orcid": "0000-0002-8861-5397", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f2fe02e097b342508301397260ef7cc3.json"}}, {"family": "Pr\u00e6bel", "given": "Kim", "initials": "K", "orcid": "0000-0002-0681-1854", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/95c9602002d042cf874a93c895f37776.json"}}, {"family": "Jentoft", "given": "Sissel", "initials": "S", "orcid": "0000-0001-8707-531X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/52961bc2c6574c6085059f52a16b5fb6.json"}}], "type": "journal article", "published": "2025-10-15", "journal": {"title": "Genome Biol.", "issn": "1474-760X", "volume": "26", "issue": "1", "pages": "355", "issn-l": "1474-7596"}, "abstract": "Whole-genome sequencing efforts, have during the past decade, unveiled the central role of genomic rearrangements-such as chromosomal inversions-in evolutionary processes, including local adaptation in a wide range of taxa. However, employment of reference genomes from distantly or even closely related species for mapping and the subsequent variant calling can lead to errors and/or biases in the datasets generated for downstream analyses.\n\nHere, we capitalize on the recently generated chromosome-anchored genome assemblies for Arctic cod (Arctogadus glacialis), polar cod (Boreogadus saida), and Atlantic cod (Gadus morhua) to evaluate the extent and consequences of reference bias on population sequencing datasets (approx. 15-20 \u00d7 coverage) for both Arctic cod and polar cod. Our findings demonstrate that the choice of reference genome impacts the mapping statistics, including mapping depth and mapping quality, as well as core population genetic estimates, such as heterozygosity levels, nucleotide diversity (\u03c0), and cross-species genetic divergence (DXY). Furthermore, using a more distantly related reference genome can lead to inaccurate detection and characterization of chromosomal inversions, i.e., in terms of size (length) and location (position), due to inter-chromosomal reorganizations between species. Additionally, we observe that some of the verified species-specific inversions are split across multiple genomic regions when mapped against a heterospecific reference.\n\nInaccurate identification of chromosomal rearrangements as well as biased population genetic measures could potentially lead to erroneous interpretation of species-specific genomic diversity, impede the resolution of local adaptation, and thus, impact predictions of their genomic potential to respond to climatic and other environmental perturbations.", "doi": "10.1186/s13059-025-03761-w", "pmid": "41094588", "labels": {"Jos\u00e9 Cerca": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC12523119"}, {"db": "pii", "key": "10.1186/s13059-025-03761-w"}], "notes": [], "created": "2026-08-20T12:21:55.840Z", "modified": "2026-09-23T09:12:29.220Z"}, {"entity": "publication", "iuid": "323bbe2a3c6e444081e24c57fa16df77", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/323bbe2a3c6e444081e24c57fa16df77.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/323bbe2a3c6e444081e24c57fa16df77"}}, "title": "Artificial intelligence-assisted prostate cancer diagnosis for reduced use of immunohistochemistry.", "authors": [{"family": "Blilie", "given": "Anders", "initials": "A", "orcid": "0009-0002-9546-5443", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d778d06e206948e5ac99017ce1ae8434.json"}}, {"family": "Mulliqi", "given": "Nita", "initials": "N"}, {"family": "Ji", "given": "Xiaoyi", "initials": "X"}, {"family": "Szolnoky", "given": "Kelvin", "initials": "K", "orcid": "0000-0002-0554-1872", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5059c9f881d4434f9b64f3bb381478fe.json"}}, {"family": "Boman", "given": "Sol Erika", "initials": "SE", "orcid": "0009-0001-5733-3178", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8a605b0dadad4b3696396827ebac9348.json"}}, {"family": "Titus", "given": "Matteo", "initials": "M", "orcid": "0009-0008-7893-7385", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/049f236217f147f78635b9d3a361db98.json"}}, {"family": "Gonzalez", "given": "Geraldine Martinez", "initials": "GM"}, {"family": "Asenjo", "given": "Jos\u00e9", "initials": "J"}, {"family": "Gambacorta", "given": "Marcello", "initials": "M"}, {"family": "Libretti", "given": "Paolo", "initials": "P"}, {"family": "Gudlaugsson", "given": "Einar", "initials": "E"}, {"family": "Kjosavik", "given": "Svein R", "initials": "SR", "orcid": "0000-0002-7004-5533", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/97167c1ee44443108098eb823bd18fa7.json"}}, {"family": "Egevad", "given": "Lars", "initials": "L", "orcid": "0000-0001-8531-222X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a7d46f1f5fc047dc8edb910eb4f0645c.json"}}, {"family": "Janssen", "given": "Emiel A M", "initials": "EAM"}, {"family": "Eklund", "given": "Martin", "initials": "M", "orcid": "0000-0001-5032-5266", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/06721510ebc8462386e0e6fc6c84315b.json"}}, {"family": "Kartasalo", "given": "Kimmo", "initials": "K", "orcid": "0000-0002-9470-4783", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7c6fc97c06ed456c8bdd1f03db8a9b72.json"}}], "type": "journal article", "published": "2025-10-15", "journal": {"title": "Commun Med (Lond)", "issn": "2730-664X", "volume": "5", "issue": "1", "pages": "425", "issn-l": null}, "abstract": "Prostate cancer diagnosis heavily relies on histopathological evaluation, which is subject to variability. While immunohistochemical staining (IHC) assists in distinguishing benign from malignant tissue, it increases workload, costs, and leads to diagnostic delays. Artificial intelligence (AI) presents a promising solution to reduce reliance on IHC by accurately classifying atypical glands and borderline morphologies in hematoxylin and eosin (H&E) stained tissue sections.\n\nIn this study, we evaluated an AI model's ability to minimize IHC use without compromising diagnostic accuracy. We retrospectively analyzed prostate core needle biopsies from routine diagnostics at three different pathology sites. These cohorts consisted exclusively of diagnostically challenging cases where pathologists had required IHC to finalize the diagnosis.\n\nWe show that the AI model achieves high performance, with area under the curve values ranging from 0.951 to 0.993 for detecting cancer in routine H&E-stained slides. When applying sensitivity-prioritized diagnostic thresholds, the model reduces the need for IHC staining by 44.4%, 42.0%, and 20.7% across the three cohorts, without a single false negative prediction. Among slides with a benign ground truth label, IHC use is reduced by up to 80.6%.\n\nThis AI model shows promise for reducing unnecessary IHC use in difficult prostate biopsy cases while maintaining diagnostic safety. Its integration into clinical workflows could streamline decision-making in prostate pathology and alleviate resource burdens.", "doi": "10.1038/s43856-025-01185-y", "pmid": "41094148", "labels": {"DDLS Fellow": "", "Kimmo Kartasalo": ""}, "xrefs": [{"db": "pmc", "key": "PMC12528698"}, {"db": "pii", "key": "10.1038/s43856-025-01185-y"}], "notes": [], "created": "2025-10-30T15:41:17.882Z", "modified": "2026-09-23T11:34:24.112Z"}, {"entity": "publication", "iuid": "7a652176313a4a5aa38ae6053ee7f46f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/7a652176313a4a5aa38ae6053ee7f46f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/7a652176313a4a5aa38ae6053ee7f46f"}}, "title": "Discovering the unseen: a performance comparison of taxonomic classification methods for unknown DNA barcodes", "authors": [{"family": "Orsholm", "given": "Johanna", "initials": "J", "orcid": "0009-0008-4879-8847", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/754e9f66db2f4a62b365beffc63aad30.json"}}, {"family": "Zito", "given": "Alessandro", "initials": "A", "orcid": "0000-0001-8515-6503", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6e686d08f8584087812f7ab16f988773.json"}}, {"family": "Somervuo", "given": "Panu", "initials": "P", "orcid": "0000-0003-3121-4047", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2019ca5fc5e742c5bad89efc09e35a75.json"}}, {"family": "Harrison", "given": "Jesse P", "initials": "JP", "orcid": "0000-0002-4877-4684", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ab049ed3d7704b018621b0bc41deeb8b.json"}}, {"family": "Koskela", "given": "Markus", "initials": "M", "orcid": "0000-0001-6515-587X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8b0127a3629c4b6bb4fee1a1d928d5df.json"}}, {"family": "Ovaskainen", "given": "Otso", "initials": "O", "orcid": "0000-0001-9750-4421", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9c73c582d24a44bd895c5ee7084487a4.json"}}, {"family": "Braga", "given": "Mariana P", "initials": "MP", "orcid": "0000-0002-1253-2536", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4f9064ed501545dca268c351c993aa26.json"}}, {"family": "Chazot", "given": "Nicolas", "initials": "N", "orcid": "0000-0002-5237-8043", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1224343fe35b490ea5d1e1b5ff0ca734.json"}}, {"family": "Roslin", "given": "Tomas", "initials": "T", "orcid": "0000-0002-2957-4791", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4b6e491ae382479b8e92eda9a11cabae.json"}}, {"family": "Furneaux", "given": "Brendan", "initials": "B", "orcid": "0000-0003-3522-7363", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f849ec266aaa4531be87b29c71ab2778.json"}}], "type": "posted-content", "published": "2025-10-14", "journal": {"title": null, "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2025.10.13.681976", "pmid": null, "labels": {"Mariana Pires Braga": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2025-11-28T12:33:11.073Z", "modified": "2026-08-18T12:48:31.528Z"}, {"entity": "publication", "iuid": "0f940366e32a487088053ca05174d12e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0f940366e32a487088053ca05174d12e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0f940366e32a487088053ca05174d12e"}}, "title": "Accurate and Robust Characterization of Structural Variants at Low Coverages with ARCLID", "authors": [{"family": "Tavakoli", "given": "Sajad", "initials": "S", "orcid": "0000-0002-0510-6491", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5aae5d84417c4fc0a0ece3be48bd1d5d.json"}}, {"family": "Frandsen", "given": "Rasmus John Normand", "initials": "RJN", "orcid": "0000-0002-3799-6062", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ee6354f31a7549d78b3ab988338d58d0.json"}}, {"family": "Majidian", "given": "Sina", "initials": "S", "orcid": "0000-0001-5345-6982", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a14f17e8c2dc470dae5250c36d32cb27.json"}}, {"family": "Mansourvar", "given": "Marjan", "initials": "M", "orcid": "0000-0001-6492-7858", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3d5ba9c3906e4b9babd2e839a86d0e8b.json"}}], "type": "posted-content", "published": "2025-10-13", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2025.10.10.681591", "pmid": null, "labels": {"Sina Majidian": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2026-09-23T15:51:54.433Z", "modified": "2026-09-23T15:51:54.585Z"}, {"entity": "publication", "iuid": "d128ec504c8042cfb896a437a4fba061", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d128ec504c8042cfb896a437a4fba061.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d128ec504c8042cfb896a437a4fba061"}}, "title": "Genomic insights into a diarrheal outbreak in Bangladesh reveal novel ETEC lineages and expansion of CS23 colonization factor.", "authors": [{"family": "Rahman", "given": "Sadia Isfat Ara", "initials": "SIA", "orcid": "0000-0002-7983-087X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fe5824c40b4d4270bee5e9d14754cd72.json"}}, {"family": "Jubair", "given": "Mohammad", "initials": "M"}, {"family": "Akhtar", "given": "Marjahan", "initials": "M"}, {"family": "Akter", "given": "Afroza", "initials": "A"}, {"family": "Tauheed", "given": "Imam", "initials": "I"}, {"family": "Begum", "given": "Yasmin Ara", "initials": "YA"}, {"family": "Bhattacharjee", "given": "Piyash", "initials": "P"}, {"family": "Afrad", "given": "Mokibul Hassan", "initials": "MH"}, {"family": "Khanam", "given": "Farhana", "initials": "F"}, {"family": "Islam", "given": "Md Taufiqul", "initials": "MT"}, {"family": "Khan", "given": "Ashraful Islam", "initials": "AI"}, {"family": "Rahman", "given": "Mustafizur", "initials": "M", "orcid": "0000-0002-6876-0191", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6fcb082b5c5b4bb7ad6d01fbd9fdeece.json"}}, {"family": "Ryan", "given": "Edward T", "initials": "ET", "orcid": "0009-0005-0169-394X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f15509942724428b8a3682ca9cd6efb5.json"}}, {"family": "Fleckenstein", "given": "James M", "initials": "JM"}, {"family": "Bhuiyan", "given": "Taufiqur Rahman", "initials": "TR", "orcid": "0000-0003-3755-4763", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/609d6c318a79458fa15a9a6f556dfcee.json"}}, {"family": "Thomson", "given": "Nicholas Robert", "initials": "NR"}, {"family": "Qadri", "given": "Firdausi", "initials": "F", "orcid": "0000-0002-8928-9888", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a24c8900720f4d9c88577a77bb695a3a.json"}}, {"family": "von Mentzer", "given": "Astrid", "initials": "A", "orcid": "0000-0002-2167-1394", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/36cefe255ba14d8684826fae58598036.json"}}, {"family": "Chowdhury", "given": "Fahima", "initials": "F", "orcid": "0000-0002-7082-0720", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/141d8156ab194f19919c199206768905.json"}}], "type": "journal article", "published": "2025-10-07", "journal": {"title": "Microbiol Spectr", "issn": "2165-0497", "volume": "13", "issue": "10", "pages": "e0331524", "issn-l": null}, "abstract": "Enterotoxigenic Escherichia coli (ETEC), a leading cause of diarrhea, is defined by heat-stable (ST) and/or heat-labile (LT) toxins and associated colonization factors (CFs). However, there is still a knowledge gap in understanding ETEC's evolution, particularly in endemic regions like Bangladesh. This study investigates the genomic attributes contributing to the rise of ETEC-associated diarrhea in Bangladesh during 2022-2023. Whole genome sequencing of 325 ETEC isolates (2022-2023), compared with historical strains (1980-2021), revealed significant evolutionary changes. Our findings showed a significant shift in ETEC toxin from LT to ST over the period 2013-2023. The most frequent virulence profile during this period was CFA/I + CS21 compared with previous years (1980-2021). The emergence of CS23-positive ETEC was reported for the first time in Bangladesh, which was considered a less common CF in previous studies. Notably, we report the four novel lineages \"L26-L29\" in this study through phylogenetic analysis, partly encompassing emergent CS23-positive ETEC strains. Additionally, the high prevalence of multi-drug-resistant ETEC strains and the presence of ESBL-CTX-M-resistant gene during 2022-2023 are a matter of great concern, underscoring the need for preventive measures. The switch of distinct toxin and CF combinations, the rapid emergence of CS23, ESBL-CTX-M resistance, and novel lineages may be the reason behind the increased number of ETEC diarrheal cases between 2022 and 2023. These findings highlight the rapid ETEC evolution that underscores the necessity of continued genomic surveillance to track ongoing changes.IMPORTANCEThis study expands on previous evidence, demonstrating a remarkable genomic diversity in ETEC strains from 2022 to 2023, particularly in virulence factors and AMR genes. The combined findings from these studies will be important for mitigating future diarrheal outbreaks by informing preventive measures, including future vaccine targets, and implementing antibiotic stewardship programs against ETEC infection. Importantly, this research underscores the necessity of continued genomic surveillance to track ongoing changes in ETEC. Such monitoring is essential for understanding the pathogen's evolving population structure, transmission dynamics, and resistance mechanisms.", "doi": "10.1128/spectrum.03315-24", "pmid": "40928300", "labels": {"Astrid von Mentzer": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC12502627"}, {"db": "BioProject", "key": "PRJNA1130082"}], "notes": [], "created": "2025-12-02T15:46:55.948Z", "modified": "2026-09-23T13:24:16.198Z"}, {"entity": "publication", "iuid": "a1465d5737e140339ba159b60f80581d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a1465d5737e140339ba159b60f80581d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a1465d5737e140339ba159b60f80581d"}}, "title": "Plasma Metabolome, Long-term Body Weight Change, and Type 2 Diabetes in U.S. Individuals.", "authors": [{"family": "Wu", "given": "Zhiyuan", "initials": "Z", "orcid": "0000-0001-5694-2441", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b04f84427ffd4651b23ef1b57a2223b6.json"}}, {"family": "Liu", "given": "Binkai", "initials": "B", "orcid": "0000-0002-5478-5208", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6fa88e28316b4770a9ea759e084c01c4.json"}}, {"family": "Li", "given": "Jun", "initials": "J", "orcid": "0000-0003-3519-8638", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/77d0c8cac07b47228b383aa851382852.json"}}, {"family": "Zeleznik", "given": "Oana", "initials": "O"}, {"family": "Eliassen", "given": "A Heather", "initials": "AH"}, {"family": "Wittenbecher", "given": "Clemens", "initials": "C", "orcid": "0000-0001-7792-877X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2f7d2c289b3c47d5a79d23bd48a3225a.json"}}, {"family": "Hu", "given": "Frank B", "initials": "FB"}, {"family": "Wang", "given": "Molin", "initials": "M"}, {"family": "Song", "given": "Mingyang", "initials": "M"}, {"family": "Hu", "given": "Yang", "initials": "Y"}, {"family": "Sun", "given": "Qi", "initials": "Q", "orcid": "0000-0002-8480-1563", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4a65407257ac4518ac5cb19317ee3b32.json"}}], "type": "journal article", "published": "2025-10-01", "journal": {"title": "Diabetes Care", "issn": "1935-5548", "volume": "48", "issue": "10", "pages": "1818-1826", "issn-l": null}, "abstract": "Body weight influences the blood metabolome, but whether specific plasma metabolomic profiles predict long-term weight change remains unclear. We aimed to investigate associations among plasma metabolites, current weight, weight change trajectories, and incident type 2 diabetes (T2D) in adults.\n\nWe profiled 260 plasma metabolites in 7,499 U.S. health professionals. A metabolomic score predicting BMI change over time was derived using elastic net regression with a training/testing approach. Associations with incident T2D were examined using multivariable Cox models.\n\nMetabolomic predictors of BMI change varied by baseline weight status. In lean individuals, 46 metabolites significantly predicted BMI change slope compared with 20 individuals in the group with overweight and 13 in the group with obesity, with no overlapping metabolites across groups. A metabolomic score of BMI slope derived in lean participants correlated with BMI slope in the lean group (Spearman r = 0.31), but the correlation was weaker in the groups with overweight (r = 0.16) and obesity (r = 0.10). The score was associated with higher T2D risk in the lean group (hazard ratio [HR] per 1 SD 1.42; 95% CI 1.26-1.60) and group with overweight (HR 1.29; 95% CI 1.17-1.42) but not in the group with obesity.\n\nPlasma metabolomic profiles predictive of future weight change differ by body weight status. Distinct metabolic signatures may help identify certain lean individuals at an elevated risk of future weight gain and T2D, offering opportunities for earlier, more targeted prevention.", "doi": "10.2337/dc25-0902", "pmid": "40802109", "labels": {"Clemens Wittenbecher": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC12451841"}, {"db": "pii", "key": "163202"}], "notes": [], "created": "2025-11-28T07:17:32.259Z", "modified": "2025-12-09T13:25:59.345Z"}, {"entity": "publication", "iuid": "53cac8349892424e93f3a56bb6932f84", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/53cac8349892424e93f3a56bb6932f84.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/53cac8349892424e93f3a56bb6932f84"}}, "title": "Image based subcellular mapping of the protein landscape of SARS-CoV-2 infected cells for target-centric drug repurposing.", "authors": [{"family": "Tampere", "given": "Marianna", "initials": "M"}, {"family": "H Le", "given": "Trang", "initials": "T"}, {"family": "Asp", "given": "Elin", "initials": "E"}, {"family": "Kalman", "given": "Adelinn", "initials": "A"}, {"family": "Kaimal", "given": "Jayasankar Mohanakrishnan", "initials": "JM"}, {"family": "Njenda", "given": "Duncan", "initials": "D"}, {"family": "B\u00e4ckstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Axelsson", "given": "Ulrika", "initials": "U"}, {"family": "Xu", "given": "Hao", "initials": "H"}, {"family": "Ouyang", "given": "Wei", "initials": "W"}, {"family": "Axelsson", "given": "Hanna", "initials": "H"}, {"family": "Marabita", "given": "Francesco", "initials": "F"}, {"family": "Moussaud-Lamodi\u00e8re", "given": "Elisabeth", "initials": "E"}, {"family": "Sepulveda", "given": "Carolina Oses", "initials": "CO"}, {"family": "Seashore-Ludlow", "given": "Brinton", "initials": "B"}, {"family": "Vernersson", "given": "Caroline", "initials": "C"}, {"family": "Mirazimi", "given": "Ali", "initials": "A"}, {"family": "Lundberg", "given": "Emma", "initials": "E"}, {"family": "\u00d6stling", "given": "P\u00e4ivi", "initials": "P"}, {"family": "Stadler", "given": "Charlotte", "initials": "C"}], "type": "journal article", "published": "2025-10-00", "journal": {"title": "Biomed. Pharmacother.", "issn": "1950-6007", "volume": "191", "pages": "118447", "issn-l": "0753-3322"}, "abstract": "The COVID-19 pandemic has resulted in millions of deaths and affected socioeconomic structure worldwide and the search for new antivirals and treatments are still ongoing. In the search for new drug targets and to increase our understanding of the disease, we applied large-scale immunofluorescence profiling to explore host cell response to SARS-CoV-2 infection. Among the 602 host proteins studied in this host response profiling, changes in abundance and subcellular localization were observed for 97 proteins, with 45 proteins showing increased abundance and 10 reduced abundance. 20 proteins displayed changed localization upon infection and an additional 22 proteins displayed altered abundance and localization, together contributing to diverse reshuffling of the host cell protein landscape during infection. We then selected existing and approved small-molecule drugs (n = 123) against our identified host response proteins and identified one compound - elesclomol, that significantly reduced antiviral activity. Our study introduces a novel, targeted and systematic approach based on host protein profiling, to identify new targets for drug repurposing. The dataset of > 100,000 immunofluorescence images from this study are published as a resource available for further studies. AUTHOR SUMMARY: In this study we have evaluated a new approach for identifying drugs that could be used as antiviral drugs, in this case demonstrated for SARS CoV-2. By mining the literature for reported interactions between SARS CoV-2 viral components and host cell proteins, we identified a few hundred host proteins suggested to interact with the virus upon infection. To explore these viral-host interaction proteins further, we developed an image based assay using immunofluorescence and confocal microscopy to visualize the host proteins within infected and non infected cells. This was possible due to the proteome wide collection of antibodies generated within the Human Protein Atlas project, with the aim to systematically map the human proteome in cells and across tissues. The host proteins that altered their location or abundance level upon infection were regarded as putative targets for drug repurposing and we subsequently tested 123 drugs that were targeting a subset of these host proteins. Applying these drugs on two different cell types infected with SARS-CoV-2, revealed a non toxic antiviral effect for one compound that can be explored further as a treatment regimen for SARS-CoV-2 infection. The approach is novel since it combines a targeted approach for drug repurposing screening, giving insight into mechanism of action from start. As such it has the potential to accelerate drug repurposing or identification of targets for new drugs.", "doi": "10.1016/j.biopha.2025.118447", "pmid": "40819539", "labels": {"Wei Ouyang": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pii", "key": "S0753-3322(25)00641-9"}], "notes": [], "created": "2025-12-15T10:04:48.439Z", "modified": "2026-09-23T15:50:14.232Z"}, {"entity": "publication", "iuid": "af5b1bed406e47ad890769e1d8f42bbd", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/af5b1bed406e47ad890769e1d8f42bbd.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/af5b1bed406e47ad890769e1d8f42bbd"}}, "title": "Hierarchical Vision Transformers for prostate biopsy grading: Towards bridging the generalization gap.", "authors": [{"family": "Grisi", "given": "Cl\u00e9ment", "initials": "C"}, {"family": "Kartasalo", "given": "Kimmo", "initials": "K", "orcid": "0000-0002-9470-4783", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7c6fc97c06ed456c8bdd1f03db8a9b72.json"}}, {"family": "Eklund", "given": "Martin", "initials": "M", "orcid": "0000-0001-5032-5266", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/06721510ebc8462386e0e6fc6c84315b.json"}}, {"family": "Egevad", "given": "Lars", "initials": "L", "orcid": "0000-0001-8531-222X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a7d46f1f5fc047dc8edb910eb4f0645c.json"}}, {"family": "van der Laak", "given": "Jeroen", "initials": "J", "orcid": "0000-0001-7982-0754", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/188f689ad0304f28b42bc9d3dbf6a56e.json"}}, {"family": "Litjens", "given": "Geert", "initials": "G", "orcid": "0000-0003-1554-1291", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3792b285bcf04c11b268da1088160a9d.json"}}], "type": "journal article", "published": "2025-10-00", "journal": {"title": "Med Image Anal", "issn": "1361-8423", "volume": "105", "pages": "103663", "issn-l": null}, "abstract": "Practical deployment of Vision Transformers in computational pathology has largely been constrained by the sheer size of whole-slide images. Transformers faced a similar limitation when applied to long documents, and Hierarchical Transformers were introduced to circumvent it. This work explores the capabilities of Hierarchical Vision Transformers for prostate cancer grading in WSIs and presents a novel technique to combine attention scores smartly across hierarchical transformers. Our best-performing model matches state-of-the-art algorithms with a 0.916 quadratic kappa on the Prostate cANcer graDe Assessment (PANDA) test set. It exhibits superior generalization capacities when evaluated in more diverse clinical settings, achieving a quadratic kappa of 0.877, outperforming existing solutions. These results demonstrate our approach's robustness and practical applicability, paving the way for its broader adoption in computational pathology and possibly other medical imaging tasks. Our code is publicly available at https://github.com/computationalpathologygroup/hvit.", "doi": "10.1016/j.media.2025.103663", "pmid": "40644915", "labels": {"DDLS Fellow": null, "Kimmo Kartasalo": null}, "xrefs": [{"db": "pii", "key": "S1361-8415(25)00210-5"}], "notes": [], "created": "2025-10-30T15:42:14.631Z", "modified": "2025-11-04T09:38:52.902Z"}, {"entity": "publication", "iuid": "be2ce01e822b40be8a0c5bcd58728f1d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/be2ce01e822b40be8a0c5bcd58728f1d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/be2ce01e822b40be8a0c5bcd58728f1d"}}, "title": "Geographical variation in mitogenomes of the largetooth sawfish Pristis pristis: Challenges and perspectives for conservation efforts", "authors": [{"family": "Rodrigues", "given": "Alan \u00c9rik S", "initials": "A\u00c9S"}, {"family": "Brito", "given": "Rafaela Maria S", "initials": "RMS"}, {"family": "Charvet", "given": "Patricia", "initials": "P"}, {"family": "Faria", "given": "Vicente V", "initials": "VV"}, {"family": "Cabanillas-Torpoco", "given": "Mariano", "initials": "M"}, {"family": "Aleixo", "given": "Alexandre", "initials": "A"}, {"family": "Burlamaqui", "given": "Tib\u00e9rio C\u00e9sar T", "initials": "TCT"}, {"family": "Rodrigues-Filho", "given": "Luis Fernando da S", "initials": "LFdS"}, {"family": "Asenjo", "given": "Angelico", "initials": "A"}, {"family": "Siccha-Ramirez", "given": "Raquel", "initials": "R"}, {"family": "Nunes", "given": "Jorge Luiz S", "initials": "JLS"}, {"family": "de Boer", "given": "Hugo J", "initials": "HJ"}, {"family": "Cerca", "given": "Jos\u00e9", "initials": "J"}, {"family": "Mauvisseau", "given": "Quentin", "initials": "Q", "orcid": "0000-0003-1215-2987", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dceece4fb16b4ae7801b572e79c9e8e1.json"}}, {"family": "Ready", "given": "Jonathan S", "initials": "JS"}, {"family": "Sales", "given": "Jo\u00e3o Br\u00e1ullio L", "initials": "JBL"}], "type": "journal-article", "published": "2025-10-00", "journal": {"title": "Global Ecology and Conservation", "issn": "2351-9894", "volume": "62", "pages": "e03757", "issn-l": null}, "abstract": null, "doi": "10.1016/j.gecco.2025.e03757", "pmid": null, "labels": {"Jos\u00e9 Cerca": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T07:56:03.940Z", "modified": "2026-09-23T11:36:45.071Z"}, {"entity": "publication", "iuid": "e167a2e134e6423ab0a2407d65e4da58", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e167a2e134e6423ab0a2407d65e4da58.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e167a2e134e6423ab0a2407d65e4da58"}}, "title": "A roadmap for equitable reuse of public microbiome data.", "authors": [{"family": "Hug", "given": "Laura A", "initials": "LA", "orcid": "0000-0001-5974-9428", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e481202df2d94d9db8636e0884acdb6f.json"}}, {"family": "Hatzenpichler", "given": "Roland", "initials": "R", "orcid": "0000-0002-5489-3444", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/17cf2bcc013440b78ba2632712a10045.json"}}, {"family": "Moraru", "given": "Cristina", "initials": "C", "orcid": "0000-0002-5375-5437", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6c3a15ec4c4e40cf8939a39e5485c6fc.json"}}, {"family": "Soares", "given": "Andr\u00e9 R", "initials": "AR", "orcid": "0000-0002-5013-3034", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/729d22b579fe4eac8abb6af144e3c874.json"}}, {"family": "Meyer", "given": "Folker", "initials": "F", "orcid": "0000-0003-1112-2284", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1d86d4611c6744e0a7866b3156e11a2f.json"}}, {"family": "Heyder", "given": "Anke", "initials": "A", "orcid": "0000-0002-1578-4894", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/086fa8628fef41808ceb737d84eb980c.json"}}, {"family": "Data Reuse Consortium", "given": "", "initials": ""}, {"family": "Probst", "given": "Alexander J", "initials": "AJ", "orcid": "0000-0002-9392-6544", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c9f5404bb1be4e5f8ae5c9ad10974797.json"}}], "type": "journal article", "published": "2025-10-00", "journal": {"title": "Nat. Microbiol", "issn": "2058-5276", "volume": "10", "issue": "10", "pages": "2384-2395", "issn-l": "2058-5276"}, "abstract": "Science benefits from rapid open data sharing, but current guidelines for data reuse were established two decades ago, when databases were several million times smaller than they are today. These guidelines are largely unfamiliar to the scientific community, and, owing to the rapid increase in biological data generated in the past decade, they are also outdated. As a result, there is a lack of community standards suited to the current landscape and inconsistent implementation of data sharing policies across institutions. Here we discuss current sequence data sharing policies and their benefits and drawbacks, and present a roadmap to establish guidelines for equitable sequence data reuse, developed in consultation with a data consortium of 167 microbiome scientists. We propose the use of a Data Reuse Information (DRI) tag for public sequence data, which will be associated with at least one Open Researcher and Contributor ID (ORCID) account. The machine-readable DRI tag indicates that the data creators prefer to be contacted before data reuse, and simultaneously provides data consumers with a mechanism to get in touch with the data creators. The DRI aims to facilitate and foster collaborations, and serve as a guideline that can be expanded to other data types.", "doi": "10.1038/s41564-025-02116-2", "pmid": "41006832", "labels": {"DDLS Fellow": "", "Luisa Hugerth": ""}, "xrefs": [{"db": "pii", "key": "10.1038/s41564-025-02116-2"}], "notes": [], "created": "2026-08-20T08:55:29.339Z", "modified": "2026-09-23T09:09:54.689Z"}, {"entity": "publication", "iuid": "4b62a54122f741a095b9996db38e4310", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4b62a54122f741a095b9996db38e4310.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4b62a54122f741a095b9996db38e4310"}}, "title": "Liquid biomarkers associate with TGF-\u03b2 Type I receptor and hypoxia in kidney cancer.", "authors": [{"family": "Mallikarjuna", "given": "Pramod", "initials": "P"}, {"family": "Erdem", "given": "Cemal", "initials": "C", "orcid": "0000-0003-3663-3646", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f71b5af589264614a52eefa8baba3132.json"}}, {"family": "Beorlegui", "given": "Ruben Ilundain", "initials": "RI"}, {"family": "Larsson", "given": "Anders", "initials": "A", "orcid": "0000-0003-3161-0402", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5b44e49c49f644cfa3348bcc4bb0080f.json"}}, {"family": "Ljungberg", "given": "B\u00f6rje", "initials": "B"}, {"family": "Kamali-Moghaddam", "given": "Masood", "initials": "M"}, {"family": "Landstr\u00f6m", "given": "Mar\u00e9ne", "initials": "M", "orcid": "0000-0001-6737-7230", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8cbb0a1e30bf44a2a267e6a3090acf01.json"}}], "type": "letter", "published": "2025-09-26", "journal": {"title": "Signal Transduct Target Ther", "issn": "2059-3635", "volume": "10", "issue": "1", "pages": "309", "issn-l": null}, "abstract": null, "doi": "10.1038/s41392-025-02404-7", "pmid": "40998794", "labels": {"Cemal Erdem": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC12464240"}, {"db": "pii", "key": "10.1038/s41392-025-02404-7"}], "notes": [], "created": "2025-11-26T12:30:53.241Z", "modified": "2026-09-23T13:24:26.124Z"}, {"entity": "publication", "iuid": "420a0bbc01614b8a8e996e0a27dbc995", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/420a0bbc01614b8a8e996e0a27dbc995.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/420a0bbc01614b8a8e996e0a27dbc995"}}, "title": "Retrospective Validation of an Artificial Intelligence System for Diagnostic Assessment of Prostate Biopsies on the ProMort Cohort: Study Protocol", "authors": [{"family": "Ji", "given": "Xiaoyi", "initials": "X", "orcid": "0009-0005-8431-7906", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e2e50c016e1040a5995a50a049280577.json"}}, {"family": "Zelic", "given": "Renata", "initials": "R", "orcid": "0000-0002-8842-5964", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/121ec02a5a924a899b913c600b3b3763.json"}}, {"family": "Aspegren", "given": "Oskar", "initials": "O", "orcid": "0000-0002-5309-7737", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d267fe4993d14025a303ba9a1f5863da.json"}}, {"family": "Mulliqi", "given": "Nita", "initials": "N", "orcid": "0009-0002-7448-4960", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/306c43e2841c4ad098db7a5ac481a1bf.json"}}, {"family": "Fiorentino", "given": "Michelangelo", "initials": "M", "orcid": "0000-0002-1749-150X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/adb2abeaee404c04b373ac96157340bf.json"}}, {"family": "Giunchi", "given": "Francesca", "initials": "F", "orcid": "0000-0001-5298-939X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3d3cc40c9d2e4fc9a796549fa6677e30.json"}}, {"family": "Molinaro", "given": "Luca", "initials": "L"}, {"family": "Boman", "given": "Sol Erika", "initials": "SE", "orcid": "0009-0001-5733-3178", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8a605b0dadad4b3696396827ebac9348.json"}}, {"family": "Szolnoky", "given": "Kelvin", "initials": "K", "orcid": "0000-0002-0554-1872", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5059c9f881d4434f9b64f3bb381478fe.json"}}, {"family": "Liu", "given": "Luana Xuan", "initials": "LX"}, {"family": "Pettersson", "given": "Andreas", "initials": "A"}, {"family": "Vincent", "given": "Per Henrik", "initials": "PH", "orcid": "0000-0002-9895-5803", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d5490a9e6c334e48b301e64fdd747504.json"}}, {"family": "Eklund", "given": "Martin", "initials": "M", "orcid": "0000-0001-5032-5266", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/06721510ebc8462386e0e6fc6c84315b.json"}}, {"family": "Akre", "given": "Olof", "initials": "O", "orcid": "0000-0002-3750-3029", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3f25f3b240644cda828e4744b30020a9.json"}}, {"family": "Kartasalo", "given": "Kimmo", "initials": "K", "orcid": "0000-0002-9470-4783", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7c6fc97c06ed456c8bdd1f03db8a9b72.json"}}], "type": "posted-content", "published": "2025-09-23", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2025.09.22.25336169", "pmid": null, "labels": {"Kimmo Kartasalo": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T11:07:11.947Z", "modified": "2026-09-23T15:51:23.285Z"}, {"entity": "publication", "iuid": "38c4c360894945348775e8b57bc4b5c7", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/38c4c360894945348775e8b57bc4b5c7.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/38c4c360894945348775e8b57bc4b5c7"}}, "title": "U-FISH: a fluorescent spot detector for imaging-based spatial-omics analysis and AI-assisted FISH diagnosis.", "authors": [{"family": "Xu", "given": "Weize", "initials": "W"}, {"family": "Cai", "given": "Huaiyuan", "initials": "H"}, {"family": "Zhang", "given": "Qian", "initials": "Q"}, {"family": "Wang", "given": "Zhengze", "initials": "Z"}, {"family": "Yang", "given": "Jiajun", "initials": "J"}, {"family": "Wu", "given": "Xiaofeng", "initials": "X"}, {"family": "Li", "given": "Chengwen", "initials": "C"}, {"family": "Cui", "given": "Chenghua", "initials": "C"}, {"family": "Liu", "given": "Changzhi", "initials": "C"}, {"family": "He", "given": "Jin", "initials": "J"}, {"family": "Mueller", "given": "Florian", "initials": "F"}, {"family": "Dai", "given": "Jinxia", "initials": "J"}, {"family": "Hao", "given": "Chen", "initials": "C"}, {"family": "Ouyang", "given": "Wei", "initials": "W"}, {"family": "Cao", "given": "Gang", "initials": "G"}], "type": "evaluation study", "published": "2025-09-01", "journal": {"title": "Genome Biol.", "issn": "1474-760X", "volume": "26", "issue": "1", "pages": "261", "issn-l": "1474-7596"}, "abstract": "Imaging-based spatial-omics advances biomedical discoveries with subcellular resolution and high sensitivity, but accurately identifying signal spots from diverse images remains challenging. We develop U-FISH, a deep learning method that enhances images for consistent spot detection across various spatial-omics data. We establish a comprehensive FISH image dataset from seven spatial-omics methods. Benchmark analysis shows U-FISH has superior accuracy and generalizability compared to existing methods and can effectively decode 3D FISH data. U-FISH is the first spot detection software integrated with large language models, as demonstrated in AI-assisted diagnostics. Our study provides a valuable tool for spatial-omics analysis and diagnostics.", "doi": "10.1186/s13059-025-03736-x", "pmid": "40890868", "labels": {"Wei Ouyang": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC12400573"}, {"db": "pii", "key": "10.1186/s13059-025-03736-x"}], "notes": [], "created": "2025-12-15T10:05:32.557Z", "modified": "2026-09-23T09:11:35.418Z"}, {"entity": "publication", "iuid": "2fa854b8d5b14823948e2948daa7b0b4", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/2fa854b8d5b14823948e2948daa7b0b4.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/2fa854b8d5b14823948e2948daa7b0b4"}}, "title": "Small Bugs, Big Data: Metagenomics for Arthropod Biodiversity Monitoring.", "authors": [{"family": "L\u00f3pez Clinton", "given": "Samantha", "initials": "S", "orcid": "0000-0003-1364-9135", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb3097a7dd3342e6ae0d1532ae0d18f3.json"}}, {"family": "Iwaszkiewicz-Eggebrecht", "given": "Ela", "initials": "E", "orcid": "0000-0003-1412-1711", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/06a3ef4263454d75a27cbd714c41cfdc.json"}}, {"family": "Miraldo", "given": "Andreia", "initials": "A", "orcid": "0000-0001-6107-006X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3edeaea21c024ee0ac9cbc0000e10c7f.json"}}, {"family": "Goodsell", "given": "Robert", "initials": "R"}, {"family": "Webster", "given": "Matthew T", "initials": "MT"}, {"family": "Ronquist", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-3929-251X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/69b01802bbbd477ca4e9b3f6204fb391.json"}}, {"family": "van der Valk", "given": "Tom", "initials": "T", "orcid": "0000-0001-6582-3452", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/aa0dba3cc12143cba213f7f3a052216c.json"}}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "Ecol Evol", "issn": "2045-7758", "volume": "15", "issue": "9", "pages": "e72163", "issn-l": "2045-7758"}, "abstract": "Obtaining genome-wide data from complex samples, such as environmental material or bulk species collections, is increasingly feasible, yet inferring species presence and population genomic insights remains challenging. We applied metagenomic sequencing to 40 arthropod bulk samples collected with Malaise traps across Sweden and compared results with metabarcoding of the same material. Using a custom genome database, we achieved genus-level classification largely consistent with metabarcoding. While metagenomics detected all genera identified by metabarcoding, conservative filtering thresholds designed to minimise false positives also excluded some true signals, particularly for low-abundance taxa. Taxonomic overlap between methods was further constrained by limited reference database representation. Beyond taxonomic assignment, metagenomic sequencing yielded genome-level information: we inferred haplotype diversity, heterozygosity and geographic population structure for several abundant species, including variable degrees of hybrid origin in red wood ants and the genetic distinctiveness of Gotland bumblebees. Finally, by-catch plant DNA present in the bulk samples revealed plausible arthropod-plant interactions, several of which align with known ecological associations. Together, these results demonstrate the potential of metagenomics for biodiversity monitoring and population genomics, while underscoring the importance of filtering criteria and comprehensive reference databases.", "doi": "10.1002/ece3.72163", "pmid": "40964625", "labels": {"DDLS Fellow": "", "Tom van der Valk": ""}, "xrefs": [{"db": "pmc", "key": "PMC12440566"}, {"db": "pii", "key": "ECE372163"}], "notes": [], "created": "2026-09-23T15:51:16.948Z", "modified": "2026-09-23T15:51:17.022Z"}, {"entity": "publication", "iuid": "3ee8c8956ad54903b231c884ce595b7f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3ee8c8956ad54903b231c884ce595b7f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3ee8c8956ad54903b231c884ce595b7f"}}, "title": "Genomic profiling of enterotoxigenic Escherichia coli toxins and adhesins in livestock isolates from Kenya.", "authors": [{"family": "Njoroge", "given": "Samuel M", "initials": "SM"}, {"family": "Kulohoma", "given": "Benard W", "initials": "BW"}, {"family": "Falzon", "given": "Laura C", "initials": "LC"}, {"family": "Kamanu", "given": "Timothy K", "initials": "TK"}, {"family": "Momanyi", "given": "Kelvin", "initials": "K"}, {"family": "Muinde", "given": "Patrick", "initials": "P"}, {"family": "Murungi", "given": "Maurice K", "initials": "MK"}, {"family": "Ogendo", "given": "Allan", "initials": "A"}, {"family": "Ogola", "given": "Joseph", "initials": "J"}, {"family": "Wambua", "given": "Lilian", "initials": "L"}, {"family": "Kangethe", "given": "Erastus", "initials": "E"}, {"family": "Rushton", "given": "Jonathan", "initials": "J"}, {"family": "Woolhouse", "given": "Mark", "initials": "M"}, {"family": "Thomson", "given": "Nicholas R", "initials": "NR"}, {"family": "Kariuki", "given": "Samuel", "initials": "S"}, {"family": "von Mentzer", "given": "Astrid", "initials": "A"}, {"family": "F\u00e8vre", "given": "Eric M", "initials": "EM"}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "Microb Genom", "issn": "2057-5858", "volume": "11", "issue": "9", "issn-l": null}, "abstract": "Enterotoxigenic Escherichia coli (ETEC) is a significant cause of diarrhoea in livestock and humans. The epidemiology of ETEC in animals remains understudied, prompting an investigation into the virulence factors and associated adhesins of ETEC in livestock from Western Kenya. Also, there is limited evidence supporting the role of livestock as possible zoonotic reservoirs for ETEC. ETEC strains harbour colonization factors/adhesins and enterotoxins, with animal ETECs exhibiting various adhesins (F4, F5, F6, F17, F18 and F41). Enterotoxins include heat-labile (LT) and heat-stable (ST) toxins and are further divided into LT-I and LT-II and STa and STb, respectively. Additional toxin combinations occur, with ETEC and Shiga toxin-producing E. coli (STEC) hybrids garnering public health significance. Here, we analysed faecal and mesenteric lymph node samples from diverse livestock across three Western Kenyan counties (Busia, Bungoma and Kakamega), using whole-genome sequencing. In silico screening determined the presence of AB5 and A2B5-like toxin genes, including cytolethal distending toxin (cdtABC) along with associated adhesins. To broaden the screening panel, adhesin genes identified were further characterized to identify both known and novel alleles, particularly focusing on human-ETEC colonization factors. Two estA alleles (estA-4-06, estA-6-02) and six eltAB-II toxin alleles (eltAB-II-a2-01, eltAB-II-a3-01, eltAB-II-c1-02, eltAB-II-c6-03, eltAB-II-c6-04 and eltAB-II-c7-02) were identified in livestock. Hybrid ETECs identified were ETEC/STEC present in 6.7% (4/60) of ETEC strains and ETEC with cdtABC type I. An A2B5-like tripartite toxin, potentially resembling the typhoid toxin, was detected in 8.7% (4/46) of the eltAB-II-positive strains. It may have unique effects on enterocytes distinct from known toxins. These findings expand our understanding of ETEC pathogenicity and genetic diversity in animal reservoirs, while also highlighting potential zoonotic risks. They broaden the toxin repertoire, offer adhesin-based vaccine candidates for livestock and provide valuable insights for future vaccine development and public health strategies in the Lake Victoria Crescent ecosystem and beyond.", "doi": "10.1099/mgen.0.001515", "pmid": "40996892", "labels": {"Astrid von Mentzer": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC13293299"}, {"db": "BioProject", "key": "PRJEB33365"}], "notes": [], "created": "2025-12-02T15:46:58.131Z", "modified": "2026-09-23T15:51:29.508Z"}, {"entity": "publication", "iuid": "aa413e1fb96e4f6391507ad3484529c7", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/aa413e1fb96e4f6391507ad3484529c7.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/aa413e1fb96e4f6391507ad3484529c7"}}, "title": "Genomic and morphological analysis reveals long-term mammoth hybridization in British Columbia, Canada.", "authors": [{"family": "Dehasque", "given": "Marianne", "initials": "M", "orcid": "0000-0002-4640-8306", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/873b625c6ce44ec48f30d92fbc9b3e2f.json"}}, {"family": "van der Valk", "given": "Tom", "initials": "T", "orcid": "0000-0001-6582-3452", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/aa0dba3cc12143cba213f7f3a052216c.json"}}, {"family": "Chac\u00f3n-Duque", "given": "J Camilo", "initials": "JC"}, {"family": "Termes", "given": "Laura", "initials": "L"}, {"family": "Larsson", "given": "Petter", "initials": "P"}, {"family": "Moots", "given": "Hannah M", "initials": "HM"}, {"family": "Tubbesing", "given": "Florentine", "initials": "F"}, {"family": "Larsdotter", "given": "Juliana", "initials": "J"}, {"family": "Oteo-Garc\u00eda", "given": "Gonzalo", "initials": "G"}, {"family": "Moreland", "given": "Kelsey", "initials": "K"}, {"family": "van Essen", "given": "Hans", "initials": "H"}, {"family": "Arbour", "given": "Victoria", "initials": "V"}, {"family": "Keddie", "given": "Grant", "initials": "G"}, {"family": "Richards", "given": "Michael P", "initials": "MP"}, {"family": "D\u00edez-Del-Molino", "given": "David", "initials": "D"}, {"family": "Heintzman", "given": "Peter D", "initials": "PD"}, {"family": "Lister", "given": "Adrian", "initials": "A"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L"}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "Biol. Lett.", "issn": "1744-957X", "volume": "21", "issue": "9", "pages": "20250305", "issn-l": "1744-9561"}, "abstract": "Climate changes profoundly impact species distributions and can drastically alter dynamics between formerly isolated taxa. The evolution of mammoths within North America was characterized by repeated cycles of dispersal and putative gene flow between woolly and Columbian mammoths. However, as genome-wide studies on mammoths have predominantly focused on Siberia, the consequences of these North American range shifts remain unclear. Here, we generated genome-wide and morphological data for two Late Pleistocene mammoth molars from British Columbia, Canada (BC), and jointly analysed these with previously published data. Our genome-wide analysis (n = 16) revealed gene flow between woolly and Columbian mammoths that would have gone undiscovered based on morphological (n = 48) and mitochondrial analysis (n = 124) alone. Consistent with their hybrid nature, our analyses suggest that these two BC mammoths had elevated genomic diversity. Our results highlight the importance of combining data types to reconstruct past evolutionary events. These findings demonstrate how the geographical range expansion of woolly mammoths resulted in long-term hybridization with local Columbian mammoths and enhance our understanding of the genomic and morphological consequences of climate-mediated dispersal.", "doi": "10.1098/rsbl.2025.0305", "pmid": "40994021", "labels": {"DDLS Fellow": "", "Tom van der Valk": ""}, "xrefs": [{"db": "pmc", "key": "PMC12461089"}], "notes": [], "created": "2026-09-23T12:33:27.255Z", "modified": "2026-09-23T12:33:27.288Z"}, {"entity": "publication", "iuid": "5a8b441b81b34d0d989e18950ffd3808", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5a8b441b81b34d0d989e18950ffd3808.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5a8b441b81b34d0d989e18950ffd3808"}}, "title": "Gene and pathway analysis of genome-wide genetic associations of bladder cancer.", "authors": [{"family": "Shi", "given": "Mingjun", "initials": "M"}, {"family": "Meng", "given": "Xiangyu", "initials": "X", "orcid": "0000-0001-5669-3502", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7c234a6170a1406e9d163c9aeffa83b4.json"}}, {"family": "Xu", "given": "Xuan", "initials": "X"}, {"family": "Wang", "given": "Qiaoli", "initials": "Q"}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "Curr Urol", "issn": "1661-7649", "volume": "19", "issue": "5", "pages": "321-330", "issn-l": null}, "abstract": "Although genetic variants associated with bladder cancer (BCa) risk have been identified through hypothesis-driven and genome-wide association studies, a systematic understanding of BCa genetic susceptibility at the gene and pathway levels remains to be achieved.\n\nIn this 2-stage functional genomics study, we used 5 independent tools for genome-wide gene mapping and ranking based on BCa genome-wide association studies summary statistics, followed by a meta-analysis of gene-level significance p values, to obtain a consensus gene ranking in terms of association with BCa. Subsequently, we performed preranked gene-set enrichment analysis to identify the functional pathways involved in BCa genetic susceptibility. Joint analysis with gene-set enrichment analysis, based on somatic alteration frequency, was performed to explore the pathway-level relationships between genetic susceptibility and somatic alterations in BCa.\n\nOther than the well-known BCa genes (such as FGFR3, MYC, TERT, CCNE1, and TP63), we additionally prioritized a set of novel genes likely to be genetically implicated in BCa development, including SETD2, a possible tumor suppressor gene involved in chromatin remodeling. We further demonstrated convergence between genetic associations and somatic alterations at both the gene (eg, FGFR3 and TERT) and pathway levels (eg, cell cycle and chromatin modification), as well as functional ontologies specifically implicated in germline predisposition to BCa (eg, CD8/TCR signaling, immune checkpoints, and cytokine signaling).\n\nWe identified several novel genes associated with BCa and demonstrated that genetic variants contribute to the development of BCa by affecting antitumor immunity, response to toxic exposure, and RNA and protein homeostasis and synergizing with somatic alterations in various cancer-related pathways.", "doi": "10.1097/CU9.0000000000000289", "pmid": "40894278", "labels": {"DDLS Fellow": null, "Qiaoli Wang": null}, "xrefs": [{"db": "pmc", "key": "PMC12398375"}, {"db": "pii", "key": "Curr-Urol-24-0153"}], "notes": [], "created": "2025-11-28T12:24:46.558Z", "modified": "2025-11-28T12:24:46.627Z"}, {"entity": "publication", "iuid": "260fb2c77a4b4503bf0c8647bdc84883", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/260fb2c77a4b4503bf0c8647bdc84883.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/260fb2c77a4b4503bf0c8647bdc84883"}}, "title": "In silico docking yields small molecule compounds targeting the core of Frizzled 7 as negative allosteric modulators", "authors": [{"family": "Schulte", "given": "Gunnar", "initials": "G", "orcid": "0000-0002-2700-7013", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ca48082cc934a8494ac50e756be0f3e.json"}}, {"family": "Scharf", "given": "Magdalena", "initials": "M", "orcid": "0000-0002-3305-3956", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca43ba6516014fe597ead17e737f697a.json"}}, {"family": "Gr\u00e4tz", "given": "Lukas", "initials": "L"}, {"family": "Kinsolving", "given": "Julia", "initials": "J", "orcid": "0000-0002-0431-8222", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/db117db4a1f54b2281020100a5de834d.json"}}, {"family": "Voss", "given": "Jan", "initials": "J", "orcid": "0000-0003-0595-4607", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f917ae3e8a384e37ab569ed8b3a6a3e4.json"}}, {"family": "Carrasco-Busturia", "given": "David", "initials": "D", "orcid": "0000-0003-1588-338X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/266c497cacdb47938ff6818655864c9d.json"}}, {"family": "Forsberg", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0002-6247-4063", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/36ea51bfa66d48b7a43559c3d0eaa59f.json"}}, {"family": "Kolb", "given": "Peter", "initials": "P", "orcid": "0000-0003-4089-614X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4b8d1c7a084e4870b3b7e94788c0c3cc.json"}}], "type": "posted-content", "published": "2025-08-15", "journal": {"issn-l": null}, "abstract": null, "doi": "10.21203/rs.3.rs-6908411/v2", "pmid": null, "labels": {"DDLS Fellow": "", "Bj\u00f6rn Forsberg": ""}, "xrefs": [], "notes": [], "created": "2026-10-01T08:34:43.437Z", "modified": "2026-10-01T08:34:43.517Z"}, {"entity": "publication", "iuid": "4646807d8f2048c7be81d65df4d86d55", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4646807d8f2048c7be81d65df4d86d55.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4646807d8f2048c7be81d65df4d86d55"}}, "title": "Immune cell activation produces locally scrambled foci of plasma membrane lipids.", "authors": [{"family": "Sputay", "given": "Daryna", "initials": "D", "orcid": "0009-0008-9987-5582", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3dedb072e04d447c87728ea160049cf0.json"}}, {"family": "Doktorova", "given": "Milka", "initials": "M", "orcid": "0000-0003-4366-2242", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/791384c319f04584bac8ffb21df7271f.json"}}, {"family": "Chan", "given": "Sze Ham", "initials": "SH", "orcid": "0000-0002-3235-0852", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4854c445b24541adbfcb1a44a1d02305.json"}}, {"family": "Guo", "given": "Emma Han", "initials": "EH"}, {"family": "Wang", "given": "Hong-Yin", "initials": "HY"}, {"family": "Lorent", "given": "Joseph H", "initials": "JH", "orcid": "0000-0002-7537-8521", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6c6a5fdf28de42ff8a14a7ae259939cb.json"}}, {"family": "Levental", "given": "Ilya", "initials": "I", "orcid": "0000-0002-1206-9545", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7fe40c2b810348cab78616402d4d1f1f.json"}}, {"family": "Levental", "given": "Kandice R", "initials": "KR", "orcid": "0000-0002-2234-3683", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dcde4d3042b349b199c48509444ac8f9.json"}}], "type": "journal article", "published": "2025-08-13", "journal": {"title": "Faraday Discuss", "issn": "1364-5498", "volume": "259", "issue": "0", "pages": "45-59", "issn-l": null}, "abstract": "Most eukaryotic cells maintain a large disparity in lipid compositions between the cytosolic and external leaflets of the plasma membrane (PM) bilayer. This lipid asymmetry is maintained by energy-consuming flippase enzymes that selectively drive phospholipids into the cytosolic leaflet, often against large concentration gradients. Scramblases, activated by intracellular Ca2+ or apoptotic signaling, shuttle phospholipids down their concentration gradient to release lipid asymmetry. Such scrambling is typically evidenced by exposure of phosphatidylserine (PS) to the external leaflet and is associated with many physiological processes, most notably blood clotting and cell death, but also activation of immune cells. Here, we show that both PS and phosphatidylethanolamine (PE) appear on the PM external leaflet following immune receptor-mediated activation of mast cells. We also observe similar effects in T cells. Importantly, in contrast to wholesale release of PM asymmetry induced by calcium ionophores or apoptosis, we show that scrambling in activated immune cells is focal, with small, stable regions of surface exposed PS. These scrambled foci are calcium dependent, have lower lipid packing than their surrounding outer leaflet, and are reversible. These observations of local, transient scrambling during physiological activation of healthy immune cells suggest important roles for the lateral and transbilayer organization of membrane lipids.", "doi": "10.1039/d4fd00205a", "pmid": "40351229", "labels": {"Milka Doktorova": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC12067185"}], "notes": [], "created": "2026-08-20T09:27:53.683Z", "modified": "2026-09-23T11:30:21.873Z"}, {"entity": "publication", "iuid": "c0b91b9a58314b17b3cb74be5ef1beaa", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c0b91b9a58314b17b3cb74be5ef1beaa.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c0b91b9a58314b17b3cb74be5ef1beaa"}}, "title": "Exploring the sensitivities of experimental techniques to various types of membrane asymmetry using atomistic simulations.", "authors": [{"family": "Heberle", "given": "Frederick A", "initials": "FA", "orcid": "0000-0002-0424-3240", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2557f5621a0b4c87b5f4702fbc7b6bdb.json"}}, {"family": "Doktorova", "given": "Milka", "initials": "M", "orcid": "0000-0003-4366-2242", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/791384c319f04584bac8ffb21df7271f.json"}}], "type": "journal article", "published": "2025-08-13", "journal": {"title": "Faraday Discuss", "issn": "1364-5498", "volume": "259", "issue": "0", "pages": "300-320", "issn-l": null}, "abstract": "Biological membranes have two leaflets that can differ in both lipid composition and total lipid abundance. These different types of asymmetries play a major role in determining the biophysical properties of the membrane; however, they have proven challenging to assay experimentally even in simpler model systems. Molecular dynamics simulations offer the means for detailed computational investigation of systematically varied interleaflet lipid distributions, but opportunities for critical validation with wet lab experiments are scarce. To help address this problem, here we use atomistic simulations of asymmetric bilayers to generate synthetic experimental data and thus investigate the sensitivity of various approaches to changes in relative lipid composition, number, and cholesterol distribution. Contrary to trends in symmetric bilayers, the simulations showed a decrease in lipid packing with increasing cholesterol in differentially stressed asymmetric bilayers, with more pronounced changes in the more loosely packed leaflet. Representative experimental data computed from the simulation trajectories indicated that the detection of asymmetry-induced changes in leaflet properties should be possible with environment-sensitive fluorescent probes and NMR observables, but may require optimization of sample preparation conditions. On the other hand, small-angle scattering data are already experimentally accessible and can reveal differential leaflet packing densities through a model-free analysis. We further show that computationally generated cryo-EM intensity profiles are highly sensitive to phospholipid imbalance between membrane leaflets. Together, these findings provide a roadmap for developing targeted applications of the in vitro techniques and obtaining experimental data critical for validating computationally derived principles related to membrane asymmetry.", "doi": "10.1039/d4fd00200h", "pmid": "40338116", "labels": {"Milka Doktorova": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC12060774"}], "notes": [], "created": "2026-08-20T09:27:51.743Z", "modified": "2026-09-23T11:30:12.057Z"}, {"entity": "publication", "iuid": "922815f4f6544556a02646ea90aa51a9", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/922815f4f6544556a02646ea90aa51a9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/922815f4f6544556a02646ea90aa51a9"}}, "title": "Systems analysis of clinical malaria reveals proteomic perturbation and innate-adaptive crosstalk linked to disease severity.", "authors": [{"family": "Lautenbach", "given": "Maximilian Julius", "initials": "MJ"}, {"family": "Wyss", "given": "Katja", "initials": "K"}, {"family": "Yman", "given": "Victor", "initials": "V"}, {"family": "Foroogh", "given": "Fariba", "initials": "F"}, {"family": "Satarvandi", "given": "Donya", "initials": "D"}, {"family": "Mousavian", "given": "Zaynab", "initials": "Z"}, {"family": "Sond\u00e9n", "given": "Klara", "initials": "K"}, {"family": "Wang", "given": "Jun", "initials": "J"}, {"family": "\u00c1lvez", "given": "Mar\u00eda Bueno", "initials": "MB"}, {"family": "Bergstr\u00f6m", "given": "Sofia", "initials": "S"}, {"family": "Nilsson", "given": "Peter", "initials": "P"}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Brodin", "given": "Petter", "initials": "P"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Sundling", "given": "Christopher", "initials": "C"}, {"family": "F\u00e4rnert", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2025-08-12", "journal": {"title": "Immunity", "issn": "1097-4180", "volume": "58", "issue": "8", "pages": "2120-2136.e5", "issn-l": null}, "abstract": "Malaria presents with varying degrees of severity. To improve clinical management and prevention, it is crucial to understand the pathogenesis and host response. We analyzed 1,463 plasma proteins during and after acute Plasmodium falciparum malaria in adult travelers and linked responses to peripheral immune cells by integrating with single-cell RNA sequencing (RNA-seq) data from a subset of donors. We identified extensive perturbations in over 250 proteins with diverse origins, including many not previously analyzed in malaria patients, such as hormones, circulating receptors, and intracellular or membrane-bound proteins from affected tissues. The protein profiles clustered participants according to disease severity, enabling the identification of a compressed 11-protein signature enriched in severe malaria. Conceptually, this study advances our understanding of malaria by linking systemic proteomic changes to immune cell communication and organ-specific responses. This resource, which includes an interactive platform to explore data, opens new avenues for hypothesis generation, biomarker discovery, and therapeutic target identification.", "doi": "10.1016/j.immuni.2025.06.014", "pmid": "40664217", "labels": {"Fredrik Edfors": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pii", "key": "S1074-7613(25)00283-3"}], "notes": [], "created": "2026-09-23T11:34:11.382Z", "modified": "2026-09-23T11:34:11.402Z"}, {"entity": "publication", "iuid": "e6075902b59241839112106d956001ab", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e6075902b59241839112106d956001ab.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e6075902b59241839112106d956001ab"}}, "title": "Risk of atherosclerotic cardiovascular disease after cancer diagnosis: findings from 3 prospective cohort studies.", "authors": [{"family": "Liu", "given": "Qiang", "initials": "Q"}, {"family": "Wang", "given": "Qiaoli", "initials": "Q", "orcid": "0000-0003-4152-7821", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/357edb3116b64ad5aa929dcb7d07a1be.json"}}, {"family": "Wang", "given": "Kai", "initials": "K", "orcid": "0000-0002-5614-5618", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f651a57b4d8c4ba9a10c056b39bfbcb5.json"}}, {"family": "Han", "given": "Han", "initials": "H", "orcid": "0000-0002-8784-9001", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9de0c752caf041819ad59238d9e590fd.json"}}, {"family": "Wang", "given": "Molin", "initials": "M"}, {"family": "Wang", "given": "Jing", "initials": "J", "orcid": "0000-0002-3224-3993", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3d5de488eacf4c058a2c6e7080355b0d.json"}}, {"family": "Song", "given": "Mingyang", "initials": "M", "orcid": "0000-0002-1324-0316", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dc64686b70104e30b57c1376d935d56f.json"}}, {"family": "Giovannucci", "given": "Edward", "initials": "E", "orcid": "0000-0002-6123-0219", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4958abe8f85b417cae3009a782e9f69d.json"}}], "type": "journal article", "published": "2025-08-01", "journal": {"title": "J. Natl. Cancer Inst.", "issn": "1460-2105", "volume": "117", "issue": "8", "pages": "1707-1716", "issn-l": "0027-8874"}, "abstract": "We sought to determine the association between cancer diagnosis and subsequent risk of atherosclerotic cardiovascular disease (ASCVD) and examine the trajectory of the association over time after cancer diagnosis.\n\nWe prospectively followed 108 689 women in the Nurses' Health Study (1984-2020), 113 569 women in the Nurses' Health Study II (1991-2019), and 45 328 men in the Health Professionals Follow-Up Study (1986-2016) who were free of ASCVD and cancer at baseline. We conducted multivariable-adjusted, time-varying Cox proportional hazards regression models to assess ASCVD risk following an individual's cancer diagnosis.\n\nDuring up to 36 years of follow-up, 4334 new-onset ASCVD events among 49 603 incident cancer cases were documented. After adjusting for shared risk factors, cervical cancer (hazard ratio [HR] = 1.56, 95% confidence interval [CI] = 1.06 to 2.29) and Hodgkin lymphoma (HR = 2.80, 95% CI = 1.89 to 4.15) was associated with increased risk of ASCVD incidence, whereas prostate cancer was associated with a lower ASCVD incidence (HR = 0.91, 95% CI = 0.85 to 0.97). Compared with cancer-free individuals, breast cancer survivors experienced lower ASCVD risk during the first 7.5 years, but risk gradually increased afterward (Pnonlinearity = .01). The risk of ASCVD increased over time among patients with cancers of the colorectum (P = .003), lung (P = .002), and endometrium (P = .04). No statistically significant association with ASCVD risk was observed for cancers of the oral cavity and pharynx, kidney, or ovary; sarcoma; melanoma; or leukemia.\n\nCervical cancer and Hodgkin lymphoma were associated with an increased risk of new-onset ASCVD, independent of shared risk factors. No increased risk was found with other cancers. Risk trajectories of ASCVD varied over time after diagnosis by cancer type.", "doi": "10.1093/jnci/djaf122", "pmid": "40445187", "labels": {"DDLS Fellow": null, "Qiaoli Wang": null}, "xrefs": [{"db": "mid", "key": "NIHMS2095411"}, {"db": "pmc", "key": "PMC12290291"}, {"db": "pii", "key": "8153926"}], "notes": [], "created": "2025-11-28T12:26:12.130Z", "modified": "2025-11-28T12:26:12.278Z"}, {"entity": "publication", "iuid": "8383db59b6414fd383474a65633a722e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8383db59b6414fd383474a65633a722e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8383db59b6414fd383474a65633a722e"}}, "title": "Mechanistic modeling of cell viability assays with in silico lineage tracing.", "authors": [{"family": "Mutsuddy", "given": "Arnab", "initials": "A", "orcid": "0000-0001-6488-7067", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8e14f7a9dc804ab1bccf030cc31a121b.json"}}, {"family": "Huggins", "given": "Jonah R", "initials": "JR", "orcid": "0000-0001-7468-4626", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7cba794166d94144af105b8894423e35.json"}}, {"family": "Amrit", "given": "Aurore K", "initials": "AK"}, {"family": "Harley-Gasaway", "given": "Atalanta Manuela", "initials": "AM"}, {"family": "Erdem", "given": "Cemal", "initials": "C", "orcid": "0000-0003-3663-3646", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f71b5af589264614a52eefa8baba3132.json"}}, {"family": "Jones", "given": "Evan T", "initials": "ET"}, {"family": "Laurine", "given": "Olivia G", "initials": "OG"}, {"family": "Calhoun", "given": "Jon C", "initials": "JC", "orcid": "0000-0001-7191-4422", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f7fd93361af9415f94fef93a4d60783c.json"}}, {"family": "Birtwistle", "given": "Marc R", "initials": "MR", "orcid": "0000-0002-0341-0705", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/df52e09a2f984f10833bda7b554b1a22.json"}}], "type": "journal article", "published": "2025-08-00", "journal": {"title": "PLoS Comput Biol", "issn": "1553-7358", "volume": "21", "issue": "8", "pages": "e1013156", "issn-l": "1553-734X"}, "abstract": "Data from cell viability assays, which measure cumulative division and death events in a population and reflect substantial cellular heterogeneity, are widely available. However, interpreting such data with mechanistic computational models is hindered because direct model/data comparison is often muddled. We developed an algorithm that tracks simulated division and death events in mechanistically-detailed single-cell lineages to enable such a model/data comparison and suggest causes of cell-cell drug response variability. Using our previously developed model of mammalian single-cell proliferation and death signaling, we simulated drug dose response experiments for four targeted anti-cancer drugs (alpelisib, neratinib, trametinib and palbociclib) and compared them to experimental data. Simulations are consistent with data for strong growth inhibition by trametinib (MEK inhibitor) and overall lack of efficacy for alpelisib (PI-3K inhibitor), but are inconsistent with data for palbociclib (CDK4/6 inhibitor) and neratinib (EGFR inhibitor). Model/data inconsistencies suggest that (i) the importance of CDK4/6 for driving the cell cycle may be overestimated, and (ii) the cellular balance between basal (tonic) and ligand-induced signaling is a critical determinant of receptor inhibitor response. Simulations show subpopulations of rapidly and slowly dividing cells in both control and drug-treated conditions. Variations in mother cells prior to drug treatment impinging on ERK pathway activity are associated with the rapidly dividing phenotype and trametinib resistance. This work lays a foundation for the application of mechanistic modeling to large-scale cell viability datasets and better understanding determinants of cellular heterogeneity in drug response.", "doi": "10.1371/journal.pcbi.1013156", "pmid": "40880521", "labels": {"Cemal Erdem": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC12416836"}, {"db": "pii", "key": "PCOMPBIOL-D-24-01441"}], "notes": [], "created": "2025-11-26T12:30:51.116Z", "modified": "2026-10-01T08:34:49.597Z"}, {"entity": "publication", "iuid": "a43536e195f64a35a033e6e8d4d2e0a4", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a43536e195f64a35a033e6e8d4d2e0a4.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a43536e195f64a35a033e6e8d4d2e0a4"}}, "title": "Germline genetic variation impacts clonal hematopoiesis landscape and progression to malignancy.", "authors": [{"family": "Liu", "given": "Jie", "initials": "J", "orcid": "0000-0001-6365-1888", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ddad30666cdd405aa37bb60d42f29348.json"}}, {"family": "Tran", "given": "Duc", "initials": "D", "orcid": "0000-0003-2918-8601", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f911948879504edd8870280ef9293a1c.json"}}, {"family": "Xue", "given": "Liying", "initials": "L"}, {"family": "Wiley", "given": "Brian J", "initials": "BJ"}, {"family": "Vlasschaert", "given": "Caitlyn", "initials": "C"}, {"family": "Watson", "given": "Caroline J", "initials": "CJ", "orcid": "0000-0002-8351-268X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c61f7e01d88b48f29b0909570d2eec97.json"}}, {"family": "MacGregor", "given": "Hamish A J", "initials": "HAJ"}, {"family": "Zong", "given": "Xiaoyu", "initials": "X"}, {"family": "Chan", "given": "Irenaeus C C", "initials": "ICC"}, {"family": "Das", "given": "Indraniel", "initials": "I"}, {"family": "Uddin", "given": "Md Mesbah", "initials": "MM", "orcid": "0000-0003-1846-0411", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/42f1ac7010c34ba997a3fd9e56c6a56a.json"}}, {"family": "Niroula", "given": "Abhishek", "initials": "A", "orcid": "0000-0002-5904-0635", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/05df7afc7a494ba5af8a378e5ffa53f0.json"}}, {"family": "Griffin", "given": "Gabriel", "initials": "G", "orcid": "0000-0002-4042-6757", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f6153204e19d4660b640dc4467605973.json"}}, {"family": "Ebert", "given": "Benjamin L", "initials": "BL", "orcid": "0000-0003-0197-5451", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56e4f1c53a4348e2b0ceb44a38850a17.json"}}, {"family": "Mack", "given": "Taralynn", "initials": "T", "orcid": "0000-0003-1043-2950", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b126c40c737b4b06a8702801ee227b04.json"}}, {"family": "Pershad", "given": "Yash", "initials": "Y", "orcid": "0000-0002-2282-1403", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ba3556fc94884dee9cc2bb4a79415631.json"}}, {"family": "Sharber", "given": "Brian", "initials": "B", "orcid": "0009-0005-9598-8211", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cbee42b03e8943e4b6ea4e5690b8dca0.json"}}, {"family": "Berger", "given": "Michael", "initials": "M", "orcid": "0000-0003-3882-5000", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/38cae43288b94d39a9261c1790cb51ea.json"}}, {"family": "Zehir", "given": "Ahmet", "initials": "A", "orcid": "0000-0001-5406-4104", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a0c0313e93434df3bdf14217e4b5aea2.json"}}, {"family": "Ptashkin", "given": "Ryan", "initials": "R"}, {"family": "Levine", "given": "Ross L", "initials": "RL", "orcid": "0000-0002-7884-1905", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/db32b99e8427494c93dbce3366801c54.json"}}, {"family": "Papaemmanuil", "given": "Elli", "initials": "E", "orcid": "0000-0003-1709-8983", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6ea61c4aa9324a398fffe747c0e7824d.json"}}, {"family": "Joseph", "given": "Vijai", "initials": "V", "orcid": "0000-0002-7933-151X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a056e9c694a14da8a883ac07a4c039c9.json"}}, {"family": "Gao", "given": "Teng", "initials": "T", "orcid": "0000-0002-0196-689X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/553d7ec1abd34703bb7145d35b484c29.json"}}, {"family": "Kemel", "given": "Yelena", "initials": "Y", "orcid": "0000-0002-5042-5651", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0cea60ee959b44c19549b815cb31a1eb.json"}}, {"family": "Mandelker", "given": "Diana", "initials": "D", "orcid": "0000-0003-4154-0567", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/03937c44ffc94ba79aa713ea4b93c6ee.json"}}, {"family": "Stopsack", "given": "Konrad H", "initials": "KH", "orcid": "0000-0002-0722-1311", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/120f5a25b7254b7f834cc9cebfa6c0d3.json"}}, {"family": "Pharoah", "given": "Paul D P", "initials": "PDP", "orcid": "0000-0001-8494-732X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/723de78b315e47bcb52e2c89a2d3918a.json"}}, {"family": "Mukherjee", "given": "Semanti", "initials": "S"}, {"family": "Ding", "given": "Li", "initials": "L", "orcid": "0000-0003-1517-2975", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/148794e8a0a84be98b9c47b5d1fa8b27.json"}}, {"family": "Cao", "given": "Yin", "initials": "Y", "orcid": "0000-0001-9835-7662", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a34eb276a5514342adb104aa5df642c9.json"}}, {"family": "Walter", "given": "Matthew J", "initials": "MJ", "orcid": "0000-0002-7753-1091", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/055099b1d98c4b43bf1163a4553c1f34.json"}}, {"family": "Blundell", "given": "Jamie R", "initials": "JR"}, {"family": "Chatterjee", "given": "Nilanjan", "initials": "N", "orcid": "0000-0002-9060-008X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4ec346fd556e40bda203b75825b4324b.json"}}, {"family": "Offit", "given": "Kenneth", "initials": "K"}, {"family": "Godley", "given": "Lucy A", "initials": "LA", "orcid": "0000-0003-1914-9158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3364441e62b7475086fea2db834a3760.json"}}, {"family": "Link", "given": "Daniel C", "initials": "DC", "orcid": "0000-0002-3170-7581", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/48661b793e284fd480d5d070a0b9a7e5.json"}}, {"family": "Stadler", "given": "Zsofia K", "initials": "ZK", "orcid": "0000-0002-6985-2864", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/726b7892e14b40ba8a6569a9de8a39b1.json"}}, {"family": "Bick", "given": "Alexander G", "initials": "AG"}, {"family": "Natarajan", "given": "Pradeep", "initials": "P"}, {"family": "Bolton", "given": "Kelly L", "initials": "KL", "orcid": "0000-0001-6584-3357", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/74eb7c71cebc4e8c888ff2b7426b4438.json"}}], "type": "journal article", "published": "2025-08-00", "journal": {"title": "Nat. Genet.", "issn": "1546-1718", "volume": "57", "issue": "8", "pages": "1872-1880", "issn-l": "1061-4036"}, "abstract": "With age, clonal expansions occur pervasively across normal tissues yet only in rare instances lead to cancer, despite being driven by well-established cancer drivers. Characterization of the factors that influence clonal progression is needed to inform interventional approaches. Germline genetic variation influences cancer risk and shapes tumor mutational profile, but its influence on the mutational landscape of normal tissues is not well known. Here we studied the impact of germline genetic variation on clonal hematopoiesis (CH) in 731,835 individuals. We identified 22 new CH-predisposition genes, most of which predispose to CH driven by specific mutational events. CH-predisposition genes contribute to unique somatic landscapes, reflecting the influence of germline genetic backdrop on gene-specific CH fitness. Correspondingly, somatic-germline interactions influence the risk of CH progression to hematologic malignancies. These results demonstrate that germline genetic variation influences somatic evolution in the blood, findings that likely extend to other tissues.", "doi": "10.1038/s41588-025-02250-x", "pmid": "40664769", "labels": {"DDLS Fellow": "", "Abhishek Niroula": ""}, "xrefs": [{"db": "pmc", "key": "PMC12339400"}, {"db": "pii", "key": "10.1038/s41588-025-02250-x"}], "notes": [], "created": "2025-11-17T15:51:13.415Z", "modified": "2026-09-23T09:07:46.350Z"}, {"entity": "publication", "iuid": "4ec73e602d0d425fb81dd9b99f1dd724", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4ec73e602d0d425fb81dd9b99f1dd724.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4ec73e602d0d425fb81dd9b99f1dd724"}}, "title": "Design of linear and cyclic peptide binders from protein sequence information.", "authors": [{"family": "Li", "given": "Qiuzhen", "initials": "Q"}, {"family": "Vlachos", "given": "Efstathios Nikolaos", "initials": "EN"}, {"family": "Bryant", "given": "Patrick", "initials": "P", "orcid": "0000-0003-3439-1866", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a683bcf98234ff09b2398976583b66f.json"}}], "type": "journal article", "published": "2025-07-22", "journal": {"title": "Commun Chem", "issn": "2399-3669", "volume": "8", "issue": "1", "pages": "211", "issn-l": null}, "abstract": "Structure prediction technology has transformed protein design, yet key challenges remain, particularly in designing novel functions. Many proteins function through interactions with other proteins, making the rational design of these interactions a central problem. While most efforts focus on large, stable proteins, shorter peptides offer advantages such as lower manufacturing costs, reduced steric hindrance, and improved cell permeability when cyclised. However, their flexibility and limited structural data make them difficult to design. Here, we introduce EvoBind2, a method for designing novel linear and cyclic peptide binders of varying lengths using only the sequence of a target protein. Unlike existing approaches, EvoBind2 does not require prior knowledge of binding sites or predefined binder lengths, making it a fully blind design process. For one target protein, we demonstrate that linear and cyclic peptide binders of different lengths can be designed in a single shot, and adversarial designs can be avoided through orthogonal in silico evaluation.", "doi": "10.1038/s42004-025-01601-3", "pmid": "40691301", "labels": {"Patrick Bryant": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC12280060"}, {"db": "pii", "key": "10.1038/s42004-025-01601-3"}], "notes": [], "created": "2026-08-20T09:25:40.568Z", "modified": "2026-09-23T09:06:06.239Z"}, {"entity": "publication", "iuid": "4cbaa979b3cc49c3bb40ccc04b73b5a0", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4cbaa979b3cc49c3bb40ccc04b73b5a0.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4cbaa979b3cc49c3bb40ccc04b73b5a0"}}, "title": "The Impact of Reference Genome Divergence on Ancient DNA Damage Detection in Metagenomic Contexts", "authors": [{"family": "Guinet", "given": "Benjamin", "initials": "B", "orcid": "0000-0002-9922-2118", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c17993b1fc0450eb9808706576983eb.json"}}, {"family": "Sharif", "given": "Bilal Muhammad", "initials": "BM", "orcid": "0000-0002-0581-0542", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2deb1c150e3942dfbb9b33c7b875dd21.json"}}, {"family": "van der Valk", "given": "Tom", "initials": "T", "orcid": "0000-0001-6582-3452", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/aa0dba3cc12143cba213f7f3a052216c.json"}}], "type": "posted-content", "published": "2025-07-20", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2025.07.16.665190", "pmid": null, "labels": {"DDLS Fellow": "", "Tom van der Valk": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T11:06:33.990Z", "modified": "2026-09-23T14:54:11.732Z"}, {"entity": "publication", "iuid": "b318e188406a4478bd4a165c76621e10", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b318e188406a4478bd4a165c76621e10.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b318e188406a4478bd4a165c76621e10"}}, "title": "In silico docking yields small molecule compounds targeting the core of Frizzled 7 as negative allosteric modulators", "authors": [{"family": "Schulte", "given": "Gunnar", "initials": "G", "orcid": "0000-0002-2700-7013", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ca48082cc934a8494ac50e756be0f3e.json"}}, {"family": "Scharf", "given": "Magdalena", "initials": "M", "orcid": "0000-0002-3305-3956", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca43ba6516014fe597ead17e737f697a.json"}}, {"family": "Gr\u00e4tz", "given": "Lukas", "initials": "L"}, {"family": "Kinsolving", "given": "Julia", "initials": "J", "orcid": "0000-0002-0431-8222", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/db117db4a1f54b2281020100a5de834d.json"}}, {"family": "Voss", "given": "Jan", "initials": "J", "orcid": "0000-0003-0595-4607", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f917ae3e8a384e37ab569ed8b3a6a3e4.json"}}, {"family": "Carrasco-Busturia", "given": "David", "initials": "D", "orcid": "0000-0003-1588-338X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/266c497cacdb47938ff6818655864c9d.json"}}, {"family": "Forsberg", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0002-6247-4063", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/36ea51bfa66d48b7a43559c3d0eaa59f.json"}}, {"family": "Kolb", "given": "Peter", "initials": "P", "orcid": "0000-0003-4089-614X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4b8d1c7a084e4870b3b7e94788c0c3cc.json"}}], "type": "posted-content", "published": "2025-07-17", "journal": {"issn-l": null}, "abstract": null, "doi": "10.21203/rs.3.rs-6908411/v1", "pmid": null, "labels": {"DDLS Fellow": "", "Bj\u00f6rn Forsberg": ""}, "xrefs": [], "notes": [], "created": "2026-10-01T08:34:39.505Z", "modified": "2026-10-01T08:34:39.579Z"}, {"entity": "publication", "iuid": "307665d33d674fab8a8bb311a886a496", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/307665d33d674fab8a8bb311a886a496.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/307665d33d674fab8a8bb311a886a496"}}, "title": "ApoB-containing lipoproteins: count, type, size, and risk of coronary artery disease.", "authors": [{"family": "Morze", "given": "Jakub", "initials": "J", "orcid": "0000-0002-7119-0273", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/91e8ec498bc6462986a824de9c42af47.json"}}, {"family": "Melloni", "given": "Giorgio E M", "initials": "GEM", "orcid": "0000-0001-6371-1334", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/087c83130a4c42ce8272d5cdd3f7360b.json"}}, {"family": "Wittenbecher", "given": "Clemens", "initials": "C"}, {"family": "Ala-Korpela", "given": "Mika", "initials": "M", "orcid": "0000-0001-5905-1206", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ae14f1b50f314ecb999a631b0e93d718.json"}}, {"family": "Rynkiewicz", "given": "Andrzej", "initials": "A"}, {"family": "Guasch-Ferr\u00e9", "given": "Marta", "initials": "M"}, {"family": "Ruff", "given": "Christian T", "initials": "CT"}, {"family": "Hu", "given": "Frank B", "initials": "FB"}, {"family": "Sabatine", "given": "Marc S", "initials": "MS"}, {"family": "Marston", "given": "Nicholas A", "initials": "NA", "orcid": "0000-0001-6164-4617", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/89a8b4146615443da4ec58d21add95be.json"}}], "type": "journal article", "published": "2025-07-14", "journal": {"title": "Eur. Heart J.", "issn": "1522-9645", "volume": "46", "issue": "27", "pages": "2691-2701", "issn-l": "0195-668X"}, "abstract": "Apolipoprotein B concentration reflects the number of atherogenic lipoproteins and is recognized as a key lipid risk marker. Whether the type or size of apoB particle (apoB-P) adds predictive value for coronary artery disease (CAD) remains unclear.\n\nA prospective analysis of 207 368 UK Biobank participants with comprehensive lipoprotein profiling and no prior history of atherosclerotic disease, diabetes, or active lipid-lowering therapy was conducted. Multivariable-adjusted Cox regression models were used to examine the association between each of the following lipid parameters with incident CAD: (i) nuclear magnetic resonance-measured apoB-P, (ii) concentrations of individual lipoprotein classes [very-low-density lipoprotein (VLDL), low-density lipoprotein (LDL)], (iii) size subclasses, (iv) average particle diameter, and (v) immunoassay-measured lipoprotein(a) [Lp(a)].\n\nA one standard deviation (SD) increase in apoB-P was associated with a 33% higher CAD risk [hazard ratio (HR): 1.33, 95% CI: 1.30-1.36]. Although VLDL particles were observed to carry a higher per-particle risk (HR per 100 nmol/L: 1.22, 1.11-1.34) compared with LDL (HR per 100 nmol/L: 1.07, 1.05-1.08), this difference was counterbalanced after considering relative particle abundance (LDL 91% vs VLDL 9% of total apoB-P). Thus the respective HR per 1-SD were 1.09 (1.05-1.14) and 1.24 (1.19-1.30). Particle diameter or size subclasses were not associated with CAD after apoB-P adjustment. The association of Lp(a) was robust even after apoB-P adjustment (HR:1.18, 1.16-1.20) and added independent prognostic value for CAD (area under curve: 0.769 vs 0.774, P < .001).\n\nLipid-related atherosclerotic risk is most accurately reflected by the total count of apoB-P and is largely unaffected by the major particle type (VLDL, LDL) or size. Elevated count of Lp(a) adds additional risk, and thus adequate assessment of atherogenic risk from dyslipidemia is best accomplished by consideration of both apoB-P and Lp(a) concentrations.", "doi": "10.1093/eurheartj/ehaf207", "pmid": "40289348", "labels": {"Clemens Wittenbecher": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pii", "key": "8118996"}], "notes": [], "created": "2025-11-28T07:19:58.641Z", "modified": "2026-09-23T08:55:27.197Z"}, {"entity": "publication", "iuid": "7ee72f71c959444b9e7be4d5eb89f6fe", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/7ee72f71c959444b9e7be4d5eb89f6fe.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/7ee72f71c959444b9e7be4d5eb89f6fe"}}, "title": "Seeking Knowledge or Efficiency: Profiling students\u2019 AI-use through survey-based Latent Class Analysis", "authors": [{"family": "Hugerth", "given": "Mattias Wickberg", "initials": "MW", "orcid": "0009-0006-2406-5214", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eb42b13600614f78bcf7fad7734277bc.json"}}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW"}], "type": "posted-content", "published": "2025-07-08", "journal": {"issn-l": null}, "abstract": null, "doi": "10.35542/osf.io/kh5xq_v2", "pmid": null, "labels": {"DDLS Fellow": "", "Luisa Hugerth": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T13:43:47.481Z", "modified": "2026-09-23T15:49:22.867Z"}, {"entity": "publication", "iuid": "f905ca88a80f42109bb997cd17743470", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f905ca88a80f42109bb997cd17743470.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f905ca88a80f42109bb997cd17743470"}}, "title": "Development and retrospective validation of an artificial intelligence system for diagnostic assessment of prostate biopsies: study protocol.", "authors": [{"family": "Mulliqi", "given": "Nita", "initials": "N"}, {"family": "Blilie", "given": "Anders", "initials": "A", "orcid": "0009-0002-9546-5443", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d778d06e206948e5ac99017ce1ae8434.json"}}, {"family": "Ji", "given": "Xiaoyi", "initials": "X"}, {"family": "Szolnoky", "given": "Kelvin", "initials": "K", "orcid": "0000-0002-0554-1872", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5059c9f881d4434f9b64f3bb381478fe.json"}}, {"family": "Olsson", "given": "Henrik", "initials": "H", "orcid": "0000-0002-2270-2017", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/da0547e978264d9c88fc6a222dcbfd5f.json"}}, {"family": "Titus", "given": "Matteo", "initials": "M", "orcid": "0009-0008-7893-7385", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/049f236217f147f78635b9d3a361db98.json"}}, {"family": "Martinez Gonzalez", "given": "Geraldine", "initials": "G"}, {"family": "Boman", "given": "Sol Erika", "initials": "SE", "orcid": "0009-0001-5733-3178", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8a605b0dadad4b3696396827ebac9348.json"}}, {"family": "Valkonen", "given": "Masi", "initials": "M", "orcid": "0000-0003-3091-2484", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ae4841e8a4124dc79c921b3af09096fe.json"}}, {"family": "Gudlaugsson", "given": "Einar", "initials": "E"}, {"family": "Kjosavik", "given": "Svein Reidar", "initials": "SR", "orcid": "0000-0002-7004-5533", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/97167c1ee44443108098eb823bd18fa7.json"}}, {"family": "Asenjo", "given": "Jos\u00e9", "initials": "J"}, {"family": "Gambacorta", "given": "Marcello", "initials": "M"}, {"family": "Libretti", "given": "Paolo", "initials": "P"}, {"family": "Braun", "given": "Marcin", "initials": "M"}, {"family": "Kordek", "given": "Radzislaw", "initials": "R"}, {"family": "\u0141owicki", "given": "Roman", "initials": "R"}, {"family": "Hotakainen", "given": "Kristina", "initials": "K"}, {"family": "V\u00e4re", "given": "P\u00e4ivi", "initials": "P"}, {"family": "Pedersen", "given": "Bodil Ginnerup", "initials": "BG", "orcid": "0000-0003-2792-7343", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/926d2e6e88a049f8ba5e50dbdd4fe210.json"}}, {"family": "S\u00f8rensen", "given": "Karina Dalsgaard", "initials": "KD"}, {"family": "Ulh\u00f8i", "given": "Benedicte Parm", "initials": "BP"}, {"family": "Rantalainen", "given": "Mattias", "initials": "M"}, {"family": "Ruusuvuori", "given": "Pekka", "initials": "P", "orcid": "0000-0001-9086-9591", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb947cd395e84612a53569f4a39abd19.json"}}, {"family": "Delahunt", "given": "Brett", "initials": "B", "orcid": "0000-0002-5398-0300", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/433a3f884f95451383cc746925d9a08c.json"}}, {"family": "Samaratunga", "given": "Hemamali", "initials": "H"}, {"family": "Tsuzuki", "given": "Toyonori", "initials": "T", "orcid": "0000-0002-4855-4366", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/42c993c2c0ab4b50afa03134f70118d9.json"}}, {"family": "Janssen", "given": "Emilius Adrianus Maria", "initials": "EAM"}, {"family": "Egevad", "given": "Lars", "initials": "L", "orcid": "0000-0001-8531-222X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a7d46f1f5fc047dc8edb910eb4f0645c.json"}}, {"family": "Kartasalo", "given": "Kimmo", "initials": "K", "orcid": "0000-0002-9470-4783", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7c6fc97c06ed456c8bdd1f03db8a9b72.json"}}, {"family": "Eklund", "given": "Martin", "initials": "M", "orcid": "0000-0001-5032-5266", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/06721510ebc8462386e0e6fc6c84315b.json"}}], "type": "journal article", "published": "2025-07-07", "journal": {"title": "BMJ Open", "issn": "2044-6055", "volume": "15", "issue": "7", "pages": "e097591", "issn-l": "2044-6055"}, "abstract": "Histopathological evaluation of prostate biopsies using the Gleason scoring system is critical for prostate cancer diagnosis and treatment selection. However, grading variability among pathologists can lead to inconsistent assessments, risking inappropriate treatment. Similar challenges complicate the assessment of other prognostic features like cribriform cancer morphology and perineural invasion. Many pathology departments are also facing an increasingly unsustainable workload due to rising prostate cancer incidence and a decreasing pathologist workforce coinciding with increasing requirements for more complex assessments and reporting. Digital pathology and artificial intelligence (AI) algorithms for analysing whole slide images show promise in improving the accuracy and efficiency of histopathological assessments. Studies have demonstrated AI's capability to diagnose and grade prostate cancer comparably to expert pathologists. However, external validations on diverse data sets have been limited and often show reduced performance. Historically, there have been no well-established guidelines for AI study designs and validation methods. Diagnostic assessments of AI systems often lack preregistered protocols and rigorous external cohort sampling, essential for reliable evidence of their safety and accuracy.\n\nThis study protocol covers the retrospective validation of an AI system for prostate biopsy assessment. The primary objective of the study is to develop a high-performing and robust AI model for diagnosis and Gleason scoring of prostate cancer in core needle biopsies, and at scale evaluate whether it can generalise to fully external data from independent patients, pathology laboratories and digitalisation platforms. The secondary objectives cover AI performance in estimating cancer extent and detecting cribriform prostate cancer and perineural invasion. This protocol outlines the steps for data collection, predefined partitioning of data cohorts for AI model training and validation, model development and predetermined statistical analyses, ensuring systematic development and comprehensive validation of the system. The protocol adheres to Transparent Reporting of a multivariable prediction model of Individual Prognosis Or Diagnosis+AI (TRIPOD+AI), Protocol Items for External Cohort Evaluation of a Deep Learning System in Cancer Diagnostics (PIECES), Checklist for AI in Medical Imaging (CLAIM) and other relevant best practices.\n\nData collection and usage were approved by the respective ethical review boards of each participating clinical laboratory, and centralised anonymised data handling was approved by the Swedish Ethical Review Authority. The study will be conducted in agreement with the Helsinki Declaration. The findings will be disseminated in peer-reviewed publications (open access).", "doi": "10.1136/bmjopen-2024-097591", "pmid": "40623883", "labels": {"DDLS Fellow": "", "Kimmo Kartasalo": ""}, "xrefs": [{"db": "pmc", "key": "PMC12258300"}, {"db": "pii", "key": "bmjopen-2024-097591"}], "notes": [], "created": "2025-10-30T15:40:42.132Z", "modified": "2026-09-23T11:28:50.741Z"}, {"entity": "publication", "iuid": "2e8b08e9f0aa4d66b8cc118cdc21ab10", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/2e8b08e9f0aa4d66b8cc118cdc21ab10.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/2e8b08e9f0aa4d66b8cc118cdc21ab10"}}, "title": "A genome-wide association study in 10,000 individuals links plasma N-glycome to liver disease and anti-inflammatory proteins.", "authors": [{"family": "Sharapov", "given": "Sodbo", "initials": "S", "orcid": "0000-0003-0279-4900", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b435f6d60c674f969172aeb5216a24ae.json"}}, {"family": "Timoshchuk", "given": "Anna", "initials": "A", "orcid": "0000-0001-8529-4498", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2f9b4737e1f94049bd6ac5a35b02846b.json"}}, {"family": "Zaytseva", "given": "Olga", "initials": "O", "orcid": "0000-0003-3960-5157", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/19ba0a0f572549f6b8a8331a66e787ee.json"}}, {"family": "Maslov", "given": "Denis E", "initials": "DE", "orcid": "0000-0003-2806-5933", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e8f6b346d03a48bdab23a9b67062935b.json"}}, {"family": "Soplenkova", "given": "Anna", "initials": "A", "orcid": "0000-0003-0703-146X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c6b607493ace4c4581e6042b74d85539.json"}}, {"family": "Elgaeva", "given": "Elizaveta E", "initials": "EE", "orcid": "0000-0002-2484-553X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4f6a8d7e3cee4b22967b3d5a125e67db.json"}}, {"family": "Tiys", "given": "Evgeny S", "initials": "ES", "orcid": "0000-0001-5820-8646", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3b3e32a6d1c2408ba24e83619c791713.json"}}, {"family": "Mangino", "given": "Massimo", "initials": "M", "orcid": "0000-0002-2167-7470", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f1c90171562c487392b4257d272d3c17.json"}}, {"family": "Wittenbecher", "given": "Clemens", "initials": "C", "orcid": "0000-0001-7792-877X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2f7d2c289b3c47d5a79d23bd48a3225a.json"}}, {"family": "Karssen", "given": "Lennart", "initials": "L", "orcid": "0000-0002-1959-342X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e6fe3ae2526141e6b1bb72a9d4aca5c2.json"}}, {"family": "Timofeeva", "given": "Maria", "initials": "M", "orcid": "0000-0002-2503-4253", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ac41dc46e4104e16b755320a54213a05.json"}}, {"family": "Nostaeva", "given": "Arina", "initials": "A", "orcid": "0000-0001-9291-7550", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0d7a78e8d3bc4fa98f01a1b3d901d867.json"}}, {"family": "Vuckovic", "given": "Frano", "initials": "F", "orcid": "0000-0002-4845-0882", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a288cb0350534629a44b981c2ca5eda0.json"}}, {"family": "Trbojevi\u0107-Akma\u010di\u0107", "given": "Irena", "initials": "I", "orcid": "0000-0003-0106-0155", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ddc3c9fa41cb41bfac30c3cecd7a303d.json"}}, {"family": "\u0160tambuk", "given": "Tamara", "initials": "T", "orcid": "0000-0003-3174-120X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ac05b90c0c4e46f6a4daf2fadfb36de5.json"}}, {"family": "Feoktistova", "given": "Sofya", "initials": "S", "orcid": "0000-0002-7608-439X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4a524cf6628b484c8a9ca39681c2df67.json"}}, {"family": "Potapova", "given": "Nadezhda A", "initials": "NA", "orcid": "0000-0002-3818-9270", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f24fd89a7fa54e40a49588aeaf393f29.json"}}, {"family": "Voroshilova", "given": "Viktoria", "initials": "V"}, {"family": "Williams", "given": "Frances", "initials": "F", "orcid": "0000-0002-2998-2744", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4d3235062dfe4581a02a6add4aabfe2c.json"}}, {"family": "Primorac", "given": "Dragan", "initials": "D", "orcid": "0000-0001-5565-080X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3db145fe96c34f1893d10d4a2abe2815.json"}}, {"family": "Van Zundert", "given": "Jan", "initials": "J", "orcid": "0000-0002-5389-2036", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/519a0055fb7c456293e2987380b62064.json"}}, {"family": "Georges", "given": "Michel", "initials": "M", "orcid": "0000-0003-4124-2375", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4b41687b7ab94cd8b684052988977107.json"}}, {"family": "Suhre", "given": "Karsten", "initials": "K", "orcid": "0000-0001-9638-3912", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4b707ecb6c7d4cb6b075a153ffda31eb.json"}}, {"family": "Allegri", "given": "Massimo", "initials": "M", "orcid": "0000-0002-8201-980X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/36970320c42b4252a27c93a412dacf69.json"}}, {"family": "Chaturvedi", "given": "Nishi", "initials": "N", "orcid": "0000-0002-6211-2775", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/66a657e6bdd74191a02b307a371e044c.json"}}, {"family": "Dunlop", "given": "Malcolm", "initials": "M", "orcid": "0000-0002-3033-5851", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3d974c43789c47eea55d0b0173bd9a87.json"}}, {"family": "Schulze", "given": "Matthias B", "initials": "MB", "orcid": "0000-0002-0830-5277", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/853ded2c43b64f26a8b47da7ea7b79c0.json"}}, {"family": "Spector", "given": "Tim", "initials": "T", "orcid": "0000-0002-9795-0365", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6d79b7af2d7a4f1da46ac2ee2bb1eb0b.json"}}, {"family": "Tsepilov", "given": "Yakov A", "initials": "YA", "orcid": "0000-0002-4931-6052", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c48088d7d8034a67b3760b0453e5ee88.json"}}, {"family": "Lauc", "given": "Gordan", "initials": "G", "orcid": "0000-0003-1840-9560", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/82836005f8274ce28febe52377b316cc.json"}}, {"family": "Aulchenko", "given": "Yurii S", "initials": "YS", "orcid": "0000-0002-7899-1575", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8d581818861a47f6965867c1b1138994.json"}}], "type": "journal article", "published": "2025-07-01", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "5525", "issn-l": "2041-1723"}, "abstract": "More than a half of plasma proteins are N-glycosylated. Most of them are synthesized, glycosylated, and secreted to the bloodstream by liver and lymphoid tissues. While associations with N-glycosylation are implicated in the rising number of liver, cardiometabolic, and immune diseases, little is known about the genetic regulation of this process. Here, we performed the largest genome-wide association study of N-glycosylation of the blood plasma proteome in 10,000 individuals. We doubled the number of genetic loci known to be associated with blood N-glycosylation by identifying 16 novel loci and prioritizing 13 novel genes contributing to N-glycosylation. Among these were the GCKR, TRIB1, HP, SERPINA1 and CFH genes. These genes are predominantly expressed in the liver and show a previously unknown genetic link between plasma protein N-glycosylation, metabolic and liver diseases, and inflammatory response. By integrating glycomics, proteomics, transcriptomics, and genomics, we provide a resource that facilitates deeper exploration of disease pathogenesis and supports the discovery of glycan-based biomarkers.", "doi": "10.1038/s41467-025-60431-y", "pmid": "40593539", "labels": {"Clemens Wittenbecher": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC12218978"}, {"db": "pii", "key": "10.1038/s41467-025-60431-y"}], "notes": [], "created": "2025-11-28T07:19:55.050Z", "modified": "2025-12-19T09:07:19.543Z"}, {"entity": "publication", "iuid": "59649424e0994b35b56f74ad1aecd8e4", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/59649424e0994b35b56f74ad1aecd8e4.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/59649424e0994b35b56f74ad1aecd8e4"}}, "title": "Bending the Course of Evolution: How Mutualistic Interactions Affect Macroevolutionary Dynamics of Diversification in Mimetic Ithomiini Butterflies.", "authors": [{"family": "Chazot", "given": "Nicolas", "initials": "N", "orcid": "0000-0002-5237-8043", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1224343fe35b490ea5d1e1b5ff0ca734.json"}}, {"family": "Braga", "given": "Mariana P", "initials": "MP", "orcid": "0000-0002-1253-2536", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4f9064ed501545dca268c351c993aa26.json"}}, {"family": "Aubier", "given": "Thomas G", "initials": "TG"}, {"family": "Llaurens", "given": "Violaine", "initials": "V"}, {"family": "Willmott", "given": "Keith R", "initials": "KR"}, {"family": "Elias", "given": "Marianne", "initials": "M"}], "type": "journal article", "published": "2025-07-00", "journal": {"title": "Am Nat", "issn": "1537-5323", "issn-l": null, "volume": "206", "issue": "1", "pages": "1-15"}, "abstract": "AbstractDisentangling the relative importance of biotic versus abiotic factors at a macroevolutionary scale is key to our understanding of the processes of diversification. Mutualistic M\u00fcllerian mimicry is a compelling example of an ecological interaction that affects population and species ecology and evolution. Here, we test how M\u00fcllerian mimicry shapes macroevolutionary patterns of diversification in the Ithomiini butterflies. We show that the age of color patterns is the most important predictor of species richness within mimicry rings but does not predict phylogenetic diversity of mimicry rings. We find pervasive phylogenetic signal in mimicry rings and in color patterns associated within polymorphic species. Only a small set of mimicry rings show high phylogenetic diversity. We identify patterns of saturation in the accumulation of new mimicry rings and in the number of evolutionary convergences toward the most species-rich mimicry rings. We discuss how the time-dependent effects detected in our study illustrate how neutral processes and ecological interactions interact and shape species and phenotypic diversification. Our results show that selection driven by mimetic interaction has not erased the effect of time and phylogenetic signal on the formation of mimicry rings but ecological saturation linked to mimetic interactions affected the dynamics of color pattern evolution and species diversification.", "doi": "10.1086/735835", "pmid": "40577833", "labels": {"Mariana Pires Braga": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2025-11-28T12:32:13.598Z", "modified": "2025-11-30T11:16:52.763Z"}, {"entity": "publication", "iuid": "07ec7b15007941bca54fa4fa13113751", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/07ec7b15007941bca54fa4fa13113751.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/07ec7b15007941bca54fa4fa13113751"}}, "title": "Scalable single-cell metagenomic analysis with Bascet and Zorn", "authors": [{"family": "Gourl\u00e9", "given": "Hadrien", "initials": "H", "orcid": "0000-0001-9807-1082", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d5485a48dfde4e53b14d39c54f2b2483.json"}}, {"family": "Yakovenko", "given": "Iryna", "initials": "I", "orcid": "0009-0003-5235-2999", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/03c9f5e054fb4eaaadec42a6e484df3b.json"}}, {"family": "Verma", "given": "Jyoti", "initials": "J", "orcid": "0009-0005-5907-7525", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b697986b1f1a487aa34c3d607432f5a7.json"}}, {"family": "Dicken", "given": "Julian", "initials": "J", "orcid": "0009-0009-8614-7321", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2aab055274d045738c660769e3616061.json"}}, {"family": "Albrecht", "given": "Florian", "initials": "F", "orcid": "0009-0002-9253-5290", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e40b1d1a00264144bd7b26aa005bb0b2.json"}}, {"family": "Ma\u017eutis", "given": "Linas", "initials": "L", "orcid": "0000-0002-5552-6427", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c7ed72d89c814cc2bde7364b6f75da7e.json"}}, {"family": "Normark", "given": "Johan", "initials": "J", "orcid": "0000-0001-5831-4369", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/914d4091260b48f880d163e575d56645.json"}}, {"family": "Sheng", "given": "Nongfei", "initials": "N", "orcid": "0009-0004-0642-3394", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c5989895054a4c8789ed4afc612d2fe4.json"}}, {"family": "Str\u00f6mberg", "given": "Nicklas", "initials": "N", "orcid": "0000-0002-8417-3560", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e974641051a54b1e8efd918caa19244f.json"}}, {"family": "L\u00f6fstedt", "given": "Tommy", "initials": "T", "orcid": "0000-0001-7119-7646", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ee41326217e4031bd7e0e57357f2ad8.json"}}, {"family": "Carroll", "given": "Laura M", "initials": "LM", "orcid": "0000-0002-3677-0192", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02112eccb0664819af916a3c3dc79daa.json"}}, {"family": "Henriksson", "given": "Johan", "initials": "J", "orcid": "0000-0002-7745-2844", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/598b7031d1c9448a91de58d8544af7fa.json"}}], "type": "posted-content", "published": "2025-06-21", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2025.06.20.660799", "pmid": null, "labels": {"Laura Carroll": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2026-09-23T14:53:55.870Z", "modified": "2026-09-23T14:53:56.186Z"}, {"entity": "publication", "iuid": "a2a287ee37064d3b8147bb1b735d729d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a2a287ee37064d3b8147bb1b735d729d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a2a287ee37064d3b8147bb1b735d729d"}}, "title": "Longitudinal analysis of genetic and environmental interplay in human metabolic profiles and the implication for metabolic health.", "authors": [{"family": "Wang", "given": "Jing", "initials": "J"}, {"family": "Zenere", "given": "Alberto", "initials": "A"}, {"family": "Wang", "given": "Xingyue", "initials": "X"}, {"family": "Bergstr\u00f6m", "given": "G\u00f6ran", "initials": "G"}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Zhong", "given": "Wen", "initials": "W"}], "type": "journal article", "published": "2025-06-17", "journal": {"title": "Genome Med", "issn": "1756-994X", "volume": "17", "issue": "1", "pages": "68", "issn-l": "1756-994X"}, "abstract": "Understanding how genetics and environmental factors shape human metabolic profiles is crucial for advancing metabolic health. Variability in metabolic profiles, influenced by genetic makeup, lifestyle, and environmental exposures, plays a critical role in disease susceptibility and progression.\n\nWe conducted a two-year longitudinal study involving 101 clinically healthy individuals aged 50 to 65, integrating genomics, metabolomics, lipidomics, proteomics, clinical measurements, and lifestyle questionnaire data from repeat sampling. We evaluated the influence of both external and internal factors, including genetic predispositions, lifestyle factors, and physiological conditions, on individual metabolic profiles. Additionally, we developed an integrative metabolite-protein network to analyze protein-metabolite associations under both genetic and environmental regulations.\n\nOur findings highlighted the significant role of genetics in determining metabolic variability, identifying 22 plasma metabolites as genetically predetermined. Environmental factors such as seasonal variation, weight management, smoking, and stress also significantly influenced metabolite levels. The integrative metabolite-protein network comprised 5,649 significant protein-metabolite pairs and identified 87 causal metabolite-protein associations under genetic regulation, validated by showing a high replication rate in an independent cohort. This network revealed stable and unique protein-metabolite profiles for each individual, emphasizing metabolic individuality. Notably, our results demonstrated the importance of plasma proteins in capturing individualized metabolic variabilities. Key proteins related to individual metabolic profiles were identified and validated in the UK Biobank, showing great potential for metabolic risk assessment.\n\nOur study provides longitudinal insights into how genetic and environmental factors shape human metabolic profiles, revealing unique and stable individual metabolic profiles. Plasma proteins emerged as key indicators for capturing the variability in human metabolism and assessing metabolic risks. These findings offer valuable tools for personalized medicine and the development of diagnostics for metabolic diseases.", "doi": "10.1186/s13073-025-01492-y", "pmid": "40528258", "labels": {"DDLS Fellow": "", "Fredrik Edfors": ""}, "xrefs": [{"db": "pmc", "key": "PMC12172340"}, {"db": "pii", "key": "10.1186/s13073-025-01492-y"}], "notes": [], "created": "2026-08-21T12:40:37.534Z", "modified": "2026-10-01T08:26:47.278Z"}, {"entity": "publication", "iuid": "c569a4a92f6d4a78ad2b3bdf24ceefa4", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c569a4a92f6d4a78ad2b3bdf24ceefa4.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c569a4a92f6d4a78ad2b3bdf24ceefa4"}}, "title": "Correction: Low coverage of species constrains the use of DNA barcoding to assess mosquito biodiversity.", "authors": [{"family": "Moraes Zenker", "given": "Maur\u00edcio", "initials": "M"}, {"family": "Portella", "given": "Tatiana Pineda", "initials": "TP"}, {"family": "Pessoa", "given": "Felipe Arley Costa", "initials": "FAC"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Galetti", "given": "Pedro Manoel", "initials": "PM"}], "type": "published erratum", "published": "2025-06-11", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "20045", "issn-l": "2045-2322"}, "abstract": null, "doi": "10.1038/s41598-025-02631-6", "pmid": "40500336", "labels": {"DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC12159141"}, {"db": "pii", "key": "10.1038/s41598-025-02631-6"}], "notes": [], "created": "2026-08-20T09:24:14.304Z", "modified": "2026-09-23T15:48:15.854Z"}, {"entity": "publication", "iuid": "c779c1cba84c4c2595cf59774de80e18", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c779c1cba84c4c2595cf59774de80e18.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c779c1cba84c4c2595cf59774de80e18"}}, "title": "Blind De Novo Design of Dual Cyclic Peptide Agonists Targeting GCGR and GLP1R", "authors": [{"family": "Li", "given": "Qiuzhen", "initials": "Q", "orcid": "0009-0009-2913-4786", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f3d7b87dcea3440d8eaa4b574a88da3e.json"}}, {"family": "Wiita", "given": "Elisee", "initials": "E"}, {"family": "Helleday", "given": "Thomas", "initials": "T", "orcid": "0000-0002-7384-092X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/385586c159494955a9a72c3381e3ad47.json"}}, {"family": "Bryant", "given": "Patrick", "initials": "P", "orcid": "0000-0003-3439-1866", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a683bcf98234ff09b2398976583b66f.json"}}], "type": "posted-content", "published": "2025-06-08", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2025.06.06.658268", "pmid": null, "labels": {"Patrick Bryant": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T11:06:04.818Z", "modified": "2026-09-23T14:12:10.571Z"}, {"entity": "publication", "iuid": "70db0602765f45758a5e9e9ed97df7c6", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/70db0602765f45758a5e9e9ed97df7c6.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/70db0602765f45758a5e9e9ed97df7c6"}}, "title": "Contrasting Becker and Duchenne muscular dystrophy serum biomarker candidates by using data independent acquisition LC-MS/MS.", "authors": [{"family": "Johansson", "given": "Camilla", "initials": "C"}, {"family": "Schrama", "given": "Esther J", "initials": "EJ"}, {"family": "Kotol", "given": "David", "initials": "D"}, {"family": "Hober", "given": "Andreas", "initials": "A"}, {"family": "Koeks", "given": "Za\u00efda", "initials": "Z"}, {"family": "van de Velde", "given": "Nienke M", "initials": "NM"}, {"family": "Verschuuren", "given": "Jan J G M", "initials": "JJGM"}, {"family": "Niks", "given": "Erik H", "initials": "EH"}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Spitali", "given": "Pietro", "initials": "P"}, {"family": "Al-Khalili Szigyarto", "given": "Cristina", "initials": "C"}], "type": "journal article", "published": "2025-06-07", "journal": {"title": "Skelet Muscle", "issn": "2044-5040", "volume": "15", "issue": "1", "pages": "15", "issn-l": "2044-5040"}, "abstract": "Becker muscular dystrophy (BMD) is a rare and heterogeneous form of dystrophinopathy caused by expression of altered dystrophin proteins, as a consequence of in-frame genetic mutations. The majority of the BMD biomarker studies employ targeted approaches and focus on translating findings from Duchenne Muscular Dystrophy (DMD), a more severe disease form with clinical similarities but caused by out-of-frame mutations in the dystrophin gene. Importantly, DMD therapies assume that disease progression can be slowed by promoting the expression of truncated dystrophin comparable to what occurs in BMD patients. In this study, we explore similarities and differences in protein trajectories over time between BMD and DMD serum, and explore proteins related to motor function performance.\n\nSerum samples collected from 34 BMD patients, in a prospective longitudinal 3-year study, and 19 DMD patients, were analyzed by using Data Independent Acquisition Tandem Mass Spectrometry (DIA-MS). Subsequent normalization, linear mixed effects model was employed to identify proteins associated with physical tests and dystrophin expression in skeletal muscle. Analysis was also performed to explore the discrepancy between DMD and BMD biomarker abundance trajectories over time.\n\nLinear mixed effects models identified 20 proteins with altered longitudinal signatures between DMD and BMD, including creatine kinase M-type (CKM) pyruvate kinase (PKM), fibrinogen gamma chain (FGG), lactate dehydrogenase B (LDHB) and alpha-2-macroglobulin (A2M). Furthermore, several proteins related to innate immune response were associated with motor function in BMD patients. In particular, A2M displayed an altered time-dependent decline in relation to dystrophin expression in the tibialis anterior muscle.\n\nOur study revealed differences in the serum proteome between BMD and DMD, which comprises proteins involved in the immune response, extracellular matrix organization and hemostasis but not muscle leakage proteins significantly associated with disease progression in DMD. If further evaluated and validated, these biomarker candidates may offer means to monitor disease progression in BMD patients. A2M is of particular interest due to its association with dystrophin expression in BMD muscle and higher abundance in DMD patients in comparison to BMD. If validated, A2M could be used as a pharmacodynamic biomarker in therapeutic clinical trials aiming to restore dystrophin expression.", "doi": "10.1186/s13395-025-00385-3", "pmid": "40483507", "labels": {"DDLS Fellow": "", "Fredrik Edfors": ""}, "xrefs": [{"db": "pmc", "key": "PMC12144774"}, {"db": "pii", "key": "10.1186/s13395-025-00385-3"}], "notes": [], "created": "2026-08-21T12:41:13.565Z", "modified": "2026-10-01T08:26:45.569Z"}, {"entity": "publication", "iuid": "4b5045598b814dcda27402c715beddc3", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4b5045598b814dcda27402c715beddc3.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4b5045598b814dcda27402c715beddc3"}}, "title": "A resource for whole-body gene expression map of human tissues based on integration of single cell and bulk transcriptomics.", "authors": [{"family": "Shi", "given": "Mengnan", "initials": "M"}, {"family": "M\u00e9ar", "given": "Loren", "initials": "L"}, {"family": "Karlsson", "given": "Max", "initials": "M"}, {"family": "\u00c1lvez", "given": "Mar\u00eda Bueno", "initials": "MB"}, {"family": "Digre", "given": "Andreas", "initials": "A"}, {"family": "Schutten", "given": "Rutger", "initials": "R"}, {"family": "Katona", "given": "Borbala", "initials": "B"}, {"family": "Vuu", "given": "Jimmy", "initials": "J"}, {"family": "Lindstr\u00f6m", "given": "Emil", "initials": "E"}, {"family": "Hikmet", "given": "Feria", "initials": "F"}, {"family": "Jin", "given": "Han", "initials": "H"}, {"family": "Yuan", "given": "Meng", "initials": "M"}, {"family": "Li", "given": "Xiangyu", "initials": "X"}, {"family": "Yang", "given": "Hong", "initials": "H"}, {"family": "Song", "given": "Xiya", "initials": "X"}, {"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E"}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Oksvold", "given": "Per", "initials": "P"}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K"}, {"family": "Zwahlen", "given": "Martin", "initials": "M"}, {"family": "Forsberg", "given": "Mattias", "initials": "M"}, {"family": "Johansson", "given": "Fredric", "initials": "F"}, {"family": "Mulder", "given": "Jan", "initials": "J"}, {"family": "H\u00f6kfelt", "given": "Tomas", "initials": "T"}, {"family": "Luo", "given": "Yonglun", "initials": "Y"}, {"family": "Butler", "given": "Lynn", "initials": "L"}, {"family": "Zhong", "given": "Wen", "initials": "W"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Sivertsson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Ponten", "given": "Fredrik", "initials": "F"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Lindskog", "given": "Cecilia", "initials": "C"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Zhang", "given": "Cheng", "initials": "C"}], "type": "journal article", "published": "2025-06-03", "journal": {"title": "Genome Biol.", "issn": "1474-760X", "volume": "26", "issue": "1", "pages": "152", "issn-l": "1474-7596"}, "abstract": "New technologies enable single-cell transcriptome analysis, mapping genome-wide expression across the human body. Here, we present an extended analysis of protein-coding genes in all major human tissues and organs, combining single-cell and bulk transcriptomics. To enhance transcriptome depth, 31 tissues were analyzed using a pooling method, identifying 557 unique cell clusters, manually annotated by marker gene expression. Genes were classified by body-wide expression and validated through antibody-based profiling. All results are available in the updated open-access Single Cell Type section of the Human Protein Atlas for genome-wide exploration of genes, proteins, and their spatial distribution in cells.", "doi": "10.1186/s13059-025-03616-4", "pmid": "40462185", "labels": {"SciLifeLab Fellow": "", "Fredrik Edfors": "", "DDLS Fellow": "", "Adil Mardinoglu": ""}, "xrefs": [{"db": "pmc", "key": "PMC12131445"}, {"db": "pii", "key": "10.1186/s13059-025-03616-4"}], "notes": [], "created": "2026-08-20T12:21:53.598Z", "modified": "2026-09-23T11:26:55.590Z"}, {"entity": "publication", "iuid": "5337a44be73f498b8a344ca81cc3be3b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5337a44be73f498b8a344ca81cc3be3b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5337a44be73f498b8a344ca81cc3be3b"}}, "title": "Wastewater surveillance of SARS-CoV-2 from aircraft to citywide monitoring.", "authors": [{"family": "Perez-Zabaleta", "given": "Mariel", "initials": "M"}, {"family": "Berg", "given": "Carlo", "initials": "C", "orcid": "0000-0001-7815-1077", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3b3513d1aca744b89e15d05dfc5498e7.json"}}, {"family": "Latorre-Margalef", "given": "Neus", "initials": "N"}, {"family": "Owusu-Agyeman", "given": "Isaac", "initials": "I"}, {"family": "Kiyar", "given": "Ayda", "initials": "A"}, {"family": "Botnen", "given": "Helene", "initials": "H", "orcid": "0009-0008-1027-0676", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/db3daea2906b417ea9711fb265d69fe0.json"}}, {"family": "Sch\u00f6nning", "given": "Caroline", "initials": "C"}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW", "orcid": "0000-0001-5432-1764", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/246ed7b405dd4c3f9ec5e7ff9f1d3ade.json"}}, {"family": "Cetecioglu", "given": "Zeynep", "initials": "Z", "orcid": "0000-0002-8170-379X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7cd2bf37c08b4c88a62e48130c066c61.json"}}], "type": "journal article", "published": "2025-06-02", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "5125", "issn-l": "2041-1723"}, "abstract": "Wastewater monitoring is highly efficient in SARS-CoV-2 surveillance for tracking virus spread through travel, surpassing traditional airport passenger testing. This study explored the links between SARS-CoV-2 contents and variants from aircraft to city, assessing the impact of detected variants from international travellers versus the local population. A total of 969 variants using next-generation sequencing (NGS) were examined to understand the links between-aircraft, Arlanda airport, wastewater treatment plants (WWTPs), and Stockholm city-and compared these to variants detected in Stockholm hospitals from January to May 2023. SARS-CoV-2 contents in WWTPs reflected local infection rates, requiring analysis from multiple plants for an accurate city-wide infection assessment. Variants initially detected in aircraft arriving from China did not spread widely during the study period. RT-qPCR is adequate for the detection of specific variants in wastewater, including Variants Under Monitoring. However, NGS remains a powerful method for identifying novel variants. Wastewater monitoring was more effective than clinical testing in the early detection of specific variants, with notable delays observed in clinical surveillance. Furthermore, a broad range of variants are detected in wastewater that surpasses clinical tests. This underscores the vital role of wastewater-based epidemiology in managing future outbreaks and enhancing global health security.", "doi": "10.1038/s41467-025-60490-1", "pmid": "40456842", "labels": {"DDLS Fellow": "", "Luisa Hugerth": ""}, "xrefs": [{"db": "pmc", "key": "PMC12130461"}, {"db": "pii", "key": "10.1038/s41467-025-60490-1"}], "notes": [], "created": "2026-09-23T09:09:28.911Z", "modified": "2026-09-23T09:09:29.084Z"}, {"entity": "publication", "iuid": "fd992c03bb8c4b279e1694bfe511de0d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/fd992c03bb8c4b279e1694bfe511de0d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/fd992c03bb8c4b279e1694bfe511de0d"}}, "title": "P-499 The Influence of the Rectal, Vaginal, and Seminal Microbiomes on Reproductive Outcome in Assisted Reproduction - A Multicenter Prospective Cohort Study", "authors": [{"family": "Behrendt-M\u00f8ller", "given": "I", "initials": "I"}, {"family": "Vomstein", "given": "T K", "initials": "TK"}, {"family": "Pereira", "given": "M", "initials": "M"}, {"family": "Yde", "given": "A M", "initials": "AM"}, {"family": "Dalgaard", "given": "C V", "initials": "CV"}, {"family": "Eskildsen", "given": "K Z", "initials": "KZ"}, {"family": "N\u00f8hr", "given": "B", "initials": "B"}, {"family": "Gr\u00f8ndahl", "given": "M L", "initials": "ML"}, {"family": "L\u00f8kkegaard", "given": "E", "initials": "E"}, {"family": "Zedeler", "given": "A", "initials": "A"}, {"family": "Petersen", "given": "M R", "initials": "MR"}, {"family": "Freiesleben", "given": "N L C", "initials": "NLC"}, {"family": "Pinborg", "given": "A", "initials": "A"}, {"family": "Hugerth", "given": "L W", "initials": "LW"}, {"family": "Nielsen", "given": "H S", "initials": "HS"}], "type": "journal-article", "published": "2025-06-01", "journal": {"issn": "0268-1161", "volume": "40", "issue": "Supplement_1", "title": "Hum. Reprod.", "issn-l": null}, "abstract": null, "doi": "10.1093/humrep/deaf097.805", "pmid": null, "labels": {"DDLS Fellow": "", "Luisa Hugerth": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T09:41:54.176Z", "modified": "2026-09-23T14:54:00.680Z"}, {"entity": "publication", "iuid": "66336b690657447d83f04afbe7981f31", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/66336b690657447d83f04afbe7981f31.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/66336b690657447d83f04afbe7981f31"}}, "title": "Shaping the future of precision medicine: plasma proteomics to uncover insights in thrombosis.", "authors": [{"family": "Johansson", "given": "Emil", "initials": "E"}, {"family": "Iglesias", "given": "Maria Jesus", "initials": "MJ"}, {"family": "Odeberg", "given": "Jacob", "initials": "J"}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2025-06-00", "journal": {"title": "Expert Rev Proteomics", "issn": "1744-8387", "volume": "22", "issue": "6", "pages": "237-254", "issn-l": "1478-9450"}, "abstract": "Advances in various proteomics technologies, especially high-throughput and reproducibility, have enabled the systematic exploration of the circulating thrombosis proteome. This includes dissecting biological systems and pathways imperative to thrombosis, such as platelet activation, coagulation cascade, complement system, and endothelial cells. These insights strengthen our understanding of the cause and effect of thrombosis and improve precision medicine by identifying better biomarkers and biomarker panels, which may aid clinicians in decision-making in venous thromboembolism (VTE) and other thrombotic patients. This progress has the potential to reduce thrombosis-related morbidity and mortality, ultimately improving patient quality of life.\n\nThis review highlights recent advances and applications of mass spectrometry and affinity-based proteomics in thrombosis over the past three years (2022-2024), focusing on the thrombotic proteome signature related to VTE.\n\nPlasma proteomics, predominantly driven by mass spectrometry and affinity-based proteomics, has shown promise in identifying novel disease biomarkers and pathways. With the recent advances in the field, proteomics holds the potential to revolutionize precision medicine. As thrombosis is an intravascular disease, analysis of the blood proteome can capture environmental, genetic, and epigenetic contributors to risk variation in thrombosis, revealing novel protein biomarkers for diagnosis and risk prediction and new biological pathways.", "doi": "10.1080/14789450.2025.2517146", "pmid": "40472045", "labels": {"DDLS Fellow": "", "Fredrik Edfors": ""}, "xrefs": [], "notes": [], "created": "2026-08-21T12:05:06.197Z", "modified": "2026-10-01T08:28:31.385Z"}, {"entity": "publication", "iuid": "5390c711c29d41839ea48ec1574949c4", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5390c711c29d41839ea48ec1574949c4.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5390c711c29d41839ea48ec1574949c4"}}, "title": "Postdiagnosis physical activity and dietary inflammatory and insulinemic potential with overall survival in men with nonmetastatic prostate cancer.", "authors": [{"family": "Lee", "given": "Dong Hoon", "initials": "DH", "orcid": "0000-0003-1329-4637", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/43e0e71f4ccd4f5290a0909ba3a1b7ce.json"}}, {"family": "Rezende", "given": "Leandro F M", "initials": "LFM"}, {"family": "Ferrari", "given": "Gerson", "initials": "G"}, {"family": "Zhang", "given": "Yiwen", "initials": "Y"}, {"family": "Wang", "given": "Qiao-Li", "initials": "QL"}, {"family": "Oh", "given": "Hannah", "initials": "H"}, {"family": "Keum", "given": "NaNa", "initials": "N"}, {"family": "Hu", "given": "Jinbo", "initials": "J"}, {"family": "Jeon", "given": "Justin Y", "initials": "JY"}, {"family": "Mucci", "given": "Lorelei A", "initials": "LA"}, {"family": "Giovannucci", "given": "Edward L", "initials": "EL"}], "type": "journal article", "published": "2025-06-00", "journal": {"title": "Eur. J. Epidemiol.", "issn": "1573-7284", "volume": "40", "issue": "6", "pages": "669-679", "issn-l": "0393-2990"}, "abstract": "Inflammation and insulin resistance are associated with increased mortality in the general population. However, it remains unclear how physical activity and proinflammatory/hyperinsulinemic diets influence overall survival in prostate cancer patients. We analyzed 4779 men with nonmetastatic prostate cancer from the Health Professionals Follow-up Study. Postdiagnosis physical activity and diet were assessed using validated self-reported questionnaires. We used the validated dietary scores to empirically assess the anti-inflammatory (rEDIP) and anti-insulinemic (rEDIH) potential of dietary patterns based upon specific combinations of food groups. Cox regression model was used to estimate hazard ratios (HRs) and 95% confidence intervals (CIs). During a median of 15 years of follow-up, we identified 2282 deaths. Compared to men with < 3 MET-h/week of postdiagnosis physical activity, multivariable-adjusted HRs (95% CI) were 0.80 (0.68-0.95) for 9-< 24 MET-h/week, 0.63 (0.53-0.75) for 24-< 48 MET-hours/week and 0.61 (0.51-0.73) for \u2265 48 MET-hours/week in relation to all-cause mortality (P-trend < 0.001). Both vigorous and non-vigorous activities after diagnosis were associated with lower all-cause mortality (P-trend < 0.001). Moreover, post-diagnosis rEDIP and rEDIH scores were inversely associated with all-cause mortality (HR per 1-SD increase: 0.93 (0.89-0.99) for rEDIP; 0.91 (0.86-0.96) for rEDIH). In joint analyses, men with high physical activity and high rEDIP (or rEDIH) score showed approximately 30-36% lower risks of all-cause mortality, compared to those with low physical activity and low diet scores. In conclusion, high physical activity and low proinflammatory and hyperinsulinemic diets were independently associated with decreased risk of all-cause mortality in men with prostate cancer. Men with both high physical activity and low proinflammatory and hyperinsulinemic diets after diagnosis have the lowest mortality rate.", "doi": "10.1007/s10654-025-01240-x", "pmid": "40426002", "labels": {"DDLS Fellow": null, "Qiaoli Wang": null}, "xrefs": [{"db": "pii", "key": "10.1007/s10654-025-01240-x"}], "notes": [], "created": "2025-11-28T12:24:44.802Z", "modified": "2025-11-28T12:24:44.827Z"}, {"entity": "publication", "iuid": "fd78ef4d1eb142daa15397e72f19853d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/fd78ef4d1eb142daa15397e72f19853d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/fd78ef4d1eb142daa15397e72f19853d"}}, "title": "Fish are poor sentinels for surveillance of riverine antimicrobial resistance.", "authors": [{"family": "Tskhay", "given": "Faina", "initials": "F", "orcid": "0000-0001-8700-3279", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/66867423459544e7a72b0a9090a46cee.json"}}, {"family": "K\u00f6bsch", "given": "Christoph", "initials": "C", "orcid": "0000-0002-9748-2039", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ebe319eddda54827bf9ac3970e91a733.json"}}, {"family": "Elena", "given": "Alan X", "initials": "AX", "orcid": "0000-0001-5372-0923", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/005e2b93413c4627a222eb7a5ef66e04.json"}}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J", "orcid": "0000-0002-6528-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c666068e9d34939b0252a627007cec7.json"}}, {"family": "Berendonk", "given": "Thomas U", "initials": "TU", "orcid": "0000-0002-9301-1803", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c66286f83a8430f954fbc5c52db10c5.json"}}, {"family": "Kl\u00fcmper", "given": "Uli", "initials": "U", "orcid": "0000-0002-4169-6548", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7d8605cdbfc14403b607a3b5ace7249d.json"}}], "type": "journal article", "published": "2025-06-00", "journal": {"title": "One Health", "issn": "2352-7714", "volume": "20", "pages": "101026", "issn-l": null}, "abstract": "Effective surveillance of antimicrobial resistance (AMR) in the environment is crucial for assessing the human and animal health risk of AMR pollution. Wastewater treatment plants (WWTPs) are one of the main sources of AMR pollutants discharged into water bodies. One important factor for assessing the risks associated with such pollution is the colonization potential of the resistant bacteria (ARB) and resistance genes (ARGs) from the environment into human or animal microbiomes upon exposure. This study explores whether fish can act as sentinels for surveillance of AMR pollution in general and specifically the human colonization potential of ARB in rivers impacted by WWTP effluents. Two riverine fish species, Brown trout, and European bullhead, were sampled up- and downstream a German WWTP. The two fish species were chosen due to their different lifestyles: Trout are mainly actively swimming in the water phase, while bullheads are sedentary and river sediment-associated. The bacterial microbiomes and resistomes of fish gills, skin, and feces were compared with those of the respective river water and sediment up- and downstream of the WWTP. Microbiomes of both fish mirrored the changes in river water and sediment downstream of the WWTP, with significant shifts in bacterial community composition, particularly an increase in Proteobacteria and Verrucomicrobia. However, increases in ARG abundances observed in water and sediment downstream of the WWTP were not reflected in any of the fish-associated resistomes. This indicates that while the fish microbiome is sensitive to environmental changes, resistomes of poikilothermic animals such as fish are less responsive to colonization by ARB originating from WWTPs and may not serve as effective sentinels for assessing AMR pollution and colonization risks in freshwater environments. This study highlights the complexity of using wildlife as indicators for environmental AMR pollution and suggests that other species are better suited for surveillance efforts.", "doi": "10.1016/j.onehlt.2025.101026", "pmid": "40236740", "labels": {"DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC11999348"}, {"db": "pii", "key": "S2352-7714(25)00062-X"}], "notes": [], "created": "2025-06-04T08:12:42.896Z", "modified": "2026-09-23T12:27:49.148Z"}, {"entity": "publication", "iuid": "ec28119bd1694596ac362b533bb1f623", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ec28119bd1694596ac362b533bb1f623.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ec28119bd1694596ac362b533bb1f623"}}, "title": "Emerging multi-drug resistant and extended-spectrum \u03b2-lactamase (ESBL)-positive enterotoxigenic E. coli (ETEC) clones circulating in aquatic environments and in patients.", "authors": [{"family": "Joffr\u00e9", "given": "Enrique", "initials": "E"}, {"family": "Mart\u00edn-Rodr\u00edguez", "given": "Alberto J", "initials": "AJ"}, {"family": "Justh de Neczpal", "given": "Annie", "initials": "A"}, {"family": "von Mentzer", "given": "Astrid", "initials": "A"}, {"family": "Sj\u00f6ling", "given": "\u00c5sa", "initials": "\u00c5"}], "type": "journal article", "published": "2025-06-00", "journal": {"title": "One Health", "issn": "2352-7714", "volume": "20", "pages": "100968", "issn-l": null}, "abstract": "Diarrheal disease pathogens often spread through water-borne routes. Enterotoxigenic Escherichia coli (ETEC) is a major bacterial agent causing diarrheal disease in children, adults, and travelers in endemic areas. In addition, ETEC is responsible for outbreaks of water and food-borne gasteroenteritis globally, ETEC isolates also show robust survival capacity in various environmental settings, including aquatic environments. During the last decade, studies of ETEC isolates have indicated a rapid increase in multi-drug resistant and extended-spectrum \u03b2-lactamase (ESBL)-positive human-specific ETEC strains. These have been found in both environmental water sources and human patients, warranting the urgent need for focused monitoring of antibiotic resistance development in ETEC. Whole genome sequencing (WGS) of isolates from environmental, animal, and human sources enables in silico surveillance of emerging pathogenic and multi-drug resistant strains. This method allows for re-analysis of genomic data, aiding in identification of new variants of pathogenic clones. By integrating data from diverse sources inclusing sequenced isolates, we found that certain ETEC clonal lineages e.g., those expressing certain toxin-colonization factor profiles including STp/CS6, LT STh/CS2 + CS3, and LT STh/CFA/I are more at risk to develop multi-drug resistance than other ETEC lineages. Comparizon of multi-locus sequence types from papers with WGS data indicated ST182, ST4, ST2332 and new ST types to be emerging multi-drug resistant ETEC. We conclude that further studies on sequenced ETEC/E. coli genomes are needed to enhance our understanding of the dynamics of ETEC evolution, and the relation of virulence and resistance profiles in both environmental and clinical isolates.", "doi": "10.1016/j.onehlt.2025.100968", "pmid": "39898314", "labels": {"Astrid von Mentzer": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC11786893"}, {"db": "pii", "key": "S2352-7714(25)00004-7"}], "notes": [], "created": "2025-12-02T15:47:00.162Z", "modified": "2025-12-02T15:47:00.164Z"}, {"entity": "publication", "iuid": "6b000114117d463389b8268aa09d576f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/6b000114117d463389b8268aa09d576f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/6b000114117d463389b8268aa09d576f"}}, "title": "AI-first structural identification of pathogenic protein target interfaces.", "authors": [{"family": "Saluri", "given": "Mihkel", "initials": "M"}, {"family": "Landreh", "given": "Michael", "initials": "M"}, {"family": "Bryant", "given": "Patrick", "initials": "P", "orcid": "0000-0003-3439-1866", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a683bcf98234ff09b2398976583b66f.json"}}], "type": "journal article", "published": "2025-06-00", "journal": {"title": "PLoS Comput Biol", "issn": "1553-7358", "volume": "21", "issue": "6", "pages": "e1013168", "issn-l": "1553-734X"}, "abstract": "The risk of pandemics is increasing as global population growth and interconnectedness accelerate. Understanding the structural basis of protein-protein interactions between pathogens and hosts is critical for elucidating pathogenic mechanisms and guiding treatment or vaccine development. Despite 21,064 experimentally supported human-pathogen interactions in the HPIDB, only 52 have resolved structures in the PDB, representing just 0.2%. Advances in protein complex structure prediction, such as AlphaFold, now enable highly accurate modelling of heterodimeric complexes, though their application to host-pathogen interactions, which have distinct evolutionary dynamics, remains underexplored. Here, we investigate the structural protein-protein interaction network between humans and ten pathogens, predicting structures for 9,452 interactions, only 10 of which have known structures. We identify 30 interactions with an expected TM-score \u22650.9, tripling the structural coverage in these networks. A detailed analysis of the Francisella tularensis dihydroprolyl dehydrogenase (IPD) complex with human immunoglobulin kappa constant (IGKC) using homology modelling and native mass spectrometry confirms a predicted 1:2:1 heterotetramer, suggesting potential roles in immune evasion. These findings highlight the transformative potential of structure prediction for rapidly advancing vaccine and drug development against novel pathogenic targets.", "doi": "10.1371/journal.pcbi.1013168", "pmid": "40570050", "labels": {"Patrick Bryant": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC12225977"}, {"db": "pii", "key": "PCOMPBIOL-D-25-00468"}], "notes": [], "created": "2026-08-20T12:43:19.933Z", "modified": "2026-09-23T11:36:35.514Z"}, {"entity": "publication", "iuid": "3e403f038c0a4d619f329f91cceb2adc", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3e403f038c0a4d619f329f91cceb2adc.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3e403f038c0a4d619f329f91cceb2adc"}}, "title": "No evidence of transposable element bursts in the Gal\u00e1pagos Scalesia adaptive radiation despite hybridization, diversification and ecological niche shifts.", "authors": [{"family": "Cerca", "given": "Jos\u00e9", "initials": "J"}, {"family": "D\u00edaz", "given": "Patricia Jaramillo", "initials": "PJ"}, {"family": "Goubert", "given": "Cl\u00e9ment", "initials": "C"}, {"family": "Yang", "given": "Heidi", "initials": "H"}, {"family": "Bieker", "given": "Vanessa C", "initials": "VC"}, {"family": "Fern\u00e1ndez-Mazuecos", "given": "Mario", "initials": "M"}, {"family": "Vargas", "given": "Pablo", "initials": "P"}, {"family": "Schley", "given": "Rowan", "initials": "R"}, {"family": "Li", "given": "Siyu", "initials": "S"}, {"family": "Guevara-Andino", "given": "Juan Ernesto", "initials": "JE"}, {"family": "Petersen", "given": "Bent", "initials": "B"}, {"family": "Petersen", "given": "Gitte", "initials": "G"}, {"family": "Sinha", "given": "Neelima R", "initials": "NR"}, {"family": "Nielsen", "given": "Lene R", "initials": "LR"}, {"family": "Leebens-Mack", "given": "James H", "initials": "JH"}, {"family": "Rivas-Torres", "given": "Gonzalo", "initials": "G"}, {"family": "Rieseberg", "given": "Loren H", "initials": "LH"}, {"family": "Martin", "given": "Michael D", "initials": "MD"}], "type": "journal article", "published": "2025-05-31", "journal": {"title": "Mobile DNA", "issn": "1759-8753", "volume": "16", "issue": "1", "pages": "23", "issn-l": "1759-8753"}, "abstract": "Transposable elements (TEs) have been hypothesized to play a pivotal role in driving diversification by facilitating the emergence of novel phenotypes and the accumulation of divergence between species. Hybridization and adaptation to novel niches have been proposed to destabilize mechanisms constraining TE proliferation, potentially inducing a 'TE burst' that promotes TE accumulation on the genome. The rapid speciation and ecological diversification characteristic of adaptive radiations offer a unique opportunity to examine the link between TE accumulation and speciation, diversification, hybridization and adaptation. Here, focusing on all 15 species of the genus Scalesia (Asteraceae), a radiation endemic to the Gal\u00e1pagos Islands, we test whether diversification, hybridization, or shifts in ecological niche are associated with changes in TE accumulation in genomes. Our analyses reveal little to no variation in TE accumulation among Scalesia species nor its hybrid populations. Shifts in ecological niches, linked to climatic variation, did not result in discernible changes in TE accumulation, a surprising finding given the anticipated selective pressure imposed by aridity, a factor often linked to genome size reduction. We found no distinct patterns in the temporal accumulation of TEs, and no effects at the class or superfamily level. Our findings suggest that while TEs may play a key role in evolution at the locus level, their macroevolutionary association with diversification or speciation appears weak. Rather than actively driving evolutionary diversification, TEs may simply be'along for the ride.", "doi": "10.1186/s13100-025-00362-z", "pmid": "40450335", "labels": {"Jos\u00e9 Cerca": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC12125827"}, {"db": "pii", "key": "10.1186/s13100-025-00362-z"}], "notes": [], "created": "2026-08-20T12:22:08.353Z", "modified": "2026-09-23T12:32:43.897Z"}, {"entity": "publication", "iuid": "7d80eacd707b42e79fdec1d031200057", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/7d80eacd707b42e79fdec1d031200057.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/7d80eacd707b42e79fdec1d031200057"}}, "title": "Environmental reservoir of resistance genes for the last resort antibiotic Cefiderocol", "authors": [{"family": "Gschwind", "given": "Remi", "initials": "R", "orcid": "0000-0001-7741-9764", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/287bf0d97cad4eb7b389fa0a8495e86b.json"}}, {"family": "Bonnet", "given": "Mehdi", "initials": "M"}, {"family": "Abramova", "given": "Anna", "initials": "A", "orcid": "0000-0002-0493-7808", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dd75cbcc659c4ca398eb678fad1dc498.json"}}, {"family": "Jarqu\u00edn-D\u00edaz", "given": "Victor Hugo", "initials": "VH", "orcid": "0000-0003-3758-1091", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d573d1cb515a4c75b3c8ff2f97be419a.json"}}, {"family": "Wenne", "given": "Marcus", "initials": "M", "orcid": "0009-0008-1941-4146", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/90d60a98a3b54120b369ffe5dd29c854.json"}}, {"family": "L\u00f6ber", "given": "Ulrike", "initials": "U", "orcid": "0000-0001-7468-9531", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b71c22b8d28b46e490fa499603ada68d.json"}}, {"family": "Godron", "given": "Nicolas", "initials": "N", "orcid": "0009-0004-4143-5462", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0285cb4da845488b97f091bc0d3acac5.json"}}, {"family": "Kampouris", "given": "Ioannis D", "initials": "ID", "orcid": "0000-0003-2093-5930", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2a58d348ca1f496d8c3915e23c411a6c.json"}}, {"family": "Tskhay", "given": "Faina", "initials": "F", "orcid": "0000-0001-8700-3279", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/66867423459544e7a72b0a9090a46cee.json"}}, {"family": "Naheed", "given": "Fouzia", "initials": "F"}, {"family": "Debroucker", "given": "Chlo\u00e9", "initials": "C"}, {"family": "Bui-Hai", "given": "Maximilien", "initials": "M"}, {"family": "Aiba", "given": "In\u00e8s El", "initials": "IE"}, {"family": "Kl\u00fcmper", "given": "Uli", "initials": "U", "orcid": "0000-0002-4169-6548", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7d8605cdbfc14403b607a3b5ace7249d.json"}}, {"family": "Berendonk", "given": "Thomas U", "initials": "TU", "orcid": "0000-0002-9301-1803", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c66286f83a8430f954fbc5c52db10c5.json"}}, {"family": "Forslund-Startceva", "given": "Sofia K", "initials": "SK", "orcid": "0000-0003-4285-6993", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/80bd453b4d084425948404417485140b.json"}}, {"family": "Zahra", "given": "Rabaab", "initials": "R", "orcid": "0000-0001-8784-0114", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a678f0c2414244ac894b5f0540b5ef5f.json"}}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J", "orcid": "0000-0002-6528-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c666068e9d34939b0252a627007cec7.json"}}, {"family": "Ruppe", "given": "Etienne", "initials": "E"}], "type": "posted-content", "published": "2025-05-26", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2025.05.26.656069", "pmid": null, "labels": {"DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2025-06-04T08:15:56.666Z", "modified": "2026-09-23T14:38:17.661Z"}, {"entity": "publication", "iuid": "4b2bd02c88e246a39e79bf13c9bafb55", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4b2bd02c88e246a39e79bf13c9bafb55.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4b2bd02c88e246a39e79bf13c9bafb55"}}, "title": "1000 conifer genomes: Genome innovation, organisation and diversity", "authors": [{"family": "Nilsson", "given": "Ove", "initials": "O"}, {"family": "Kalman", "given": "Teitur Ahlgren", "initials": "TA"}, {"family": "Delhomme", "given": "Nicolas", "initials": "N"}, {"family": "Eriksson", "given": "Mimmi", "initials": "M", "orcid": "0000-0002-9548-8226", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e8736c6470734a65a6b4bb81efd4ce84.json"}}, {"family": "Hill", "given": "Jason", "initials": "J"}, {"family": "Kumar", "given": "Vikash", "initials": "V"}, {"family": "Larsson", "given": "Tomas", "initials": "T"}, {"family": "M\u00e4hler", "given": "Niklas", "initials": "N"}, {"family": "Nandi", "given": "Soumyadeep", "initials": "S"}, {"family": "Unneberg", "given": "Per", "initials": "P", "orcid": "0000-0001-5735-3315", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/47dae455224d4af4a35865907088f0b1.json"}}, {"family": "Valk", "given": "Tom van der", "initials": "Tvd"}, {"family": "Zuccolo", "given": "Andrea", "initials": "A"}, {"family": "Chen", "given": "Zhi Qiang", "initials": "ZQ"}, {"family": "Barcala", "given": "Maximiliano Estravis", "initials": "ME"}, {"family": "Rodriguez", "given": "Eduardo", "initials": "E"}, {"family": "Funda", "given": "Tom\u00e1\u0161", "initials": "T"}, {"family": "Chaudhary", "given": "Rajiv", "initials": "R"}, {"family": "Birkeland", "given": "Siri", "initials": "S"}, {"family": "Olsen", "given": "Remi Andre", "initials": "RA"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Mccann", "given": "Jamie", "initials": "J"}, {"family": "Tuominen", "given": "Hannele", "initials": "H"}, {"family": "Canovi", "given": "Camilla", "initials": "C"}, {"family": "Piombo", "given": "Edoardo", "initials": "E"}, {"family": "Lorenzo", "given": "Zulema Carracedo", "initials": "ZC"}, {"family": "Zalen", "given": "Elena van", "initials": "Ev"}, {"family": "Suontama", "given": "Mari", "initials": "M"}, {"family": "Hallingb\u00e4ck", "given": "Henrik", "initials": "H"}, {"family": "Mosbech", "given": "Mai Britt", "initials": "MB"}, {"family": "Vassilieff", "given": "Helena", "initials": "H"}, {"family": "Schiffthaler", "given": "Bastian", "initials": "B"}, {"family": "Grabherr", "given": "Manfred", "initials": "M"}, {"family": "Bakker", "given": "Linda", "initials": "L"}, {"family": "Schijlen", "given": "Elio", "initials": "E"}, {"family": "Benstein", "given": "Ruben", "initials": "R", "orcid": "0000-0002-5799-7572", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c22a29452d1548d9939ba592587c322c.json"}}, {"family": "Sundstr\u00f6m", "given": "Jens", "initials": "J", "orcid": "0000-0003-2848-5284", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3f874bf5d22d447293d5fa7f774baa5d.json"}}, {"family": "Westrin", "given": "Karl Johan", "initials": "KJ"}, {"family": "Emanuelsson", "given": "Olof", "initials": "O"}, {"family": "Pettersson", "given": "Olga", "initials": "O"}, {"family": "Hvidsten", "given": "Torgeir", "initials": "T", "orcid": "0000-0001-6097-2539", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9f385ace6dda41249296c3ca55adaaf6.json"}}, {"family": "Sherwood", "given": "Ellen", "initials": "E"}, {"family": "Ingvarsson", "given": "P\u00e4r", "initials": "P", "orcid": "0000-0001-9225-7521", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fb09a6889bc64651ac6eb90b67edca3d.json"}}, {"family": "Wu", "given": "Harry", "initials": "H", "orcid": "0000-0002-7072-4704", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d09d9cea430d4bf7907374fd9fc44b18.json"}}, {"family": "Gyllensten", "given": "Ulf", "initials": "U", "orcid": "0000-0002-6316-3355", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eacfdf2095e947e99ac45fe994261b72.json"}}, {"family": "Nilsson", "given": "Ove", "initials": "O"}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/33ba67b99d2b477d9588d40e8cc0fed2.json"}}, {"family": "Street", "given": "Nathaniel", "initials": "N", "orcid": "0000-0001-6031-005X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9fee0b9ea71c4a54abee68132840b274.json"}}], "type": "posted-content", "published": "2025-05-26", "journal": {"issn-l": null}, "abstract": null, "doi": "10.21203/rs.3.rs-6502828/v1", "pmid": null, "labels": {"DDLS Fellow": "", "Tom van der Valk": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T12:59:45.001Z", "modified": "2026-09-23T14:15:06.352Z"}, {"entity": "publication", "iuid": "b195c8eb580347c3a35ed0111691ba59", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b195c8eb580347c3a35ed0111691ba59.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b195c8eb580347c3a35ed0111691ba59"}}, "title": "RareFold: Structure Prediction and Design of Proteins with Noncanonical Amino Acids", "authors": [{"family": "Li", "given": "Qiuzhen", "initials": "Q", "orcid": "0009-0009-2913-4786", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f3d7b87dcea3440d8eaa4b574a88da3e.json"}}, {"family": "Daumiller", "given": "Diandra", "initials": "D", "orcid": "0009-0009-5387-1292", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0021818d47ef4ce6b5cd53c92c4cd540.json"}}, {"family": "Zuo", "given": "Fanglei", "initials": "F", "orcid": "0000-0002-4545-1265", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/aff6db3e84404d4b90e9ecfb2e6d8a77.json"}}, {"family": "Marcotte", "given": "Harold", "initials": "H", "orcid": "0000-0002-7168-349X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6e082f9bcfa8424987aa9e205396e5f3.json"}}, {"family": "Pan-Hammarstr\u00f6m", "given": "Qiang", "initials": "Q", "orcid": "0000-0003-1990-8804", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3ba17712dd394791a8813f7643e72aaf.json"}}, {"family": "Bryant", "given": "Patrick", "initials": "P", "orcid": "0000-0003-3439-1866", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a683bcf98234ff09b2398976583b66f.json"}}], "type": "posted-content", "published": "2025-05-23", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2025.05.19.654846", "pmid": null, "labels": {"Patrick Bryant": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2026-09-23T13:50:21.062Z", "modified": "2026-09-23T13:50:21.132Z"}, {"entity": "publication", "iuid": "1daf186d98b44d7788ab8df587133b27", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1daf186d98b44d7788ab8df587133b27.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1daf186d98b44d7788ab8df587133b27"}}, "title": "Library-based single-cell analysis of CAR signaling reveals drivers of in vivo persistence.", "authors": [{"family": "Perez", "given": "Caleb R", "initials": "CR"}, {"family": "Garmilla", "given": "Andrea", "initials": "A"}, {"family": "Nilsson", "given": "Avlant", "initials": "A"}, {"family": "Baghdassarian", "given": "Hratch M", "initials": "HM"}, {"family": "Gordon", "given": "Khloe S", "initials": "KS"}, {"family": "Lima", "given": "Louise G", "initials": "LG"}, {"family": "Smith", "given": "Blake E", "initials": "BE"}, {"family": "Maus", "given": "Marcela V", "initials": "MV"}, {"family": "Lauffenburger", "given": "Douglas A", "initials": "DA"}, {"family": "Birnbaum", "given": "Michael E", "initials": "ME", "orcid": "0000-0002-2281-3518", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ccd63276499445cae3ad2346409847e.json"}}], "type": "journal article", "published": "2025-05-21", "journal": {"title": "Cell Syst", "issn": "2405-4720", "volume": "16", "issue": "5", "pages": "101260", "issn-l": null}, "abstract": "The anti-tumor function of engineered T cells expressing chimeric antigen receptors (CARs) is dependent on signals transduced through intracellular signaling domains (ICDs). Different ICDs are known to drive distinct phenotypes, but systematic investigations into how ICD architectures direct T cell function-particularly at the molecular level-are lacking. Here, we use single-cell sequencing to map diverse signaling inputs to transcriptional outputs, focusing on a defined library of clinically relevant ICD architectures. Informed by these observations, we functionally characterize transcriptionally distinct ICD variants across various contexts to build comprehensive maps from ICD composition to phenotypic output. We identify a unique tonic signaling signature associated with a subset of ICD architectures that drives durable in vivo persistence and efficacy in liquid, but not solid, tumors. Our findings work toward decoding CAR signaling design principles, with implications for the rational design of next-generation ICD architectures optimized for in vivo function.", "doi": "10.1016/j.cels.2025.101260", "pmid": "40215972", "labels": {"Avlant Nilsson": null, "DDLS Fellow": null}, "xrefs": [{"db": "mid", "key": "NIHMS2074196"}, {"db": "pmc", "key": "PMC12097926"}, {"db": "pii", "key": "S2405-4712(25)00093-6"}], "notes": [], "created": "2025-11-28T13:09:37.440Z", "modified": "2025-12-04T19:42:10.117Z"}, {"entity": "publication", "iuid": "52e8a7565f594b1f83b7ec6dc5066de9", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/52e8a7565f594b1f83b7ec6dc5066de9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/52e8a7565f594b1f83b7ec6dc5066de9"}}, "title": "Caveolin assemblies displace one bilayer leaflet to organize and bend membranes.", "authors": [{"family": "Doktorova", "given": "Milka", "initials": "M", "orcid": "0000-0003-4366-2242", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/791384c319f04584bac8ffb21df7271f.json"}}, {"family": "Daum", "given": "Sebastian", "initials": "S"}, {"family": "Reagle", "given": "Tyler R", "initials": "TR"}, {"family": "Cannon", "given": "Hannah I", "initials": "HI"}, {"family": "Ebenhan", "given": "Jan", "initials": "J"}, {"family": "Neudorf", "given": "Sarah", "initials": "S"}, {"family": "Han", "given": "Bing", "initials": "B"}, {"family": "Sharma", "given": "Satyan", "initials": "S"}, {"family": "Kasson", "given": "Peter", "initials": "P"}, {"family": "Levental", "given": "Kandice R", "initials": "KR", "orcid": "0000-0002-2234-3683", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dcde4d3042b349b199c48509444ac8f9.json"}}, {"family": "Bacia", "given": "Kirsten", "initials": "K"}, {"family": "Kenworthy", "given": "Anne K", "initials": "AK", "orcid": "0000-0001-6567-9059", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/16cb5a7a473b4373a243bcfa6ff36708.json"}}, {"family": "Levental", "given": "Ilya", "initials": "I", "orcid": "0000-0002-1206-9545", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7fe40c2b810348cab78616402d4d1f1f.json"}}], "type": "journal article", "published": "2025-05-20", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "122", "issue": "20", "pages": "e2417024122", "issn-l": "0027-8424"}, "abstract": "Caveolin is a monotopic integral membrane protein, widely expressed in metazoans and responsible for constructing enigmatic membrane invaginations known as caveolae. Recently, the high-resolution structure of a purified human caveolin assembly, the CAV1-8S complex, revealed a unique organization of 11 protomers arranged in a tightly packed, radially symmetric spiral disc. One face and the outer rim of this disc are hydrophobic, suggesting that the complex incorporates into membranes by displacing hundreds of lipids from one leaflet. The feasibility of this unique molecular architecture and its biophysical and functional consequences are currently unknown. Using Langmuir film balance measurements, we find that CAV1-8S is highly surface active, intercalating into lipid monolayers of various compositions. CAV1-8S can also incorporate into preformed bilayers, but only upon removal of phospholipids from the outer-facing leaflet. Atomistic and coarse-grained simulations of biomimetic bilayers support this \"leaflet replacement\" model and also reveal that CAV1-8S accumulates 40 to 70 cholesterol molecules into a disordered monolayer between the complex and its distal lipid leaflet. We find that CAV1-8S preferentially associates with positively curved membrane surfaces due to its influence on the conformations of distal leaflet lipids, and that these effects laterally sort lipids. Large-scale simulations of multiple caveolin assemblies confirmed their association with large, positively curved membrane morphologies consistent with the shape of caveolae. Further, association with curved membranes regulates the exposure of caveolin residues implicated in protein-protein interactions. Altogether, the unique structure of CAV1-8S imparts unusual modes of membrane interaction with implications for membrane organization, morphology, and physiology.", "doi": "10.1073/pnas.2417024122", "pmid": "40359049", "labels": {"Milka Doktorova": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC12107156"}], "notes": [], "created": "2026-08-20T09:31:41.385Z", "modified": "2026-09-23T09:07:44.382Z"}, {"entity": "publication", "iuid": "ad4d81de09004be6a9da87374e7dc612", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ad4d81de09004be6a9da87374e7dc612.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ad4d81de09004be6a9da87374e7dc612"}}, "title": "Gender differences in global antimicrobial resistance.", "authors": [{"family": "Salehi", "given": "Mahkameh", "initials": "M"}, {"family": "Laitinen", "given": "Ville", "initials": "V"}, {"family": "Bhanushali", "given": "Shivang", "initials": "S"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J", "orcid": "0000-0002-6528-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c666068e9d34939b0252a627007cec7.json"}}, {"family": "Collignon", "given": "Peter", "initials": "P"}, {"family": "Beggs", "given": "John J", "initials": "JJ"}, {"family": "P\u00e4rn\u00e4nen", "given": "Katariina", "initials": "K"}, {"family": "Lahti", "given": "Leo", "initials": "L"}], "type": "journal article", "published": "2025-05-19", "journal": {"title": "NPJ Biofilms Microbiomes", "issn": "2055-5008", "volume": "11", "issue": "1", "pages": "79", "issn-l": null}, "abstract": "Antimicrobial resistance is one of the leading causes of mortality globally. However, little is known about the distribution of antibiotic resistance genes (ARGs) in human gut metagenomes, collectively referred to as the resistome, across socio-demographic gradients. In particular, limited evidence exists on gender-based differences. We investigated how the resistomes differ between women and men in a global dataset of 14,641 publicly available human gut metagenomes encompassing countries with widely variable economic statuses. We observed a 9% higher total ARG load in women than in men in high-income countries. However, in low- and middle-income countries, the difference between genders was reversed in univariate models, but not significant after adjusting for covariates. Interestingly, the differences in ARG load between genders emerged in adulthood, suggesting resistomes differentiate between genders after childhood. Collectively, our data-driven analyses shed light on global, gendered antibiotic resistance patterns, which may help guide further research and targeted interventions.", "doi": "10.1038/s41522-025-00715-9", "pmid": "40389466", "labels": {"DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC12089330"}, {"db": "pii", "key": "10.1038/s41522-025-00715-9"}], "notes": [], "created": "2025-06-04T08:12:37.852Z", "modified": "2026-09-23T09:06:58.101Z"}, {"entity": "publication", "iuid": "636ade3645a445628ee42ef4730d546a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/636ade3645a445628ee42ef4730d546a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/636ade3645a445628ee42ef4730d546a"}}, "title": "Fast, flexible gene cluster family delineation with IGUA", "authors": [{"family": "Larralde", "given": "Martin", "initials": "M", "orcid": "0000-0002-3947-4444", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6e048b839197434d8af8ab34bd50cf5e.json"}}, {"family": "Blom", "given": "Josefin", "initials": "J", "orcid": "0009-0000-9910-7374", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/361785c07fb04b5497ce209141d2c337.json"}}, {"family": "Gourl\u00e9", "given": "Hadrien", "initials": "H", "orcid": "0000-0001-9807-1082", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d5485a48dfde4e53b14d39c54f2b2483.json"}}, {"family": "Carroll", "given": "Laura M", "initials": "LM", "orcid": "0000-0002-3677-0192", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02112eccb0664819af916a3c3dc79daa.json"}}, {"family": "Zeller", "given": "Georg", "initials": "G", "orcid": "0000-0003-1429-7485", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/414382373eb5447186a7e6c925aa067f.json"}}], "type": "posted-content", "published": "2025-05-19", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2025.05.15.654203", "pmid": null, "labels": {"DDLS Fellow": "", "Laura Carroll": ""}, "xrefs": [], "notes": [], "created": "2026-10-01T08:31:02.314Z", "modified": "2026-10-01T08:31:02.379Z"}, {"entity": "publication", "iuid": "d26c5004293a4ea7b4613b8f3053e8ac", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d26c5004293a4ea7b4613b8f3053e8ac.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d26c5004293a4ea7b4613b8f3053e8ac"}}, "title": "Chromosome-level genome assembly of Norwegian wild alpine reindeer ( Rangifer tarandus tarandus )", "authors": [{"family": "T\u00f8rresen", "given": "Ole K", "initials": "OK", "orcid": "0000-0002-1932-8212", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9d2f90dfcdde43d597ac37a347c44ff5.json"}}, {"family": "Tooming-Klunderud", "given": "Ave", "initials": "A", "orcid": "0009-0008-0057-2873", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a83f56872d6a4b0fb91504e15cafa9eb.json"}}, {"family": "Skage", "given": "Morten", "initials": "M", "orcid": "0000-0002-5312-8038", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b3f666519e7d400fa772046cad3844f4.json"}}, {"family": "Streitlien", "given": "Anne Eline", "initials": "AE"}, {"family": "Strand", "given": "Olav", "initials": "O"}, {"family": "Rolandsen", "given": "Christer M", "initials": "CM", "orcid": "0000-0002-5628-0385", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/72a91e483949447789bd7230f8bc5b7e.json"}}, {"family": "Ferrari", "given": "Giada", "initials": "G", "orcid": "0000-0002-0850-1518", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6679779a21914fb496849057cccbf984.json"}}, {"family": "Cerca", "given": "Jos\u00e9", "initials": "J", "orcid": "0000-0001-7788-4367", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b9119ffe17f1400ea74e0eaf43c105fc.json"}}, {"family": "Mysterud", "given": "Atle", "initials": "A", "orcid": "0000-0001-8993-7382", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f36192bbe8634b818745104303041e90.json"}}, {"family": "Jakobsen", "given": "Kjetill S", "initials": "KS", "orcid": "0000-0002-8861-5397", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f2fe02e097b342508301397260ef7cc3.json"}}], "type": "posted-content", "published": "2025-05-16", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2025.05.15.652595", "pmid": null, "labels": {"Jos\u00e9 Cerca": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T11:03:51.677Z", "modified": "2026-09-23T15:47:42.740Z"}, {"entity": "publication", "iuid": "ba2006e120954777a021042ee6d1b63e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ba2006e120954777a021042ee6d1b63e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ba2006e120954777a021042ee6d1b63e"}}, "title": "Cell shapes decode molecular phenotypes in image-based spatial proteomics.", "authors": [{"family": "Le", "given": "Trang", "initials": "T"}, {"family": "Leineweber", "given": "William D", "initials": "WD", "orcid": "0000-0003-3069-398X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f6f5dd2023994301867b8bb3948a2274.json"}}, {"family": "Viana", "given": "Matheus P", "initials": "MP", "orcid": "0000-0001-9288-2108", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/57b1be92b4f549df8b09af4a7532493f.json"}}, {"family": "Cesnik", "given": "Anthony", "initials": "A", "orcid": "0000-0002-5326-7134", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0fda549f3795457fb60ec3372b98e2d5.json"}}, {"family": "Hansen", "given": "Jan N", "initials": "JN", "orcid": "0000-0002-0489-7535", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4047064d44674e229a3b2dd10f241607.json"}}, {"family": "Ouyang", "given": "Wei", "initials": "W", "orcid": "0000-0002-0291-926X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56f601e1d1c6448aab0c3a1e3cffdbfc.json"}}, {"family": "Rafelski", "given": "Susanne M", "initials": "SM", "orcid": "0000-0002-1399-5970", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/33f5be9729bf4ff280b958d85df287d4.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb07e6d0122c4528a927c1fe922e3bc8.json"}}], "type": "journal article", "published": "2025-05-16", "journal": {"title": "bioRxiv", "issn": "2692-8205", "issn-l": null}, "abstract": "The diversity of cellular and tissue structures can arise from a few basic cell shapes, which undergo various transformations based on biophysical constraints on cytoskeletal organization. While cellular geometry has been linked with selected biological processes such as polarity, signaling or morphogenesis, the orchestration of the whole proteome in association to cell shape is still poorly understood. In this study, using more than 1 million images of single cells stained for 11,998 proteins across 10 cell lines in the Human Protein Atlas database, we performed an integrated analysis of organelle, pathway and single protein levels in association to a 2D cellular shapespace. We found that cell and nuclear shapes across cell lines exist in a shared continuum. We also found that the subcellular organelle topology varies across cell lines, but remains robust within each cell line's shapespace. At the single protein level, we found that cells of different shapes in the same cell cycle phase might be preparing for different fates, and that many non-cell cycle proteins expressed shape-based abundance variation. Using the same coordinate framework defined by shape, we could analyze the distribution shift of protein spatial localization under drug perturbation.", "doi": "10.1101/2025.05.13.653868", "pmid": "40463127", "labels": {"Wei Ouyang": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC12132440"}, {"db": "pii", "key": "2025.05.13.653868"}], "notes": [], "created": "2025-12-15T10:06:41.544Z", "modified": "2026-09-23T14:28:41.175Z"}, {"entity": "publication", "iuid": "a91b13df641f4c78b410d3628b3b13a6", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a91b13df641f4c78b410d3628b3b13a6.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a91b13df641f4c78b410d3628b3b13a6"}}, "title": "Community-promoted antibiotic resistance genes show increased dissemination among pathogens", "authors": [{"family": "Lund", "given": "David", "initials": "D", "orcid": "0000-0003-4075-7529", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/20d4ac6decf34a9791cd8c1aa0cc0eaf.json"}}, {"family": "Johnning", "given": "Anna", "initials": "A", "orcid": "0000-0003-2185-2432", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ed3d27417904d79b3615483b936d63d.json"}}, {"family": "Holmstr\u00f6m", "given": "Michaela", "initials": "M"}, {"family": "Varghaei", "given": "Laleh", "initials": "L"}, {"family": "Inda-D\u00edaz", "given": "Juan Salvador", "initials": "JS", "orcid": "0000-0002-3735-8300", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2eaba7e7cf3f4fdeb9883a16f5c6d9fe.json"}}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J", "orcid": "0000-0002-6528-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c666068e9d34939b0252a627007cec7.json"}}, {"family": "Kristiansson", "given": "Erik", "initials": "E", "orcid": "0000-0002-8609-2414", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/18d5538c8c0749199a6f1b51d15eec69.json"}}], "type": "posted-content", "published": "2025-05-15", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2025.05.12.653433", "pmid": null, "labels": {"DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2025-06-04T08:15:59.392Z", "modified": "2026-09-23T14:38:13.641Z"}, {"entity": "publication", "iuid": "a38b9cc5b27b4a82bcf11a7e599b4eed", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a38b9cc5b27b4a82bcf11a7e599b4eed.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a38b9cc5b27b4a82bcf11a7e599b4eed"}}, "title": "Cell membranes sustain phospholipid imbalance via cholesterol asymmetry.", "authors": [{"family": "Doktorova", "given": "Milka", "initials": "M"}, {"family": "Symons", "given": "Jessica L", "initials": "JL"}, {"family": "Zhang", "given": "Xiaoxuan", "initials": "X"}, {"family": "Wang", "given": "Hong-Yin", "initials": "HY"}, {"family": "Schlegel", "given": "Jan", "initials": "J"}, {"family": "Lorent", "given": "Joseph H", "initials": "JH"}, {"family": "Heberle", "given": "Frederick A", "initials": "FA"}, {"family": "Sezgin", "given": "Erdinc", "initials": "E"}, {"family": "Lyman", "given": "Edward", "initials": "E"}, {"family": "Levental", "given": "Kandice R", "initials": "KR"}, {"family": "Levental", "given": "Ilya", "initials": "I"}], "type": "journal article", "published": "2025-05-15", "journal": {"title": "Cell", "issn": "1097-4172", "volume": "188", "issue": "10", "pages": "2586-2602.e24", "issn-l": "0092-8674"}, "abstract": "Membranes are molecular interfaces that compartmentalize cells to control the flow of nutrients and information. These functions are facilitated by diverse collections of lipids, nearly all of which are distributed asymmetrically between the two bilayer leaflets. Most models of biomembrane structure and function include the implicit assumption that these leaflets have similar abundances of phospholipids. Here, we show that this assumption is generally invalid and investigate the consequences of lipid abundance imbalances in mammalian plasma membranes (PMs). Using lipidomics, we report that cytoplasmic leaflets of human erythrocyte membranes have >50% overabundance of phospholipids compared with exoplasmic leaflets. This imbalance is enabled by an asymmetric interleaflet distribution of cholesterol, which regulates cellular cholesterol homeostasis. These features produce unique functional characteristics, including low PM permeability and resting tension in the cytoplasmic leaflet that regulates protein localization.", "doi": "10.1016/j.cell.2025.02.034", "pmid": "40179882", "labels": {"SciLifeLab Fellow": "", "Milka Doktorova": "", "DDLS Fellow": "", "Erdinc Sezgin": ""}, "xrefs": [{"db": "mid", "key": "NIHMS2062685"}, {"db": "pmc", "key": "PMC12085300"}, {"db": "pii", "key": "S0092-8674(25)00270-3"}], "notes": [], "created": "2026-09-23T07:31:16.036Z", "modified": "2026-09-23T07:31:16.059Z"}, {"entity": "publication", "iuid": "a4ae10b23b9244769817f28db610716f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a4ae10b23b9244769817f28db610716f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a4ae10b23b9244769817f28db610716f"}}, "title": "Metagenomic biodiversity assessment within an offshore wind farm.", "authors": [{"family": "Serivichyaswat", "given": "Phanu Theodore", "initials": "PT"}, {"family": "Scholte", "given": "Thijs", "initials": "T"}, {"family": "Wilms", "given": "Tim", "initials": "T"}, {"family": "Stranddorf", "given": "Liv", "initials": "L"}, {"family": "van der Valk", "given": "Tom", "initials": "T"}], "type": "journal article", "published": "2025-05-14", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "16786", "issn-l": "2045-2322"}, "abstract": "Environmental DNA (eDNA) analysis can be a powerful tool for monitoring biodiversity and assessing human impacts on ecosystems. In this study, we employed a genome-wide metagenomic eDNA approach to assess the marine biodiversity within and around the Horns Rev 1 offshore wind farm in the Danish North Sea. Seawater samples were collected from both within the windfarm and surrounding control sites, sequenced, and analyzed using a combination of DNA k-mer matching and alignment-based classification methods. We identified a wide range of species across the tree of life-highlighting the species richness of this marine ecosystem. Our results revealed a high degree of species diversity congruence between the wind farm and control sites. While this could suggest minimal ecological disruption of the wind farm, we cannot rule out that the influence of ocean currents and water mixing the DNA from different regions dominate the species detection. We detected bioindicator species, such as Thalassiosira, Phaeocystis and Skeletonema, which can provide insights into water quality. Our metagenomic approach also enabled us to obtain population genomics insights for species, such as the European anchovy (Engraulis encrasicolus) and the diatom Rhizosolenia setigera, and genetically confirmed the origin of the invasive Sea walnut (Mnemiopsis leidyi) in the North Sea. This study highlights the potential of genome-wide eDNA metagenomics as a framework for assessing marine biodiversity and detecting population-level genetic signals, contributing to informed and scalable ecosystem monitoring strategies.", "doi": "10.1038/s41598-025-01541-x", "pmid": "40368948", "labels": {"DDLS Fellow": "", "Tom van der Valk": ""}, "xrefs": [{"db": "pmc", "key": "PMC12078662"}, {"db": "pii", "key": "10.1038/s41598-025-01541-x"}], "notes": [], "created": "2026-09-23T12:28:04.299Z", "modified": "2026-09-23T12:28:04.326Z"}, {"entity": "publication", "iuid": "7e5bd66642ac43a3a8c76d8c34eefdae", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/7e5bd66642ac43a3a8c76d8c34eefdae.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/7e5bd66642ac43a3a8c76d8c34eefdae"}}, "title": "AI4CellFate: Interpretable Early Cell Fate Prediction with Generative AI", "authors": [{"family": "Cunha", "given": "In\u00eas", "initials": "I", "orcid": "0000-0002-1327-9018", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/77f0773f41cc4f1191aaba0d21ec745a.json"}}, {"family": "Panconi", "given": "Luca", "initials": "L", "orcid": "0000-0001-6025-8597", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/25ef9b2e880e487ab860720826e438b0.json"}}, {"family": "Bauer", "given": "Sebastian", "initials": "S", "orcid": "0009-0009-7265-1527", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/13207e5919484106ba3126c36880802c.json"}}, {"family": "Gestin", "given": "Maxime", "initials": "M", "orcid": "0000-0002-4164-166X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1df5b46bb33b4a54935024ac6efb31e3.json"}}, {"family": "Latron", "given": "Emma", "initials": "E"}, {"family": "Sahai", "given": "Erik", "initials": "E", "orcid": "0000-0002-3932-5086", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8cc2504741b948499d681721a1b519b2.json"}}, {"family": "Le Marois", "given": "Alix", "initials": "A", "orcid": "0000-0003-4464-4089", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/464758d00f7f4a9d826c1315d1eabaa4.json"}}, {"family": "Griffi\u00e9", "given": "Juliette", "initials": "J", "orcid": "0000-0001-6438-0119", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2650e9aa00f7499aba2f222c49a95e71.json"}}], "type": "posted-content", "published": "2025-05-14", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2025.05.12.653464", "pmid": null, "labels": {"DDLS Fellow": "", "Juliette Griffie": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T11:03:47.691Z", "modified": "2026-09-23T14:53:39.745Z"}, {"entity": "publication", "iuid": "a2fd7d47dd5148bdb0f5170e51a2f92d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a2fd7d47dd5148bdb0f5170e51a2f92d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a2fd7d47dd5148bdb0f5170e51a2f92d"}}, "title": "Loss of lipid asymmetry facilitates plasma membrane blebbing by decreasing membrane lipid packing.", "authors": [{"family": "Wang", "given": "Hong-Yin", "initials": "HY", "orcid": "0000-0002-8704-2814", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b2e12db192d04321b4c232a49181b8ff.json"}}, {"family": "Rumin", "given": "Alissa", "initials": "A", "orcid": "0009-0006-0314-1353", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/17d45c7578b4489499e15e99132e466d.json"}}, {"family": "Doktorova", "given": "Milka", "initials": "M", "orcid": "0000-0003-4366-2242", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/791384c319f04584bac8ffb21df7271f.json"}}, {"family": "Sputay", "given": "Daryna", "initials": "D", "orcid": "0009-0008-9987-5582", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3dedb072e04d447c87728ea160049cf0.json"}}, {"family": "Chan", "given": "Sze Ham", "initials": "SH", "orcid": "0000-0002-3235-0852", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4854c445b24541adbfcb1a44a1d02305.json"}}, {"family": "Wehman", "given": "Ann M", "initials": "AM", "orcid": "0000-0001-9826-4132", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a8575abcc457452d91ec3f61e81616e7.json"}}, {"family": "Levental", "given": "Kandice R", "initials": "KR", "orcid": "0000-0002-2234-3683", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dcde4d3042b349b199c48509444ac8f9.json"}}, {"family": "Levental", "given": "Ilya", "initials": "I", "orcid": "0000-0002-1206-9545", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7fe40c2b810348cab78616402d4d1f1f.json"}}], "type": "journal article", "published": "2025-05-13", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "122", "issue": "19", "pages": "e2417145122", "issn-l": "0027-8424"}, "abstract": "Membrane blebs have important roles in cell migration, apoptosis, and intercellular communication through extracellular vesicles (EVs). While plasma membranes (PM) typically maintain phosphatidylserine (PS) on their cytoplasmic leaflet, most blebs have PS exposed on their outer leaflet, revealing that loss of steady-state lipid asymmetry often accompanies PM blebbing. How these changes in PM lipid organization regulate membrane properties and affect bleb formation remains unknown. We confirmed that lipid scrambling through the scramblase TMEM16F is essential for chemically induced membrane blebbing across cell types, with the kinetics of PS exposure being tightly coupled to the kinetics of bleb formation. Measurement of lipid packing with environment-sensitive probes revealed that lipid scrambling changes the physical properties of the PM, reducing lipid packing and facilitating the bilayer bending required for bleb formation. Accordingly, reducing lipid packing of the PM through cholesterol extraction, elevated temperature, or treatment with biological amphiphiles promoted blebbing in the absence of TMEM16F. Consistent with these cellular observations, blebbing in Caenorhabditis elegans embryos measured via EV production was significantly reduced by depleting the TMEM16-homolog ANOH-2. Our findings suggest that changing membrane biophysical properties by lipid scrambling is an important contributor to the formation of blebs and EVs and potentially other cellular processes involving PM deformation.", "doi": "10.1073/pnas.2417145122", "pmid": "40324083", "labels": {"Milka Doktorova": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC12088411"}], "notes": [], "created": "2026-08-20T09:31:46.422Z", "modified": "2026-09-23T09:10:43.480Z"}, {"entity": "publication", "iuid": "7b6876e0da1547e08cf8eb2484a67e5e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/7b6876e0da1547e08cf8eb2484a67e5e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/7b6876e0da1547e08cf8eb2484a67e5e"}}, "title": "The effectiveness of selection in a species affects the direction of amino acid frequency evolution.", "authors": [{"family": "McShea", "given": "Hanon", "initials": "H", "orcid": "0000-0002-9341-4899", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/04a9138ad6834af4be9e2d3c255cc1c9.json"}}, {"family": "Wheeler", "given": "Andrew L", "initials": "AL"}, {"family": "Goodman", "given": "Peter", "initials": "P"}, {"family": "Weibel", "given": "Catherine", "initials": "C", "orcid": "0000-0003-1837-5209", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/54d6dc2af7084fc58d9ab18aa72423e7.json"}}, {"family": "Wehbi", "given": "Sawsan", "initials": "S", "orcid": "0000-0001-9498-9582", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d2a9b28368f5476d9ff5e4cc7886c9ab.json"}}, {"family": "James", "given": "Jennifer E", "initials": "JE", "orcid": "0000-0003-0518-6783", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4b807f7ab8f46f8a5e927e1b090d662.json"}}, {"family": "Huttley", "given": "Gavin", "initials": "G", "orcid": "0000-0001-7224-2074", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/89918f0414cb43c591dfc534bc95d6e6.json"}}, {"family": "Masel", "given": "Joanna", "initials": "J", "orcid": "0000-0002-7398-2127", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eed69f257e574f4aa53f59349c3ff384.json"}}], "type": "journal article", "published": "2025-05-10", "journal": {"title": "bioRxiv", "issn": "2692-8205", "issn-l": null}, "abstract": "Nearly neutral theory predicts that species with higher effective population size are better at purging slightly deleterious mutations. We compare evolution in high- N e vs. low- N e vertebrates to reveal subtle selective preferences among amino acids. We take three complementary approaches. First, we fit non-stationary substitution models using maximum likelihood, comparing the high- N e clade of rodents and lagomorphs to its low- N e sister clade of primates and colugos. Second, we compared evolutionary outcomes across a wider range of vertebrates, via correlations between amino acid frequencies and N e . Third, we dissected which amino acids substitutions occurred in human, chimpanzee, mouse, and rat, as scored by parsimony - this also enabled comparison to a historical paper. All methods agree on amino acid preference under more effective selection. Preferred amino acids are less costly to synthesize and use GC-rich codons, which are hard to maintain under AT-biased mutation. These factors explain 85% of the variance in amino acid preferences. Parsimony-induced bias in the historical study produces an apparent reduction in structural disorder, perhaps driven by slightly deleterious substitutions in rapidly evolving regions. Within highly exchangeable pairs of amino acids, arginine is strongly preferred over lysine, aspartate over glutamate, and valine over isoleucine, consistent with more effective selection preferring a marginally larger free energy of folding. Two of these preferences (K\u2192R and I\u2192V), but not a third (E\u2192D) match differences between thermophiles and mesophilic relatives. These results reveal the biophysical consequences of mutation-selection-drift balance, and demonstrate the utility of nearly neutral theory for understanding protein evolution. N e", "doi": "10.1101/2023.02.01.526552", "pmid": "38948853", "labels": {"DDLS Fellow": "", "Jennifer James": ""}, "xrefs": [{"db": "pmc", "key": "PMC11212923"}, {"db": "pii", "key": "2023.02.01.526552"}], "notes": [], "created": "2026-08-20T10:43:39.130Z", "modified": "2026-09-23T14:14:23.788Z"}, {"entity": "publication", "iuid": "de8979bc70314b06becac1e654fdde9e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/de8979bc70314b06becac1e654fdde9e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/de8979bc70314b06becac1e654fdde9e"}}, "title": "Single-Shot Design of a Cyclic Peptide Inhibitor of HIV-1 Membrane Fusion with EvoBind", "authors": [{"family": "Daumiller", "given": "Diandra", "initials": "D", "orcid": "0009-0009-5387-1292", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0021818d47ef4ce6b5cd53c92c4cd540.json"}}, {"family": "Giammarino", "given": "Federica", "initials": "F", "orcid": "0000-0001-6775-3574", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f65a4d11c82c4850bf74a083617ff475.json"}}, {"family": "Li", "given": "Qiuzhen", "initials": "Q", "orcid": "0009-0009-2913-4786", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f3d7b87dcea3440d8eaa4b574a88da3e.json"}}, {"family": "S\u00f6nnerborg", "given": "Anders", "initials": "A", "orcid": "0000-0001-8928-3374", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f67d8f8e70a548ec9872d92df85e438f.json"}}, {"family": "Ce\u00f1a Diez", "given": "Rafael", "initials": "R", "orcid": "0000-0001-9987-395X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2c133152b24541ac8c8b5ab3b7a2d601.json"}}, {"family": "Bryant", "given": "Patrick", "initials": "P", "orcid": "0000-0003-3439-1866", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a683bcf98234ff09b2398976583b66f.json"}}], "type": "posted-content", "published": "2025-05-05", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2025.04.30.651413", "pmid": null, "labels": {"Patrick Bryant": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T11:02:38.453Z", "modified": "2026-09-23T14:22:27.882Z"}, {"entity": "publication", "iuid": "f07317bcb2454384a6400697aca03b3a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f07317bcb2454384a6400697aca03b3a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f07317bcb2454384a6400697aca03b3a"}}, "title": "Gene regulatory networks linked to GABA signalling emerge as relevant for glioblastoma pathogenesis", "authors": [{"family": "Nissen", "given": "Itzel", "initials": "I"}, {"family": "Dakhel", "given": "Soran", "initials": "S"}, {"family": "Chakraborty", "given": "Chaitali", "initials": "C"}, {"family": "Nygaard", "given": "Amalie Holm", "initials": "AH", "orcid": "0009-0006-4376-8679", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8d9e02b7a8a94b92b3f1d3e005deeb70.json"}}, {"family": "Kirkeby", "given": "Agnete", "initials": "A", "orcid": "0000-0001-8203-6901", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/032019fd440849ecbef295171adfd567.json"}}, {"family": "H\u00f6rnblad", "given": "Andreas", "initials": "A", "orcid": "0000-0003-1283-0784", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/52e17bc600544fdb845d01c21e7af3b7.json"}}, {"family": "Erdem", "given": "Cemal", "initials": "C", "orcid": "0000-0003-3663-3646", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f71b5af589264614a52eefa8baba3132.json"}}, {"family": "Remeseiro", "given": "Silvia", "initials": "S", "orcid": "0000-0001-5343-007X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ccb0543bf564256983df104e716dbf3.json"}}], "type": "posted-content", "published": "2025-05-05", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2025.04.30.651564", "pmid": null, "labels": {"Cemal Erdem": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2025-11-26T12:30:48.833Z", "modified": "2026-09-23T14:28:39.258Z"}, {"entity": "publication", "iuid": "8edb5e1fae454101ad0818b70bbeee25", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8edb5e1fae454101ad0818b70bbeee25.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8edb5e1fae454101ad0818b70bbeee25"}}, "title": "The Role of Artificial Intelligence in the Evaluation of Prostate Pathology.", "authors": [{"family": "Egevad", "given": "Lars", "initials": "L", "orcid": "0000-0001-8531-222X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a7d46f1f5fc047dc8edb910eb4f0645c.json"}}, {"family": "Camilloni", "given": "Andrea", "initials": "A"}, {"family": "Delahunt", "given": "Brett", "initials": "B"}, {"family": "Samaratunga", "given": "Hemamali", "initials": "H"}, {"family": "Eklund", "given": "Martin", "initials": "M"}, {"family": "Kartasalo", "given": "Kimmo", "initials": "K"}], "type": "journal article", "published": "2025-05-00", "journal": {"title": "Pathol Int", "issn": "1440-1827", "volume": "75", "issue": "5", "pages": "213-220", "issn-l": null}, "abstract": "Artificial intelligence (AI) is an emerging tool in diagnostic pathology, including prostate pathology. This review summarizes the possibilities offered by AI and also discusses the challenges and risks. AI has the potential to assist in the diagnosis and grading of prostate cancer. Diagnostic safety can be enhanced by avoiding the accidental underdiagnosis of small lesions. Another possible benefit is a greater degree of standardization of grading. AI for clinical use needs to be trained on large, high-quality data sets that have been assessed by experienced pathologists. A problem with the use of AI in prostate pathology is the plethora of benign mimics of prostate cancer and morphological variants of cancer that are too unusual to allow sufficient training of AI. AI systems need to be able to account for variations in local routines for cutting, staining, and scanning of slides. We also need to be aware of the risk that users will rely too much on the output of an AI system, leading to diagnostic errors and loss of clinical competence. The reporting pathologist must ultimately be responsible for accepting or rejecting the diagnosis proposed by AI.", "doi": "10.1111/pin.70015", "pmid": "40226937", "labels": {"DDLS Fellow": "", "Kimmo Kartasalo": ""}, "xrefs": [{"db": "pmc", "key": "PMC12101047"}], "notes": [], "created": "2025-10-30T15:41:55.249Z", "modified": "2026-09-23T11:36:31.623Z"}, {"entity": "publication", "iuid": "a804f602902f4ca0ae3c0399525b1651", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a804f602902f4ca0ae3c0399525b1651.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a804f602902f4ca0ae3c0399525b1651"}}, "title": "Reply to the Letter to the Editor regarding \"Early detection of pancreatic cancer: Study design and analytical considerations in biomarker discovery and early phase validation studies\".", "authors": [{"family": "Mahoney", "given": "Douglas M", "initials": "DM"}, {"family": "Smith", "given": "Lynette M", "initials": "LM"}, {"family": "Wang", "given": "Qiao-Li", "initials": "QL"}, {"family": "Izmirlian", "given": "Grant", "initials": "G"}, {"family": "Cot\u00e9", "given": "Gregory A", "initials": "GA"}, {"family": "Goggins", "given": "Michael G", "initials": "MG"}, {"family": "Brand", "given": "Randall", "initials": "R"}, {"family": "Oberg", "given": "Ann L", "initials": "AL"}, {"family": "PCDC Biostatistics Subcommittee", "given": "", "initials": ""}], "type": "letter", "published": "2025-05-00", "journal": {"title": "Pancreatology", "issn": "1424-3911", "volume": "25", "issue": "3", "pages": "487-488", "issn-l": null}, "abstract": null, "doi": "10.1016/j.pan.2025.04.017", "pmid": "40379559", "labels": {"DDLS Fellow": "", "Qiaoli Wang": ""}, "xrefs": [{"db": "mid", "key": "NIHMS2170289"}, {"db": "pmc", "key": "PMC13191428"}, {"db": "pii", "key": "S1424-3903(25)00082-1"}], "notes": [], "created": "2025-11-28T12:24:43.736Z", "modified": "2026-10-01T08:34:19.128Z"}, {"entity": "publication", "iuid": "4a65ad20d9274dcbbe03aac505dc8da5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4a65ad20d9274dcbbe03aac505dc8da5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4a65ad20d9274dcbbe03aac505dc8da5"}}, "title": "Precision nutrition for cardiometabolic diseases.", "authors": [{"family": "Guasch-Ferr\u00e9", "given": "Marta", "initials": "M", "orcid": "0000-0001-8525-1404", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2d1a49f5df124e96a9285b43d628cee9.json"}}, {"family": "Wittenbecher", "given": "Clemens", "initials": "C", "orcid": "0000-0001-7792-877X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2f7d2c289b3c47d5a79d23bd48a3225a.json"}}, {"family": "Palmn\u00e4s", "given": "Marie", "initials": "M", "orcid": "0000-0002-3906-7638", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/75f49e36c7f24bb6b51714c592922f9a.json"}}, {"family": "Ben-Yacov", "given": "Orly", "initials": "O"}, {"family": "Blaak", "given": "Ellen E", "initials": "EE", "orcid": "0000-0002-2496-3464", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/daef0918ddac4cb6b3ad41a95dfbad17.json"}}, {"family": "Dahm", "given": "Christina C", "initials": "CC"}, {"family": "Fall", "given": "Tove", "initials": "T", "orcid": "0000-0003-2071-5866", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7dbbd468e6da4727b69333ade942c071.json"}}, {"family": "Heitmann", "given": "Berit L", "initials": "BL"}, {"family": "Licht", "given": "Tine R", "initials": "TR", "orcid": "0000-0002-6399-9574", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/78ff232ace63404a85f293a188bd92c2.json"}}, {"family": "L\u00f6f", "given": "Marie", "initials": "M", "orcid": "0000-0002-2273-4430", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d9f868890cf04250bbdee6d9c6a12254.json"}}, {"family": "Loos", "given": "Ruth", "initials": "R", "orcid": "0000-0002-8532-5087", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/179eb6511eba4d33b633599c5652e344.json"}}, {"family": "Patel", "given": "Chirag J", "initials": "CJ", "orcid": "0000-0002-8756-8525", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4e3b6c075b794875b60c6af39aa402b9.json"}}, {"family": "Quarta", "given": "Carmelo", "initials": "C"}, {"family": "Redman", "given": "Leanne M", "initials": "LM"}, {"family": "Segal", "given": "Eran", "initials": "E", "orcid": "0000-0002-6859-1164", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6ccb86fba84a43a7bd6c17d81b349051.json"}}, {"family": "Segata", "given": "Nicola", "initials": "N", "orcid": "0000-0002-1583-5794", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c12044ea5ac54151a34118799775c301.json"}}, {"family": "Snyder", "given": "Michael", "initials": "M", "orcid": "0000-0003-0784-7987", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ce9e294ff3b64f7caa770c883d12514c.json"}}, {"family": "Sun", "given": "Qi", "initials": "Q", "orcid": "0000-0002-8480-1563", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4a65407257ac4518ac5cb19317ee3b32.json"}}, {"family": "Tobias", "given": "Deirdre K", "initials": "DK", "orcid": "0000-0003-0020-9552", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b5e79c8580904d65bbd35821a2371239.json"}}, {"family": "Hu", "given": "Frank B", "initials": "FB"}, {"family": "Franks", "given": "Paul W", "initials": "PW", "orcid": "0000-0002-0520-7604", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8263a26f474946de8b61a2080051d37b.json"}}, {"family": "Landberg", "given": "Rikard", "initials": "R", "orcid": "0000-0002-6399-7608", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c523f452e91246cc9543d12342bec624.json"}}, {"family": "Sargent", "given": "Jennifer L", "initials": "JL", "orcid": "0009-0008-3697-1737", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cbc6f423959746efafbfc1555927aaa7.json"}}, {"family": "Merino", "given": "Jordi", "initials": "J", "orcid": "0000-0001-8312-1438", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0474f391b6e0478ca3008a4e851b95f9.json"}}], "type": "journal article", "published": "2025-05-00", "journal": {"title": "Nat. Med.", "issn": "1546-170X", "volume": "31", "issue": "5", "pages": "1444-1453", "issn-l": "1078-8956"}, "abstract": "Precision nutrition is a vibrant and rapidly evolving field of scientific research and innovation with the potential to deliver health, societal and economic benefits by improving healthcare delivery and policies. Advances in deep phenotyping technologies, digital tools and artificial intelligence have made possible early proof-of-concept research that expands the understanding of within- and between-person variability in responses to diet. These studies illustrate the promise of precision nutrition to complement the traditional 'one size fits all' dietary guidelines, which, while considering broad life-stage and disease-specific nutritional requirements, often lack the granularity to account fully for individual variations in nutritional needs and dietary responses. Despite these developments, however, considerable challenges remain before precision nutrition can be implemented on a broader scale. This Review examines the current state of precision nutrition research, with a focus on its application to reducing the incidence and burden of cardiometabolic diseases. We critically examine the evidence base, explore the potential benefits and discuss the challenges and opportunities ahead.", "doi": "10.1038/s41591-025-03669-9", "pmid": "40307513", "labels": {"Clemens Wittenbecher": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pii", "key": "10.1038/s41591-025-03669-9"}], "notes": [], "created": "2025-11-28T07:19:56.877Z", "modified": "2026-09-23T08:51:46.149Z"}, {"entity": "publication", "iuid": "bbade1c2653e46e499c3c21ba7711761", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/bbade1c2653e46e499c3c21ba7711761.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/bbade1c2653e46e499c3c21ba7711761"}}, "title": "Physical Color Calibration of Digital Pathology Scanners for Robust Artificial Intelligence-Assisted Cancer Diagnosis.", "authors": [{"family": "Ji", "given": "Xiaoyi", "initials": "X"}, {"family": "Salmon", "given": "Richard", "initials": "R"}, {"family": "Mulliqi", "given": "Nita", "initials": "N"}, {"family": "Khan", "given": "Umair", "initials": "U"}, {"family": "Wang", "given": "Yinxi", "initials": "Y"}, {"family": "Blilie", "given": "Anders", "initials": "A"}, {"family": "Olsson", "given": "Henrik", "initials": "H"}, {"family": "Pedersen", "given": "Bodil Ginnerup", "initials": "BG"}, {"family": "S\u00f8rensen", "given": "Karina Dalsgaard", "initials": "KD"}, {"family": "Ulh\u00f8i", "given": "Benedicte Parm", "initials": "BP"}, {"family": "Kjosavik", "given": "Svein R", "initials": "SR"}, {"family": "Janssen", "given": "Emilius A M", "initials": "EAM"}, {"family": "Rantalainen", "given": "Mattias", "initials": "M"}, {"family": "Egevad", "given": "Lars", "initials": "L"}, {"family": "Ruusuvuori", "given": "Pekka", "initials": "P"}, {"family": "Eklund", "given": "Martin", "initials": "M"}, {"family": "Kartasalo", "given": "Kimmo", "initials": "K"}], "type": "journal article", "published": "2025-05-00", "journal": {"title": "Mod. Pathol.", "issn": "1530-0285", "volume": "38", "issue": "5", "pages": "100715", "issn-l": "0893-3952"}, "abstract": "The potential of artificial intelligence (AI) in digital pathology is limited by technical inconsistencies in the production of whole slide images (WSIs). This causes degraded AI performance and poses a challenge for widespread clinical application, as fine-tuning algorithms for each site is impractical. Changes in the imaging workflow can also compromise diagnostic accuracy and patient safety. Physical color calibration of scanners, relying on a biomaterial-based calibrant slide and a spectrophotometric reference measurement, has been proposed for standardizing WSI appearance, but its impact on AI performance has not been investigated. We evaluated whether physical color calibration can enable robust AI performance. We trained fully supervised and foundation model-based AI systems for detecting and Gleason grading prostate cancer using WSIs of prostate biopsies from the STHLM3 clinical trial (n = 3651) and evaluated their performance in 3 external cohorts (n = 1161) with and without calibration. With physical color calibration, the fully supervised system's concordance with pathologists' grading (Cohen linearly weighted \u03ba) improved from 0.439 to 0.619 in the Stavanger University Hospital cohort (n = 860), from 0.354 to 0.738 in the Karolinska University Hospital cohort (n = 229), and from 0.423 to 0.452 in the Aarhus University Hospital cohort (n = 72). The foundation model's concordance improved as follows: from 0.739 to 0.760 (Karolinska), from 0.424 to 0.459 (Aarhus), and from 0.547 to 0.670 (Stavanger). This study demonstrated that physical color calibration provides a potential solution to the variation introduced by different scanners, making AI-based cancer diagnostics more reliable and applicable in diverse clinical settings.", "doi": "10.1016/j.modpat.2025.100715", "pmid": "39826798", "labels": {"DDLS Fellow": "", "Kimmo Kartasalo": ""}, "xrefs": [{"db": "pii", "key": "S0893-3952(25)00011-0"}], "notes": [], "created": "2025-10-30T15:41:38.928Z", "modified": "2026-10-01T08:24:44.828Z"}, {"entity": "publication", "iuid": "b6d11842314245849594ec1f1ab68adc", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b6d11842314245849594ec1f1ab68adc.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b6d11842314245849594ec1f1ab68adc"}}, "title": "Investigating the Microbiome in Relation to Mental Distress Across Two Points During Pregnancy: Data From U.S. and Swedish Cohorts.", "authors": [{"family": "Kimmel", "given": "Mary", "initials": "M"}, {"family": "Tong", "given": "Bangzhuo", "initials": "B"}, {"family": "Devall", "given": "Alfons Edbom", "initials": "AE"}, {"family": "Bj\u00f6rvang", "given": "Richelle D", "initials": "RD"}, {"family": "Schuppe-Koistinen", "given": "Ina", "initials": "I"}, {"family": "Engstrand", "given": "Lars", "initials": "L"}, {"family": "Fransson", "given": "Emma", "initials": "E"}, {"family": "Skalkidou", "given": "Alkistis", "initials": "A"}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW"}], "type": "journal article", "published": "2025-05-00", "journal": {"title": "Biol Psychiatry Glob Open Sci", "issn": "2667-1743", "volume": "5", "issue": "3", "pages": "100453", "issn-l": null}, "abstract": "In this study, we aimed to characterize the gut microbiome and its potential functioning in 2 populations at 2 time points during pregnancy in relation to mental distress.\n\nDuring the second and third trimester, individuals from the United States and Sweden completed the Edinburgh Postnatal Depression Scale and provided fecal samples for whole-genome metagenomics. A total of 832 and 161 samples were sequenced and analyzed from the Swedish cohort and the U.S. cohort, respectively. Multiple characterizations of the microbial community were analyzed in relation to distress measured using the Edinburgh Postnatal Depression Scale. Principal coordinate analysis and distance-based redundancy analysis assessed variation in functional gut-brain modules. For the U.S. cohort, the Trier Social Stress Test was administered 8 weeks postpartum while collecting salivary cortisol.\n\nPrincipal coordinate analysis identified 4 sample clusters based on the gut-brain modules distinguished by functions such as short-chain fatty acid synthesis and cortisol degradation. While with distance-based redundancy analysis, mental distress subtypes did not significantly contribute to variation in gut-brain modules (p = .085 for Sweden, p = .23 for the U.S.), a U.S. sample cluster distinguished by lower cortisol degradation from another cluster with higher gut microbial cortisol degradation abundance had significantly higher odds of being associated with depression (p = .024). The U.S. sample cluster with lower gut microbial cortisol degradation abundance also had significantly higher cortisol levels after a postpartum social stressor.\n\nFurther studies are warranted to investigate the potential for the gut microbiome to serve as biomarkers of gut-brain axis health during pregnancy across disparate populations.", "doi": "10.1016/j.bpsgos.2025.100453", "pmid": "40115744", "labels": {"DDLS Fellow": "", "Luisa Hugerth": ""}, "xrefs": [{"db": "pmc", "key": "PMC11925571"}, {"db": "pii", "key": "S2667-1743(25)00007-2"}], "notes": [], "created": "2026-08-20T06:49:27.372Z", "modified": "2026-09-23T12:30:13.926Z"}, {"entity": "publication", "iuid": "ede95c30809a47069b0a6542a20cddc9", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ede95c30809a47069b0a6542a20cddc9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ede95c30809a47069b0a6542a20cddc9"}}, "title": "Advancing transdisciplinary research on Madagascar's grassy biomes to support resilience in ecosystems and livelihoods", "authors": [{"family": "Phelps", "given": "Leanne N", "initials": "LN", "orcid": "0000-0002-7385-3907", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9bdc38406efd41a1868e6b73df5da116.json"}}, {"family": "Razanatsoa", "given": "Estelle", "initials": "E", "orcid": "0000-0002-7219-1411", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6af21892343b4c95bd50d9d1ea4d16ad.json"}}, {"family": "Davis", "given": "Dylan S", "initials": "DS", "orcid": "0000-0002-5783-3578", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/374ff871c73149ec9bbe5c6951d9fe4b.json"}}, {"family": "Hackel", "given": "Jan", "initials": "J", "orcid": "0000-0002-9657-5372", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b0474875c79f4955bfc9e5bda7736ba8.json"}}, {"family": "Rasolondrainy", "given": "Tanambelo", "initials": "T", "orcid": "0000-0002-3962-1504", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2015efecd96f46c09257eb079303b72e.json"}}, {"family": "Tiley", "given": "George P", "initials": "GP", "orcid": "0000-0003-0053-0207", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4e5ddbbd7e1d47319652f8583036f8ba.json"}}, {"family": "Burney", "given": "David", "initials": "D", "orcid": "0000-0002-1029-8926", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/37909e97f4c0437099d5662ad4ff6601.json"}}, {"family": "Cox", "given": "Ronadh", "initials": "R", "orcid": "0000-0002-1743-2702", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/806e08d41c2445f9a72fb6ec823016ad.json"}}, {"family": "Godfrey", "given": "Laurie", "initials": "L", "orcid": "0000-0001-9997-0207", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/31cb9143232a4d9ab581e07cecb075a5.json"}}, {"family": "Hempson", "given": "Gareth P", "initials": "GP", "orcid": "0000-0001-8055-4895", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/da2d6f1443bd465cbb5c18ed801d957a.json"}}, {"family": "Hixon", "given": "Sean", "initials": "S", "orcid": "0000-0001-6147-7118", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0bf6dd8fc53c48c5870f12bd28de50f3.json"}}, {"family": "Andermann", "given": "Tobias", "initials": "T", "orcid": "0000-0002-0932-1623", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dfff478dfcfc43ddbd40bb1bafbcb0a7.json"}}, {"family": "Andriambololonera", "given": "Sylvie", "initials": "S"}, {"family": "Andriamiarisoa", "given": "Lala Roger", "initials": "LR"}, {"family": "Antonelli", "given": "Alexandre", "initials": "A", "orcid": "0000-0003-1842-9297", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1de98df1bb2140fc9666507cb2fb5614.json"}}, {"family": "Besnard", "given": "Guillaume", "initials": "G", "orcid": "0000-0003-2275-6012", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/404d0f6fab9d4231b431d96dfd0cb87c.json"}}, {"family": "Birkinshaw", "given": "Chris", "initials": "C"}, {"family": "Bond", "given": "William", "initials": "W", "orcid": "0000-0002-3441-2084", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c6f415d864ca465a9981c95fe32748a4.json"}}, {"family": "Chikhi", "given": "Loun\u00e8s", "initials": "L", "orcid": "0000-0002-1140-0718", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0e6ba1f261a3430a94f41d3b688404b8.json"}}, {"family": "Fern\u00e1ndez\u2010Garc\u00eda", "given": "V\u00edctor", "initials": "V", "orcid": "0000-0003-3217-3814", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/008fc2c5314f4bb4abca27522975824e.json"}}, {"family": "Gillson", "given": "Lindsey", "initials": "L"}, {"family": "Haberle", "given": "Simon", "initials": "S", "orcid": "0000-0001-5802-6535", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/489117b8d60e43afa2dfa15da7425e5c.json"}}, {"family": "Hansford", "given": "James", "initials": "J", "orcid": "0000-0002-5702-8915", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3b60030441fa4c8c8e853be0f36b9ff4.json"}}, {"family": "Joseph", "given": "Grant S", "initials": "GS", "orcid": "0000-0002-8731-9828", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/213509e2c5b045b39db049447ce5acad.json"}}, {"family": "Kull", "given": "Christian A", "initials": "CA", "orcid": "0000-0002-7516-7898", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9475cca34b8a4f9aba99555d97e4bedc.json"}}, {"family": "Mangut", "given": "Chiamaka L", "initials": "CL"}, {"family": "Marchant", "given": "Rob", "initials": "R"}, {"family": "Montade", "given": "Vincent", "initials": "V", "orcid": "0000-0002-8518-2610", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4d1f4f3e4bca4b2d988722f0b8363b26.json"}}, {"family": "Pham", "given": "Karen V", "initials": "KV"}, {"family": "Rabehevitra", "given": "David", "initials": "D"}, {"family": "Radespiel", "given": "Ute", "initials": "U"}, {"family": "Raharimampionona", "given": "Jeannie", "initials": "J"}, {"family": "Rajaonah", "given": "Mamy Tiana", "initials": "MT"}, {"family": "Rakotomalala", "given": "Nantenaina", "initials": "N"}, {"family": "Ramiadantsoa", "given": "Tanjona", "initials": "T", "orcid": "0000-0003-4689-0267", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/980b0bc1d6e14f53b208d73fa0662d11.json"}}, {"family": "Ramiandrisoa", "given": "Botovao Auguste", "initials": "BA"}, {"family": "Ranarijaona", "given": "Hery Lisy Tiana", "initials": "HLT"}, {"family": "Randriamboavonjy", "given": "Tianjanahary", "initials": "T"}, {"family": "Randrianarimanana", "given": "Fenitra", "initials": "F"}, {"family": "Randriatsara", "given": "Fetra", "initials": "F"}, {"family": "Ratsirarson", "given": "Joelisoa", "initials": "J"}, {"family": "Razafimanantsoa", "given": "Andriantsilavo Hery Isandratana", "initials": "AHI", "orcid": "0000-0002-9933-6991", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a4634650f1094842a020efd4b5fd33e1.json"}}, {"family": "Salmona", "given": "Jordi", "initials": "J"}, {"family": "Samonds", "given": "Karen", "initials": "K"}, {"family": "Scroxton", "given": "Nick", "initials": "N", "orcid": "0000-0003-2315-9199", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/09a590ea5dcd41d98d96102976547b8b.json"}}, {"family": "Seymour", "given": "Colleen", "initials": "C", "orcid": "0000-0002-6729-2576", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b6746fb8df3d435fa7e134c0a59e1ada.json"}}, {"family": "Steffens", "given": "Travis S", "initials": "TS"}, {"family": "Teixeira", "given": "Helena", "initials": "H", "orcid": "0000-0001-9032-4575", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ffec5c06bab0482e9287e238e1d273bc.json"}}, {"family": "Voarintsoa", "given": "Ny Riavo G", "initials": "NRG"}, {"family": "Waeber", "given": "Patrick O", "initials": "PO", "orcid": "0000-0002-3229-0124", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a0b957e1a4684347b01f2f5acbbf8224.json"}}, {"family": "Wilm\u00e9", "given": "Lucienne", "initials": "L", "orcid": "0000-0002-8344-1957", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d7532b96f38744d88587758d1c62165e.json"}}, {"family": "Yoder", "given": "Anne D", "initials": "AD"}, {"family": "Convery Fisher", "given": "Elliot", "initials": "E"}, {"family": "Solofondranohatra", "given": "C\u00e9drique", "initials": "C"}, {"family": "van Elst", "given": "Tobias", "initials": "T"}, {"family": "Crowley", "given": "Brooke", "initials": "B", "orcid": "0000-0002-8462-6806", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8b2dd1b41d6c4ec08e3467533eed6d60.json"}}, {"family": "Douglass", "given": "Kristina", "initials": "K", "orcid": "0000-0003-0931-3428", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/506be33c09634d7987ea58cad09afda5.json"}}, {"family": "Vorontsova", "given": "Maria S", "initials": "MS", "orcid": "0000-0003-0899-1120", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/658bd52a89af4667bf9fc6bfa6f14b39.json"}}, {"family": "Lehmann", "given": "Caroline E R", "initials": "CER", "orcid": "0000-0002-6825-124X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/24173f034c8c432292645d0db47d4803.json"}}], "type": "journal-article", "published": "2025-05-00", "journal": {"title": "Ecological Monographs", "issn": "0012-9615", "volume": "95", "issue": "2", "issn-l": null}, "abstract": null, "doi": "10.1002/ecm.70011", "pmid": null, "labels": {"Tobias Andermann": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T06:32:10.674Z", "modified": "2026-09-23T11:35:33.467Z"}, {"entity": "publication", "iuid": "be6e123262664fba87fb4902f91c49cb", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/be6e123262664fba87fb4902f91c49cb.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/be6e123262664fba87fb4902f91c49cb"}}, "title": "GenePioneer: a comprehensive Python package for identification of essential genes and modules in cancer.", "authors": [{"family": "Haerianardakani", "given": "Amirhossein", "initials": "A"}, {"family": "Taheri", "given": "Golnaz", "initials": "G", "orcid": "0000-0002-2741-0355", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/014c217121d346b2b371bbc1c2fede57.json"}}], "type": "journal article", "published": "2025-04-29", "journal": {"title": "Bioinform Adv", "issn": "2635-0041", "volume": "5", "issue": "1", "pages": "vbaf094", "issn-l": null}, "abstract": "We propose a network-based unsupervised learning model to identify essential cancer genes and modules for 12 different cancer types, supported by a Python package for practical application. The model constructs a gene network from frequently mutated genes and biological processes, ranks genes using topological features, and detects critical modules. Evaluation across cancer types confirms its effectiveness in prioritizing cancer-related genes and uncovering relevant modules. The Python package allows users to input gene lists, retrieve rankings, and identify associated modules. This work provides a robust method for gene prioritization and module detection, along with a user-friendly package to support research and clinical decision-making in cancer genomics.\n\nGenePioneer is released as an open-source software under the MIT license. The source code is available on GitHub at https://github.com/Golnazthr/ModuleDetection.", "doi": "10.1093/bioadv/vbaf094", "pmid": "40417653", "labels": {"Golnaz Taheri": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC12098931"}, {"db": "pii", "key": "vbaf094"}], "notes": [], "created": "2026-08-20T09:39:08.522Z", "modified": "2026-09-23T15:47:16.324Z"}, {"entity": "publication", "iuid": "7737851a912241f4960b61fa42bdb87f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/7737851a912241f4960b61fa42bdb87f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/7737851a912241f4960b61fa42bdb87f"}}, "title": "Quantifying Acyl Chain Interdigitation in Simulated Bilayers via Direct Transbilayer Interactions.", "authors": [{"family": "Chaisson", "given": "Emily H", "initials": "EH", "orcid": "0009-0002-7876-9736", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/47f6b458684f4496933d3ebeb32f0aab.json"}}, {"family": "Heberle", "given": "Frederick A", "initials": "FA", "orcid": "0000-0002-0424-3240", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2557f5621a0b4c87b5f4702fbc7b6bdb.json"}}, {"family": "Doktorova", "given": "Milka", "initials": "M", "orcid": "0000-0003-4366-2242", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/791384c319f04584bac8ffb21df7271f.json"}}], "type": "journal article", "published": "2025-04-28", "journal": {"title": "J Chem Inf Model", "issn": "1549-960X", "volume": "65", "issue": "8", "pages": "3879-3885", "issn-l": "1549-9596"}, "abstract": "In a lipid bilayer, the interactions between the lipid hydrocarbon chains from opposing leaflets can influence membrane properties. These interactions include the phenomenon of interdigitation, in which an acyl chain of one leaflet extends past the bilayer midplane and into the opposing leaflet. While static interdigitation is well understood in gel-phase bilayers from X-ray diffraction measurements, much less is known about dynamic interdigitation in fluid phases. In this regard, atomistic molecular dynamics simulations can provide mechanistic information on interleaflet interactions that can be used to generate experimentally testable hypotheses. To address limitations of existing computational methodologies that provide results that are either indirect or averaged over time and space, here we introduce three novel ways of quantifying the extent of chain interdigitation. Our protocols include the analysis of instantaneous interactions at the level of individual carbon atoms, thus providing temporal and spatial resolution for a more nuanced picture of dynamic interdigitation. We compare the methods on bilayers composed of lipids with an equal total number of carbon atoms, but different mismatches between the sn-1 and sn-2 chain lengths. We find that these metrics, which are based on freely available software packages and are easy to implement, provide complementary details that help characterize various features of lipid-lipid contacts at the bilayer midplane. The new frameworks thus allow for a deeper look at fundamental molecular mechanisms underlying bilayer structure and dynamics and present a valuable expansion of the membrane biophysics toolkit.", "doi": "10.1021/acs.jcim.4c02287", "pmid": "40237313", "labels": {"Milka Doktorova": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC12042268"}], "notes": [], "created": "2026-08-20T08:10:32.619Z", "modified": "2026-09-23T12:27:57.021Z"}, {"entity": "publication", "iuid": "4b81c7d357004c78a377a337d44faf89", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4b81c7d357004c78a377a337d44faf89.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4b81c7d357004c78a377a337d44faf89"}}, "title": "PCSK9 Regulates Cardiac Mitochondrial Cholesterol by Promoting TSPO Degradation.", "authors": [{"family": "Laudette", "given": "Marion", "initials": "M"}, {"family": "Lindbom", "given": "Malin", "initials": "M"}, {"family": "Cinato", "given": "Mathieu", "initials": "M", "orcid": "0000-0002-8490-4335", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5b2d3790356a446e85061a007b50bb28.json"}}, {"family": "Bergh", "given": "Per-Olof", "initials": "PO", "orcid": "0000-0001-9993-6965", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0340d8f630034124a106f49ebd3101f3.json"}}, {"family": "Sk\u00e5l\u00e9n", "given": "Kristina", "initials": "K", "orcid": "0009-0003-5693-4339", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6074b6582bf34bf185edcd91046860cb.json"}}, {"family": "Arif", "given": "Muhammad", "initials": "M", "orcid": "0000-0003-2261-0881", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c8ffc9889ace44e3b992816601b817e2.json"}}, {"family": "Miljanovic", "given": "Azra", "initials": "A", "orcid": "0000-0003-0290-5711", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3c6bf97776c845c6a598449a78102267.json"}}, {"family": "Czuba", "given": "Tomasz", "initials": "T", "orcid": "0009-0001-0232-0425", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ab8dfef96691491bab3c222812e529b7.json"}}, {"family": "Perkins", "given": "Rosie", "initials": "R", "orcid": "0000-0003-2447-3286", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/47f33fc99e8147a6b7bda7ce799c87cb.json"}}, {"family": "Smith", "given": "J Gustav", "initials": "JG"}, {"family": "Lezoualc'h", "given": "Frank", "initials": "F", "orcid": "0000-0001-5239-6017", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/83e10db1e01644f5bc9d432b9c1dd2d0.json"}}, {"family": "Levin", "given": "Malin C", "initials": "MC"}, {"family": "Bor\u00e9n", "given": "Jan", "initials": "J", "orcid": "0000-0003-0786-8091", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/73a770eb9e614448a046b8e9199052e9.json"}}], "type": "journal article", "published": "2025-04-25", "journal": {"title": "Circ. Res.", "issn": "1524-4571", "volume": "136", "issue": "9", "pages": "924-942", "issn-l": "0009-7330"}, "abstract": "Cholesterol is critical for mitochondrial membrane structure and function. Given the emergence of mitochondria as a key factor in the pathogenesis of heart failure, mitochondrial cholesterol homeostasis may be crucial for maintaining mitochondrial properties and thus cardiac function. We previously showed that CM-Pcsk9-/- mice (mice with cardiomyocyte-specific deletion of the gene encoding PCSK9 [proprotein convertase subtilisin-kexin type 9]) have impaired cardiomyocyte mitochondrial bioenergetics and heart function, paralleled by cardiomyocyte mitochondrial cholesterol accumulation and an increased number of mitochondria-endoplasmic reticulum contacts. However, the mechanisms linking PCSK9 to mitochondrial cholesterol homeostasis remain unclear. We hypothesized that PCSK9 acts on proteins involved in mitochondrial cholesterol trafficking in the heart to maintain cardiac mitochondrial function.\n\nBy performing RNA sequencing and immunoblot on hearts from CM-Pcsk9-/- and CM-Pcsk9+/+ (without cardiomyocyte-specific deletion of Pcsk9) mice, we showed that TSPO (translocator protein) was increased by Pcsk9 deficiency. To investigate the relationship between TSPO levels and heart function in humans, we compared the transcriptome of human left ventricles with high versus low TSPO levels. We used H9c2 (a rat cardiomyoblast cell line) cardiomyocytes to explore the mechanism linking PCSK9/TSPO to mitochondrial cholesterol content and function. The impact of reduced TSPO levels on cardiac function and mitochondrial oxidation in CM-Pcsk9-/- mice was tested using adeno-associated virus serotype 9 short hairpin TSPO.\n\nBoth gene and protein levels of TSPO, a mitochondrial protein involved in cholesterol transport, were increased in CM-Pcsk9-/- mouse hearts. Transcriptome analysis showed that high TSPO expression in human left ventricles was associated with impaired mitochondrial and cardiac function. We showed that PCSK9 induced TSPO degradation through a proteasomal mechanism that occurs in cardiomyocytes but not hepatocytes and contributes to maintaining normal mitochondrial cholesterol composition and function. At the molecular level, endoplasmic reticulum-resident PCSK9 interacted with GRP78 (glucose regulatory protein 78) , reducing GRP78-TSPO interactions and leading to TSPO misfolding and degradation by the ubiquitin-proteasome pathway. Importantly, gene therapy-induced downregulation of TSPO in CM-Pcsk9-/- mice prevented mitochondrial cholesterol accumulation and improved cardiac function.\n\nThese findings indicate that PCSK9 regulates mitochondrial cholesterol levels by modulating the TSPO degradation in the heart. Modulation of mitochondrial cholesterol by targeting TSPO may be a promising therapeutic approach for heart failure.", "doi": "10.1161/CIRCRESAHA.124.325629", "pmid": "40171648", "labels": {"DDLS Fellow": "", "Muhammad Arif": ""}, "xrefs": [], "notes": [], "created": "2026-10-01T08:26:22.515Z", "modified": "2026-10-01T08:26:22.762Z"}, {"entity": "publication", "iuid": "99a47993dec34e92b6761a4c5f3e3568", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/99a47993dec34e92b6761a4c5f3e3568.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/99a47993dec34e92b6761a4c5f3e3568"}}, "title": "Sex differences in DNMT3A-mutant clonal hematopoiesis and the effects of estrogen.", "authors": [{"family": "Stomper", "given": "Julia", "initials": "J"}, {"family": "Niroula", "given": "Abhishek", "initials": "A"}, {"family": "Belizaire", "given": "Roger", "initials": "R"}, {"family": "McConkey", "given": "Marie", "initials": "M"}, {"family": "Bandaru", "given": "Tagore Sanketh", "initials": "TS"}, {"family": "Ebert", "given": "Benjamin L", "initials": "BL"}], "type": "journal article", "published": "2025-04-22", "journal": {"title": "Cell Reports", "issn": "2211-1247", "volume": "44", "issue": "4", "pages": "115494", "issn-l": null}, "abstract": "Blood cancers are generally more common in males, and the prevalence of most mutations that drive clonal hematopoiesis and myeloid malignancies is higher in males. In contrast, hematopoietic DNMT3A mutations are more common in females. Among \u223c450,000 participants in the UK Biobank, the prevalence of DNMT3A mutations and copy-number abnormalities is higher in females than males. In a murine model, Dnmt3a-mutant hematopoietic stem cells (HSCs) from unperturbed female mice had increased stemness gene expression compared to male and wild-type (WT) mice. Estrogen regulates HSCs, and we found that Dnmt3a mutations maintain stemness in the setting of estrogen-induced proliferative stress. Dnmt3a-mutant myeloid cells outcompeted WT cells under chronic estrogen treatment, an effect that was dependent on cell-intrinsic estrogen receptor alpha activity. Our studies indicate that estrogen might contribute to the female predominance of DNMT3A-mutant clonal hematopoiesis.", "doi": "10.1016/j.celrep.2025.115494", "pmid": "40178977", "labels": {"DDLS Fellow": "", "Abhishek Niroula": ""}, "xrefs": [{"db": "pii", "key": "S2211-1247(25)00265-7"}], "notes": [], "created": "2025-11-17T15:51:12.235Z", "modified": "2026-10-01T08:24:48.531Z"}, {"entity": "publication", "iuid": "2435a148ee5f4c80be82567ceda77ac7", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/2435a148ee5f4c80be82567ceda77ac7.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/2435a148ee5f4c80be82567ceda77ac7"}}, "title": "Omics Approach for Personalised Prevention of Type 2 Diabetes Mellitus for African and European Populations (OPTIMA): a protocol paper.", "authors": [{"family": "Goedecke", "given": "Julia H", "initials": "JH", "orcid": "0000-0001-6795-4771", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2d3111aa93554291a9d85becaea7d41c.json"}}, {"family": "Danquah", "given": "Ina", "initials": "I"}, {"family": "Abidha", "given": "Carol Akinyi", "initials": "CA"}, {"family": "Agyemang", "given": "Charles", "initials": "C"}, {"family": "Albers", "given": "Hannah Maike", "initials": "HM"}, {"family": "Amoah", "given": "Stephen", "initials": "S"}, {"family": "Brunius", "given": "Carl", "initials": "C"}, {"family": "Chorell", "given": "Elin", "initials": "E"}, {"family": "Hoosen", "given": "Fatima", "initials": "F"}, {"family": "Fortuin-de Smidt", "given": "Melony", "initials": "M"}, {"family": "H\u00f6rnsten", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Karlsson", "given": "Therese", "initials": "T"}, {"family": "Lindholm", "given": "Lars", "initials": "L"}, {"family": "Mendham", "given": "Amy E", "initials": "AE", "orcid": "0000-0002-1959-6698", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1301a064a29a4b2ea6634ca93e51bacc.json"}}, {"family": "Micklesfield", "given": "Lisa K", "initials": "LK", "orcid": "0000-0002-4994-0779", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/af359e74210340d793d9897f052631ae.json"}}, {"family": "Meili", "given": "Kaspar Walter", "initials": "KW"}, {"family": "Noerman", "given": "Stefania", "initials": "S"}, {"family": "Otten", "given": "Julia", "initials": "J", "orcid": "0000-0001-9016-1139", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5c63fe7e464f40c89c4712cafa3384c7.json"}}, {"family": "S\u00f6derberg", "given": "Stefan", "initials": "S", "orcid": "0000-0001-9225-1306", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/26c8e954ebf1429b95afc1fcdbc597eb.json"}}, {"family": "van der Linden", "given": "Eva L", "initials": "EL", "orcid": "0000-0002-4037-1717", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e80b753dbf84f93b88286b754c96599.json"}}, {"family": "Wittenbecher", "given": "Clemens", "initials": "C"}, {"family": "Landberg", "given": "Rikard", "initials": "R"}, {"family": "Olsson", "given": "Tommy", "initials": "T"}], "type": "journal article", "published": "2025-04-22", "journal": {"title": "BMJ Open", "issn": "2044-6055", "volume": "15", "issue": "4", "pages": "e099108", "issn-l": "2044-6055"}, "abstract": "The prevalence of type 2 diabetes (T2D) within sub-Saharan Africa (SSA) is increasing. Despite the pathophysiology of T2D differing by ethnicity and sex, risk stratification and guidelines for the prevention of T2D are generic, relying on evidence from studies including predominantly Europeans. Accordingly, this study aims to develop ethnic-specific and sex-specific risk prediction models for the early detection of dysglycaemia (impaired glucose tolerance and T2D) to inform clinically feasible, culturally acceptable and cost-effective risk management and prevention strategies using dietary modification in SSA and European populations.\n\nThis multinational collaboration will include the prospective cohort data from two African cohorts, the Middle-Aged Soweto Cohort from South Africa and the Research on Obesity and Diabetes among African Migrants Prospective cohort from Ghana and migrants living in Europe, and a Swedish cohort, the Pre-Swedish CArdioPulmonary bioImage Study. Targeted proteomics, as well as targeted and untargeted metabolomics, will be performed at baseline to discover known and novel ethnic-specific and sex-specific biomarkers that predict incident dysglycaemia in the different longitudinal cohorts. Dietary patterns that explain maximum variation in the biomarker profiles and that associate with dysglycaemia will be identified in the SSA and European cohorts and used to build the prototypes for dietary interventions to prevent T2D. A comparative cost-effectiveness analysis of the dietary interventions will be estimated in the different populations. Finally, the perceptions of at-risk participants and healthcare providers regarding ethnic-specific and sex-specific dietary recommendations for the prevention of T2D will be assessed using focus group discussions and in-depth interviews in South Africa, Ghana, Germany (Ghanaian migrants) and Sweden.\n\nEthical clearance has been obtained from all participating sites. The study results will be disseminated at scientific conferences and in journal publications, and through community engagement events and diabetes organisations in the respective countries.", "doi": "10.1136/bmjopen-2025-099108", "pmid": "40262963", "labels": {"Clemens Wittenbecher": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC12015709"}, {"db": "pii", "key": "bmjopen-2025-099108"}], "notes": [], "created": "2025-11-28T07:19:59.870Z", "modified": "2026-09-23T11:35:10.040Z"}, {"entity": "publication", "iuid": "9f52d4026e054c489cc4c94a5de91017", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9f52d4026e054c489cc4c94a5de91017.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9f52d4026e054c489cc4c94a5de91017"}}, "title": "Rapid traversal of vast chemical space using machine learning-guided docking screens.", "authors": [{"family": "Luttens", "given": "Andreas", "initials": "A", "orcid": "0000-0003-2915-7901", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d2944edc47eb4b639f1c61ae7b94b60a.json"}}, {"family": "Cabeza de Vaca", "given": "Israel", "initials": "I"}, {"family": "Sparring", "given": "Leonard", "initials": "L"}, {"family": "Brea", "given": "Jos\u00e9", "initials": "J"}, {"family": "Mart\u00ednez", "given": "Ant\u00f3n Leandro", "initials": "AL", "orcid": "0000-0002-1595-3459", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ccf0b72b679f424cac5adb240ed16b7a.json"}}, {"family": "Kahlous", "given": "Nour Aldin", "initials": "NA", "orcid": "0000-0002-7744-1491", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ed14cfbd31384338928150f4a97aee16.json"}}, {"family": "Radchenko", "given": "Dmytro S", "initials": "DS", "orcid": "0000-0001-5444-7754", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5a8f8993ce024259aa09cfae9a745a20.json"}}, {"family": "Moroz", "given": "Yurii S", "initials": "YS", "orcid": "0000-0001-6073-002X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/85e5c6a40d854426b96476233f59ccfa.json"}}, {"family": "Loza", "given": "Mar\u00eda Isabel", "initials": "MI", "orcid": "0000-0003-4730-0863", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/177c0793b32b44f2b46cdf286da0d3f3.json"}}, {"family": "Norinder", "given": "Ulf", "initials": "U", "orcid": "0000-0003-3107-331X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/da36a1cdadab4126b4e2527721ac2710.json"}}, {"family": "Carlsson", "given": "Jens", "initials": "J", "orcid": "0000-0003-4623-2977", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/792c1cd4aca248dc94b967115ffa82df.json"}}], "type": "journal article", "published": "2025-04-00", "journal": {"title": "Nat Comput Sci", "issn": "2662-8457", "volume": "5", "issue": "4", "pages": "301-312", "issn-l": null}, "abstract": "The accelerating growth of make-on-demand chemical libraries provides unprecedented opportunities to identify starting points for drug discovery with virtual screening. However, these multi-billion-scale libraries are challenging to screen, even for the fastest structure-based docking methods. Here we explore a strategy that combines machine learning and molecular docking to enable rapid virtual screening of databases containing billions of compounds. In our workflow, a classification algorithm is trained to identify top-scoring compounds based on molecular docking of 1 million compounds to the target protein. The conformal prediction framework is then used to make selections from the multi-billion-scale library, reducing the number of compounds to be scored by docking. The CatBoost classifier showed an optimal balance between speed and accuracy and was used to adapt the workflow for screens of ultralarge libraries. Application to a library of 3.5 billion compounds demonstrated that our protocol can reduce the computational cost of structure-based virtual screening by more than 1,000-fold. Experimental testing of predictions identified ligands of G protein-coupled receptors and demonstrated that our approach enables discovery of compounds with multi-target activity tailored for therapeutic effect.", "doi": "10.1038/s43588-025-00777-x", "pmid": "40082701", "labels": {"SciLifeLab Fellow": "", "Jens Carlsson": "", "Andreas Luttens": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC12021657"}, {"db": "pii", "key": "10.1038/s43588-025-00777-x"}, {"db": "Protein", "key": "7CMV, 8GNE, 6CM4, 4EIY, 6DPT, 6XUE,"}], "notes": [], "created": "2026-09-23T08:32:11.684Z", "modified": "2026-09-23T08:32:12.183Z"}, {"entity": "publication", "iuid": "c048cd2c24e74516983dbf38b10ba8f3", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c048cd2c24e74516983dbf38b10ba8f3.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c048cd2c24e74516983dbf38b10ba8f3"}}, "title": "Occurrence and spread of carbapenemase\u2010producing Enterobacterales (CPE) in the food chain in the EU/EFTA. Part 1: 2025 update", "authors": [{"family": "Allende", "given": "Ana", "initials": "A"}, {"family": "\u00c1lvarez\u2010Ord\u00f3\u00f1ez", "given": "Avelino", "initials": "A"}, {"family": "Bortolaia", "given": "Valeria", "initials": "V"}, {"family": "Bover\u2010Cid", "given": "Sara", "initials": "S"}, {"family": "De Cesare", "given": "Alessandra", "initials": "A"}, {"family": "Dohmen", "given": "Wietske", "initials": "W"}, {"family": "Guillier", "given": "Laurent", "initials": "L"}, {"family": "Herman", "given": "Lieve", "initials": "L"}, {"family": "Jacxsens", "given": "Liesbeth", "initials": "L"}, {"family": "Mughini\u2010Gras", "given": "Lapo", "initials": "L"}, {"family": "Nauta", "given": "Maarten", "initials": "M"}, {"family": "Ottoson", "given": "Jakob", "initials": "J"}, {"family": "P\u00e9rez\u2010Rodr\u00edguez", "given": "Fernando", "initials": "F"}, {"family": "Skandamis", "given": "Panagiotis", "initials": "P"}, {"family": "Suffredini", "given": "Elisabetta", "initials": "E"}, {"family": "Arg\u00fcello", "given": "Hector", "initials": "H"}, {"family": "Bengtsson\u2010Palme", "given": "Johan", "initials": "J"}, {"family": "Carattoli", "given": "Alessandra", "initials": "A"}, {"family": "Kohlenberg", "given": "Anke", "initials": "A"}, {"family": "Monnet", "given": "Dominique L", "initials": "DL"}, {"family": "Poirel", "given": "Laurent", "initials": "L"}, {"family": "Guerra", "given": "Beatriz", "initials": "B"}, {"family": "Garc\u00eda\u2010Fierro", "given": "Raquel", "initials": "R"}, {"family": "Li\u00e9bana", "given": "Ernesto", "initials": "E"}, {"family": "Goudjihounde", "given": "Sonagnon Martin", "initials": "SM"}, {"family": "Ferrer\u2010Bustins", "given": "N\u00faria", "initials": "N"}, {"family": "Rabb\u00e5s", "given": "Hanne", "initials": "H"}, {"family": "Peixe", "given": "Luisa", "initials": "L"}], "type": "journal-article", "published": "2025-04-00", "journal": {"title": "EFSA J", "issn": "1831-4732", "volume": "23", "issue": "4", "issn-l": null}, "abstract": null, "doi": "10.2903/j.efsa.2025.9336", "pmid": null, "labels": {"Johan Bengtsson-Palme": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2025-06-04T08:12:40.338Z", "modified": "2025-12-05T10:15:10.775Z"}, {"entity": "publication", "iuid": "fbb534254dff438b83a95bb8dbbe741d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/fbb534254dff438b83a95bb8dbbe741d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/fbb534254dff438b83a95bb8dbbe741d"}}, "title": "Protocol to infer off-target effects of drugs on cellular signaling using interactome-based deep learning.", "authors": [{"family": "Meimetis", "given": "Nikolaos", "initials": "N", "orcid": "0000-0003-2333-0187", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e0e968cb5cc44b52818647cea77762d9.json"}}, {"family": "Lauffenburger", "given": "Douglas A", "initials": "DA", "orcid": "0000-0002-0050-989X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ac0a09cb7c9c49de95b660756a4e5464.json"}}, {"family": "Nilsson", "given": "Avlant", "initials": "A", "orcid": "0000-0002-9476-4516", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f2e21dbc1c624f6a841c59e959e948e4.json"}}], "type": "journal article", "published": "2025-03-21", "journal": {"title": "STAR Protoc", "issn": "2666-1667", "issn-l": null, "volume": "6", "issue": "1", "pages": "103573"}, "abstract": "Drugs that target specific proteins often have off-target effects. We present a protocol using artificial neural networks to model cellular transcriptional responses to drugs, aiming to understand their mechanisms of action. We detail steps for predicting transcriptional activities, inferring drug-target interactions, and explaining the off-target mechanism of action. As a case study, we analyze the off-target effects of lestaurtinib on FOXM1 in the A375 cell line. For complete details on the use and execution of this protocol, please refer to Meimetis et al.1.", "doi": "10.1016/j.xpro.2024.103573", "pmid": "39823233", "labels": {"Avlant Nilsson": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC11786766"}, {"db": "pii", "key": "S2666-1667(24)00738-X"}], "notes": [], "created": "2025-03-20T10:57:36.917Z", "modified": "2026-10-01T08:29:33.039Z"}, {"entity": "publication", "iuid": "a1b3bb93902b454c91aef9f982b2e5ff", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a1b3bb93902b454c91aef9f982b2e5ff.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a1b3bb93902b454c91aef9f982b2e5ff"}}, "title": "Seal milk oligosaccharides rival human milk complexity and exhibit functional dynamics during lactation", "authors": [{"family": "Jin", "given": "Chunsheng", "initials": "C"}, {"family": "Lundstr\u00f8m", "given": "Jon", "initials": "J", "orcid": "0000-0003-2733-7124", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/143dd0ab2b034524ab081ebd3e4d4e84.json"}}, {"family": "Cori", "given": "Carmen R", "initials": "CR", "orcid": "0009-0004-6876-3204", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/35c1d8b451f64511858bb6fd5a79607c.json"}}, {"family": "Guu", "given": "Shih Yun", "initials": "SY", "orcid": "0009-0007-1886-5140", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/de887755da0e46e890bbc3d14e5ab26d.json"}}, {"family": "Bennett", "given": "Alexander R", "initials": "AR", "orcid": "0000-0003-4869-9132", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/72c3e68726ee4b1c94df835a395d1db0.json"}}, {"family": "Dannborg", "given": "Mirjam", "initials": "M", "orcid": "0000-0003-3171-9379", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3379f6c1295741a9ba945f9e92a552eb.json"}}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J", "orcid": "0000-0002-6528-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c666068e9d34939b0252a627007cec7.json"}}, {"family": "Hevey", "given": "Rachel", "initials": "R", "orcid": "0000-0002-2649-3427", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1eb0458f8032456db2515a98ebb1603e.json"}}, {"family": "Khoo", "given": "Kay Hooi", "initials": "KH", "orcid": "0000-0003-2906-406X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ec5a1fbecb024bef97d689d14e0848d5.json"}}, {"family": "Bojar", "given": "Daniel", "initials": "D", "orcid": "0000-0002-3008-7851", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e478a4f31d694706a63d5d71e02ecf1c.json"}}], "type": "posted-content", "published": "2025-03-20", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2025.03.20.644374", "pmid": null, "labels": {"Johan Bengtsson-Palme": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2025-06-04T08:16:04.305Z", "modified": "2025-06-04T08:16:04.728Z"}, {"entity": "publication", "iuid": "f5473aa949af412d900bdeab47f175d8", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f5473aa949af412d900bdeab47f175d8.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f5473aa949af412d900bdeab47f175d8"}}, "title": "Survival and adaptative strategies of Enterotoxigenic E. coli (ETEC) to the freshwater environment.", "authors": [{"family": "Sj\u00f6ling", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Ashokkumar", "given": "Eswari", "initials": "E"}, {"family": "Bjurnemark", "given": "Caroline", "initials": "C"}, {"family": "Thorell", "given": "Kaisa", "initials": "K"}, {"family": "Xiao", "given": "Xue", "initials": "X"}, {"family": "von Mentzer", "given": "Astrid", "initials": "A"}, {"family": "Hu", "given": "Yue O O", "initials": "YOO"}, {"family": "Zhu", "given": "Baoli", "initials": "B"}, {"family": "Joffr\u00e9", "given": "Enrique", "initials": "E", "orcid": "0000-0003-0328-518X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d0a7d88da85f4dbfab455ac2df10a8de.json"}}], "type": "journal article", "published": "2025-03-19", "journal": {"title": "Res Sq", "issn": "2693-5015", "issn-l": null}, "abstract": "Waterborne pathogenic enterobacteria are adapted for infection of human hosts but can also survive for long periods in water environments. To understand how the human pathogen enterotoxigenic Escherichia coli (ETEC) adapts to acute and long-term hypo-osmotic stress and oligotrophic water conditions, this study aimed to explore the effects of short- and long-term freshwater exposure on ETEC isolates by examining transcriptional responses, survival mechanisms, and antibiotic resistance development. RNA sequencing revealed that over 1,700 genes were differentially expressed, with significant transcriptional reprogramming occurring early within the first two hours of water exposure. Early responses included activation of catabolic pathways for nitrogen and carbon assimilation and downregulation of energy metabolism and anabolic processes to mitigate osmotic stress. Notably, the arnBCADTEF operon was upregulated, facilitating lipid A modification and membrane enforcement which also confers colistin tolerance. ETEC carries virulence genes on large plasmids which cause diarrheal disease in humans. Plasmid gene analysis indicated repression of virulence genes and upregulation of mobilization and toxin-antitoxin systems during the first 48 hours in water, suggesting a shift towards genetic adaptability. Prolonged exposure over weeks enhanced biofilm formation capacity and adherence to human epithelial cells, and ETEC isolates evolved towards increased colistin resistance. These findings stress the significant influence of freshwater on ETEC adaptive strategies, suggesting a role of waterborne transmission for human pathogens in development of persistence, biofilm formation capability and the emergence of antibiotic tolerance.", "doi": "10.21203/rs.3.rs-6252921/v1", "pmid": "40166005", "labels": {"Astrid von Mentzer": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC11957205"}, {"db": "pii", "key": "rs.3.rs-6252921"}], "notes": [], "created": "2025-12-02T15:47:02.145Z", "modified": "2025-12-02T15:47:02.177Z"}, {"entity": "publication", "iuid": "72fb93708492426787e659dd3bc5fdc7", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/72fb93708492426787e659dd3bc5fdc7.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/72fb93708492426787e659dd3bc5fdc7"}}, "title": "Early gonadotoxic effects of cyclophosphamide on the prepubertal testis and the feasibility of reducing toxicity through combined antioxidant therapy", "authors": [{"family": "Eskafinoghani", "given": "Amirhesam", "initials": "A", "orcid": "0000-0002-9717-4810", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/870acfdb0dcb4f978107a194d485df9f.json"}}, {"family": "Reyes Palomares", "given": "Arturo", "initials": "A"}, {"family": "Hao", "given": "Xia", "initials": "X"}, {"family": "Mohammadi", "given": "Roudabeh", "initials": "R"}, {"family": "Lundberg", "given": "Arian", "initials": "A", "orcid": "0000-0002-6630-2787", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/baa2c7c8963840bfb6a22d7c5cfe35f9.json"}}, {"family": "Rodriguez-Walberg", "given": "Kenny A", "initials": "KA", "orcid": "0000-0003-4378-6181", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ab738f3602664a20bb1db36e55156d8b.json"}}], "type": "posted-content", "published": "2025-03-19", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2025.03.18.643799", "pmid": null, "labels": {"DDLS Fellow": "", "Arian Lundberg": ""}, "xrefs": [], "notes": [], "created": "2026-04-18T06:33:10.419Z", "modified": "2026-09-23T15:46:00.738Z"}, {"entity": "publication", "iuid": "dbd9f08cebd64013a251af7cb65f8352", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/dbd9f08cebd64013a251af7cb65f8352.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/dbd9f08cebd64013a251af7cb65f8352"}}, "title": "Disinfecting eukaryotic reference genomes to improve taxonomic inference from ancient environmental metagenomic data", "authors": [{"family": "Oskolkov", "given": "Nikolay", "initials": "N", "orcid": "0000-0001-5326-8893", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3c448f1b878442c687d58549f90ba4e9.json"}}, {"family": "Jin", "given": "Chenyu", "initials": "C", "orcid": "0000-0002-2392-7090", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/afcc4905564e41868967d9cfef968b07.json"}}, {"family": "Clinton", "given": "Samantha L\u00f3pez", "initials": "SL", "orcid": "0000-0003-1364-9135", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb3097a7dd3342e6ae0d1532ae0d18f3.json"}}, {"family": "Guinet", "given": "Benjamin", "initials": "B", "orcid": "0000-0002-9922-2118", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c17993b1fc0450eb9808706576983eb.json"}}, {"family": "Wijnands", "given": "Flore", "initials": "F", "orcid": "0009-0009-6254-8964", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/557893083c5a469ea1285294e2a2ac3a.json"}}, {"family": "Johnson", "given": "Ernst", "initials": "E", "orcid": "0009-0004-0745-2437", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ff7522013ba43ebb1fe72b5e3d4037d.json"}}, {"family": "Kutschera", "given": "Verena E", "initials": "VE", "orcid": "0000-0002-8930-534X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c7185df2f7d44872960d604e9c70c551.json"}}, {"family": "Kinsella", "given": "Cormac M", "initials": "CM", "orcid": "0000-0001-9865-4608", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/772bfbaa9ca14161980526ba81082d3c.json"}}, {"family": "Heintzman", "given": "Peter D", "initials": "PD", "orcid": "0000-0002-6449-0219", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/54774bc7db094262b111c5245207579f.json"}}, {"family": "van der Valk", "given": "Tom", "initials": "T", "orcid": "0000-0001-6582-3452", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/aa0dba3cc12143cba213f7f3a052216c.json"}}], "type": "posted-content", "published": "2025-03-19", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2025.03.19.644176", "pmid": null, "labels": {"DDLS Fellow": "", "Tom van der Valk": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T11:01:37.613Z", "modified": "2026-09-23T14:18:05.285Z"}, {"entity": "publication", "iuid": "c804939c8e134ac29252c0780fdc327f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c804939c8e134ac29252c0780fdc327f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c804939c8e134ac29252c0780fdc327f"}}, "title": "Abstract 072: Plasma Metabolome Predicts Long-term Body Weight Gain and Type 2 Diabetes in Non-Obese Individuals", "authors": [{"family": "Wu", "given": "Zhiyuan", "initials": "Z"}, {"family": "Liu", "given": "Binkai", "initials": "B"}, {"family": "Li", "given": "Jun", "initials": "J"}, {"family": "Zeleznik", "given": "Oana", "initials": "O"}, {"family": "Eliassen", "given": "A Heather", "initials": "AH"}, {"family": "Wittenbecher", "given": "Clemens", "initials": "C"}, {"family": "Hu", "given": "Frank", "initials": "F"}, {"family": "Wang", "given": "Molin", "initials": "M"}, {"family": "Song", "given": "Mingyang", "initials": "M"}, {"family": "Hu", "given": "Yang", "initials": "Y"}, {"family": "Sun", "given": "Qi", "initials": "Q"}], "type": "journal-article", "published": "2025-03-11", "journal": {"title": "Circulation", "issn": "0009-7322", "volume": "151", "issue": "Suppl_1", "issn-l": null}, "abstract": null, "doi": "10.1161/cir.151.suppl_1.072", "pmid": null, "labels": {"Clemens Wittenbecher": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2025-12-09T13:24:36.160Z", "modified": "2025-12-09T13:25:53.297Z"}, {"entity": "publication", "iuid": "c432e16534c042828949dad3d3c7d52e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c432e16534c042828949dad3d3c7d52e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c432e16534c042828949dad3d3c7d52e"}}, "title": "Predicting allergy and postpartum depression from an incomplete compositional microbiome", "authors": [{"family": "Shternshis", "given": "Andrey", "initials": "A", "orcid": "0000-0002-9299-369X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c813415242504d84878495f76514059a.json"}}, {"family": "Tong", "given": "Bangzhuo", "initials": "B", "orcid": "0000-0002-5463-5699", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/95b7213f0ed449718c2bd47c2ab0bd0e.json"}}, {"family": "Skalkidou", "given": "Alkistis", "initials": "A", "orcid": "0000-0002-4935-7532", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/882f68bd159a46e5999dedb151bd7ea4.json"}}, {"family": "W\u00e4hlby", "given": "Carolina", "initials": "C", "orcid": "0000-0002-4139-7003", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/833afe3444d84c24be12ea1468563bea.json"}}, {"family": "Zachariah", "given": "Dave", "initials": "D", "orcid": "0000-0002-6698-0166", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/76aa850a94d44237b89940bf4d007a6e.json"}}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW", "orcid": "0000-0001-5432-1764", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/246ed7b405dd4c3f9ec5e7ff9f1d3ade.json"}}, {"family": "Singh", "given": "Prashant", "initials": "P", "orcid": "0000-0002-3123-3478", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f19f17dbc48047f98bf209175b935bc3.json"}}], "type": "posted-content", "published": "2025-03-06", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2025.02.28.640766", "pmid": null, "labels": {"Prashant Singh": "", "SciLifeLab Fellow": "", "DDLS Fellow": "", "Luisa Hugerth": ""}, "xrefs": [], "notes": [], "created": "2025-11-28T05:42:26.583Z", "modified": "2026-09-23T15:45:34.669Z"}, {"entity": "publication", "iuid": "7e85702edc4b4d74a4a1a9c16174cbb5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/7e85702edc4b4d74a4a1a9c16174cbb5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/7e85702edc4b4d74a4a1a9c16174cbb5"}}, "title": "Amino Acid Properties, Substitution Rates, and the Nearly Neutral Theory.", "authors": [{"family": "James", "given": "Jennifer E", "initials": "JE", "orcid": "0000-0003-0518-6783", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4b807f7ab8f46f8a5e927e1b090d662.json"}}, {"family": "Lascoux", "given": "Martin", "initials": "M", "orcid": "0000-0003-1699-9042", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0730d0f9c2524eb19383640612924701.json"}}], "type": "journal article", "published": "2025-03-06", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "17", "issue": "3", "issn-l": "1759-6653"}, "abstract": "Do the properties of amino acids affect their rates of substitution? The neutral theory predicts that greater selective constraint leads to slower rates of evolution; similarly, we expect amino acids that are more different from each other to have lower rates of exchange because such changes are most likely to affect protein structure and function. Here, we test these predictions, using substitution rates estimated from empirical amino acid exchangeability matrices. To measure degree of amino acid difference, we focused on two physicochemical properties, charge and size, uncorrelated metrics that are known to have important implications for protein structure and function. We find that for both charge and size, amino acid pairs with large differences had lower rates of substitution. We also found that amino acids that differed in both properties had the lowest rates of substitution, suggesting that both physicochemical properties are under selective constraint. Mutation properties, such as the number of mutations or the number of transitions as opposed to transversions separating amino acid pairs, were also important predictors of substitution rates. The relationship between amino acid substitution rates and differences in their physiochemical properties holds across several taxonomically restricted datasets. This finding suggests that purifying selection affects amino acid substitution rates in a similar manner across taxonomic groups with different effective population sizes.", "doi": "10.1093/gbe/evaf025", "pmid": "39971341", "labels": {"DDLS Fellow": "", "Jennifer James": ""}, "xrefs": [{"db": "pmc", "key": "PMC11884779"}, {"db": "pii", "key": "8024405"}], "notes": [], "created": "2026-08-20T09:41:25.179Z", "modified": "2026-09-23T15:45:07.027Z"}, {"entity": "publication", "iuid": "1d81ac07fdfe4adea0206e44bfcb3c82", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1d81ac07fdfe4adea0206e44bfcb3c82.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1d81ac07fdfe4adea0206e44bfcb3c82"}}, "title": "Androgen Receptor Inhibition Increases MHC Class I Expression and Improves Immune Response in Prostate Cancer.", "authors": [{"family": "Chesner", "given": "Lisa N", "initials": "LN", "orcid": "0009-0007-2779-8824", 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cancer, are limited. We show that AR downregulates MHCI expression/antigen presentation and that AR inhibition improves T-cell responses and tumor control. This suggests that treatments combining AR inhibitors and checkpoint blockade may improve tumor immune surveillance and antitumor immunity in patients.", "doi": "10.1158/2159-8290.CD-24-0559", "pmid": "39652470", "labels": {"Arian Lundberg": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC11873725"}, {"db": "pii", "key": "750492"}], "notes": [], "created": "2025-03-20T14:05:18.677Z", "modified": "2026-10-01T08:24:21.712Z"}, {"entity": "publication", "iuid": "2fff6d7c8b744137b3d70f78c899b66b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/2fff6d7c8b744137b3d70f78c899b66b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/2fff6d7c8b744137b3d70f78c899b66b"}}, "title": "Recent advances in precision nutrition and cardiometabolic diseases.", "authors": [{"family": "Mart\u00ednez-Gonz\u00e1lez", "given": "Miguel A", "initials": "MA", "orcid": "0000-0002-3917-9808", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7852fa98fe3a4da285d79f04e09cbd34.json"}}, {"family": "Planes", "given": "Francisco J", "initials": "FJ"}, {"family": "Ruiz-Canela", "given": "Miguel", "initials": "M", "orcid": "0000-0002-7684-2787", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4f947f7399034daeb6778d0781b6e789.json"}}, {"family": "Toledo", "given": "Estefan\u00eda", "initials": "E", "orcid": "0000-0002-6263-4434", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d04ea61c7230463ab64e537f97fb07fe.json"}}, {"family": "Estruch", "given": "Ram\u00f3n", "initials": "R", "orcid": "0000-0003-1260-4445", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/122cb01329f24931ae77ae5ac5a05059.json"}}, {"family": "Salas-Salvad\u00f3", "given": "Jordi", "initials": "J"}, {"family": "Vald\u00e9s-M\u00e1s", "given": "Rafael", "initials": "R"}, {"family": "Mena", "given": "Pedro", "initials": "P"}, {"family": "Casta\u00f1er", "given": "Olga", "initials": "O"}, {"family": "Fit\u00f3", "given": "Montse", "initials": "M"}, {"family": "Clish", "given": "Clary", "initials": "C", "orcid": "0000-0001-8259-9245", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/25b862e77efe474ca91bce1bd96fd366.json"}}, {"family": "Landberg", "given": "Rikard", "initials": "R"}, {"family": "Wittenbecher", "given": "Clemens", "initials": "C", "orcid": "0000-0001-7792-877X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2f7d2c289b3c47d5a79d23bd48a3225a.json"}}, {"family": "Liang", "given": "Liming", "initials": "L", "orcid": "0000-0001-8261-3174", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7da355304cad4309ab4dee783a341611.json"}}, {"family": "Guasch-Ferr\u00e9", "given": "Marta", "initials": "M", "orcid": "0000-0001-8525-1404", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2d1a49f5df124e96a9285b43d628cee9.json"}}, {"family": "Lamuela-Ravent\u00f3s", "given": "Rosa M", "initials": "RM"}, {"family": "Wang", "given": "Dong D", "initials": "DD"}, {"family": "Forouhi", "given": "Nita", "initials": "N"}, {"family": "Razquin", "given": "Cristina", "initials": "C"}, {"family": "Hu", "given": "Frank B", "initials": "FB"}], "type": "journal article", "published": "2025-03-00", "journal": {"title": "Rev Esp Cardiol (Engl Ed)", "issn": "1885-5857", "volume": "78", "issue": "3", "pages": "263-271", "issn-l": null}, "abstract": "A growing body of research on nutrition omics has led to recent advances in cardiovascular disease epidemiology and prevention. Within the PREDIMED trial, significant associations between diet-related metabolites and cardiovascular disease were identified, which were subsequently replicated in independent cohorts. Some notable metabolites identified include plasma levels of ceramides, acyl-carnitines, branched-chain amino acids, tryptophan, urea cycle pathways, and the lipidome. These metabolites and their related pathways have been associated with incidence of both cardiovascular disease and type 2 diabetes. Future directions in precision nutrition research include: a) developing more robust multimetabolomic scores to predict long-term risk of cardiovascular disease and mortality; b) incorporating more diverse populations and a broader range of dietary patterns; and c) conducting more translational research to bridge the gap between precision nutrition studies and clinical applications.", "doi": "10.1016/j.rec.2024.09.003", "pmid": "39357800", "labels": {"Clemens Wittenbecher": "", "DDLS Fellow": ""}, "xrefs": [{"db": "mid", "key": "NIHMS2043685"}, {"db": "pmc", "key": "PMC11875914"}, {"db": "pii", "key": "S1885-5857(24)00279-2"}], "notes": [], "created": "2025-03-19T08:18:39.467Z", "modified": "2026-09-23T11:31:46.929Z"}, {"entity": "publication", "iuid": "58d2dc413d8a48d9a278f1beb582d0f1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/58d2dc413d8a48d9a278f1beb582d0f1.json"}, "display": {"href": 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"584526a65f14426b83e9c9ad79978582", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/584526a65f14426b83e9c9ad79978582.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/584526a65f14426b83e9c9ad79978582"}}, "title": "Geographical variation in mitogenomes of the largetooth sawfish Pristis pristis : challenges and perspectives for conservation efforts", "authors": [{"family": "Rodrigues", "given": "Alan \u00c9rik S", "initials": "A\u00c9S"}, {"family": "Brito", "given": "Rafaela Maria S", "initials": "RMS"}, {"family": "Charvet", "given": "Patricia", "initials": "P"}, {"family": "Faria", "given": "Vicente V", "initials": "VV"}, {"family": "Cabanillas-Torpoco", "given": "Mariano", "initials": "M"}, {"family": "Aleixo", "given": "Alexandre", "initials": "A", "orcid": "0000-0002-7816-9725", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d113ccfdbfb74ab9a43deef86d07e1bb.json"}}, {"family": "Burlamaqui", "given": "Tib\u00e9rio C\u00e9sar T", "initials": "TCT"}, {"family": "Rodrigues-Filho", "given": "Luis Fernando da S", "initials": "LFdS"}, {"family": "Asenjo", "given": "Angelico", "initials": "A"}, {"family": "Siccha-Ramirez", "given": "Raquel", "initials": "R"}, {"family": "Nunes", "given": "Jorge Luiz S", "initials": "JLS"}, {"family": "de Boer", "given": "Hugo J", "initials": "HJ"}, {"family": "Cerca", "given": "Jos\u00e9", "initials": "J"}, {"family": "Mauvisseau", "given": "Quentin", "initials": "Q"}, {"family": "Ready", "given": "Jonathan S", "initials": "JS"}, {"family": "Sales", "given": "Jo\u00e3o Br\u00e1ullio L", "initials": "JBL"}], "type": "posted-content", "published": "2025-02-27", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2025.02.22.639618", "pmid": null, "labels": {"Jos\u00e9 Cerca": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T11:01:06.388Z", "modified": "2026-09-23T14:53:06.037Z"}, {"entity": "publication", "iuid": "889b1d49e4b64d8498be41da2c00fea8", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/889b1d49e4b64d8498be41da2c00fea8.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/889b1d49e4b64d8498be41da2c00fea8"}}, "title": "Applying 3D cultures and high-throughput technologies to study host-pathogen interactions.", "authors": [{"family": "De Martinis", "given": "Elaine Cristina Pereira", "initials": "ECP"}, {"family": "Alves", "given": "Virg\u00ednia Farias", "initials": "VF"}, {"family": "Pereira", "given": "Marita Gimenez", "initials": "MG"}, {"family": "Andrade", "given": "Leonardo Neves", "initials": "LN"}, {"family": "Abichabki", "given": "Nath\u00e1lia", "initials": "N"}, {"family": "Abramova", "given": "Anna", "initials": "A", "orcid": "0000-0002-0493-7808", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dd75cbcc659c4ca398eb678fad1dc498.json"}}, {"family": "Dannborg", "given": "Mirjam", "initials": "M", "orcid": "0000-0003-3171-9379", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3379f6c1295741a9ba945f9e92a552eb.json"}}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J", "orcid": "0000-0002-6528-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c666068e9d34939b0252a627007cec7.json"}}], "type": "journal article", "published": "2025-02-20", "journal": {"title": "Front Immunol", "issn": "1664-3224", "volume": "16", "pages": "1488699", "issn-l": "1664-3224"}, "abstract": "Recent advances in cell culturing and DNA sequencing have dramatically altered the field of human microbiome research. Three-dimensional (3D) cell culture is an important tool in cell biology, in cancer research, and for studying host-microbe interactions, as it mimics the in vivo characteristics of the host environment in an in vitro system, providing reliable and reproducible models. This work provides an overview of the main 3D culture techniques applied to study interactions between host cells and pathogenic microorganisms, how these systems can be integrated with high-throughput molecular methods, and how multi-species model systems may pave the way forward to pinpoint interactions among host, beneficial microbes and pathogens.", "doi": "10.3389/fimmu.2025.1488699", "pmid": "40051624", "labels": {"DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC11882522"}], "notes": [], "created": "2025-06-04T08:12:47.630Z", "modified": "2026-09-23T12:27:45.119Z"}, {"entity": "publication", "iuid": "86e33ce298c34535bec9ee06e20f9dd3", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/86e33ce298c34535bec9ee06e20f9dd3.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/86e33ce298c34535bec9ee06e20f9dd3"}}, "title": "Genetic adaptation to amoxicillin in Escherichia coli: The limited role of dinB and katE.", "authors": [{"family": "Teichmann", "given": "Lisa", "initials": "L"}, {"family": "Wenne", "given": "Marcus", "initials": "M"}, {"family": "Luitwieler", "given": "Sam", "initials": "S"}, {"family": "Dugar", "given": "Gaurav", "initials": "G"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Ter Kuile", "given": "Benno", "initials": "B", "orcid": "0000-0002-8523-8135", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3c87f0fedd1d4b208ff99000dbade32c.json"}}], "type": "journal article", "published": "2025-02-19", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "20", "issue": "2", "pages": "e0312223", "issn-l": "1932-6203"}, "abstract": "Bacteria can quickly adapt to sub-lethal concentrations of antibiotics. Several stress and DNA repair genes contribute to this adaptation process. However, the pathways leading to adaptation by acquisition of de novo mutations remain poorly understood. This study explored the roles of DNA polymerase IV (dinB) and catalase HP2 (katE) in E. coli's adaptation to amoxicillin. These genes are thought to play essential roles in beta-lactam resistance-dinB in increasing mutation rates and katE in managing oxidative stress. By comparing the adaptation rates, transcriptomic profiles, and genetic changes of wild-type and knockout strains, we aimed to clarify the contributions of these genes to beta-lactam resistance. While all strains exhibited similar adaptation rates and mutations in the frdD gene and ampC operon, several unique mutations were acquired in the \u0394katE and \u0394dinB strains. Overall, this study distinguishes the contributions of general stress-related genes on the one hand, and dinB, and katE on the other hand, in development of beta-lactam resistance.", "doi": "10.1371/journal.pone.0312223", "pmid": "39970152", "labels": {"DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC11838884"}, {"db": "pii", "key": "PONE-D-24-43795"}], "notes": [], "created": "2025-06-04T08:12:45.234Z", "modified": "2026-09-23T13:15:57.089Z"}, {"entity": "publication", "iuid": "584e5a83218d4ee481f1071ddaa2c952", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/584e5a83218d4ee481f1071ddaa2c952.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/584e5a83218d4ee481f1071ddaa2c952"}}, "title": "Virtual fragment screening for DNA repair inhibitors in vast chemical space.", "authors": [{"family": "Luttens", "given": "Andreas", "initials": "A", "orcid": "0000-0003-2915-7901", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d2944edc47eb4b639f1c61ae7b94b60a.json"}}, {"family": "Vo", "given": "Duc Duy", "initials": "DD"}, {"family": "Scaletti", "given": "Emma R", "initials": "ER"}, {"family": "Wiita", "given": "Elis\u00e9e", "initials": "E"}, {"family": "Alml\u00f6f", "given": "Ingrid", "initials": "I"}, {"family": "Wallner", "given": "Olov", "initials": "O"}, {"family": "Davies", "given": "Jonathan", "initials": "J"}, {"family": "Ko\u0161enina", "given": "Sara", "initials": "S", "orcid": "0000-0001-7893-0249", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/04654f973aba4ecc9d8b45445741c38f.json"}}, {"family": "Meng", "given": "Liuzhen", "initials": "L"}, {"family": "Long", "given": "Maeve", "initials": "M"}, {"family": "Mortusewicz", "given": "Oliver", "initials": "O", "orcid": "0000-0002-4290-4994", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6f546fe8f2c54824b942f7f88976e3bd.json"}}, {"family": "Masuyer", "given": "Geoffrey", "initials": "G", "orcid": "0000-0002-9527-2310", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c62ba219d3e34662aaa458dbd361cf31.json"}}, {"family": "Ballante", "given": "Flavio", "initials": "F", "orcid": "0000-0002-4831-3423", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8ce9aad230aa414886e3bf519937aad9.json"}}, {"family": "Michel", "given": "Maurice", "initials": "M"}, {"family": "Homan", "given": "Evert", "initials": "E"}, {"family": "Scobie", "given": "Martin", "initials": "M"}, {"family": "Kalder\u00e9n", "given": "Christina", "initials": "C"}, {"family": "Warpman Berglund", "given": "Ulrika", "initials": "U"}, {"family": "Tarnovskiy", "given": "Andrii V", "initials": "AV"}, {"family": "Radchenko", "given": "Dmytro S", "initials": "DS", "orcid": "0000-0001-5444-7754", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5a8f8993ce024259aa09cfae9a745a20.json"}}, {"family": "Moroz", "given": "Yurii S", "initials": "YS", "orcid": "0000-0001-6073-002X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/85e5c6a40d854426b96476233f59ccfa.json"}}, {"family": "Kihlberg", "given": "Jan", "initials": "J", "orcid": "0000-0002-4205-6040", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7edb4dfa7c4b4d6c8c4cf0282a9c9a1a.json"}}, {"family": "Stenmark", "given": "P\u00e5l", "initials": "P", "orcid": "0000-0003-4777-3417", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9791bc0d7463417899d6953b5ca1bac3.json"}}, {"family": "Helleday", "given": "Thomas", "initials": "T"}, {"family": "Carlsson", "given": "Jens", "initials": "J", "orcid": "0000-0003-4623-2977", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/792c1cd4aca248dc94b967115ffa82df.json"}}], "type": "journal article", "published": "2025-02-18", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "1741", "issn-l": "2041-1723"}, "abstract": "Fragment-based screening can catalyze drug discovery by identifying novel scaffolds, but this approach is limited by the small chemical libraries studied by biophysical experiments and the challenging optimization process. To expand the explored chemical space, we employ structure-based docking to evaluate orders-of-magnitude larger libraries than those used in traditional fragment screening. We computationally dock a set of 14 million fragments to 8-oxoguanine DNA glycosylase (OGG1), a difficult drug target involved in cancer and inflammation, and evaluate 29 highly ranked compounds experimentally. Four of these bind to OGG1 and X-ray crystallography confirms the binding modes predicted by docking. Furthermore, we show how fragment elaboration using searches among billions of readily synthesizable compounds identifies submicromolar inhibitors with anti-inflammatory and anti-cancer effects in cells. Comparisons of virtual screening strategies to explore a chemical space of 1022 compounds illustrate that fragment-based design enables enumeration of all molecules relevant for inhibitor discovery. Virtual fragment screening is hence a highly efficient strategy for navigating the rapidly growing combinatorial libraries and can serve as a powerful tool to accelerate drug discovery efforts for challenging therapeutic targets.", "doi": "10.1038/s41467-025-56893-9", "pmid": "39966348", "labels": {"SciLifeLab Fellow": "", "Jens Carlsson": "", "Andreas Luttens": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC11836371"}, {"db": "pii", "key": "10.1038/s41467-025-56893-9"}], "notes": [], "created": "2026-09-23T09:09:46.413Z", "modified": "2026-09-23T09:09:46.668Z"}, {"entity": "publication", "iuid": "e608034f8699475b897a7ea9a05b34d3", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e608034f8699475b897a7ea9a05b34d3.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e608034f8699475b897a7ea9a05b34d3"}}, "title": "PyOrthoANI, PyFastANI, and Pyskani: a suite of Python libraries for computation of average nucleotide identity", "authors": [{"family": "Larralde", "given": "Martin", "initials": "M", "orcid": "0000-0002-3947-4444", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6e048b839197434d8af8ab34bd50cf5e.json"}}, {"family": "Zeller", "given": "Georg", "initials": "G", "orcid": "0000-0003-1429-7485", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/414382373eb5447186a7e6c925aa067f.json"}}, {"family": "Carroll", "given": "Laura M", "initials": "LM", "orcid": "0000-0002-3677-0192", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02112eccb0664819af916a3c3dc79daa.json"}}], "type": "posted-content", "published": "2025-02-17", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2025.02.13.638148", "pmid": null, "labels": {"Laura Carroll": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2025-03-18T17:33:38.582Z", "modified": "2026-10-01T08:31:39.104Z"}, {"entity": "publication", "iuid": "86edd1bfedc24087afc1752b92c4dbab", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/86edd1bfedc24087afc1752b92c4dbab.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/86edd1bfedc24087afc1752b92c4dbab"}}, "title": "Towards an interpretable deep learning model of cancer.", "authors": [{"family": "Nilsson", "given": "Avlant", "initials": "A", "orcid": "0000-0002-9476-4516", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f2e21dbc1c624f6a841c59e959e948e4.json"}}, {"family": "Meimetis", "given": "Nikolaos", "initials": "N", "orcid": "0000-0003-2333-0187", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e0e968cb5cc44b52818647cea77762d9.json"}}, {"family": "Lauffenburger", "given": "Douglas A", "initials": "DA", "orcid": "0000-0002-0050-989X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ac0a09cb7c9c49de95b660756a4e5464.json"}}], "type": "journal article", "published": "2025-02-14", "journal": {"title": "NPJ Precis Oncol", "issn": "2397-768X", "issn-l": null, "volume": "9", "issue": "1", "pages": "46"}, "abstract": "Cancer is a manifestation of dysfunctional cell states. It emerges from an interplay of intrinsic and extrinsic factors that disrupt cellular dynamics, including genetic and epigenetic alterations, as well as the tumor microenvironment. This complexity can make it challenging to infer molecular causes for treating the disease. This may be addressed by system-wide computer models of cells, as they allow rapid generation and testing of hypotheses that would be too slow or impossible to perform in the laboratory and clinic. However, so far, such models have been impeded by both experimental and computational limitations. In this perspective, we argue that they can now be achieved using deep learning algorithms to integrate omics data and prior knowledge of molecular networks. Such models would have many applications in precision oncology, e.g., for identifying drug targets and biomarkers, predicting resistance mechanisms and toxicity effects of drugs, or simulating cell-cell interactions in the microenvironment.", "doi": "10.1038/s41698-025-00822-y", "pmid": "39948231", "labels": {"Avlant Nilsson": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC11825879"}, {"db": "pii", "key": "10.1038/s41698-025-00822-y"}], "notes": [], "created": "2025-03-20T11:42:04.334Z", "modified": "2026-09-23T11:28:17.272Z"}, {"entity": "publication", "iuid": "5c2c696877584a1fbe6be7f6a20c727b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5c2c696877584a1fbe6be7f6a20c727b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5c2c696877584a1fbe6be7f6a20c727b"}}, "title": "Rapid Evolution of Host Repertoire and Geographic Range in a Young and Diverse Genus of Montane Butterflies.", "authors": [{"family": "Mo", "given": "Shifang", "initials": "S"}, {"family": "Zhu", "given": "Yaowei", "initials": "Y"}, {"family": "Braga", "given": "Mariana P", "initials": "MP", "orcid": "0000-0002-1253-2536", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4f9064ed501545dca268c351c993aa26.json"}}, {"family": "Lohman", "given": "David J", "initials": "DJ"}, {"family": "Nylin", "given": "S\u00f6ren", "initials": "S", "orcid": "0000-0003-4195-8920", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bd67adc20d4b4deda715bc3ef8b05560.json"}}, {"family": "Moumou", "given": "Ashraf", "initials": "A"}, {"family": "Wheat", "given": "Christopher W", "initials": "CW", "orcid": "0000-0003-1863-2340", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/77b0fc9157fe4852b14f55a804f5f13c.json"}}, {"family": "Wahlberg", "given": "Niklas", "initials": "N", "orcid": "0000-0002-1259-3363", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/18850e1316e74948b7e33abe0ba1492a.json"}}, {"family": "Wang", "given": "Min", "initials": "M"}, {"family": "Ma", "given": "Fangzhou", "initials": "F"}, {"family": "Zhang", "given": "Peng", "initials": "P"}, {"family": "Wang", "given": "Houshuai", "initials": "H", "orcid": "0000-0001-7475-0136", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/77429d26b3884b328ef827033ff1e7b6.json"}}], "type": "journal article", "published": "2025-02-10", "journal": {"title": "Syst. Biol.", "issn": "1076-836X", "issn-l": "1063-5157", "volume": "74", "issue": "1", "pages": "141-157"}, "abstract": "Evolutionary changes in geographic distribution and larval host plants may promote the rapid diversification of montane insects, but this scenario has been rarely investigated. We studied the rapid radiation of the butterfly genus Colias, which has diversified in mountain ecosystems in Eurasia, Africa, and the Americas. Based on a data set of 150 nuclear protein-coding genetic loci and mitochondrial genomes, we constructed a time-calibrated phylogenetic tree of Colias species with broad taxon sampling. We then inferred their ancestral geographic ranges, historical diversification rates, and the evolution of host use. We found that the most recent common ancestor of Colias was likely geographically widespread and originated ~3.5 Ma. The group subsequently diversified in different regions across the world, often in tandem with geographic expansion events. No aspect of elevation was found to have a direct effect on diversification. The genus underwent a burst of diversification soon after the divergence of the Neotropical lineage, followed by an exponential decline in diversification rate toward the present. The ancestral host repertoire included the legume genera Astragalus and Trifolium but later expanded to include a wide range of Fabaceae genera and plants in more distantly related families, punctuated with periods of host range expansion and contraction. We suggest that the widespread distribution of the ancestor of all extant Colias lineages set the stage for diversification by isolation of populations that locally adapted to the various different environments they encountered, including different host plants. In this scenario, elevation is not the main driver but might have accelerated diversification by isolating populations.", "doi": "10.1093/sysbio/syae061", "pmid": "39484941", "labels": {"Mariana Pires Braga": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC11809587"}, {"db": "pii", "key": "7862722"}], "notes": [], "created": "2025-11-28T12:34:46.863Z", "modified": "2025-11-30T11:17:12.915Z"}, {"entity": "publication", "iuid": "a1f3cf40d1734ddcb3e8773591019a01", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a1f3cf40d1734ddcb3e8773591019a01.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a1f3cf40d1734ddcb3e8773591019a01"}}, "title": "Seven blood biomarkers are associated with TGF-\u03b2 and VHL-HIF signaling in patients with clear cell renal cell carcinoma", "authors": [{"family": "Mallikarjuna", "given": "Pramod", "initials": "P"}, {"family": "Erdem", "given": "Cemal", "initials": "C", "orcid": "0000-0003-3663-3646", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f71b5af589264614a52eefa8baba3132.json"}}, {"family": "Hedman", "given": "Harald", "initials": "H"}, {"family": "Sitaram", "given": "Raviprakash T", "initials": "RT"}, {"family": "Beorlegui", "given": "Ruben Ilundain", "initials": "RI"}, {"family": "Aripaka", "given": "Karthik", "initials": "K"}, {"family": "Larsson", "given": "Anders", "initials": "A", "orcid": "0000-0003-3161-0402", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5b44e49c49f644cfa3348bcc4bb0080f.json"}}, {"family": "Ljungberg", "given": "B\u00f6rje", "initials": "B"}, {"family": "Kamali-Moghaddam", "given": "Masood", "initials": "M"}, {"family": "Landstr\u00f6m", "given": "Mar\u00e9ne", "initials": "M"}], "type": "posted-content", "published": "2025-02-08", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2025.02.07.636864", "pmid": null, "labels": {"DDLS Fellow": "", "Cemal Erdem": ""}, "xrefs": [], "notes": [], "created": "2026-10-01T08:34:00.410Z", "modified": "2026-10-01T08:34:00.459Z"}, {"entity": "publication", "iuid": "22579707ed15411491e1427f9cb0cef6", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/22579707ed15411491e1427f9cb0cef6.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/22579707ed15411491e1427f9cb0cef6"}}, "title": "Ceftazidime-avibactam tolerance and persistence among difficult-to-treat KPC-producing Klebsiella pneumoniae clinical isolates from bloodstream infections.", "authors": [{"family": "Abichabki", "given": "N", "initials": "N"}, {"family": "Gaspar", "given": "G G", "initials": "GG"}, {"family": "Bortolato", "given": "L R", "initials": "LR"}, {"family": "Lima", "given": "D A F S", "initials": "DAFS"}, {"family": "Silva", "given": "L N", "initials": "LN"}, {"family": "Pocente", "given": "R H C", "initials": "RHC"}, {"family": "Ferreira", "given": "J C", "initials": "JC"}, {"family": "Ogasawara", "given": "T C", "initials": "TC"}, {"family": "Pereira", "given": "D", "initials": "D"}, {"family": "Guerra", "given": "R R", "initials": "RR"}, {"family": "Wilhelm", "given": "C", "initials": "C"}, {"family": "Barth", "given": "P", "initials": "P"}, {"family": "Martins", "given": "A F", "initials": "AF"}, {"family": "Barth", "given": "A", "initials": "A"}, {"family": "Braga", "given": "G U L", "initials": "GUL"}, {"family": "De Martinis", "given": "E C P", "initials": "ECP"}, {"family": "Bengtsson-Palme", "given": "J", "initials": "J", "orcid": "0000-0002-6528-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c666068e9d34939b0252a627007cec7.json"}}, {"family": "Bellissimo-Rodrigues", "given": "F", "initials": "F"}, {"family": "Bollela", "given": "V R", "initials": "VR"}, {"family": "Darini", "given": "A L C", "initials": "ALC"}, {"family": "Andrade", "given": "L N", "initials": "LN"}], "type": "journal article", "published": "2025-02-00", "journal": {"title": "Eur. J. Clin. Microbiol. Infect. Dis.", "issn": "1435-4373", "volume": "44", "issue": "2", "pages": "343-353", "issn-l": "0934-9723"}, "abstract": "Tolerance and persistence occur \"silently\" in bacteria categorized as susceptible by antimicrobial susceptibility testing in clinical microbiology laboratories. They are different from resistance phenomena, not well-studied, and often remain unnoticeable. We aimed to investigate and characterize ceftazidime-avibactam (CZA) tolerance/persistence in 80 Klebsiella pneumoniae isolates from bloodstream infections.\n\nWe used the Tolerance Disk Test (TDtest) to detect CZA tolerance/persistence and investigate the avibactam (AVI) influence on them, and time-kill assays with minimal duration for killing (MDK) determination to characterize/differentiate CZA tolerance from persistence, for selected isolates. Whole genome sequencing was performed for 49/80 selected isolates to investigate genes related to beta-lactam tolerance/persistence and resistance as well as phylogeny studies.\n\nTolerance/persistence to CZA was detected in 48/80 (60%) isolates, all extensively drug-resistant (XDR) or multidrug-resistant, carbapenem-resistant K. pneumoniae (CRKp), KPC producers, and previously categorized as susceptible (not resistant) to CZA. No heteroresistance was detected. CZA tolerance/persistence occurred due to ceftazidime tolerance/persistence and was not related to AVI in the CZA combination. 5/11 isolates were characterized as CZA-tolerant and 5/11 as CZA-persistent. The single (1/11) XDR and CRKp non-KPC producer was truly susceptible. All the CZA-tolerant/persistent isolates (ST11, ST258, ST340, ST437, ST16, ST17, and ST307) harbored the carbapenemase-encoding gene blaKPC-2. Mutation in only two genes (rpoS and degQ) related to beta-lactam tolerance/persistence was found in only 7/49 CZA-tolerant/persistent isolates, suggesting the presence of yet unknown beta-lactam tolerance/persistence genes.\n\nAmong the K. pneumoniae bloodstream isolates studied, 60%, previously categorized as susceptible to CZA, were, actually, tolerant/persistent to this antibiotic, all these KPC producers.", "doi": "10.1007/s10096-024-05005-4", "pmid": "39614972", "labels": {"DDLS Fellow": ""}, "xrefs": [{"db": "pii", "key": "10.1007/s10096-024-05005-4"}], "notes": [], "created": "2025-06-04T08:15:04.773Z", "modified": "2026-09-23T11:34:48.679Z"}, {"entity": "publication", "iuid": "9496dbd57e89474da8a764a1dfe12504", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9496dbd57e89474da8a764a1dfe12504.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9496dbd57e89474da8a764a1dfe12504"}}, "title": "Adaptation of Escherichia coli to ciprofloxacin and enrofloxacin: Differential proteomics of the SOS response and RecA-independent mechanisms.", "authors": [{"family": "Teichmann", "given": "Lisa", "initials": "L"}, {"family": "Pasman", "given": "Raymond", "initials": "R"}, {"family": "Luitwieler", "given": "Sam", "initials": "S"}, {"family": "Varriale", "given": "Chiara", "initials": "C"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J", "orcid": "0000-0002-6528-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c666068e9d34939b0252a627007cec7.json"}}, {"family": "Ter Kuile", "given": "Benno", "initials": "B"}], "type": "journal article", "published": "2025-02-00", "journal": {"title": "Int. J. Antimicrob. Agents", "issn": "1872-7913", "volume": "65", "issue": "2", "pages": "107420", "issn-l": "0924-8579"}, "abstract": "Antibiotic resistance is a growing global healthcare challenge, treatment of bacterial infections with fluoroquinolones being no exception. These antibiotics can induce genetic instability through several mechanisms, one of the most significant being the activation of the SOS response. During exposure to sublethal concentration, this stress response increases mutation rates, accelerating resistance evolution.\n\nTo explore the role of the SOS response in fluoroquinolone adaptation, we induced de novo resistance by exposure to step-wise increasing concentrations Escherichia coli wild-type (MG1655) and a \u0394recA mutant strain, which is deficient in SOS activation. Both strains were exposed to stepwise increasing concentrations of ciprofloxacin and enrofloxacin - two fluoroquinolones that differ only by a single methyl group.\n\nDevelopment of resistance against both fluoroquinolones was severely hampered in the \u0394recA mutant. While these antibiotics are often assumed to elicit similar cellular responses, our data revealed distinct genomic and adaptive differences. Building on these findings, we performed a comparative proteomics analysis to investigate how E. coli adapts to ciprofloxacin and enrofloxacin at the protein level.\n\nThe results demonstrate that the slight structural variation between ciprofloxacin and enrofloxacin leads to unique proteomic adaptations. These findings suggest that even subtle chemical differences can lead to distinct adaptive trajectories and illustrate the flexibility of cellular stress responses.", "doi": "10.1016/j.ijantimicag.2024.107420", "pmid": "39742892", "labels": {"DDLS Fellow": ""}, "xrefs": [{"db": "pii", "key": "S0924-8579(24)00336-4"}], "notes": [], "created": "2025-06-04T08:14:28.371Z", "modified": "2026-10-01T08:26:35.949Z"}, {"entity": "publication", "iuid": "bb208e8865fc4192b2c539f6a8e46c82", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/bb208e8865fc4192b2c539f6a8e46c82.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/bb208e8865fc4192b2c539f6a8e46c82"}}, "title": "Telomemore enables single-cell analysis of cell cycle and chromatin condensation.", "authors": [{"family": "Yakovenko", "given": "Iryna", "initials": "I", "orcid": "0009-0003-5235-2999", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/03c9f5e054fb4eaaadec42a6e484df3b.json"}}, {"family": "Mihai", "given": "Ionut Sebastian", "initials": "IS", "orcid": "0000-0002-9322-5879", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a992010c915b42e8a5d3b1ab8e6302ee.json"}}, {"family": "Selinger", "given": "Martin", "initials": "M", "orcid": "0000-0002-5420-9702", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/178f194601f84780a0cdee01ab25a12d.json"}}, {"family": "Rosenbaum", "given": "William", "initials": "W", "orcid": "0000-0003-2274-7343", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/452d1628f9ca4fb88ccc432a0258c517.json"}}, {"family": "Dernstedt", "given": "Andy", "initials": "A", "orcid": "0000-0001-6048-5300", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/63ec9ea5d1d64327a301381d7496561a.json"}}, {"family": "Gr\u00f6ning", "given": "Remigius", "initials": "R", "orcid": "0000-0001-5384-8038", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/554e7b2b64da4db890e3330c3766b1d6.json"}}, {"family": "Trygg", "given": "Johan", "initials": "J", "orcid": "0000-0003-3799-6094", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3e227e1e1bb84083b9534f4124830f6d.json"}}, {"family": "Carroll", "given": "Laura", "initials": "L", "orcid": "0000-0002-3677-0192", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02112eccb0664819af916a3c3dc79daa.json"}}, {"family": "Forsell", "given": "Mattias", "initials": "M", "orcid": "0000-0001-6904-742X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c3209b86680246b898a8442ea43bba0e.json"}}, {"family": "Henriksson", "given": "Johan", "initials": "J", "orcid": "0000-0002-7745-2844", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/598b7031d1c9448a91de58d8544af7fa.json"}}], "type": "journal article", "published": "2025-01-24", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "volume": "53", "issue": "3", "issn-l": "0305-1048"}, "abstract": "Single-cell RNA-seq methods can be used to delineate cell types and states at unprecedented resolution but do little to explain why certain genes are expressed. Single-cell ATAC-seq and multiome (ATAC + RNA) have emerged to give a complementary view of the cell state. It is however unclear what additional information can be extracted from ATAC-seq data besides transcription factor binding sites. Here, we show that ATAC-seq telomere-like reads counter-inituively cannot be used to infer telomere length, as they mostly originate from the subtelomere, but can be used as a biomarker for chromatin condensation. Using long-read sequencing, we further show that modern hyperactive Tn5 does not duplicate 9 bp of its target sequence, contrary to common belief. We provide a new tool, Telomemore, which can quantify nonaligning subtelomeric reads. By analyzing several public datasets and generating new multiome fibroblast and B-cell atlases, we show how this new readout can aid single-cell data interpretation. We show how drivers of condensation processes can be inferred, and how it complements common RNA-seq-based cell cycle inference, which fails for monocytes. Telomemore-based analysis of the condensation state is thus a valuable complement to the single-cell analysis toolbox.", "doi": "10.1093/nar/gkaf031", "pmid": "39878215", "labels": {"Laura Carroll": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC11775621"}, {"db": "pii", "key": "7986050"}], "notes": [], "created": "2025-03-18T17:32:33.811Z", "modified": "2025-03-18T17:32:34.241Z"}, {"entity": "publication", "iuid": "b90234c03b76414d948c1214faefadb8", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b90234c03b76414d948c1214faefadb8.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b90234c03b76414d948c1214faefadb8"}}, "title": "Fluoroquinolone-specific resistance trajectories in E. coli and their dependence on the SOS-response.", "authors": [{"family": "Teichmann", "given": "Lisa", "initials": "L"}, {"family": "Luitwieler", "given": "Sam", "initials": "S"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J", "orcid": "0000-0002-6528-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c666068e9d34939b0252a627007cec7.json"}}, {"family": "Ter Kuile", "given": "Benno", "initials": "B"}], "type": "journal article", "published": "2025-01-21", "journal": {"title": "BMC Microbiol.", "issn": "1471-2180", "volume": "25", "issue": "1", "pages": "37", "issn-l": "1471-2180"}, "abstract": "Fluoroquinolones are indispensable antibiotics used in treating bacterial infections in both human and veterinary medicine. However, resistance to these drugs presents a growing challenge. The SOS response, a DNA repair pathway activated by DNA damage, is known to influence resistance development, yet its role in fluoroquinolone resistance is not fully understood. This study aims to unfold the mechanisms of fluoroquinolone resistance by investigating the impact of the SOS response on bacterial adaptation.\n\nWe exposed Escherichia coli to four fluoroquinolones-ciprofloxacin, enrofloxacin, levofloxacin, and moxifloxacin. Using a recA knockout mutant, deficient in the SOS response, as a control, we assessed how the presence or absence of this pathway affects resistance development. Our findings demonstrated that the rate of resistance evolution varied between the different fluoroquinolones. Ciprofloxacin, enrofloxacin, and moxifloxacin exposures led to the most evident reliance on the SOS response for resistance, whereas levofloxacin exposed cultures showed less dependency. Whole genome analysis indicated distinct genetic changes associated with each fluoroquinolone, highlighting potential different pathways and mechanisms involved in resistance.\n\nThis study shows that the SOS response plays a crucial role in resistance development to certain fluoroquinolones, with varying dependencies per drug. The characteristic impact of fluoroquinolones on resistance mechanisms emphasizes the need to consider the unique properties of each antibiotic in resistance studies and treatment strategies. These findings are essential for improving antibiotic stewardship and developing more effective, tailored interventions to combat resistance.", "doi": "10.1186/s12866-025-03771-5", "pmid": "39838279", "labels": {"DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC11748515"}, {"db": "pii", "key": "10.1186/s12866-025-03771-5"}, {"db": "BioProject", "key": "PRJNA1163877"}], "notes": [], "created": "2025-06-04T08:12:49.937Z", "modified": "2026-09-23T12:22:14.453Z"}, {"entity": "publication", "iuid": "a2eda393befd4a169ee1b9567b07bdf3", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a2eda393befd4a169ee1b9567b07bdf3.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a2eda393befd4a169ee1b9567b07bdf3"}}, "title": "Advancing Chronic Liver Disease Diagnoses: Targeted Proteomics for the Non-Invasive Detection of Fibrosis", "authors": [{"family": "Villanueva Raisman", "given": "Andrea", "initials": "A", "orcid": "0009-0006-5973-2814", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d2596360054e454da5a68e006208730a.json"}}, {"family": "Kotol", "given": "David", "initials": "D"}, {"family": "Altay", "given": "Ozlem", "initials": "O"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca58bf2d214047e0ae5e38a42a0f2808.json"}}, {"family": "Atak", "given": "Dila", "initials": "D", "orcid": "0000-0001-8882-0019", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/03d108c4e22b435a90b4cb91cc0bc7f6.json"}}, {"family": "Yurdaydin", "given": "Cihan", "initials": "C", "orcid": "0000-0002-5419-7158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/53825e71e1994442b474df83c61f751d.json"}}, {"family": "Akyildiz", "given": "Murat", "initials": "M"}, {"family": "Dayangac", "given": "Murat", "initials": "M", "orcid": "0000-0002-1240-7233", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/574c0b430ae74d0e93c67146256f97f7.json"}}, {"family": "Kirimlioglu", "given": "Hale", "initials": "H"}, {"family": "Zeybel", "given": "M\u00fcjdat", "initials": "M"}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}], "type": "journal-article", "published": "2025-01-14", "journal": {"title": "Livers", "issn": "2673-4389", "volume": "5", "issue": "1", "pages": "2", "issn-l": null}, "abstract": null, "doi": "10.3390/livers5010002", "pmid": null, "labels": {"SciLifeLab Fellow": "", "Fredrik Edfors": "", "DDLS Fellow": "", "Adil Mardinoglu": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T13:42:10.273Z", "modified": "2026-09-23T13:36:46.869Z"}, {"entity": "publication", "iuid": "fc0b71fbdcab40c59d6f3fff158457a1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/fc0b71fbdcab40c59d6f3fff158457a1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/fc0b71fbdcab40c59d6f3fff158457a1"}}, "title": "DTPPI: predicting drug interactions using a weighted drug-protein network", "authors": [{"family": "Szydlik", "given": "Szymon", "initials": "S"}, {"family": "Taheri", "given": "Golnaz", "initials": "G", "orcid": "0000-0002-2741-0355", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/014c217121d346b2b371bbc1c2fede57.json"}}], "type": "posted-content", "published": "2025-01-08", "journal": {"title": null, "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2025.01.06.631638", "pmid": null, "labels": {"Golnaz Taheri": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2025-03-21T09:11:24.047Z", "modified": "2025-03-21T09:32:03.091Z"}, {"entity": "publication", "iuid": "10dbf64b9a3c469bbf8dcaab7407fdf6", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/10dbf64b9a3c469bbf8dcaab7407fdf6.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/10dbf64b9a3c469bbf8dcaab7407fdf6"}}, "title": "Multi-omics characterization of improved cognitive functions in Parkinson's disease patients after the combined metabolic activator treatment: a randomized, double-blinded, placebo-controlled phase II trial.", "authors": [{"family": "Yulug", "given": "Burak", "initials": "B", "orcid": "0000-0002-9704-6173", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eaa4a645a0ec49d79f44335b7c335f89.json"}}, {"family": "Altay", "given": "Ozlem", "initials": "O"}, {"family": "Li", "given": "Xiangyu", "initials": "X"}, {"family": "Hanoglu", "given": "Lutfu", "initials": "L"}, {"family": "Cankaya", "given": "Seyda", "initials": "S"}, {"family": "Velioglu", "given": "Halil A", "initials": "HA", "orcid": "0000-0002-2306-5937", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7627e2e2cd174f29b452e11103dffeb1.json"}}, {"family": "Lam", "given": "Simon", "initials": "S", "orcid": "0000-0002-4476-0971", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bdf5adecfed749b4a66cdda5cd08ee24.json"}}, {"family": "Yang", "given": "Hong", "initials": "H"}, {"family": "Coskun", "given": "Ebru", "initials": "E", "orcid": "0000-0003-1028-6703", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/69a8b6b9414c400f874350b09c3ba808.json"}}, {"family": "Idil", "given": "Ezgi", "initials": "E"}, {"family": "Bayraktaroglu", "given": "Zubeyir", "initials": "Z", "orcid": "0000-0001-5118-4776", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f6854bf743b24240b3e6e364fd33890f.json"}}, {"family": "Nogaylar", "given": "Rahim", "initials": "R"}, {"family": "Ozsimsek", "given": "Ahmet", "initials": "A"}, {"family": "Yildirim", "given": "Serkan", "initials": "S"}, {"family": "Bolat", "given": "Ismail", "initials": "I"}, {"family": "Kiliclioglu", "given": "Metin", "initials": "M"}, {"family": "Bayram", "given": "Cemil", "initials": "C"}, {"family": "Yuksel", "given": "Nursena", "initials": "N"}, {"family": "Tozlu", "given": "Ozlem O", "initials": "OO"}, {"family": "Arif", "given": "Muhammad", "initials": "M", "orcid": "0000-0003-2261-0881", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c8ffc9889ace44e3b992816601b817e2.json"}}, {"family": "Shoaie", "given": "Saeed", "initials": "S"}, {"family": "Hacimuftuoglu", "given": "Ahmet", "initials": "A"}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f46e4161be08458994efddb75ed75874.json"}}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/33f2b49a39ed4e54ba77dfe397ed3087.json"}}, {"family": "Turkez", "given": "Hasan", "initials": "H"}, {"family": "Bor\u00e9n", "given": "Jan", "initials": "J"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}], "type": "clinical trial", "published": "2025-01-06", "journal": {"title": "Brain Commun", "issn": "2632-1297", "volume": "7", "issue": "1", "pages": "fcae478", "issn-l": null}, "abstract": "Parkinson's disease is primarily marked by mitochondrial dysfunction and metabolic abnormalities. We recently reported that the combined metabolic activators improved the immunohistochemical parameters and behavioural functions in Parkinson's disease and Alzheimer's disease animal models and the cognitive functions in Alzheimer's disease patients. These metabolic activators serve as the precursors of nicotinamide adenine dinucleotide and glutathione, and they can be used to activate mitochondrial metabolism and eventually treat mitochondrial dysfunction. Here, we designed a randomized, double-blinded, placebo-controlled phase II study in Parkinson's disease patients with 84 days combined metabolic activator administration. A single dose of combined metabolic activator contains L-serine (12.35 g), N-acetyl-L-cysteine (2.55 g), nicotinamide riboside (1 g) and L-carnitine tartrate (3.73 g). Patients were administered either one dose of combined metabolic activator or a placebo daily for the initial 28 days, followed by twice-daily dosing for the next 56 days. The main goal of the study was to evaluate the clinical impact on motor functions using the Unified Parkinson's Disease Rating Scale and to determine the safety and tolerability of combined metabolic activator. A secondary objective was to assess cognitive functions utilizing the Montreal Cognitive Assessment and to analyse brain activity through functional MRI. We also performed comprehensive plasma metabolomics and proteomics analysis for detailed characterization of Parkinson's disease patients who participated in the study. Although no improvement in motor functions was observed, cognitive function was shown to be significantly improved (P < 0.0000) in Parkinson's disease patients treated with the combined metabolic activator group over 84 days, whereas no such improvement was noted in the placebo group (P > 0.05). Moreover, a significant reduction (P = 0.001) in Montreal Cognitive Assessment scores was observed in the combined metabolic activator group, with no decline (P > 0.05) in the placebo group among severe Parkinson's disease patients with lower baseline Montreal Cognitive Assessment scores. We showed that improvement in cognition was associated with critical brain network alterations based on functional MRI analysis, especially relevant to areas with cognitive functions in the brain. Finally, through a comprehensive multi-omics analysis, we elucidated the molecular mechanisms underlying cognitive improvements observed in Parkinson's disease patients. Our results show that combined metabolic activator administration leads to enhanced cognitive function and improved metabolic health in Parkinson's disease patients as recently shown in Alzheimer's disease patients. The trial was registered in ClinicalTrials.gov NCT04044131 (17 July 2019, https://clinicaltrials.gov/ct2/show/NCT04044131).", "doi": "10.1093/braincomms/fcae478", "pmid": "39816194", "labels": {"SciLifeLab Fellow": "", "Saeed Shoaie": "", "DDLS Fellow": "", "Adil Mardinoglu": "", "Muhammad Arif": ""}, "xrefs": [{"db": "pmc", "key": "PMC11733689"}, {"db": "pii", "key": "fcae478"}, {"db": "ClinicalTrials.gov", "key": "NCT04044131"}], "notes": [], "created": "2026-08-20T09:40:32.415Z", "modified": "2026-09-23T11:36:17.382Z"}, {"entity": "publication", "iuid": "b124e674af774eddbade26681d170b30", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b124e674af774eddbade26681d170b30.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b124e674af774eddbade26681d170b30"}}, "title": "Improving taxonomic inference from ancient environmental metagenomes by masking microbial-like regions in reference genomes.", "authors": [{"family": "Oskolkov", "given": "Nikolay", "initials": "N", "orcid": "0000-0001-5326-8893", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3c448f1b878442c687d58549f90ba4e9.json"}}, {"family": "Jin", "given": "Chenyu", "initials": "C", "orcid": "0000-0002-2392-7090", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/afcc4905564e41868967d9cfef968b07.json"}}, {"family": "Clinton", "given": "Samantha L\u00f3pez", "initials": "SL", "orcid": "0000-0003-1364-9135", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb3097a7dd3342e6ae0d1532ae0d18f3.json"}}, {"family": "Guinet", "given": "Benjamin", "initials": "B", "orcid": "0000-0002-9922-2118", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c17993b1fc0450eb9808706576983eb.json"}}, {"family": "Wijnands", "given": "Flore", "initials": "F", "orcid": "0009-0009-6254-8964", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/557893083c5a469ea1285294e2a2ac3a.json"}}, {"family": "Johnson", "given": "Ernst", "initials": "E", "orcid": "0009-0004-0745-2437", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ff7522013ba43ebb1fe72b5e3d4037d.json"}}, {"family": "Kutschera", "given": "Verena E", "initials": "VE", "orcid": "0000-0002-8930-534X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c7185df2f7d44872960d604e9c70c551.json"}}, {"family": "Kinsella", "given": "Cormac M", "initials": "CM", "orcid": "0000-0001-9865-4608", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/772bfbaa9ca14161980526ba81082d3c.json"}}, {"family": "Heintzman", "given": "Peter D", "initials": "PD", "orcid": "0000-0002-6449-0219", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/54774bc7db094262b111c5245207579f.json"}}, {"family": "van der Valk", "given": "Tom", "initials": "T", "orcid": "0000-0001-6582-3452", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/aa0dba3cc12143cba213f7f3a052216c.json"}}], "type": "journal article", "published": "2025-01-06", "journal": {"title": "Gigascience", "issn": "2047-217X", "volume": "14", "issn-l": "2047-217X"}, "abstract": "Ancient environmental DNA is increasingly vital for reconstructing past ecosystems, particularly when paleontological and archaeological tissue remains are absent. Detecting ancient plant and animal DNA in environmental samples relies on using extensive eukaryotic reference genome databases for profiling metagenomics data. However, many eukaryotic genomes contain regions with high sequence similarity to microbial DNA, which can lead to the misclassification of bacterial and archaeal reads as eukaryotic. This issue is especially problematic in ancient eDNA datasets, where plant and animal DNA is typically present at very low abundance. In this study, we present a method for identifying bacterial- and archaeal-like sequences in eukaryotic genomes and apply it to nearly 3,000 reference genomes from NCBI RefSeq and GenBank (vertebrates, invertebrates, plants) as well as the 1,323 PhyloNorway plant genome assemblies from herbarium material from northern high-latitude regions. We find that microbial-like regions are widespread across eukaryotic genomes and provide a comprehensive resource of their genomic coordinates and taxonomic annotations. This resource enables the masking of microbial-like regions during profiling analyses, thereby improving the reliability of ancient environmental metagenomic datasets for downstream analyses.", "doi": "10.1093/gigascience/giaf108", "pmid": "41041810", "labels": {"DDLS Fellow": "", "Tom van der Valk": ""}, "xrefs": [{"db": "pmc", "key": "PMC12491943"}, {"db": "pii", "key": "8271467"}], "notes": [], "created": "2026-09-23T12:35:53.353Z", "modified": "2026-09-23T12:35:53.469Z"}, {"entity": "publication", "iuid": "5565dc781ccf4db88283613d8ae34168", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5565dc781ccf4db88283613d8ae34168.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5565dc781ccf4db88283613d8ae34168"}}, "title": "Unveiling Driver Modules in Lung Cancer: A Clustering-Based Gene-Gene Interaction Network Analysis", "authors": [{"family": "Taheri", "given": "Golnaz", "initials": "G", "orcid": "0000-0002-2741-0355", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/014c217121d346b2b371bbc1c2fede57.json"}}, {"family": "Szalai", "given": "Marcell", "initials": "M"}, {"family": "Habibi", "given": "Mahnaz", "initials": "M", "orcid": "0000-0002-8969-2706", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f04af4e059814b78bfb107c3a5782f70.json"}}, {"family": "Papapetrou", "given": "Panagiotis", "initials": "P"}], "type": "book-chapter", "published": "2025-00-00", "journal": {"title": null, "issn": "1865-0929", "issn-l": null, "volume": null, "issue": null, "pages": "41-58"}, "abstract": null, "doi": "10.1007/978-3-031-74640-6_4", "pmid": null, "labels": {"Golnaz Taheri": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2025-03-21T09:08:42.934Z", "modified": "2025-03-21T10:33:09.106Z"}, {"entity": "publication", "iuid": "536be351277c4da096195356a1a97714", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/536be351277c4da096195356a1a97714.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/536be351277c4da096195356a1a97714"}}, "title": "The Utility of Deep Learning for Modeling Seasonal Biodiversity Changes Across the Landscape", "authors": [{"family": "Baggstr\u00f6m", "given": "Adrian", "initials": "A"}, {"family": "Goodsell", "given": "Robert", "initials": "R"}, {"family": "van Dijk", "given": "Laura", "initials": "L"}, {"family": "Iwaszkiewicz-Eggebrecht", "given": "Ela", "initials": "E"}, {"family": "Miraldo", "given": "Andreia", "initials": "A"}, {"family": "Tack", "given": "Ayco", "initials": "A", "orcid": "0000-0002-3550-1070", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/20531f32048b4cd498311138500cc6bc.json"}}, {"family": "Andermann", "given": "Tobias", "initials": "T", "orcid": "0000-0002-0932-1623", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dfff478dfcfc43ddbd40bb1bafbcb0a7.json"}}], "type": "posted-content", "published": "2025-00-00", "journal": {"issn-l": null}, "abstract": null, "doi": "10.2139/ssrn.5123378", "pmid": null, "labels": {"Tobias Andermann": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2025-03-18T16:05:27.007Z", "modified": "2025-04-03T08:25:01.032Z"}, {"entity": "publication", "iuid": "3f0b8d3a98de4d11803b835f00f67d49", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3f0b8d3a98de4d11803b835f00f67d49.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3f0b8d3a98de4d11803b835f00f67d49"}}, "title": "Strategies for taxonomic and functional annotation of metagenomes", "authors": [{"family": "Abramova", "given": "Anna", "initials": "A", "orcid": "0000-0002-0493-7808", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dd75cbcc659c4ca398eb678fad1dc498.json"}}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J", "orcid": "0000-0002-6528-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c666068e9d34939b0252a627007cec7.json"}}], "type": "book-chapter", "published": "2025-00-00", "journal": {"pages": "57-81", "issn-l": null}, "abstract": null, "doi": "10.1016/b978-0-323-91631-8.00002-0", "pmid": null, "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [], "notes": [], "created": "2024-11-18T11:46:26.151Z", "modified": "2025-03-26T11:39:35.922Z"}, {"entity": "publication", "iuid": "8dfc8924633947c19ceaad89e691e329", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8dfc8924633947c19ceaad89e691e329.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8dfc8924633947c19ceaad89e691e329"}}, "title": "Limited Effects of Tetracycline and Ciprofloxacin on Soil Bacterial Communities", "authors": [{"family": "Wenne", "given": "Marcus", "initials": "M", "orcid": "0009-0008-1941-4146", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/90d60a98a3b54120b369ffe5dd29c854.json"}}, {"family": "Abramova", "given": "Anna", "initials": "A", "orcid": "0000-0002-0493-7808", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dd75cbcc659c4ca398eb678fad1dc498.json"}}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J", "orcid": "0000-0002-6528-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c666068e9d34939b0252a627007cec7.json"}}], "type": "posted-content", "published": "2025-00-00", "journal": {"issn-l": null}, "abstract": null, "doi": "10.2139/ssrn.5249550", "pmid": null, "labels": {"Johan Bengtsson-Palme": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2025-06-04T08:16:02.193Z", "modified": "2025-12-05T10:15:22.934Z"}, {"entity": "publication", "iuid": "c7ca7531e471429bbded939e900f5892", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c7ca7531e471429bbded939e900f5892.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c7ca7531e471429bbded939e900f5892"}}, "title": "GenePioneer: A Comprehensive Python Package for Identification of Essential Genes and Modules in Cancer", "authors": [{"family": "Taheri", "given": "Golnaz", "initials": "G", "orcid": "0000-0002-2741-0355", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/014c217121d346b2b371bbc1c2fede57.json"}}, {"family": "Haerianardakani", "given": "Amirhossein", "initials": "A"}], "type": "posted-content", "published": "2024-12-21", "journal": {"title": null, "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2024.12.16.628633", "pmid": null, "labels": {"Golnaz Taheri": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2025-03-21T09:08:29.820Z", "modified": "2025-03-21T10:34:39.651Z"}, {"entity": "publication", "iuid": "4bf036fbbfcd4865b3d7e92a30739123", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4bf036fbbfcd4865b3d7e92a30739123.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4bf036fbbfcd4865b3d7e92a30739123"}}, "title": "AI-first structural identification of pathogenic protein targets", "authors": [{"family": "Saluri", "given": "Mihkel", "initials": "M"}, {"family": "Landreh", "given": "Michael", "initials": "M", "orcid": "0000-0002-7958-4074", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fccd56038e8a4c2992ed2b49f3d8d2bd.json"}}, {"family": "Bryant", "given": "Patrick", "initials": "P", "orcid": "0000-0003-3439-1866", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a683bcf98234ff09b2398976583b66f.json"}}], "type": "posted-content", "published": "2024-12-16", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2024.12.12.628104", "pmid": null, "labels": {"Patrick Bryant": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T10:59:32.934Z", "modified": "2026-09-23T14:52:37.073Z"}, {"entity": "publication", "iuid": "cee11f4ab587455b89473bdc8546bab5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/cee11f4ab587455b89473bdc8546bab5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/cee11f4ab587455b89473bdc8546bab5"}}, "title": "Author Correction: AutoTransOP: translating omics signatures without orthologue requirements using deep learning.", "authors": [{"family": "Meimetis", "given": "Nikolaos", "initials": "N", "orcid": "0000-0003-2333-0187", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e0e968cb5cc44b52818647cea77762d9.json"}}, {"family": "Pullen", "given": "Krista M", "initials": "KM", "orcid": "0000-0002-4857-8907", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6930c9935ef740479a3052b4796d7d6d.json"}}, {"family": "Zhu", "given": "Daniel Y", "initials": "DY"}, {"family": "Nilsson", "given": "Avlant", "initials": "A", "orcid": "0000-0002-9476-4516", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f2e21dbc1c624f6a841c59e959e948e4.json"}}, {"family": "Hoang", "given": "Trong Nghia", "initials": "TN"}, {"family": "Magliacane", "given": "Sara", "initials": "S"}, {"family": "Lauffenburger", "given": "Douglas A", "initials": "DA", "orcid": "0000-0002-0050-989X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ac0a09cb7c9c49de95b660756a4e5464.json"}}], "type": "published erratum", "published": "2024-12-13", "journal": {"title": "NPJ Syst Biol Appl", "issn": "2056-7189", "issn-l": "2056-7189", "volume": "10", "issue": "1", "pages": "148"}, "abstract": null, "doi": "10.1038/s41540-024-00456-z", "pmid": "39672816", "labels": {"Avlant Nilsson": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC11645403"}, {"db": "pii", "key": "10.1038/s41540-024-00456-z"}], "notes": [], "created": "2025-03-20T11:12:01.570Z", "modified": "2025-03-21T10:38:14.626Z"}, {"entity": "publication", "iuid": "b5cb34f60b154d46943268cc516c2cec", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b5cb34f60b154d46943268cc516c2cec.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b5cb34f60b154d46943268cc516c2cec"}}, "title": "Elucidating acquired PARP inhibitor resistance in advanced prostate cancer.", "authors": [{"family": "Seed", "given": "George", "initials": "G"}, {"family": "Beije", "given": "Nick", "initials": "N"}, {"family": "Yuan", "given": "Wei", "initials": "W"}, {"family": "Bertan", "given": "Claudia", "initials": "C"}, {"family": "Goodall", "given": "Jane", "initials": "J"}, {"family": "Lundberg", "given": "Arian", "initials": "A", "orcid": "0000-0002-6630-2787", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/baa2c7c8963840bfb6a22d7c5cfe35f9.json"}}, {"family": "Tyler", "given": "Matthew", "initials": "M"}, {"family": "Figueiredo", "given": "Ines", "initials": "I"}, {"family": "Pereira", "given": "Rita", "initials": "R"}, {"family": "Baker", "given": "Chloe", "initials": "C"}, {"family": "Bogdan", "given": "Denisa", "initials": "D"}, {"family": "Gallagher", "given": "Lewis", "initials": "L"}, {"family": "Cieslik", "given": "Jan-Phillipp", "initials": "JP"}, {"family": "Greening", "given": "Semini", "initials": "S"}, {"family": "Lambros", "given": "Maryou", "initials": "M"}, {"family": "Neves", "given": "Rui", "initials": "R"}, {"family": "Magraner-Pardo", "given": "Lorena", "initials": "L"}, {"family": "Fowler", "given": "Gemma", "initials": "G"}, {"family": "Ebbs", "given": "Berni", "initials": "B"}, {"family": "Miranda", "given": "Susana", "initials": "S"}, {"family": "Flohr", "given": "Penny", "initials": "P"}, {"family": "Bianchini", "given": "Diletta", "initials": "D"}, {"family": "Rescigno", "given": "Pasquale", "initials": "P"}, {"family": "Porta", "given": "Nuria", "initials": "N"}, {"family": "Hall", "given": "Emma", "initials": "E"}, {"family": "Gurel", "given": "Bora", "initials": "B"}, {"family": "Tunariu", "given": "Nina", "initials": "N"}, {"family": "Sharp", "given": "Adam", "initials": "A"}, {"family": "Pettit", "given": "Stephen", "initials": "S"}, {"family": "Stoecklein", "given": "Nikolas H", "initials": "NH"}, {"family": "Sandhu", "given": "Shahneen", "initials": "S"}, {"family": "Quigley", "given": "David", "initials": "D"}, {"family": "Lord", "given": "Christopher J", "initials": "CJ"}, {"family": "Mateo", "given": "Joaquin", "initials": "J"}, {"family": "Carreira", "given": "Suzanne", "initials": "S"}, {"family": "de Bono", "given": "Johann", "initials": "J"}], "type": "journal article", "published": "2024-12-09", "journal": {"title": "Cancer Cell", "issn": "1878-3686", "volume": "42", "issue": "12", "pages": "2113-2123.e4", "issn-l": "1535-6108"}, "abstract": "PARP inhibition (PARPi) has anti-tumor activity against castration-resistant prostate cancer (CRPC) with homologous recombination repair (HRR) defects. However, mechanisms underlying PARPi resistance are not fully understood. While acquired mutations restoring BRCA genes are well documented, their clinical relevance, frequency, and mechanism of generation remain unclear. Moreover, how resistance emerges in BRCA2 homozygously deleted (HomDel) CRPC is unknown. Evaluating samples from patients with metastatic CRPC treated in the TOPARP-B trial, we identify reversion mutations in most BRCA2/PALB2-mutated tumors (79%) by end of treatment. Among reversions mediated by frameshift deletions, 60% are flanked by DNA microhomologies, implicating POLQ-mediated repair. The number of reversions and time of their detection associate with radiological progression-free survival and overall survival (p < 0.01). For BRCA2 HomDels, selection for rare subclones without BRCA2-HomDel is observed following PARPi, confirmed by single circulating-tumor-cell genomics, biopsy fluorescence in situ hybridization (FISH), and RNAish. These data support the need for restored HRR function in PARPi resistance.", "doi": "10.1016/j.ccell.2024.10.015", "pmid": "39577422", "labels": {"DDLS Fellow": null, "Arian Lundberg": null}, "xrefs": [{"db": "mid", "key": "EMS207307"}, {"db": "pmc", "key": "PMC7618010"}, {"db": "pii", "key": "S1535-6108(24)00403-3"}], "notes": [], "created": "2025-11-14T07:48:35.081Z", "modified": "2026-01-03T12:41:34.396Z"}, {"entity": "publication", "iuid": "9af490f5e1374bb19136107d78484d9d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9af490f5e1374bb19136107d78484d9d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9af490f5e1374bb19136107d78484d9d"}}, "title": "Cell membranes sustain phospholipid imbalance via cholesterol asymmetry.", "authors": [{"family": "Doktorova", "given": "Milka", "initials": "M", "orcid": "0000-0003-4366-2242", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/791384c319f04584bac8ffb21df7271f.json"}}, {"family": "Symons", "given": "Jessica L", "initials": "JL"}, {"family": "Zhang", "given": "Xiaoxuan", "initials": "X", "orcid": "0000-0002-8728-8849", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/65a68d96961247bb8bb9890b20fa2305.json"}}, {"family": "Wang", "given": "Hong-Yin", "initials": "HY"}, {"family": "Schlegel", "given": "Jan", "initials": "J", "orcid": "0000-0003-3159-8079", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e34faeab2a0c466bb17c323d668ef339.json"}}, {"family": "Lorent", "given": "Joseph H", "initials": "JH", "orcid": "0000-0002-7537-8521", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6c6a5fdf28de42ff8a14a7ae259939cb.json"}}, {"family": "Heberle", "given": "Frederick A", "initials": "FA", "orcid": "0000-0002-0424-3240", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2557f5621a0b4c87b5f4702fbc7b6bdb.json"}}, {"family": "Sezgin", "given": "Erdinc", "initials": "E", "orcid": "0000-0002-4915-388X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f7bd3619c7fd48318bc4c1e7a9910df8.json"}}, {"family": "Lyman", "given": "Edward", "initials": "E"}, {"family": "Levental", "given": "Kandice R", "initials": "KR", "orcid": "0000-0002-2234-3683", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dcde4d3042b349b199c48509444ac8f9.json"}}, {"family": "Levental", "given": "Ilya", "initials": "I", "orcid": "0000-0002-1206-9545", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7fe40c2b810348cab78616402d4d1f1f.json"}}], "type": "journal article", "published": "2024-12-09", "journal": {"title": "bioRxiv", "issn": "2692-8205", "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": "Membranes are molecular interfaces that compartmentalize cells to control the flow of nutrients and information. These functions are facilitated by diverse collections of lipids, nearly all of which are distributed asymmetrically between the two bilayer leaflets. Most models of biomembrane structure and function often include the implicit assumption that these leaflets have similar abundances of phospholipids. Here, we show that this assumption is generally invalid and investigate the consequences of lipid abundance imbalances in mammalian plasma membranes (PM). Using quantitative lipidomics, we discovered that cytoplasmic leaflets of human erythrocyte membranes have >50% overabundance of phospholipids compared to exoplasmic leaflets. This imbalance is enabled by an asymmetric interleaflet distribution of cholesterol, which regulates cellular cholesterol homeostasis. These features produce unique functional characteristics, including low PM permeability and resting tension in the cytoplasmic leaflet that regulates protein localization. These largely overlooked aspects of membrane asymmetry represent an evolution of classic paradigms of biomembrane structure and physiology.", "doi": "10.1101/2023.07.30.551157", "pmid": "39713443", "labels": {"Milka Doktorova": "", "DDLS Fellow": "", "SciLifeLab Fellow": "", "Erdinc Sezgin": ""}, "xrefs": [{"db": "pmc", "key": "PMC11661119"}, {"db": "pii", "key": "2023.07.30.551157"}], "notes": [], "created": "2024-11-27T12:25:48.071Z", "modified": "2026-09-23T13:43:03.251Z"}, {"entity": "publication", "iuid": "6234890ec4f9490bbc0a7d0677b47d65", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/6234890ec4f9490bbc0a7d0677b47d65.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/6234890ec4f9490bbc0a7d0677b47d65"}}, "title": "Plasma proteomics for novel biomarker discovery in childhood tuberculosis", "authors": [{"family": "Fossati", "given": "Andrea", "initials": "A", "orcid": "0000-0001-5170-4903", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/658637b885384441943698722fad5944.json"}}, {"family": "Wambi", "given": "Peter", "initials": "P"}, {"family": "Jaganath", "given": "Devan", "initials": "D"}, {"family": "Calderon", "given": "Roger", "initials": "R"}, {"family": "Castro", "given": "Robert", "initials": "R"}, {"family": "Mohapatra", "given": "Alexander", "initials": "A"}, {"family": "McKetney", "given": "Justin", "initials": "J"}, {"family": "Luiz", "given": "Juaneta", "initials": "J"}, {"family": "Nerurkar", "given": "Rutuja", "initials": "R"}, {"family": "Nkereuwem", "given": "Esin", "initials": "E"}, {"family": "Franke", "given": "Molly F", "initials": "MF"}, {"family": "Mousavian", "given": "Zaynab", "initials": "Z"}, {"family": "Collins", "given": "Jeffrey M", "initials": "JM", "orcid": "0000-0002-2903-797X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8e55c6f4136342ad8c1874d0c0e13924.json"}}, {"family": "Sigal", "given": "George B", "initials": "GB"}, {"family": "Segal", "given": "Mark R", "initials": "MR"}, {"family": "Kampman", "given": "Beate", "initials": "B"}, {"family": "Wobudeya", "given": "Eric", "initials": "E"}, {"family": "Cattamanchi", "given": "Adithya", "initials": "A"}, {"family": "Ernst", "given": "Joel D", "initials": "JD"}, {"family": "Zar", "given": "Heather J", "initials": "HJ"}, {"family": "Swaney", "given": "Danielle L", "initials": "DL", "orcid": "0000-0001-6119-6084", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56317207941d4aaf81ab4d55de5fcba4.json"}}], "type": "posted-content", "published": "2024-12-08", "journal": {"title": null, "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2024.12.05.24318340", "pmid": null, "labels": {"Andrea Fossati": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2025-03-18T16:51:17.973Z", "modified": "2025-03-21T13:33:21.345Z"}, {"entity": "publication", "iuid": "47fd732a27064ac6ad542fa347d7dc8b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/47fd732a27064ac6ad542fa347d7dc8b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/47fd732a27064ac6ad542fa347d7dc8b"}}, "title": "The Circulating Proteome\u2500Technological Developments, Current Challenges, and Future Trends.", "authors": [{"family": "Geyer", "given": "Philipp E", "initials": "PE", "orcid": "0000-0001-7980-4826", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9d69184685884e28ac1557b8bf354920.json"}}, {"family": "Hornburg", "given": "Daniel", "initials": "D", "orcid": "0000-0002-6618-7774", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0cee5a39e5314a03ab14899eff0f9b11.json"}}, {"family": "Pernemalm", "given": "Maria", "initials": "M"}, {"family": "Hauck", "given": "Stefanie M", "initials": "SM", "orcid": "0000-0002-1630-6827", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c34e958b66ea4d4f90bc5d77a1ef2fbb.json"}}, {"family": "Palaniappan", "given": "Krishnan K", "initials": "KK", "orcid": "0000-0003-0203-9016", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ad180add9d14755b44834d00ea88fb4.json"}}, {"family": "Albrecht", "given": "Vincent", "initials": "V"}, {"family": "Dagley", "given": "Laura F", "initials": "LF", "orcid": "0000-0003-4171-3712", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/37484d809bd244978484d49d685d5520.json"}}, {"family": "Moritz", "given": "Robert L", "initials": "RL"}, {"family": "Yu", "given": "Xiaobo", "initials": "X"}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Vandenbrouck", "given": "Yves", "initials": "Y", "orcid": "0000-0002-1292-373X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1ed616edf97c454aa6b79c56e565ce64.json"}}, {"family": "Mueller-Reif", "given": "Johannes B", "initials": "JB"}, {"family": "Sun", "given": "Zhi", "initials": "Z"}, {"family": "Brun", "given": "Virginie", "initials": "V", "orcid": "0000-0002-9098-8707", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/075e825949ea4031bbcf6a2449ce1051.json"}}, {"family": "Ahadi", "given": "Sara", "initials": "S"}, {"family": "Omenn", "given": "Gilbert S", "initials": "GS", "orcid": "0000-0002-8976-6074", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8271c48d1bc6477ca3ba90d05d3854ad.json"}}, {"family": "Deutsch", "given": "Eric W", "initials": "EW", "orcid": "0000-0001-8732-0928", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2463c206245a4dbb979cad9d201d73c4.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/022e140799b6466ea123319c3d70c76e.json"}}], "type": "journal article", "published": "2024-12-06", "journal": {"title": "J. Proteome Res.", "issn": "1535-3907", "volume": "23", "issue": "12", "pages": "5279-5295", "issn-l": "1535-3893"}, "abstract": "Recent improvements in proteomics technologies have fundamentally altered our capacities to characterize human biology. There is an ever-growing interest in using these novel methods for studying the circulating proteome, as blood offers an accessible window into human health. However, every methodological innovation and analytical progress calls for reassessing our existing approaches and routines to ensure that the new data will add value to the greater biomedical research community and avoid previous errors. As representatives of HUPO's Human Plasma Proteome Project (HPPP), we present our 2024 survey of the current progress in our community, including the latest build of the Human Plasma Proteome PeptideAtlas that now comprises 4608 proteins detected in 113 data sets. We then discuss the updates of established proteomics methods, emerging technologies, and investigations of proteoforms, protein networks, extracellualr vesicles, circulating antibodies and microsamples. Finally, we provide a prospective view of using the current and emerging proteomics tools in studies of circulating proteins.", "doi": "10.1021/acs.jproteome.4c00586", "pmid": "39479990", "labels": {"Fredrik Edfors": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC11629384"}], "notes": [], "created": "2026-08-20T08:11:51.037Z", "modified": "2026-09-23T08:43:11.528Z"}, {"entity": "publication", "iuid": "2bec5b85c0034a5584897d8f2f96a21c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/2bec5b85c0034a5584897d8f2f96a21c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/2bec5b85c0034a5584897d8f2f96a21c"}}, "title": "A landscape of X-inactivation during human T cell development.", "authors": [{"family": "Gylemo", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-5253-6737", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/87b7679215e543d285e315e5dc841b9e.json"}}, {"family": "Bensberg", "given": "Maike", "initials": "M", "orcid": "0000-0003-2395-6083", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3fe8907522864854b5d2c87cd8144e73.json"}}, {"family": "Hennings", "given": "Viktoria", "initials": "V"}, {"family": "Lundqvist", "given": "Christina", "initials": "C", "orcid": "0000-0002-2256-4072", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a9603a8805c14393b04222e0fa277d5e.json"}}, {"family": "Camponeschi", "given": "Alessandro", "initials": "A", "orcid": "0000-0002-6472-2438", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/94baec0c542a4f4c991860a1797e212d.json"}}, {"family": "Goldmann", "given": "D\u00f3ra", "initials": "D"}, {"family": "Zhang", "given": "Huan", "initials": "H"}, {"family": "Selimovi\u0107-Pa\u0161i\u0107", "given": "Aida", "initials": "A"}, {"family": "Lentini", "given": "Antonio", "initials": "A", "orcid": "0000-0003-1239-5495", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c5042d3005814ad0a2d1eaeee5d2de3b.json"}}, {"family": "Ekwall", "given": "Olov", "initials": "O", "orcid": "0000-0002-4506-9955", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eab7f16bfd5f42fab025afc23b79d395.json"}}, {"family": "Nestor", "given": "Colm E", "initials": "CE", "orcid": "0000-0001-5853-1769", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/53da1d2e5d714a368bcb61c4001abd0f.json"}}], "type": "journal article", "published": "2024-12-04", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "10527", "issn-l": "2041-1723"}, "abstract": "Females exhibit a more robust immune response to both self-antigens and non-self-antigens than males, resulting in a higher prevalence of autoimmune diseases but more effective responses against infection. Increased expression of X-linked immune genes in female T cells is thought to underlie this enhanced response. Here we isolate thymocytes from pediatric thymi of healthy males (46, XY), females (46, XX), a female with completely skewed X-chromosome inactivation (46, XX, cXCI) and a female with Turner syndrome (45, X0). Using whole exome sequencing, RNA sequencing and DNA methylation data, we present a sex-aware expression profile of T cell development and generate a high-resolution map of escape from X-chromosome inactivation (XCI). Unexpectedly, XCI is transcriptionally and epigenetically stable throughout T cell development, and is independent of expression of XIST, the lncRNA responsible for XCI initiation during early embryonic development. In thymocytes, several genes known to escape XCI are expressed from only one X-chromosome. Additionally, we further reveal that a second X-chromosome is dispensable for T cell development. Our study thus provides a high-resolution map of XCI during human development and suggests a re-evaluation of XCI in sex differences in T cell function.", "doi": "10.1038/s41467-024-54110-7", "pmid": "39632794", "labels": {"Antonio Lentini": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC11618795"}, {"db": "pii", "key": "10.1038/s41467-024-54110-7"}], "notes": [], "created": "2025-03-28T07:03:00.279Z", "modified": "2025-03-28T07:03:00.528Z"}, {"entity": "publication", "iuid": "aa01b1824c8b4ae3809b1d60ee41a333", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/aa01b1824c8b4ae3809b1d60ee41a333.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/aa01b1824c8b4ae3809b1d60ee41a333"}}, "title": "The paradox of predictability provides a bridge between micro- and macroevolution.", "authors": [{"family": "Tsuboi", "given": "Masahito", "initials": "M", "orcid": "0000-0002-0144-2893", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8c8800dd5c384be2bc50cb0fe9fb9299.json"}}, {"family": "Sztepanacz", "given": "Jacqueline", "initials": "J"}, {"family": "De Lisle", "given": "Stephen", "initials": "S", "orcid": "0000-0001-9587-8665", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/27c7578386ea4bea8d797a43e91cdf90.json"}}, {"family": "Voje", "given": "Kjetil L", "initials": "KL", "orcid": "0000-0003-2556-3080", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/66caf8f6c228405eb065b599e6533df2.json"}}, {"family": "Grabowski", "given": "Mark", "initials": "M", "orcid": "0000-0001-7045-9472", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/55d4c151f9c742e6979da1795440091f.json"}}, {"family": "Hopkins", "given": "Melanie J", "initials": "MJ", "orcid": "0000-0002-3580-2172", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/327a6c543c464ee7903455fe30f24139.json"}}, {"family": "Porto", "given": "Arthur", "initials": "A"}, {"family": "Balk", "given": "Meghan", "initials": "M", "orcid": "0000-0003-2699-3066", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/265402a72daf443faa9042db75b1b25a.json"}}, {"family": "Pontarp", "given": "Mikael", "initials": "M"}, {"family": "Rossoni", "given": "Daniela", "initials": "D"}, {"family": "Hildesheim", "given": "Laura S", "initials": "LS", "orcid": "0000-0002-4938-8478", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4e8a91a4dd14f758c540f62d607e884.json"}}, {"family": "Horta-Lacueva", "given": "Quentin J-B", "initials": "QJ", "orcid": "0000-0001-9656-1731", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3b260d75ab0c4b9c95504cbf6062e395.json"}}, {"family": "Hohmann", "given": "Niklas", "initials": "N"}, {"family": "Holstad", "given": "Agnes", "initials": "A", "orcid": "0000-0003-3154-1857", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/311a30f62bea4b26bae0584cca7b36b6.json"}}, {"family": "L\u00fcrig", "given": "Moritz", "initials": "M"}, {"family": "Milocco", "given": "Lisandro", "initials": "L"}, {"family": "Nil\u00e9n", "given": "Sofie", "initials": "S", "orcid": "0009-0002-0996-0182", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b6c1cf4d020f4be1bfea851ad8fd7035.json"}}, {"family": "Passarotto", "given": "Arianna", "initials": "A"}, {"family": "Svensson", "given": "Erik I", "initials": "EI", "orcid": "0000-0001-9006-016X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c9e346763c2b439a8055b1d72f492634.json"}}, {"family": "Villegas", "given": "Cristina", "initials": "C", "orcid": "0000-0002-6402-5288", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/66ceb26d9aa24dc4a6a8a576f79aa08b.json"}}, {"family": "Winslott", "given": "Erica", "initials": "E", "orcid": "0000-0001-6556-2272", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/41454a34cbfd42f4a7043aeb708fa26d.json"}}, {"family": "Liow", "given": "Lee Hsiang", "initials": "LH", "orcid": "0000-0002-3732-6069", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/500a0405f863427f8bddb0b39f6e8705.json"}}, {"family": "Hunt", "given": "Gene", "initials": "G", "orcid": "0000-0001-6430-5020", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ccdd02611f2b4b4dae93f9c64767ed7a.json"}}, {"family": "Love", "given": "Alan C", "initials": "AC", "orcid": "0000-0003-4422-7779", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d51ba04090154290934b5ea737b946ce.json"}}, {"family": "Houle", "given": "David", "initials": "D", "orcid": "0000-0002-8095-3156", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/991b5213c61b447f8c6fca30eee55f40.json"}}], "type": "journal article", "published": "2024-12-02", "journal": {"title": "J Evol Biol", "issn": "1420-9101", "volume": "37", "issue": "12", "pages": "1413-1432", "issn-l": null}, "abstract": "The relationship between the evolutionary dynamics observed in contemporary populations (microevolution) and evolution on timescales of millions of years (macroevolution) has been a topic of considerable debate. Historically, this debate centers on inconsistencies between microevolutionary processes and macroevolutionary patterns. Here, we characterize a striking exception: emerging evidence indicates that standing variation in contemporary populations and macroevolutionary rates of phenotypic divergence is often positively correlated. This apparent consistency between micro- and macroevolution is paradoxical because it contradicts our previous understanding of phenotypic evolution and is so far unexplained. Here, we explore the prospects for bridging evolutionary timescales through an examination of this \"paradox of predictability.\" We begin by explaining why the divergence-variance correlation is a paradox, followed by data analysis to show that the correlation is a general phenomenon across a broad range of temporal scales, from a few generations to tens of millions of years. Then we review complementary approaches from quantitative genetics, comparative morphology, evo-devo, and paleontology to argue that they can help to address the paradox from the shared vantage point of recent work on evolvability. In conclusion, we recommend a methodological orientation that combines different kinds of short-term and long-term data using multiple analytical frameworks in an interdisciplinary research program. Such a program will increase our general understanding of how evolution works within and across timescales.", "doi": "10.1093/jeb/voae103", "pmid": "39208440", "labels": {"DDLS Fellow": null, "Lisandro Milocco": null}, "xrefs": [{"db": "pii", "key": "7745387"}], "notes": [], "created": "2025-11-28T14:28:20.845Z", "modified": "2025-11-28T14:28:59.200Z"}, {"entity": "publication", "iuid": "2721b972cb2e40c5b6f64f2285aec738", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/2721b972cb2e40c5b6f64f2285aec738.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/2721b972cb2e40c5b6f64f2285aec738"}}, "title": "The last of their kind: Is the genus Scutiger (Anura: Megophryidae) a relict element of the paleo-Transhimalaya biota?", "authors": [{"family": "Hofmann", "given": "Sylvia", "initials": "S", "orcid": "0000-0003-0621-9049", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5e89cec6cf1d4923a3e8c142c15040c9.json"}}, {"family": "Podsiadlowski", "given": "Lars", "initials": "L"}, {"family": "Andermann", "given": "Tobias", "initials": "T", "orcid": "0000-0002-0932-1623", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dfff478dfcfc43ddbd40bb1bafbcb0a7.json"}}, {"family": "Matschiner", "given": "Michael", "initials": "M", "orcid": "0000-0003-4741-3884", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2afde3b4ccad4b0d91d9330781efb8be.json"}}, {"family": "Baniya", "given": "Chitra B", "initials": "CB"}, {"family": "Litvinchuk", "given": "Spartak N", "initials": "SN"}, {"family": "Martin", "given": "Sebastian", "initials": "S", "orcid": "0000-0002-0747-7456", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/68ae66fad62c4ebdb028816ec56a4283.json"}}, {"family": "Masroor", "given": "Rafaqat", "initials": "R"}, {"family": "Yang", "given": "Jianhuan", "initials": "J", "orcid": "0000-0002-4497-9615", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/813a309f6b5c46ff9bff0ac129512c48.json"}}, {"family": "Zheng", "given": "Yuchi", "initials": "Y"}, {"family": "Jablonski", "given": "Daniel", "initials": "D"}, {"family": "Schmidt", "given": "Joachim", "initials": "J"}], "type": "journal article", "published": "2024-12-00", "journal": {"title": "Mol. Phylogenet. Evol.", "issn": "1095-9513", "volume": "201", "pages": "108166", "issn-l": "1055-7903"}, "abstract": "The orographic evolution of the Himalaya-Tibet Mountain system continues to be a subject of controversy, leading to considerable uncertainty regarding the environment and surface elevation of the Tibetan Plateau during the Cenozoic era. As many geoscientific (but not paleontological) studies suggest, elevations close to modern heights exist in vast areas of Tibet since at least the late Paleogene, implicating the presence of large-scale alpine environments for more than 30 million years. To explore a recently proposed alternative model that assumes a warm temperate environment across paleo-Tibet, we carried out a phylogeographic survey using genomic analyses of samples covering the range of endemic lazy toads (Scutiger) across the Himalaya-Tibet orogen. We identified two main clades, with several, geographically distinct subclades. The long temporal gap between the stem and crown age of Scutiger may suggest high extinction rates. Diversification within the crown group, depending on the calibration, occurred either from the Mid-Miocene or Late-Miocene and continued until the Holocene. The present-day Himalayan Scutiger fauna could have evolved from lineages that existed on the southern edges of the paleo-Tibetan area (the Transhimalaya = Gangdese Shan), while extant species living on the eastern edge of the Plateau originated probably from the eastern edges of northern parts of the ancestral Tibetan area (Hoh Xil, Tanggula Shan). Based on the Mid-Miocene divergence time estimation and ancestral area reconstruction, we propose that uplift-associated aridification of a warm temperate Miocene-Tibet, coupled with high extirpation rates of ancestral populations, and species range shifts along drainage systems and epigenetic transverse valleys of the rising mountains, is a plausible scenario explaining the phylogenetic structure of Scutiger. This hypothesis aligns with the fossil record but conflicts with geoscientific concepts of high elevated Tibetan Plateau since the late Paleogene. Considering a Late-Miocene/Pliocene divergence time, an alternative scenario of dispersal from SE Asia into the East, Central, and West Himalaya cannot be excluded, although essential evolutionary and biogeographic aspects remain unresolved within this model.", "doi": "10.1016/j.ympev.2024.108166", "pmid": "39127262", "labels": {"Tobias Andermann": null, "DDLS Fellow": null}, "xrefs": [{"db": "pii", "key": "S1055-7903(24)00158-1"}], "notes": [], "created": "2025-03-18T16:05:23.392Z", "modified": "2025-04-07T06:59:26.098Z"}, {"entity": "publication", "iuid": "5e29e009d86b4cb781d38abaee53167a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5e29e009d86b4cb781d38abaee53167a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5e29e009d86b4cb781d38abaee53167a"}}, "title": "New developments for the Quest for Orthologs benchmark service.", "authors": [{"family": "Altenhoff", "given": "Adrian", "initials": "A"}, {"family": "Nevers", "given": "Yannis", "initials": "Y", "orcid": "0000-0002-8604-2943", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7e5e2aea9cc2433c880a3d650d4d0d5b.json"}}, {"family": "Tran", "given": "Vinh", "initials": "V"}, {"family": "Jyothi", "given": "Dushyanth", "initials": "D"}, {"family": "Martin", "given": "Maria", "initials": "M"}, {"family": "Cosentino", "given": "Salvatore", "initials": "S"}, {"family": "Majidian", "given": "Sina", "initials": "S", "orcid": "0000-0001-5345-6982", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a14f17e8c2dc470dae5250c36d32cb27.json"}}, {"family": "Marcet-Houben", "given": "Marina", "initials": "M"}, {"family": "Fuentes-Palacios", "given": "Diego", "initials": "D"}, {"family": "Persson", "given": "Emma", "initials": "E"}, {"family": "Walsh", "given": "Thomas", "initials": "T"}, {"family": "Lecompte", "given": "Odile", "initials": "O"}, {"family": "Gabald\u00f3n", "given": "Toni", "initials": "T"}, {"family": "Kelly", "given": "Steven", "initials": "S"}, {"family": "Hu", "given": "Yanhui", "initials": "Y", "orcid": "0000-0003-1494-1402", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d048ac84bf934c9d87774c6cab7430c6.json"}}, {"family": "Iwasaki", "given": "Wataru", "initials": "W"}, {"family": "Capella-Gutierrez", "given": "Salvador", "initials": "S", "orcid": "0000-0002-0309-604X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c76a6ff4986b42f58a0be702993eef42.json"}}, {"family": "Dessimoz", "given": "Christophe", "initials": "C", "orcid": "0000-0002-2170-853X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8d9dc970f3da45a4a46ecfdf4ab0893f.json"}}, {"family": "Thomas", "given": "Paul D", "initials": "PD", "orcid": "0000-0002-9074-3507", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4af1f8a10ced487196829d162e22d314.json"}}, {"family": "Ebersberger", "given": "Ingo", "initials": "I", "orcid": "0000-0001-8187-9253", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/946c40da21e441d196dd8b88ea126df0.json"}}, {"family": "Sonnhammer", "given": "Erik", "initials": "E", "orcid": "0000-0002-9015-5588", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8c4fb5f5a50a4dbb91bbea3cc6861ffa.json"}}], "type": "journal article", "published": "2024-12-00", "journal": {"title": "NAR Genomics and Bioinformatics", "issn": "2631-9268", "volume": "6", "issue": "4", "pages": "lqae167", "issn-l": null}, "abstract": "The Quest for Orthologs (QfO) orthology benchmark service (https://orthology.benchmarkservice.org) hosts a wide range of standardized benchmarks for orthology inference evaluation. It is supported and maintained by the QfO consortium, and is used to gather ortholog predictions and to examine strengths and weaknesses of newly developed and existing orthology inference methods. The web server allows different inference methods to be compared in a standardized way using the same proteome data. The benchmark results are useful for developing new methods and can help researchers to guide their choice of orthology method for applications in comparative genomics and phylogenetic analysis. We here present a new release of the Orthology Benchmark Service with a new benchmark based on feature architecture similarity as well as updated reference proteomes. We further provide a meta-analysis of the public predictions from 18 different orthology assignment methods to reveal how they relate in terms of ortholog predictions and benchmark performance. These results can guide users of orthologs to the best suited method for their purpose.", "doi": "10.1093/nargab/lqae167", "pmid": "39664814", "labels": {"Sina Majidian": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC11632614"}, {"db": "pii", "key": "lqae167"}], "notes": [], "created": "2026-08-20T09:43:00.453Z", "modified": "2026-09-23T11:26:36.697Z"}, {"entity": "publication", "iuid": "b1dbcd43ab2144a7b770d84866dad8d5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b1dbcd43ab2144a7b770d84866dad8d5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b1dbcd43ab2144a7b770d84866dad8d5"}}, "title": "Early detection of pancreatic cancer: Study design and analytical considerations in biomarker discovery and early phase validation studies.", "authors": [{"family": "Smith", "given": "Lynette M", "initials": "LM"}, {"family": "Mahoney", "given": "Douglas W", "initials": "DW"}, {"family": "Bamlet", "given": "William R", "initials": "WR"}, {"family": "Yu", "given": "Fang", "initials": "F"}, {"family": "Liu", "given": "Suyu", "initials": "S"}, {"family": "Goggins", "given": "Michael G", "initials": "MG"}, {"family": "Darabi", "given": "Sourat", "initials": "S"}, {"family": "Majumder", "given": "Shounak", "initials": "S"}, {"family": "Wang", "given": "Qiao-Li", "initials": "QL"}, {"family": "Cot\u00e9", "given": "Gregory A", "initials": "GA"}, {"family": "Demeure", "given": "Michael J", "initials": "MJ"}, {"family": "Zhang", "given": "Zhen", "initials": "Z"}, {"family": "Srivastava", "given": "Sudhir", "initials": "S"}, {"family": "Chawla", "given": "Akhil", "initials": "A"}, {"family": "Izmirlian", "given": "Grant", "initials": "G"}, {"family": "Olson", "given": "Janet E", "initials": "JE"}, {"family": "Wolpin", "given": "Brian M", "initials": "BM"}, {"family": "Genkinger", "given": "Jeanine M", "initials": "JM"}, {"family": "Zaret", "given": "Kenneth S", "initials": "KS"}, {"family": "Brand", "given": "Randall", "initials": "R"}, {"family": "Koay", "given": "Eugene J", "initials": "EJ"}, {"family": "Oberg", "given": "Ann L", "initials": "AL"}], "type": "journal article", "published": "2024-12-00", "journal": {"title": "Pancreatology", "issn": "1424-3911", "volume": "24", "issue": "8", "pages": "1265-1279", "issn-l": null}, "abstract": "Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal disease that is challenging to detect at an early stage. Biomarkers are needed that can detect PDAC early in the course of disease when interventions lead to the best outcomes. We highlight study design and statistical considerations that inform pancreatic cancer early detection biomarker evaluation.\n\nWe describe experimental design strategies in this setting useful for streamlining biomarker evaluation at each Early Detection Research Network (EDRN) phase of biomarker development. We break the early EDRN phases into sub-phases, proposing objectives, study design strategies, and biomarker performance benchmarks.\n\nThe goal of early detection in populations at high-risk of PDAC is described. Evaluating biomarker behavior in patients under surveillance without disease can winnow candidate biomarkers. Potential resources for biomarker validation studies are described.\n\nMultisite and multidisciplinary collaboration can facilitate study design strategies in this lethal but low incidence disease and streamline the path from biomarker discovery to clinical use. Improvements in analytical and experimental design methods could help accelerate biomarker evaluation through the phases of biomarker development.", "doi": "10.1016/j.pan.2024.10.012", "pmid": "39516175", "labels": {"DDLS Fellow": null, "Qiaoli Wang": null}, "xrefs": [{"db": "mid", "key": "NIHMS2034711"}, {"db": "pmc", "key": "PMC11780679"}, {"db": "pii", "key": "S1424-3903(24)00784-1"}], "notes": [], "created": "2025-11-28T12:24:41.531Z", "modified": "2025-11-28T12:24:41.573Z"}, {"entity": "publication", "iuid": "1840a8a90ea843e8874a0033568988d2", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1840a8a90ea843e8874a0033568988d2.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1840a8a90ea843e8874a0033568988d2"}}, "title": "Bridging the gap: Integrating cutting-edge techniques into biological imaging with deepImageJ.", "authors": [{"family": "Fuster-Barcel\u00f3", "given": "Caterina", "initials": "C", "orcid": "0000-0002-4784-6957", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/881d36fa227445c9b381a03990b5ed49.json"}}, {"family": "Garc\u00eda-L\u00f3pez-de-Haro", "given": "Carlos", "initials": "C"}, {"family": "G\u00f3mez-de-Mariscal", "given": "Estibaliz", "initials": "E"}, {"family": "Ouyang", "given": "Wei", "initials": "W"}, {"family": "Olivo-Marin", "given": "Jean-Christophe", "initials": "JC", "orcid": "0000-0001-6796-0696", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f2558d56edd54d0e87904930c8ec54f6.json"}}, {"family": "Sage", "given": "Daniel", "initials": "D", "orcid": "0000-0002-1150-1623", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/919b0180005444d88757db8e63b80d83.json"}}, {"family": "Mu\u00f1oz-Barrutia", "given": "Arrate", "initials": "A", "orcid": "0000-0002-1573-1661", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1f71dcceb0284105a7033f2ed195b9c1.json"}}], "type": "journal article", "published": "2024-11-22", "journal": {"title": "Biol Imaging", "issn": "2633-903X", "volume": "4", "pages": "e14", "issn-l": null}, "abstract": "This manuscript showcases the latest advancements in deepImageJ, a pivotal Fiji/ImageJ plugin for bioimage analysis in life sciences. The plugin, known for its user-friendly interface, facilitates the application of diverse pre-trained convolutional neural networks to custom data. The manuscript demonstrates several deepImageJ capabilities, particularly in deploying complex pipelines, three-dimensional (3D) image analysis, and processing large images. A key development is the integration of the Java Deep Learning Library, expanding deepImageJ's compatibility with various deep learning (DL) frameworks, including TensorFlow, PyTorch, and ONNX. This allows for running multiple engines within a single Fiji/ImageJ instance, streamlining complex bioimage analysis workflows. The manuscript details three case studies to demonstrate these capabilities. The first case study explores integrated image-to-image translation followed by nuclei segmentation. The second case study focuses on 3D nuclei segmentation. The third case study showcases large image volume segmentation and compatibility with the BioImage Model Zoo. These use cases underscore deepImageJ's versatility and power to make advanced DLmore accessible and efficient for bioimage analysis. The new developments within deepImageJ seek to provide a more flexible and enriched user-friendly framework to enable next-generation image processing in life science.", "doi": "10.1017/S2633903X24000114", "pmid": "39776608", "labels": {"DDLS Fellow": "", "Wei Ouyang": ""}, "xrefs": [{"db": "pmc", "key": "PMC11704127"}, {"db": "pii", "key": "S2633903X24000114"}], "notes": [], "created": "2026-08-20T08:08:11.844Z", "modified": "2026-09-23T13:22:20.906Z"}, {"entity": "publication", "iuid": "b64612886bb34b5c8ecf3ea6d4152dc7", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b64612886bb34b5c8ecf3ea6d4152dc7.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b64612886bb34b5c8ecf3ea6d4152dc7"}}, "title": "A Phylogenomic Analysis of Genipa (Rubiaceae) Using Target Sequence Capture Data", "authors": [{"family": "Ridley", "given": "Rhonda", "initials": "R"}, {"family": "Persson", "given": "Claes", "initials": "C"}, {"family": "Oxelman", "given": "Bengt", "initials": "B"}, {"family": "Andermann", "given": "Tobias", "initials": "T", "orcid": "0000-0002-0932-1623", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dfff478dfcfc43ddbd40bb1bafbcb0a7.json"}}, {"family": "Bacon", "given": "Christine D", "initials": "CD"}], "type": "journal-article", "published": "2024-11-19", "journal": {"title": "Systematic Botany", "issn": "0363-6445", "volume": "49", "issue": "3", "pages": "617-625", "issn-l": null}, "abstract": null, "doi": "10.1600/036364424x17267811220489", "pmid": null, "labels": {"Tobias Andermann": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2025-03-18T16:05:19.676Z", "modified": "2026-09-23T15:43:04.202Z"}, {"entity": "publication", "iuid": "f02fcde08768426d99f8dcf240ea146e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f02fcde08768426d99f8dcf240ea146e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f02fcde08768426d99f8dcf240ea146e"}}, "title": "Enterotoxigenic Escherichia coli in Blantyre, Malawi.", "authors": [{"family": "Ashton", "given": "Philip M", "initials": "PM", "orcid": "0000-0002-1545-9661", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/69650b51cc0f499a852dd9f7b4462173.json"}}, {"family": "Katuah", "given": "Zefaniah Joel", "initials": "ZJ"}, {"family": "Botomani", "given": "Arnold", "initials": "A"}, {"family": "Kutambe", "given": "Belson M", "initials": "BM"}, {"family": "Cunliffe", "given": "Nigel A", "initials": "NA"}, {"family": "von Mentzer", "given": "Astrid", "initials": "A"}, {"family": "Msefula", "given": "Chisomo", "initials": "C"}, {"family": "Jere", "given": "Khuzwayo C", "initials": "KC"}], "type": "journal article", "published": "2024-11-18", "journal": {"title": "Access Microbiol", "issn": "2516-8290", "volume": "6", "issue": "11", "issn-l": null}, "abstract": "We announce the deposition of the first two enterotoxigenic Escherichia coli (ETEC) genomes from Malawi. They were isolated from the faeces of asymptomatically infected children obtained in 2014. Both genomes encode the porcine variant of the heat-labile toxin and no known ETEC colonization factors.", "doi": "10.1099/acmi.0.000885.v3", "pmid": "39559263", "labels": {"Astrid von Mentzer": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC11572489"}, {"db": "pii", "key": "000885.v3"}], "notes": [], "created": "2025-12-02T15:47:04.071Z", "modified": "2025-12-02T15:47:04.126Z"}, {"entity": "publication", "iuid": "cefda4bf897a46c995c7eb0eee6f05cf", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/cefda4bf897a46c995c7eb0eee6f05cf.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/cefda4bf897a46c995c7eb0eee6f05cf"}}, "title": "JAK2-mutant clonal hematopoiesis is associated with venous thromboembolism.", "authors": [{"family": "Zon", "given": "Rebecca L", "initials": "RL", "orcid": "0000-0002-6980-5996", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d4cf161e73c148f1bac9d32678208869.json"}}, {"family": "Sekar", "given": "Aswin", "initials": "A", "orcid": "0000-0003-0406-0935", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2cff21c3699340a3a10c13447b59c7ff.json"}}, {"family": "Clapham", "given": "Katharine", "initials": "K", "orcid": "0000-0003-3659-4755", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/375b74fa831a497a9f68bfb85acb0251.json"}}, {"family": "Oren", "given": "Ohad", "initials": "O", "orcid": "0000-0003-4700-8037", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f5260704910442c7adca85f434355dae.json"}}, {"family": "Niroula", "given": "Abhishek", "initials": "A", "orcid": "0000-0002-5904-0635", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/05df7afc7a494ba5af8a378e5ffa53f0.json"}}, {"family": "Bick", "given": "Alexander G", "initials": "AG", "orcid": "0000-0001-5824-9595", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d2da5a35a4984921b19dfafe64cea2de.json"}}, {"family": "Gibson", "given": "Christopher J", "initials": "CJ", "orcid": "0000-0002-3700-5310", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/71ce9f64755e483496f8c28a76a2a1ff.json"}}, {"family": "Griffin", "given": "Gabriel", "initials": "G", "orcid": "0000-0002-4042-6757", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f6153204e19d4660b640dc4467605973.json"}}, {"family": "Uddin", "given": "Md Mesbah", "initials": "MM", "orcid": "0000-0003-1846-0411", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/42f1ac7010c34ba997a3fd9e56c6a56a.json"}}, {"family": "Neuberg", "given": "Donna", "initials": "D", "orcid": "0000-0003-2566-3145", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/70b2f9e23251469987cbe7b42d38dc58.json"}}, {"family": "Natarajan", "given": "Pradeep", "initials": "P", "orcid": "0000-0001-8402-7435", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fe8bd48c61c047cd8e61c35d9e9ac650.json"}}, {"family": "Ebert", "given": "Benjamin L", "initials": "BL", "orcid": "0000-0003-0197-5451", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56e4f1c53a4348e2b0ceb44a38850a17.json"}}], "type": "journal article", "published": "2024-11-14", "journal": {"title": "Blood", "issn": "1528-0020", "volume": "144", "issue": "20", "pages": "2149-2154", "issn-l": "0006-4971"}, "abstract": "Venous thromboembolism (VTE) is common among older individuals, but provoking factors are not identified in many cases. Patients with myeloid malignancies, especially myeloproliferative neoplasms (MPNs), are at increased risk for venous thrombosis. Clonal hematopoiesis of indeterminate potential (CHIP), a precursor state to myeloid malignancies, is common among older individuals and may similarly predispose to venous thrombosis. We evaluated overall and genotype-specific associations between CHIP and prevalent and incident VTE in >400 000 samples from the UK Biobank. CHIP was modestly associated with incident VTE with a hazard ratio (HR) of 1.17 (95% confidence interval [CI], 1.09-1.3; P = .002) but was not significantly associated with prevalent VTE with an odds ratio (OR) of 1.02 (95% CI, 0.81-1.23; P = .81). TET2-mutant CHIP was associated with incident VTE with a HR of 1.33 (95% CI, 1.05-1.69; P = .02). JAK2 mutations were highly associated with both prevalent and incident VTE risk, with an OR of 6.58 (95% CI, 2.65-16.29; P = 4.7 \u00d7 10-5) and a HR of 4.2 (95% CI, 2.18-8.08; P = 1.7 \u00d7 10-5), respectively, consistent with the thrombophilia associated with JAK2-mutant MPN. The association between JAK2-mutant CHIP and VTE remained significant after excluding potential undiagnosed MPN based on laboratory parameters. JAK2-mutant CHIP was more strongly associated with VTE but was less common than heterozygous factor V Leiden and heterozygous prothrombin gene mutation. These results indicate that most individuals with CHIP do not have an altered risk of thrombosis, but individuals with JAK2-mutant CHIP have a significantly elevated risk of VTE.", "doi": "10.1182/blood.2024024187", "pmid": "39102652", "labels": {"DDLS Fellow": "", "Abhishek Niroula": ""}, "xrefs": [{"db": "pmc", "key": "PMC11600088"}, {"db": "pii", "key": "517042"}], "notes": [], "created": "2025-03-18T15:49:49.285Z", "modified": "2026-09-23T08:44:19.623Z"}, {"entity": "publication", "iuid": "01ddbbc30bef43d4bf0950f19dda70fc", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/01ddbbc30bef43d4bf0950f19dda70fc.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/01ddbbc30bef43d4bf0950f19dda70fc"}}, "title": "Colchicine prevents accelerated atherosclerosis in TET2-mutant clonal haematopoiesis.", "authors": [{"family": "Zuriaga", "given": "Mar\u00eda A", "initials": "MA", "orcid": "0000-0003-0422-2965", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e6d822a55f86424880dab59ade3a52b7.json"}}, {"family": "Yu", "given": "Zhi", "initials": "Z", "orcid": "0000-0003-4810-3474", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4b810efe02244148b701c1468543ea3.json"}}, {"family": "Matesanz", "given": "Nuria", "initials": "N"}, {"family": "Truong", "given": "Buu", "initials": "B"}, {"family": "Ramos-Neble", "given": "Beatriz L", "initials": "BL"}, {"family": "Asensio-L\u00f3pez", "given": "Mari C", "initials": "MC"}, {"family": "Uddin", "given": "Md Mesbah", "initials": "MM"}, {"family": "Nakao", "given": "Tetsushi", "initials": "T"}, {"family": "Niroula", "given": "Abhishek", "initials": "A"}, {"family": "Zorita", "given": "Virginia", "initials": "V"}, {"family": "Amor\u00f3s-P\u00e9rez", "given": "Marta", "initials": "M"}, {"family": "Moro", "given": "Rosa", "initials": "R"}, {"family": "Ebert", "given": "Benjamin L", "initials": "BL"}, {"family": "Honigberg", "given": "Michael C", "initials": "MC"}, {"family": "Pascual-Figal", "given": "Domingo", "initials": "D"}, {"family": "Natarajan", "given": "Pradeep", "initials": "P", "orcid": "0000-0001-8402-7435", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fe8bd48c61c047cd8e61c35d9e9ac650.json"}}, {"family": "Fuster", "given": "Jos\u00e9 J", "initials": "JJ", "orcid": "0000-0002-5970-629X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6f051a754bdc49f0b7b6b23893d9600d.json"}}], "type": "journal article", "published": "2024-11-14", "journal": {"title": "Eur. Heart J.", "issn": "1522-9645", "volume": "45", "issue": "43", "pages": "4601-4615", "issn-l": "0195-668X"}, "abstract": "Somatic mutations in the TET2 gene that lead to clonal haematopoiesis (CH) are associated with accelerated atherosclerosis development in mice and a higher risk of atherosclerotic disease in humans. Mechanistically, these observations have been linked to exacerbated vascular inflammation. This study aimed to evaluate whether colchicine, a widely available and inexpensive anti-inflammatory drug, prevents the accelerated atherosclerosis associated with TET2-mutant CH.\n\nIn mice, TET2-mutant CH was modelled using bone marrow transplantations in atherosclerosis-prone Ldlr-/- mice. Haematopoietic chimeras carrying initially 10% Tet2-/- haematopoietic cells were fed a high-cholesterol diet and treated with colchicine or placebo. In humans, whole-exome sequencing data and clinical data from 37 181 participants in the Mass General Brigham Biobank and 437 236 participants in the UK Biobank were analysed to examine the potential modifying effect of colchicine prescription on the relationship between CH and myocardial infarction.\n\nColchicine prevented accelerated atherosclerosis development in the mouse model of TET2-mutant CH, in parallel with suppression of interleukin-1\u03b2 overproduction in conditions of TET2 loss of function. In humans, patients who were prescribed colchicine had attenuated associations between TET2 mutations and myocardial infarction. This interaction was not observed for other mutated genes.\n\nThese results highlight the potential value of colchicine to mitigate the higher cardiovascular risk of carriers of somatic TET2 mutations in blood cells. These observations set the basis for the development of clinical trials that evaluate the efficacy of precision medicine approaches tailored to the effects of specific mutations linked to CH.", "doi": "10.1093/eurheartj/ehae546", "pmid": "39212933", "labels": {"Abhishek Niroula": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC11560281"}, {"db": "pii", "key": "7742978"}], "notes": [], "created": "2025-03-18T15:49:50.895Z", "modified": "2026-09-23T08:28:55.463Z"}, {"entity": "publication", "iuid": "59c25b7e2d9f4e3c9fcae99b03f3e1f4", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/59c25b7e2d9f4e3c9fcae99b03f3e1f4.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/59c25b7e2d9f4e3c9fcae99b03f3e1f4"}}, "title": "Annotated genome sequences of Salmonella Haifa, Salmonella Bangkok, and Salmonella Reading, isolated from chicken meat in South Africa.", "authors": [{"family": "Mathole", "given": "Masenyabu", "initials": "M", "orcid": "0009-0004-1795-9434", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/abc9cb36374d4a7db5163ce252543ec8.json"}}, {"family": "Carroll", "given": "Laura", "initials": "L"}, {"family": "Khabo-Mmekoa", "given": "Collette", "initials": "C"}, {"family": "Mabogoane", "given": "Nomsa", "initials": "N"}, {"family": "Matle", "given": "Itumeleng", "initials": "I", "orcid": "0000-0002-1495-357X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dd13d91d769e49738063ce04919c589f.json"}}], "type": "journal article", "published": "2024-11-12", "journal": {"title": "Microbiol Resour Announc", "issn": "2576-098X", "volume": "13", "issue": "11", "pages": "e0028424", "issn-l": null}, "abstract": "This paper presents the annotated genomes of Salmonella Haifa, Salmonella Bangkok, and Salmonella Reading, which are uncommonly isolated from meat in South Africa. Despite their rarity in South Africa, these serotypes have been linked to several high-profile outbreaks in other parts of the world.", "doi": "10.1128/mra.00284-24", "pmid": "39382302", "labels": {"Laura Carroll": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC11556139"}], "notes": [], "created": "2025-03-18T17:32:21.635Z", "modified": "2026-09-23T13:22:09.586Z"}, {"entity": "publication", "iuid": "94a2df5cd41942ef97efe84a5bd7651f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/94a2df5cd41942ef97efe84a5bd7651f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/94a2df5cd41942ef97efe84a5bd7651f"}}, "title": "Building pangenome graphs.", "authors": [{"family": "Garrison", "given": "Erik", "initials": "E", "orcid": "0000-0003-3821-631X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bcc0030d6ede4d6692ff94cbda4a976f.json"}}, {"family": "Guarracino", "given": "Andrea", "initials": "A", "orcid": "0000-0001-9744-131X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e3880127b26141e3ba9c9bb053417d46.json"}}, {"family": "Heumos", "given": "Simon", "initials": "S", "orcid": "0000-0003-3326-817X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ad244d3f8841444abfc67853bd403e18.json"}}, {"family": "Villani", "given": "Flavia", "initials": "F", "orcid": "0000-0003-3633-0610", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/307974836f164367befa9d1ab46be71d.json"}}, {"family": "Bao", "given": "Zhigui", "initials": "Z", "orcid": "0000-0003-3601-460X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/41ce9c6be70e4e09b284c71d17b5fba1.json"}}, {"family": "Tattini", "given": "Lorenzo", "initials": "L"}, {"family": "Hagmann", "given": "J\u00f6rg", "initials": "J", "orcid": "0000-0002-7232-3103", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f6ff97238b604758833d438decae8a53.json"}}, {"family": "Vorbrugg", "given": "Sebastian", "initials": "S"}, {"family": "Marco-Sola", "given": "Santiago", "initials": "S", "orcid": "0000-0001-7951-3914", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7374a893465044fc8da560f9295d3867.json"}}, {"family": "Kubica", "given": "Christian", "initials": "C"}, {"family": "Ashbrook", "given": "David G", "initials": "DG", "orcid": "0000-0002-7397-8910", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1b61127e078144d0835d40d797a1088c.json"}}, {"family": "Thorell", "given": "Kaisa", "initials": "K", "orcid": "0000-0002-4447-8968", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/789d4029a5c14d3c83df7c47b3b514c7.json"}}, {"family": "Rusholme-Pilcher", "given": "Rachel L", "initials": "RL", "orcid": "0000-0003-0000-0038", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/75d7f80346a54b03b6a979d706df7aa7.json"}}, {"family": "Liti", "given": "Gianni", "initials": "G"}, {"family": "Rudbeck", "given": "Emilio", "initials": "E"}, {"family": "Golicz", "given": "Agnieszka A", "initials": "AA", "orcid": "0000-0002-9711-4826", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/00e6ce757691402eab951b2d4f3456af.json"}}, {"family": "Nahnsen", "given": "Sven", "initials": "S", "orcid": "0000-0002-4375-0691", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/822afa4ff0b041bcb7743d15d23b0c22.json"}}, {"family": "Yang", "given": "Zuyu", "initials": "Z", "orcid": "0000-0002-0651-848X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ff490cb664cb423a9df6e73fd4d0af3c.json"}}, {"family": "Mwaniki", "given": "Moses Njagi", "initials": "MN"}, {"family": "Nobrega", "given": "Franklin L", "initials": "FL", "orcid": "0000-0002-8238-1083", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e0e4489785ca4c789e5c3b026f7cf4d1.json"}}, {"family": "Wu", "given": "Yi", "initials": "Y"}, {"family": "Chen", "given": "Hao", "initials": "H"}, {"family": "de Ligt", "given": "Joep", "initials": "J", "orcid": "0000-0002-0348-419X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/119cc9aa12a44667a5bbdf2a711c3a63.json"}}, {"family": "Sudmant", "given": "Peter H", "initials": "PH", "orcid": "0000-0002-9573-8248", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/51dce83846184d3697a56d8d6bb06db7.json"}}, {"family": "Huang", "given": "Sanwen", "initials": "S", "orcid": "0000-0002-8547-5309", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3234328fbd4741638d4464e2de00f72a.json"}}, {"family": "Weigel", "given": "Detlef", "initials": "D", "orcid": "0000-0002-2114-7963", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/869682094103499d9e61cb48d8fda862.json"}}, {"family": "Soranzo", "given": "Nicole", "initials": "N"}, {"family": "Colonna", "given": "Vincenza", "initials": "V", "orcid": "0000-0002-3966-0474", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/817771f5031644c3b995c37be8c112ac.json"}}, {"family": "Williams", "given": "Robert W", "initials": "RW"}, {"family": "Prins", "given": "Pjotr", "initials": "P", "orcid": "0000-0002-8021-9162", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/be784d1883984d6bbf587a060417c1ed.json"}}], "type": "journal article", "published": "2024-11-00", "journal": {"title": "Nat. Methods", "issn": "1548-7105", "issn-l": "1548-7091", "volume": "21", "issue": "11", "pages": "2008-2012"}, "abstract": "Pangenome graphs can represent all variation between multiple reference genomes, but current approaches to build them exclude complex sequences or are based upon a single reference. In response, we developed the PanGenome Graph Builder, a pipeline for constructing pangenome graphs without bias or exclusion. The PanGenome Graph Builder uses all-to-all alignments to build a variation graph in which we can identify variation, measure conservation, detect recombination events and infer phylogenetic relationships.", "doi": "10.1038/s41592-024-02430-3", "pmid": "39433878", "labels": {"Kaisa Thorell": null, "DDLS Fellow": null}, "xrefs": [{"db": "pii", "key": "10.1038/s41592-024-02430-3"}], "notes": [], "created": "2025-03-19T17:07:47.110Z", "modified": "2025-03-21T13:34:53.012Z"}, {"entity": "publication", "iuid": "3e55948203104658ab74310562478c6d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3e55948203104658ab74310562478c6d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3e55948203104658ab74310562478c6d"}}, "title": "An ancient ecospecies of Helicobacter pylori.", "authors": [{"family": "Tourrette", "given": "Elise", "initials": "E", "orcid": "0000-0002-0822-5330", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8a2633bd0cd04e9981429f449e3d3248.json"}}, {"family": "Torres", "given": "Roberto C", "initials": "RC", "orcid": "0000-0001-6990-9114", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7ba4620c612a481989a81983eb9f405a.json"}}, {"family": "Svensson", "given": "Sarah L", "initials": "SL", "orcid": "0000-0002-3183-6084", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2b41514d94c442c98e9e8b4e4ce98242.json"}}, {"family": "Matsumoto", "given": "Takashi", "initials": "T", "orcid": "0000-0002-6899-1686", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f06a8462b1034c5ab2114555cc6ccae0.json"}}, {"family": "Miftahussurur", "given": "Muhammad", "initials": "M", "orcid": "0000-0003-1415-6033", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0cd1c83607a44aa786bb746860e24c0f.json"}}, {"family": "Fauzia", "given": "Kartika Afrida", "initials": "KA"}, {"family": "Alfaray", "given": "Ricky Indra", "initials": "RI", "orcid": "0000-0001-7721-9455", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7e1b6b6e420d40f4b386f23f36733514.json"}}, {"family": "Vilaichone", "given": "Ratha-Korn", "initials": "R"}, {"family": "Tuan", "given": "Vo Phuoc", "initials": "VP"}, {"family": "Helicobacter Genomics Consortium", "given": "", "initials": ""}, {"family": "Wang", "given": "Difei", "initials": "D", "orcid": "0000-0003-4088-3859", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/47af1e6daf8641d089d6def9b137e677.json"}}, {"family": "Yadegar", "given": "Abbas", "initials": "A", "orcid": "0000-0002-2135-7581", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ef1ab6bffbb64bdd828d0491d9f16136.json"}}, {"family": "Olsson", "given": "Lisa M", "initials": "LM", "orcid": "0000-0001-9730-1915", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ebc33ee3a5840c8b3c71ce912057c39.json"}}, {"family": "Zhou", "given": "Zhemin", "initials": "Z", "orcid": "0000-0001-9783-0366", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f2659842e6f74c4187b1d6a032d7b6d8.json"}}, {"family": "Yamaoka", "given": "Yoshio", "initials": "Y", "orcid": "0000-0002-1222-5819", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a710e567386a47d283402e7f05d8a500.json"}}, {"family": "Thorell", "given": "Kaisa", "initials": "K", "orcid": "0000-0002-4447-8968", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/789d4029a5c14d3c83df7c47b3b514c7.json"}}, {"family": "Falush", "given": "Daniel", "initials": "D", "orcid": "0000-0002-2956-0795", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eb315b1088084cf59f2a0ab3767f03b2.json"}}], "type": "journal article", "published": "2024-11-00", "journal": {"title": "Nature", "issn": "1476-4687", "issn-l": "0028-0836", "volume": "635", "issue": "8037", "pages": "178-185"}, "abstract": "Helicobacter pylori disturbs the stomach lining during long-term colonization of its human host, with sequelae including ulcers and gastric cancer1,2. Numerous H. pylori virulence factors have been identified, showing extensive geographic variation1. Here we identify a 'Hardy' ecospecies of H. pylori that shares the ancestry of 'Ubiquitous' H. pylori from the same region in most of the genome but has nearly fixed single-nucleotide polymorphism differences in 100 genes, many of which encode outer membrane proteins and host interaction factors. Most Hardy strains have a second urease, which uses iron as a cofactor rather than nickel3, and two additional copies of the vacuolating cytotoxin VacA. Hardy strains currently have a limited distribution, including in Indigenous populations in Siberia and the Americas and in lineages that have jumped from humans to other mammals. Analysis of polymorphism data implies that Hardy and Ubiquitous coexisted in the stomachs of modern humans since before we left Africa and that both were dispersed around the world by our migrations. Our results also show that highly distinct adaptive strategies can arise and be maintained stably within bacterial populations, even in the presence of continuous genetic exchange between strains.", "doi": "10.1038/s41586-024-07991-z", "pmid": "39415013", "labels": {"Kaisa Thorell": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC11541087"}, {"db": "pii", "key": "10.1038/s41586-024-07991-z"}], "notes": [], "created": "2025-03-19T17:07:43.934Z", "modified": "2025-03-21T13:35:08.471Z"}, {"entity": "publication", "iuid": "7d17c7de81cf4c79af7dcb60c8a3d885", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/7d17c7de81cf4c79af7dcb60c8a3d885.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/7d17c7de81cf4c79af7dcb60c8a3d885"}}, "title": "Fish are poor sentinels for surveillance of riverine AMR", "authors": [{"family": "Tskhay", "given": "Faina", "initials": "F", "orcid": "0000-0001-8700-3279", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/66867423459544e7a72b0a9090a46cee.json"}}, {"family": "K\u00f6bsch", "given": "Christoph", "initials": "C", "orcid": "0000-0002-9748-2039", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ebe319eddda54827bf9ac3970e91a733.json"}}, {"family": "Elena", "given": "Alan X", "initials": "AX", "orcid": "0000-0001-5372-0923", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/005e2b93413c4627a222eb7a5ef66e04.json"}}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J", "orcid": "0000-0002-6528-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c666068e9d34939b0252a627007cec7.json"}}, {"family": "Berendonk", "given": "Thomas U", "initials": "TU", "orcid": "0000-0002-9301-1803", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c66286f83a8430f954fbc5c52db10c5.json"}}, {"family": "Kl\u00fcmper", "given": "Uli", "initials": "U", "orcid": "0000-0002-4169-6548", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7d8605cdbfc14403b607a3b5ace7249d.json"}}], "type": "posted-content", "published": "2024-10-22", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2024.10.22.619632", "pmid": null, "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [], "notes": [], "created": "2024-11-18T11:45:27.075Z", "modified": "2025-12-04T16:53:36.360Z"}, {"entity": "publication", "iuid": "983f5cce99e346089c9358266a353b6c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/983f5cce99e346089c9358266a353b6c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/983f5cce99e346089c9358266a353b6c"}}, "title": "ESPressoscope: A small and powerful approach for in situ microscopy.", "authors": [{"family": "Li", "given": "Ethan", "initials": "E", "orcid": "0000-0002-3041-0428", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d18c3583619e4e5e8d2f7a4596ff557a.json"}}, {"family": "Saggiomo", "given": "Vittorio", "initials": "V"}, {"family": "Ouyang", "given": "Wei", "initials": "W"}, {"family": "Prakash", "given": "Manu", "initials": "M", "orcid": "0000-0002-8046-8388", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ffb31ee2e27483b9303ce73a9e6f3d1.json"}}, {"family": "Diederich", "given": "Benedict", "initials": "B", "orcid": "0000-0003-0453-6286", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/25fb1523d3854ce59fdfe3841250ac3c.json"}}], "type": "journal article", "published": "2024-10-16", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "19", "issue": "10", "pages": "e0306654", "issn-l": "1932-6203"}, "abstract": "Microscopy is essential for detecting, identifying, analyzing, and measuring small objects. Access to modern microscopy equipment is crucial for scientific research, especially in the biomedical and analytical sciences. However, the high cost of equipment, limited availability of parts, and challenges associated with transporting equipment often limit the accessibility and operational capabilities of these tools, particularly in field sites and other remote or resource-limited settings. Thus, there is a need for affordable and accessible alternatives to traditional microscopy systems. We address this challenge by investigating the feasibility of using a simple microcontroller board not only as a portable and field-ready digital microscope, but furthermore as a versatile platform which can easily be adapted to a variety of imaging applications. By adding a few external components, we demonstrate that a low-cost ESP32 camera board can be used to build an autonomous in situ platform for digital time-lapse imaging of cells. Our prototype of this approach, which we call ESPressoscope, can be adapted to applications ranging from monitoring incubator cell cultures in the lab to observing ecological phenomena in the sea, and it can be adapted for other techniques such as microfluidics or spectrophotometry. Our prototype of the ESPressoscope concept achieves a low power consumption and small size, which makes it ideal for field research in environments and applications where microscopy was previously infeasible. Its Wi-Fi connectivity enables integration with external image processing and storage systems, including on cloud platforms when internet access is available. Finally, we present several web browser-based tools to help users operate and manage our prototype's software. Our findings demonstrate the potential for low-cost, portable microscopy solutions to enable new and more accessible experiments for biological and analytical applications.", "doi": "10.1371/journal.pone.0306654", "pmid": "39413076", "labels": {"DDLS Fellow": "", "Wei Ouyang": ""}, "xrefs": [{"db": "pmc", "key": "PMC11482665"}, {"db": "pii", "key": "PONE-D-24-07702"}], "notes": [], "created": "2026-08-20T12:44:30.457Z", "modified": "2026-09-23T12:27:19.556Z"}, {"entity": "publication", "iuid": "c89237bd61794c2aa244bb46bbc6c899", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c89237bd61794c2aa244bb46bbc6c899.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c89237bd61794c2aa244bb46bbc6c899"}}, "title": "Machine learning in microscopy - insights, opportunities and challenges.", "authors": [{"family": "Cunha", "given": "In\u00eas", "initials": "I", "orcid": "0000-0002-1327-9018", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/77f0773f41cc4f1191aaba0d21ec745a.json"}}, {"family": "Latron", "given": "Emma", "initials": "E"}, {"family": "Bauer", "given": "Sebastian", "initials": "S"}, {"family": "Sage", "given": "Daniel", "initials": "D", "orcid": "0000-0002-1150-1623", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/919b0180005444d88757db8e63b80d83.json"}}, {"family": "Griffi\u00e9", "given": "Juliette", "initials": "J", "orcid": "0000-0001-6438-0119", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2650e9aa00f7499aba2f222c49a95e71.json"}}], "type": "journal article", "published": "2024-10-15", "journal": {"title": "J. Cell. Sci.", "issn": "1477-9137", "volume": "137", "issue": "20", "issn-l": "0021-9533"}, "abstract": "Machine learning (ML) is transforming the field of image processing and analysis, from automation of laborious tasks to open-ended exploration of visual patterns. This has striking implications for image-driven life science research, particularly microscopy. In this Review, we focus on the opportunities and challenges associated with applying ML-based pipelines for microscopy datasets from a user point of view. We investigate the significance of different data characteristics - quantity, transferability and content - and how this determines which ML model(s) to use, as well as their output(s). Within the context of cell biological questions and applications, we further discuss ML utility range, namely data curation, exploration, prediction and explanation, and what they entail and translate to in the context of microscopy. Finally, we explore the challenges, common artefacts and risks associated with ML in microscopy. Building on insights from other fields, we propose how these pitfalls might be mitigated for in microscopy.", "doi": "10.1242/jcs.262095", "pmid": "39465533", "labels": {"DDLS Fellow": "", "Juliette Griffie": ""}, "xrefs": [{"db": "pii", "key": "362505"}], "notes": [], "created": "2026-08-20T12:38:31.317Z", "modified": "2026-09-23T09:08:07.757Z"}, {"entity": "publication", "iuid": "07bb5f0d9127493089db67eec353c920", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/07bb5f0d9127493089db67eec353c920.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/07bb5f0d9127493089db67eec353c920"}}, "title": "Metagenomic assemblies tend to break around antibiotic resistance genes.", "authors": [{"family": "Abramova", "given": "Anna", "initials": "A", "orcid": "0000-0002-0493-7808", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dd75cbcc659c4ca398eb678fad1dc498.json"}}, {"family": "Karkman", "given": "Antti", "initials": "A", "orcid": "0000-0003-0983-3319", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/51ba670092f8496d8ebedcb07d0b6e62.json"}}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J", "orcid": "0000-0002-6528-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c666068e9d34939b0252a627007cec7.json"}}], "type": "journal article", "published": "2024-10-14", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "25", "issue": "1", "pages": "959", "issn-l": "1471-2164"}, "abstract": "Assembly of metagenomic samples can provide essential information about the mobility potential and taxonomic origin of antibiotic resistance genes (ARGs) and inform interventions to prevent further spread of resistant bacteria. However, similar to other conserved regions, such as ribosomal RNA genes and mobile genetic elements, almost identical ARGs typically occur in multiple genomic contexts across different species, representing a considerable challenge for the assembly process. Usually, this results in many fragmented contigs of unclear origin, complicating the risk assessment of ARG detections. To systematically investigate the impact of this issue on detection, quantification and contextualization of ARGs, we evaluated the performance of different assembly approaches, including genomic-, metagenomic- and transcriptomic-specialized assemblers. We quantified recovery and accuracy rates of each tool for ARGs both from in silico spiked metagenomic samples as well as real samples sequenced using both long- and short-read sequencing technologies.\n\nThe results revealed that none of the investigated tools can accurately capture genomic contexts present in samples of high complexity. The transcriptomic assembler Trinity showed a better performance in terms of reconstructing longer and fewer contigs matching unique genomic contexts, which can be beneficial for deciphering the taxonomic origin of ARGs. The currently commonly used metagenomic assembly tools metaSPAdes and MEGAHIT were able to identify the ARG repertoire but failed to fully recover the diversity of genomic contexts present in a sample. On top of that, in a complex scenario MEGAHIT produced very short contigs, which can lead to considerable underestimation of the resistome in a given sample.\n\nOur study shows that metaSPAdes and Trinity would be the preferable tools in terms of accuracy to recover correct genomic contexts around ARGs in metagenomic samples characterized by uneven coverages. Overall, the inability of assemblers to reconstruct long ARG-containing contigs has impacts on ARG quantification, suggesting that directly mapping reads to an ARG database should be performed as a complementary strategy to get accurate ARG abundance and diversity measures.", "doi": "10.1186/s12864-024-10876-0", "pmid": "39402510", "labels": {"DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC11479545"}, {"db": "pii", "key": "10.1186/s12864-024-10876-0"}], "notes": [], "created": "2024-11-18T11:43:50.298Z", "modified": "2026-09-23T08:48:28.468Z"}, {"entity": "publication", "iuid": "3e3149ba56534f57be85c69020b838aa", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3e3149ba56534f57be85c69020b838aa.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3e3149ba56534f57be85c69020b838aa"}}, "title": "Coagulation factor X promotes resistance to androgen-deprivation therapy in prostate cancer.", "authors": [{"family": "Cal\u00ec", "given": "Bianca", "initials": "B"}, {"family": "Troiani", "given": "Martina", "initials": "M"}, {"family": "Bressan", "given": "Silvia", "initials": "S"}, {"family": "Attanasio", "given": "Giuseppe", "initials": "G"}, {"family": "Merler", "given": "Sara", "initials": "S"}, {"family": "Moscarda", "given": "Viola", "initials": "V"}, {"family": "Mosole", "given": "Simone", "initials": "S"}, {"family": "Ricci", "given": "Elena", "initials": "E"}, {"family": "Guo", "given": "Christina", "initials": "C"}, {"family": "Yuan", "given": "Wei", "initials": "W"}, {"family": "Gallagher", "given": "Lewis", "initials": "L"}, {"family": "Lundberg", "given": "Arian", "initials": "A", "orcid": "0000-0002-6630-2787", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/baa2c7c8963840bfb6a22d7c5cfe35f9.json"}}, {"family": "Bernett", "given": "Ilona", "initials": "I"}, {"family": "Figueiredo", "given": "Ines", "initials": "I"}, {"family": "Arzola", "given": "Rydell Alvarez", "initials": "RA"}, {"family": "Abreut", "given": "Ernesto Bermudez", "initials": "EB"}, {"family": "D'Ambrosio", "given": "Mariantonietta", "initials": "M"}, {"family": "Bancaro", "given": "Nicol\u00f2", "initials": "N"}, {"family": "Brina", "given": "Daniela", "initials": "D"}, {"family": "Zumerle", "given": "Sara", "initials": "S"}, {"family": "Pasquini", "given": "Emiliano", "initials": "E"}, {"family": "Maddalena", "given": "Martino", "initials": "M"}, {"family": "Lai", "given": "Ping", "initials": "P"}, {"family": "Colucci", "given": "Manuel", "initials": "M"}, {"family": "Pernigoni", "given": "Nicol\u00f2", "initials": "N"}, {"family": "Rinaldi", "given": "Andrea", "initials": "A"}, {"family": "Minardi", "given": "Davide", "initials": "D"}, {"family": "Morlacco", "given": "Alessandro", "initials": "A"}, {"family": "Moro", "given": "Fabrizio Dal", "initials": "FD"}, {"family": "Sabbadin", "given": "Marianna", "initials": "M"}, {"family": "Galuppini", "given": "Francesca", "initials": "F"}, {"family": "Fassan", "given": "Matteo", "initials": "M"}, {"family": "R\u00fcschoff", "given": "Jan Hendrik", "initials": "JH"}, {"family": "Moch", "given": "Holger", "initials": "H"}, {"family": "Rescigno", "given": "Pasquale", "initials": "P"}, {"family": "Francini", "given": "Edoardo", "initials": "E"}, {"family": "Saieva", "given": "Calogero", "initials": "C"}, {"family": "Modesti", "given": "Mikol", "initials": "M"}, {"family": "Theurillat", "given": "Jean-Philippe", "initials": "JP"}, {"family": "Gillessen", "given": "Silke", "initials": "S"}, {"family": "Wilgenbus", "given": "Petra", "initials": "P"}, {"family": "Graf", "given": "Claudine", "initials": "C"}, {"family": "Ruf", "given": "Wolfram", "initials": "W"}, {"family": "de Bono", "given": "Johann", "initials": "J"}, {"family": "Alimonti", "given": "Andrea", "initials": "A"}], "type": "journal article", "published": "2024-10-14", "journal": {"title": "Cancer Cell", "issn": "1878-3686", "volume": "42", "issue": "10", "pages": "1676-1692.e11", "issn-l": "1535-6108"}, "abstract": "Although hypercoagulability is commonly associated with malignancies, whether coagulation factors directly affect tumor cell proliferation remains unclear. Herein, by performing single-cell RNA sequencing (scRNA-seq) of the prostate tumor microenvironment (TME) of mouse models of castration-resistant prostate cancer (CRPC), we report that immunosuppressive neutrophils (PMN-MDSCs) are a key extra-hepatic source of coagulation factor X (FX). FX activation within the TME enhances androgen-independent tumor growth by activating the protease-activated receptor 2 (PAR2) and the phosphorylation of ERK1/2 in tumor cells. Genetic and pharmacological inhibition of factor Xa (FXa) antagonizes the oncogenic activity of PMN-MDSCs, reduces tumor progression, and synergizes with enzalutamide therapy. Intriguingly, F10high PMN-MDSCs express the surface marker CD84 and CD84 ligation enhances F10 expression. Elevated levels of FX, CD84, and PAR2 in prostate tumors associate with worse survival in CRPC patients. This study provides evidence that FXa directly promotes cancer and highlights additional targets for PMN-MDSCs for cancer therapies.", "doi": "10.1016/j.ccell.2024.08.018", "pmid": "39303726", "labels": {"DDLS Fellow": null, "Arian Lundberg": null}, "xrefs": [{"db": "pii", "key": "S1535-6108(24)00317-9"}], "notes": [], "created": "2025-11-14T07:48:48.647Z", "modified": "2026-01-03T12:41:52.036Z"}, {"entity": "publication", "iuid": "ac33ff29f6394ef190d5183e3826a588", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ac33ff29f6394ef190d5183e3826a588.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ac33ff29f6394ef190d5183e3826a588"}}, "title": "Properties and limitations of eDNA substrates for terrestrial animal monitoring", "authors": [{"family": "Zhao", "given": "Beilun", "initials": "B", "orcid": "0000-0003-1495-9717", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2ba7a63991cd4bc3ab299795cc6914f1.json"}}, {"family": "Andermann", "given": "Tobias", "initials": "T", "orcid": "0000-0002-0932-1623", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dfff478dfcfc43ddbd40bb1bafbcb0a7.json"}}], "type": "posted-content", "published": "2024-10-10", "journal": {"issn-l": null}, "abstract": null, "doi": "10.22541/au.172854903.36594897/v1", "pmid": null, "labels": {"Tobias Andermann": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2025-03-18T16:05:17.264Z", "modified": "2025-03-18T16:06:34.531Z"}, {"entity": "publication", "iuid": "9b255b8a99944228a707e155419fd870", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9b255b8a99944228a707e155419fd870.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9b255b8a99944228a707e155419fd870"}}, "title": "Quest for Orthologs in the Era of Biodiversity Genomics.", "authors": [{"family": "Langschied", "given": "Felix", "initials": "F", "orcid": "0009-0004-3348-3130", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e1a6e133f7fe44bf96dd05a90d8fc273.json"}}, {"family": "Bordin", "given": "Nicola", "initials": "N", "orcid": "0000-0002-6568-9035", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3ec6e6c9fb67478580b946a6ecae062b.json"}}, {"family": "Cosentino", "given": "Salvatore", "initials": "S", "orcid": "0000-0002-1066-8659", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/99f2695b80684c87addfbc751534e7d7.json"}}, {"family": "Fuentes-Palacios", "given": "Diego", "initials": "D", "orcid": "0000-0002-9977-6786", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cc15167b6b1943a3a07e911fef77b942.json"}}, {"family": "Glover", "given": "Natasha", "initials": "N", "orcid": "0000-0003-1811-4340", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fe6ec892c5404ac3a0aaf4e8ac907ee9.json"}}, {"family": "Hiller", "given": "Michael", "initials": "M", "orcid": "0000-0003-3024-1449", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1005d0d1f4264b46b1cfe214c7aca246.json"}}, {"family": "Hu", "given": "Yanhui", "initials": "Y", "orcid": "0000-0003-1494-1402", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d048ac84bf934c9d87774c6cab7430c6.json"}}, {"family": "Huerta-Cepas", "given": "Jaime", "initials": "J", "orcid": "0000-0003-4195-5025", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0c8c00b0396840c480fa3f57a376ce00.json"}}, {"family": "Coelho", "given": "Luis Pedro", "initials": "LP", "orcid": "0000-0002-9280-7885", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3630792233fd4118b12a548dba98f8bc.json"}}, {"family": "Iwasaki", "given": "Wataru", "initials": "W", "orcid": "0000-0002-9169-9245", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/77399cc41820467ba6e32dd3ee6eaaec.json"}}, {"family": "Majidian", "given": "Sina", "initials": "S", "orcid": "0000-0001-5345-6982", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a14f17e8c2dc470dae5250c36d32cb27.json"}}, {"family": "Manzano-Morales", "given": "Saioa", "initials": "S", "orcid": "0000-0001-5138-3871", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c23facda0fef49a8a038195ac49b6ee2.json"}}, {"family": "Persson", "given": "Emma", "initials": "E", "orcid": "0000-0003-0532-8251", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c17b5ab61d4949d4818f653f43fa11f6.json"}}, {"family": "Richards", "given": "Thomas A", "initials": "TA", "orcid": "0000-0002-9692-0973", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c4778e4e15ce4ce6af7a4f07b27943b9.json"}}, {"family": "Gabald\u00f3n", "given": "Toni", "initials": "T", "orcid": "0000-0003-0019-1735", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1ae849222ff5490d816ec645b9e3cda3.json"}}, {"family": "Sonnhammer", "given": "Erik", "initials": "E", "orcid": "0000-0002-9015-5588", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8c4fb5f5a50a4dbb91bbea3cc6861ffa.json"}}, {"family": "Thomas", "given": "Paul D", "initials": "PD", "orcid": "0000-0002-9074-3507", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4af1f8a10ced487196829d162e22d314.json"}}, {"family": "Dessimoz", "given": "Christophe", "initials": "C", "orcid": "0000-0002-2170-853X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8d9dc970f3da45a4a46ecfdf4ab0893f.json"}}, {"family": "Ebersberger", "given": "Ingo", "initials": "I", "orcid": "0000-0001-8187-9253", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/946c40da21e441d196dd8b88ea126df0.json"}}], "type": "journal article", "published": "2024-10-09", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "16", "issue": "10", "issn-l": "1759-6653"}, "abstract": "The era of biodiversity genomics is characterized by large-scale genome sequencing efforts that aim to represent each living taxon with an assembled genome. Generating knowledge from this wealth of data has not kept up with this pace. We here discuss major challenges to integrating these novel genomes into a comprehensive functional and evolutionary network spanning the tree of life. In summary, the expanding datasets create a need for scalable gene annotation methods. To trace gene function across species, new methods must seek to increase the resolution of ortholog analyses, e.g. by extending analyses to the protein domain level and by accounting for alternative splicing. Additionally, the scope of orthology prediction should be pushed beyond well-investigated proteomes. This demands the development of specialized methods for the identification of orthologs to short proteins and noncoding RNAs and for the functional characterization of novel gene families. Furthermore, protein structures predicted by machine learning are now readily available, but this new information is yet to be integrated with orthology-based analyses. Finally, an increasing focus should be placed on making orthology assignments adhere to the findable, accessible, interoperable, and reusable (FAIR) principles. This fosters green bioinformatics by avoiding redundant computations and helps integrating diverse scientific communities sharing the need for comparative genetics and genomics information. It should also help with communicating orthology-related concepts in a format that is accessible to the public, to counteract existing misinformation about evolution.", "doi": "10.1093/gbe/evae224", "pmid": "39404012", "labels": {"Sina Majidian": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC11523110"}, {"db": "pii", "key": "7822254"}], "notes": [], "created": "2026-08-20T09:41:22.699Z", "modified": "2026-09-23T09:05:59.758Z"}, {"entity": "publication", "iuid": "b074a8eba6254039acd8bedf1ce89a8d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b074a8eba6254039acd8bedf1ce89a8d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b074a8eba6254039acd8bedf1ce89a8d"}}, "title": "Genetic Adaptation to Amoxicillin inEscherichia coli: The Limited Role ofdinBandkatE", "authors": [{"family": "Teichmann", "given": "Lisa", "initials": "L"}, {"family": "Wenne", "given": "Marcus", "initials": "M"}, {"family": "Luitwieler", "given": "Sam", "initials": "S"}, {"family": "Dugar", "given": "Gaurav", "initials": "G"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J", "orcid": "0000-0002-6528-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c666068e9d34939b0252a627007cec7.json"}}, {"family": "Kuile", "given": "Benno ter", "initials": "Bt", "orcid": "0000-0002-8523-8135", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3c87f0fedd1d4b208ff99000dbade32c.json"}}], "type": "posted-content", "published": "2024-10-06", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2024.10.05.616818", "pmid": null, "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [], "notes": [], "created": "2024-11-18T11:45:29.434Z", "modified": "2025-04-07T06:57:51.755Z"}, {"entity": "publication", "iuid": "6defc26e37704bc18722bc1e8d65512b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/6defc26e37704bc18722bc1e8d65512b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/6defc26e37704bc18722bc1e8d65512b"}}, "title": "The ACROBAT 2022 challenge: Automatic registration of breast cancer tissue.", "authors": [{"family": "Weitz", "given": "Philippe", "initials": "P", "orcid": "0000-0002-1788-0716", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a70939bc05a04f87b9a61e7d98448e09.json"}}, {"family": "Valkonen", "given": "Masi", "initials": "M", "orcid": "0000-0003-3091-2484", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ae4841e8a4124dc79c921b3af09096fe.json"}}, {"family": "Solorzano", "given": "Leslie", "initials": "L", "orcid": "0000-0001-8658-6417", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f5c33a5b8cef4cad8b9f57b4510fb0c2.json"}}, {"family": "Carr", "given": "Circe", "initials": "C"}, {"family": "Kartasalo", "given": "Kimmo", "initials": "K", "orcid": "0000-0002-9470-4783", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7c6fc97c06ed456c8bdd1f03db8a9b72.json"}}, {"family": "Boissin", "given": "Constance", "initials": "C"}, {"family": "Koivukoski", "given": "Sonja", "initials": "S", "orcid": "0000-0002-4909-3522", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1889b0f9c9f943609f51e8d8d15041f1.json"}}, {"family": "Kuusela", "given": "Aino", "initials": "A"}, {"family": "Rasic", "given": "Dusan", "initials": "D", "orcid": "0000-0003-4610-5265", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/42ddfdb3b820417197cedfd1b96ab172.json"}}, {"family": "Feng", "given": "Yanbo", "initials": "Y"}, {"family": "Pouplier", "given": "Sandra Sinius", "initials": "SS"}, {"family": "Sharma", "given": "Abhinav", "initials": "A"}, {"family": "Eriksson", "given": "Kajsa Ledesma", "initials": "KL"}, {"family": "Robertson", "given": "Stephanie", "initials": "S"}, {"family": "Marzahl", "given": "Christian", "initials": "C"}, {"family": "Gatenbee", "given": "Chandler D", "initials": "CD"}, {"family": "Anderson", "given": "Alexander R A", "initials": "ARA"}, {"family": "Wodzinski", "given": "Marek", "initials": "M"}, {"family": "Jurgas", "given": "Artur", "initials": "A"}, {"family": "Marini", "given": "Niccol\u00f2", "initials": "N"}, {"family": "Atzori", "given": "Manfredo", "initials": "M"}, {"family": "M\u00fcller", "given": "Henning", "initials": "H"}, {"family": "Budelmann", "given": "Daniel", "initials": "D"}, {"family": "Weiss", "given": "Nick", "initials": "N"}, {"family": "Heldmann", "given": "Stefan", "initials": "S"}, {"family": "Lotz", "given": "Johannes", "initials": "J"}, {"family": "Wolterink", "given": "Jelmer M", "initials": "JM"}, {"family": "De Santi", "given": "Bruno", "initials": "B"}, {"family": "Patil", "given": "Abhijeet", "initials": "A"}, {"family": "Sethi", "given": "Amit", "initials": "A"}, {"family": "Kondo", "given": "Satoshi", "initials": "S"}, {"family": "Kasai", "given": "Satoshi", "initials": "S"}, {"family": "Hirasawa", "given": "Kousuke", "initials": "K"}, {"family": "Farrokh", "given": "Mahtab", "initials": "M"}, {"family": "Kumar", "given": "Neeraj", "initials": "N"}, {"family": "Greiner", "given": "Russell", "initials": "R"}, {"family": "Latonen", "given": "Leena", "initials": "L", "orcid": "0000-0003-4502-2193", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f85efd5db6e74874acdb8d14237ae732.json"}}, {"family": "Laenkholm", "given": "Anne-Vibeke", "initials": "A"}, {"family": "Hartman", "given": "Johan", "initials": "J", "orcid": "0000-0002-6500-8527", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d62d622200d443b7b5be34ff3c0945be.json"}}, {"family": "Ruusuvuori", "given": "Pekka", "initials": "P", "orcid": "0000-0001-9086-9591", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb947cd395e84612a53569f4a39abd19.json"}}, {"family": "Rantalainen", "given": "Mattias", "initials": "M"}], "type": "journal article", "published": "2024-10-00", "journal": {"title": "Med Image Anal", "issn": "1361-8423", "issn-l": null, "volume": "97", "issue": null, "pages": "103257"}, "abstract": "The alignment of tissue between histopathological whole-slide-images (WSI) is crucial for research and clinical applications. Advances in computing, deep learning, and availability of large WSI datasets have revolutionised WSI analysis. Therefore, the current state-of-the-art in WSI registration is unclear. To address this, we conducted the ACROBAT challenge, based on the largest WSI registration dataset to date, including 4,212 WSIs from 1,152 breast cancer patients. The challenge objective was to align WSIs of tissue that was stained with routine diagnostic immunohistochemistry to its H&E-stained counterpart. We compare the performance of eight WSI registration algorithms, including an investigation of the impact of different WSI properties and clinical covariates. We find that conceptually distinct WSI registration methods can lead to highly accurate registration performances and identify covariates that impact performances across methods. These results provide a comparison of the performance of current WSI registration methods and guide researchers in selecting and developing methods.", "doi": "10.1016/j.media.2024.103257", "pmid": "38981282", "labels": {"Kimmo Kartasalo": null, "DDLS Fellow": null}, "xrefs": [{"db": "pii", "key": "S1361-8415(24)00182-8"}], "notes": [], "created": "2024-11-05T16:12:17.237Z", "modified": "2025-04-07T06:58:23.491Z"}, {"entity": "publication", "iuid": "aa9f95b4639a44068ad80705aba1ec45", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/aa9f95b4639a44068ad80705aba1ec45.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/aa9f95b4639a44068ad80705aba1ec45"}}, "title": "The 'queen of the Andes' (Puya raimondii) is genetically fragile and fragmented: a consequence of long generation time and semelparity?", "authors": [{"family": "Liu", "given": "Lu", "initials": "L", "orcid": "0000-0001-7168-5017", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c659b1c306424989af636398dd57f975.json"}}, {"family": "James", "given": "Jennifer", "initials": "J", "orcid": "0000-0003-0518-6783", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4b807f7ab8f46f8a5e927e1b090d662.json"}}, {"family": "Zhang", "given": "Yu-Qu", "initials": "YQ", "orcid": "0000-0003-1517-9229", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8c109ec2712f46d197ca0c8e702c967b.json"}}, {"family": "Wang", "given": "Zheng-Feng", "initials": "ZF", "orcid": "0000-0002-7599-7891", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ed6c9ca81aab4d4d9563578777bf3012.json"}}, {"family": "Arakaki", "given": "M\u00f3nica", "initials": "M", "orcid": "0000-0003-1081-2507", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b63566a5a85d4b75817fd1bb59b3f99a.json"}}, {"family": "Vadillo", "given": "Giovana", "initials": "G", "orcid": "0000-0002-0145-0367", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/29a2f91d2eab4066a098317b92075a8c.json"}}, {"family": "Zhou", "given": "Qiu-Jie", "initials": "QJ", "orcid": "0000-0001-7351-2371", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/15244ffd4f4746ddb9ec39e4c038204e.json"}}, {"family": "Lascoux", "given": "Martin", "initials": "M", "orcid": "0000-0003-1699-9042", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0730d0f9c2524eb19383640612924701.json"}}, {"family": "Ge", "given": "Xue-Jun", "initials": "XJ", "orcid": "0000-0002-5008-9475", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ef81044779a4cf08dec7e2f062da88c.json"}}], "type": "journal article", "published": "2024-10-00", "journal": {"title": "New Phytol.", "issn": "1469-8137", "issn-l": "0028-646X", "volume": "244", "issue": "1", "pages": "277-291"}, "abstract": "Understanding how life history shapes genetic diversity is a fundamental issue in evolutionary biology, with important consequences for conservation. However, we still have an incomplete picture of the impact of life history on genome-wide patterns of diversity, especially in long-lived semelparous plants. Puya raimondii is a high-altitude semelparous species from the Andes that flowers at 40-100 years of age. We sequenced the whole genome and estimated the nucleotide diversity of 200 individuals sampled from nine populations. Coalescent-based approaches were then used to infer past population dynamics. Finally, these results were compared with results obtained for the iteroparous species, Puya macrura. The nine populations of P. raimondii were highly divergent, highly inbred, and carried an exceptionally high genetic load. They are genetically depauperate, although, locally in the genome, balancing selection contributed to the maintenance of genetic polymorphism. While both P. raimondii and P. macrura went through a severe bottleneck during the Pleistocene, P. raimondii did not recover from it and continuously declined, while P. macrura managed to bounce back. Our results demonstrate the importance of life history, in particular generation time and reproductive strategy, in affecting population dynamics and genomic variation, and illustrate the genetic fragility of long-lived semelparous plants.", "doi": "10.1111/nph.20036", "pmid": "39135394", "labels": {"Jennifer James": "", "DDLS Fellow": ""}, "xrefs": [{"db": "BioProject", "key": "PRJNA939266"}, {"db": "BioProject", "key": "SRR23677054"}, {"db": "BioProject", "key": "SRR23677115"}, {"db": "BioProject", "key": "SRR23692597"}, {"db": "BioProject", "key": "SRR23692642"}, {"db": "BioProject", "key": "SRR23692647"}, {"db": "BioProject", "key": "SRR23692743"}], "notes": [], "created": "2024-11-27T09:19:02.046Z", "modified": "2026-09-23T12:25:04.375Z"}, {"entity": "publication", "iuid": "1e7452ca26b74a918d5df7e1ae26d7b3", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1e7452ca26b74a918d5df7e1ae26d7b3.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1e7452ca26b74a918d5df7e1ae26d7b3"}}, "title": "Sex bias in FGFR3 somatic mutations in bladder cancer", "authors": [{"family": "Meng", "given": "Xiangyu", "initials": "X"}, {"family": "Wang", "given": "Qiaoli", "initials": "Q"}], "type": "journal-article", "published": "2024-10-00", "journal": {"title": "Oncol Transl Med", "issn": "2995-5858", "volume": "10", "issue": "5", "pages": "252-256", "issn-l": null}, "abstract": null, "doi": "10.1097/ot9.0000000000000054", "pmid": null, "labels": {"DDLS Fellow": null, "Qiaoli Wang": null}, "xrefs": [], "notes": [], "created": "2025-11-28T12:24:40.368Z", "modified": "2025-12-04T19:43:06.125Z"}, {"entity": "publication", "iuid": "1070918999b3451da1cb45b9ab4e789c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1070918999b3451da1cb45b9ab4e789c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1070918999b3451da1cb45b9ab4e789c"}}, "title": "Proteomic changes in Alzheimer's disease associated with progressive A\u03b2 plaque and tau tangle pathologies.", "authors": [{"family": "Pichet Binette", "given": "Alexa", "initials": "A", "orcid": "0000-0001-5218-3337", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e8f0967b7b694bcf96e30a051a5bbe9a.json"}}, {"family": "Gaiteri", "given": "Chris", "initials": "C"}, {"family": "Wennstr\u00f6m", "given": "Malin", "initials": "M"}, {"family": "Kumar", "given": "Atul", "initials": "A"}, {"family": "Hristovska", "given": "Ines", "initials": "I"}, {"family": "Spotorno", "given": "Nicola", "initials": "N"}, {"family": "Salvad\u00f3", "given": "Gemma", "initials": "G", "orcid": "0000-0002-5210-9230", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c3b7599000404d618d84b389ba47f19a.json"}}, {"family": "Strandberg", "given": "Olof", "initials": "O"}, {"family": "Mathys", "given": "Hansruedi", "initials": "H", "orcid": "0000-0003-0186-2115", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/38b5ab2013214cc7845021e2460b3433.json"}}, {"family": "Tsai", "given": "Li-Huei", "initials": "LH", "orcid": "0000-0003-1262-0592", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fd0b5f35b80a4fb580612e498d06c75b.json"}}, {"family": "Palmqvist", "given": "Sebastian", "initials": "S", "orcid": "0000-0002-9267-1930", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6fbd05e87cfb4057a1a7e41d9fb94aef.json"}}, {"family": "Mattsson-Carlgren", "given": "Niklas", "initials": "N"}, {"family": "Janelidze", "given": "Shorena", "initials": "S"}, {"family": "Stomrud", "given": "Erik", "initials": "E"}, {"family": "Vogel", "given": "Jacob W", "initials": "JW"}, {"family": "Hansson", "given": "Oskar", "initials": "O", "orcid": "0000-0001-8467-7286", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9292115deece4d9fafc8a02d4a430707.json"}}], "type": "journal article", "published": "2024-10-00", "journal": {"title": "Nat. Neurosci.", "issn": "1546-1726", "volume": "27", "issue": "10", "pages": "1880-1891", "issn-l": "1097-6256"}, "abstract": "Proteomics can shed light on the dynamic and multifaceted alterations in neurodegenerative disorders like Alzheimer's disease (AD). Combining radioligands measuring \u03b2-amyloid (A\u03b2) plaques and tau tangles with cerebrospinal fluid proteomics, we uncover molecular events mirroring different stages of AD pathology in living humans. We found 127 differentially abundant proteins (DAPs) across the AD spectrum. The strongest A\u03b2-related proteins were mainly expressed in glial cells and included SMOC1 and ITGAM. A dozen proteins linked to ATP metabolism and preferentially expressed in neurons were independently associated with tau tangle load and tau accumulation. Only 20% of the DAPs were also altered in other neurodegenerative diseases, underscoring AD's distinct proteome. Two co-expression modules related, respectively, to protein metabolism and microglial immune response encompassed most DAPs, with opposing, staggered trajectories along the AD continuum. We unveil protein signatures associated with A\u03b2 and tau proteinopathy in vivo, offering insights into complex neural responses and potential biomarkers and therapeutics targeting different disease stages.", "doi": "10.1038/s41593-024-01737-w", "pmid": "39187705", "labels": {"Jacob W Vogel": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC11452344"}, {"db": "pii", "key": "10.1038/s41593-024-01737-w"}], "notes": [], "created": "2025-03-19T11:17:10.669Z", "modified": "2025-03-19T11:19:18.053Z"}, {"entity": "publication", "iuid": "79604ac5d21c4943bf6880d0b11664ae", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/79604ac5d21c4943bf6880d0b11664ae.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/79604ac5d21c4943bf6880d0b11664ae"}}, "title": "Lipidome changes due to improved dietary fat quality inform cardiometabolic risk reduction and precision nutrition.", "authors": [{"family": "Eichelmann", "given": "Fabian", "initials": "F", "orcid": "0000-0002-3975-5596", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4f6083a259c6440ab3201d53f44a0d55.json"}}, {"family": "Prada", "given": "Marcela", "initials": "M"}, {"family": "Sellem", "given": "Laury", "initials": "L"}, {"family": "Jackson", "given": "Kim G", "initials": "KG", "orcid": "0000-0002-0070-3203", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/95c9d516d1814fb0aaebc54107f59e0a.json"}}, {"family": "Salas Salvad\u00f3", "given": "Jordi", "initials": "J", "orcid": "0000-0003-2700-7459", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/49e886d4d7e346e1a65f949699f620a4.json"}}, {"family": "Razquin Burillo", "given": "Cristina", "initials": "C", "orcid": "0000-0003-3480-2645", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f0f5c529e0a647528ca99b42fe8a9e8b.json"}}, {"family": "Estruch", "given": "Ramon", "initials": "R", "orcid": "0000-0003-1260-4445", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/122cb01329f24931ae77ae5ac5a05059.json"}}, {"family": "Fried\u00e9n", "given": "Michael", "initials": "M"}, {"family": "Rosqvist", "given": "Frederik", "initials": "F"}, {"family": "Ris\u00e9rus", "given": "Ulf", "initials": "U"}, {"family": "Rexrode", "given": "Kathryn M", "initials": "KM", "orcid": "0000-0003-3387-8429", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a3600b145b304aa7959c0f85fa198192.json"}}, {"family": "Guasch-Ferr\u00e9", "given": "Marta", "initials": "M", "orcid": "0000-0001-8525-1404", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2d1a49f5df124e96a9285b43d628cee9.json"}}, {"family": "Sun", "given": "Qi", "initials": "Q", "orcid": "0000-0002-8480-1563", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4a65407257ac4518ac5cb19317ee3b32.json"}}, {"family": "Willett", "given": "Walter C", "initials": "WC"}, {"family": "Martinez-Gonzalez", "given": "Miguel Angel", "initials": "MA", "orcid": "0000-0002-3917-9808", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7852fa98fe3a4da285d79f04e09cbd34.json"}}, {"family": "Lovegrove", "given": "Julie A", "initials": "JA"}, {"family": "Hu", "given": "Frank B", "initials": "FB"}, {"family": "Schulze", "given": "Matthias B", "initials": "MB", "orcid": "0000-0002-0830-5277", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/853ded2c43b64f26a8b47da7ea7b79c0.json"}}, {"family": "Wittenbecher", "given": "Clemens", "initials": "C", "orcid": "0000-0001-7792-877X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2f7d2c289b3c47d5a79d23bd48a3225a.json"}}], "type": "journal article", "published": "2024-10-00", "journal": {"title": "Nat. Med.", "issn": "1546-170X", "volume": "30", "issue": "10", "pages": "2867-2877", "issn-l": "1078-8956"}, "abstract": "Current cardiometabolic disease prevention guidelines recommend increasing dietary unsaturated fat intake while reducing saturated fats. Here we use lipidomics data from a randomized controlled dietary intervention trial to construct a multilipid score (MLS), summarizing the effects of replacing saturated fat with unsaturated fat on 45 lipid metabolite concentrations. In the EPIC-Potsdam cohort, a difference in the MLS, reflecting better dietary fat quality, was associated with a significant reduction in the incidence of cardiovascular disease (-32%; 95% confidence interval (95% CI): -21% to -42%) and type 2 diabetes (-26%; 95% CI: -15% to -35%). We built a closely correlated simplified score, reduced MLS (rMLS), and observed that beneficial rMLS changes, suggesting improved dietary fat quality over 10 years, were associated with lower diabetes risk (odds ratio per standard deviation of 0.76; 95% CI: 0.59 to 0.98) in the Nurses' Health Study. Furthermore, in the PREDIMED trial, an olive oil-rich Mediterranean diet intervention primarily reduced diabetes incidence among participants with unfavorable preintervention rMLS levels, suggestive of disturbed lipid metabolism before intervention. Our findings indicate that the effects of dietary fat quality on the lipidome can contribute to a more precise understanding and possible prediction of the health outcomes of specific dietary fat modifications.", "doi": "10.1038/s41591-024-03124-1", "pmid": "38992128", "labels": {"Clemens Wittenbecher": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC11485259"}, {"db": "pii", "key": "10.1038/s41591-024-03124-1"}], "notes": [], "created": "2025-03-19T08:18:40.856Z", "modified": "2026-09-23T08:32:52.010Z"}, {"entity": "publication", "iuid": "4f5de8bb669447038121a19d8969f906", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4f5de8bb669447038121a19d8969f906.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4f5de8bb669447038121a19d8969f906"}}, "title": "Blood lipid profiling indicates that dietary fat quality is associated with cardiometabolic risk.", "authors": [], "type": "journal article", "published": "2024-10-00", "journal": {"title": "Nat. Med.", "issn": "1546-170X", "volume": "30", "issue": "10", "pages": "2735-2736", "issn-l": "1078-8956"}, "abstract": null, "doi": "10.1038/s41591-024-03234-w", "pmid": "39215152", "labels": {"Clemens Wittenbecher": null, "DDLS Fellow": null}, "xrefs": [{"db": "pii", "key": "10.1038/s41591-024-03234-w"}], "notes": [], "created": "2025-12-09T13:24:46.133Z", "modified": "2025-12-09T13:26:03.251Z"}, {"entity": "publication", "iuid": "c8c8b612d5d246f9974a8c23c21d64eb", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c8c8b612d5d246f9974a8c23c21d64eb.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c8c8b612d5d246f9974a8c23c21d64eb"}}, "title": "Author Correction: Immune system adaptation during gender-affirming testosterone treatment.", "authors": [{"family": "Lakshmikanth", "given": "Tadepally", "initials": "T", "orcid": "0000-0001-7256-5770", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/28e45f00f5f247389409f0411d412da1.json"}}, {"family": "Consiglio", "given": "Camila", "initials": "C", "orcid": "0000-0002-8901-2328", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a786e29de11b41dd9da2b680ad5b351f.json"}}, {"family": "Sardh", "given": "Fabian", "initials": "F"}, {"family": "Forlin", "given": "Rikard", "initials": "R"}, {"family": "Wang", "given": "Jun", "initials": "J"}, {"family": "Tan", "given": "Ziyang", "initials": "Z"}, {"family": "Barcenilla", "given": "Hugo", "initials": "H", "orcid": "0000-0002-7255-362X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7bbd3a04481c4423856fd02092b32b89.json"}}, {"family": "Rodriguez", "given": "Lucie", "initials": "L", "orcid": "0000-0002-3692-9060", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4bc5e1ca94da426495051d3db0dd7a88.json"}}, {"family": "Sugrue", "given": "Jamie", "initials": "J"}, {"family": "Noori", "given": "Peri", "initials": "P"}, {"family": "Ivanchenko", "given": "Margarita", "initials": "M"}, {"family": "Pi\u00f1ero P\u00e1ez", "given": "Laura", "initials": "L"}, {"family": "Gonzalez", "given": "Laura", "initials": "L"}, {"family": "Habimana Mugabo", "given": "Constantin", "initials": "C"}, {"family": "Johnsson", "given": "Anette", "initials": "A"}, {"family": "Ryberg", "given": "Henrik", "initials": "H"}, {"family": "Hallgren", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Pou", "given": "Christian", "initials": "C"}, {"family": "Chen", "given": "Yang", "initials": "Y"}, {"family": "Mike\u0161", "given": "Jarom\u00edr", "initials": "J", "orcid": "0000-0002-9941-7855", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b486baedd784487dbf3e5b7b33f950da.json"}}, {"family": "James", "given": "Anna", "initials": "A"}, {"family": "Dahlqvist", "given": "Per", "initials": "P", "orcid": "0000-0002-6471-9503", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/47c69bcb5cf147879083cfd43c73a82c.json"}}, {"family": "Wahlberg", "given": "Jeanette", "initials": "J", "orcid": "0000-0003-4061-6830", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b1efae9cc4d84ab999328eb418d55d45.json"}}, {"family": "Hagelin", "given": "Anders", "initials": "A"}, {"family": "Holmberg", "given": "Mats", "initials": "M", "orcid": "0000-0003-2884-9981", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/243bc33834b54a49b5ad873e12ed73b0.json"}}, {"family": "Degerblad", "given": "Marie", "initials": "M"}, {"family": "Isaksson", "given": "Magnus", "initials": "M"}, {"family": "Duffy", "given": "Darragh", "initials": "D", "orcid": "0000-0002-8875-2308", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7b526f87dac847bca71b52d02a79f33f.json"}}, {"family": "K\u00e4mpe", "given": "Olle", "initials": "O", "orcid": "0000-0001-6091-9914", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/48f52710708f4b3291e5b5a4eefca8f5.json"}}, {"family": "Landegren", "given": "Nils", "initials": "N"}, {"family": "Brodin", "given": "Petter", "initials": "P", "orcid": "0000-0002-8103-0046", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b5fe1b70e79d48b1bc07ceeec842c3a3.json"}}], "type": "published erratum", "published": "2024-10-00", "journal": {"title": "Nature", "issn": "1476-4687", "volume": "634", "issue": "8033", "pages": "E5", "issn-l": "0028-0836"}, "abstract": null, "doi": "10.1038/s41586-024-08081-w", "pmid": "39317781", "labels": {"Camila Consiglio": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC11464365"}, {"db": "pii", "key": "10.1038/s41586-024-08081-w"}], "notes": [], "created": "2026-08-20T08:59:03.505Z", "modified": "2026-09-23T14:37:35.012Z"}, {"entity": "publication", "iuid": "cbcaa04a1b9846fbb2f642e717396e4c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/cbcaa04a1b9846fbb2f642e717396e4c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/cbcaa04a1b9846fbb2f642e717396e4c"}}, "title": "Assessment of the exposure to cytotoxic Bacillus cereus group genotypes through high-temperature, short-time milk consumption.", "authors": [{"family": "Su", "given": "Jun", "initials": "J"}, {"family": "Chandross-Cohen", "given": "Tyler", "initials": "T"}, {"family": "Qian", "given": "Chenhao", "initials": "C"}, {"family": "Carroll", "given": "Laura", "initials": "L", "orcid": "0000-0002-3677-0192", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02112eccb0664819af916a3c3dc79daa.json"}}, {"family": "Kimble", "given": "Kayla", "initials": "K"}, {"family": "Yount", "given": "Mackenna", "initials": "M"}, {"family": "Wiedmann", "given": "Martin", "initials": "M", "orcid": "0000-0002-4168-5662", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ff5ceeea60684abeb83951c53f7b6e31.json"}}, {"family": "Kovac", "given": "Jasna", "initials": "J", "orcid": "0000-0002-9465-4552", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d18e6f5bd24644e18030b59391d1a755.json"}}], "type": "journal article", "published": "2024-10-00", "journal": {"title": "J Dairy Sci", "issn": "1525-3198", "volume": "107", "issue": "10", "pages": "7631-7647", "issn-l": null}, "abstract": "This study addresses the limited tools available for assessing food safety risks from cytotoxic Bacillus cereus group strains in contaminated food. We quantified the growth, in skim milk broth, of 17 cytotoxic B. cereus strains across 6 phylogenetic groups with various virulence gene profiles. The strains did not grow in HTST milk at 4 or 6\u00b0C. At 10\u00b0C, 15 strains exhibited growth; at 8\u00b0C, one strain grew; and all strains grew at temperatures \u226514\u00b0C. Using growth data from 16 strains, we developed linear secondary growth models and an exposure assessment model. This model, simulating a 5-stage HTST milk supply chain and up to 35 d of consumer storage with an initial contamination of 100 cfu/mL, estimated that 2.81 \u00b1 0.66% and 4.13 \u00b1 2.53% of milk containers would surpass 105 cfu/mL of B. cereus by d 21 and 35, respectively. A sensitivity analysis identified the initial physiological state of cells as the most influential variable affecting predictions for specific isolates. What-if scenarios indicated that increases in mean and variability of consumer storage temperatures significantly affected the predicted B. cereus concentrations in milk. This model serves as an initial tool for risk-based food safety decision-making regarding low-level B. cereus contamination.", "doi": "10.3168/jds.2024-24703", "pmid": "38851576", "labels": {"Laura Carroll": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pii", "key": "S0022-0302(24)00896-8"}], "notes": [], "created": "2025-03-18T17:32:09.737Z", "modified": "2026-09-23T11:33:16.806Z"}, {"entity": "publication", "iuid": "5e60bd26094541689abe0ed9d66ae3c4", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5e60bd26094541689abe0ed9d66ae3c4.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5e60bd26094541689abe0ed9d66ae3c4"}}, "title": "Introducing synthetic thermostable RNase inhibitors to single-cell RNA-seq.", "authors": [{"family": "Noble", "given": "Joyce Carol", "initials": "JC", "orcid": "0000-0002-4450-429X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/26bf6f7884b341c9b1f69a357395ddf7.json"}}, {"family": "Lentini", "given": "Antonio", "initials": "A", "orcid": "0000-0003-1239-5495", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c5042d3005814ad0a2d1eaeee5d2de3b.json"}}, {"family": "Hagemann-Jensen", "given": "Michael", "initials": "M", "orcid": "0000-0002-6423-8216", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7a67d94769764d37a2bf3febd4f79101.json"}}, {"family": "Sandberg", "given": "Rickard", "initials": "R", "orcid": "0000-0001-6473-1740", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/55acae2b727144ddac3ac6bfe51fc74d.json"}}, {"family": "Reinius", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0002-7021-5248", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a7c1abacc8d446bf8855254246b8d899.json"}}], "type": "journal article", "published": "2024-09-27", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "8373", "issn-l": "2041-1723"}, "abstract": "Single-cell RNA-sequencing (scRNAseq) is revolutionizing biomedicine, propelled by advances in methodology, ease of use, and cost reduction of library preparation. Over the past decade, there have been remarkable technical improvements in most aspects of single-cell transcriptomics. Yet, little to no progress has been made in advancing RNase inhibition despite maintained RNA integrity being critical during cell collection, storage, and cDNA library generation. Here, we demonstrate that a synthetic thermostable RNase inhibitor (SEQURNA) yields single-cell libraries of equal or superior quality compared to ubiquitously used protein-based recombinant RNase inhibitors (RRIs). Importantly, the synthetic RNase inhibitor provides additional unique improvements in reproducibility and throughput, enables new experimental workflows including retained RNase inhibition throughout heat cycles, and can reduce the need for dry-ice transports. In summary, replacing RRIs represents a substantial advancement in the field of single-cell transcriptomics.", "doi": "10.1038/s41467-024-52717-4", "pmid": "39333520", "labels": {"Antonio Lentini": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC11437267"}, {"db": "pii", "key": "10.1038/s41467-024-52717-4"}], "notes": [], "created": "2025-03-28T07:03:02.650Z", "modified": "2025-03-28T07:03:02.757Z"}, {"entity": "publication", "iuid": "f2be797a2d714005b3d085b39efb9e16", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f2be797a2d714005b3d085b39efb9e16.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f2be797a2d714005b3d085b39efb9e16"}}, "title": "The Organelle in the Ointment: improved detection of cryptic mitochondrial reads resolves many unknown sequences in cross-species microbiome analyses", "authors": [{"family": "Sonett", "given": "Dylan", "initials": "D", "orcid": "0000-0001-6821-4695", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8b5856f98b0d4ff4b60fbaa463bf1169.json"}}, {"family": "Brown", "given": "Tanya", "initials": "T", "orcid": "0000-0003-0103-7510", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/52bb2f5a91994e0286961713fb099a5d.json"}}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J", "orcid": "0000-0002-6528-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c666068e9d34939b0252a627007cec7.json"}}, {"family": "Padilla-Gami\u00f1o", "given": "Jacqueline L", "initials": "JL", "orcid": "0000-0003-0478-9953", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8c4d81e0f7044728ab945b296b0e3cc9.json"}}, {"family": "Zaneveld", "given": "Jesse R", "initials": "JR", "orcid": "0000-0002-9823-810X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ebe78647d72540e5b42a82874eb6d5c7.json"}}], "type": "journal-article", "published": "2024-09-24", "journal": {"issn": "2730-6151", "title": "ISME Commun", "issn-l": null}, "abstract": null, "doi": "10.1093/ismeco/ycae114", "pmid": null, "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [], "notes": [], "created": "2024-11-18T11:43:52.710Z", "modified": "2025-04-07T06:58:48.764Z"}, {"entity": "publication", "iuid": "51d3f83358734fb0ab52f65ac307207b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/51d3f83358734fb0ab52f65ac307207b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/51d3f83358734fb0ab52f65ac307207b"}}, "title": "Longitudinal analysis of genetic and environmental interplay in human metabolic profiles and the implication for metabolic health", "authors": [{"family": "Wang", "given": "Jing", "initials": "J", "orcid": "0000-0002-9272-5628", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/55d9f6c22c454b938d46b5541d59c995.json"}}, {"family": "Zenere", "given": "Alberto", "initials": "A", "orcid": "0000-0001-5791-7686", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/496af089725f4f67aae0c3b45f8c80e2.json"}}, {"family": "Wang", "given": "Xingyue", "initials": "X", "orcid": "0000-0002-4960-5882", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/73d95100422f464f948451ff0c3bc2f6.json"}}, {"family": "Bergstr\u00f6m", "given": "G\u00f6ran", "initials": "G"}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ea446aa574042a295d5f69437402f76.json"}}, {"family": "Zhong", "given": "Wen", "initials": "W"}], "type": "posted-content", "published": "2024-09-24", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2024.09.23.24314199", "pmid": null, "labels": {"Fredrik Edfors": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T10:58:31.078Z", "modified": "2026-09-23T14:52:04.824Z"}, {"entity": "publication", "iuid": "f60395474e8144699451cb34b3db1c84", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f60395474e8144699451cb34b3db1c84.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f60395474e8144699451cb34b3db1c84"}}, "title": "Longitudinal Exposomics in a Multiomic Wellness Cohort Reveals Distinctive and Dynamic Environmental Chemical Mixtures in Blood.", "authors": [{"family": "Sdougkou", "given": "Kalliroi", "initials": "K", "orcid": "0000-0001-9463-655X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f07679bf36604909b7533419e618a68e.json"}}, {"family": "Papazian", "given": "Stefano", "initials": "S", "orcid": "0000-0003-2538-8702", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/27c56d6b160c42d4b3782d78210e80ff.json"}}, {"family": "Bonnefille", "given": "B\u00e9nilde", "initials": "B", "orcid": "0000-0001-5141-7111", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8df2bdf31f21411a90ccc2f9bb6eaf10.json"}}, {"family": "Xie", "given": "Hongyu", "initials": "H", "orcid": "0000-0002-2422-0492", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/871a1de2d146412693d3cfea85e8e293.json"}}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Bergstr\u00f6m", "given": "G\u00f6ran", "initials": "G"}, {"family": "Martin", "given": "Leah J", "initials": "LJ"}, {"family": "Martin", "given": "Jonathan W", "initials": "JW", "orcid": "0000-0001-6265-4294", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02199c0d99674e2ea5e96e6589c07a00.json"}}], "type": "journal article", "published": "2024-09-17", "journal": {"title": "Environ. Sci. Technol.", "issn": "1520-5851", "volume": "58", "issue": "37", "pages": "16302-16315", "issn-l": "0013-936X"}, "abstract": "Chemical exposomes can now be comprehensively measured in human blood, but knowledge of their variability and longitudinal stability is required for robust application in cohort studies. Here, we applied high-resolution chemical exposomics to plasma of 46 adults, each sampled 6 times over 2 years in a multiomic cohort, resulting in 276 individual exposomes. In addition to quantitative analysis of 83 priority target analytes, we discovered and semiquantified substances that have rarely or never been reported in humans, including personal care products, pesticide transformation products, and polymer additives. Hierarchical cluster analysis for 519 confidently annotated substances revealed unique and distinctive coexposures, including clustered pesticides, poly(ethylene glycols), chlorinated phenols, or natural substances from tea and coffee; interactive heatmaps were publicly deposited to support open exploration of the complex (meta)data. Intraclass correlation coefficients (ICC) for all annotated substances demonstrated the relatively low stability of the exposome compared to that of proteome, microbiome, and endogenous small molecules. Implications are that the chemical exposome must be measured more frequently than other omics in longitudinal studies and four longitudinal exposure types are defined that can be considered in study design. In this small cohort, mixed-effect models nevertheless revealed significant associations between testosterone and perfluoroalkyl substances, demonstrating great potential for longitudinal exposomics in precision health research.", "doi": "10.1021/acs.est.4c05235", "pmid": "39236221", "labels": {"Fredrik Edfors": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC11411717"}], "notes": [], "created": "2026-09-23T09:08:19.813Z", "modified": "2026-09-23T09:08:19.959Z"}, {"entity": "publication", "iuid": "66598865387641aabc6f82b3fa85c7f5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/66598865387641aabc6f82b3fa85c7f5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/66598865387641aabc6f82b3fa85c7f5"}}, "title": "BCL2 expression is enriched in advanced prostate cancer with features of lineage plasticity.", "authors": [{"family": "Westaby", "given": "Daniel", "initials": "D"}, {"family": "Jim\u00e9nez-Vacas", "given": "Juan M", "initials": "JM"}, {"family": "Figueiredo", "given": "Ines", "initials": "I"}, {"family": "Rekowski", "given": "Jan", "initials": "J"}, {"family": "Pettinger", "given": "Claire", "initials": "C"}, {"family": "Gurel", "given": "Bora", "initials": "B"}, {"family": "Lundberg", "given": "Arian", "initials": "A", "orcid": "0000-0002-6630-2787", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/baa2c7c8963840bfb6a22d7c5cfe35f9.json"}}, {"family": "Bogdan", "given": "Denisa", "initials": "D"}, {"family": "Buroni", "given": "Lorenzo", "initials": "L"}, {"family": "Neeb", "given": "Antje", "initials": "A"}, {"family": "Padilha", "given": "Ana", "initials": "A"}, {"family": "Taylor", "given": "Joe", "initials": "J"}, {"family": "Zeng", "given": "Wanting", "initials": "W"}, {"family": "Das", "given": "Souvik", "initials": "S"}, {"family": "Hobern", "given": "Emily", "initials": "E"}, {"family": "Riisnaes", "given": "Ruth", "initials": "R"}, {"family": "Crespo", "given": "Mateus", "initials": "M"}, {"family": "Miranda", "given": "Susana", "initials": "S"}, {"family": "Ferreira", "given": "Ana", "initials": "A"}, {"family": "Hanratty", "given": "Brian P", "initials": "BP"}, {"family": "Nava Rodrigues", "given": "Daniel", "initials": "D"}, {"family": "Bertan", "given": "Claudia", "initials": "C"}, {"family": "Seed", "given": "George", "initials": "G"}, {"family": "Fenor de La Maza", "given": "Maria de Los Dolores", "initials": "MLD"}, {"family": "Guo", "given": "Christina", "initials": "C"}, {"family": "Carmichael", "given": "Juliet", "initials": "J"}, {"family": "Grochot", "given": "Rafael", "initials": "R"}, {"family": "Chandran", "given": "Khobe", "initials": "K"}, {"family": "Stavridi", "given": "Anastasia", "initials": "A"}, {"family": "Varkaris", "given": "Andreas", "initials": "A"}, {"family": "Stylianou", "given": "Nataly", "initials": "N"}, {"family": "Hollier", "given": "Brett G", "initials": "BG"}, {"family": "Tunariu", "given": "Nina", "initials": "N"}, {"family": "Balk", "given": "Steven P", "initials": "SP"}, {"family": "Carreira", "given": "Suzanne", "initials": "S"}, {"family": "Yuan", "given": "Wei", "initials": "W"}, {"family": "Nelson", "given": "Peter S", "initials": "PS"}, {"family": "Corey", "given": "Eva", "initials": "E"}, {"family": "Haffner", "given": "Michael", "initials": "M"}, {"family": "de Bono", "given": "Johann", "initials": "J"}, {"family": "Sharp", "given": "Adam", "initials": "A"}], "type": "journal article", "published": "2024-09-17", "journal": {"title": "J. Clin. Invest.", "issn": "1558-8238", "volume": "134", "issue": "18", "issn-l": "0021-9738"}, "abstract": "The widespread use of potent androgen receptor signaling inhibitors (ARSIs) has led to an increasing emergence of AR-independent castration-resistant prostate cancer (CRPC), typically driven by loss of AR expression, lineage plasticity, and transformation to prostate cancers (PCs) that exhibit phenotypes of neuroendocrine or basal-like cells. The anti-apoptotic protein BCL2 is upregulated in neuroendocrine cancers and may be a therapeutic target for this aggressive PC disease subset. There is an unmet clinical need, therefore, to clinically characterize BCL2 expression in metastatic CRPC (mCRPC), determine its association with AR expression, uncover its mechanisms of regulation, and evaluate BCL2 as a therapeutic target and/or biomarker with clinical utility. Here, using multiple PC biopsy cohorts and models, we demonstrate that BCL2 expression is enriched in AR-negative mCRPC, associating with shorter overall survival and resistance to ARSIs. Moreover, high BCL2 expression associates with lineage plasticity features and neuroendocrine marker positivity. We provide evidence that BCL2 expression is regulated by DNA methylation, associated with epithelial-mesenchymal transition, and increased by the neuronal transcription factor ASCL1. Finally, BCL2 inhibition had antitumor activity in some, but not all, BCL2-positive PC models, highlighting the need for combination strategies to enhance tumor cell apoptosis and enrich response.", "doi": "10.1172/JCI179998", "pmid": "39286979", "labels": {"DDLS Fellow": null, "Arian Lundberg": null}, "xrefs": [{"db": "pmc", "key": "PMC11405043"}, {"db": "pii", "key": "179998"}], "notes": [], "created": "2025-11-14T07:49:55.957Z", "modified": "2026-01-03T12:42:01.813Z"}, {"entity": "publication", "iuid": "2749014de2334181bacad583b927535e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/2749014de2334181bacad583b927535e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/2749014de2334181bacad583b927535e"}}, "title": "An Atlas of Accessible Chromatin in Advanced Prostate Cancer Reveals the Epigenetic Evolution during Tumor Progression.", "authors": [{"family": "Shrestha", "given": "Raunak", "initials": "R", "orcid": "0000-0002-1144-1413", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1ee8056667cd46ecbec79e2789ae8029.json"}}, {"family": "Chesner", "given": "Lisa N", "initials": "LN", "orcid": "0009-0007-2779-8824", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ee8b85578474244893baffac823a58c.json"}}, {"family": "Zhang", "given": "Meng", "initials": "M", "orcid": "0000-0003-1042-6294", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3d24c6c51c024ac0b27a5162c4c2fa91.json"}}, {"family": "Zhou", "given": "Stanley", "initials": "S", "orcid": "0000-0001-8187-0128", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e22a4caa4fe04b2bbf6af8d5149f0383.json"}}, {"family": "Foye", "given": "Adam", "initials": "A", "orcid": "0000-0002-9910-9836", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/74c8c402b4a243ab95b9d20ecc43d4b9.json"}}, {"family": "Lundberg", "given": "Arian", "initials": "A", "orcid": "0000-0002-6630-2787", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/baa2c7c8963840bfb6a22d7c5cfe35f9.json"}}, {"family": "Weinstein", "given": "Alana S", "initials": "AS", "orcid": "0000-0002-1563-9072", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e16ba4d459704a96adc34a85197bab05.json"}}, {"family": "Sj\u00f6str\u00f6m", "given": "Martin", "initials": "M", "orcid": "0000-0002-2629-9966", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b42d7aeedc844018bbe28980b73cb6c6.json"}}, {"family": "Zhu", "given": "Xiaolin", "initials": "X", "orcid": "0000-0002-3221-595X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/30d1c66f02ef4b5abc414a110705ccf9.json"}}, {"family": "Moreno-Rodriguez", "given": "Thaidy", "initials": "T", "orcid": "0000-0003-3588-3889", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/be9adfae1d354f85a76d66de8bc08cba.json"}}, {"family": "Li", "given": "Haolong", "initials": "H", "orcid": "0000-0002-8628-9698", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fbc2d2abba854008b56d417e6083614c.json"}}, {"family": "SU2C/PCF West Coast Prostate Cancer Dream Team", "given": "", "initials": ""}, {"family": "Alumkal", "given": "Joshi J", "initials": "JJ", "orcid": "0000-0003-1278-0166", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/92169d39d28f4819959b032eff1b1b80.json"}}, {"family": "Aggarwal", "given": "Rahul", "initials": "R", "orcid": "0000-0001-7003-7982", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dc6eb510bedd42bbb6f57e03e724efba.json"}}, {"family": "Small", "given": "Eric J", "initials": "EJ", "orcid": "0000-0003-3191-6268", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a5a6d3bacede42059d6bf0f2cbfe0fec.json"}}, {"family": "Lupien", "given": "Mathieu", "initials": "M", "orcid": "0000-0003-0929-9478", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1967a3e4d1ff43998c93ea10d874cd01.json"}}, {"family": "Quigley", "given": "David A", "initials": "DA", "orcid": "0000-0002-4726-1473", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a7672a24a905407c8b5f9d1e28deea02.json"}}, {"family": "Feng", "given": "Felix Y", "initials": "FY", "orcid": "0000-0002-0963-7687", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c5af5c0e774941ac97890f17640a339e.json"}}], "type": "journal article", "published": "2024-09-16", "journal": {"title": "Cancer Res.", "issn": "1538-7445", "volume": "84", "issue": "18", "pages": "3086-3100", "issn-l": "0008-5472"}, "abstract": "Metastatic castration-resistant prostate cancer (mCRPC) is a lethal disease that resists therapy targeting androgen signaling, the primary driver of prostate cancer. mCRPC resists androgen receptor (AR) inhibitors by amplifying AR signaling or by evolving into therapy-resistant subtypes that do not depend on AR. Elucidation of the epigenetic underpinnings of these subtypes could provide important insights into the drivers of therapy resistance. In this study, we produced chromatin accessibility maps linked to the binding of lineage-specific transcription factors (TF) by performing assay for transposase-accessible chromatin sequencing on 70 mCRPC tissue biopsies integrated with transcriptome and whole-genome sequencing. mCRPC had a distinct global chromatin accessibility profile linked to AR function. Analysis of TF occupancy across accessible chromatin revealed 203 TFs associated with mCRPC subtypes. Notably, ZNF263 was identified as a putative prostate cancer TF with a significant impact on gene activity in the double-negative subtype (AR- neuroendocrine-), potentially activating MYC targets. Overall, this analysis of chromatin accessibility in mCRPC provides valuable insights into epigenetic changes that occur during progression to mCRPC. Significance: Integration of a large cohort of transcriptome, whole-genome, and ATAC sequencing characterizes the chromatin accessibility changes in advanced prostate cancer and identifies therapy-resistant prostate cancer subtype-specific transcription factors that modulate oncogenic programs.", "doi": "10.1158/0008-5472.CAN-24-0890", "pmid": "38990734", "labels": {"DDLS Fellow": null, "Arian Lundberg": null}, "xrefs": [{"db": "mid", "key": "NIHMS2049608"}, {"db": "pmc", "key": "PMC12248187"}, {"db": "pii", "key": "746391"}], "notes": [], "created": "2025-11-14T07:49:57.398Z", "modified": "2025-11-14T07:49:57.837Z"}, {"entity": "publication", "iuid": "fa85625093c64a4f8d5f54b783ecbdce", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/fa85625093c64a4f8d5f54b783ecbdce.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/fa85625093c64a4f8d5f54b783ecbdce"}}, "title": "Sequence variants influencing the regulation of serum IgG subclass levels.", "authors": [{"family": "Olafsdottir", "given": "Thorunn A", "initials": "TA", "orcid": "0000-0001-5454-938X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/417237ea231141ce83a9f314aacc4714.json"}}, {"family": "Thorleifsson", "given": "Gudmar", "initials": "G", "orcid": "0000-0003-4623-9087", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3460ce8189d243829543bd5919c42588.json"}}, {"family": "Lopez de Lapuente Portilla", "given": "Aitzkoa", "initials": "A"}, {"family": "Jonsson", "given": "Stefan", "initials": "S"}, {"family": "Stefansdottir", "given": "Lilja", "initials": "L"}, {"family": "Niroula", "given": "Abhishek", "initials": "A", "orcid": "0000-0002-5904-0635", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/05df7afc7a494ba5af8a378e5ffa53f0.json"}}, {"family": "Jonasdottir", "given": "Aslaug", "initials": "A"}, {"family": "Eggertsson", "given": "Hannes P", "initials": "HP", "orcid": "0000-0002-1674-9978", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8c1148fbfcc6416ca8e3229341b6c3c9.json"}}, {"family": "Halldorsson", "given": "Gisli H", "initials": "GH", "orcid": "0000-0001-7067-9862", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/28549aa56c4543178dd7626dbc9e4667.json"}}, {"family": "Thorlacius", "given": "Gudny E", "initials": "GE"}, {"family": "Arnthorsson", "given": "Asgeir O", "initials": "AO"}, {"family": "Bjornsdottir", "given": "Unnur S", "initials": "US"}, {"family": "Asselbergs", "given": "Folkert W", "initials": "FW", "orcid": "0000-0002-1692-8669", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/181a8a467ca54344b574d248cc98f1d3.json"}}, {"family": "Bentlage", "given": "Arthur E H", "initials": "AEH", "orcid": "0000-0002-7924-554X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/381bbbaf3dd942029554efdfd15c425a.json"}}, {"family": "Eyjolfsson", "given": "Gudmundur I", "initials": "GI"}, {"family": "Gudmundsdottir", "given": "Steinunn", "initials": "S", "orcid": "0000-0001-9317-0903", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ab6ef8f8394e4892b48792cb0795a03b.json"}}, {"family": "Gunnarsdottir", "given": "Kristbjorg", "initials": "K"}, {"family": "Halldorsson", "given": "Bjarni V", "initials": "BV", "orcid": "0000-0003-0756-0767", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fb4e875f04154f40b3f50fd7596d083f.json"}}, {"family": "Holm", "given": "Hilma", "initials": "H", "orcid": "0000-0002-9517-6636", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4c040c4c22346f8902fe25320c0c8f5.json"}}, {"family": "Ludviksson", "given": "Bjorn R", "initials": "BR"}, {"family": "Melsted", "given": "Pall", "initials": "P"}, {"family": "Norddahl", "given": "Gudmundur L", "initials": "GL"}, {"family": "Olafsson", "given": "Isleifur", "initials": "I"}, {"family": "Saevarsdottir", "given": "Saedis", "initials": "S", "orcid": "0000-0001-9392-6184", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eb3c8823bb4d41d1a207f7be6d9ac63b.json"}}, {"family": "Sigurdardottir", "given": "Olof", "initials": "O"}, {"family": "Sigurdsson", "given": "Asgeir", "initials": "A"}, {"family": "Temming", "given": "Robin", "initials": "R"}, {"family": "\u00d6nundarson", "given": "Pall T", "initials": "PT"}, {"family": "Thorsteinsdottir", "given": "Unnur", "initials": "U"}, {"family": "Vidarsson", "given": "Gestur", "initials": "G", "orcid": "0000-0001-5621-003X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5bfa1f126aaa46f99f6c5151caab36d0.json"}}, {"family": "Sulem", "given": "Patrick", "initials": "P", "orcid": "0000-0001-7123-6123", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/587ca1614f654c4e9a96a84fdab962f4.json"}}, {"family": "Gudbjartsson", "given": "Daniel F", "initials": "DF", "orcid": "0000-0002-5222-9857", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/11758dde6b6e4d0cad421e39719b2821.json"}}, {"family": "Jonsdottir", "given": "Ingileif", "initials": "I", "orcid": "0000-0001-8339-150X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4f4e82de44504a55b50b0378447318f8.json"}}, {"family": "Nilsson", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-5542-0254", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2e9df5bbe6f948b196a65176963748c8.json"}}, {"family": "Stefansson", "given": "Kari", "initials": "K", "orcid": "0000-0003-1676-864X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9edf80871ac84e76a4d1316fc7079d7d.json"}}], "type": "journal article", "published": "2024-09-14", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "8054", "issn-l": "2041-1723"}, "abstract": "Immunoglobulin G (IgG) is the main isotype of antibody in human blood. IgG consists of four subclasses (IgG1 to IgG4), encoded by separate constant region genes within the Ig heavy chain locus (IGH). Here, we report a genome-wide association study on blood IgG subclass levels. Across 4334 adults and 4571 individuals under 18 years, we discover ten new and identify four known variants at five loci influencing IgG subclass levels. These variants also affect the risk of asthma, autoimmune diseases, and blood traits. Seven variants map to the IGH locus, three to the Fc\u03b3 receptor (FCGR) locus, and two to the human leukocyte antigen (HLA) region, affecting the levels of all IgG subclasses. The most significant associations are observed between the G1m (f), G2m(n) and G3m(b*) allotypes, and IgG1, IgG2 and IgG3, respectively. Additionally, we describe selective associations with IgG4 at 16p11.2 (ITGAX) and 17q21.1 (IKZF3, ZPBP2, GSDMB, ORMDL3). Interestingly, the latter coincides with a highly pleiotropic signal where the allele associated with lower IgG4 levels protects against childhood asthma but predisposes to inflammatory bowel disease. Our results provide insight into the regulation of antibody-mediated immunity that can potentially be useful in the development of antibody based therapeutics.", "doi": "10.1038/s41467-024-52470-8", "pmid": "39277589", "labels": {"Abhishek Niroula": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC11401918"}, {"db": "pii", "key": "10.1038/s41467-024-52470-8"}], "notes": [], "created": "2025-03-18T15:48:56.925Z", "modified": "2025-03-18T15:49:15.318Z"}, {"entity": "publication", "iuid": "e201025534c2440d959f408409bef326", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e201025534c2440d959f408409bef326.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e201025534c2440d959f408409bef326"}}, "title": "Long-term longitudinal analysis of 4,187 participants reveals insights into determinants of clonal hematopoiesis.", "authors": [{"family": "Uddin", "given": "Md Mesbah", "initials": "MM", "orcid": "0000-0003-1846-0411", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/42f1ac7010c34ba997a3fd9e56c6a56a.json"}}, {"family": "Saadatagah", "given": "Seyedmohammad", "initials": "S"}, {"family": "Niroula", "given": "Abhishek", "initials": "A", "orcid": "0000-0002-5904-0635", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/05df7afc7a494ba5af8a378e5ffa53f0.json"}}, {"family": "Yu", "given": "Bing", "initials": "B", "orcid": "0000-0003-4818-1077", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e408849bd8f14fd99a2ae255990c1f49.json"}}, {"family": "Hornsby", "given": "Whitney E", "initials": "WE"}, {"family": "Ganesh", "given": "Shriienidhie", "initials": "S", "orcid": "0000-0002-4226-7526", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ab02750ae47045b08d78ad814c146e00.json"}}, {"family": "Lannery", "given": "Kim", "initials": "K"}, {"family": "Schuermans", "given": "Art", "initials": "A", "orcid": "0000-0001-8146-9692", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/af284c3bd9304f54ac7b8c9970ce56be.json"}}, {"family": "Honigberg", "given": "Michael C", "initials": "MC", "orcid": "0000-0001-8630-5021", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c541cd0864c947a6bafa7ad6e78bfe49.json"}}, {"family": "Bick", "given": "Alexander G", "initials": "AG", "orcid": "0000-0001-5824-9595", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d2da5a35a4984921b19dfafe64cea2de.json"}}, {"family": "Libby", "given": "Peter", "initials": "P", "orcid": "0000-0002-1502-502X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/39fb20acff0442bd92fc7931d3ee6cf9.json"}}, {"family": "Ebert", "given": "Benjamin L", "initials": "BL", "orcid": "0000-0003-0197-5451", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56e4f1c53a4348e2b0ceb44a38850a17.json"}}, {"family": "Ballantyne", "given": "Christie M", "initials": "CM", "orcid": "0000-0002-6432-1730", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/27dc5297c262410bad3bbb66a488d4b4.json"}}, {"family": "Natarajan", "given": "Pradeep", "initials": "P", "orcid": "0000-0001-8402-7435", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fe8bd48c61c047cd8e61c35d9e9ac650.json"}}], "type": "journal article", "published": "2024-09-09", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "7858", "issn-l": "2041-1723"}, "abstract": "Clonal hematopoiesis of indeterminate potential (CHIP) is linked to diverse aging-related diseases, including hematologic malignancy and atherosclerotic cardiovascular disease (ASCVD). While CHIP is common among older adults, the underlying factors driving its development are largely unknown. To address this, we performed whole-exome sequencing on 8,374 blood DNA samples collected from 4,187 Atherosclerosis Risk in Communities Study (ARIC) participants over a median follow-up of 21 years. During this period, 735 participants developed incident CHIP. Splicing factor genes (SF3B1, SRSF2, U2AF1, and ZRSR2) and TET2 CHIP grow significantly faster than DNMT3A non-R882 clones. We find that age at baseline and sex significantly influence the incidence of CHIP, while ASCVD and other traditional ASCVD risk factors do not exhibit such associations. Additionally, baseline synonymous passenger mutations are strongly associated with CHIP status and are predictive of new CHIP clone acquisition and clonal growth over extended follow-up, providing valuable insights into clonal dynamics of aging hematopoietic stem and progenitor cells. This study also reveals associations between germline genetic variants and incident CHIP. Our comprehensive longitudinal assessment yields insights into cell-intrinsic and -extrinsic factors contributing to the development and progression of CHIP clones in older adults.", "doi": "10.1038/s41467-024-52302-9", "pmid": "39251642", "labels": {"Abhishek Niroula": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC11385577"}, {"db": "pii", "key": "10.1038/s41467-024-52302-9"}], "notes": [], "created": "2025-03-18T15:48:55.530Z", "modified": "2026-09-23T08:51:41.660Z"}, {"entity": "publication", "iuid": "c848f64abd814890b0e81b905eea5401", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c848f64abd814890b0e81b905eea5401.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c848f64abd814890b0e81b905eea5401"}}, "title": "The protein domains of vertebrate species in which selection is more effective have greater intrinsic structural disorder", "authors": [{"family": "Weibel", "given": "Catherine A", "initials": "CA", "orcid": "0000-0003-1837-5209", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/54d6dc2af7084fc58d9ab18aa72423e7.json"}}, {"family": "Wheeler", "given": "Andrew L", "initials": "AL", "orcid": "0000-0002-5347-5419", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d5be19398f37475282b6d184b7e77cfe.json"}}, {"family": "James", "given": "Jennifer E", "initials": "JE", "orcid": "0000-0003-0518-6783", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4b807f7ab8f46f8a5e927e1b090d662.json"}}, {"family": "Willis", "given": "Sara M", "initials": "SM", "orcid": "0000-0002-1605-6426", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6316b06885844b32a451c3b8ab502060.json"}}, {"family": "McShea", "given": "Hanon", "initials": "H", "orcid": "0000-0002-9341-4899", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/04a9138ad6834af4be9e2d3c255cc1c9.json"}}, {"family": "Masel", "given": "Joanna", "initials": "J", "orcid": "0000-0002-7398-2127", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eed69f257e574f4aa53f59349c3ff384.json"}}], "type": "journal-article", "published": "2024-09-06", "journal": {"title": "Elife", "issn": "2050-084X", "issn-l": "2050-084X", "volume": "12", "issue": null, "pages": null}, "abstract": null, "doi": "10.7554/elife.87335.3", "pmid": null, "labels": {"Jennifer James": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2024-11-27T09:19:34.636Z", "modified": "2024-11-29T09:34:08.559Z"}, {"entity": "publication", "iuid": "1841172623c942da95a8488067ca4e7d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1841172623c942da95a8488067ca4e7d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1841172623c942da95a8488067ca4e7d"}}, "title": "Deep learning segmentation model produces accurate biodiversity predictions at 10 m spatial resolution", "authors": [{"family": "Andermann", "given": "Tobias", "initials": "T", "orcid": "0000-0002-0932-1623", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dfff478dfcfc43ddbd40bb1bafbcb0a7.json"}}, {"family": "H\u00e4ggmark", "given": "Johan", "initials": "J"}, {"family": "Olsson", "given": "Patrik", "initials": "P"}, {"family": "H\u00f6gstr\u00f6m", "given": "Alice", "initials": "A"}], "type": "posted-content", "published": "2024-09-05", "journal": {"issn-l": null}, "abstract": null, "doi": "10.21203/rs.3.rs-4734879/v1", "pmid": null, "labels": {"Tobias Andermann": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2025-03-18T16:05:15.169Z", "modified": "2025-03-18T16:06:32.582Z"}, {"entity": "publication", "iuid": "d0d9f4529b454091948f6278108b824f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d0d9f4529b454091948f6278108b824f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d0d9f4529b454091948f6278108b824f"}}, "title": "Caveolin assemblies displace one bilayer leaflet to organize and bend membranes.", "authors": [{"family": "Doktorova", "given": "Milka", "initials": "M", "orcid": "0000-0003-4366-2242", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/791384c319f04584bac8ffb21df7271f.json"}}, {"family": "Daum", "given": "Sebastian", "initials": "S"}, {"family": "Ebenhan", "given": "Jan", "initials": "J"}, {"family": "Neudorf", "given": "Sarah", "initials": "S"}, {"family": "Han", "given": "Bing", "initials": "B"}, {"family": "Sharma", "given": "Satyan", "initials": "S"}, {"family": "Kasson", "given": "Peter", "initials": "P"}, {"family": "Levental", "given": "Kandice R", "initials": "KR", "orcid": "0000-0002-2234-3683", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dcde4d3042b349b199c48509444ac8f9.json"}}, {"family": "Bacia", "given": "Kirsten", "initials": "K"}, {"family": "Kenworthy", "given": "Anne K", "initials": "AK", "orcid": "0000-0001-6567-9059", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/16cb5a7a473b4373a243bcfa6ff36708.json"}}, {"family": "Levental", "given": "Ilya", "initials": "I", "orcid": "0000-0002-1206-9545", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7fe40c2b810348cab78616402d4d1f1f.json"}}], "type": "journal article", "published": "2024-09-04", "journal": {"title": "bioRxiv", "issn": "2692-8205", "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": "Caveolin is a monotopic integral membrane protein, widely expressed in metazoa and responsible for constructing enigmatic membrane invaginations known as caveolae. Recently, the high-resolution structure of a purified human caveolin assembly, the CAV1-8S complex, revealed a unique organization of 11 protomers arranged in a tightly packed, radially symmetric spiral disc. One face and the outer rim of this disc are highly hydrophobic, suggesting that the complex incorporates into membranes by displacing hundreds of lipids from one leaflet. The feasibility of this unique molecular architecture and its biophysical and functional consequences are currently unknown. Using Langmuir film balance measurements, we find that CAV1-8S is highly surface active and intercalates into lipid monolayers. Molecular simulations of biomimetic bilayers support this 'leaflet replacement' model and reveal that while CAV1-8S effectively displaces phospholipids from one bilayer leaflet, it accumulates 40-70 cholesterol molecules into a disordered monolayer between the complex and its distal lipid leaflet. We find that CAV1-8S preferentially associates with positively curved membrane surfaces due to its influence on the conformations of distal leaflet lipids, and that these effects laterally sort lipids of the distal leaflet. Large-scale simulations of multiple caveolin assemblies confirmed their association with large, positively curved membrane morphologies, consistent with the shape of caveolae. Further, association with curved membranes regulates the exposure of caveolin residues implicated in protein-protein interactions. Altogether, the unique structure of CAV1-8S imparts unusual modes of membrane interaction with implications for membrane organization, morphology, and physiology.", "doi": "10.1101/2024.08.28.610209", "pmid": "39257813", "labels": {"Milka Doktorova": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC11383982"}, {"db": "pii", "key": "2024.08.28.610209"}], "notes": [], "created": "2024-11-27T12:17:07.688Z", "modified": "2024-11-29T08:18:08.278Z"}, {"entity": "publication", "iuid": "df7405442f3c44d5ab58e01a7d89a1a3", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/df7405442f3c44d5ab58e01a7d89a1a3.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/df7405442f3c44d5ab58e01a7d89a1a3"}}, "title": "Cryo-EM images of phase-separated lipid bilayer vesicles analyzed with a machine-learning approach.", "authors": [{"family": "Sharma", "given": "Karan D", "initials": "KD"}, {"family": "Doktorova", "given": "Milka", "initials": "M", "orcid": "0000-0003-4366-2242", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/791384c319f04584bac8ffb21df7271f.json"}}, {"family": "Waxham", "given": "M Neal", "initials": "MN", "orcid": "0000-0003-4801-1190", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ba2f5e1eeb4144ecbf0ef9a7bb01cdae.json"}}, {"family": "Heberle", "given": "Frederick A", "initials": "FA", "orcid": "0000-0002-0424-3240", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2557f5621a0b4c87b5f4702fbc7b6bdb.json"}}], "type": "journal article", "published": "2024-09-03", "journal": {"title": "Biophys. J.", "issn": "1542-0086", "issn-l": "0006-3495", "volume": "123", "issue": "17", "pages": "2877-2891"}, "abstract": "Lateral lipid heterogeneity (i.e., raft formation) in biomembranes plays a functional role in living cells. Three-component mixtures of low- and high-melting lipids plus cholesterol offer a simplified experimental model for raft domains in which a liquid-disordered (Ld) phase coexists with a liquid-ordered (Lo) phase. Using such models, we recently showed that cryogenic electron microscopy (cryo-EM) can detect phase separation in lipid vesicles based on differences in bilayer thickness. However, the considerable noise within cryo-EM data poses a significant challenge for accurately determining the membrane phase state at high spatial resolution. To this end, we have developed an image-processing pipeline that utilizes machine learning (ML) to predict the bilayer phase in projection images of lipid vesicles. Importantly, the ML method exploits differences in both the thickness and molecular density of Lo compared to Ld, which leads to improved phase identification. To assess accuracy, we used artificial images of phase-separated lipid vesicles generated from all-atom molecular dynamics simulations of Lo and Ld phases. Synthetic ground-truth data sets mimicking a series of compositions along a tieline of Ld + Lo coexistence were created and then analyzed with various ML models. For all tieline compositions, we find that the ML approach can correctly identify the bilayer phase with >90% accuracy, thus providing a means to isolate the intensity profiles of coexisting Ld and Lo phases, as well as accurately determine domain-size distributions, number of domains, and phase-area fractions. The method described here provides a framework for characterizing nanoscopic lateral heterogeneities in membranes and paves the way for a more detailed understanding of raft properties in biological contexts.", "doi": "10.1016/j.bpj.2024.04.029", "pmid": "38689500", "labels": {"Milka Doktorova": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC11393711"}, {"db": "pii", "key": "S0006-3495(24)00291-1"}], "notes": [], "created": "2024-11-27T12:18:13.240Z", "modified": "2024-11-29T08:17:29.429Z"}, {"entity": "publication", "iuid": "b56b283fd207440294400d3c909cf1d7", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b56b283fd207440294400d3c909cf1d7.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b56b283fd207440294400d3c909cf1d7"}}, "title": "Immune system adaptation during gender-affirming testosterone treatment.", "authors": [{"family": "Lakshmikanth", "given": "Tadepally", "initials": "T", "orcid": "0000-0001-7256-5770", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/28e45f00f5f247389409f0411d412da1.json"}}, {"family": "Consiglio", "given": "Camila", "initials": "C", "orcid": "0000-0002-8901-2328", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a786e29de11b41dd9da2b680ad5b351f.json"}}, {"family": "Sardh", "given": "Fabian", "initials": "F"}, {"family": "Forlin", "given": "Rikard", "initials": "R"}, {"family": "Wang", "given": "Jun", "initials": "J"}, {"family": "Tan", "given": "Ziyang", "initials": "Z"}, {"family": "Barcenilla", "given": "Hugo", "initials": "H", "orcid": "0000-0002-7255-362X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7bbd3a04481c4423856fd02092b32b89.json"}}, {"family": "Rodriguez", "given": "Lucie", "initials": "L", "orcid": "0000-0002-3692-9060", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4bc5e1ca94da426495051d3db0dd7a88.json"}}, {"family": "Sugrue", "given": "Jamie", "initials": "J"}, {"family": "Noori", "given": "Peri", "initials": "P"}, {"family": "Ivanchenko", "given": "Margarita", "initials": "M"}, {"family": "Pi\u00f1ero P\u00e1ez", "given": "Laura", "initials": "L"}, {"family": "Gonzalez", "given": "Laura", "initials": "L"}, {"family": "Habimana Mugabo", "given": "Constantin", "initials": "C"}, {"family": "Johnsson", "given": "Anette", "initials": "A"}, {"family": "Ryberg", "given": "Henrik", "initials": "H"}, {"family": "Hallgren", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Pou", "given": "Christian", "initials": "C"}, {"family": "Chen", "given": "Yang", "initials": "Y"}, {"family": "Mike\u0161", "given": "Jarom\u00edr", "initials": "J", "orcid": "0000-0002-9941-7855", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b486baedd784487dbf3e5b7b33f950da.json"}}, {"family": "James", "given": "Anna", "initials": "A"}, {"family": "Dahlqvist", "given": "Per", "initials": "P", "orcid": "0000-0002-6471-9503", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/47c69bcb5cf147879083cfd43c73a82c.json"}}, {"family": "Wahlberg", "given": "Jeanette", "initials": "J", "orcid": "0000-0003-4061-6830", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b1efae9cc4d84ab999328eb418d55d45.json"}}, {"family": "Hagelin", "given": "Anders", "initials": "A"}, {"family": "Holmberg", "given": "Mats", "initials": "M", "orcid": "0000-0003-2884-9981", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/243bc33834b54a49b5ad873e12ed73b0.json"}}, {"family": "Degerblad", "given": "Marie", "initials": "M"}, {"family": "Isaksson", "given": "Magnus", "initials": "M"}, {"family": "Duffy", "given": "Darragh", "initials": "D", "orcid": "0000-0002-8875-2308", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7b526f87dac847bca71b52d02a79f33f.json"}}, {"family": "K\u00e4mpe", "given": "Olle", "initials": "O", "orcid": "0000-0001-6091-9914", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/48f52710708f4b3291e5b5a4eefca8f5.json"}}, {"family": "Landegren", "given": "Nils", "initials": "N"}, {"family": "Brodin", "given": "Petter", "initials": "P", "orcid": "0000-0002-8103-0046", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b5fe1b70e79d48b1bc07ceeec842c3a3.json"}}], "type": "journal article", "published": "2024-09-00", "journal": {"title": "Nature", "issn": "1476-4687", "volume": "633", "issue": "8028", "pages": "155-164", "issn-l": "0028-0836"}, "abstract": "Infectious, inflammatory and autoimmune conditions present differently in males and females. SARS-CoV-2 infection in naive males is associated with increased risk of death, whereas females are at increased risk of long COVID1, similar to observations in other infections2. Females respond more strongly to vaccines, and adverse reactions are more frequent3, like most autoimmune diseases4. Immunological sex differences stem from genetic, hormonal and behavioural factors5 but their relative importance is only partially understood6-8. In individuals assigned female sex at birth and undergoing gender-affirming testosterone therapy (trans men), hormone concentrations change markedly but the immunological consequences are poorly understood. Here we performed longitudinal systems-level analyses in 23 trans men and found that testosterone modulates a cross-regulated axis between type-I interferon and tumour necrosis factor. This is mediated by functional attenuation of type-I interferon responses in both plasmacytoid dendritic cells and monocytes. Conversely, testosterone potentiates monocyte responses leading to increased tumour necrosis factor, interleukin-6 and interleukin-15 production and downstream activation of nuclear factor kappa B-regulated genes and potentiation of interferon-\u03b3 responses, primarily in natural killer cells. These findings in trans men are corroborated by sex-divergent responses in public datasets and illustrate the dynamic regulation of human immunity by sex hormones, with implications for the health of individuals undergoing hormone therapy and our understanding of sex-divergent immune responses in cisgender individuals.", "doi": "10.1038/s41586-024-07789-z", "pmid": "39232147", "labels": {"Camila Consiglio": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC11374716"}, {"db": "pii", "key": "10.1038/s41586-024-07789-z"}], "notes": [], "created": "2026-09-23T07:30:18.956Z", "modified": "2026-09-23T07:30:19.110Z"}, {"entity": "publication", "iuid": "45c0b7df1fa142928e4779500f9ec487", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/45c0b7df1fa142928e4779500f9ec487.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/45c0b7df1fa142928e4779500f9ec487"}}, "title": "Characterization of reduced astrocyte creatine kinase levels in Alzheimer's disease.", "authors": [{"family": "Zheng", "given": "Tianyu", "initials": "T"}, {"family": "Kotol", "given": "David", "initials": "D", "orcid": "0000-0002-5388-3826", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c41f8f491c474e6bba2047b5d04b4af5.json"}}, {"family": "Sj\u00f6berg", "given": "Rebecca", "initials": "R"}, {"family": "Mitsios", "given": "Nicholas", "initials": "N", "orcid": "0000-0001-6243-4953", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9443771d4c464bf6b18fc130b329444b.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Zhong", "given": "Wen", "initials": "W"}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Mulder", "given": "Jan", "initials": "J", "orcid": "0000-0003-3717-5018", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/40ed8170792444b491519e499d51c434.json"}}], "type": "journal article", "published": "2024-09-00", "journal": {"title": "Glia", "issn": "1098-1136", "volume": "72", "issue": "9", "pages": "1590-1603", "issn-l": "0894-1491"}, "abstract": "The creatine-phosphocreatine cycle serves as a crucial temporary energy buffering system in the brain, regulated by brain creatine kinase (CKB), in maintaining Adenosine triphosphate (ATP) levels. Alzheimer's disease (AD) has been linked to increased CKB oxidation and loss of its regulatory function, although specific pathological processes and affected cell types remain unclear. In our study, cerebral cortex samples from individuals with AD, dementia with Lewy bodies (DLB), and age-matched controls were analyzed using antibody-based methods to quantify CKB levels and assess alterations associated with disease processes. Two independently validated antibodies exclusively labeled astrocytes in the human cerebral cortex. Combining immunofluorescence (IF) and mass spectrometry (MS), we explored CKB availability in AD and DLB cases. IF and Western blot analysis demonstrated a loss of CKB immunoreactivity correlated with increased plaque load, severity of tau pathology, and Lewy body pathology. However, transcriptomics data and targeted MS demonstrated unaltered total CKB levels, suggesting posttranslational modifications (PTMs) affecting antibody binding. This aligns with altered efficiency at proteolytic cleavage sites indicated in the targeted MS experiment. These findings highlight that the proper function of astrocytes, understudied in the brain compared with neurons, is highly affected by PTMs. Reduction in ATP levels within astrocytes can disrupt ATP-dependent processes, such as the glutamate-glutamine cycle. As CKB and the creatine-phosphocreatine cycle are important in securing constant ATP availability, PTMs in CKB, and astrocyte dysfunction may disturb homeostasis, driving excitotoxicity in the AD brain. CKB and its activity could be promising biomarkers for monitoring early-stage energy deficits in AD.", "doi": "10.1002/glia.24569", "pmid": "38856187", "labels": {"Fredrik Edfors": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T06:33:00.041Z", "modified": "2026-09-23T11:20:39.849Z"}, {"entity": "publication", "iuid": "9d3ae19204374be7af05422af89c88cc", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9d3ae19204374be7af05422af89c88cc.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9d3ae19204374be7af05422af89c88cc"}}, "title": "Structure prediction of alternative protein conformations.", "authors": [{"family": "Bryant", "given": "Patrick", "initials": "P", "orcid": "0000-0003-3439-1866", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a683bcf98234ff09b2398976583b66f.json"}}, {"family": "No\u00e9", "given": "Frank", "initials": "F", "orcid": "0000-0003-4169-9324", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/852838b35de241a38712a04dbbd6b938.json"}}], "type": "journal article", "published": "2024-08-26", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "15", "issue": "1", "pages": "7328"}, "abstract": "Proteins are dynamic molecules whose movements result in different conformations with different functions. Neural networks such as AlphaFold2 can predict the structure of single-chain proteins with conformations most likely to exist in the PDB. However, almost all protein structures with multiple conformations represented in the PDB have been used while training these models. Therefore, it is unclear whether alternative protein conformations can be genuinely predicted using these networks, or if they are simply reproduced from memory. Here, we train a structure prediction network, Cfold, on a conformational split of the PDB to generate alternative conformations. Cfold enables efficient exploration of the conformational landscape of monomeric protein structures. Over 50% of experimentally known nonredundant alternative protein conformations evaluated here are predicted with high accuracy (TM-score > 0.8).", "doi": "10.1038/s41467-024-51507-2", "pmid": "39187507", "labels": {"Patrick Bryant": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC11347660"}, {"db": "pii", "key": "10.1038/s41467-024-51507-2"}], "notes": [], "created": "2024-10-17T12:20:23.876Z", "modified": "2026-09-23T07:41:00.939Z"}, {"entity": "publication", "iuid": "abb9b59b3c704c368ae9354c12331e64", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/abb9b59b3c704c368ae9354c12331e64.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/abb9b59b3c704c368ae9354c12331e64"}}, "title": "Mechanistic modeling of cell viability assays with in silico lineage tracing.", "authors": [{"family": "Mutsuddy", "given": "Arnab", "initials": "A", "orcid": "0000-0001-6488-7067", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8e14f7a9dc804ab1bccf030cc31a121b.json"}}, {"family": "Huggins", "given": "Jonah R", "initials": "JR", "orcid": "0000-0001-7468-4626", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7cba794166d94144af105b8894423e35.json"}}, {"family": "Amrit", "given": "Aurore", "initials": "A"}, {"family": "Erdem", "given": "Cemal", "initials": "C", "orcid": "0000-0003-3663-3646", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f71b5af589264614a52eefa8baba3132.json"}}, {"family": "Calhoun", "given": "Jon C", "initials": "JC", "orcid": "0000-0001-7191-4422", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f7fd93361af9415f94fef93a4d60783c.json"}}, {"family": "Birtwistle", "given": "Marc R", "initials": "MR", "orcid": "0000-0002-0341-0705", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/df52e09a2f984f10833bda7b554b1a22.json"}}], "type": "journal article", "published": "2024-08-26", "journal": {"title": "bioRxiv", "issn": "2692-8205", "issn-l": null}, "abstract": "Data from cell viability assays, which measure cumulative division and death events in a population and reflect substantial cellular heterogeneity, are widely available. However, interpreting such data with mechanistic computational models is hindered because direct model/data comparison is often muddled. We developed an algorithm that tracks simulated division and death events in mechanistically detailed single-cell lineages to enable such a model/data comparison and suggest causes of cell-cell drug response variability. Using our previously developed model of mammalian single-cell proliferation and death signaling, we simulated drug dose response experiments for four targeted anti-cancer drugs (alpelisib, neratinib, trametinib and palbociclib) and compared them to experimental data. Simulations are consistent with data for strong growth inhibition by trametinib (MEK inhibitor) and overall lack of efficacy for alpelisib (PI-3K inhibitor), but are inconsistent with data for palbociclib (CDK4/6 inhibitor) and neratinib (EGFR inhibitor). Model/data inconsistencies suggest (i) the importance of CDK4/6 for driving the cell cycle may be overestimated, and (ii) that the cellular balance between basal (tonic) and ligand-induced signaling is a critical determinant of receptor inhibitor response. Simulations show subpopulations of rapidly and slowly dividing cells in both control and drug-treated conditions. Variations in mother cells prior to drug treatment all impinging on ERK pathway activity are associated with the rapidly dividing phenotype and trametinib resistance. This work lays a foundation for the application of mechanistic modeling to large-scale cell viability assay datasets and better understanding determinants of cellular heterogeneity in drug response.", "doi": "10.1101/2024.08.23.609433", "pmid": "39253474", "labels": {"DDLS Fellow": null, "Cemal Erdem": null}, "xrefs": [{"db": "pmc", "key": "PMC11383287"}, {"db": "pii", "key": "2024.08.23.609433"}], "notes": [], "created": "2024-11-27T20:00:23.828Z", "modified": "2024-11-27T20:00:23.965Z"}, {"entity": "publication", "iuid": "af34a78ef45b4385ac61311527634ea9", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/af34a78ef45b4385ac61311527634ea9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/af34a78ef45b4385ac61311527634ea9"}}, "title": "Multi-layered dosage compensation of the avian Z chromosome", "authors": [{"family": "Papanicolaou", "given": "Natali", "initials": "N", "orcid": "0000-0002-2931-3241", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ffb7037b0b6e453ba9aab04fd1eec4bf.json"}}, {"family": "Lentini", "given": "Antonio", "initials": "A", "orcid": "0000-0003-1239-5495", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c5042d3005814ad0a2d1eaeee5d2de3b.json"}}, {"family": "Wettersten", "given": "Sebastian", "initials": "S", "orcid": "0009-0008-3414-9299", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2c7abebfbe1f4b568cb8a72393d3166f.json"}}, {"family": "Hagemann-Jensen", "given": "Michael", "initials": "M", "orcid": "0000-0002-6423-8216", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7a67d94769764d37a2bf3febd4f79101.json"}}, {"family": "Kr\u00fcger", "given": "Annika", "initials": "A", "orcid": "0000-0002-2482-0316", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c45726bfa8be44969c411364691a469a.json"}}, {"family": "Zhang", "given": "Jilin", "initials": "J", "orcid": "0000-0002-9976-1605", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/59d5fd56d8bc40a9b96e1b495de959fd.json"}}, {"family": "Coucoravas", "given": "Christos", "initials": "C"}, {"family": "Petrosian", "given": "Ioannis", "initials": "I"}, {"family": "Xin", "given": "Xian", "initials": "X", "orcid": "0000-0003-1460-5978", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2c9a25d6dd5f4a2dab3917305298b34c.json"}}, {"family": "Ceyhan", "given": "Ilhan", "initials": "I", "orcid": "0000-0002-3495-1264", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/29b4386e3b3e4ad9adc637df1a8fad85.json"}}, {"family": "Rorbach", "given": "Joanna", "initials": "J", "orcid": "0000-0002-2891-2840", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0a00abe0efcc458d8879f14186202a63.json"}}, {"family": "Wright", "given": "Dominic", "initials": "D", "orcid": "0000-0003-2329-2635", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/57c57f05024e4508902848b015aac021.json"}}, {"family": "Reinius", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0002-7021-5248", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a7c1abacc8d446bf8855254246b8d899.json"}}], "type": "posted-content", "published": "2024-08-20", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2024.08.20.608780", "pmid": null, "labels": {"Antonio Lentini": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2025-03-28T07:03:10.677Z", "modified": "2025-03-28T07:03:10.909Z"}, {"entity": "publication", "iuid": "f90df874d6ad48c58ed647c139f3997e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f90df874d6ad48c58ed647c139f3997e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f90df874d6ad48c58ed647c139f3997e"}}, "title": "Defining Vaginal Community Dynamics: daily microbiome transitions, the role of menstruation, bacteriophages, and bacterial genes.", "authors": [{"family": "Hugerth", "given": "Luisa W", "initials": "LW", "orcid": "0000-0001-5432-1764", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/246ed7b405dd4c3f9ec5e7ff9f1d3ade.json"}}, {"family": "Krog", "given": "Maria Christine", "initials": "MC", "orcid": "0000-0002-2110-0479", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bdd65c5105f4480692383dae8d4ac986.json"}}, {"family": "Vomstein", "given": "Kilian", "initials": "K"}, {"family": "Du", "given": "Juan", "initials": "J", "orcid": "0000-0001-7649-9571", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f67834a614ca4cd4aff026e5e9a1a1e4.json"}}, {"family": "Bashir", "given": "Zahra", "initials": "Z", "orcid": "0000-0002-2497-282X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2d15fce497fe4cdabd82e994e7cd83ad.json"}}, {"family": "Kaldhusdal", "given": "Vilde", "initials": "V"}, {"family": "Fransson", "given": "Emma", "initials": "E", "orcid": "0000-0001-9010-8522", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8c05290187ec426b8804eefc3d954971.json"}}, {"family": "Engstrand", "given": "Lars", "initials": "L", "orcid": "0000-0002-7713-2373", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02d8684df81e42169e613de803446fbf.json"}}, {"family": "Nielsen", "given": "Henriette Svarre", "initials": "HS", "orcid": "0000-0003-2106-8103", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9a99fa7ebb204c618ed70f29be0085b3.json"}}, {"family": "Schuppe-Koistinen", "given": "Ina", "initials": "I", "orcid": "0000-0002-1423-3089", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/659fb04e6a1a430cbd707b8a50d500a3.json"}}], "type": "journal article", "published": "2024-08-19", "journal": {"title": "Microbiome", "issn": "2049-2618", "volume": "12", "issue": "1", "pages": "153", "issn-l": "2049-2618"}, "abstract": "The composition of the vaginal microbiota during the menstrual cycle is dynamic, with some women remaining eu- or dysbiotic and others transitioning between these states. What defines these dynamics, and whether these differences are microbiome-intrinsic or mostly driven by the host is unknown. To address this, we characterized 49 healthy, young women by metagenomic sequencing of daily vaginal swabs during a menstrual cycle. We classified the dynamics of the vaginal microbiome and assessed the impact of host behavior as well as microbiome differences at the species, strain, gene, and phage levels.\n\nBased on the daily shifts in community state types (CSTs) during a menstrual cycle, the vaginal microbiome was classified into four Vaginal Community Dynamics (VCDs) and reported in a classification tool, named VALODY: constant eubiotic, constant dysbiotic, menses-related, and unstable dysbiotic. The abundance of bacteria, phages, and bacterial gene content was compared between the four VCDs. Women with different VCDs showed significant differences in relative phage abundance and bacterial composition even when assigned to the same CST. Women with unstable VCDs had higher phage counts and were more likely dominated by L. iners. Their Gardnerella spp. strains were also more likely to harbor bacteriocin-coding genes.\n\nThe VCDs present a novel time series classification that highlights the complexity of varying degrees of vaginal dysbiosis. Knowing the differences in phage gene abundances and the genomic strains present allows a deeper understanding of the initiation and maintenance of permanent dysbiosis. Applying the VCDs to further characterize the different types of microbiome dynamics qualifies the investigation of disease and enables comparisons at individual and population levels. Based on our data, to be able to classify a dysbiotic sample into the accurate VCD, clinicians would need two to three mid-cycle samples and two samples during menses. In the future, it will be important to address whether transient VCDs pose a similar risk profile to persistent dysbiosis with similar clinical outcomes. This framework may aid interdisciplinary translational teams in deciphering the role of the vaginal microbiome in women's health and reproduction. Video Abstract.", "doi": "10.1186/s40168-024-01870-5", "pmid": "39160615", "labels": {"Luisa Hugerth": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC11331738"}, {"db": "pii", "key": "10.1186/s40168-024-01870-5"}], "notes": [], "created": "2025-03-19T07:35:44.797Z", "modified": "2026-09-23T08:48:26.480Z"}, {"entity": "publication", "iuid": "7f64126faf774b5f82b51639f91b2e8a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/7f64126faf774b5f82b51639f91b2e8a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/7f64126faf774b5f82b51639f91b2e8a"}}, "title": "Escherichia coli in urban marine sediments: interpreting virulence, biofilm formation, halotolerance, and antibiotic resistance to infer contamination or naturalization.", "authors": [{"family": "Erb", "given": "Isabel K", "initials": "IK"}, {"family": "Suarez", "given": "Carolina", "initials": "C"}, {"family": "Frank", "given": "Ellinor M", "initials": "EM"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J", "orcid": "0000-0002-6528-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c666068e9d34939b0252a627007cec7.json"}}, {"family": "Lindberg", "given": "Elisabet", "initials": "E"}, {"family": "Paul", "given": "Catherine J", "initials": "CJ", "orcid": "0000-0003-0323-8359", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/adaa89b4cf6945bebfe382aa1dbfd1a0.json"}}], "type": "journal article", "published": "2024-08-14", "journal": {"title": "FEMS Microbes", "issn": "2633-6685", "volume": "5", "pages": "xtae024", "issn-l": null}, "abstract": "Marine sediments have been suggested as a reservoir for pathogenic bacteria, including Escherichia coli. The origins, and properties promoting survival of E. coli in marine sediments (including osmotolerance, biofilm formation capacity, and antibiotic resistance), have not been well-characterized. Phenotypes and genotypes of 37 E. coli isolates from coastal marine sediments were characterized. The isolates were diverse: 30 sequence types were identified that have been previously documented in humans, livestock, and other animals. Virulence genes were found in all isolates, with more virulence genes found in isolates sampled from sediment closer to the effluent discharge point of a wastewater treatment plant. Antibiotic resistance was demonstrated phenotypically for one isolate, which also carried tetracycline resistance genes on a plasmid. Biofilm formation capacity varied for the different isolates, with most biofilm formed by phylogroup B1 isolates. All isolates were halotolerant, growing at 3.5% NaCl. This suggests that the properties of some isolates may facilitate survival in marine environments and can explain in part how marine sediments can be a reservoir for pathogenic E. coli. As disturbance of sediment could resuspend bacteria, this should be considered as a potential contributor to compromised bathing water quality at nearby beaches.", "doi": "10.1093/femsmc/xtae024", "pmid": "39246828", "labels": {"DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC11378635"}, {"db": "pii", "key": "xtae024"}], "notes": [], "created": "2024-11-18T11:43:54.851Z", "modified": "2026-09-23T11:27:50.175Z"}, {"entity": "publication", "iuid": "66ba9aefeb424a47927a105ce3d9e02a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/66ba9aefeb424a47927a105ce3d9e02a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/66ba9aefeb424a47927a105ce3d9e02a"}}, "title": "Genomic and transcriptomic features of androgen receptor signaling inhibitor resistance in metastatic castration-resistant prostate cancer.", "authors": [{"family": "Zhu", "given": "Xiaolin", "initials": "X"}, {"family": "Farsh", "given": "Tatyanah", "initials": "T"}, {"family": "Vis", "given": "Dani\u00ebl", "initials": "D"}, {"family": "Yu", "given": "Ivan", "initials": "I"}, {"family": "Li", "given": "Haolong", "initials": "H"}, {"family": "Liu", "given": "Tianyi", "initials": "T"}, {"family": "Sj\u00f6str\u00f6m", "given": "Martin", "initials": "M"}, {"family": "Shrestha", "given": "Raunak", "initials": "R"}, {"family": "Kneppers", "given": "Jeroen", "initials": "J"}, {"family": "Severson", "given": "Tesa", "initials": "T"}, {"family": "Zhang", "given": "Meng", "initials": "M"}, {"family": "Lundberg", "given": "Arian", "initials": "A", "orcid": "0000-0002-6630-2787", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/baa2c7c8963840bfb6a22d7c5cfe35f9.json"}}, {"family": "Moreno Rodriguez", "given": "Thaidy", "initials": "T"}, {"family": "Weinstein", "given": "Alana S", "initials": "AS"}, {"family": "Foye", "given": "Adam", "initials": "A"}, {"family": "Mehra", "given": "Niven", "initials": "N"}, {"family": "Aggarwal", "given": "Rahul R", "initials": "RR"}, {"family": "Bergman", "given": "Andries M", "initials": "AM"}, {"family": "Small", "given": "Eric J", "initials": "EJ"}, {"family": "Lack", "given": "Nathan A", "initials": "NA"}, {"family": "Zwart", "given": "Wilbert", "initials": "W"}, {"family": "Quigley", "given": "David A", "initials": "DA"}, {"family": "van der Heijden", "given": "Michiel S", "initials": "MS"}, {"family": "Feng", "given": "Felix Y", "initials": "FY"}], "type": "journal article", "published": "2024-08-13", "journal": {"title": "J. Clin. Invest.", "issn": "1558-8238", "volume": "134", "issue": "19", "issn-l": "0021-9738"}, "abstract": "BACKGROUNDAndrogen receptor signaling inhibitors (ARSIs) have improved outcomes for patients with metastatic castration-resistant prostate cancer (mCRPC), but their clinical benefit is limited by treatment resistance.METHODSTo investigate the mechanisms of ARSI resistance, we analyzed the whole-genome (n = 45) and transcriptome (n = 31) sequencing data generated from paired metastatic biopsies obtained before initiation of first-line ARSI therapy for mCRPC and after radiographic disease progression. We investigated the effects of genetic and pharmacologic modulation of SSTR1 in 22Rv1 cells, a representative mCRPC cell line.RESULTSWe confirmed the predominant role of tumor genetic alterations converging on augmenting androgen receptor (AR) signaling and the increased transcriptional heterogeneity and lineage plasticity during the emergence of ARSI resistance. We further identified amplifications involving a putative enhancer downstream of the AR and transcriptional downregulation of SSTR1, encoding somatostatin receptor 1, in ARSI-resistant tumors. We found that patients with SSTR1-low mCRPC tumors derived less benefit from subsequent ARSI therapy in a retrospective cohort. We showed that SSTR1 was antiproliferative in 22Rv1 cells and that the FDA-approved drug pasireotide suppressed 22Rv1 cell proliferation.CONCLUSIONOur findings expand the knowledge of ARSI resistance and point out actionable next steps, exemplified by potentially targeting SSTR1, to improve patient outcomes.FUNDINGNational Cancer Institute (NCI), NIH; Prostate Cancer Foundation; Conquer Cancer, American Society of Clinical Oncology Foundation; UCSF Benioff Initiative for Prostate Cancer Research; Netherlands Cancer Institute.", "doi": "10.1172/JCI178604", "pmid": "39352383", "labels": {"DDLS Fellow": null, "Arian Lundberg": null}, "xrefs": [{"db": "pmc", "key": "PMC11444163"}, {"db": "pii", "key": "178604"}], "notes": [], "created": "2025-11-14T07:50:00.511Z", "modified": "2026-01-03T12:42:33.115Z"}, {"entity": "publication", "iuid": "c0fc1ac6d9704cacb375132e24f50c91", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c0fc1ac6d9704cacb375132e24f50c91.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c0fc1ac6d9704cacb375132e24f50c91"}}, "title": "Deciphering the genetics and mechanisms of predisposition to multiple myeloma.", "authors": [{"family": "Went", "given": "Molly", "initials": "M", "orcid": "0000-0003-3271-975X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0ec75486d11444c89b8f8a8d81d22bda.json"}}, {"family": "Duran-Lozano", "given": "Laura", "initials": "L"}, {"family": "Halldorsson", "given": "Gisli H", "initials": "GH", "orcid": "0000-0001-7067-9862", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/28549aa56c4543178dd7626dbc9e4667.json"}}, {"family": "Gunnell", "given": "Andrea", "initials": "A", "orcid": "0000-0001-5162-5391", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/879f235469b443259ce663d029e7cdf8.json"}}, {"family": "Ugidos-Damboriena", "given": "Nerea", "initials": "N"}, {"family": "Law", "given": "Philip", "initials": "P", "orcid": "0000-0001-9663-4611", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/499974f99dfe4fdd87a73034acb98d3e.json"}}, {"family": "Ekdahl", "given": "Ludvig", "initials": "L"}, {"family": "Sud", "given": "Amit", "initials": "A", "orcid": "0000-0002-6133-0164", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/058d01f444ad44469b82a5b08ffe6aa2.json"}}, {"family": "Thorleifsson", "given": "Gudmar", "initials": "G", "orcid": "0000-0003-4623-9087", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3460ce8189d243829543bd5919c42588.json"}}, {"family": "Thodberg", "given": "Malte", "initials": "M", "orcid": "0000-0001-6244-3841", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7f2c232400714922bdbd28e77ede971e.json"}}, {"family": "Olafsdottir", "given": "Thorunn", "initials": "T", "orcid": "0000-0001-5454-938X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/417237ea231141ce83a9f314aacc4714.json"}}, {"family": "Lamarca-Arrizabalaga", "given": "Antton", "initials": "A", "orcid": "0009-0008-3426-2347", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8c28e60407d84e159c09d6789d087264.json"}}, {"family": "Cafaro", "given": "Caterina", "initials": "C"}, {"family": "Niroula", "given": "Abhishek", "initials": "A", "orcid": "0000-0002-5904-0635", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/05df7afc7a494ba5af8a378e5ffa53f0.json"}}, {"family": "Ajore", "given": "Ram", "initials": "R"}, {"family": "Lopez de Lapuente Portilla", "given": "Aitzkoa", "initials": "A"}, {"family": "Ali", "given": "Zain", "initials": "Z"}, {"family": "Pertesi", "given": "Maroulio", "initials": "M", "orcid": "0000-0002-4869-8925", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1395ddcc49604bc1a05ea52f7b1ad79a.json"}}, {"family": "Goldschmidt", "given": "Hartmut", "initials": "H", "orcid": "0000-0003-0961-0035", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f634b54dfdbd48bb9f53f574e0cfd023.json"}}, {"family": "Stefansdottir", "given": "Lilja", "initials": "L"}, {"family": "Kristinsson", "given": "Sigurdur Y", "initials": "SY"}, {"family": "Stacey", "given": "Simon N", "initials": "SN", "orcid": "0000-0002-4732-7380", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c0dcdf7567e1416482442d565b8005c0.json"}}, {"family": "Love", "given": "Thorvardur J", "initials": "TJ"}, {"family": "Rognvaldsson", "given": "Saemundur", "initials": "S"}, {"family": "Hajek", "given": "Roman", "initials": "R", "orcid": "0000-0001-6955-6267", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7099912b8d2d400d864ba440cacd434c.json"}}, {"family": "Vodicka", "given": "Pavel", "initials": "P"}, {"family": "Pettersson-Kymmer", "given": "Ulrika", "initials": "U", "orcid": "0000-0002-0557-9803", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6e219143aebf4a5386f19f01f6e1d237.json"}}, {"family": "Sp\u00e4th", "given": "Florentin", "initials": "F"}, {"family": "Schinke", "given": "Carolina", "initials": "C", "orcid": "0000-0002-2699-1741", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a0367de9c18a41b5ba34821157acc0b1.json"}}, {"family": "Van Rhee", "given": "Frits", "initials": "F", "orcid": "0000-0001-9959-1282", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b7cb56c62bce4c51947aed1b0ee21887.json"}}, {"family": "Sulem", "given": "Patrick", "initials": "P", "orcid": "0000-0001-7123-6123", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/587ca1614f654c4e9a96a84fdab962f4.json"}}, {"family": "Ferkingstad", "given": "Egil", "initials": "E", "orcid": "0000-0001-8090-7988", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/503c894e23fc4ceea1316b6a089ab889.json"}}, {"family": "Hjorleifsson Eldjarn", "given": "Grimur", "initials": "G", "orcid": "0000-0002-9580-6685", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/98aff0e76e114696aaaabadc5ec18388.json"}}, {"family": "Mellqvist", "given": "Ulf-Henrik", "initials": "UH"}, {"family": "Jonsdottir", "given": "Ingileif", "initials": "I", "orcid": "0000-0001-8339-150X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4f4e82de44504a55b50b0378447318f8.json"}}, {"family": "Morgan", "given": "Gareth", "initials": "G", "orcid": "0000-0002-4271-6360", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bf94973d06d4414a98855c4506453f6c.json"}}, {"family": "Sonneveld", "given": "Pieter", "initials": "P"}, {"family": "Waage", "given": "Anders", "initials": "A", "orcid": "0000-0001-9072-1220", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/04b9b219373b4dea9950e8a7ae9f6f0b.json"}}, {"family": "Weinhold", "given": "Niels", "initials": "N"}, {"family": "Thomsen", "given": "Hauke", "initials": "H"}, {"family": "F\u00f6rsti", "given": "Asta", "initials": "A", "orcid": "0000-0002-9857-4728", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a2356cdc19c040348a7924e3dd4b8c32.json"}}, {"family": "Hansson", "given": "Markus", "initials": "M", "orcid": "0000-0002-7715-4548", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9aabef8e26ba40d9abd8e229d954795d.json"}}, {"family": "Juul-Vangsted", "given": "Annette", "initials": "A", "orcid": "0000-0002-2131-731X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7eadc85ce9564aeb838718479df147ff.json"}}, {"family": "Thorsteinsdottir", "given": "Unnur", "initials": "U"}, {"family": "Hemminki", "given": "Kari", "initials": "K"}, {"family": "Kaiser", "given": "Martin", "initials": "M", "orcid": "0000-0002-3677-4804", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/61695044f08e4490a7feaf7db2aacc07.json"}}, {"family": "Rafnar", "given": "Thorunn", "initials": "T", "orcid": "0000-0003-0491-7046", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/67a01e1ebd79473dbc0059d38f066e55.json"}}, {"family": "Stefansson", "given": "Kari", "initials": "K", "orcid": "0000-0003-1676-864X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9edf80871ac84e76a4d1316fc7079d7d.json"}}, {"family": "Houlston", "given": "Richard", "initials": "R", "orcid": "0000-0002-5268-0242", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e7605f3f03f94e1b95c011318f5e5d4c.json"}}, {"family": "Nilsson", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-5542-0254", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2e9df5bbe6f948b196a65176963748c8.json"}}], "type": "journal article", "published": "2024-08-05", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "6644", "issn-l": "2041-1723"}, "abstract": "Multiple myeloma (MM) is an incurable malignancy of plasma cells. Epidemiological studies indicate a substantial heritable component, but the underlying mechanisms remain unclear. Here, in a genome-wide association study totaling 10,906 cases and 366,221 controls, we identify 35 MM risk loci, 12 of which are novel. Through functional fine-mapping and Mendelian randomization, we uncover two causal mechanisms for inherited MM risk: longer telomeres; and elevated levels of B-cell maturation antigen (BCMA) and interleukin-5 receptor alpha (IL5RA) in plasma. The largest increase in BCMA and IL5RA levels is mediated by the risk variant rs34562254-A at TNFRSF13B. While individuals with loss-of-function variants in TNFRSF13B develop B-cell immunodeficiency, rs34562254-A exerts a gain-of-function effect, increasing MM risk through amplified B-cell responses. Our results represent an analysis of genetic MM predisposition, highlighting causal mechanisms contributing to MM development.", "doi": "10.1038/s41467-024-50932-7", "pmid": "39103364", "labels": {"Abhishek Niroula": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC11300596"}, {"db": "pii", "key": "10.1038/s41467-024-50932-7"}], "notes": [], "created": "2025-03-18T15:48:53.213Z", "modified": "2025-03-18T15:49:12.903Z"}, {"entity": "publication", "iuid": "06ce21f88b7a4e7cadca5ce894dc8666", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/06ce21f88b7a4e7cadca5ce894dc8666.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/06ce21f88b7a4e7cadca5ce894dc8666"}}, "title": "Structure-based virtual screening of vast chemical space as a starting point for drug discovery.", "authors": [{"family": "Carlsson", "given": "Jens", "initials": "J"}, {"family": "Luttens", "given": "Andreas", "initials": "A"}], "type": "journal article", "published": "2024-08-00", "journal": {"title": "Curr. Opin. Struct. Biol.", "issn": "1879-033X", "volume": "87", "pages": "102829", "issn-l": "0959-440X"}, "abstract": "Structure-based virtual screening aims to find molecules forming favorable interactions with a biological macromolecule using computational models of complexes. The recent surge of commercially available chemical space provides the opportunity to search for ligands of therapeutic targets among billions of compounds. This review offers a compact overview of structure-based virtual screens of vast chemical spaces, highlighting successful applications in early drug discovery for therapeutically important targets such as G protein-coupled receptors and viral enzymes. Emphasis is placed on strategies to explore ultra-large chemical libraries and synergies with emerging machine learning techniques. The current opportunities and future challenges of virtual screening are discussed, indicating that this approach will play an important role in the next-generation drug discovery pipeline.", "doi": "10.1016/j.sbi.2024.102829", "pmid": "38848655", "labels": {"SciLifeLab Fellow": "", "Jens Carlsson": "", "Andreas Luttens": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pii", "key": "S0959-440X(24)00056-3"}], "notes": [], "created": "2026-08-20T08:04:21.833Z", "modified": "2026-09-23T08:32:50.144Z"}, {"entity": "publication", "iuid": "468d8c3dab1c48d889d35d3e63b16ac1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/468d8c3dab1c48d889d35d3e63b16ac1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/468d8c3dab1c48d889d35d3e63b16ac1"}}, "title": "Integrated analyses highlight interactions between the three-dimensional genome and DNA, RNA and epigenomic alterations in metastatic prostate cancer.", "authors": [{"family": "Zhao", "given": "Shuang G", "initials": "SG", "orcid": "0000-0002-9166-6507", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c7d9e7e456be4376adb63a3e5ab895a7.json"}}, {"family": "Bootsma", "given": "Matthew", "initials": "M"}, {"family": "Zhou", "given": "Stanley", "initials": "S", "orcid": "0000-0001-8187-0128", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e22a4caa4fe04b2bbf6af8d5149f0383.json"}}, {"family": "Shrestha", "given": "Raunak", "initials": "R", "orcid": "0000-0002-1144-1413", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1ee8056667cd46ecbec79e2789ae8029.json"}}, {"family": "Moreno-Rodriguez", "given": "Thaidy", "initials": "T", "orcid": "0000-0003-3588-3889", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/be9adfae1d354f85a76d66de8bc08cba.json"}}, {"family": "Lundberg", "given": "Arian", "initials": "A", "orcid": "0000-0002-6630-2787", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/baa2c7c8963840bfb6a22d7c5cfe35f9.json"}}, {"family": "Pan", "given": "Chu", "initials": "C"}, {"family": "Arlidge", "given": "Christopher", "initials": "C"}, {"family": "Hawley", "given": "James R", "initials": "JR"}, {"family": "Foye", "given": "Adam", "initials": "A"}, {"family": "Weinstein", "given": "Alana S", "initials": "AS", "orcid": "0000-0002-1563-9072", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e16ba4d459704a96adc34a85197bab05.json"}}, {"family": "Sj\u00f6str\u00f6m", "given": "Martin", "initials": "M", "orcid": "0000-0002-2629-9966", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b42d7aeedc844018bbe28980b73cb6c6.json"}}, {"family": "Zhang", "given": "Meng", "initials": "M", "orcid": "0000-0003-1042-6294", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3d24c6c51c024ac0b27a5162c4c2fa91.json"}}, {"family": "Li", "given": "Haolong", "initials": "H", "orcid": "0000-0002-8628-9698", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fbc2d2abba854008b56d417e6083614c.json"}}, {"family": "Chesner", "given": "Lisa N", "initials": "LN"}, {"family": "Rydzewski", "given": "Nicholas R", "initials": "NR"}, {"family": "Helzer", "given": "Kyle T", "initials": "KT", "orcid": "0000-0003-3853-5564", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7011e2b72c254794baf945f716d3372d.json"}}, {"family": "Shi", "given": "Yue", "initials": "Y", "orcid": "0000-0002-2860-2666", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6128013110c14fedaef6e2ad9924006c.json"}}, {"family": "West Coast Dream Team Consortium", "given": "", "initials": ""}, {"family": "Lynch", "given": "Molly", "initials": "M"}, {"family": "Dehm", "given": "Scott M", "initials": "SM", "orcid": "0000-0002-7827-5579", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eb947d721b424bb190ddf41a808a2cb0.json"}}, {"family": "Lang", "given": "Joshua M", "initials": "JM", "orcid": "0000-0002-0943-8872", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d37a2599fa044894abc8642baa80e00b.json"}}, {"family": "Alumkal", "given": "Joshi J", "initials": "JJ", "orcid": "0000-0003-1278-0166", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/92169d39d28f4819959b032eff1b1b80.json"}}, {"family": "He", "given": "Hansen H", "initials": "HH", "orcid": "0000-0003-2898-3363", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/487cb044249647b2a1608be1a33dff98.json"}}, {"family": "Wyatt", "given": "Alexander W", "initials": "AW", "orcid": "0000-0003-2399-0329", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/41e8ef800a344c68be341f0691438260.json"}}, {"family": "Aggarwal", "given": "Rahul", "initials": "R", "orcid": "0000-0001-7003-7982", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dc6eb510bedd42bbb6f57e03e724efba.json"}}, {"family": "Zwart", "given": "Wilbert", "initials": "W", "orcid": "0000-0002-9823-7289", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/014603af06df4629b83fb3e7aa17710a.json"}}, {"family": "Small", "given": "Eric J", "initials": "EJ", "orcid": "0000-0003-3191-6268", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a5a6d3bacede42059d6bf0f2cbfe0fec.json"}}, {"family": "Quigley", "given": "David A", "initials": "DA", "orcid": "0000-0002-4726-1473", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a7672a24a905407c8b5f9d1e28deea02.json"}}, {"family": "Lupien", "given": "Mathieu", "initials": "M"}, {"family": "Feng", "given": "Felix Y", "initials": "FY", "orcid": "0000-0002-0963-7687", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c5af5c0e774941ac97890f17640a339e.json"}}], "type": "journal article", "published": "2024-08-00", "journal": {"title": "Nat. Genet.", "issn": "1546-1718", "volume": "56", "issue": "8", "pages": "1689-1700", "issn-l": "1061-4036"}, "abstract": "The impact of variations in the three-dimensional structure of the genome has been recognized, but solid cancer tissue studies are limited. Here, we performed integrated deep Hi-C sequencing with matched whole-genome sequencing, whole-genome bisulfite sequencing, 5-hydroxymethylcytosine (5hmC) sequencing and RNA sequencing across a cohort of 80 biopsy samples from patients with metastatic castration-resistant prostate cancer. Dramatic differences were present in gene expression, 5-methylcytosine/5hmC methylation and in structural variation versus mutation rate between A and B (open and closed) chromatin compartments. A subset of tumors exhibited depleted regional chromatin contacts at the AR locus, linked to extrachromosomal circular DNA (ecDNA) and worse response to AR signaling inhibitors. We also identified topological subtypes associated with stark differences in methylation structure, gene expression and prognosis. Our data suggested that DNA interactions may predispose to structural variant formation, exemplified by the recurrent TMPRSS2-ERG fusion. This comprehensive integrated sequencing effort represents a unique clinical tumor resource.", "doi": "10.1038/s41588-024-01826-3", "pmid": "39020220", "labels": {"DDLS Fellow": null, "Arian Lundberg": null}, "xrefs": [{"db": "pmc", "key": "PMC11319208"}, {"db": "pii", "key": "10.1038/s41588-024-01826-3"}], "notes": [], "created": "2025-11-14T07:50:01.698Z", "modified": "2025-11-14T07:50:01.999Z"}, {"entity": "publication", "iuid": "d6df3b28b3934727b1a5080d0cdb303e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d6df3b28b3934727b1a5080d0cdb303e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d6df3b28b3934727b1a5080d0cdb303e"}}, "title": "Exploring Paleogene Tibet's warm temperate environments through target enrichment and phylogenetic niche modelling of Himalayan spiny frogs (Paini, Dicroglossidae).", "authors": [{"family": "Hofmann", "given": "Sylvia", "initials": "S", "orcid": "0000-0003-0621-9049", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5e89cec6cf1d4923a3e8c142c15040c9.json"}}, {"family": "R\u00f6dder", "given": "Dennis", "initials": "D", "orcid": "0000-0002-6108-1639", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6bb748ab1a45479f80ff59042a9f7926.json"}}, {"family": "Andermann", "given": "Tobias", "initials": "T", "orcid": "0000-0002-0932-1623", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dfff478dfcfc43ddbd40bb1bafbcb0a7.json"}}, {"family": "Matschiner", "given": "Michael", "initials": "M", "orcid": "0000-0003-4741-3884", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2afde3b4ccad4b0d91d9330781efb8be.json"}}, {"family": "Riedel", "given": "Jendrian", "initials": "J"}, {"family": "Baniya", "given": "Chitra B", "initials": "CB"}, {"family": "Flecks", "given": "Morris", "initials": "M"}, {"family": "Yang", "given": "Jianhuan", "initials": "J"}, {"family": "Jiang", "given": "Ke", "initials": "K"}, {"family": "Jianping", "given": "Jiang", "initials": "J", "orcid": "0000-0002-1051-7797", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/978939d6044b442a80ea747a418664bd.json"}}, {"family": "Litvinchuk", "given": "Spartak N", "initials": "SN"}, {"family": "Martin", "given": "Sebastian", "initials": "S"}, {"family": "Masroor", "given": "Rafaqat", "initials": "R"}, {"family": "Nothnagel", "given": "Michael", "initials": "M"}, {"family": "Vershinin", "given": "Vladimir", "initials": "V"}, {"family": "Zheng", "given": "Yuchi", "initials": "Y", "orcid": "0000-0002-1155-5293", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/76ed52ac493947af8f56df5e26f3fb22.json"}}, {"family": "Jablonski", "given": "Daniel", "initials": "D"}, {"family": "Schmidt", "given": "Joachim", "initials": "J"}, {"family": "Podsiadlowski", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2024-08-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "volume": "33", "issue": "15", "pages": "e17446", "issn-l": "0962-1083"}, "abstract": "The Cenozoic topographic development of the Himalaya-Tibet orogen (HTO) substantially affected the paleoenvironment and biodiversity patterns of High Asia. However, concepts on the evolution and paleoenvironmental history of the HTO differ massively in timing, elevational increase and sequence of surface uplift of the different elements of the orogen. Using target enrichment of a large set of transcriptome-derived markers, ancestral range estimation and paleoclimatic niche modelling, we assess a recently proposed concept of a warm temperate paleo-Tibet in Asian spiny frogs of the tribe Paini and reconstruct their historical biogeography. That concept was previously developed in invertebrates. Because of their early evolutionary origin, low dispersal capacity, high degree of local endemism, and strict dependence on temperature and humidity, the cladogenesis of spiny frogs may echo the evolution of the HTO paleoenvironment. We show that diversification of main lineages occurred during the early to Mid-Miocene, while the evolution of alpine taxa started during the late Miocene/early Pliocene. Our distribution and niche modelling results indicate range shifts and niche stability that may explain the modern disjunct distributions of spiny frogs. They probably maintained their (sub)tropical or (warm)temperate preferences and moved out of the ancestral paleo-Tibetan area into the Himalaya as the climate shifted, as opposed to adapting in situ. Based on ancestral range estimation, we assume the existence of low-elevation, climatically suitable corridors across paleo-Tibet during the Miocene along the Kunlun, Qiangtang and/or Gangdese Shan. Our results contribute to a deeper understanding of the mechanisms and processes of faunal evolution in the HTO.", "doi": "10.1111/mec.17446", "pmid": "38946613", "labels": {"Tobias Andermann": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2025-03-18T16:02:06.158Z", "modified": "2025-03-18T16:06:30.626Z"}, {"entity": "publication", "iuid": "366e34c3da3349c080465133e71a0427", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/366e34c3da3349c080465133e71a0427.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/366e34c3da3349c080465133e71a0427"}}, "title": "BioImage.IO Chatbot: a community-driven AI assistant for integrative computational bioimaging.", "authors": [{"family": "Lei", "given": "Wanlu", "initials": "W"}, {"family": "Fuster-Barcel\u00f3", "given": "Caterina", "initials": "C", "orcid": "0000-0002-4784-6957", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/881d36fa227445c9b381a03990b5ed49.json"}}, {"family": "Reder", "given": "Gabriel", "initials": "G", "orcid": "0000-0001-8918-0789", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5246d02b7efe4cdb9359e9ae5e8db74d.json"}}, {"family": "Mu\u00f1oz-Barrutia", "given": "Arrate", "initials": "A", "orcid": "0000-0002-1573-1661", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1f71dcceb0284105a7033f2ed195b9c1.json"}}, {"family": "Ouyang", "given": "Wei", "initials": "W", "orcid": "0000-0002-0291-926X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56f601e1d1c6448aab0c3a1e3cffdbfc.json"}}], "type": "letter", "published": "2024-08-00", "journal": {"title": "Nat. Methods", "issn": "1548-7105", "volume": "21", "issue": "8", "pages": "1368-1370", "issn-l": "1548-7091"}, "abstract": null, "doi": "10.1038/s41592-024-02370-y", "pmid": "39122937", "labels": {"Wei Ouyang": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pii", "key": "10.1038/s41592-024-02370-y"}], "notes": [], "created": "2025-12-15T10:00:07.665Z", "modified": "2026-09-23T09:09:19.496Z"}, {"entity": "publication", "iuid": "cd29ce0f417e4e118befac4bc3d0e76c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/cd29ce0f417e4e118befac4bc3d0e76c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/cd29ce0f417e4e118befac4bc3d0e76c"}}, "title": "Complex Polyploids: Origins, Genomic Composition, and Role of Introgressed Alleles.", "authors": [{"family": "Leal", "given": "J Luis", "initials": "JL", "orcid": "0000-0003-0731-7329", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5c8ad8376a7f483ebe91ed2d15d9147a.json"}}, {"family": "Milesi", "given": "Pascal", "initials": "P"}, {"family": "Hodkov\u00e1", "given": "Eva", "initials": "E"}, {"family": "Zhou", "given": "Qiujie", "initials": "Q", "orcid": "0000-0001-7351-2371", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/15244ffd4f4746ddb9ec39e4c038204e.json"}}, {"family": "James", "given": "Jennifer", "initials": "J", "orcid": "0000-0003-0518-6783", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4b807f7ab8f46f8a5e927e1b090d662.json"}}, {"family": "Eklund", "given": "D Magnus", "initials": "DM"}, {"family": "Pyh\u00e4j\u00e4rvi", "given": "Tanja", "initials": "T", "orcid": "0000-0001-6958-5172", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7256c4910788401f873272cf29fedf91.json"}}, {"family": "Saloj\u00e4rvi", "given": "Jarkko", "initials": "J"}, {"family": "Lascoux", "given": "Martin", "initials": "M", "orcid": "0000-0003-1699-9042", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0730d0f9c2524eb19383640612924701.json"}}], "type": "journal article", "published": "2024-07-27", "journal": {"title": "Syst. Biol.", "issn": "1076-836X", "issn-l": "1063-5157", "volume": "73", "issue": "2", "pages": "392-418"}, "abstract": "Introgression allows polyploid species to acquire new genomic content from diploid progenitors or from other unrelated diploid or polyploid lineages, contributing to genetic diversity and facilitating adaptive allele discovery. In some cases, high levels of introgression elicit the replacement of large numbers of alleles inherited from the polyploid's ancestral species, profoundly reshaping the polyploid's genomic composition. In such complex polyploids, it is often difficult to determine which taxa were the progenitor species and which taxa provided additional introgressive blocks through subsequent hybridization. Here, we use population-level genomic data to reconstruct the phylogenetic history of Betula pubescens (downy birch), a tetraploid species often assumed to be of allopolyploid origin and which is known to hybridize with at least four other birch species. This was achieved by modeling polyploidization and introgression events under the multispecies coalescent and then using an approximate Bayesian computation rejection algorithm to evaluate and compare competing polyploidization models. We provide evidence that B. pubescens is the outcome of an autoploid genome doubling event in the common ancestor of B. pendula and its extant sister species, B. platyphylla, that took place approximately 178,000-188,000 generations ago. Extensive hybridization with B. pendula, B. nana, and B. humilis followed in the aftermath of autopolyploidization, with the relative contribution of each of these species to the B. pubescens genome varying markedly across the species' range. Functional analysis of B. pubescens loci containing alleles introgressed from B. nana identified multiple genes involved in climate adaptation, while loci containing alleles derived from B. humilis revealed several genes involved in the regulation of meiotic stability and pollen viability in plant species.", "doi": "10.1093/sysbio/syae012", "pmid": "38613229", "labels": {"SciLifeLab Fellow": "", "Pascal Milesi": "", "Jennifer James": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC11282369"}, {"db": "pii", "key": "7645150"}], "notes": [], "created": "2024-11-26T09:22:05.553Z", "modified": "2026-09-23T09:07:13.460Z"}, {"entity": "publication", "iuid": "442cfbe882b344b6b586a3c9a349c165", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/442cfbe882b344b6b586a3c9a349c165.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/442cfbe882b344b6b586a3c9a349c165"}}, "title": "Multiscale photocatalytic proximity labeling reveals cell surface neighbors on and between cells.", "authors": [{"family": "Lin", "given": "Zhi", "initials": "Z", "orcid": "0000-0001-6662-7330", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/059b4f81da244058a9e7442b149daadf.json"}}, {"family": "Schaefer", "given": "Kaitlin", "initials": "K", "orcid": "0000-0003-4825-1389", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5601fa03584f40e887f7c12e005737ea.json"}}, {"family": "Lui", "given": "Irene", "initials": "I", "orcid": "0000-0002-6171-5443", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1eca2b8ec2d9461b89c962e8f225e192.json"}}, {"family": "Yao", "given": "Zi", "initials": "Z"}, {"family": "Fossati", "given": "Andrea", "initials": "A", "orcid": "0000-0001-5170-4903", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/658637b885384441943698722fad5944.json"}}, {"family": "Swaney", "given": "Danielle L", "initials": "DL", "orcid": "0000-0001-6119-6084", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56317207941d4aaf81ab4d55de5fcba4.json"}}, {"family": "Palar", "given": "Ajikarunia", "initials": "A", "orcid": "0000-0001-9357-6970", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/155427eafdb8474589a735c36ca9f149.json"}}, {"family": "Sali", "given": "Andrej", "initials": "A", "orcid": "0000-0003-0435-6197", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dd70ba581f7e49b886339e8883b7f053.json"}}, {"family": "Wells", "given": "James A", "initials": "JA", "orcid": "0000-0001-8267-5519", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f0c1fc2f2b584824bd489884424e333c.json"}}], "type": "journal article", "published": "2024-07-19", "journal": {"title": "Science (New York, N.Y.)", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "385", "issue": "6706", "pages": "eadl5763"}, "abstract": "Proximity labeling proteomics (PLP) strategies are powerful approaches to yield snapshots of protein neighborhoods. Here, we describe a multiscale PLP method with adjustable resolution that uses a commercially available photocatalyst, Eosin Y, which upon visible light illumination activates different photo-probes with a range of labeling radii. We applied this platform to profile neighborhoods of the oncogenic epidermal growth factor receptor and orthogonally validated more than 20 neighbors using immunoassays and AlphaFold-Multimer prediction. We further profiled the protein neighborhoods of cell-cell synapses induced by bispecific T cell engagers and chimeric antigen receptor T cells. This integrated multiscale PLP platform maps local and distal protein networks on and between cell surfaces, which will aid in the systematic construction of the cell surface interactome, revealing horizontal signaling partners and reveal new immunotherapeutic opportunities.", "doi": "10.1126/science.adl5763", "pmid": "39024454", "labels": {"Andrea Fossati": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2025-03-18T16:51:05.008Z", "modified": "2025-03-21T13:32:58.593Z"}, {"entity": "publication", "iuid": "add7868f9a864a50937dd0d74848f5ba", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/add7868f9a864a50937dd0d74848f5ba.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/add7868f9a864a50937dd0d74848f5ba"}}, "title": "Retraction notice to \"Combined metabolic activators improve metabolic functions in the animal models of neurodegenerative diseases\" [Life Sci. 314 (2023) 121325].", "authors": [{"family": "Turkez", "given": "Hasan", "initials": "H"}, {"family": "Altay", "given": "Ozlem", "initials": "O"}, {"family": "Yildirim", "given": "Serkan", "initials": "S"}, {"family": "Li", "given": "Xiangyu", "initials": "X"}, {"family": "Yang", "given": "Hong", "initials": "H"}, {"family": "Bayram", "given": "Cemil", "initials": "C"}, {"family": "Bolat", "given": "Ismail", "initials": "I"}, {"family": "Oner", "given": "Sena", "initials": "S"}, {"family": "Tozlu", "given": "Ozlem Ozdemir", "initials": "OO"}, {"family": "Arslan", "given": "Mehmet Enes", "initials": "ME"}, {"family": "Arif", "given": "Muhammad", "initials": "M"}, {"family": "Yulug", "given": "Burak", "initials": "B"}, {"family": "Hanoglu", "given": "Lutfu", "initials": "L"}, {"family": "Cankaya", "given": "Seyda", "initials": "S"}, {"family": "Lam", "given": "Simon", "initials": "S"}, {"family": "Velioglu", "given": "Halil Aziz", "initials": "HA"}, {"family": "Coskun", "given": "Ebru", "initials": "E"}, {"family": "Idil", "given": "Ezgi", "initials": "E"}, {"family": "Nogaylar", "given": "Rahim", "initials": "R"}, {"family": "Ozsimsek", "given": "Ahmet", "initials": "A"}, {"family": "Hacimuftuoglu", "given": "Ahmet", "initials": "A"}, {"family": "Shoaie", "given": "Saeed", "initials": "S"}, {"family": "Zhang", "given": "Cheng", "initials": "C"}, {"family": "Nielsen", "given": "Jens", "initials": "J"}, {"family": "Bor\u00e9n", "given": "Jan", "initials": "J"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}], "type": "journal article", "published": "2024-07-15", "journal": {"title": "Life Sci", "issn": "1879-0631", "volume": "349", "pages": "122712", "issn-l": null}, "abstract": null, "doi": "10.1016/j.lfs.2024.122712", "pmid": "38762436", "labels": {"SciLifeLab Fellow": "", "Saeed Shoaie": "", "DDLS Fellow": "", "Adil Mardinoglu": "", "Muhammad Arif": ""}, "xrefs": [{"db": "pii", "key": "S0024-3205(24)00302-3"}], "notes": [], "created": "2026-08-20T08:00:21.484Z", "modified": "2026-09-23T15:38:42.423Z"}, {"entity": "publication", "iuid": "c516e4f79f7c41a6a7bc7b7822cd4a73", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c516e4f79f7c41a6a7bc7b7822cd4a73.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c516e4f79f7c41a6a7bc7b7822cd4a73"}}, "title": "Temporal dynamics of woolly mammoth genome erosion prior to extinction.", "authors": [{"family": "Dehasque", "given": "Marianne", "initials": "M"}, {"family": "Morales", "given": "Hern\u00e1n E", "initials": "HE"}, {"family": "D\u00edez-Del-Molino", "given": "David", "initials": "D"}, {"family": "Pe\u010dnerov\u00e1", "given": "Patr\u00edcia", "initials": "P"}, {"family": "Chac\u00f3n-Duque", "given": "J Camilo", "initials": "JC"}, {"family": "Kanellidou", "given": "Foteini", "initials": "F"}, {"family": "Muller", "given": "H\u00e9lo\u00efse", "initials": "H"}, {"family": "Plotnikov", "given": "Valerii", "initials": "V"}, {"family": "Protopopov", "given": "Albert", "initials": "A"}, {"family": "Tikhonov", "given": "Alexei", "initials": "A"}, {"family": "Nikolskiy", "given": "Pavel", "initials": "P"}, {"family": "Danilov", "given": "Gleb K", "initials": "GK"}, {"family": "Giann\u00ec", "given": "Maddalena", "initials": "M"}, {"family": "van der Sluis", "given": "Laura", "initials": "L"}, {"family": "Higham", "given": "Tom", "initials": "T"}, {"family": "Heintzman", "given": "Peter D", "initials": "PD"}, {"family": "Oskolkov", "given": "Nikolay", "initials": "N"}, {"family": "Gilbert", "given": "M Thomas P", "initials": "MTP"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "van der Valk", "given": "Tom", "initials": "T"}, {"family": "Vartanyan", "given": "Sergey", "initials": "S"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L"}], "type": "journal article", "published": "2024-07-11", "journal": {"title": "Cell", "issn": "1097-4172", "volume": "187", "issue": "14", "pages": "3531-3540.e13", "issn-l": "0092-8674"}, "abstract": "A number of species have recently recovered from near-extinction. Although these species have avoided the immediate extinction threat, their long-term viability remains precarious due to the potential genetic consequences of population declines, which are poorly understood on a timescale beyond a few generations. Woolly mammoths (Mammuthus primigenius) became isolated on Wrangel Island around 10,000 years ago and persisted for over 200 generations before becoming extinct around 4,000 years ago. To study the evolutionary processes leading up to the mammoths' extinction, we analyzed 21 Siberian woolly mammoth genomes. Our results show that the population recovered quickly from a severe bottleneck and remained demographically stable during the ensuing six millennia. We find that mildly deleterious mutations gradually accumulated, whereas highly deleterious mutations were purged, suggesting ongoing inbreeding depression that lasted for hundreds of generations. The time-lag between demographic and genetic recovery has wide-ranging implications for conservation management of recently bottlenecked populations.", "doi": "10.1016/j.cell.2024.05.033", "pmid": "38942016", "labels": {"DDLS Fellow": "", "Tom van der Valk": ""}, "xrefs": [{"db": "pii", "key": "S0092-8674(24)00577-4"}], "notes": [], "created": "2026-09-23T08:54:54.097Z", "modified": "2026-09-23T08:54:54.139Z"}, {"entity": "publication", "iuid": "0effefb552b64f16b9d47b8e0bd4482f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0effefb552b64f16b9d47b8e0bd4482f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0effefb552b64f16b9d47b8e0bd4482f"}}, "title": "Characterization of a lipid-based jumbo phage compartment as a hub for early phage infection.", "authors": [{"family": "Mozumdar", "given": "Deepto", "initials": "D"}, {"family": "Fossati", "given": "Andrea", "initials": "A", "orcid": "0000-0001-5170-4903", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/658637b885384441943698722fad5944.json"}}, {"family": "Stevenson", "given": "Erica", "initials": "E"}, {"family": "Guan", "given": "Jingwen", "initials": "J"}, {"family": "Nieweglowska", "given": "Eliza", "initials": "E"}, {"family": "Rao", "given": "Sanjana", "initials": "S"}, {"family": "Agard", "given": "David", "initials": "D"}, {"family": "Swaney", "given": "Danielle L", "initials": "DL", "orcid": "0000-0001-6119-6084", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56317207941d4aaf81ab4d55de5fcba4.json"}}, {"family": "Bondy-Denomy", "given": "Joseph", "initials": "J"}], "type": "journal article", "published": "2024-07-10", "journal": {"title": "Cell Host Microbe", "issn": "1934-6069", "issn-l": "1931-3128", "volume": "32", "issue": "7", "pages": "1050-1058.e7"}, "abstract": "Viral genomes are most vulnerable to cellular defenses at the start of the infection. A family of jumbo phages related to phage \u03a6KZ, which infects Pseudomonas aeruginosa, assembles a protein-based phage nucleus to protect replicating phage DNA, but how it is protected prior to phage nucleus assembly is unclear. We find that host proteins related to membrane and lipid biology interact with injected phage protein, clustering in an early phage infection (EPI) vesicle. The injected virion RNA polymerase (vRNAP) executes early gene expression until phage genome separation from the vRNAP and the EPI vesicle, moving into the nascent proteinaceous phage nucleus. Enzymes involved in DNA replication and CRISPR/restriction immune nucleases are excluded by the EPI vesicle. We propose that the EPI vesicle is rapidly constructed with injected phage proteins, phage DNA, host lipids, and host membrane proteins to enable genome protection, early transcription, localized translation, and to ensure faithful genome transfer to the proteinaceous nucleus.", "doi": "10.1016/j.chom.2024.05.016", "pmid": "38870941", "labels": {"Andrea Fossati": null, "DDLS Fellow": null}, "xrefs": [{"db": "mid", "key": "NIHMS2004244"}, {"db": "pmc", "key": "PMC11239273"}, {"db": "pii", "key": "S1931-3128(24)00188-4"}], "notes": [], "created": "2025-03-18T16:51:13.029Z", "modified": "2025-03-21T13:20:33.888Z"}, {"entity": "publication", "iuid": "93a531466f604c84bd9fe1c6e880c846", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/93a531466f604c84bd9fe1c6e880c846.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/93a531466f604c84bd9fe1c6e880c846"}}, "title": "Broadcasters, receivers, functional groups of metabolites, and the link to heart failure by revealing metabolomic network connectivity.", "authors": [{"family": "Yazdani", "given": "Azam", "initials": "A"}, {"family": "Mendez-Giraldez", "given": "Raul", "initials": "R"}, {"family": "Yazdani", "given": "Akram", "initials": "A"}, {"family": "Wang", "given": "Rui-Sheng", "initials": "RS"}, {"family": "Schaid", "given": "Daniel J", "initials": "DJ"}, {"family": "Kong", "given": "Sek Won", "initials": "SW"}, {"family": "Hadi", "given": "M Reza", "initials": "MR"}, {"family": "Samiei", "given": "Ahmad", "initials": "A"}, {"family": "Samiei", "given": "Esmat", "initials": "E"}, {"family": "Wittenbecher", "given": "Clemens", "initials": "C", "orcid": "0000-0001-7792-877X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2f7d2c289b3c47d5a79d23bd48a3225a.json"}}, {"family": "Lasky-Su", "given": "Jessica", "initials": "J"}, {"family": "Clish", "given": "Clary B", "initials": "CB"}, {"family": "Muehlschlegel", "given": "Jochen D", "initials": "JD"}, {"family": "Marotta", "given": "Francesco", "initials": "F"}, {"family": "Loscalzo", "given": "Joseph", "initials": "J"}, {"family": "Mora", "given": "Samia", "initials": "S", "orcid": "0000-0001-6283-0980", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e1189d5d8e634514b0272b8aad38641f.json"}}, {"family": "Chasman", "given": "Daniel I", "initials": "DI"}, {"family": "Larson", "given": "Martin G", "initials": "MG"}, {"family": "Elsea", "given": "Sarah H", "initials": "SH"}], "type": "journal article", "published": "2024-07-07", "journal": {"title": "Metabolomics", "issn": "1573-3890", "volume": "20", "issue": "4", "pages": "71", "issn-l": "1573-3882"}, "abstract": "Blood-based small molecule metabolites offer easy accessibility and hold significant potential for insights into health processes, the impact of lifestyle, and genetic variation on disease, enabling precise risk prevention. In a prospective study with records of heart failure (HF) incidence, we present metabolite profiling data from individuals without HF at baseline.\n\nWe uncovered the interconnectivity of metabolites using data-driven and causal networks augmented with polygenic factors. Exploring the networks, we identified metabolite broadcasters, receivers, mediators, and subnetworks corresponding to functional classes of metabolites, and provided insights into the link between metabolomic architecture and regulation in health. We incorporated the network structure into the identification of metabolites associated with HF to control the effect of confounding metabolites.\n\nWe identified metabolites associated with higher and lower risk of HF incidence, such as glycine, ureidopropionic and glycocholic acids, and LPC 18:2. These associations were not confounded by the other metabolites due to uncovering the connectivity among metabolites and adjusting each association for the confounding metabolites. Examples of our findings include the direct influence of asparagine on glycine, both of which were inversely associated with HF. These two metabolites were influenced by polygenic factors and only essential amino acids, which are not synthesized in the human body and are obtained directly from the diet.\n\nMetabolites may play a critical role in linking genetic background and lifestyle factors to HF incidence. Revealing the underlying connectivity of metabolites associated with HF strengthens the findings and facilitates studying complex conditions like HF.", "doi": "10.1007/s11306-024-02141-y", "pmid": "38972029", "labels": {"Clemens Wittenbecher": null, "DDLS Fellow": null}, "xrefs": [{"db": "mid", "key": "NIHMS2063675"}, {"db": "pmc", "key": "PMC12060728"}, {"db": "pii", "key": "10.1007/s11306-024-02141-y"}], "notes": [], "created": "2025-03-19T08:18:42.593Z", "modified": "2025-12-09T13:32:41.885Z"}, {"entity": "publication", "iuid": "ca4e877fc2674394b71d586581237b4d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ca4e877fc2674394b71d586581237b4d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ca4e877fc2674394b71d586581237b4d"}}, "title": "A generalizable data-driven model of atrophy heterogeneity and progression in memory clinic settings.", "authors": [{"family": "Baumeister", "given": "Hannah", "initials": "H", "orcid": "0000-0001-5503-6308", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/302449c1b3f840e196daf1c8a17c6fa2.json"}}, {"family": "Vogel", "given": "Jacob W", "initials": "JW", "orcid": "0000-0001-6394-9940", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d2ad5af780c245da9b59a8c80a0b00ff.json"}}, {"family": "Insel", "given": "Philip S", "initials": "PS", "orcid": "0000-0002-6270-5490", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/74882821894141eda7f061a520925d4e.json"}}, {"family": "Kleineidam", "given": "Luca", "initials": "L"}, {"family": "Wolfsgruber", "given": "Steffen", "initials": "S"}, {"family": "Stark", "given": "Melina", "initials": "M"}, {"family": "Gellersen", "given": "Helena M", "initials": "HM"}, {"family": "Yakupov", "given": "Renat", "initials": "R", "orcid": "0000-0002-3868-284X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/30f21cde956f4e3da51f71770efcb8d3.json"}}, {"family": "Schmid", "given": "Matthias C", "initials": "MC"}, {"family": "L\u00fcsebrink", "given": "Falk", "initials": "F"}, {"family": "Brosseron", "given": "Frederic", "initials": "F"}, {"family": "Ziegler", "given": "Gabriel", "initials": "G"}, {"family": "Freiesleben", "given": "Silka D", "initials": "SD"}, {"family": "Preis", "given": "Lukas", "initials": "L"}, {"family": "Schneider", "given": "Luisa-Sophie", "initials": "LS"}, {"family": "Spruth", "given": "Eike J", "initials": "EJ"}, {"family": "Altenstein", "given": "Slawek", "initials": "S"}, {"family": "Lohse", "given": "Andrea", "initials": "A"}, {"family": "Fliessbach", "given": "Klaus", "initials": "K"}, {"family": "Vogt", "given": "Ina R", "initials": "IR"}, {"family": "Bartels", "given": "Claudia", "initials": "C"}, {"family": "Schott", "given": "Bj\u00f6rn H", "initials": "BH", "orcid": "0000-0002-8237-4481", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/231a7bad31c74f6f822c89c59872768b.json"}}, {"family": "Rostamzadeh", "given": "Ayda", "initials": "A"}, {"family": "Glanz", "given": "Wenzel", "initials": "W"}, {"family": "Incesoy", "given": "Enise I", "initials": "EI"}, {"family": "Butryn", "given": "Michaela", "initials": "M"}, {"family": "Janowitz", "given": "Daniel", "initials": "D"}, {"family": "Rauchmann", "given": "Boris-Stephan", "initials": "BS"}, {"family": "Kilimann", "given": "Ingo", "initials": "I"}, {"family": "Goerss", "given": "Doreen", "initials": "D"}, {"family": "Munk", "given": "Matthias H", "initials": "MH"}, {"family": "Hetzer", "given": "Stefan", "initials": "S"}, {"family": "Dechent", "given": "Peter", "initials": "P"}, {"family": "Ewers", "given": "Michael", "initials": "M", "orcid": "0000-0001-5231-1714", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d2368c66c8ea44e4a04f798487a6242a.json"}}, {"family": "Scheffler", "given": "Klaus", "initials": "K"}, {"family": "Wuestefeld", "given": "Anika", "initials": "A"}, {"family": "Strandberg", "given": "Olof", "initials": "O"}, {"family": "van Westen", "given": "Danielle", "initials": "D", "orcid": "0000-0001-8649-9874", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/38afd81dca574f4a9884a1ce97b78e50.json"}}, {"family": "Mattsson-Carlgren", "given": "Niklas", "initials": "N", "orcid": "0000-0002-8885-7724", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb26ae59b2a04f369c5ebc2f2375195a.json"}}, {"family": "Janelidze", "given": "Shorena", "initials": "S"}, {"family": "Stomrud", "given": "Erik", "initials": "E"}, {"family": "Palmqvist", "given": "Sebastian", "initials": "S", "orcid": "0000-0002-9267-1930", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6fbd05e87cfb4057a1a7e41d9fb94aef.json"}}, {"family": "Spottke", "given": "Annika", "initials": "A"}, {"family": "Laske", "given": "Christoph", "initials": "C"}, {"family": "Teipel", "given": "Stefan", "initials": "S", "orcid": "0000-0002-3586-3194", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e9b449fbff504b1484eaac2bb2fb1252.json"}}, {"family": "Perneczky", "given": "Robert", "initials": "R"}, {"family": "Buerger", "given": "Katharina", "initials": "K"}, {"family": "Schneider", "given": "Anja", "initials": "A"}, {"family": "Priller", "given": "Josef", "initials": "J"}, {"family": "Peters", "given": "Oliver", "initials": "O"}, {"family": "Ramirez", "given": "Alfredo", "initials": "A", "orcid": "0000-0003-4991-763X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/da390d70e47a4b4883f4221fe96148b4.json"}}, {"family": "Wiltfang", "given": "Jens", "initials": "J"}, {"family": "Heneka", "given": "Michael T", "initials": "MT"}, {"family": "Wagner", "given": "Michael", "initials": "M"}, {"family": "D\u00fczel", "given": "Emrah", "initials": "E", "orcid": "0000-0002-0139-5388", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/83a4ff611c18448295e1e6d449d8c8fc.json"}}, {"family": "Jessen", "given": "Frank", "initials": "F"}, {"family": "Hansson", "given": "Oskar", "initials": "O", "orcid": "0000-0001-8467-7286", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9292115deece4d9fafc8a02d4a430707.json"}}, {"family": "Berron", "given": "David", "initials": "D", "orcid": "0000-0003-1558-1883", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7a3f4829ce644c23a65a4c13359f17fe.json"}}], "type": "journal article", "published": "2024-07-05", "journal": {"title": "Brain", "issn": "1460-2156", "volume": "147", "issue": "7", "pages": "2400-2413", "issn-l": "0006-8950"}, "abstract": "Memory clinic patients are a heterogeneous population representing various aetiologies of pathological ageing. It is not known whether divergent spatiotemporal progression patterns of brain atrophy, as previously described in Alzheimer's disease patients, are prevalent and clinically meaningful in this group of older adults. To uncover distinct atrophy subtypes, we applied the Subtype and Stage Inference (SuStaIn) algorithm to baseline structural MRI data from 813 participants enrolled in the DELCODE cohort (mean \u00b1 standard deviation, age = 70.67 \u00b1 6.07 years, 52% females). Participants were cognitively unimpaired (n = 285) or fulfilled diagnostic criteria for subjective cognitive decline (n = 342), mild cognitive impairment (n = 118) or dementia of the Alzheimer's type (n = 68). Atrophy subtypes were compared in baseline demographics, fluid Alzheimer's disease biomarker levels, the Preclinical Alzheimer Cognitive Composite (PACC-5) as well as episodic memory and executive functioning. PACC-5 trajectories over up to 240 weeks were examined. To test whether baseline atrophy subtype and stage predicted clinical trajectories before manifest cognitive impairment, we analysed PACC-5 trajectories and mild cognitive impairment conversion rates of cognitively unimpaired participants and those with subjective cognitive decline. Limbic-predominant and hippocampal-sparing atrophy subtypes were identified. Limbic-predominant atrophy initially affected the medial temporal lobes, followed by further temporal regions and, finally, the remaining cortical regions. At baseline, this subtype was related to older age, more pathological Alzheimer's disease biomarker levels, APOE \u03b54 carriership and an amnestic cognitive impairment. Hippocampal-sparing atrophy initially occurred outside the temporal lobe, with the medial temporal lobe spared up to advanced atrophy stages. This atrophy pattern also affected individuals with positive Alzheimer's disease biomarkers and was associated with more generalized cognitive impairment. Limbic-predominant atrophy, in all participants and in only unimpaired participants, was linked to more negative longitudinal PACC-5 slopes than observed in participants without or with hippocampal-sparing atrophy and increased the risk of mild cognitive impairment conversion. SuStaIn modelling was repeated in a sample from the Swedish BioFINDER-2 cohort. Highly similar atrophy progression patterns and associated cognitive profiles were identified. Cross-cohort model generalizability, at both the subject and the group level, was excellent, indicating reliable performance in previously unseen data. The proposed model is a promising tool for capturing heterogeneity among older adults at early at-risk states for Alzheimer's disease in applied settings. The implementation of atrophy subtype- and stage-specific end points might increase the statistical power of pharmacological trials targeting early Alzheimer's disease.", "doi": "10.1093/brain/awae118", "pmid": "38654513", "labels": {"Jacob W Vogel": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC11224599"}, {"db": "pii", "key": "7657064"}], "notes": [], "created": "2025-03-19T11:17:08.204Z", "modified": "2025-03-19T11:19:16.050Z"}, {"entity": "publication", "iuid": "b6884adebcd44c5f85555627116b94ea", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b6884adebcd44c5f85555627116b94ea.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b6884adebcd44c5f85555627116b94ea"}}, "title": "Investigations of microbiota composition and neuroactive pathways in association with symptoms of stress and depression in a cohort of healthy women.", "authors": [{"family": "Bashir", "given": "Zahra", "initials": "Z", "orcid": "0000-0002-2497-282X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2d15fce497fe4cdabd82e994e7cd83ad.json"}}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW", "orcid": "0000-0001-5432-1764", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/246ed7b405dd4c3f9ec5e7ff9f1d3ade.json"}}, {"family": "Krog", "given": "Maria Christine", "initials": "MC", "orcid": "0000-0002-2110-0479", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bdd65c5105f4480692383dae8d4ac986.json"}}, {"family": "Prast-Nielsen", "given": "Stefanie", "initials": "S", "orcid": "0000-0001-5877-7988", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fe13dffa03b24588a919b6b028788a6e.json"}}, {"family": "Edfeldt", "given": "Gabriella", "initials": "G", "orcid": "0000-0003-0366-5588", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bc30318aa3ca4720ac5aa3a982c9f730.json"}}, {"family": "Boulund", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-3806-323X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a5c6814a31e644b9bc544d4da759a438.json"}}, {"family": "Schacht", "given": "Simon R\u00f8nnow", "initials": "SR"}, {"family": "Tetens", "given": "Inge", "initials": "I"}, {"family": "Engstrand", "given": "Lars", "initials": "L", "orcid": "0000-0002-7713-2373", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02d8684df81e42169e613de803446fbf.json"}}, {"family": "Schuppe-Koistinen", "given": "Ina", "initials": "I", "orcid": "0000-0002-1423-3089", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/659fb04e6a1a430cbd707b8a50d500a3.json"}}, {"family": "Fransson", "given": "Emma", "initials": "E", "orcid": "0000-0001-9010-8522", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8c05290187ec426b8804eefc3d954971.json"}}, {"family": "Nielsen", "given": "Henriette Svarre", "initials": "HS", "orcid": "0000-0003-2106-8103", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9a99fa7ebb204c618ed70f29be0085b3.json"}}], "type": "journal article", "published": "2024-07-02", "journal": {"title": "Front. Cell. Infect. Microbiol.", "issn": "2235-2988", "volume": "14", "pages": "1324794", "issn-l": "2235-2988"}, "abstract": "Despite mounting evidence of gut-brain involvement in psychiatric conditions, functional data remain limited, and analyses of other microbial niches, such as the vaginal microbiota, are lacking in relation to mental health. This aim of this study was to investigate if the connections between the gut microbiome and mental health observed in populations with a clinical diagnosis of mental illness extend to healthy women experiencing stress and depressive symptoms. Additionally, this study examined the functional pathways of the gut microbiota according to the levels of psychological symptoms. Furthermore, the study aimed to explore potential correlations between the vaginal microbiome and mental health parameters in young women without psychiatric diagnoses.\n\nIn this cross-sectional study, 160 healthy Danish women (aged 18-40 years) filled out questionnaires with validated scales measuring symptoms of stress and depression and frequency of dietary intake. Fecal and vaginal microbiota samples were collected at the beginning of the menstrual cycle and vaginal samples were also collected at cycle day 8-12 and 18-22. Shotgun metagenomic profiling of the gut and vaginal microbiome was performed. The Kyoto Encyclopedia of Genes and Genomes (KEGG) was used for functional profiling and 56 Gut Brain Modules were analyzed in the fecal samples.\n\nThe relative abundance in the gut of the genera Escherichia, Parabacteroides, and Shigella was higher in women with elevated depressive symptoms. Women with high perceived stress showed a tendency of increased abundance of Escherichia, Shigella, and Blautia. Amongst others, the potentially pathogenic genera, Escherichia and Shigella correlate with alterations in the neuroactive pathways such as the glutamatergic, GABAeric, dopaminergic, and Kynurenine pathways. Vaginosis symptoms were more prevalent in women reporting high levels of stress and depressive symptoms.\n\nThe findings of this study support the concept of a microbiota-associated effect on the neuroactive pathways even in healthy young women. This suggest, that targeting the gut microbiome could be a promising approach for future psychiatric interventions.", "doi": "10.3389/fcimb.2024.1324794", "pmid": "39015337", "labels": {"Luisa Hugerth": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC11249552"}], "notes": [], "created": "2025-03-19T07:35:43.556Z", "modified": "2026-09-23T11:26:14.203Z"}, {"entity": "publication", "iuid": "47790ad3ab044123af522895aed77545", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/47790ad3ab044123af522895aed77545.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/47790ad3ab044123af522895aed77545"}}, "title": "Vaginal Microbiota Transplantation (VMT) for treatment of vaginal dysbiosis without the use of antibiotics \u2013 A Double-Blinded Randomized Controlled Trial in healthy women with vaginal dysbiosis", "authors": [{"family": "Wr\u00f8nding", "given": "Tine", "initials": "T", "orcid": "0009-0008-9670-7241", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/995111ab46cc44fbabcd722a61cd8427.json"}}, {"family": "Vomstein", "given": "Kilian", "initials": "K", "orcid": "0000-0003-2981-4211", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/de8dcc493f994095b2bb66bbf7e5624a.json"}}, {"family": "DeLong", "given": "Kevin", "initials": "K", "orcid": "0000-0002-8710-9601", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fd442f18cf304ff08475fb5967adad88.json"}}, {"family": "Lundgaard", "given": "Agnete Troen", "initials": "AT", "orcid": "0000-0001-7447-6560", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e6d31459d60f4ce789790f6a6ef62328.json"}}, {"family": "Mollerup", "given": "Sarah", "initials": "S", "orcid": "0000-0003-2429-4018", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/afd1d20a9cc94d36bb201279f495f9b8.json"}}, {"family": "Mortensen", "given": "Brynjulf", "initials": "B", "orcid": "0009-0009-3191-778X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/969fe325b43f4f6896844a6ab751b478.json"}}, {"family": "Bosma", "given": "Elleke F", "initials": "EF", "orcid": "0000-0001-6189-7753", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb2afc88a2194bd581b6d03c86bdd68d.json"}}, {"family": "Hellerung", "given": "Ann Marie", "initials": "AM"}, {"family": "Engel", "given": "Emilie Vester", "initials": "EV"}, {"family": "Wiil", "given": "Klara Dortea", "initials": "KD"}, {"family": "Heintz", "given": "Julie Elm", "initials": "JE"}, {"family": "Halkj\u00e6r", "given": "Sofie Ingdam", "initials": "SI"}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW"}, {"family": "Hartwig", "given": "Tanja Schlaikj\u00e6r", "initials": "TS", "orcid": "0000-0003-4220-5947", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a0d4ad16b03d445296c051fa6472c5b5.json"}}, {"family": "Petersen", "given": "Andreas Munk", "initials": "AM", "orcid": "0000-0003-0531-0553", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7b471a95019d4791af5d7151ce5334bb.json"}}, {"family": "Thomsen", "given": "Anne Bloch", "initials": "AB"}, {"family": "Westergaard", "given": "David", "initials": "D", "orcid": "0000-0003-0128-8432", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ef3dd4caeaab419dbf3addb16f903206.json"}}, {"family": "Freiesleben", "given": "Nina La Cour", "initials": "NLC", "orcid": "0000-0002-5670-2015", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fcde9aee66774b038c570b2773f36300.json"}}, {"family": "Westh", "given": "Henrik", "initials": "H", "orcid": "0000-0001-5681-647X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e926cbb026264ed68bacef326e20fc3d.json"}}, {"family": "van Hylckama Vlieg", "given": "Johan E T", "initials": "JET", "orcid": "0000-0001-6656-8668", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/52a8cb2eea2648e6aba006926ca58a9a.json"}}, {"family": "Ensign", "given": "Laura M", "initials": "LM", "orcid": "0000-0002-6949-7911", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ef7038e1a1f3439a9627a68d74a70881.json"}}, {"family": "Nielsen", "given": "Henriette Svarre", "initials": "HS", "orcid": "0000-0003-2106-8103", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9a99fa7ebb204c618ed70f29be0085b3.json"}}], "type": "posted-content", "published": "2024-07-01", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2024.06.28.24309465", "pmid": null, "labels": {"DDLS Fellow": "", "Luisa Hugerth": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T10:55:29.580Z", "modified": "2026-09-23T14:17:46.393Z"}, {"entity": "publication", "iuid": "40306463bf3a40fd9b42f4cef692e4a1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/40306463bf3a40fd9b42f4cef692e4a1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/40306463bf3a40fd9b42f4cef692e4a1"}}, "title": "Unravelling reference bias in ancient DNA datasets.", "authors": [{"family": "Dolenz", "given": "Stephanie", "initials": "S"}, {"family": "van der Valk", "given": "Tom", "initials": "T", "orcid": "0000-0001-6582-3452", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/aa0dba3cc12143cba213f7f3a052216c.json"}}, {"family": "Jin", "given": "Chenyu", "initials": "C", "orcid": "0000-0002-2392-7090", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/afcc4905564e41868967d9cfef968b07.json"}}, {"family": "Oppenheimer", "given": "Jonas", "initials": "J"}, {"family": "Sharif", "given": "Muhammad Bilal", "initials": "MB"}, {"family": "Orlando", "given": "Ludovic", "initials": "L"}, {"family": "Shapiro", "given": "Beth", "initials": "B"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L"}, {"family": "Heintzman", "given": "Peter D", "initials": "PD", "orcid": "0000-0002-6449-0219", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/54774bc7db094262b111c5245207579f.json"}}], "type": "journal article", "published": "2024-07-01", "journal": {"title": "Bioinformatics", "issn": "1367-4811", "volume": "40", "issue": "7", "issn-l": "1367-4803"}, "abstract": "The alignment of sequencing reads is a critical step in the characterization of ancient genomes. However, reference bias and spurious mappings pose a significant challenge, particularly as cutting-edge wet lab methods generate datasets that push the boundaries of alignment tools. Reference bias occurs when reference alleles are favoured over alternative alleles during mapping, whereas spurious mappings stem from either contamination or when endogenous reads fail to align to their correct position. Previous work has shown that these phenomena are correlated with read length but a more thorough investigation of reference bias and spurious mappings for ancient DNA has been lacking. Here, we use a range of empirical and simulated palaeogenomic datasets to investigate the impacts of mapping tools, quality thresholds, and reference genome on mismatch rates across read lengths.\n\nFor these analyses, we introduce AMBER, a new bioinformatics tool for assessing the quality of ancient DNA mapping directly from BAM-files and informing on reference bias, read length cut-offs and reference selection. AMBER rapidly and simultaneously computes the sequence read mapping bias in the form of the mismatch rates per read length, cytosine deamination profiles at both CpG and non-CpG sites, fragment length distributions, and genomic breadth and depth of coverage. Using AMBER, we find that mapping algorithms and quality threshold choices dictate reference bias and rates of spurious alignment at different read lengths in a predictable manner, suggesting that optimized mapping parameters for each read length will be a key step in alleviating reference bias and spurious mappings.\n\nAMBER is available for noncommercial use on GitHub (https://github.com/tvandervalk/AMBER.git). Scripts used to generate and analyse simulated datasets are available on Github (https://github.com/sdolenz/refbias_scripts).", "doi": "10.1093/bioinformatics/btae436", "pmid": "38960861", "labels": {"DDLS Fellow": "", "Tom van der Valk": ""}, "xrefs": [{"db": "pmc", "key": "PMC11254355"}, {"db": "pii", "key": "7705522"}], "notes": [], "created": "2026-09-23T09:03:26.907Z", "modified": "2026-09-23T09:03:26.954Z"}, {"entity": "publication", "iuid": "b9950ef7523f4c7880d948806d4a7f0d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b9950ef7523f4c7880d948806d4a7f0d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b9950ef7523f4c7880d948806d4a7f0d"}}, "title": "Integrative analysis of ultra-deep RNA-seq reveals alternative promoter usage as a mechanism of activating oncogenic programmes during prostate cancer progression.", "authors": [{"family": "Zhang", "given": "Meng", "initials": "M", "orcid": "0000-0003-1042-6294", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3d24c6c51c024ac0b27a5162c4c2fa91.json"}}, {"family": "Sj\u00f6str\u00f6m", "given": "Martin", "initials": "M", "orcid": "0000-0002-2629-9966", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b42d7aeedc844018bbe28980b73cb6c6.json"}}, {"family": "Cui", "given": "Xiekui", "initials": "X"}, {"family": "Foye", "given": "Adam", "initials": "A"}, {"family": "Farh", "given": "Kyle", "initials": "K"}, {"family": "Shrestha", "given": "Raunak", "initials": "R", "orcid": "0000-0002-1144-1413", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1ee8056667cd46ecbec79e2789ae8029.json"}}, {"family": "Lundberg", "given": "Arian", "initials": "A", "orcid": "0000-0002-6630-2787", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/baa2c7c8963840bfb6a22d7c5cfe35f9.json"}}, {"family": "Dang", "given": "Ha X", "initials": "HX", "orcid": "0000-0002-9342-9249", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0a111bbe28044d3c93a4476769bcfb6c.json"}}, {"family": "Li", "given": "Haolong", "initials": "H"}, {"family": "Febbo", "given": "Phillip G", "initials": "PG", "orcid": "0000-0002-6496-4664", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fb238880a5de47579326ae0d8008119d.json"}}, {"family": "Aggarwal", "given": "Rahul", "initials": "R"}, {"family": "Alumkal", "given": "Joshi J", "initials": "JJ", "orcid": "0000-0003-1278-0166", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/92169d39d28f4819959b032eff1b1b80.json"}}, {"family": "Small", "given": "Eric J", "initials": "EJ"}, {"family": "SU2C/PCF West Coast Prostate Cancer Dream Team", "given": "", "initials": ""}, {"family": "Maher", "given": "Christopher A", "initials": "CA", "orcid": "0000-0002-9035-603X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6d6e57151d8f42b3af517e57cd09baa0.json"}}, {"family": "Feng", "given": "Felix Y", "initials": "FY", "orcid": "0000-0002-0963-7687", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c5af5c0e774941ac97890f17640a339e.json"}}, {"family": "Quigley", "given": "David A", "initials": "DA", "orcid": "0000-0002-4726-1473", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a7672a24a905407c8b5f9d1e28deea02.json"}}], "type": "journal article", "published": "2024-07-00", "journal": {"title": "Nat. Cell Biol.", "issn": "1476-4679", "volume": "26", "issue": "7", "pages": "1176-1186", "issn-l": "1465-7392"}, "abstract": "Transcription factor (TF) proteins regulate gene activity by binding to regulatory regions, most importantly at gene promoters. Many genes have alternative promoters (APs) bound by distinct TFs. The role of differential TF activity at APs during tumour development is poorly understood. Here we show, using deep RNA sequencing in 274 biopsies of benign prostate tissue, localized prostate tumours and metastatic castration-resistant prostate cancer, that AP usage increases as tumours progress and APs are responsible for a disproportionate amount of tumour transcriptional activity. Expression of the androgen receptor (AR), the key driver of prostate tumour activity, is correlated with elevated AP usage. We identified AR, FOXA1 and MYC as potential drivers of AP activation. DNA methylation is a likely mechanism for AP activation during tumour progression and lineage plasticity. Our data suggest that prostate tumours activate APs to magnify the transcriptional impact of tumour drivers, including AR and MYC.", "doi": "10.1038/s41556-024-01438-3", "pmid": "38871824", "labels": {"DDLS Fellow": null, "Arian Lundberg": null}, "xrefs": [{"db": "mid", "key": "NIHMS2049615"}, {"db": "pmc", "key": "PMC11844022"}, {"db": "pii", "key": "10.1038/s41556-024-01438-3"}], "notes": [], "created": "2025-11-14T07:50:03.288Z", "modified": "2025-11-14T07:50:03.458Z"}, {"entity": "publication", "iuid": "3c64b24bafd54f689e620174b358a06d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3c64b24bafd54f689e620174b358a06d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3c64b24bafd54f689e620174b358a06d"}}, "title": "Improved protein complex prediction with AlphaFold-multimer by denoising the MSA profile.", "authors": [{"family": "Bryant", "given": "Patrick", "initials": "P", "orcid": "0000-0003-3439-1866", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a683bcf98234ff09b2398976583b66f.json"}}, {"family": "No\u00e9", "given": "Frank", "initials": "F"}], "type": "journal article", "published": "2024-07-00", "journal": {"title": "PLoS Comput Biol", "issn": "1553-7358", "issn-l": "1553-734X", "volume": "20", "issue": "7", "pages": "e1012253"}, "abstract": "Structure prediction of protein complexes has improved significantly with AlphaFold2 and AlphaFold-multimer (AFM), but only 60% of dimers are accurately predicted. Here, we learn a bias to the MSA representation that improves the predictions by performing gradient descent through the AFM network. We demonstrate the performance on seven difficult targets from CASP15 and increase the average MMscore to 0.76 compared to 0.63 with AFM. We evaluate the procedure on 487 protein complexes where AFM fails and obtain an increased success rate (MMscore>0.75) of 33% on these difficult targets. Our protocol, AFProfile, provides a way to direct predictions towards a defined target function guided by the MSA. We expect gradient descent over the MSA to be useful for different tasks.", "doi": "10.1371/journal.pcbi.1012253", "pmid": "39052676", "labels": {"Patrick Bryant": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC11302914"}, {"db": "pii", "key": "PCOMPBIOL-D-23-01693"}], "notes": [], "created": "2024-10-17T12:18:09.786Z", "modified": "2026-09-23T08:52:44.621Z"}, {"entity": "publication", "iuid": "3e5dc3fefbf2424d9aae1cfdd9e8483d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3e5dc3fefbf2424d9aae1cfdd9e8483d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3e5dc3fefbf2424d9aae1cfdd9e8483d"}}, "title": "Corrigendum to \"Discovery of therapeutic agents targeting PKLR for NAFLD using drug repositioning\" [eBioMedicine, 2022;83:104214].", "authors": [{"family": "Zhang", "given": "Cheng", "initials": "C"}, {"family": "Shi", "given": "Mengnan", "initials": "M"}, {"family": "Kim", "given": "Woonghee", "initials": "W"}, {"family": "Arif", "given": "Muhammad", "initials": "M"}, {"family": "Klevstig", "given": "Martina", "initials": "M"}, {"family": "Li", "given": "Xiangyu", "initials": "X"}, {"family": "Yang", "given": "Hong", "initials": "H"}, {"family": "Bayram", "given": "Cemil", "initials": "C"}, {"family": "Bolat", "given": "Ismail", "initials": "I"}, {"family": "Tozlu", "given": "\u00d6zlem \u00d6zdemir", "initials": "\u00d6\u00d6"}, {"family": "Hac\u0131muftuoglu", "given": "Ahmet", "initials": "A"}, {"family": "Y\u0131ld\u0131r\u0131m", "given": "Serkan", "initials": "S"}, {"family": "Sebhaoui", "given": "Jihad", "initials": "J"}, {"family": "Iqbal", "given": "Shazia", "initials": "S"}, {"family": "Wei", "given": "Yongjun", "initials": "Y"}, {"family": "Shi", "given": "Xiaojing", "initials": "X"}, {"family": "Nielsen", "given": "Jens", "initials": "J"}, {"family": "Turkez", "given": "Hasan", "initials": "H"}, {"family": "Uhlen", "given": "Mathias", "initials": "M"}, {"family": "Boren", "given": "Jan", "initials": "J"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}], "type": "published erratum", "published": "2024-07-00", "journal": {"title": "EBioMedicine", "issn": "2352-3964", "volume": "105", "pages": "105224", "issn-l": "2352-3964"}, "abstract": null, "doi": "10.1016/j.ebiom.2024.105224", "pmid": "38943726", "labels": {"SciLifeLab Fellow": "", "DDLS Fellow": "", "Adil Mardinoglu": "", "Muhammad Arif": ""}, "xrefs": [{"db": "pmc", "key": "PMC11261410"}, {"db": "pii", "key": "S2352-3964(24)00259-7"}], "notes": [], "created": "2026-08-20T07:54:09.596Z", "modified": "2026-09-23T15:39:35.359Z"}, {"entity": "publication", "iuid": "2259da8d1cc84184a1c2fe394aab1f51", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/2259da8d1cc84184a1c2fe394aab1f51.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/2259da8d1cc84184a1c2fe394aab1f51"}}, "title": "Being Breastfed in Infancy and Risk of Colorectal Cancer and Precursor Lesions.", "authors": [{"family": "Yuan", "given": "Chen", "initials": "C"}, {"family": "Wang", "given": "Qiao-Li", "initials": "QL"}, {"family": "Kim", "given": "Hanseul", "initials": "H"}, {"family": "Babic", "given": "Ana", "initials": "A"}, {"family": "Zhang", "given": "Jinming", "initials": "J"}, {"family": "Wolpin", "given": "Brian M", "initials": "BM"}, {"family": "Wu", "given": "Kana", "initials": "K"}, {"family": "Song", "given": "Mingyang", "initials": "M"}, {"family": "Ogino", "given": "Shuji", "initials": "S"}, {"family": "Meyerhardt", "given": "Jeffrey A", "initials": "JA"}, {"family": "Chan", "given": "Andrew T", "initials": "AT"}, {"family": "Cao", "given": "Yin", "initials": "Y"}, {"family": "Giovannucci", "given": "Edward L", "initials": "EL"}, {"family": "Ng", "given": "Kimmie", "initials": "K"}], "type": "journal article", "published": "2024-07-00", "journal": {"title": "Clin Gastroenterol Hepatol", "issn": "1542-7714", "volume": "22", "issue": "7", "pages": "1508-1517.e11", "issn-l": null}, "abstract": "Emerging evidence implicates the importance of perinatal and early-life exposures in colorectal cancer (CRC) development. However, it remains unclear whether being breastfed in infancy is associated with CRC risk in adult life, particularly early adulthood.\n\nWe prospectively investigated the association between history of being breastfed and risk of CRC and its precursor lesions among 66,634 women 46-93 years of age from the Nurses' Health Study and 92,062 women 27-68 years of age from the Nurses' Health Study II. Cox regression and logistic regression for clustered data were used to estimate hazard ratios for CRC and odds ratios for CRC precursors, respectively.\n\nDuring 3.5 million person-years of follow-up, we identified 1490 incident cases of CRC in 2 cohorts. Having been breastfed was associated with a 23% (95% confidence interval [CI], 10% to 38%) increased risk of CRC. The risk of CRC increased with duration of being breastfed (Ptrend < .001). These findings were validated using breastfeeding information from the mothers of a subset of participants. Among younger participants from the Nurses' Health Study II, a significant association was observed between being breastfed and increased risk of high-risk adenomas under 50 years of age (odds ratio, 1.46; 95% CI, 1.16 to 1.83). Consistently, having been breastfed was associated with increased risk of CRC among participants \u226455 years of age (hazard ratio, 1.38; 95% CI, 1.06 to 1.80).\n\nBeing breastfed in infancy was associated with increased risk of CRC in adulthood, including among younger adults. However, further research is needed to understand the underlying biological mechanisms, as this association does not establish causation.", "doi": "10.1016/j.cgh.2023.08.023", "pmid": "37683882", "labels": {"DDLS Fellow": null, "Qiaoli Wang": null}, "xrefs": [{"db": "mid", "key": "NIHMS1930442"}, {"db": "pmc", "key": "PMC10915099"}, {"db": "pii", "key": "S1542-3565(23)00673-0"}], "notes": [], "created": "2025-11-28T12:23:10.019Z", "modified": "2025-11-28T12:23:10.053Z"}, {"entity": "publication", "iuid": "edac8cecdb7c46b6aa5fd11f2e98bb69", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/edac8cecdb7c46b6aa5fd11f2e98bb69.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/edac8cecdb7c46b6aa5fd11f2e98bb69"}}, "title": "Design of linear and cyclic peptide binders of different lengths from protein sequence information", "authors": [{"family": "Li", "given": "Qiuzhen", "initials": "Q", "orcid": "0009-0009-2913-4786", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f3d7b87dcea3440d8eaa4b574a88da3e.json"}}, {"family": "Vlachos", "given": "Efstathios Nikolaos", "initials": "EN", "orcid": "0009-0007-0050-6350", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6ee58b57a01c4571a212b19026ce3d10.json"}}, {"family": "Bryant", "given": "Patrick", "initials": "P", "orcid": "0000-0003-3439-1866", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a683bcf98234ff09b2398976583b66f.json"}}], "type": "posted-content", "published": "2024-06-22", "journal": {"title": null, "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2024.06.20.599739", "pmid": null, "labels": {"Patrick Bryant": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2024-10-17T12:18:46.824Z", "modified": "2026-09-23T13:49:40.909Z"}, {"entity": "publication", "iuid": "79aa247e93ee44d09554e5a7ed663886", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/79aa247e93ee44d09554e5a7ed663886.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/79aa247e93ee44d09554e5a7ed663886"}}, "title": "Construction of the ETECFinder database for the characterization of enterotoxigenic Escherichia coli (ETEC) and revision of the VirulenceFinder web tool at the CGE website.", "authors": [{"family": "Scheutz", "given": "Flemming", "initials": "F", "orcid": "0000-0002-3931-4846", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/173c759fd89f457197319ff51c68748a.json"}}, {"family": "Nielsen", "given": "Camilla Hald", "initials": "CH"}, {"family": "von Mentzer", "given": "Astrid", "initials": "A"}], "type": "journal article", "published": "2024-06-12", "journal": {"title": "J. Clin. Microbiol.", "issn": "1098-660X", "volume": "62", "issue": "6", "pages": "e0057023", "issn-l": "0095-1137"}, "abstract": "The identification of pathogens is essential for effective surveillance and outbreak detection, which lately has been facilitated by the decreasing cost of whole-genome sequencing (WGS). However, extracting relevant virulence genes from WGS data remains a challenge. In this study, we developed a web-based tool to predict virulence-associated genes in enterotoxigenic Escherichia coli (ETEC), which is a major concern for human and animal health. The database includes genes encoding the heat-labile toxin (LT) (eltA and eltB), heat-stable toxin (ST) (est), colonization factors CS1 through 30, F4, F5, F6, F17, F18, and F41, as well as toxigenic invasion and adherence loci (tia, tibAC, etpBAC, eatA, yghJ, and tleA). To construct the database, we revised the existing ETEC nomenclature and used the VirulenceFinder webtool at the CGE website [VirulenceFinder 2.0 (dtu.dk)]. The database was tested on 1,083 preassembled ETEC genomes, two BioProjects (PRJNA421191 with 305 and PRJNA416134 with 134 sequences), and the ETEC reference genome H10407. In total, 455 new virulence gene alleles were added, 50 alleles were replaced or renamed, and two were removed. Overall, our tool has the potential to greatly facilitate ETEC identification and improve the accuracy of WGS analysis. It can also help identify potential new virulence genes in ETEC. The revised nomenclature and expanded gene repertoire provide a better understanding of the genetic diversity of ETEC. Additionally, the user-friendly interface makes it accessible to users with limited bioinformatics experience.\n\nDetecting colonization factors in enterotoxigenic Escherichia coli (ETEC) is challenging due to their large number, heterogeneity, and lack of standardized tests. Therefore, it is important to include these ETEC-related genes in a more comprehensive VirulenceFinder database in order to obtain a more complete coverage of the virulence gene repertoire of pathogenic types of E. coli. ETEC vaccines are of great importance due to the severity of the infections, primarily in children. A tool such as this could assist in the surveillance of ETEC in order to determine the prevalence of relevant types in different parts of the world, allowing vaccine developers to target the most prevalent types and, thus, a more effective vaccine.", "doi": "10.1128/jcm.00570-23", "pmid": "38656142", "labels": {"Astrid von Mentzer": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC11237473"}], "notes": [], "created": "2025-12-02T15:47:06.094Z", "modified": "2025-12-02T15:47:06.151Z"}, {"entity": "publication", "iuid": "176e2b85f83744e8be1dae971831b33b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/176e2b85f83744e8be1dae971831b33b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/176e2b85f83744e8be1dae971831b33b"}}, "title": "Fluoroquinolone-Specific Resistance Trajectories in E. coli and their Dependence on the SOS-Response", "authors": [{"family": "Teichmann", "given": "Lisa", "initials": "L"}, {"family": "Luitwieler", "given": "Sam", "initials": "S"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "ter Kuile", "given": "Benno", "initials": "B", "orcid": "0000-0002-8523-8135", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3c87f0fedd1d4b208ff99000dbade32c.json"}}], "type": "posted-content", "published": "2024-06-06", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2024.06.06.597756", "pmid": null, "labels": {"DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T10:55:08.695Z", "modified": "2026-09-23T14:51:31.347Z"}, {"entity": "publication", "iuid": "b4823945d72846b7905667c994234140", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b4823945d72846b7905667c994234140.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b4823945d72846b7905667c994234140"}}, "title": "Author Correction: Gene-expression memory-based prediction of cell lineages from scRNA-seq datasets.", "authors": [{"family": "Eisele", "given": "A S", "initials": "AS", "orcid": "0000-0001-8376-4089", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2bff45c62e2f426b99ca66c8d772fa12.json"}}, {"family": "Tarbier", "given": "M", "initials": "M", "orcid": "0000-0003-0556-2531", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9678d0797def441e9870afe6ffbb08d0.json"}}, {"family": "Dormann", "given": "A A", "initials": "AA"}, {"family": "Pelechano", "given": "V", "initials": "V", "orcid": "0000-0002-9415-788X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e893b93b7654d10b4072e1b5de0bd71.json"}}, {"family": "Suter", "given": "D M", "initials": "DM", "orcid": "0000-0001-5644-4899", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3a3dd88c76314449ad1823ac1f067db7.json"}}], "type": "published erratum", "published": "2024-06-04", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "4752", "issn-l": "2041-1723"}, "abstract": null, "doi": "10.1038/s41467-024-48978-8", "pmid": "38834555", "labels": {"SciLifeLab Fellow": "", "DDLS Fellow": "", "Marcel Tarbier": ""}, "xrefs": [{"db": "pmc", "key": "PMC11150479"}, {"db": "pii", "key": "10.1038/s41467-024-48978-8"}], "notes": [], "created": "2026-08-20T08:53:21.082Z", "modified": "2026-09-23T15:39:02.788Z"}, {"entity": "publication", "iuid": "2e800d3226134053b0cc35a85b918107", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/2e800d3226134053b0cc35a85b918107.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/2e800d3226134053b0cc35a85b918107"}}, "title": "Atrial Fibrillation and Clonal Hematopoiesis in TET2 and ASXL1.", "authors": [{"family": "Saadatagah", "given": "Seyedmohammad", "initials": "S"}, {"family": "Naderian", "given": "Mohammadreza", "initials": "M"}, {"family": "Uddin", "given": "Mesbah", "initials": "M", "orcid": "0000-0003-1846-0411", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/42f1ac7010c34ba997a3fd9e56c6a56a.json"}}, {"family": "Dikilitas", "given": "Ozan", "initials": "O"}, {"family": "Niroula", "given": "Abhishek", "initials": "A", "orcid": "0000-0002-5904-0635", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/05df7afc7a494ba5af8a378e5ffa53f0.json"}}, {"family": "Schuermans", "given": "Art", "initials": "A", "orcid": "0000-0001-8146-9692", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/af284c3bd9304f54ac7b8c9970ce56be.json"}}, {"family": "Selvin", "given": "Elizabeth", "initials": "E"}, {"family": "Hoogeveen", "given": "Ron C", "initials": "RC"}, {"family": "Matsushita", "given": "Kunihiro", "initials": "K"}, {"family": "Nambi", "given": "Vijay", "initials": "V"}, {"family": "Yu", "given": "Bing", "initials": "B", "orcid": "0000-0003-4818-1077", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e408849bd8f14fd99a2ae255990c1f49.json"}}, {"family": "Chen", "given": "Lin Yee", "initials": "LY"}, {"family": "Bick", "given": "Alexander G", "initials": "AG", "orcid": "0000-0001-5824-9595", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d2da5a35a4984921b19dfafe64cea2de.json"}}, {"family": "Ebert", "given": "Benjamin L", "initials": "BL", "orcid": "0000-0003-0197-5451", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56e4f1c53a4348e2b0ceb44a38850a17.json"}}, {"family": "Honigberg", "given": "Michael C", "initials": "MC", "orcid": "0000-0001-8630-5021", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c541cd0864c947a6bafa7ad6e78bfe49.json"}}, {"family": "Li", "given": "Na", "initials": "N"}, {"family": "Shah", "given": "Amil", "initials": "A"}, {"family": "Natarajan", "given": "Pradeep", "initials": "P", "orcid": "0000-0001-8402-7435", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fe8bd48c61c047cd8e61c35d9e9ac650.json"}}, {"family": "Kullo", "given": "Iftikhar J", "initials": "IJ"}, {"family": "Ballantyne", "given": "Christie M", "initials": "CM", "orcid": "0000-0002-6432-1730", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/27dc5297c262410bad3bbb66a488d4b4.json"}}], "type": "journal article", "published": "2024-06-01", "journal": {"title": "JAMA Cardiol", "issn": "2380-6591", "volume": "9", "issue": "6", "pages": "497-506", "issn-l": "2380-6583"}, "abstract": "Clonal hematopoiesis of indeterminate potential (CHIP) may contribute to the risk of atrial fibrillation (AF) through its association with inflammation and cardiac remodeling.\n\nTo determine whether CHIP was associated with AF, inflammatory and cardiac biomarkers, and cardiac structural changes.\n\nThis was a population-based, prospective cohort study in participants of the Atherosclerosis Risk in Communities (ARIC) study and UK Biobank (UKB) cohort. Samples were collected and echocardiography was performed from 2011 to 2013 in the ARIC cohort, and samples were collected from 2006 to 2010 in the UKB cohort. Included in this study were adults without hematologic malignancies, mitral valve stenosis, or previous mitral valve procedure from both the ARIC and UKB cohorts; additionally, participants without hypertrophic cardiomyopathy and congenital heart disease from the UKB cohort were also included. Data analysis was completed in 2023.\n\nCHIP (variant allele frequency [VAF] \u22652%), common gene-specific CHIP subtypes (DNMT3A, TET2, ASXL1), large CHIP (VAF \u226510%), inflammatory and cardiac biomarkers (high-sensitivity C-reactive protein, interleukin 6 [IL-6], IL-18, high-sensitivity troponin T [hs-TnT] and hs-TnI, N-terminal pro-B-type natriuretic peptide), and echocardiographic indices.\n\nIncident AF.\n\nA total of 199 982 adults were included in this study. In ARIC participants (4131 [2.1%]; mean [SD] age, 76 [5] years; 2449 female [59%]; 1682 male [41%]; 935 Black [23%] and 3196 White [77%]), 1019 had any CHIP (24.7%), and 478 had large CHIP (11.6%). In UKB participants (195 851 [97.9%]; mean [SD] age, 56 [8] years; 108 370 female [55%]; 87 481 male [45%]; 3154 Black [2%], 183 747 White [94%], and 7971 other race [4%]), 11 328 had any CHIP (5.8%), and 5189 had large CHIP (2.6%). ARIC participants were followed up for a median (IQR) period of 7.0 (5.3-7.7) years, and UKB participants were followed up for a median (IQR) period of 12.2 (11.3-13.0) years. Meta-analyzed hazard ratios for AF were 1.12 (95% CI, 1.01-1.25; P = .04) for participants with vs without large CHIP, 1.29 (95% CI, 1.05-1.59; P = .02) for those with vs without large TET2 CHIP (seen in 1340 of 197 209 [0.67%]), and 1.45 (95% CI, 1.02-2.07; P = .04) for those with vs without large ASXL1 CHIP (seen in 314 of 197 209 [0.16%]). Large TET2 CHIP was associated with higher IL-6 levels. Additionally, large ASXL1 was associated with higher hs-TnT level and increased left ventricular mass index.\n\nLarge TET2 and ASXL1, but not DNMT3A, CHIP was associated with higher IL-6 level, indices of cardiac remodeling, and increased risk for AF. Future research is needed to elaborate on the mechanisms driving the associations and to investigate potential interventions to reduce the risk.", "doi": "10.1001/jamacardio.2024.0459", "pmid": "38598228", "labels": {"Abhishek Niroula": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC11007653"}, {"db": "pii", "key": "2817222"}], "notes": [], "created": "2025-03-18T15:48:50.593Z", "modified": "2026-09-23T08:49:39.822Z"}, {"entity": "publication", "iuid": "d6ea7c71d8004a8ab13ab559f981cd12", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d6ea7c71d8004a8ab13ab559f981cd12.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d6ea7c71d8004a8ab13ab559f981cd12"}}, "title": "Malat1 affects transcription and splicing through distinct pathways in mouse embryonic stem cells.", "authors": [{"family": "Aslanzadeh", "given": "Morteza", "initials": "M"}, {"family": "Stanicek", "given": "Laura", "initials": "L"}, {"family": "Tarbier", "given": "Marcel", "initials": "M", "orcid": "0000-0003-0556-2531", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9678d0797def441e9870afe6ffbb08d0.json"}}, {"family": "M\u00e1rmol-S\u00e1nchez", "given": "Emilio", "initials": "E"}, {"family": "Biryukova", "given": "Inna", "initials": "I"}, {"family": "Friedl\u00e4nder", "given": "Marc R", "initials": "MR", "orcid": "0000-0001-6577-4363", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ac5a2794be7c4cab89d1e4f1570c9417.json"}}], "type": "journal article", "published": "2024-06-00", "journal": {"title": "NAR Genomics and Bioinformatics", "issn": "2631-9268", "volume": "6", "issue": "2", "pages": "lqae045", "issn-l": null}, "abstract": "Malat1 is a long-noncoding RNA with critical roles in gene regulation and cancer metastasis, however its functional role in stem cells is largely unexplored. We here perform a nuclear knockdown of Malat1 in mouse embryonic stem cells, causing the de-regulation of 320 genes and aberrant splicing of 90 transcripts, some of which potentially affecting the translated protein sequence. We find evidence that Malat1 directly interacts with gene bodies and aberrantly spliced transcripts, and that it locates upstream of down-regulated genes at their putative enhancer regions, in agreement with functional genomics data. Consistent with this, we find these genes affected at both exon and intron levels, suggesting that they are transcriptionally regulated by Malat1. Besides, the down-regulated genes are regulated by specific transcription factors and bear both activating and repressive chromatin marks, suggesting that some of them might be regulated by bivalent promoters. We propose a model in which Malat1 facilitates the transcription of genes involved in chromatid dynamics and mitosis in one pathway, and affects the splicing of transcripts that are themselves involved in RNA processing in a distinct pathway. Lastly, we compare our findings with Malat1 perturbation studies performed in other cell systems and in vivo.", "doi": "10.1093/nargab/lqae045", "pmid": "38711862", "labels": {"Marcel Tarbier": "", "DDLS Fellow": "", "SciLifeLab Fellow": "", "Marc Friedl\u00e4nder": ""}, "xrefs": [{"db": "pmc", "key": "PMC11071118"}, {"db": "pii", "key": "lqae045"}], "notes": [], "created": "2025-12-03T10:28:05.413Z", "modified": "2026-09-23T12:19:14.317Z"}, {"entity": "publication", "iuid": "b4fbfad8723d40e2bb1acd11774120fb", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b4fbfad8723d40e2bb1acd11774120fb.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b4fbfad8723d40e2bb1acd11774120fb"}}, "title": "DL4MicEverywhere: deep learning for microscopy made flexible, shareable and reproducible.", "authors": [{"family": "Hidalgo-Cenalmor", "given": "Iv\u00e1n", "initials": "I", "orcid": "0009-0000-8923-568X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fb7011ce4fb646318568c7c5a9f2f9b8.json"}}, {"family": "Pylv\u00e4n\u00e4inen", "given": "Joanna W", "initials": "JW", "orcid": "0000-0002-3540-5150", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dc3dcdba0dc9406592b31ccbe4f3862e.json"}}, {"family": "G Ferreira", "given": "Mariana", "initials": "M", "orcid": "0009-0002-2886-4612", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/99ce24339a974d4d94d000defe684bb5.json"}}, {"family": "Russell", "given": "Craig T", "initials": "CT", "orcid": "0000-0002-2447-5911", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/01b58f5bd05d4d46824927306d536c4f.json"}}, {"family": "Saguy", "given": "Alon", "initials": "A"}, {"family": "Arganda-Carreras", "given": "Ignacio", "initials": "I"}, {"family": "Shechtman", "given": "Yoav", "initials": "Y", "orcid": "0000-0001-8498-5203", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1d6ecca729644b5d92ed29f88c3688e2.json"}}, {"family": "AI4Life Horizon Europe Program Consortium", "given": "", "initials": ""}, {"family": "Jacquemet", "given": "Guillaume", "initials": "G", "orcid": "0000-0002-9286-920X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b7a1bac74d1946259e319f067f61e88d.json"}}, {"family": "Henriques", "given": "Ricardo", "initials": "R", "orcid": "0000-0002-2043-5234", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/91d3a7ea2f3b4eba8c87c36d2b9bcf0c.json"}}, {"family": "G\u00f3mez-de-Mariscal", "given": "Estibaliz", "initials": "E", "orcid": "0000-0003-2082-3277", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cdcc04b3b1534abc8457380935970dd5.json"}}], "type": "letter", "published": "2024-06-00", "journal": {"title": "Nat. Methods", "issn": "1548-7105", "volume": "21", "issue": "6", "pages": "925-927", "issn-l": "1548-7091"}, "abstract": null, "doi": "10.1038/s41592-024-02295-6", "pmid": "38760611", "labels": {"DDLS Fellow": "", "Wei Ouyang": ""}, "xrefs": [{"db": "mid", "key": "EMS196336"}, {"db": "pmc", "key": "PMC7616093"}, {"db": "pii", "key": "10.1038/s41592-024-02295-6"}], "notes": [], "created": "2026-08-20T09:03:04.132Z", "modified": "2026-09-23T10:56:37.005Z"}, {"entity": "publication", "iuid": "e5d94e4974c84c5093fbda5b3e7fd244", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e5d94e4974c84c5093fbda5b3e7fd244.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e5d94e4974c84c5093fbda5b3e7fd244"}}, "title": "Structure prediction of protein-ligand complexes from sequence information with Umol.", "authors": [{"family": "Bryant", "given": "Patrick", "initials": "P", "orcid": "0000-0003-3439-1866", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a683bcf98234ff09b2398976583b66f.json"}}, {"family": "Kelkar", "given": "Atharva", "initials": "A"}, {"family": "Guljas", "given": "Andrea", "initials": "A"}, {"family": "Clementi", "given": "Cecilia", "initials": "C", "orcid": "0000-0001-9221-2358", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/39158db40ee146a7bced89add1ddb55a.json"}}, {"family": "No\u00e9", "given": "Frank", "initials": "F", "orcid": "0000-0003-4169-9324", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/852838b35de241a38712a04dbbd6b938.json"}}], "type": "journal article", "published": "2024-05-28", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "15", "issue": "1", "pages": "4536"}, "abstract": "Protein-ligand docking is an established tool in drug discovery and development to narrow down potential therapeutics for experimental testing. However, a high-quality protein structure is required and often the protein is treated as fully or partially rigid. Here we develop an AI system that can predict the fully flexible all-atom structure of protein-ligand complexes directly from sequence information. We find that classical docking methods are still superior, but depend upon having crystal structures of the target protein. In addition to predicting flexible all-atom structures, predicted confidence metrics (plDDT) can be used to select accurate predictions as well as to distinguish between strong and weak binders. The advances presented here suggest that the goal of AI-based drug discovery is one step closer, but there is still a way to go to grasp the complexity of protein-ligand interactions fully. Umol is available at: https://github.com/patrickbryant1/Umol .", "doi": "10.1038/s41467-024-48837-6", "pmid": "38806453", "labels": {"Patrick Bryant": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC11133481"}, {"db": "pii", "key": "10.1038/s41467-024-48837-6"}], "notes": [], "created": "2024-10-17T12:18:16.739Z", "modified": "2026-09-23T08:36:52.546Z"}, {"entity": "publication", "iuid": "0032013e4e1a4d598d2e1c183adb5f66", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0032013e4e1a4d598d2e1c183adb5f66.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0032013e4e1a4d598d2e1c183adb5f66"}}, "title": "Bacillamide D produced by Bacillus cereus from the mouse intestinal bacterial collection (miBC) is a potent cytotoxin in vitro.", "authors": [{"family": "Hohmann", "given": "Maximilian", "initials": "M"}, {"family": "Brunner", "given": "Valentina", "initials": "V"}, {"family": "Johannes", "given": "Widya", "initials": "W"}, {"family": "Schum", "given": "Dominik", "initials": "D", "orcid": "0009-0001-2706-6208", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7ed4ed5f3f264263a9c3e0b16895c5f4.json"}}, {"family": "Carroll", "given": "Laura M", "initials": "LM", "orcid": "0000-0002-3677-0192", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02112eccb0664819af916a3c3dc79daa.json"}}, {"family": "Liu", "given": "Tianzhe", "initials": "T"}, {"family": "Sasaki", "given": "Daisuke", "initials": "D"}, {"family": "Bosch", "given": "Johanna", "initials": "J", "orcid": "0000-0003-3982-849X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9219b59c825f4c6d95b753db69fcc604.json"}}, {"family": "Clavel", "given": "Thomas", "initials": "T", "orcid": "0000-0002-7229-5595", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4e2197de37974b5c91d68b955f9ee3ec.json"}}, {"family": "Sieber", "given": "Stephan A", "initials": "SA", "orcid": "0000-0002-9400-906X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ed221037cc8f4af18984505bc69cd193.json"}}, {"family": "Zeller", "given": "Georg", "initials": "G", "orcid": "0000-0003-1429-7485", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/414382373eb5447186a7e6c925aa067f.json"}}, {"family": "Tschurtschenthaler", "given": "Markus", "initials": "M", "orcid": "0000-0002-0060-4790", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/88ddb86362d1430791cbf916b8091d50.json"}}, {"family": "Jan\u00dfen", "given": "Klaus-Peter", "initials": "KP", "orcid": "0000-0002-4707-7887", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6b6efb5e10ce471780a443fbbcba2615.json"}}, {"family": "Gulder", "given": "Tobias A M", "initials": "TAM", "orcid": "0000-0001-6013-3161", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/649b2a17f6964525acada09aa3a652eb.json"}}], "type": "journal article", "published": "2024-05-28", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "7", "issue": "1", "pages": "655", "issn-l": "2399-3642"}, "abstract": "The gut microbiota influences human health and the development of chronic diseases. However, our understanding of potentially protective or harmful microbe-host interactions at the molecular level is still in its infancy. To gain further insights into the hidden gut metabolome and its impact, we identified a cryptic non-ribosomal peptide BGC in the genome of Bacillus cereus DSM 28590 from the mouse intestine ( www.dsmz.de/miBC ), which was predicted to encode a thiazol(in)e substructure. Cloning and heterologous expression of this BGC revealed that it produces bacillamide D. In-depth functional evaluation showed potent cytotoxicity and inhibition of cell migration using the human cell lines HCT116 and HEK293, which was validated using primary mouse organoids. This work establishes the bacillamides as selective cytotoxins from a bacterial gut isolate that affect mammalian cells. Our targeted structure-function-predictive approach is demonstrated to be a streamlined method to discover deleterious gut microbial metabolites with potential effects on human health.", "doi": "10.1038/s42003-024-06208-3", "pmid": "38806706", "labels": {"Laura Carroll": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC11133360"}, {"db": "pii", "key": "10.1038/s42003-024-06208-3"}], "notes": [], "created": "2025-03-18T17:31:56.201Z", "modified": "2025-04-08T06:10:47.544Z"}, {"entity": "publication", "iuid": "db32d2e1e6d3436890bcffb81878f88b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/db32d2e1e6d3436890bcffb81878f88b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/db32d2e1e6d3436890bcffb81878f88b"}}, "title": "Effectiveness and Cost-effectiveness of Artificial Intelligence-assisted Pathology for Prostate Cancer Diagnosis in Sweden: A Microsimulation Study.", "authors": [{"family": "Du", "given": "Xiaoyang", "initials": "X"}, {"family": "Hao", "given": "Shuang", "initials": "S"}, {"family": "Olsson", "given": "Henrik", "initials": "H"}, {"family": "Kartasalo", "given": "Kimmo", "initials": "K"}, {"family": "Mulliqi", "given": "Nita", "initials": "N"}, {"family": "Rai", "given": "Balram", "initials": "B"}, {"family": "Menges", "given": "Dominik", "initials": "D"}, {"family": "Heintz", "given": "Emelie", "initials": "E"}, {"family": "Egevad", "given": "Lars", "initials": "L"}, {"family": "Eklund", "given": "Martin", "initials": "M"}, {"family": "Clements", "given": "Mark", "initials": "M"}], "type": "journal article", "published": "2024-05-23", "journal": {"title": "Eur Urol Oncol", "issn": "2588-9311", "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": "Image-based artificial intelligence (AI) methods have shown high accuracy in prostate cancer (PCa) detection. Their impact on patient outcomes and cost effectiveness in comparison to human pathologists remains unknown. Our aim was to evaluate the effectiveness and cost-effectiveness of AI-assisted pathology for PCa diagnosis in Sweden.\r\n\r\nWe modeled quadrennial prostate-specific antigen (PSA) screening for men between the ages of 50 and 74 yr over a lifetime horizon using a health care perspective. Men with PSA \u22653 ng/ml were referred for standard biopsy (SBx), for which cores were either examined via AI followed by a pathologist for AI-labeled positive cores, or a pathologist alone. The AI performance characteristics were estimated using an internal STHLM3 validation data set. Outcome measures included the number of tests, PCa incidence and mortality, overdiagnosis, quality-adjusted life years (QALYs), and the potential reduction in pathologist-evaluated biopsy cores if AI were used. Cost-effectiveness was assessed using the incremental cost-effectiveness ratio.\r\n\r\nIn comparison to a pathologist alone, the AI-assisted workflow increased the number of PSA tests, SBx procedures, and PCa deaths by \u22640.03%, and slightly reduced PCa incidence and overdiagnosis. AI would reduce the proportion of biopsy cores evaluated by a pathologist by 80%. At a cost of \u20ac10 per case, the AI-assisted workflow would cost less and result in <0.001% lower QALYs in comparison to a pathologist alone. The results were sensitive to the AI cost.\r\n\r\nAccording to our model, AI-assisted pathology would significantly decrease the workload of pathologists, would not affect patient quality of life, and would yield cost savings in Sweden when compared to a human pathologist alone.\r\n\r\nWe compared outcomes for prostate cancer patients and relevant costs for two methods of assessing prostate biopsies in Sweden: (1) artificial intelligence (AI) technology and review of positive biopsies by a human pathologist; and (2) a human pathologist alone for all biopsies. We found that addition of AI would reduce the pathology workload and save money, and would not affect patient outcomes when compared to a human pathologist alone. The results suggest that adding AI to prostate pathology in Sweden would save costs.", "doi": "10.1016/j.euo.2024.05.004", "pmid": "38789385", "labels": {"Kimmo Kartasalo": null, "DDLS Fellow": null}, "xrefs": [{"db": "pii", "key": "S2588-9311(24)00133-0"}], "notes": [], "created": "2024-11-05T16:12:19.243Z", "modified": "2024-11-29T10:41:09.255Z"}, {"entity": "publication", "iuid": "c9eaed9f58a04b4a8beb68e86d7161d5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c9eaed9f58a04b4a8beb68e86d7161d5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c9eaed9f58a04b4a8beb68e86d7161d5"}}, "title": "Diagnosis of Cancer After Recent Weight Loss-Reply.", "authors": [{"family": "Wang", "given": "Qiao-Li", "initials": "QL"}, {"family": "Yuan", "given": "Chen", "initials": "C"}, {"family": "Wolpin", "given": "Brian M", "initials": "BM"}], "type": "letter", "published": "2024-05-21", "journal": {"title": "JAMA", "issn": "1538-3598", "volume": "331", "issue": "19", "pages": "1678-1679", "issn-l": null}, "abstract": null, "doi": "10.1001/jama.2024.5419", "pmid": "38656760", "labels": {"DDLS Fellow": null, "Qiaoli Wang": null}, "xrefs": [{"db": "pii", "key": "2818052"}], "notes": [], "created": "2025-11-28T12:24:42.587Z", "modified": "2025-11-28T12:24:42.603Z"}, {"entity": "publication", "iuid": "65da812e265149fba8d4c311774023e2", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/65da812e265149fba8d4c311774023e2.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/65da812e265149fba8d4c311774023e2"}}, "title": "An atlas of protein-protein associations of human tissues prioritizes candidate disease genes", "authors": [{"family": "Laman Trip", "given": "Diederik S", "initials": "DS"}, {"family": "van Oostrum", "given": "Marc", "initials": "M"}, {"family": "Memon", "given": "Danish", "initials": "D"}, {"family": "Frommelt", "given": "Fabian", "initials": "F", "orcid": "0000-0003-3666-8005", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e71a93da1624a17bcbace26ba50c5a5.json"}}, {"family": "Baptista", "given": "Delora", "initials": "D"}, {"family": "Panneerselvam", "given": "Kalpana", "initials": "K"}, {"family": "Bradley", "given": "Glyn", "initials": "G"}, {"family": "Licata", "given": "Luana", "initials": "L"}, {"family": "Hermjakob", "given": "Henning", "initials": "H", "orcid": "0000-0001-8479-0262", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7ef7fa5ba29447fba798a69b305c0228.json"}}, {"family": "Orchard", "given": "Sandra", "initials": "S"}, {"family": "Trynka", "given": "Gosia", "initials": "G"}, {"family": "McDonagh", "given": "Ellen", "initials": "E"}, {"family": "Fossati", "given": "Andrea", "initials": "A", "orcid": "0000-0001-5170-4903", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/658637b885384441943698722fad5944.json"}}, {"family": "Aebersold", "given": "Ruedi", "initials": "R", "orcid": "0000-0002-9576-3267", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4aa50db862e94831b8cac04c4426daf1.json"}}, {"family": "Gstaiger", "given": "Matthias", "initials": "M", "orcid": "0000-0002-3245-3253", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8370f12358274bb2a5a4cd524ae4f465.json"}}, {"family": "Wollscheid", "given": "Bernd", "initials": "B", "orcid": "0000-0002-3923-1610", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fecd11050305473ca698ba6c6ee54a52.json"}}, {"family": "Beltrao", "given": "Pedro", "initials": "P", "orcid": "0000-0002-2724-7703", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/952eba119d2e4d4b89e14b294c5c6885.json"}}], "type": "posted-content", "published": "2024-05-17", "journal": {"title": null, "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2024.05.15.594301", "pmid": null, "labels": {"Andrea Fossati": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2025-03-18T16:51:07.686Z", "modified": "2025-03-21T13:32:48.505Z"}, {"entity": "publication", "iuid": "c02cf8e5eac24ecfa226cc6368b1aecc", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c02cf8e5eac24ecfa226cc6368b1aecc.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c02cf8e5eac24ecfa226cc6368b1aecc"}}, "title": "Compositional and functional differences of the vaginal microbiota of women with and without cervical dysplasia.", "authors": [{"family": "Norenhag", "given": "Johanna", "initials": "J"}, {"family": "Edfeldt", "given": "Gabriella", "initials": "G", "orcid": "0000-0003-0366-5588", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bc30318aa3ca4720ac5aa3a982c9f730.json"}}, {"family": "St\u00e5lberg", "given": "Karin", "initials": "K", "orcid": "0000-0001-5527-8796", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ca801fe1aba4d04a06eaf9f6e3407dd.json"}}, {"family": "Garcia", "given": "Fabricio", "initials": "F"}, {"family": "Hugerth", "given": "Luisa Warchavchik", "initials": "LW", "orcid": "0000-0001-5432-1764", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/246ed7b405dd4c3f9ec5e7ff9f1d3ade.json"}}, {"family": "Engstrand", "given": "Lars", "initials": "L", "orcid": "0000-0002-7713-2373", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02d8684df81e42169e613de803446fbf.json"}}, {"family": "Fransson", "given": "Emma", "initials": "E", "orcid": "0000-0001-9010-8522", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8c05290187ec426b8804eefc3d954971.json"}}, {"family": "Du", "given": "Juan", "initials": "J", "orcid": "0000-0001-7649-9571", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f67834a614ca4cd4aff026e5e9a1a1e4.json"}}, {"family": "Schuppe-Koistinen", "given": "Ina", "initials": "I", "orcid": "0000-0002-1423-3089", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/659fb04e6a1a430cbd707b8a50d500a3.json"}}, {"family": "Olovsson", "given": "Matts", "initials": "M"}], "type": "journal article", "published": "2024-05-16", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "11183", "issn-l": "2045-2322"}, "abstract": "Alterations in the vaginal microbiota, including both species composition and functional pathways, have been associated with HPV infection and progression of dysplasia to cervical cancer. To further explore this, shotgun metagenomic sequencing was used to taxonomically and functionally characterize the vaginal microbiota of women with and without cervical dysplasia. Women with histologically verified dysplasia (n = 177; low grade dysplasia (LSIL) n = 81, high-grade dysplasia (HSIL) n = 94, cancer n = 2) were compared with healthy controls recruited from the cervical screening programme (n = 177). Women with dysplasia had a higher vaginal microbial diversity, and higher abundances of Gardnerella vaginalis, Aerococcus christensenii, Peptoniphilus lacrimalis and Fannyhessea vaginae, while healthy controls had higher relative abundance of Lactobacillus crispatus. Genes involved in e.g. nucleotide biosynthesis and peptidoglycan biosynthesis were more abundant in women with dysplasia. Healthy controls showed higher abundance of genes important for e.g. amino acid biosynthesis, (especially L-lysine) and sugar degradation. These findings suggest that the microbiota may have a role in creating a pro-oncogenic environment in women with dysplasia. Its role and potential interactions with other components in the microenvironment deserve further exploration.", "doi": "10.1038/s41598-024-61942-2", "pmid": "38755259", "labels": {"Luisa Hugerth": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC11099171"}, {"db": "pii", "key": "10.1038/s41598-024-61942-2"}], "notes": [], "created": "2025-03-19T07:35:42.306Z", "modified": "2026-09-23T09:03:25.027Z"}, {"entity": "publication", "iuid": "6bd48c8800034578818f777808b875a6", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/6bd48c8800034578818f777808b875a6.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/6bd48c8800034578818f777808b875a6"}}, "title": "TPP1 is associated with risk of advanced precursors and cervical cancer survival.", "authors": [{"family": "Wang", "given": "Qiao-Li", "initials": "QL", "orcid": "0000-0003-4152-7821", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/357edb3116b64ad5aa929dcb7d07a1be.json"}}, {"family": "Gong", "given": "Caifeng", "initials": "C"}, {"family": "Meng", "given": "Xiang-Yu", "initials": "XY"}, {"family": "Fu", "given": "Min", "initials": "M"}, {"family": "Yang", "given": "Hui", "initials": "H"}, {"family": "Zhou", "given": "Fuxiang", "initials": "F"}, {"family": "Wu", "given": "Qiuji", "initials": "Q", "orcid": "0000-0002-4655-3108", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/39eb919e325d4b428319792599fa9ccc.json"}}, {"family": "Zhou", "given": "Yunfeng", "initials": "Y"}], "type": "journal article", "published": "2024-05-09", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "19", "issue": "5", "pages": "e0298118", "issn-l": "1932-6203"}, "abstract": "It is unclear how telomere-binding protein TPP1 interacts with human telomerase reverse transcriptase (hTERT) and influences cervical cancer development and progression. This study included all eligible 156 cervical cancers diagnosed during 2003-2008 and followed up through 2014, 102 cervical intraepithelial neoplasia (CIN) patients, and 16 participants with normal cervix identified at the same period. Correlation of expression of TPP1 and hTERT in these lesions was assessed using Kappa statistics. TPP1 was knocked down by siRNA in three cervical cancer cell lines. We assessed mRNA expression using quantitative real-time polymerase chain reaction and protein expression using tissue microarray-based immunohistochemical staining. We further analyzed the impact of TPP1 expression on the overall survival of cervical cancer patients by calculating the hazard ratio (HR) with 95% confidence intervals (CIs) using the multivariable-adjusted Cox regression model. Compared to the normal cervix, high TPP1expression was significantly associated with CIN 3 and cervical cancers (P<0.001 for both). Expressions of TPP1 and hTERT were highly correlated in CIN 3 (Kappa statistics = 0.50, P = 0.005), squamous cell carcinoma (Kappa statistics = 0.22, P = 0.011), and adenocarcinoma/adenosquamous carcinoma (Kappa statistics = 0.77, P = 0.001). Mechanistically, knockdown of TPP1 inhibited the expression of hTERT in both mRNA and protein levels. High expression of TPP1 (HR = 2.61, 95% CI 1.23-5.51) and co-high expression of TPP1 and hTERT (HR = 2.38, 95% CI 1.28-4.43) were independently associated with worse survival in cervical cancer patients. TPP1 and hTERT expression was correlated and high expression of TPP1 was associated with high risk of CIN 3 and cervical cancer and could predict a worse survival in cervical cancer.", "doi": "10.1371/journal.pone.0298118", "pmid": "38722833", "labels": {"DDLS Fellow": null, "Qiaoli Wang": null}, "xrefs": [{"db": "pmc", "key": "PMC11081309"}, {"db": "pii", "key": "PONE-D-23-25037"}], "notes": [], "created": "2025-11-28T12:24:35.649Z", "modified": "2025-11-28T12:24:35.705Z"}, {"entity": "publication", "iuid": "2195d3173411440cbf65e96d7e61cb60", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/2195d3173411440cbf65e96d7e61cb60.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/2195d3173411440cbf65e96d7e61cb60"}}, "title": "Gastrointestinal cancer precursor risk and mortality in pancreatic intraductal papillary mucinous neoplasms: a nationwide cohort study.", "authors": [{"family": "Vujasinovic", "given": "Miroslav", "initials": "M", "orcid": "0000-0002-6496-295X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/df1d05afd7a649e6b62a3a9ee6784ea8.json"}}, {"family": "Elbe", "given": "Peter", "initials": "P"}, {"family": "Ekheden", "given": "Isabella", "initials": "I"}, {"family": "Wang", "given": "Qiao-Li", "initials": "QL"}, {"family": "Thuresson", "given": "Marcus", "initials": "M"}, {"family": "Roelstraete", "given": "Bjorn", "initials": "B"}, {"family": "Ghazi", "given": "Sam", "initials": "S"}, {"family": "L\u00f6hr", "given": "J-Matthias", "initials": "JM"}, {"family": "Ludvigsson", "given": "Jonas F", "initials": "JF", "orcid": "0000-0003-1024-5602", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2bbd74e2ef664d9687a2c8bc616dec07.json"}}], "type": "journal article", "published": "2024-05-00", "journal": {"title": "Scand. J. Gastroenterol.", "issn": "1502-7708", "volume": "59", "issue": "5", "pages": "600-607", "issn-l": "0036-5521"}, "abstract": "Intraductal papillary mucinous neoplasm (IPMN) of the pancreas is a precursor of pancreatic cancer. While earlier research has shown a high prevalence of synchronous/metachronous extrapancreatic tumors in IPMN patients, these studies have often been small with retrospective data collection. The aim of the study was to examine absolute and relative risks of non-pancreatic gastrointestinal (GI) cancer precursors and mortality in histologically confirmed IPMN.\n\nThrough the nationwide ESPRESSO histopathology cohort, we retrieved data on IPMN between 1965 and 2016. Each index case was matched to \u22645 general population controls. Through Cox regression, we estimated hazard ratios (HRs) for future GI cancer precursors and death.\n\nA total of 117 patients with IPMN and 539 age- and sex-matched controls were included. Over a median of 2.1 years of follow up, we confirmed two (1.7%) incident GI cancer precursors in IPMN vs. four (0.7%) in controls, corresponding to an HR of 1.89 (95%CI = 0.34-10.55). By contrast, IPMN patients were at increased risk of death (HR 3.61 (95%CI = 1.79-7.27)). The most common cause of death in IPMN was pancreatic cancer (n = 14; 45.2% of all deaths).\n\nWe found no association between IPMN and other GI cancer precursors. This argues against comprehensive routine surveillance for other GI cancer precursors in IPMN patients. Mortality was increased in IPMN with pancreatic cancer being the most common cause of death, indicating the need for lifelong follow up in all resected and non-resected patients with IPMN. However, results should be confirmed in larger cohorts.", "doi": "10.1080/00365521.2024.2310162", "pmid": "38351653", "labels": {"DDLS Fellow": null, "Qiaoli Wang": null}, "xrefs": [], "notes": [], "created": "2025-11-28T12:24:34.540Z", "modified": "2025-11-28T12:24:34.584Z"}, {"entity": "publication", "iuid": "119372bc0180412e8486e4b2fa20522b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/119372bc0180412e8486e4b2fa20522b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/119372bc0180412e8486e4b2fa20522b"}}, "title": "Disease staging of Alzheimer's disease using a CSF-based biomarker model.", "authors": [{"family": "Salvad\u00f3", "given": "Gemma", "initials": "G", "orcid": "0000-0002-5210-9230", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c3b7599000404d618d84b389ba47f19a.json"}}, {"family": "Horie", "given": "Kanta", "initials": "K", "orcid": "0000-0001-7736-2614", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a39cbb87fbd940fe830fef9c5d1ad9d5.json"}}, {"family": "Barth\u00e9lemy", "given": "Nicolas R", "initials": "NR", "orcid": "0000-0003-4937-2860", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2e2661ed001644c68ff9513b271bbe7b.json"}}, {"family": "Vogel", "given": "Jacob W", "initials": "JW", "orcid": "0000-0001-6394-9940", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d2ad5af780c245da9b59a8c80a0b00ff.json"}}, {"family": "Pichet Binette", "given": "Alexa", "initials": "A", "orcid": "0000-0001-5218-3337", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e8f0967b7b694bcf96e30a051a5bbe9a.json"}}, {"family": "Chen", "given": "Charles D", "initials": "CD", "orcid": "0000-0001-6698-1268", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/aff8a335b4394feb8add3b1feb5f2812.json"}}, {"family": "Aschenbrenner", "given": "Andrew J", "initials": "AJ"}, {"family": "Gordon", "given": "Brian A", "initials": "BA", "orcid": "0000-0003-2109-2955", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5d260cb618f240bc839bdb8b607c5418.json"}}, {"family": "Benzinger", "given": "Tammie L S", "initials": "TLS", "orcid": "0000-0002-8114-0552", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/edc53d42fddc4d3db2b7abbbac246223.json"}}, {"family": "Holtzman", "given": "David M", "initials": "DM"}, {"family": "Morris", "given": "John C", "initials": "JC"}, {"family": "Palmqvist", "given": "Sebastian", "initials": "S", "orcid": "0000-0002-9267-1930", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6fbd05e87cfb4057a1a7e41d9fb94aef.json"}}, {"family": "Stomrud", "given": "Erik", "initials": "E"}, {"family": "Janelidze", "given": "Shorena", "initials": "S", "orcid": "0000-0003-2869-8378", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a3e2ab428bdc42838f5af521a4d8b862.json"}}, {"family": "Ossenkoppele", "given": "Rik", "initials": "R"}, {"family": "Schindler", "given": "Suzanne E", "initials": "SE"}, {"family": "Bateman", "given": "Randall J", "initials": "RJ", "orcid": "0000-0002-7729-1702", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0dd2354822ab40feacbdd2168370d582.json"}}, {"family": "Hansson", "given": "Oskar", "initials": "O", "orcid": "0000-0001-8467-7286", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9292115deece4d9fafc8a02d4a430707.json"}}], "type": "journal article", "published": "2024-05-00", "journal": {"title": "Nat Aging", "issn": "2662-8465", "volume": "4", "issue": "5", "pages": "694-708", "issn-l": null}, "abstract": "Biological staging of individuals with Alzheimer's disease (AD) may improve diagnostic and prognostic workup of dementia in clinical practice and the design of clinical trials. In this study, we used the Subtype and Stage Inference (SuStaIn) algorithm to establish a robust biological staging model for AD using cerebrospinal fluid (CSF) biomarkers. Our analysis involved 426 participants from BioFINDER-2 and was validated in 222 participants from the Knight Alzheimer Disease Research Center cohort. SuStaIn identified a singular biomarker sequence and revealed that five CSF biomarkers effectively constituted a reliable staging model (ordered: A\u03b242/40, pT217/T217, pT205/T205, MTBR-tau243 and non-phosphorylated mid-region tau). The CSF stages (0-5) demonstrated a correlation with increased abnormalities in other AD-related biomarkers, such as A\u03b2-PET and tau-PET, and aligned with longitudinal biomarker changes reflective of AD progression. Higher CSF stages at baseline were associated with an elevated hazard ratio of clinical decline. This study highlights a common molecular pathway underlying AD pathophysiology across all patients, suggesting that a single CSF collection can accurately indicate the presence of AD pathologies and characterize the stage of disease progression. The proposed staging model has implications for enhancing diagnostic and prognostic assessments in both clinical practice and the design of clinical trials.", "doi": "10.1038/s43587-024-00599-y", "pmid": "38514824", "labels": {"Jacob W Vogel": null, "DDLS Fellow": null}, "xrefs": [{"db": "mid", "key": "NIHMS1986363"}, {"db": "pmc", "key": "PMC11108782"}, {"db": "pii", "key": "10.1038/s43587-024-00599-y"}], "notes": [], "created": "2025-03-19T11:17:00.164Z", "modified": "2025-03-19T11:19:05.978Z"}, {"entity": "publication", "iuid": "04cfcdec61724e0ab852e7f82316d8be", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/04cfcdec61724e0ab852e7f82316d8be.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/04cfcdec61724e0ab852e7f82316d8be"}}, "title": "Colonization factors of human and animal-specific enterotoxigenic Escherichia coli (ETEC).", "authors": [{"family": "von Mentzer", "given": "Astrid", "initials": "A"}, {"family": "Svennerholm", "given": "Ann-Mari", "initials": "AM"}], "type": "journal article", "published": "2024-05-00", "journal": {"title": "Trends Microbiol.", "issn": "1878-4380", "volume": "32", "issue": "5", "pages": "448-464", "issn-l": "0966-842X"}, "abstract": "Colonization factors (CFs) are major virulence factors of enterotoxigenic Escherichia coli (ETEC). This pathogen is among the most common causes of bacterial diarrhea in children in low- and middle-income countries, travelers, and livestock. CFs are major candidate antigens in vaccines under development as preventive measures against ETEC infections in humans and livestock. Recent molecular studies have indicated that newly identified CFs on human ETEC are closely related to animal ETEC CFs. Increased knowledge of pathogenic mechanisms, immunogenicity, regulation, and expression of ETEC CFs, as well as the possible spread of animal ETEC to humans, may facilitate the future development of ETEC vaccines for humans and animals. Here, we present an updated review of CFs in ETEC.", "doi": "10.1016/j.tim.2023.11.001", "pmid": "38052687", "labels": {"Astrid von Mentzer": null, "DDLS Fellow": null}, "xrefs": [{"db": "pii", "key": "S0966-842X(23)00319-0"}], "notes": [], "created": "2025-12-02T15:47:08.175Z", "modified": "2025-12-02T15:47:08.178Z"}, {"entity": "publication", "iuid": "e0976a02cfbd40de8686848494f4beaf", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e0976a02cfbd40de8686848494f4beaf.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e0976a02cfbd40de8686848494f4beaf"}}, "title": "Clonal Hematopoiesis of Indeterminate Potential With Loss of Tet2 Enhances Risk for Atrial Fibrillation Through Nlrp3 Inflammasome Activation.", "authors": [{"family": "Lin", "given": "Amy Erica", "initials": "AE", "orcid": "0000-0002-0554-2832", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca94bff0b2bf49fda6fd77a16e6ef0fd.json"}}, {"family": "Bapat", "given": "Aneesh C", "initials": "AC", "orcid": "0000-0002-1996-522X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/aa87f4a8e0664c7e93b91941a770aa0c.json"}}, {"family": "Xiao", "given": "Ling", "initials": "L", "orcid": "0000-0002-5463-5576", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/37f99769b7f44a9d82116459fe8aea8c.json"}}, {"family": "Niroula", "given": "Abhishek", "initials": "A", "orcid": "0000-0002-5904-0635", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/05df7afc7a494ba5af8a378e5ffa53f0.json"}}, {"family": "Ye", "given": "Jiangchuan", "initials": "J"}, {"family": "Wong", "given": "Waihay J", "initials": "WJ", "orcid": "0000-0003-2023-6590", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3a4e1a5be5c54646ab5881bc338bf6cd.json"}}, {"family": "Agrawal", "given": "Mridul", "initials": "M"}, {"family": "Farady", "given": "Christopher J", "initials": "CJ", "orcid": "0000-0002-3607-9721", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3d5167b1ad30407ba72740764e1fbb83.json"}}, {"family": "Boettcher", "given": "Andreas", "initials": "A", "orcid": "0000-0002-6548-1015", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8bf2e6da2b5844e8b8e69e27905144f1.json"}}, {"family": "Hergott", "given": "Christopher B", "initials": "CB"}, {"family": "McConkey", "given": "Marie", "initials": "M", "orcid": "0000-0002-9500-018X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e5174577207f4e46b75a2f0170e76ff3.json"}}, {"family": "Flores-Bringas", "given": "Patricio", "initials": "P"}, {"family": "Shkolnik", "given": "Veronica", "initials": "V", "orcid": "0000-0002-9043-1503", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/509e4c48124649a29675f21de034504f.json"}}, {"family": "Bick", "given": "Alexander G", "initials": "AG", "orcid": "0000-0001-5824-9595", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d2da5a35a4984921b19dfafe64cea2de.json"}}, {"family": "Milan", "given": "David", "initials": "D", "orcid": "0000-0003-0149-3110", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0f5f95aea4ec44da99d8b4bfa2fe9ba2.json"}}, {"family": "Natarajan", "given": "Pradeep", "initials": "P", "orcid": "0000-0001-8402-7435", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fe8bd48c61c047cd8e61c35d9e9ac650.json"}}, {"family": "Libby", "given": "Peter", "initials": "P", "orcid": "0000-0002-1502-502X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/39fb20acff0442bd92fc7931d3ee6cf9.json"}}, {"family": "Ellinor", "given": "Patrick T", "initials": "PT", "orcid": "0000-0002-2067-0533", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fd1830794e884e6e849fd4f7645c9b61.json"}}, {"family": "Ebert", "given": "Benjamin L", "initials": "BL", "orcid": "0000-0003-0197-5451", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56e4f1c53a4348e2b0ceb44a38850a17.json"}}], "type": "journal article", "published": "2024-04-30", "journal": {"title": "Circulation", "issn": "1524-4539", "volume": "149", "issue": "18", "pages": "1419-1434", "issn-l": "0009-7322"}, "abstract": "Clonal hematopoiesis of indeterminate potential (CHIP), a common age-associated phenomenon, associates with increased risk of both hematological malignancy and cardiovascular disease. Although CHIP is known to increase the risk of myocardial infarction and heart failure, the influence of CHIP in cardiac arrhythmias, such as atrial fibrillation (AF), is less explored.\n\nCHIP prevalence was determined in the UK Biobank, and incident AF analysis was stratified by CHIP status and clone size using Cox proportional hazard models. Lethally irradiated mice were transplanted with hematopoietic-specific loss of Tet2, hematopoietic-specific loss of Tet2 and Nlrp3, or wild-type control and fed a Western diet, compounded with or without NLRP3 (NLR [NACHT, LRR {leucine rich repeat}] family pyrin domain containing protein 3) inhibitor, NP3-361, for 6 to 9 weeks. Mice underwent in vivo invasive electrophysiology studies and ex vivo optical mapping. Cardiomyocytes from Ldlr-/- mice with hematopoietic-specific loss of Tet2 or wild-type control and fed a Western diet were isolated to evaluate calcium signaling dynamics and analysis. Cocultures of pluripotent stem cell-derived atrial cardiomyocytes were incubated with Tet2-deficient bone marrow-derived macrophages, wild-type control, or cytokines IL-1\u03b2 (interleukin 1\u03b2) or IL-6 (interleukin 6).\n\nAnalysis of the UK Biobank showed individuals with CHIP, in particular TET2 CHIP, have increased incident AF. Hematopoietic-specific inactivation of Tet2 increases AF propensity in atherogenic and nonatherogenic mouse models and is associated with increased Nlrp3 expression and CaMKII (Ca2+/calmodulin-dependent protein kinase II) activation, with AF susceptibility prevented by inactivation of Nlrp3. Cardiomyocytes isolated from Ldlr-/- mice with hematopoietic inactivation of Tet2 and fed a Western diet have impaired calcium release from the sarcoplasmic reticulum into the cytosol, contributing to atrial arrhythmogenesis. Abnormal sarcoplasmic reticulum calcium release was recapitulated in cocultures of cardiomyocytes with the addition of Tet2-deficient macrophages or cytokines IL-1\u03b2 or IL-6.\n\nWe identified a modest association between CHIP, particularly TET2 CHIP, and incident AF in the UK Biobank population. In a mouse model of AF resulting from hematopoietic-specific inactivation of Tet2, we propose altered calcium handling as an arrhythmogenic mechanism, dependent on Nlrp3 inflammasome activation. Our data are in keeping with previous studies of CHIP in cardiovascular disease, and further studies into the therapeutic potential of NLRP3 inhibition for individuals with TET2 CHIP may be warranted.", "doi": "10.1161/CIRCULATIONAHA.123.065597", "pmid": "38357791", "labels": {"Abhishek Niroula": "", "DDLS Fellow": ""}, "xrefs": [{"db": "mid", "key": "NIHMS1962305"}, {"db": "pmc", "key": "PMC11058018"}], "notes": [], "created": "2025-03-18T15:48:47.159Z", "modified": "2026-10-01T08:23:51.379Z"}, {"entity": "publication", "iuid": "e8139e5e7ef04acd839fd3906a2e385e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e8139e5e7ef04acd839fd3906a2e385e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e8139e5e7ef04acd839fd3906a2e385e"}}, "title": "Inference of drug off-target effects on cellular signaling using interactome-based deep learning.", "authors": [{"family": "Meimetis", "given": "Nikolaos", "initials": "N", "orcid": "0000-0003-2333-0187", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e0e968cb5cc44b52818647cea77762d9.json"}}, {"family": "Lauffenburger", "given": "Douglas A", "initials": "DA", "orcid": "0000-0002-0050-989X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ac0a09cb7c9c49de95b660756a4e5464.json"}}, {"family": "Nilsson", "given": "Avlant", "initials": "A", "orcid": "0000-0002-9476-4516", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f2e21dbc1c624f6a841c59e959e948e4.json"}}], "type": "journal article", "published": "2024-04-19", "journal": {"title": "iScience", "issn": "2589-0042", "issn-l": null, "volume": "27", "issue": "4", "pages": "109509"}, "abstract": "Many diseases emerge from dysregulated cellular signaling, and drugs are often designed to target specific signaling proteins. Off-target effects are, however, common and may ultimately result in failed clinical trials. Here we develop a computer model of the cell's transcriptional response to drugs for improved understanding of their mechanisms of action. The model is based on ensembles of artificial neural networks and simultaneously infers drug-target interactions and their downstream effects on intracellular signaling. With this, it predicts transcription factors' activities, while recovering known drug-target interactions and inferring many new ones, which we validate with an independent dataset. As a case study, we analyze the effects of the drug Lestaurtinib on downstream signaling. Alongside its intended target, FLT3, the model predicts an inhibition of CDK2 that enhances the downregulation of the cell cycle-critical transcription factor FOXM1. Our approach can therefore enhance our understanding of drug signaling for therapeutic design.", "doi": "10.1016/j.isci.2024.109509", "pmid": "38591003", "labels": {"Avlant Nilsson": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC11000001"}, {"db": "pii", "key": "S2589-0042(24)00730-2"}], "notes": [], "created": "2025-03-20T10:57:42.060Z", "modified": "2026-09-23T11:24:18.761Z"}, {"entity": "publication", "iuid": "f6557e4bde204b0eb7e4e7bf78bf8edd", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f6557e4bde204b0eb7e4e7bf78bf8edd.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f6557e4bde204b0eb7e4e7bf78bf8edd"}}, "title": "Longitudinal Exposomics in a Multiomic Wellness Cohort Reveals Distinctive and Dynamic Environmental Chemical Mixtures in Blood", "authors": [{"family": "Sdougkou", "given": "Kalliroi", "initials": "K", "orcid": "0000-0001-9463-655X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f07679bf36604909b7533419e618a68e.json"}}, {"family": "Papazian", "given": "Stefano", "initials": "S", "orcid": "0000-0003-2538-8702", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/27c56d6b160c42d4b3782d78210e80ff.json"}}, {"family": "Bonnefille", "given": "B\u00e9nilde", "initials": "B", "orcid": "0000-0001-5141-7111", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8df2bdf31f21411a90ccc2f9bb6eaf10.json"}}, {"family": "Xie", "given": "Hongyu", "initials": "H", "orcid": "0000-0002-2422-0492", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/871a1de2d146412693d3cfea85e8e293.json"}}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e213b04f8984c8eb00c68f5bc2f6a36.json"}}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/abbbf8193d5a4376a5c726768d039439.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ea446aa574042a295d5f69437402f76.json"}}, {"family": "Bergstr\u00f6m", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0003-4289-5722", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d414b3352a4540a68227ca7eec73cfa6.json"}}, {"family": "Martin", "given": "Leah JM", "initials": "LJ"}, {"family": "Martin", "given": "Jonathan W", "initials": "JW", "orcid": "0000-0001-6265-4294", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02199c0d99674e2ea5e96e6589c07a00.json"}}], "type": "posted-content", "published": "2024-04-17", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2024.04.14.589329", "pmid": null, "labels": {"Fredrik Edfors": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T10:53:10.468Z", "modified": "2026-09-23T15:38:11.268Z"}, {"entity": "publication", "iuid": "d3f9ec4f7ab64d1c991880c490c53019", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d3f9ec4f7ab64d1c991880c490c53019.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d3f9ec4f7ab64d1c991880c490c53019"}}, "title": "Comparison of the performance of multiple whole-genome sequence-based tools for the identification of Bacillus cereus sensu stricto biovar Thuringiensis.", "authors": [{"family": "Chung", "given": "Taejung", "initials": "T", "orcid": "0000-0003-4783-6473", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7a7b898b08a84a1ab602619308a98cb8.json"}}, {"family": "Salazar", "given": "Abimel", "initials": "A"}, {"family": "Harm", "given": "Grant", "initials": "G"}, {"family": "Johler", "given": "Sophia", "initials": "S", "orcid": "0000-0003-4299-5651", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/13a16c4a1aad43f7b4ce0d0b59766b8f.json"}}, {"family": "Carroll", "given": "Laura M", "initials": "LM"}, {"family": "Kovac", "given": "Jasna", "initials": "J", "orcid": "0000-0002-9465-4552", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d18e6f5bd24644e18030b59391d1a755.json"}}], "type": "journal article", "published": "2024-04-17", "journal": {"title": "Applied and environmental microbiology", "issn": "1098-5336", "volume": "90", "issue": "4", "pages": "e0177823", "issn-l": "0099-2240"}, "abstract": "The Bacillus cereus sensu stricto (s.s.) species comprises strains of biovar Thuringiensis (Bt) known for their bioinsecticidal activity, as well as strains with foodborne pathogenic potential. Bt strains are identified (i) based on the production of insecticidal crystal proteins, also known as Bt toxins, or (ii) based on the presence of cry, cyt, and vip genes, which encode Bt toxins. Multiple bioinformatics tools have been developed for the detection of crystal protein-encoding genes based on whole-genome sequencing (WGS) data. However, the performance of these tools is yet to be evaluated using phenotypic data. Thus, the goal of this study was to assess the performance of four bioinformatics tools for the detection of crystal protein-encoding genes. The accuracy of sequence-based identification of Bt was determined in reference to phenotypic microscope-based screening for the production of crystal proteins. A total of 58 diverse B. cereus sensu lato strains isolated from clinical, food, environmental, and commercial biopesticide products underwent WGS. Isolates were examined for crystal protein production using phase contrast microscopy. Crystal protein-encoding genes were detected using BtToxin_Digger, BTyper3, IDOPS (identification of pesticidal sequences), and Cry_processor. Out of 58 isolates, the phenotypic production of crystal proteins was confirmed for 18 isolates. Specificity and sensitivity of Bt identification based on sequences were 0.85 and 0.94 for BtToxin_Digger, 0.97 and 0.89 for BTyper3, 0.95 and 0.94 for IDOPS, and 0.88 and 1.00 for Cry_processor, respectively. Cry_processor predicted crystal protein production with the highest specificity, and BtToxin_Digger and IDOPS predicted crystal protein production with the highest sensitivity. Three out of four tested bioinformatics tools performed well overall, with IDOPS achieving high sensitivity and specificity (>0.90).IMPORTANCEStrains of Bacillus cereus sensu stricto (s.s.) biovar Thuringiensis (Bt) are used as organic biopesticides. Bt is differentiated from the foodborne pathogen Bacillus cereus s.s. by the production of insecticidal crystal proteins. Thus, reliable genomic identification of biovar Thuringiensis is necessary to ensure food safety and facilitate risk assessment. This study assessed the accuracy of whole-genome sequencing (WGS)-based identification of Bt compared to phenotypic microscopy-based screening for crystal protein production. Multiple bioinformatics tools were compared to assess their performance in predicting crystal protein production. Among them, identification of pesticidal sequences performed best overall at WGS-based Bt identification.", "doi": "10.1128/aem.01778-23", "pmid": "38470126", "labels": {"Laura Carroll": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC11026089"}], "notes": [], "created": "2025-03-18T17:31:40.749Z", "modified": "2026-09-23T11:29:24.406Z"}, {"entity": "publication", "iuid": "b3d485a2b3d74f79ae1b0450b6dadd4c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b3d485a2b3d74f79ae1b0450b6dadd4c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b3d485a2b3d74f79ae1b0450b6dadd4c"}}, "title": "Efficient calculation of orientation-dependent lipid dynamics from membrane simulations.", "authors": [{"family": "Doktorova", "given": "Milka", "initials": "M", "orcid": "0000-0003-4366-2242", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/791384c319f04584bac8ffb21df7271f.json"}}, {"family": "Khelashvili", "given": "George", "initials": "G", "orcid": "0000-0001-7235-8579", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/49b73bce7f8541fd8c959b5117bbe668.json"}}, {"family": "Brown", "given": "Michael F", "initials": "MF", "orcid": "0000-0003-4154-0241", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b57572fcc90e4033b1c705a9c030e7eb.json"}}], "type": "preprint", "published": "2024-04-15", "journal": {"title": "bioRxiv", "issn": "2692-8205", "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": "Molecular dynamics simulations of lipid membranes have become increasingly impactful in biophysics because they offer atomistic resolution of structural fluctuations in relation to their functional outputs. Yet quantitative characterization of multiscale processes is a formidable challenge due to the distribution of motions that evade analysis of discrete simulation data. Here we investigate the efficient calculation of CH bond relaxation rates from membrane simulations. Widely used computational approaches offer numerical simplicity but fall short of capturing crucial aspects of the orientation dependence of the dynamics. To circumvent this problem, we introduced a robust framework based on liquid crystal theory which considers explicitly the CH bond motions with respect to the director axis (bilayer normal). Analysis of the orientation dependence of the dynamics shows excellent agreement with experiment, illustrating how the ordering potential affects the calculated relaxation rates. Furthermore, a fit-based resampling of the autocorrelation function of the bond fluctuations validates the new approach for low-temporal resolution data. The recovered relaxation rates indicate that at short timescales, both with and without cholesterol, the local motions of CH bonds describe the bilayer microviscosity and resemble liquid hydrocarbons. Our results establish the critical role of the orientational anisotropy in analysis of membrane simulations, explain fundamental aspects of lipid dynamics, and provide guidelines for extracting information that can be compared to experimental data.", "doi": "10.1101/2023.05.23.542012", "pmid": "37292992", "labels": {"Milka Doktorova": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC10245828"}, {"db": "pii", "key": "2023.05.23.542012"}], "notes": [], "created": "2024-11-27T12:18:17.246Z", "modified": "2024-11-29T08:17:49.622Z"}, {"entity": "publication", "iuid": "c6db8369a47c42b395a627a5c2925ff0", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c6db8369a47c42b395a627a5c2925ff0.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c6db8369a47c42b395a627a5c2925ff0"}}, "title": "Macromolecular condensation organizes nucleolar sub-phases to set up a pH gradient.", "authors": [{"family": "King", "given": "Matthew R", "initials": "MR"}, {"family": "Ruff", "given": "Kiersten M", "initials": "KM"}, {"family": "Lin", "given": "Andrew Z", "initials": "AZ"}, {"family": "Pant", "given": "Avnika", "initials": "A"}, {"family": "Farag", "given": "Mina", "initials": "M"}, {"family": "Lalmansingh", "given": "Jared M", "initials": "JM"}, {"family": "Wu", "given": "Tingting", "initials": "T"}, {"family": "Fossat", "given": "Martin J", "initials": "MJ"}, {"family": "Ouyang", "given": "Wei", "initials": "W"}, {"family": "Lew", "given": "Matthew D", "initials": "MD"}, {"family": "Lundberg", "given": "Emma", "initials": "E"}, {"family": "Vahey", "given": "Michael D", "initials": "MD"}, {"family": "Pappu", "given": "Rohit V", "initials": "RV"}], "type": "journal article", "published": "2024-04-11", "journal": {"title": "Cell", "issn": "1097-4172", "volume": "187", "issue": "8", "pages": "1889-1906.e24", "issn-l": "0092-8674"}, "abstract": "Nucleoli are multicomponent condensates defined by coexisting sub-phases. We identified distinct intrinsically disordered regions (IDRs), including acidic (D/E) tracts and K-blocks interspersed by E-rich regions, as defining features of nucleolar proteins. We show that the localization preferences of nucleolar proteins are determined by their IDRs and the types of RNA or DNA binding domains they encompass. In vitro reconstitutions and studies in cells showed how condensation, which combines binding and complex coacervation of nucleolar components, contributes to nucleolar organization. D/E tracts of nucleolar proteins contribute to lowering the pH of co-condensates formed with nucleolar RNAs in vitro. In cells, this sets up a pH gradient between nucleoli and the nucleoplasm. By contrast, juxta-nucleolar bodies, which have different macromolecular compositions, featuring protein IDRs with very different charge profiles, have pH values that are equivalent to or higher than the nucleoplasm. Our findings show that distinct compositional specificities generate distinct physicochemical properties for condensates.", "doi": "10.1016/j.cell.2024.02.029", "pmid": "38503281", "labels": {"DDLS Fellow": "", "Wei Ouyang": ""}, "xrefs": [{"db": "mid", "key": "NIHMS2044799"}, {"db": "pmc", "key": "PMC11938373"}, {"db": "pii", "key": "S0092-8674(24)00232-0"}], "notes": [], "created": "2026-08-20T06:50:29.412Z", "modified": "2026-09-23T06:46:49.267Z"}, {"entity": "publication", "iuid": "1a34613645e042a586322fc43704d286", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1a34613645e042a586322fc43704d286.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1a34613645e042a586322fc43704d286"}}, "title": "Utilizing developmental dynamics for evolutionary prediction and control.", "authors": [{"family": "Milocco", "given": "Lisandro", "initials": "L", "orcid": "0000-0003-3953-0407", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/74f9e4dfff0e4b008c46b75e3d319673.json"}}, {"family": "Uller", "given": "Tobias", "initials": "T", "orcid": "0000-0003-1293-5842", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/63799fa606284069a4ccf960795749e8.json"}}], "type": "journal article", "published": "2024-04-02", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "121", "issue": "14", "pages": "e2320413121", "issn-l": "0027-8424"}, "abstract": "Understanding, predicting, and controlling the phenotypic consequences of genetic and environmental change is essential to many areas of fundamental and applied biology. In evolutionary biology, the generative process of development is a major source of organismal evolvability that constrains or facilitates adaptive change by shaping the distribution of phenotypic variation that selection can act upon. While the complex interactions between genetic and environmental factors during development may appear to make it impossible to infer the consequences of perturbations, the persistent observation that many perturbations result in similar phenotypes indicates that there is a logic to what variation is generated. Here, we show that a general representation of development as a dynamical system can reveal this logic. We build a framework that allows predicting the phenotypic effects of perturbations, and conditions for when the effects of perturbations of different origins are concordant. We find that this concordance is explained by two generic features of development, namely the dynamical dependence of the phenotype on itself and the fact that all perturbations must affect the developmental process to have an effect on the phenotype. We apply our theoretical framework to classical models of development and show that it can be used to predict the evolutionary response to selection using information of plasticity and to accelerate evolution in a desired direction. The framework we introduce provides a way to quantitatively interchange perturbations, opening an avenue of perturbation design to control the generation of variation.", "doi": "10.1073/pnas.2320413121", "pmid": "38530898", "labels": {"DDLS Fellow": null, "Lisandro Milocco": null}, "xrefs": [{"db": "pmc", "key": "PMC10998628"}], "notes": [], "created": "2025-11-28T14:28:25.545Z", "modified": "2025-11-28T14:29:03.092Z"}, {"entity": "publication", "iuid": "9900d195ccee4a3b99d8a29d87b7cc7d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9900d195ccee4a3b99d8a29d87b7cc7d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9900d195ccee4a3b99d8a29d87b7cc7d"}}, "title": "Lifetime Duration of Breastfeeding and Cardiovascular Risk in Women With Type 2 Diabetes or a History of Gestational Diabetes: Findings From Two Large Prospective Cohorts.", "authors": [{"family": "Birukov", "given": "Anna", "initials": "A", "orcid": "0000-0002-8306-3351", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0485c5a948c343d78bd63652195e7253.json"}}, {"family": "Guasch-Ferr\u00e9", "given": "Marta", "initials": "M", "orcid": "0000-0001-8525-1404", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2d1a49f5df124e96a9285b43d628cee9.json"}}, {"family": "Ley", "given": "Sylvia H", "initials": "SH", "orcid": "0000-0003-0084-2630", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/23f0a3e83c1e49f3b57ff6bf2a9f7b5e.json"}}, {"family": "Tobias", "given": "Deirdre K", "initials": "DK", "orcid": "0000-0003-0020-9552", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b5e79c8580904d65bbd35821a2371239.json"}}, {"family": "Wang", "given": "Fenglei", "initials": "F"}, {"family": "Wittenbecher", "given": "Clemens", "initials": "C", "orcid": "0000-0001-7792-877X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2f7d2c289b3c47d5a79d23bd48a3225a.json"}}, {"family": "Yang", "given": "Jiaxi", "initials": "J", "orcid": "0000-0002-4497-9615", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/813a309f6b5c46ff9bff0ac129512c48.json"}}, {"family": "Manson", "given": "JoAnn E", "initials": "JE"}, {"family": "Chavarro", "given": "Jorge E", "initials": "JE", "orcid": "0000-0002-4436-9630", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bf89e1968fa1427c900cacffd0422191.json"}}, {"family": "Hu", "given": "Frank B", "initials": "FB"}, {"family": "Zhang", "given": "Cuilin", "initials": "C", "orcid": "0000-0002-8014-2708", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e842ad101b8c4110946037b230884450.json"}}], "type": "journal article", "published": "2024-04-01", "journal": {"title": "Diabetes Care", "issn": "1935-5548", "volume": "47", "issue": "4", "pages": "720-728", "issn-l": null}, "abstract": "Breastfeeding duration is inversely associated with risks of cardiovascular disease (CVD) and type 2 diabetes in parous women. However, the association among women at high risk, including women with type 2 diabetes or gestational diabetes mellitus (GDM) is unclear.\n\nWe included 15,146 parous women with type 2 diabetes from the Nurses' Health Study I and II (NHS, NHS II) and 4,537 women with a history of GDM from NHS II. Participants reported history of breastfeeding via follow-up questionnaires. Incident CVD by 2017 comprised stroke or coronary heart disease (CHD) (myocardial infarction, coronary revascularization). Adjusted hazard ratios (aHRs) and 95% CIs were estimated using Cox models.\n\nWe documented 1,159 incident CVD cases among women with type 2 diabetes in both cohorts during 188,874 person-years of follow-up and 132 incident CVD cases among women with a GDM history during 100,218 person-years of follow-up. Longer lifetime duration of breastfeeding was significantly associated with lower CVD risk among women with type 2 diabetes, with pooled aHR of 0.68 (95% CI 0.54-0.85) for >18 months versus 0 months and 0.94 (0.91-0.98) per 6-month increment in breastfeeding. Similar associations were observed with CHD (pooled aHR 0.93 [0.88-0.97]) but not with stroke (0.96 [0.91-1.02]) per 6-month increment in breastfeeding. Among women with GDM history, >18 months versus 0 months of breastfeeding was associated with an aHR of 0.49 (0.28-0.86) for total CVD.\n\nLonger duration of breastfeeding was associated with lower risk of CVD in women with type 2 diabetes or GDM.", "doi": "10.2337/dc23-1494", "pmid": "38377484", "labels": {"Clemens Wittenbecher": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC11065777"}, {"db": "pii", "key": "154273"}], "notes": [], "created": "2025-03-19T08:18:43.992Z", "modified": "2026-09-23T09:05:52.303Z"}, {"entity": "publication", "iuid": "b44b20675f284acb911d497d1301f76c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b44b20675f284acb911d497d1301f76c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b44b20675f284acb911d497d1301f76c"}}, "title": "DIP-MS: ultra-deep interaction proteomics for the deconvolution of protein complexes.", "authors": [{"family": "Frommelt", "given": "Fabian", "initials": "F", "orcid": "0000-0003-3666-8005", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e71a93da1624a17bcbace26ba50c5a5.json"}}, {"family": "Fossati", "given": "Andrea", "initials": "A", "orcid": "0000-0001-5170-4903", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/658637b885384441943698722fad5944.json"}}, {"family": "Uliana", "given": "Federico", "initials": "F"}, {"family": "Wendt", "given": "Fabian", "initials": "F", "orcid": "0000-0002-2501-536X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f9f0e10e0ff84bfdba2da72790f12c32.json"}}, {"family": "Xue", "given": "Peng", "initials": "P"}, {"family": "Heusel", "given": "Moritz", "initials": "M"}, {"family": "Wollscheid", "given": "Bernd", "initials": "B", "orcid": "0000-0002-3923-1610", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fecd11050305473ca698ba6c6ee54a52.json"}}, {"family": "Aebersold", "given": "Ruedi", "initials": "R", "orcid": "0000-0002-9576-3267", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4aa50db862e94831b8cac04c4426daf1.json"}}, {"family": "Ciuffa", "given": "Rodolfo", "initials": "R"}, {"family": "Gstaiger", "given": "Matthias", "initials": "M", "orcid": "0000-0002-3245-3253", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8370f12358274bb2a5a4cd524ae4f465.json"}}], "type": "journal article", "published": "2024-04-00", "journal": {"title": "Nat. Methods", "issn": "1548-7105", "issn-l": "1548-7091", "volume": "21", "issue": "4", "pages": "635-647"}, "abstract": "Most proteins are organized in macromolecular assemblies, which represent key functional units regulating and catalyzing most cellular processes. Affinity purification of the protein of interest combined with liquid chromatography coupled to tandem mass spectrometry (AP-MS) represents the method of choice to identify interacting proteins. The composition of complex isoforms concurrently present in the AP sample can, however, not be resolved from a single AP-MS experiment but requires computational inference from multiple time- and resource-intensive reciprocal AP-MS experiments. Here we introduce deep interactome profiling by mass spectrometry (DIP-MS), which combines AP with blue-native-PAGE separation, data-independent acquisition with mass spectrometry and deep-learning-based signal processing to resolve complex isoforms sharing the same bait protein in a single experiment. We applied DIP-MS to probe the organization of the human prefoldin family of complexes, resolving distinct prefoldin holo- and subcomplex variants, complex-complex interactions and complex isoforms with new subunits that were experimentally validated. Our results demonstrate that DIP-MS can reveal proteome modularity at unprecedented depth and resolution.", "doi": "10.1038/s41592-024-02211-y", "pmid": "38532014", "labels": {"Andrea Fossati": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC11009110"}, {"db": "pii", "key": "10.1038/s41592-024-02211-y"}], "notes": [], "created": "2025-03-18T16:51:10.645Z", "modified": "2025-03-21T13:32:23.292Z"}, {"entity": "publication", "iuid": "78aacec6207547e993b2ba7414386dd1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/78aacec6207547e993b2ba7414386dd1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/78aacec6207547e993b2ba7414386dd1"}}, "title": "Biomarker-based staging of Alzheimer disease: rationale and clinical applications.", "authors": [{"family": "Therriault", "given": "Joseph", "initials": "J", "orcid": "0000-0002-7826-4781", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ead8a0c5abeb4021b67de72780349675.json"}}, {"family": "Schindler", "given": "Suzanne E", "initials": "SE", "orcid": "0000-0002-1680-1465", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d0db66c9d2e2466e876fd6729ed3aba7.json"}}, {"family": "Salvad\u00f3", "given": "Gemma", "initials": "G", "orcid": "0000-0002-5210-9230", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c3b7599000404d618d84b389ba47f19a.json"}}, {"family": "Pascoal", "given": "Tharick A", "initials": "TA"}, {"family": "Benedet", "given": "Andr\u00e9a Lessa", "initials": "AL"}, {"family": "Ashton", "given": "Nicholas J", "initials": "NJ"}, {"family": "Karikari", "given": "Thomas K", "initials": "TK", "orcid": "0000-0003-1422-4358", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/691ac93bc83b48d6b6d56004af3fb1e3.json"}}, {"family": "Apostolova", "given": "Liana", "initials": "L"}, {"family": "Murray", "given": "Melissa E", "initials": "ME", "orcid": "0000-0001-7379-2545", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca9051ca92954b028a9848e4b99f437d.json"}}, {"family": "Verberk", "given": "Inge", "initials": "I", "orcid": "0000-0003-0341-7445", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2bc5287e5d6c4f1c86b84a0198f1bf28.json"}}, {"family": "Vogel", "given": "Jacob W", "initials": "JW"}, {"family": "La Joie", "given": "Renaud", "initials": "R", "orcid": "0000-0003-2581-8100", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7019086dee3146e6acb527f31921e5f7.json"}}, {"family": "Gauthier", "given": "Serge", "initials": "S"}, {"family": "Teunissen", "given": "Charlotte", "initials": "C"}, {"family": "Rabinovici", "given": "Gil D", "initials": "GD"}, {"family": "Zetterberg", "given": "Henrik", "initials": "H", "orcid": "0000-0003-3930-4354", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/18365a2ea4ec4ca2baeb657cd1c8bd8f.json"}}, {"family": "Bateman", "given": "Randall J", "initials": "RJ", "orcid": "0000-0002-7729-1702", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0dd2354822ab40feacbdd2168370d582.json"}}, {"family": "Scheltens", "given": "Philip", "initials": "P"}, {"family": "Blennow", "given": "Kaj", "initials": "K", "orcid": "0000-0002-1890-4193", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/57f920b41aab42f0a43a32bbe34035b2.json"}}, {"family": "Sperling", "given": "Reisa", "initials": "R"}, {"family": "Hansson", "given": "Oskar", "initials": "O", "orcid": "0000-0001-8467-7286", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9292115deece4d9fafc8a02d4a430707.json"}}, {"family": "Jack", "given": "Clifford R", "initials": "CR", "orcid": "0000-0001-7916-622X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/48c9f645872d4c408a0b7d53f4f4560e.json"}}, {"family": "Rosa-Neto", "given": "Pedro", "initials": "P", "orcid": "0000-0001-9116-1376", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/aada749a4ab6404a9954fd902f5560fd.json"}}], "type": "journal article", "published": "2024-04-00", "journal": {"title": "Nat Rev Neurol", "issn": "1759-4766", "volume": "20", "issue": "4", "pages": "232-244", "issn-l": null}, "abstract": "Disease staging, whereby the spatial extent and load of brain pathology are used to estimate the severity of Alzheimer disease (AD), is pivotal to the gold-standard neuropathological diagnosis of AD. Current in vivo diagnostic frameworks for AD are based on abnormal concentrations of amyloid-\u03b2 and tau in the cerebrospinal fluid or on PET scans, and breakthroughs in molecular imaging have opened up the possibility of in vivo staging of AD. Focusing on the key principles of disease staging shared across several areas of medicine, this Review highlights the potential for in vivo staging of AD to transform our understanding of preclinical AD, refine enrolment criteria for trials of disease-modifying therapies and aid clinical decision-making in the era of anti-amyloid therapeutics. We provide a state-of-the-art review of recent biomarker-based AD staging systems and highlight their contributions to the understanding of the natural history of AD. Furthermore, we outline hypothetical frameworks to stage AD severity using more accessible fluid biomarkers. In addition, by applying amyloid PET-based staging to recently published anti-amyloid therapeutic trials, we highlight how biomarker-based disease staging frameworks could illustrate the numerous pathological changes that have already taken place in individuals with mildly symptomatic AD. Finally, we discuss challenges related to the validation and standardization of disease staging and provide a forward-looking perspective on potential clinical applications.", "doi": "10.1038/s41582-024-00942-2", "pmid": "38429551", "labels": {"Jacob W Vogel": null, "DDLS Fellow": null}, "xrefs": [{"db": "pii", "key": "10.1038/s41582-024-00942-2"}], "notes": [], "created": "2025-03-19T11:16:55.419Z", "modified": "2025-03-19T11:19:01.219Z"}, {"entity": "publication", "iuid": "c144eed63cca443ebc5813ccf7842a70", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c144eed63cca443ebc5813ccf7842a70.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c144eed63cca443ebc5813ccf7842a70"}}, "title": "Gene-expression memory-based prediction of cell lineages from scRNA-seq datasets.", "authors": [{"family": "Eisele", "given": "A S", "initials": "AS", "orcid": "0000-0001-8376-4089", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2bff45c62e2f426b99ca66c8d772fa12.json"}}, {"family": "Tarbier", "given": "M", "initials": "M", "orcid": "0000-0003-0556-2531", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9678d0797def441e9870afe6ffbb08d0.json"}}, {"family": "Dormann", "given": "A A", "initials": "AA"}, {"family": "Pelechano", "given": "V", "initials": "V", "orcid": "0000-0002-9415-788X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e893b93b7654d10b4072e1b5de0bd71.json"}}, {"family": "Suter", "given": "D M", "initials": "DM", "orcid": "0000-0001-5644-4899", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3a3dd88c76314449ad1823ac1f067db7.json"}}], "type": "journal article", "published": "2024-03-29", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "2744", "issn-l": "2041-1723"}, "abstract": "Assigning single cell transcriptomes to cellular lineage trees by lineage tracing has transformed our understanding of differentiation during development, regeneration, and disease. However, lineage tracing is technically demanding, often restricted in time-resolution, and most scRNA-seq datasets are devoid of lineage information. Here we introduce Gene Expression Memory-based Lineage Inference (GEMLI), a computational tool allowing to robustly identify small to medium-sized cell lineages solely from scRNA-seq datasets. GEMLI allows to study heritable gene expression, to discriminate symmetric and asymmetric cell fate decisions and to reconstruct individual multicellular structures from pooled scRNA-seq datasets. In human breast cancer biopsies, GEMLI reveals previously unknown gene expression changes at the onset of cancer invasiveness. The universal applicability of GEMLI allows studying the role of small cell lineages in a wide range of physiological and pathological contexts, notably in vivo. GEMLI is available as an R package on GitHub ( https://github.com/UPSUTER/GEMLI ).", "doi": "10.1038/s41467-024-47158-y", "pmid": "38553478", "labels": {"Marcel Tarbier": "", "DDLS Fellow": "", "SciLifeLab Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC10980719"}, {"db": "pii", "key": "10.1038/s41467-024-47158-y"}], "notes": [], "created": "2025-12-03T10:24:47.889Z", "modified": "2026-09-23T11:12:16.352Z"}, {"entity": "publication", "iuid": "07c94aaeb0224da4869e1546ccdc7d66", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/07c94aaeb0224da4869e1546ccdc7d66.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/07c94aaeb0224da4869e1546ccdc7d66"}}, "title": "Low coverage of species constrains the use of DNA barcoding to assess mosquito biodiversity.", "authors": [{"family": "Moraes Zenker", "given": "Maur\u00edcio", "initials": "M"}, {"family": "Portella", "given": "Tatiana Pineda", "initials": "TP"}, {"family": "Pessoa", "given": "Felipe Arley Costa", "initials": "FAC"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J", "orcid": "0000-0002-6528-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c666068e9d34939b0252a627007cec7.json"}}, {"family": "Galetti", "given": "Pedro Manoel", "initials": "PM"}], "type": "journal article", "published": "2024-03-28", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "7432", "issn-l": "2045-2322"}, "abstract": "Mosquitoes (Culicidae) represent the main vector insects globally, and they also inhabit many of the terrestrial and aquatic habitats of the world. DNA barcoding and metabarcoding are now widely used in both research and routine practices involving mosquitoes. However, these methodologies rely on information available in databases consisting of barcode sequences representing taxonomically identified voucher specimens. In this study, we assess the availability of public data for mosquitoes in the main online databases, focusing specifically on the two most widely used DNA barcoding markers in Culicidae: COI and ITS2. In addition, we test hypotheses on possible factors affecting species coverage (i.e., the percentage of species covered in the online databases) for COI in different countries and the occurrence of the DNA barcode gap for COI. Our findings showed differences in the data publicly available in the repositories, with a taxonomic or species coverage of 28.4-30.11% for COI in BOLD + GenBank, and 12.32% for ITS2 in GenBank. Afrotropical, Australian and Oriental biogeographic regions had the lowest coverages, while Nearctic, Palearctic and Oceanian had the highest. The Neotropical region had an intermediate coverage. In general, countries with a higher diversity of mosquitoes and higher numbers of medically important species had lower coverage. Moreover, countries with a higher number of endemic species tended to have a higher coverage. Although our DNA barcode gap analyses suggested that the species boundaries need to be revised in half of the mosquito species available in the databases, additional data must be gathered to confirm these results and to allow explaining the occurrence of the DNA barcode gap. We hope this study can help guide regional species inventories of mosquitoes and the completion of a publicly available reference library of DNA barcodes for all mosquito species.", "doi": "10.1038/s41598-024-58071-1", "pmid": "38548880", "labels": {"DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC10978826"}, {"db": "pii", "key": "10.1038/s41598-024-58071-1"}], "notes": [], "created": "2024-11-18T11:43:58.938Z", "modified": "2026-09-23T11:04:44.119Z"}, {"entity": "publication", "iuid": "c42e75b03f804e06973c7a13d57bde18", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c42e75b03f804e06973c7a13d57bde18.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c42e75b03f804e06973c7a13d57bde18"}}, "title": "Landscape of microRNA and target expression variation and covariation in single mouse embryonic stem cells", "authors": [{"family": "Tarbier", "given": "Marcel", "initials": "M"}, {"family": "Mackowiak", "given": "Sebastian D", "initials": "SD"}, {"family": "Sekar", "given": "Vaishnovi", "initials": "V"}, {"family": "Bonath", "given": "Franziska", "initials": "F"}, {"family": "Yapar", "given": "Etka", "initials": "E"}, {"family": "Fromm", "given": "Bastian", "initials": "B", "orcid": "0000-0003-0352-3037", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cdc4c42e06604b759dd6225c5f8362b5.json"}}, {"family": "Faridani", "given": "Omid R", "initials": "OR"}, {"family": "Biryukova", "given": "Inna", "initials": "I"}, {"family": "Friedl\u00e4nder", "given": "Marc R", "initials": "MR", "orcid": "0000-0001-6577-4363", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ac5a2794be7c4cab89d1e4f1570c9417.json"}}], "type": "posted-content", "published": "2024-03-27", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2024.03.24.586475", "pmid": null, "labels": {"SciLifeLab Fellow": "", "DDLS Fellow": "", "Marcel Tarbier": "", "Marc Friedl\u00e4nder": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T10:53:06.618Z", "modified": "2026-09-23T14:50:40.015Z"}, {"entity": "publication", "iuid": "c32ae05406e74d31ad90908a68b3cb3d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c32ae05406e74d31ad90908a68b3cb3d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c32ae05406e74d31ad90908a68b3cb3d"}}, "title": "U-FISH: a universal deep learning approach for accurate FISH spot detection across diverse datasets", "authors": [{"family": "Xu", "given": "Weize", "initials": "W", "orcid": "0000-0002-3903-0683", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3c05e3106bf742c29151f6a51e0d3453.json"}}, {"family": "Cai", "given": "Huaiyuan", "initials": "H"}, {"family": "Zhang", "given": "Qian", "initials": "Q"}, {"family": "Mueller", "given": "Florian", "initials": "F"}, {"family": "Ouyang", "given": "Wei", "initials": "W"}, {"family": "Cao", "given": "Gang", "initials": "G"}], "type": "posted-content", "published": "2024-03-11", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2024.03.06.583706", "pmid": null, "labels": {"DDLS Fellow": "", "Wei Ouyang": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T10:52:39.743Z", "modified": "2026-09-23T14:17:42.681Z"}, {"entity": "publication", "iuid": "d7bf3f1bb74b4880a1ccb1842d76e377", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d7bf3f1bb74b4880a1ccb1842d76e377.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d7bf3f1bb74b4880a1ccb1842d76e377"}}, "title": "Plasma metabolites of a healthy lifestyle in relation to mortality and longevity: Four prospective US cohort studies.", "authors": [{"family": "Tessier", "given": "Anne-Julie", "initials": "AJ", "orcid": "0000-0003-4551-1640", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/79588c2979634d5590d2545afef7bbbe.json"}}, {"family": "Wang", "given": "Fenglei", "initials": "F", "orcid": "0000-0002-3850-2482", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/41a725cb032d4e2097b2c75a5b18e937.json"}}, {"family": "Liang", "given": "Liming", "initials": "L", "orcid": "0000-0001-8261-3174", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7da355304cad4309ab4dee783a341611.json"}}, {"family": "Wittenbecher", "given": "Clemens", "initials": "C", "orcid": "0000-0001-7792-877X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2f7d2c289b3c47d5a79d23bd48a3225a.json"}}, {"family": "Haslam", "given": "Danielle E", "initials": "DE"}, {"family": "Eliassen", "given": "A Heather", "initials": "AH"}, {"family": "Tobias", "given": "Deirdre K", "initials": "DK", "orcid": "0000-0003-0020-9552", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b5e79c8580904d65bbd35821a2371239.json"}}, {"family": "Li", "given": "Jun", "initials": "J", "orcid": "0000-0003-3519-8638", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/77d0c8cac07b47228b383aa851382852.json"}}, {"family": "Zeleznik", "given": "Oana A", "initials": "OA"}, {"family": "Ascherio", "given": "Alberto", "initials": "A"}, {"family": "Sun", "given": "Qi", "initials": "Q", "orcid": "0000-0002-8480-1563", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4a65407257ac4518ac5cb19317ee3b32.json"}}, {"family": "Stampfer", "given": "Meir J", "initials": "MJ"}, {"family": "Grodstein", "given": "Francine", "initials": "F"}, {"family": "Rexrode", "given": "Kathryn M", "initials": "KM", "orcid": "0000-0003-3387-8429", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a3600b145b304aa7959c0f85fa198192.json"}}, {"family": "Manson", "given": "JoAnn E", "initials": "JE", "orcid": "0000-0002-9426-7595", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6e39f122c5fd4f0ea0dcf2353ed4a274.json"}}, {"family": "Balasubramanian", "given": "Raji", "initials": "R"}, {"family": "Clish", "given": "Clary B", "initials": "CB"}, {"family": "Mart\u00ednez-Gonz\u00e1lez", "given": "Miguel A", "initials": "MA", "orcid": "0000-0002-3917-9808", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7852fa98fe3a4da285d79f04e09cbd34.json"}}, {"family": "Chavarro", "given": "Jorge E", "initials": "JE", "orcid": "0000-0002-4436-9630", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bf89e1968fa1427c900cacffd0422191.json"}}, {"family": "Hu", "given": "Frank B", "initials": "FB"}, {"family": "Guasch-Ferr\u00e9", "given": "Marta", "initials": "M", "orcid": "0000-0001-8525-1404", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2d1a49f5df124e96a9285b43d628cee9.json"}}], "type": "journal article", "published": "2024-03-08", "journal": {"title": "Med", "issn": "2666-6340", "volume": "5", "issue": "3", "pages": "224-238.e5", "issn-l": null}, "abstract": "A healthy lifestyle is associated with a lower premature mortality risk and with longer life expectancy. However, the metabolic pathways of a healthy lifestyle and how they relate to mortality and longevity are unclear. We aimed to identify and replicate a healthy lifestyle metabolomic signature and examine how it is related to total and cause-specific mortality risk and longevity.\n\nIn four large cohorts with 13,056 individuals and 28-year follow-up, we assessed five healthy lifestyle factors, used liquid chromatography mass spectrometry to profile plasma metabolites, and ascertained deaths with death certificates. The unique healthy lifestyle metabolomic signature was identified using an elastic regression. Multivariable Cox regressions were used to assess associations of the signature with mortality and longevity.\n\nThe identified healthy lifestyle metabolomic signature was reflective of lipid metabolism pathways. Shorter and more saturated triacylglycerol and diacylglycerol metabolite sets were inversely associated with the healthy lifestyle score, whereas cholesteryl ester and phosphatidylcholine plasmalogen sets were positively associated. Participants with a higher healthy lifestyle metabolomic signature had a 17% lower risk of all-cause mortality, 19% for cardiovascular disease mortality, and 17% for cancer mortality and were 25% more likely to reach longevity. The healthy lifestyle metabolomic signature explained 38% of the association between the self-reported healthy lifestyle score and total mortality risk and 49% of the association with longevity.\n\nThis study identifies a metabolomic signature that measures adherence to a healthy lifestyle and shows prediction of total and cause-specific mortality and longevity.\n\nThis work was funded by the NIH, CIHR, AHA, Novo Nordisk Foundation, and SciLifeLab.", "doi": "10.1016/j.medj.2024.01.010", "pmid": "38366602", "labels": {"Clemens Wittenbecher": null, "DDLS Fellow": null}, "xrefs": [{"db": "mid", "key": "NIHMS1962992"}, {"db": "pmc", "key": "PMC10940196"}, {"db": "pii", "key": "S2666-6340(24)00040-0"}], "notes": [], "created": "2025-03-19T08:18:45.492Z", "modified": "2025-12-09T13:32:50.147Z"}, {"entity": "publication", "iuid": "6f4e49de47b7421889da93060495e49e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/6f4e49de47b7421889da93060495e49e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/6f4e49de47b7421889da93060495e49e"}}, "title": "Twenty years on from Developmental Plasticity and Evolution: middle-range theories and how to test them.", "authors": [{"family": "Uller", "given": "Tobias", "initials": "T", "orcid": "0000-0003-1293-5842", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/63799fa606284069a4ccf960795749e8.json"}}, {"family": "Milocco", "given": "Lisandro", "initials": "L", "orcid": "0000-0003-3953-0407", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/74f9e4dfff0e4b008c46b75e3d319673.json"}}, {"family": "Isanta-Navarro", "given": "Jana", "initials": "J", "orcid": "0000-0002-6168-4499", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/791d53fda02a4bdc81bfe0e66dac4ac9.json"}}, {"family": "Cornwallis", "given": "Charlie K", "initials": "CK", "orcid": "0000-0003-1308-3995", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cd3a03b2536c4e2490f9610ed9845538.json"}}, {"family": "Feiner", "given": "Nathalie", "initials": "N", "orcid": "0000-0003-4648-6950", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4e39c9bdce63497b9b48db29c749cc16.json"}}], "type": "journal article", "published": "2024-03-07", "journal": {"title": "J. Exp. Biol.", "issn": "1477-9145", "volume": "227", "issue": "Suppl_1", "issn-l": "0022-0949"}, "abstract": "In Developmental Plasticity and Evolution, Mary-Jane West-Eberhard argued that the developmental mechanisms that enable organisms to respond to their environment are fundamental causes of adaptation and diversification. Twenty years after publication of this book, this once so highly controversial claim appears to have been assimilated by a wealth of studies on 'plasticity-led' evolution. However, we suggest that the role of development in explanations for adaptive evolution remains underappreciated in this body of work. By combining concepts of evolvability from evolutionary developmental biology and quantitative genetics, we outline a framework that is more appropriate to identify developmental causes of adaptive evolution. This framework demonstrates how experimental and comparative developmental biology and physiology can be leveraged to put the role of plasticity in evolution to the test.", "doi": "10.1242/jeb.246375", "pmid": "38449333", "labels": {"DDLS Fellow": null, "Lisandro Milocco": null}, "xrefs": [{"db": "pii", "key": "344074"}], "notes": [], "created": "2025-11-28T14:28:23.399Z", "modified": "2025-11-28T14:29:01.119Z"}, {"entity": "publication", "iuid": "09536763d1864e339a2b9b6589db1480", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/09536763d1864e339a2b9b6589db1480.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/09536763d1864e339a2b9b6589db1480"}}, "title": "Protein biomarkers and alternatively methylated cell-free DNA detect early stage pancreatic cancer.", "authors": [{"family": "Ben-Ami", "given": "Roni", "initials": "R", "orcid": "0000-0002-4939-0324", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/60bcd554ec164a3b944496d1ebc09d9d.json"}}, {"family": "Wang", "given": "Qiao-Li", "initials": "QL"}, {"family": "Zhang", "given": "Jinming", "initials": "J"}, {"family": "Supplee", "given": "Julianna G", "initials": "JG"}, {"family": "Fahrmann", "given": "Johannes F", "initials": "JF"}, {"family": "Lehmann-Werman", "given": "Roni", "initials": "R"}, {"family": "Brais", "given": "Lauren K", "initials": "LK"}, {"family": "Nowak", "given": "Jonathan", "initials": "J", "orcid": "0000-0002-0943-7407", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/71150fe12f15469090234f31e56fa682.json"}}, {"family": "Yuan", "given": "Chen", "initials": "C", "orcid": "0000-0002-0708-9648", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cd3904c835394e0d89bba633a0b74c54.json"}}, {"family": "Loftus", "given": "Maureen", "initials": "M"}, {"family": "Babic", "given": "Ana", "initials": "A"}, {"family": "Irajizad", "given": "Ehsan", "initials": "E"}, {"family": "Davidi", "given": "Tal", "initials": "T"}, {"family": "Zick", "given": "Aviad", "initials": "A"}, {"family": "Hubert", "given": "Ayala", "initials": "A"}, {"family": "Neiman", "given": "Daniel", "initials": "D"}, {"family": "Piyanzin", "given": "Sheina", "initials": "S"}, {"family": "Gal-Rosenberg", "given": "Ofer", "initials": "O"}, {"family": "Horn", "given": "Amit", "initials": "A"}, {"family": "Shemer", "given": "Ruth", "initials": "R"}, {"family": "Glaser", "given": "Benjamin", "initials": "B"}, {"family": "Boos", "given": "Natalia", "initials": "N"}, {"family": "Jajoo", "given": "Kunal", "initials": "K"}, {"family": "Lee", "given": "Linda", "initials": "L"}, {"family": "Clancy", "given": "Thomas E", "initials": "TE"}, {"family": "Rubinson", "given": "Douglas A", "initials": "DA"}, {"family": "Ng", "given": "Kimmie", "initials": "K"}, {"family": "Chabot", "given": "John A", "initials": "JA"}, {"family": "Kastrinos", "given": "Fay", "initials": "F"}, {"family": "Kluger", "given": "Michael", "initials": "M"}, {"family": "Aguirre", "given": "Andrew J", "initials": "AJ"}, {"family": "J\u00e4nne", "given": "Pasi A", "initials": "PA"}, {"family": "Bardeesy", "given": "Nabeel", "initials": "N"}, {"family": "Stanger", "given": "Ben", "initials": "B"}, {"family": "O'Hara", "given": "Mark H", "initials": "MH"}, {"family": "Till", "given": "Jacob", "initials": "J"}, {"family": "Maitra", "given": "Anirban", "initials": "A"}, {"family": "Carpenter", "given": "Erica L", "initials": "EL"}, {"family": "Bullock", "given": "Andrea J", "initials": "AJ"}, {"family": "Genkinger", "given": "Jeanine", "initials": "J"}, {"family": "Hanash", "given": "Samir M", "initials": "SM"}, {"family": "Paweletz", "given": "Cloud P", "initials": "CP"}, {"family": "Dor", "given": "Yuval", "initials": "Y"}, {"family": "Wolpin", "given": "Brian M", "initials": "BM"}], "type": "journal article", "published": "2024-03-07", "journal": {"title": "Gut", "issn": "1468-3288", "volume": "73", "issue": "4", "pages": "639-648", "issn-l": "0017-5749"}, "abstract": "Pancreatic ductal adenocarcinoma (PDAC) is commonly diagnosed at an advanced stage. Liquid biopsy approaches may facilitate detection of early stage PDAC when curative treatments can be employed.\n\nTo assess circulating marker discrimination in training, testing and validation patient cohorts (total n=426 patients), plasma markers were measured among PDAC cases and patients with chronic pancreatitis, colorectal cancer (CRC), and healthy controls. Using CA19-9 as an anchor marker, measurements were made of two protein markers (TIMP1, LRG1) and cell-free DNA (cfDNA) pancreas-specific methylation at 9 loci encompassing 61 CpG sites.\n\nComparative methylome analysis identified nine loci that were differentially methylated in exocrine pancreas DNA. In the training set (n=124 patients), cfDNA methylation markers distinguished PDAC from healthy and CRC controls. In the testing set of 86 early stage PDAC and 86 matched healthy controls, CA19-9 had an area under the receiver operating characteristic curve (AUC) of 0.88 (95% CI 0.83 to 0.94), which was increased by adding TIMP1 (AUC 0.92; 95% CI 0.88 to 0.96; p=0.06), LRG1 (AUC 0.92; 95% CI 0.88 to 0.96; p=0.02) or exocrine pancreas-specific cfDNA methylation markers at nine loci (AUC 0.92; 95% CI 0.88 to 0.96; p=0.02). In the validation set of 40 early stage PDAC and 40 matched healthy controls, a combined panel including CA19-9, TIMP1 and a 9-loci cfDNA methylation panel had greater discrimination (AUC 0.86, 95% CI 0.77 to 0.95) than CA19-9 alone (AUC 0.82; 95% CI 0.72 to 0.92).\n\nA combined panel of circulating markers including proteins and methylated cfDNA increased discrimination compared with CA19-9 alone for early stage PDAC.", "doi": "10.1136/gutjnl-2023-331074", "pmid": "38123998", "labels": {"DDLS Fellow": null, "Qiaoli Wang": null}, "xrefs": [{"db": "pmc", "key": "PMC10958271"}, {"db": "pii", "key": "gutjnl-2023-331074"}], "notes": [], "created": "2025-11-28T12:24:36.841Z", "modified": "2025-11-28T12:24:36.923Z"}, {"entity": "publication", "iuid": "be67824444964bf1b54995c92b87a2f8", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/be67824444964bf1b54995c92b87a2f8.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/be67824444964bf1b54995c92b87a2f8"}}, "title": "Clonal haematopoiesis of indeterminate potential predicts incident cardiac arrhythmias.", "authors": [{"family": "Schuermans", "given": "Art", "initials": "A", "orcid": "0000-0001-8146-9692", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/af284c3bd9304f54ac7b8c9970ce56be.json"}}, {"family": "Vlasschaert", "given": "Caitlyn", "initials": "C"}, {"family": "Nauffal", "given": "Victor", "initials": "V", "orcid": "0000-0001-7199-299X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ae110095a59c48cfbc03311a0b553d65.json"}}, {"family": "Cho", "given": "So Mi Jemma", "initials": "SMJ"}, {"family": "Uddin", "given": "Md Mesbah", "initials": "MM", "orcid": "0000-0003-1846-0411", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/42f1ac7010c34ba997a3fd9e56c6a56a.json"}}, {"family": "Nakao", "given": "Tetsushi", "initials": "T"}, {"family": "Niroula", "given": "Abhishek", "initials": "A"}, {"family": "Klarqvist", "given": "Marcus D R", "initials": "MDR"}, {"family": "Weeks", "given": "Lachelle D", "initials": "LD"}, {"family": "Lin", "given": "Amy E", "initials": "AE"}, {"family": "Saadatagah", "given": "Seyedmohammad", "initials": "S"}, {"family": "Lannery", "given": "Kim", "initials": "K"}, {"family": "Wong", "given": "Megan", "initials": "M", "orcid": "0000-0003-4135-633X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0e3d0466080a4885b77de32bf611056c.json"}}, {"family": "Hornsby", "given": "Whitney", "initials": "W"}, {"family": "Lubitz", "given": "Steven A", "initials": "SA", "orcid": "0000-0002-9599-4866", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/60efe6f9ed234eaca23702a92b8aa49f.json"}}, {"family": "Ballantyne", "given": "Christie", "initials": "C"}, {"family": "Jaiswal", "given": "Siddhartha", "initials": "S"}, {"family": "Libby", "given": "Peter", "initials": "P", "orcid": "0000-0002-1502-502X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/39fb20acff0442bd92fc7931d3ee6cf9.json"}}, {"family": "Ebert", "given": "Benjamin L", "initials": "BL"}, {"family": "Bick", "given": "Alexander G", "initials": "AG"}, {"family": "Ellinor", "given": "Patrick T", "initials": "PT", "orcid": "0000-0002-2067-0533", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fd1830794e884e6e849fd4f7645c9b61.json"}}, {"family": "Natarajan", "given": "Pradeep", "initials": "P", "orcid": "0000-0001-8402-7435", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fe8bd48c61c047cd8e61c35d9e9ac650.json"}}, {"family": "Honigberg", "given": "Michael C", "initials": "MC", "orcid": "0000-0001-8630-5021", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c541cd0864c947a6bafa7ad6e78bfe49.json"}}], "type": "journal article", "published": "2024-03-07", "journal": {"title": "Eur. Heart J.", "issn": "1522-9645", "volume": "45", "issue": "10", "pages": "791-805", "issn-l": "0195-668X"}, "abstract": "Clonal haematopoiesis of indeterminate potential (CHIP), the age-related expansion of blood cells with preleukemic mutations, is associated with atherosclerotic cardiovascular disease and heart failure. This study aimed to test the association of CHIP with new-onset arrhythmias.\n\nUK Biobank participants without prevalent arrhythmias were included. Co-primary study outcomes were supraventricular arrhythmias, bradyarrhythmias, and ventricular arrhythmias. Secondary outcomes were cardiac arrest, atrial fibrillation, and any arrhythmia. Associations of any CHIP [variant allele fraction (VAF) \u2265 2%], large CHIP (VAF \u226510%), and gene-specific CHIP subtypes with incident arrhythmias were evaluated using multivariable-adjusted Cox regression. Associations of CHIP with myocardial interstitial fibrosis [T1 measured using cardiac magnetic resonance (CMR)] were also tested.\n\nThis study included 410 702 participants [CHIP: n = 13 892 (3.4%); large CHIP: n = 9191 (2.2%)]. Any and large CHIP were associated with multi-variable-adjusted hazard ratios of 1.11 [95% confidence interval (CI) 1.04-1.18; P = .001] and 1.13 (95% CI 1.05-1.22; P = .001) for supraventricular arrhythmias, 1.09 (95% CI 1.01-1.19; P = .031) and 1.13 (95% CI 1.03-1.25; P = .011) for bradyarrhythmias, and 1.16 (95% CI, 1.00-1.34; P = .049) and 1.22 (95% CI 1.03-1.45; P = .021) for ventricular arrhythmias, respectively. Associations were independent of coronary artery disease and heart failure. Associations were also heterogeneous across arrhythmia subtypes and strongest for cardiac arrest. Gene-specific analyses revealed an increased risk of arrhythmias across driver genes other than DNMT3A. Large CHIP was associated with 1.31-fold odds (95% CI 1.07-1.59; P = .009) of being in the top quintile of myocardial fibrosis by CMR.\n\nCHIP may represent a novel risk factor for incident arrhythmias, indicating a potential target for modulation towards arrhythmia prevention and treatment.", "doi": "10.1093/eurheartj/ehad670", "pmid": "37952204", "labels": {"Abhishek Niroula": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC10919923"}, {"db": "pii", "key": "7320137"}], "notes": [], "created": "2025-03-18T15:48:44.753Z", "modified": "2025-03-18T15:49:09.359Z"}, {"entity": "publication", "iuid": "80fc82d4a197449ba117c3eb3d8d9c0f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/80fc82d4a197449ba117c3eb3d8d9c0f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/80fc82d4a197449ba117c3eb3d8d9c0f"}}, "title": "Patient-Centric Quantitative Microsampling for Accurate Determination of Urine Albumin to Creatinine Ratio (UACR) in a Clinical Setting.", "authors": [{"family": "L\u00f6fgren", "given": "Lars", "initials": "L"}, {"family": "von Euler Chelpin", "given": "Marianne", "initials": "M"}, {"family": "Bhat", "given": "Maria", "initials": "M"}, {"family": "Althage", "given": "Magnus", "initials": "M"}, {"family": "Hober", "given": "Andreas", "initials": "A", "orcid": "0000-0001-8947-2562", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/06cbc187628340278395a00ab9dd6c89.json"}}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Ruckh", "given": "Tim", "initials": "T"}, {"family": "Challis", "given": "Benjamin", "initials": "B"}, {"family": "Davidsson", "given": "Pia", "initials": "P", "orcid": "0000-0002-4775-5828", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a62589743acc4ae3967b343bf4bb3d33.json"}}, {"family": "Miliotis", "given": "Tasso", "initials": "T", "orcid": "0000-0003-4917-0724", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a0d5ba9b546949db95c9b8597bd1fe7e.json"}}], "type": "journal article", "published": "2024-03-01", "journal": {"title": "J Appl Lab Med", "issn": "2576-9456", "volume": "9", "issue": "2", "pages": "329-341", "issn-l": null}, "abstract": "Developing and implementing new patient-centric strategies for drug trials lowers the barrier to participation for some patients by reducing the need to travel to research sites. In early chronic kidney disease (CKD) trials, albuminuria is the key measure for determining treatment effect prior to pivotal kidney outcome trials.\n\nTo facilitate albuminuria sample collection outside of a clinical research site, we developed 2 quantitative microsampling methods to determine the urinary albumin to creatinine ratio (UACR). Readout was performed by LC-MS/MS.\n\nFor the Mitra device the within-batch precision (CV%) was 2.8% to 4.6% and the between-batch precision was 5.3% to 6.1%. Corresponding data for the Capitainer device were 4.0% to 8.6% and 6.7% to 9.0%, respectively. The storage stability at room temperature for 3 weeks was 98% to 103% for both devices. The recovery for the Mitra and Capitainer devices was 104% (SD 7.0%) and 95 (SD 7.4%), respectively. The inter-assay comparison of UACR assessment generated results that were indistinguishable regardless of microsampling technique. The accuracy based on LC-MS/MS vs analysis of neat urine using a clinical chemistry analyzer was assessed in a clinical setting, resulting in 102 \u00b1 8.0% for the Mitra device and 95 \u00b1 10.0% for the Capitainer device.\n\nBoth UACR microsampling measurements exhibit excellent accuracy and precision compared to a clinical chemistry analyzer using neat urine. We applied our patient-centric sampling strategy to subjects with heart failure in a clinical setting. Precise UACR measurements using quantitative microsampling at home would be beneficial in clinical drug development for kidney therapies.", "doi": "10.1093/jalm/jfad111", "pmid": "38113397", "labels": {"Fredrik Edfors": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pii", "key": "7479657"}], "notes": [], "created": "2026-08-20T09:42:02.090Z", "modified": "2026-09-23T12:26:26.180Z"}, {"entity": "publication", "iuid": "b0dbf3f74da04f0ab7a0ef14fc9efd27", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b0dbf3f74da04f0ab7a0ef14fc9efd27.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b0dbf3f74da04f0ab7a0ef14fc9efd27"}}, "title": "Uncovering driver genes in breast cancer through an innovative machine learning mutational analysis method.", "authors": [{"family": "Taheri", "given": "Golnaz", "initials": "G", "orcid": "0000-0002-2741-0355", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/014c217121d346b2b371bbc1c2fede57.json"}}, {"family": "Habibi", "given": "Mahnaz", "initials": "M", "orcid": "0000-0002-8969-2706", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f04af4e059814b78bfb107c3a5782f70.json"}}], "type": "journal article", "published": "2024-03-00", "journal": {"title": "Comput Biol Med", "issn": "1879-0534", "issn-l": null, "volume": "171", "issue": null, "pages": "108234"}, "abstract": "Breast cancer has become a severe public health concern and one of the leading causes of cancer-related death in women worldwide. Several genes and mutations in these genes linked to breast cancer have been identified using sophisticated techniques, despite the fact that the exact cause of breast cancer is still unknown. A commonly used feature for identifying driver mutations is the recurrence of a mutation in patients. Nevertheless, some mutations are more likely to occur than others for various reasons. Sequencing analysis has shown that cancer-driving genes operate across complex networks, often with mutations appearing in a modular pattern. In this work, as a retrospective study, we used TCGA data, which is gathered from breast cancer patients. We introduced a new machine-learning approach to examine gene functionality in networks derived from mutation associations, gene-gene interactions, and graph clustering for breast cancer analysis. These networks have uncovered crucial biological components in critical pathways, particularly those that exhibit low-frequency mutations. The statistical strength of the clinical study is significantly boosted by evaluating the network as a whole instead of just single gene effects. Our method successfully identified essential driver genes with diverse mutation frequencies. We then explored the functions of these potential driver genes and their related pathways. By uncovering low-frequency genes, we shed light on understudied pathways associated with breast cancer. Additionally, we present a novel Monte Carlo-based algorithm to identify driver modules in breast cancer. Our findings highlight the significance and role of these modules in critical signaling pathways in breast cancer, providing a comprehensive understanding of breast cancer development. Materials and implementations are available at: [https://github.com/MahnazHabibi/BreastCancer].", "doi": "10.1016/j.compbiomed.2024.108234", "pmid": "38430742", "labels": {"Golnaz Taheri": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pii", "key": "S0010-4825(24)00318-4"}], "notes": [], "created": "2025-03-21T09:08:27.575Z", "modified": "2026-09-23T12:56:42.757Z"}, {"entity": "publication", "iuid": "684825d292d0401099d492f2d7d180c0", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/684825d292d0401099d492f2d7d180c0.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/684825d292d0401099d492f2d7d180c0"}}, "title": "Association of Somatic TET2 Mutations With Giant Cell Arteritis.", "authors": [{"family": "Robinette", "given": "Michelle L", "initials": "ML"}, {"family": "Weeks", "given": "Lachelle D", "initials": "LD", "orcid": "0000-0001-8726-6212", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ec1c3cd65e44fdb9f5cc2c2bf09bbc1.json"}}, {"family": "Kramer", "given": "Ryan J", "initials": "RJ"}, {"family": "Agrawal", "given": "Mridul", "initials": "M", "orcid": "0000-0002-5455-2543", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a2e1aab434af4a05a350e2be61ae5e4f.json"}}, {"family": "Gibson", "given": "Christopher J", "initials": "CJ", "orcid": "0000-0002-3700-5310", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/71ce9f64755e483496f8c28a76a2a1ff.json"}}, {"family": "Yu", "given": "Zhi", "initials": "Z", "orcid": "0000-0003-4810-3474", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4b810efe02244148b701c1468543ea3.json"}}, {"family": "Sekar", "given": "Aswin", "initials": "A", "orcid": "0000-0003-0406-0935", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2cff21c3699340a3a10c13447b59c7ff.json"}}, {"family": "Mehta", "given": "Arnav", "initials": "A"}, {"family": "Niroula", "given": "Abhishek", "initials": "A", "orcid": "0000-0002-5904-0635", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/05df7afc7a494ba5af8a378e5ffa53f0.json"}}, {"family": "Brown", "given": "Jared T", "initials": "JT"}, {"family": "McDermott", "given": "Gregory C", "initials": "GC", "orcid": "0000-0002-9750-5448", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3fa60854a8dd4d6f825ced35cbd393e4.json"}}, {"family": "Reshef", "given": "Edith R", "initials": "ER"}, {"family": "Lu", "given": "Jonathan E", "initials": "JE"}, {"family": "Liou", "given": "Victor D", "initials": "VD"}, {"family": "Chiou", "given": "Carolina A", "initials": "CA"}, {"family": "Natarajan", "given": "Pradeep", "initials": "P", "orcid": "0000-0001-8402-7435", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fe8bd48c61c047cd8e61c35d9e9ac650.json"}}, {"family": "Freitag", "given": "Suzanne K", "initials": "SK"}, {"family": "Rao", "given": "Deepak A", "initials": "DA", "orcid": "0000-0001-9672-7746", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/769f937bc2864984abc0718f548f6265.json"}}, {"family": "Ebert", "given": "Benjamin L", "initials": "BL", "orcid": "0000-0003-0197-5451", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56e4f1c53a4348e2b0ceb44a38850a17.json"}}], "type": "journal article", "published": "2024-03-00", "journal": {"title": "Arthritis & rheumatology (Hoboken, N.J.)", "issn": "2326-5205", "volume": "76", "issue": "3", "pages": "438-443", "issn-l": "2326-5191"}, "abstract": "Giant cell arteritis (GCA) is an age-related vasculitis. Prior studies have identified an association between GCA and hematologic malignancies (HMs). How the presence of somatic mutations that drive the development of HMs, or clonal hematopoiesis (CH), may influence clinical outcomes in GCA is not well understood.\n\nTo examine an association between CH and GCA, we analyzed sequenced exomes of 470,960 UK Biobank (UKB) participants for the presence of CH and used multivariable Cox regression. To examine the clinical phenotype of GCA in patients with and without somatic mutations across the spectrum of CH to HM, we performed targeted sequencing of blood samples and electronic health record review on 114 patients with GCA seen at our institution. We then examined associations between specific clonal mutations and GCA disease manifestations.\n\nUKB participants with CH had a 1.48-fold increased risk of incident GCA compared to UKB participants without CH. GCA risk was highest among individuals with cytopenia (hazard ratio [HR] 2.98, P = 0.00178) and with TET2 mutation (HR 2.02, P = 0.00116). Mutations were detected in 27.2% of our institutional GCA cohort, three of whom had HM at GCA diagnosis. TET2 mutations were associated with vision loss in patients with GCA (odds ratio 4.33, P = 0.047).\n\nCH increases risk for development of GCA in a genotype-specific manner, with the greatest risk being conferred by the presence of mutations in TET2. Somatic TET2 mutations likewise increase the risk of GCA-associated vision loss. Integration of somatic genetic testing in GCA diagnostics may be warranted in the future.", "doi": "10.1002/art.42738", "pmid": "37909388", "labels": {"Abhishek Niroula": null, "DDLS Fellow": null}, "xrefs": [{"db": "mid", "key": "NIHMS1941121"}, {"db": "pmc", "key": "PMC10922498"}], "notes": [], "created": "2025-03-18T15:48:42.040Z", "modified": "2025-04-08T06:12:50.039Z"}, {"entity": "publication", "iuid": "95dc763234304fa2909ce46f46159e20", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/95dc763234304fa2909ce46f46159e20.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/95dc763234304fa2909ce46f46159e20"}}, "title": "From genomic threat assessment to conservation action.", "authors": [{"family": "van der Valk", "given": "Tom", "initials": "T"}, {"family": "Dal\u00e8n", "given": "Love", "initials": "L"}], "type": "journal article", "published": "2024-02-29", "journal": {"title": "Cell", "issn": "1097-4172", "volume": "187", "issue": "5", "pages": "1038-1041", "issn-l": "0092-8674"}, "abstract": "Genomic approaches have the potential to play a pivotal role in conservation, both to detect threats to species and populations and to restore biodiversity through actions. We here separate these approaches into two subdisciplines, vulnerability and restoration genomics, and discuss current applications, outstanding questions, and future potential.", "doi": "10.1016/j.cell.2024.01.038", "pmid": "38428386", "labels": {"DDLS Fellow": "", "Tom van der Valk": ""}, "xrefs": [{"db": "pii", "key": "S0092-8674(24)00106-5"}], "notes": [], "created": "2026-08-20T06:50:27.471Z", "modified": "2026-09-23T11:22:34.657Z"}, {"entity": "publication", "iuid": "1c4caf654d8645899fe13fcf25900dfa", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1c4caf654d8645899fe13fcf25900dfa.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1c4caf654d8645899fe13fcf25900dfa"}}, "title": "Risk factors for clonal hematopoiesis of indeterminate potential in people with HIV: a report from the REPRIEVE trial.", "authors": [{"family": "Bhattacharya", "given": "Romit", "initials": "R", "orcid": "0000-0002-0782-4753", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/adea681afe7c431c91b30900a92baf8f.json"}}, {"family": "Uddin", "given": "Md Mesbah", "initials": "MM", "orcid": "0000-0003-1846-0411", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/42f1ac7010c34ba997a3fd9e56c6a56a.json"}}, {"family": "Patel", "given": "Aniruddh P", "initials": "AP", "orcid": "0000-0001-7871-9638", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b7bf68d8799f4946814bc4e6ea80ef2f.json"}}, {"family": "Niroula", "given": "Abhishek", "initials": "A", "orcid": "0000-0002-5904-0635", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/05df7afc7a494ba5af8a378e5ffa53f0.json"}}, {"family": "Finneran", "given": "Phoebe", "initials": "P"}, {"family": "Bernardo", "given": "Rachel", "initials": "R", "orcid": "0000-0001-7139-6899", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c5a8588e727e4bfb80b622375ccd5d89.json"}}, {"family": "Fitch", "given": "Kathleen V", "initials": "KV"}, {"family": "Lu", "given": "Michael T", "initials": "MT"}, {"family": "Bloomfield", "given": "Gerald S", "initials": "GS"}, {"family": "Malvestutto", "given": "Carlos", "initials": "C", "orcid": "0000-0003-3156-2965", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/579e40a069684a539bd8a9aaeeb9f88b.json"}}, {"family": "Aberg", "given": "Judy A", "initials": "JA", "orcid": "0000-0001-8162-0284", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e3306ed88f5d4fedaecd6e6b130ff242.json"}}, {"family": "Fichtenbaum", "given": "Carl J", "initials": "CJ", "orcid": "0000-0002-6778-7253", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8f33fe77cc70491aa7971e8a159bd879.json"}}, {"family": "Hornsby", "given": "Whitney", "initials": "W", "orcid": "0000-0002-0672-0338", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a8ab7aefec20431caf36c130be364ec4.json"}}, {"family": "Ribaudo", "given": "Heather J", "initials": "HJ", "orcid": "0000-0002-0394-3990", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b304b28a37ac46a695a17dc359f09485.json"}}, {"family": "Libby", "given": "Peter", "initials": "P", "orcid": "0000-0002-1502-502X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/39fb20acff0442bd92fc7931d3ee6cf9.json"}}, {"family": "Ebert", "given": "Benjamin L", "initials": "BL", "orcid": "0000-0003-0197-5451", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56e4f1c53a4348e2b0ceb44a38850a17.json"}}, {"family": "Zanni", "given": "Markella V", "initials": "MV"}, {"family": "Douglas", "given": "Pamela S", "initials": "PS", "orcid": "0000-0001-9876-4049", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/48b7c5b425e542c78387242bdd4b2b53.json"}}, {"family": "Grinspoon", "given": "Steven K", "initials": "SK"}, {"family": "Natarajan", "given": "Pradeep", "initials": "P", "orcid": "0000-0001-8402-7435", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fe8bd48c61c047cd8e61c35d9e9ac650.json"}}], "type": "journal article", "published": "2024-02-27", "journal": {"title": "Blood Adv", "issn": "2473-9529", "volume": "8", "issue": "4", "pages": "959-967", "issn-l": null}, "abstract": "Clonal hematopoiesis of indeterminate potential (CHIP), the clonal expansion of myeloid cells with leukemogenic mutations, results in increased coronary artery disease (CAD) risk. CHIP is more prevalent among people with HIV (PWH), but the risk factors are unknown. CHIP was identified among PWH in REPRIEVE (Randomized Trial to Prevent Vascular Events in HIV) using whole-exome sequencing. Logistic regression was used to associate sociodemographic factors and HIV-specific factors with CHIP adjusting for age, sex, and smoking status. In the studied global cohort of 4486 PWH, mean age was 49.9 (standard deviation [SD], 6.4) years; 1650 (36.8%) were female; and 3418 (76.2%) were non-White. CHIP was identified in 223 of 4486 (4.97%) and in 38 of 373 (10.2%) among those aged \u226560 years. Age (odds ratio [OR], 1.07; 95% confidence interval [CI], 1.05-1.09; P < .0001) and smoking (OR, 1.37; 95% CI, 1.14-1.66; P < .001) associated with increased odds of CHIP. Globally, participants outside of North America had lower odds of CHIP including sub-Saharan Africa (OR, 0.57; 95% CI, 0.4-0.81; P = .0019), South Asia (OR, 0.45; 95% CI, 0.23-0.80; P = .01), and Latin America/Caribbean (OR, 0.56; 95% CI, 0.34-0.87; P = .014). Hispanic/Latino ethnicity (OR, 0.38; 95% CI, 0.23-0.54; P = .002) associated with significantly lower odds of CHIP. Among HIV-specific factors, CD4 nadir <50 cells/mm3 associated with a 1.9-fold (95%CI, 1.21-3.05; P = .006) increased odds of CHIP, with the effect being significantly stronger among individuals with short duration of antiretroviral therapy (ART; OR, 4.15; 95% CI, 1.51-11.1; P = .005) (Pinteraction= .0492). Among PWH at low-to-moderate CAD risk on stable ART, smoking, CD4 nadir, North American origin, and non-Hispanic ethnicity associated with increased odds of CHIP. This trial was registered at www.ClinicalTrials.gov as NCT02344290.", "doi": "10.1182/bloodadvances.2023011324", "pmid": "38197863", "labels": {"Abhishek Niroula": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC10877123"}, {"db": "pii", "key": "507100"}, {"db": "ClinicalTrials.gov", "key": "NCT02344290"}], "notes": [], "created": "2025-03-18T15:48:38.411Z", "modified": "2025-03-18T15:49:07.099Z"}, {"entity": "publication", "iuid": "dbf0cc07119643f4985f2a029f111340", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/dbf0cc07119643f4985f2a029f111340.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/dbf0cc07119643f4985f2a029f111340"}}, "title": "CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods.", "authors": [{"family": "Critical Assessment of Genome Interpretation Consortium", "given": "", "initials": ""}], "type": "journal article", "published": "2024-02-22", "journal": {"title": "Genome Biol.", "issn": "1474-760X", "volume": "25", "issue": "1", "pages": "53", "issn-l": "1474-7596"}, "abstract": "The Critical Assessment of Genome Interpretation (CAGI) aims to advance the state-of-the-art for computational prediction of genetic variant impact, particularly where relevant to disease. The five complete editions of the CAGI community experiment comprised 50 challenges, in which participants made blind predictions of phenotypes from genetic data, and these were evaluated by independent assessors.\n\nPerformance was particularly strong for clinical pathogenic variants, including some difficult-to-diagnose cases, and extends to interpretation of cancer-related variants. Missense variant interpretation methods were able to estimate biochemical effects with increasing accuracy. Assessment of methods for regulatory variants and complex trait disease risk was less definitive and indicates performance potentially suitable for auxiliary use in the clinic.\n\nResults show that while current methods are imperfect, they have major utility for research and clinical applications. Emerging methods and increasingly large, robust datasets for training and assessment promise further progress ahead.", "doi": "10.1186/s13059-023-03113-6", "pmid": "38389099", "labels": {"Abhishek Niroula": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC10882881"}, {"db": "pii", "key": "10.1186/s13059-023-03113-6"}], "notes": [], "created": "2025-03-18T15:48:32.891Z", "modified": "2025-03-18T15:49:04.866Z"}, {"entity": "publication", "iuid": "526124e531b54215b305dbd6549abbc0", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/526124e531b54215b305dbd6549abbc0.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/526124e531b54215b305dbd6549abbc0"}}, "title": "Exposure assessment suggests some cytotoxic Bacillus cereus group genotypes can grow over 3 logs in HTST milk throughout the shelf life at temperature abuse conditions", "authors": [{"family": "Su", "given": "Jun", "initials": "J", "orcid": "0000-0003-3627-6693", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/931ed33927b34edba4856c7e9f271698.json"}}, {"family": "Chandross-Cohen", "given": "Tyler", "initials": "T", "orcid": "0000-0003-4367-0293", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d29bbd94fb3f443d98751f3930603ab5.json"}}, {"family": "Qian", "given": "Chenhao", "initials": "C", "orcid": "0000-0002-3835-1952", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/78cd9d05a77d4c14aface616e9b4c55a.json"}}, {"family": "Carroll", "given": "Laura", "initials": "L", "orcid": "0000-0002-3677-0192", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02112eccb0664819af916a3c3dc79daa.json"}}, {"family": "Kimble", "given": "Kayla", "initials": "K", "orcid": "0009-0007-6208-0658", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4e6f7a3654744274a8365889a89733a2.json"}}, {"family": "Yount", "given": "Mackenna", "initials": "M", "orcid": "0009-0005-3250-1197", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f31ca907d4a041d9bd88e4592a21f558.json"}}, {"family": "Wiedmann", "given": "Martin", "initials": "M", "orcid": "0000-0002-4168-5662", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ff5ceeea60684abeb83951c53f7b6e31.json"}}, {"family": "Kovac", "given": "Jasna", "initials": "J", "orcid": "0000-0002-9465-4552", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d18e6f5bd24644e18030b59391d1a755.json"}}], "type": "posted-content", "published": "2024-02-20", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2024.02.20.581219", "pmid": null, "labels": {"Laura Carroll": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T10:52:20.334Z", "modified": "2026-09-23T15:32:20.891Z"}, {"entity": "publication", "iuid": "a0f29a63adeb4cbc8e076dd4e3c44d80", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a0f29a63adeb4cbc8e076dd4e3c44d80.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a0f29a63adeb4cbc8e076dd4e3c44d80"}}, "title": "Whole-genome resequencing facilitates the development of a 50K single nucleotide polymorphism genotyping array for Scots pine (Pinus sylvestris L.) and its transferability to other pine species.", "authors": [{"family": "Estravis Barcala", "given": "Maximiliano", "initials": "M", "orcid": "0000-0002-0337-023X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8051e3f7b05047099cbfa1ae8baa8000.json"}}, {"family": "van der Valk", "given": "Tom", "initials": "T"}, {"family": "Chen", "given": "Zhiqiang", "initials": "Z", "orcid": "0000-0001-9725-8929", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e8935d36e8274be3bf02f7404d85f4fc.json"}}, {"family": "Funda", "given": "Tomas", "initials": "T"}, {"family": "Chaudhary", "given": "Rajiv", "initials": "R"}, {"family": "Klingberg", "given": "Adam", "initials": "A"}, {"family": "Fundova", "given": "Irena", "initials": "I"}, {"family": "Suontama", "given": "Mari", "initials": "M"}, {"family": "Hallingb\u00e4ck", "given": "Henrik", "initials": "H"}, {"family": "Bernhardsson", "given": "Carolina", "initials": "C"}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Ingvarsson", "given": "P\u00e4r K", "initials": "PK"}, {"family": "Sherwood", "given": "Ellen", "initials": "E"}, {"family": "Street", "given": "Nathaniel", "initials": "N"}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Nilsson", "given": "Ove", "initials": "O"}, {"family": "Wu", "given": "Harry X", "initials": "HX"}], "type": "journal article", "published": "2024-02-00", "journal": {"title": "Plant J.", "issn": "1365-313X", "volume": "117", "issue": "3", "pages": "944-955", "issn-l": "0960-7412"}, "abstract": "Scots pine (Pinus sylvestris L.) is one of the most widespread and economically important conifer species in the world. Applications like genomic selection and association studies, which could help accelerate breeding cycles, are challenging in Scots pine because of its large and repetitive genome. For this reason, genotyping tools for conifer species, and in particular for Scots pine, are commonly based on transcribed regions of the genome. In this article, we present the Axiom Psyl50K array, the first single nucleotide polymorphism (SNP) genotyping array for Scots pine based on whole-genome resequencing, that represents both genic and intergenic regions. This array was designed following a two-step procedure: first, 192 trees were sequenced, and a 430K SNP screening array was constructed. Then, 480 samples, including haploid megagametophytes, full-sib family trios, breeding population, and range-wide individuals from across Eurasia were genotyped with the screening array. The best 50K SNPs were selected based on quality, replicability, distribution across the draft genome assembly, balance between genic and intergenic regions, and genotype-environment and genotype-phenotype associations. Of the final 49 877 probes tiled in the array, 20 372 (40.84%) occur inside gene models, while the rest lie in intergenic regions. We also show that the Psyl50K array can yield enough high-confidence SNPs for genetic studies in pine species from North America and Eurasia. This new genotyping tool will be a valuable resource for high-throughput fundamental and applied research of Scots pine and other pine species.", "doi": "10.1111/tpj.16535", "pmid": "37947292", "labels": {"DDLS Fellow": "", "Tom van der Valk": ""}, "xrefs": [], "notes": [], "created": "2026-09-23T11:31:05.468Z", "modified": "2026-09-23T11:31:05.566Z"}, {"entity": "publication", "iuid": "9b97a0392a214fa6b691c03be2cf6cf8", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9b97a0392a214fa6b691c03be2cf6cf8.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9b97a0392a214fa6b691c03be2cf6cf8"}}, "title": "Plasma metabolite predictors of metabolic syndrome incidence and reversion.", "authors": [{"family": "Semnani-Azad", "given": "Zhila", "initials": "Z"}, {"family": "Toledo", "given": "Estefan\u00eda", "initials": "E", "orcid": "0000-0002-6263-4434", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d04ea61c7230463ab64e537f97fb07fe.json"}}, {"family": "Babio", "given": "Nancy", "initials": "N"}, {"family": "Ruiz-Canela", "given": "Miguel", "initials": "M", "orcid": "0000-0002-7684-2787", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4f947f7399034daeb6778d0781b6e789.json"}}, {"family": "Wittenbecher", "given": "Clemens", "initials": "C", "orcid": "0000-0001-7792-877X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2f7d2c289b3c47d5a79d23bd48a3225a.json"}}, {"family": "Razquin", "given": "Cristina", "initials": "C"}, {"family": "Wang", "given": "Fenglei", "initials": "F", "orcid": "0000-0002-3850-2482", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/41a725cb032d4e2097b2c75a5b18e937.json"}}, {"family": "Dennis", "given": "Courtney", "initials": "C"}, {"family": "Deik", "given": "Amy", "initials": "A"}, {"family": "Clish", "given": "Clary B", "initials": "CB"}, {"family": "Corella", "given": "Dolores", "initials": "D", "orcid": "0000-0002-2366-4104", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5b2b00c374df498794b8623cfbd6cc30.json"}}, {"family": "Fit\u00f3", "given": "Montserrat", "initials": "M"}, {"family": "Estruch", "given": "Ramon", "initials": "R", "orcid": "0000-0003-1260-4445", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/122cb01329f24931ae77ae5ac5a05059.json"}}, {"family": "Ar\u00f3s", "given": "Fernando", "initials": "F", "orcid": "0000-0001-8337-7185", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bafd2db45467474c9f6896ada491e747.json"}}, {"family": "Ros", "given": "Emilio", "initials": "E"}, {"family": "Garc\u00eda-Gavilan", "given": "Jes\u00fas", "initials": "J", "orcid": "0000-0002-3707-5255", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/89296f9aee3146208cddcb8485c9e116.json"}}, {"family": "Liang", "given": "Liming", "initials": "L", "orcid": "0000-0001-8261-3174", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7da355304cad4309ab4dee783a341611.json"}}, {"family": "Salas-Salvad\u00f3", "given": "Jordi", "initials": "J"}, {"family": "Mart\u00ednez-Gonz\u00e1lez", "given": "Miguel A", "initials": "MA", "orcid": "0000-0002-3917-9808", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7852fa98fe3a4da285d79f04e09cbd34.json"}}, {"family": "Hu", "given": "Frank B", "initials": "FB"}, {"family": "Guasch-Ferr\u00e9", "given": "Marta", "initials": "M", "orcid": "0000-0001-8525-1404", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2d1a49f5df124e96a9285b43d628cee9.json"}}], "type": "journal article", "published": "2024-02-00", "journal": {"title": "Metabolism", "issn": "1532-8600", "volume": "151", "pages": "155742", "issn-l": null}, "abstract": "Metabolic Syndrome (MetS) is a progressive pathophysiological state defined by a cluster of cardiometabolic traits. However, little is known about metabolites that may be predictors of MetS incidence or reversion. Our objective was to identify plasma metabolites associated with MetS incidence or MetS reversion.\n\nThe study included 1468 participants without cardiovascular disease (CVD) but at high CVD risk at enrollment from two case-cohort studies nested within the PREvenci\u00f3n con DIeta MEDiterr\u00e1nea (PREDIMED) study with baseline metabolomics data. MetS was defined in accordance with the harmonized International Diabetes Federation and the American Heart Association/National Heart, Lung, and Blood Institute criteria, which include meeting 3 or more thresholds for waist circumference, triglyceride, HDL cholesterol, blood pressure, and fasting blood glucose. MetS incidence was defined by not having MetS at baseline but meeting the MetS criteria at a follow-up visit. MetS reversion was defined by MetS at baseline but not meeting MetS criteria at a follow-up visit. Plasma metabolome was profiled by LC-MS. Multivariable-adjusted Cox regression models and elastic net regularized regressions were used to assess the association of 385 annotated metabolites with MetS incidence and MetS reversion after adjusting for potential risk factors.\n\nOf the 603 participants without baseline MetS, 298 developed MetS over the median 4.8-year follow-up. Of the 865 participants with baseline MetS, 285 experienced MetS reversion. A total of 103 and 88 individual metabolites were associated with MetS incidence and MetS reversion, respectively, after adjusting for confounders and false discovery rate correction. A metabolomic signature comprised of 77 metabolites was robustly associated with MetS incidence (HR: 1.56 (95 % CI: 1.33-1.83)), and a metabolomic signature of 83 metabolites associated with MetS reversion (HR: 1.44 (95 % CI: 1.25-1.67)), both p < 0.001. The MetS incidence and reversion signatures included several lipids (mainly glycerolipids and glycerophospholipids) and branched-chain amino acids.\n\nWe identified unique metabolomic signatures, primarily comprised of lipids (including glycolipids and glycerophospholipids) and branched-chain amino acids robustly associated with MetS incidence; and several amino acids and glycerophospholipids associated with MetS reversion. These signatures provide novel insights on potential distinct mechanisms underlying the conditions leading to the incidence or reversion of MetS.", "doi": "10.1016/j.metabol.2023.155742", "pmid": "38007148", "labels": {"Clemens Wittenbecher": null, "DDLS Fellow": null}, "xrefs": [{"db": "mid", "key": "NIHMS1950047"}, {"db": "pmc", "key": "PMC10872312"}, {"db": "pii", "key": "S0026-0495(23)00346-3"}], "notes": [], "created": "2025-03-19T08:18:48.395Z", "modified": "2025-12-09T13:32:48.089Z"}, {"entity": "publication", "iuid": "bed8d1c6466a490db480fef6dafd3fd7", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/bed8d1c6466a490db480fef6dafd3fd7.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/bed8d1c6466a490db480fef6dafd3fd7"}}, "title": "Multivalent insulin receptor activation using insulin-DNA origami nanostructures.", "authors": [{"family": "Spratt", "given": "Joel", "initials": "J"}, {"family": "Dias", "given": "Jos\u00e9 M", "initials": "JM", "orcid": "0000-0002-1402-0323", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/baa189d497af4380b7db4c1aba55ae80.json"}}, {"family": "Kolonelou", "given": "Christina", "initials": "C", "orcid": "0000-0002-5625-5569", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/48cfd6b4505d4325a934fbe7d35d1875.json"}}, {"family": "Kiriako", "given": "Georges", "initials": "G", "orcid": "0000-0001-6117-6286", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0efc585788bc4e86a69e466c5670f007.json"}}, {"family": "Engstr\u00f6m", "given": "Enya", "initials": "E", "orcid": "0009-0009-6574-0652", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8a3762eb3425447e8c0805a9bb0059a0.json"}}, {"family": "Petrova", "given": "Ekaterina", "initials": "E"}, {"family": "Karampelias", "given": "Christos", "initials": "C", "orcid": "0000-0002-9990-5760", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eb41842e9b36439cbcbf097378a82378.json"}}, {"family": "Cervenka", "given": "Igor", "initials": "I"}, {"family": "Papanicolaou", "given": "Natali", "initials": "N", "orcid": "0000-0002-2931-3241", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ffb7037b0b6e453ba9aab04fd1eec4bf.json"}}, {"family": "Lentini", "given": "Antonio", "initials": "A", "orcid": "0000-0003-1239-5495", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c5042d3005814ad0a2d1eaeee5d2de3b.json"}}, {"family": "Reinius", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0002-7021-5248", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a7c1abacc8d446bf8855254246b8d899.json"}}, {"family": "Andersson", "given": "Olov", "initials": "O", "orcid": "0000-0001-6715-781X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2f39763e006e48309fc287cdb644ffe4.json"}}, {"family": "Ambrosetti", "given": "Elena", "initials": "E"}, {"family": "Ruas", "given": "Jorge L", "initials": "JL"}, {"family": "Teixeira", "given": "Ana I", "initials": "AI", "orcid": "0000-0001-8169-8815", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e1e6497a9de14f5b901fbca4a223ddad.json"}}], "type": "journal article", "published": "2024-02-00", "journal": {"title": "Nat Nanotechnol", "issn": "1748-3395", "volume": "19", "issue": "2", "pages": "237-245", "issn-l": null}, "abstract": "Insulin binds the insulin receptor (IR) and regulates anabolic processes in target tissues. Impaired IR signalling is associated with multiple diseases, including diabetes, cancer and neurodegenerative disorders. IRs have been reported to form nanoclusters at the cell membrane in several cell types, even in the absence of insulin binding. Here we exploit the nanoscale spatial organization of the IR to achieve controlled multivalent receptor activation. To control insulin nanoscale spatial organization and valency, we developed rod-like insulin-DNA origami nanostructures carrying different numbers of insulin molecules with defined spacings. Increasing the insulin valency per nanostructure markedly extended the residence time of insulin-DNA origami nanostructures at the receptors. Both insulin valency and spacing affected the levels of IR activation in adipocytes. Moreover, the multivalent insulin design associated with the highest levels of IR activation also induced insulin-mediated transcriptional responses more effectively than the corresponding monovalent insulin nanostructures. In an in vivo zebrafish model of diabetes, treatment with multivalent-but not monovalent-insulin nanostructures elicited a reduction in glucose levels. Our results show that the control of insulin multivalency and spatial organization with nanoscale precision modulates the IR responses, independent of the insulin concentration. Therefore, we propose insulin nanoscale organization as a design parameter in developing new insulin therapies.", "doi": "10.1038/s41565-023-01507-y", "pmid": "37813939", "labels": {"Antonio Lentini": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC10873203"}, {"db": "pii", "key": "10.1038/s41565-023-01507-y"}], "notes": [], "created": "2025-03-28T07:03:05.954Z", "modified": "2025-03-28T07:03:06.260Z"}, {"entity": "publication", "iuid": "12b7c1d2703f4e8680f8d1249e0bb9ad", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/12b7c1d2703f4e8680f8d1249e0bb9ad.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/12b7c1d2703f4e8680f8d1249e0bb9ad"}}, "title": "ESPressoscope: a small and powerful platform for in situ microscopy", "authors": [{"family": "Li", "given": "Ethan", "initials": "E"}, {"family": "Saggiomo", "given": "Vittorio", "initials": "V"}, {"family": "Ouyang", "given": "Wei", "initials": "W"}, {"family": "Prakash", "given": "Manu", "initials": "M", "orcid": "0000-0002-8046-8388", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ffb31ee2e27483b9303ce73a9e6f3d1.json"}}, {"family": "Diederich", "given": "Benedict", "initials": "B", "orcid": "0000-0003-0453-6286", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/25fb1523d3854ce59fdfe3841250ac3c.json"}}], "type": "posted-content", "published": "2024-01-31", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2024.01.20.576174", "pmid": null, "labels": {"DDLS Fellow": "", "Wei Ouyang": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T10:51:33.166Z", "modified": "2026-09-23T14:50:26.514Z"}, {"entity": "publication", "iuid": "b430290ce94247c285d5680d2ac53006", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b430290ce94247c285d5680d2ac53006.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b430290ce94247c285d5680d2ac53006"}}, "title": "AutoTransOP: translating omics signatures without orthologue requirements using deep learning.", "authors": [{"family": "Meimetis", "given": "Nikolaos", "initials": "N", "orcid": "0000-0003-2333-0187", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e0e968cb5cc44b52818647cea77762d9.json"}}, {"family": "Pullen", "given": "Krista M", "initials": "KM", "orcid": "0000-0002-4857-8907", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6930c9935ef740479a3052b4796d7d6d.json"}}, {"family": "Zhu", "given": "Daniel Y", "initials": "DY"}, {"family": "Nilsson", "given": "Avlant", "initials": "A", "orcid": "0000-0002-9476-4516", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f2e21dbc1c624f6a841c59e959e948e4.json"}}, {"family": "Hoang", "given": "Trong Nghia", "initials": "TN"}, {"family": "Magliacane", "given": "Sara", "initials": "S"}, {"family": "Lauffenburger", "given": "Douglas A", "initials": "DA", "orcid": "0000-0002-0050-989X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ac0a09cb7c9c49de95b660756a4e5464.json"}}], "type": "journal article", "published": "2024-01-29", "journal": {"title": "NPJ Syst Biol Appl", "issn": "2056-7189", "issn-l": "2056-7189", "volume": "10", "issue": "1", "pages": "13"}, "abstract": "The development of therapeutics and vaccines for human diseases requires a systematic understanding of human biology. Although animal and in vitro culture models can elucidate some disease mechanisms, they typically fail to adequately recapitulate human biology as evidenced by the predominant likelihood of clinical trial failure. To address this problem, we developed AutoTransOP, a neural network autoencoder framework, to map omics profiles from designated species or cellular contexts into a global latent space, from which germane information for different contexts can be identified without the typically imposed requirement of matched orthologues. This approach was found in general to perform at least as well as current alternative methods in identifying animal/culture-specific molecular features predictive of other contexts-most importantly without requiring homology matching. For an especially challenging test case, we successfully applied our framework to a set of inter-species vaccine serology studies, where 1-to-1 mapping between human and non-human primate features does not exist.", "doi": "10.1038/s41540-024-00341-9", "pmid": "38287079", "labels": {"Avlant Nilsson": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC10825146"}, {"db": "pii", "key": "10.1038/s41540-024-00341-9"}], "notes": [], "created": "2025-03-20T10:57:39.228Z", "modified": "2025-03-21T13:16:11.249Z"}, {"entity": "publication", "iuid": "1cc8e9edd2ea41958988fe669eb443bf", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1cc8e9edd2ea41958988fe669eb443bf.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1cc8e9edd2ea41958988fe669eb443bf"}}, "title": "Comparative genomic analyses provide new insights into evolutionary history and conservation genomics of gorillas.", "authors": [{"family": "van der Valk", "given": "Tom", "initials": "T"}, {"family": "Jensen", "given": "Axel", "initials": "A"}, {"family": "Caillaud", "given": "Damien", "initials": "D"}, {"family": "Guschanski", "given": "Katerina", "initials": "K"}], "type": "review", "published": "2024-01-26", "journal": {"title": "BMC Ecol Evol", "issn": "2730-7182", "volume": "24", "issue": "1", "pages": "14", "issn-l": null}, "abstract": "Genome sequencing is a powerful tool to understand species evolutionary history, uncover genes under selection, which could be informative of local adaptation, and infer measures of genetic diversity, inbreeding and mutational load that could be used to inform conservation efforts. Gorillas, critically endangered primates, have received considerable attention and with the recently sequenced Bwindi mountain gorilla population, genomic data is now available from all gorilla subspecies and both mountain gorilla populations. Here, we reanalysed this rich dataset with a focus on evolutionary history, local adaptation and genomic parameters relevant for conservation. We estimate a recent split between western and eastern gorillas of 150,000-180,000 years ago, with gene flow around 20,000 years ago, primarily between the Cross River and Grauer's gorilla subspecies. This gene flow event likely obscures evolutionary relationships within eastern gorillas: after excluding putatively introgressed genomic regions, we uncover a sister relationship between Virunga mountain gorillas and Grauer's gorillas to the exclusion of Bwindi mountain gorillas. This makes mountain gorillas paraphyletic. Eastern gorillas are less genetically diverse and more inbred than western gorillas, yet we detected lower genetic load in the eastern species. Analyses of indels fit remarkably well with differences in genetic diversity across gorilla taxa as recovered with nucleotide diversity measures. We also identified genes under selection and unique gene variants specific for each gorilla subspecies, encoding, among others, traits involved in immunity, diet, muscular development, hair morphology and behavior. The presence of this functional variation suggests that the subspecies may be locally adapted. In conclusion, using extensive genomic resources we provide a comprehensive overview of gorilla genomic diversity, including a so-far understudied Bwindi mountain gorilla population, identify putative genes involved in local adaptation, and detect population-specific gene flow across gorilla species.", "doi": "10.1186/s12862-023-02195-x", "pmid": "38273244", "labels": {"DDLS Fellow": "", "Tom van der Valk": ""}, "xrefs": [{"db": "pmc", "key": "PMC10811819"}, {"db": "pii", "key": "10.1186/s12862-023-02195-x"}], "notes": [], "created": "2026-08-20T12:19:41.126Z", "modified": "2026-09-23T11:16:30.406Z"}, {"entity": "publication", "iuid": "40b9004fe7aa46cf826e30184602bd8b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/40b9004fe7aa46cf826e30184602bd8b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/40b9004fe7aa46cf826e30184602bd8b"}}, "title": "Personalized oral care (Precaries): an intervention study customized according to genetic cause and risk", "authors": [{"family": "Westerlund", "given": "Anna", "initials": "A"}, {"family": "Khalifa", "given": "Halah", "initials": "H"}, {"family": "Yousif", "given": "Ranna", "initials": "R"}, {"family": "Araujo", "given": "Gustavo", "initials": "G"}, {"family": "Lundqvist", "given": "Evelina", "initials": "E"}, {"family": "Larsson", "given": "Erica", "initials": "E"}, {"family": "Thrastardottir", "given": "Rakel", "initials": "R"}, {"family": "Akhlaghi", "given": "Rebecka", "initials": "R"}, {"family": "Granciuc", "given": "Victoria", "initials": "V"}, {"family": "Svanberg", "given": "Charlotta", "initials": "C"}, {"family": "Andr\u00e9", "given": "Maria", "initials": "M"}, {"family": "Lehrkinder", "given": "Anna", "initials": "A"}, {"family": "Bazargani", "given": "Farhan", "initials": "F"}, {"family": "Radsj\u00f6", "given": "Christina Goriel", "initials": "CG"}, {"family": "Carlfjord", "given": "Caspar", "initials": "C"}, {"family": "Kr\u00e4mer", "given": "Anke", "initials": "A"}, {"family": "Ganzer", "given": "Niels", "initials": "N"}, {"family": "Hansson", "given": "Isabell", "initials": "I"}, {"family": "Frilund", "given": "Erik", "initials": "E"}, {"family": "Josefsson", "given": "Eva", "initials": "E"}, {"family": "Lindsten", "given": "Rune", "initials": "R"}, {"family": "Magnusson", "given": "Anders", "initials": "A"}, {"family": "Grunwald", "given": "Brygida", "initials": "B"}, {"family": "Hittini", "given": "Firas", "initials": "F"}, {"family": "Kryeziu", "given": "Nurije", "initials": "N"}, {"family": "Loostr\u00f6m", "given": "Henning", "initials": "H"}, {"family": "Sonesson", "given": "Mikael", "initials": "M"}, {"family": "Al-Taha", "given": "Reem", "initials": "R"}, {"family": "Surac", "given": "Hanna", "initials": "H"}, {"family": "Esmaili", "given": "Seifi", "initials": "S"}, {"family": "Isic", "given": "Haris", "initials": "H"}, {"family": "Tegnell", "given": "Anna", "initials": "A"}, {"family": "Andersson", "given": "Samuel", "initials": "S"}, {"family": "L\u00f6vgren", "given": "Mai Lin", "initials": "ML"}, {"family": "Kallunki", "given": "Jenny", "initials": "J"}, {"family": "Lorenzo", "given": "Anna E", "initials": "AE"}, {"family": "Arezzo", "given": "Elena", "initials": "E"}, {"family": "Jasna", "given": "Agata", "initials": "A"}, {"family": "Raviprakash", "given": "Tumkur Sitaram", "initials": "TS"}, {"family": "Str\u00f6mqvist-Engbo", "given": "Eva", "initials": "E"}, {"family": "Burstedt", "given": "Amanda", "initials": "A"}, {"family": "Rosenbaum", "given": "William", "initials": "W"}, {"family": "\u00d6hman", "given": "Oscar", "initials": "O"}, {"family": "Lohr", "given": "Wolfgang", "initials": "W"}, {"family": "R\u00f6nn", "given": "Ann Charlotte", "initials": "AC"}, {"family": "Axelsson", "given": "Tomas", "initials": "T"}, {"family": "M\u00e5rell", "given": "Lena", "initials": "L"}, {"family": "\u00d6sterman", "given": "Lennart", "initials": "L"}, {"family": "Hollox", "given": "Edward J", "initials": "EJ", "orcid": "0000-0002-0115-2298", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5f69a3dd5a3c4d27b184bd176726738d.json"}}, {"family": "Westerlind", "given": "Ulrika", "initials": "U"}, {"family": "Persson", "given": "Karina", "initials": "K"}, {"family": "Clausen", "given": "Henrik", "initials": "H"}, {"family": "Liv", "given": "Per", "initials": "P"}, {"family": "Ryd\u00e9n", "given": "Patrik", "initials": "P"}, {"family": "Henriksson", "given": "Johan", "initials": "J", "orcid": "0000-0002-7745-2844", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/598b7031d1c9448a91de58d8544af7fa.json"}}, {"family": "Carroll", "given": "Laura", "initials": "L", "orcid": "0000-0002-3677-0192", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02112eccb0664819af916a3c3dc79daa.json"}}, {"family": "Sheng", "given": "Nongfei", "initials": "N"}, {"family": "Larsson", "given": "P\u00e4r", "initials": "P"}, {"family": "Str\u00f6mberg", "given": "Nicklas", "initials": "N"}], "type": "posted-content", "published": "2024-01-24", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2024.01.23.24300787", "pmid": null, "labels": {"Laura Carroll": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T10:51:42.595Z", "modified": "2026-09-23T14:50:22.698Z"}, {"entity": "publication", "iuid": "33b5d140755749cd9d3aec0b789ceaf7", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/33b5d140755749cd9d3aec0b789ceaf7.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/33b5d140755749cd9d3aec0b789ceaf7"}}, "title": "Comparison of the performance of multiple whole-genome sequence-based tools for the identification of Bacillus cereus sensu stricto biovar Thuringiensis", "authors": [{"family": "Chung", "given": "Taejung", "initials": "T", "orcid": "0000-0003-4783-6473", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7a7b898b08a84a1ab602619308a98cb8.json"}}, {"family": "Salazar", "given": "Abimel", "initials": "A"}, {"family": "Harm", "given": "Grant", "initials": "G"}, {"family": "Johler", "given": "Sophia", "initials": "S"}, {"family": "Carroll", "given": "Laura M", "initials": "LM"}, {"family": "Kovac", "given": "Jasna", "initials": "J"}], "type": "posted-content", "published": "2024-01-24", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2024.01.23.575246", "pmid": null, "labels": {"Laura Carroll": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T10:51:44.871Z", "modified": "2026-09-23T15:31:39.403Z"}, {"entity": "publication", "iuid": "386bb7a76bcd4095b99bae786320a99a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/386bb7a76bcd4095b99bae786320a99a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/386bb7a76bcd4095b99bae786320a99a"}}, "title": "Cancer Diagnoses After Recent Weight Loss.", "authors": [{"family": "Wang", "given": "Qiao-Li", "initials": "QL"}, {"family": "Babic", "given": "Ana", "initials": "A"}, {"family": "Rosenthal", "given": "Michael H", "initials": "MH"}, {"family": "Lee", "given": "Alice A", "initials": "AA"}, {"family": "Zhang", "given": "Yin", "initials": "Y"}, {"family": "Zhang", "given": "Xuehong", "initials": "X"}, {"family": "Song", "given": "Mingyang", "initials": "M"}, {"family": "Rezende", "given": "Leandro F M", "initials": "LFM"}, {"family": "Lee", "given": "Dong Hoon", "initials": "DH"}, {"family": "Biller", "given": "Leah", "initials": "L"}, {"family": "Ng", "given": "Kimmie", "initials": "K"}, {"family": "Giannakis", "given": "Marios", "initials": "M"}, {"family": "Chan", "given": "Andrew T", "initials": "AT"}, {"family": "Meyerhardt", "given": "Jeffrey A", "initials": "JA"}, {"family": "Fuchs", "given": "Charles S", "initials": "CS"}, {"family": "Eliassen", "given": "A Heather", "initials": "AH"}, {"family": "Birmann", "given": "Brenda M", "initials": "BM"}, {"family": "Stampfer", "given": "Meir J", "initials": "MJ"}, {"family": "Giovannucci", "given": "Edward L", "initials": "EL"}, {"family": "Kraft", "given": "Peter", "initials": "P"}, {"family": "Nowak", "given": "Jonathan A", "initials": "JA"}, {"family": "Yuan", "given": "Chen", "initials": "C"}, {"family": "Wolpin", "given": "Brian M", "initials": "BM"}], "type": "journal article", "published": "2024-01-23", "journal": {"title": "JAMA", "issn": "1538-3598", "volume": "331", "issue": "4", "pages": "318-328", "issn-l": null}, "abstract": "Weight loss is common in primary care. Among individuals with recent weight loss, the rates of cancer during the subsequent 12 months are unclear compared with those without recent weight loss.\n\nTo determine the rates of subsequent cancer diagnoses over 12 months among health professionals with weight loss during the prior 2 years compared with those without recent weight loss.\n\nProspective cohort analysis of females aged 40 years or older from the Nurses' Health Study who were followed up from June 1978 until June 30, 2016, and males aged 40 years or older from the Health Professionals Follow-Up Study who were followed up from January 1988 until January 31, 2016.\n\nRecent weight change was calculated from the participant weights that were reported biennially. The intentionality of weight loss was categorized as high if both physical activity and diet quality increased, medium if only 1 increased, and low if neither increased.\n\nRates of cancer diagnosis during the 12 months after weight loss.\n\nAmong 157 474 participants (median age, 62 years [IQR, 54-70 years]; 111 912 were female [71.1%]; there were 2631 participants [1.7%] who self-identified as Asian, Native American, or Native Hawaiian; 2678 Black participants [1.7%]; and 149 903 White participants [95.2%]) and during 1.64 million person-years of follow-up, 15 809 incident cancer cases were identified (incident rate, 964 cases/100 000 person-years). During the 12 months after reported weight change, there were 1362 cancer cases/100 000 person-years among all participants with recent weight loss of greater than 10.0% of body weight compared with 869 cancer cases/100 000 person-years among those without recent weight loss (between-group difference, 493 cases/100 000 person-years [95% CI, 391-594 cases/100 000 person-years]; P < .001). Among participants categorized with low intentionality for weight loss, there were 2687 cancer cases/100 000 person-years for those with weight loss of greater than 10.0% of body weight compared with 1220 cancer cases/100 000 person-years for those without recent weight loss (between-group difference, 1467 cases/100 000 person-years [95% CI, 799-2135 cases/100 000 person-years]; P < .001). Cancer of the upper gastrointestinal tract (cancer of the esophagus, stomach, liver, biliary tract, or pancreas) was particularly common among participants with recent weight loss; there were 173 cancer cases/100 000 person-years for those with weight loss of greater than 10.0% of body weight compared with 36 cancer cases/100 000 person-years for those without recent weight loss (between-group difference, 137 cases/100 000 person-years [95% CI, 101-172 cases/100 000 person-years]; P < .001).\n\nHealth professionals with weight loss within the prior 2 years had a significantly higher risk of cancer during the subsequent 12 months compared with those without recent weight loss. Cancer of the upper gastrointestinal tract was particularly common among participants with recent weight loss compared with those without recent weight loss.", "doi": "10.1001/jama.2023.25869", "pmid": "38261044", "labels": {"DDLS Fellow": null, "Qiaoli Wang": null}, "xrefs": [{"db": "pmc", "key": "PMC10807298"}, {"db": "pii", "key": "2814132"}], "notes": [], "created": "2025-11-28T12:24:37.978Z", "modified": "2025-11-28T12:24:37.982Z"}, {"entity": "publication", "iuid": "def11a0f594d47c6a1f0259f523998a2", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/def11a0f594d47c6a1f0259f523998a2.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/def11a0f594d47c6a1f0259f523998a2"}}, "title": "Remodeling of the human skeletal muscle proteome found after long-term endurance training but not after strength training.", "authors": [{"family": "Emanuelsson", "given": "Eric B", "initials": "EB", "orcid": "0000-0002-2746-8581", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5e6f00426a2c4aa8b65497f25bce9fd3.json"}}, {"family": "Arif", "given": "Muhammad", "initials": "M", "orcid": "0000-0003-2261-0881", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c8ffc9889ace44e3b992816601b817e2.json"}}, {"family": "Reitzner", "given": "Stefan M", "initials": "SM", "orcid": "0000-0003-0151-2780", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f1d32bad414e49569ede9d7c80e2bf6f.json"}}, {"family": "Perez", "given": "Sean", "initials": "S"}, {"family": "Lindholm", "given": "Mal\u00e9ne E", "initials": "ME"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca58bf2d214047e0ae5e38a42a0f2808.json"}}, {"family": "Daub", "given": "Carsten", "initials": "C", "orcid": "0000-0002-3295-8729", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/779af7484e984ad6883a105caa008313.json"}}, {"family": "Sundberg", "given": "Carl Johan", "initials": "CJ", "orcid": "0000-0002-7000-466X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7ed337b1089b4b3ca6e7787c2228326d.json"}}, {"family": "Chapman", "given": "Mark A", "initials": "MA", "orcid": "0000-0001-9905-4022", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/71c4b747b8794745a547d635953c9960.json"}}], "type": "journal article", "published": "2024-01-19", "journal": {"title": "iScience", "issn": "2589-0042", "volume": "27", "issue": "1", "pages": "108638", "issn-l": null}, "abstract": "Exercise training has tremendous systemic tissue-specific health benefits, but the molecular adaptations to long-term exercise training are not completely understood. We investigated the skeletal muscle proteome of highly endurance-trained, strength-trained, and untrained individuals and performed exercise- and sex-specific analyses. Of the 6,000+ proteins identified, >650 were differentially expressed in endurance-trained individuals compared with controls. Strikingly, 92% of the shared proteins with higher expression in both the male and female endurance groups were known mitochondrial. In contrast to the findings in endurance-trained individuals, minimal differences were found in strength-trained individuals and between females and males. Lastly, a co-expression network and comparative literature analysis revealed key proteins and pathways related to the health benefits of exercise, which were primarily related to differences in mitochondrial proteins. This network is available as an interactive database resource where investigators can correlate clinical data with global gene and protein expression data for hypothesis generation.", "doi": "10.1016/j.isci.2023.108638", "pmid": "38213622", "labels": {"SciLifeLab Fellow": "", "DDLS Fellow": "", "Adil Mardinoglu": "", "Muhammad Arif": ""}, "xrefs": [{"db": "pmc", "key": "PMC10783619"}, {"db": "pii", "key": "S2589-0042(23)02715-3"}], "notes": [], "created": "2026-09-23T11:04:33.359Z", "modified": "2026-09-24T14:20:40.387Z"}, {"entity": "publication", "iuid": "5fa60f0f466444c08a2e0578827a4e57", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5fa60f0f466444c08a2e0578827a4e57.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5fa60f0f466444c08a2e0578827a4e57"}}, "title": "Soluble and multivalent Jag1 DNA origami nanopatterns activate Notch without pulling force.", "authors": [{"family": "Smyrlaki", "given": "Ioanna", "initials": "I"}, {"family": "F\u00f6rd\u0151s", "given": "Ferenc", "initials": "F", "orcid": "0000-0002-2274-5594", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/92e5d6f6ed814c69a85b1c09021afb28.json"}}, {"family": "Rocamonde-Lago", "given": "Iris", "initials": "I"}, {"family": "Wang", "given": "Yang", "initials": "Y", "orcid": "0000-0002-7911-9551", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b6a9aa7f9d8749b3843f4e7730e12840.json"}}, {"family": "Shen", "given": "Boxuan", "initials": "B", "orcid": "0000-0002-1107-828X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/13923ea488c649d79e28dcbb9dbeabcf.json"}}, {"family": "Lentini", "given": "Antonio", "initials": "A", "orcid": "0000-0003-1239-5495", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c5042d3005814ad0a2d1eaeee5d2de3b.json"}}, {"family": "Luca", "given": "Vincent C", "initials": "VC", "orcid": "0000-0001-9427-5520", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/45fe34fbca3245549e4df5f43df718f7.json"}}, {"family": "Reinius", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0002-7021-5248", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a7c1abacc8d446bf8855254246b8d899.json"}}, {"family": "Teixeira", "given": "Ana I", "initials": "AI", "orcid": "0000-0001-8169-8815", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e1e6497a9de14f5b901fbca4a223ddad.json"}}, {"family": "H\u00f6gberg", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0003-2715-7887", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bc6147217ff7477db7d6c14847da3d58.json"}}], "type": "journal article", "published": "2024-01-18", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "465", "issn-l": "2041-1723"}, "abstract": "The Notch signaling pathway has fundamental roles in embryonic development and in the nervous system. The current model of receptor activation involves initiation via a force-induced conformational change. Here, we define conditions that reveal pulling force-independent Notch activation using soluble multivalent constructs. We treat neuroepithelial stem-like cells with molecularly precise ligand nanopatterns displayed from solution using DNA origami. Notch signaling follows with clusters of Jag1, and with chimeric structures where most Jag1 proteins are replaced by other binders not targeting Notch. Our data rule out several confounding factors and suggest a model where Jag1 activates Notch upon prolonged binding without appearing to need a pulling force. These findings reveal a distinct mode of activation of Notch and lay the foundation for the development of soluble agonists.", "doi": "10.1038/s41467-023-44059-4", "pmid": "38238313", "labels": {"Antonio Lentini": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC10796381"}, {"db": "pii", "key": "10.1038/s41467-023-44059-4"}], "notes": [], "created": "2025-03-28T07:03:08.537Z", "modified": "2025-03-28T07:03:08.704Z"}, {"entity": "publication", "iuid": "1764d34dcf0c4b99ae17a97dac0204f0", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1764d34dcf0c4b99ae17a97dac0204f0.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1764d34dcf0c4b99ae17a97dac0204f0"}}, "title": "Bridging the Gap: Integrating Cutting-edge Techniques into Biological Imaging with deepImageJ", "authors": [{"family": "Fuster-Barcel\u00f3", "given": "Caterina", "initials": "C", "orcid": "0000-0002-4784-6957", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/881d36fa227445c9b381a03990b5ed49.json"}}, {"family": "Garc\u00eda L\u00f3pez de Haro", "given": "Carlos", "initials": "C"}, {"family": "G\u00f3mez-de-Mariscal", "given": "Estibaliz", "initials": "E", "orcid": "0000-0003-2082-3277", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cdcc04b3b1534abc8457380935970dd5.json"}}, {"family": "Ouyang", "given": "Wei", "initials": "W"}, {"family": "Olivo-Marin", "given": "Jean Christophe", "initials": "JC", "orcid": "0000-0001-6796-0696", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f2558d56edd54d0e87904930c8ec54f6.json"}}, {"family": "Sage", "given": "Daniel", "initials": "D", "orcid": "0000-0002-1150-1623", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/919b0180005444d88757db8e63b80d83.json"}}, {"family": "Mu\u00f1oz-Barrutia", "given": "Arrate", "initials": "A", "orcid": "0000-0002-1573-1661", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1f71dcceb0284105a7033f2ed195b9c1.json"}}], "type": "posted-content", "published": "2024-01-15", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2024.01.12.575015", "pmid": null, "labels": {"DDLS Fellow": "", "Wei Ouyang": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T10:51:31.337Z", "modified": "2026-09-23T14:50:14.256Z"}, {"entity": "publication", "iuid": "ca03446746b34f0686f25a8d0a0f5c78", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ca03446746b34f0686f25a8d0a0f5c78.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ca03446746b34f0686f25a8d0a0f5c78"}}, "title": "Longevity interventions modulate mechanotransduction and extracellular matrix homeostasis in C. elegans.", "authors": [{"family": "Teuscher", "given": "Alina C", "initials": "AC"}, {"family": "Statzer", "given": "Cyril", "initials": "C"}, {"family": "Goyala", "given": "Anita", "initials": "A"}, {"family": "Domenig", "given": "Seraina A", "initials": "SA"}, {"family": "Schoen", "given": "Ingmar", "initials": "I", "orcid": "0000-0002-5699-1160", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cc84aaf9916f4ba48a9b30cf012ba69f.json"}}, {"family": "Hess", "given": "Max", "initials": "M"}, {"family": "Hofer", "given": "Alexander M", "initials": "AM", "orcid": "0009-0001-5176-1622", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d3341bfd21fc49d59395ff162ffa86dc.json"}}, {"family": "Fossati", "given": "Andrea", "initials": "A", "orcid": "0000-0001-5170-4903", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/658637b885384441943698722fad5944.json"}}, {"family": "Vogel", "given": "Viola", "initials": "V", "orcid": "0000-0003-2898-7671", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fbcfc4590cd246f19a71e93f8e8ce6a0.json"}}, {"family": "Goksel", "given": "Orcun", "initials": "O", "orcid": "0000-0002-8639-7373", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/278c3104bb084bb2849b9f01582181b8.json"}}, {"family": "Aebersold", "given": "Ruedi", "initials": "R", "orcid": "0000-0002-9576-3267", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4aa50db862e94831b8cac04c4426daf1.json"}}, {"family": "Ewald", "given": "Collin Y", "initials": "CY", "orcid": "0000-0003-1166-4171", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/33cc1fe0fbcc473da386ecd1e30b3564.json"}}], "type": "journal article", "published": "2024-01-04", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "15", "issue": "1", "pages": "276"}, "abstract": "Dysfunctional extracellular matrices (ECM) contribute to aging and disease. Repairing dysfunctional ECM could potentially prevent age-related pathologies. Interventions promoting longevity also impact ECM gene expression. However, the role of ECM composition changes in healthy aging remains unclear. Here we perform proteomics and in-vivo monitoring to systematically investigate ECM composition (matreotype) during aging in C. elegans revealing three distinct collagen dynamics. Longevity interventions slow age-related collagen stiffening and prolong the expression of collagens that are turned over. These prolonged collagen dynamics are mediated by a mechanical feedback loop of hemidesmosome-containing structures that span from the exoskeletal ECM through the hypodermis, basement membrane ECM, to the muscles, coupling mechanical forces to adjust ECM gene expression and longevity via the transcriptional co-activator YAP-1 across tissues. Our results provide in-vivo evidence that coordinated ECM remodeling through mechanotransduction is required and sufficient to promote longevity, offering potential avenues for interventions targeting ECM dynamics.", "doi": "10.1038/s41467-023-44409-2", "pmid": "38177158", "labels": {"Andrea Fossati": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC10766642"}, {"db": "pii", "key": "10.1038/s41467-023-44409-2"}], "notes": [], "created": "2025-03-18T16:51:15.294Z", "modified": "2025-03-21T13:20:13.403Z"}, {"entity": "publication", "iuid": "71f8234e1edd43ef9ed90dcbeca11b4d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/71f8234e1edd43ef9ed90dcbeca11b4d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/71f8234e1edd43ef9ed90dcbeca11b4d"}}, "title": "Clonal Hematopoiesis Risk Score and All-Cause and Cardiovascular Mortality in Older Adults.", "authors": [{"family": "Saadatagah", "given": "Seyedmohammad", "initials": "S"}, {"family": "Uddin", "given": "Md Mesbah", "initials": "MM"}, {"family": "Weeks", "given": "Lachelle D", "initials": "LD"}, {"family": "Niroula", "given": "Abhishek", "initials": "A"}, {"family": "Ru", "given": "Meng", "initials": "M"}, {"family": "Takahashi", "given": "Koichi", "initials": "K"}, {"family": "Gondek", "given": "Lukasz", "initials": "L"}, {"family": "Yu", "given": "Bing", "initials": "B"}, {"family": "Bick", "given": "Alexander G", "initials": "AG"}, {"family": "Ebert", "given": "Benjamin L", "initials": "BL"}, {"family": "Platz", "given": "Elizabeth A", "initials": "EA"}, {"family": "Natarajan", "given": "Pradeep", "initials": "P"}, {"family": "Ballantyne", "given": "Christie M", "initials": "CM"}], "type": "journal article", "published": "2024-01-02", "journal": {"title": "JAMA Netw Open", "issn": "2574-3805", "volume": "7", "issue": "1", "pages": "e2351927", "issn-l": null}, "abstract": "Clonal hematopoiesis (CH) with acquired pathogenic variants in myeloid leukemia driver genes is common in older adults but of unknown prognostic value.\n\nTo investigate the prevalence of CH and the utility of the CH risk score (CHRS) in estimating all-cause and disease-specific mortality in older adults with CH.\n\nThis population-based prospective cohort study involved community-dwelling older adults (aged 67-90 years) without hematologic malignant neoplasms (HMs) who were participants in the Atherosclerosis Risk in Communities Visit 5 at 4 US centers: Forsyth County, North Carolina; Jackson, Mississippi; Minneapolis, Minnesota; and Washington County, Maryland. Samples were collected from 2011 to 2013, sequencing was performed in 2022, and data analysis was completed in 2023.\n\nThe exposure was a diagnosis of CH. CHRS scores (calculated using 8 demographic, complete blood cell count, and molecular factors) were used to categorize individuals with CH into low-risk (CHRS \u22649.5), intermediate-risk (CHRS >9.5 to <12.5), and high-risk (CHRS \u226512.5) groups.\n\nThe primary outcome was all-cause mortality, and secondary outcomes were HM mortality, cardiovascular disease mortality, and death from other causes.\n\nAmong 3871 participants without a history of HM (mean [SD] age, 75.7 [5.2] years; 2264 [58.5%] female individuals; 895 [23.1%] Black individuals; 2976 White individuals [76.9%]), 938 (24.2%) had CH. According to the CHRS, 562 (59.9%) were low risk, 318 (33.9%) were intermediate risk, and 58 (6.2%) were high risk. During a median (IQR) follow-up of 7.13 (5.63-7.78) years, 570 participants without CH (19.4%) and 254 participants with CH (27.1%) died. Mortality by CHRS risk group was 128 deaths (22.8%) for low risk, 93 (29.2%) for intermediate risk, and 33 (56.9%) for high risk. By use of multivariable competing risk regression, subdistribution hazard ratios (sHRs) for all-cause mortality were 1.08 (95% CI, 0.89-1.31; P = .42) for low-risk CH, 1.12 (95% CI, 0.89-1.41; P = .31) for intermediate-risk CH, and 2.52 (95% CI, 1.72-3.70; P < .001) for high-risk CH compared with no CH. Among individuals in the high-risk CH group, the sHR of death from HM (6 deaths [10.3%]) was 25.58 (95% CI, 7.55-86.71; P < .001) and that of cardiovascular death (12 deaths [20.7%]) was 2.91 (95% CI, 1.55-5.47; P < .001).\n\nIn this cohort study, the CHRS was associated with all-cause, HM-related, and cardiovascular disease mortality in older adults with CH and may be useful in shared decision-making to guide clinical management and identify appropriate candidates for clinical trials.", "doi": "10.1001/jamanetworkopen.2023.51927", "pmid": "38231513", "labels": {"Abhishek Niroula": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC10794939"}, {"db": "pii", "key": "2814020"}], "notes": [], "created": "2025-03-18T15:48:36.585Z", "modified": "2025-03-18T15:49:05.945Z"}, {"entity": "publication", "iuid": "c87dda99e92e48bfbcfbf63900a0dedf", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c87dda99e92e48bfbcfbf63900a0dedf.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c87dda99e92e48bfbcfbf63900a0dedf"}}, "title": "Molecular profiling of high-level athlete skeletal muscle after acute endurance or resistance exercise - A systems biology approach.", "authors": [{"family": "Reitzner", "given": "Stefan M", "initials": "SM"}, {"family": "Emanuelsson", "given": "Eric B", "initials": "EB"}, {"family": "Arif", "given": "Muhammad", "initials": "M"}, {"family": "Kaczkowski", "given": "Bogumil", "initials": "B"}, {"family": "Kwon", "given": "Andrew Tj", "initials": "AT"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Arner", "given": "Erik", "initials": "E"}, {"family": "Chapman", "given": "Mark A", "initials": "MA"}, {"family": "Sundberg", "given": "Carl Johan", "initials": "CJ"}], "type": "journal article", "published": "2024-01-00", "journal": {"title": "Mol Metab", "issn": "2212-8778", "volume": "79", "pages": "101857", "issn-l": "2212-8778"}, "abstract": "Long-term high-level exercise training leads to improvements in physical performance and multi-tissue adaptation following changes in molecular pathways. While skeletal muscle baseline differences between exercise-trained and untrained individuals have been previously investigated, it remains unclear how training history influences human multi-omics responses to acute exercise.\n\nWe recruited and extensively characterized 24 individuals categorized as endurance athletes with >15 years of training history, strength athletes or control subjects. Timeseries skeletal muscle biopsies were taken from M. vastus lateralis at three time-points after endurance or resistance exercise was performed and multi-omics molecular analysis performed.\n\nOur analyses revealed distinct activation differences of molecular processes such as fatty- and amino acid metabolism and transcription factors such as HIF1A and the MYF-family. We show that endurance athletes have an increased abundance of carnitine-derivates while strength athletes increase specific phospholipid metabolites compared to control subjects. Additionally, for the first time, we show the metabolite sorbitol to be substantially increased with acute exercise. On transcriptional level, we show that acute resistance exercise stimulates more gene expression than acute endurance exercise. This follows a specific pattern, with endurance athletes uniquely down-regulating pathways related to mitochondria, translation and ribosomes. Finally, both forms of exercise training specialize in diverging transcriptional directions, differentiating themselves from the transcriptome of the untrained control group.\n\nWe identify a \"transcriptional specialization effect\" by transcriptional narrowing and intensification, and molecular specialization effects on metabolomic level Additionally, we performed multi-omics network and cluster analysis, providing a novel resource of skeletal muscle transcriptomic and metabolomic profiling in highly trained and untrained individuals.", "doi": "10.1016/j.molmet.2023.101857", "pmid": "38141850", "labels": {"SciLifeLab Fellow": "", "DDLS Fellow": "", "Adil Mardinoglu": "", "Muhammad Arif": ""}, "xrefs": [{"db": "pmc", "key": "PMC10805945"}, {"db": "pii", "key": "S2212-8778(23)00191-6"}], "notes": [], "created": "2026-09-23T10:04:37.373Z", "modified": "2026-09-23T10:43:14.326Z"}, {"entity": "publication", "iuid": "b6a2fcc71d4e4edd8d9d294fe075227c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b6a2fcc71d4e4edd8d9d294fe075227c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b6a2fcc71d4e4edd8d9d294fe075227c"}}, "title": "JDLL: a library to run deep learning models on Java bioimage informatics platforms.", "authors": [{"family": "Garc\u00eda L\u00f3pez de Haro", "given": "Carlos", "initials": "C"}, {"family": "Dallongeville", "given": "St\u00e9phane", "initials": "S", "orcid": "0000-0002-2204-7083", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6d1860b509cf415fa512a4286d25c9f8.json"}}, {"family": "Musset", "given": "Thomas", "initials": "T"}, {"family": "G\u00f3mez-de-Mariscal", "given": "Estibaliz", "initials": "E", "orcid": "0000-0003-2082-3277", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cdcc04b3b1534abc8457380935970dd5.json"}}, {"family": "Sage", "given": "Daniel", "initials": "D", "orcid": "0000-0002-1150-1623", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/919b0180005444d88757db8e63b80d83.json"}}, {"family": "Ouyang", "given": "Wei", "initials": "W", "orcid": "0000-0002-0291-926X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56f601e1d1c6448aab0c3a1e3cffdbfc.json"}}, {"family": "Mu\u00f1oz-Barrutia", "given": "Arrate", "initials": "A", "orcid": "0000-0002-1573-1661", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1f71dcceb0284105a7033f2ed195b9c1.json"}}, {"family": "Tinevez", "given": "Jean-Yves", "initials": "JY", "orcid": "0000-0002-0998-4718", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/83f54be6102d4b4499ac702b1289e9c7.json"}}, {"family": "Olivo-Marin", "given": "Jean-Christophe", "initials": "JC", "orcid": "0000-0001-6796-0696", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f2558d56edd54d0e87904930c8ec54f6.json"}}], "type": "letter", "published": "2024-01-00", "journal": {"title": "Nat. Methods", "issn": "1548-7105", "volume": "21", "issue": "1", "pages": "7-8", "issn-l": "1548-7091"}, "abstract": null, "doi": "10.1038/s41592-023-02129-x", "pmid": "38191929", "labels": {"DDLS Fellow": "", "Wei Ouyang": ""}, "xrefs": [{"db": "pii", "key": "10.1038/s41592-023-02129-x"}], "notes": [], "created": "2026-08-20T09:02:58.057Z", "modified": "2026-09-23T13:12:22.314Z"}, {"entity": "publication", "iuid": "352a4e8c023347d9aa50342fe3d83b4b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/352a4e8c023347d9aa50342fe3d83b4b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/352a4e8c023347d9aa50342fe3d83b4b"}}, "title": "Aberrant microbiomes are associated with increased antibiotic resistance gene load in hybrid mice.", "authors": [{"family": "Jarqu\u00edn-D\u00edaz", "given": "V\u00edctor Hugo", "initials": "VH"}, {"family": "Ferreira", "given": "Susana Carolina Martins", "initials": "SCM"}, {"family": "Balard", "given": "Alice", "initials": "A"}, {"family": "\u010eureje", "given": "\u013dudov\u00edt", "initials": "\u013d"}, {"family": "Machol\u00e1n", "given": "Milos", "initials": "M"}, {"family": "Pi\u00e1lek", "given": "Jaroslav", "initials": "J"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J", "orcid": "0000-0002-6528-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c666068e9d34939b0252a627007cec7.json"}}, {"family": "Kramer-Schadt", "given": "Stephanie", "initials": "S"}, {"family": "Forslund-Startceva", "given": "Sofia Kirke", "initials": "SK"}, {"family": "Heitlinger", "given": "Emanuel", "initials": "E"}], "type": "journal article", "published": "2024-01-00", "journal": {"title": "ISME Commun", "issn": "2730-6151", "volume": "4", "issue": "1", "pages": "ycae053", "issn-l": null}, "abstract": "Antibiotic resistance is a priority public health problem resulting from eco-evolutionary dynamics within microbial communities and their interaction at a mammalian host interface or geographical scale. The links between mammalian host genetics, bacterial gut community, and antimicrobial resistance gene (ARG) content must be better understood in natural populations inhabiting heterogeneous environments. Hybridization, the interbreeding of genetically divergent populations, influences different components of the gut microbial communities. However, its impact on bacterial traits such as antibiotic resistance is unknown. Here, we present that hybridization might shape bacterial communities and ARG occurrence. We used amplicon sequencing to study the gut microbiome and to predict ARG composition in natural populations of house mice (Mus musculus). We compared gastrointestinal bacterial and ARG diversity, composition, and abundance across a gradient of pure and hybrid genotypes in the European House Mouse Hybrid Zone. We observed an increased overall predicted richness of ARG in hybrid mice. We found bacteria-ARG interactions by their co-abundance and detected phenotypes of extreme abundances in hybrid mice at the level of specific bacterial taxa and ARGs, mainly multidrug resistance genes. Our work suggests that mammalian host genetic variation impacts the gut microbiome and chromosomal ARGs. However, it raises further questions on how the mammalian host genetics impact ARGs via microbiome dynamics or environmental covariates.", "doi": "10.1093/ismeco/ycae053", "pmid": "38800129", "labels": {"DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC11128261"}, {"db": "pii", "key": "ycae053"}], "notes": [], "created": "2024-11-18T11:43:56.930Z", "modified": "2026-09-23T13:15:14.019Z"}, {"entity": "publication", "iuid": "a60b98275b9d428599f9a3d45d2f55cb", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a60b98275b9d428599f9a3d45d2f55cb.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a60b98275b9d428599f9a3d45d2f55cb"}}, "title": "Mapping of the gene network that regulates glycan clock of ageing.", "authors": [{"family": "Frkatovi\u0107-Hod\u017ei\u0107", "given": "Azra", "initials": "A"}, {"family": "Mijakovac", "given": "Anika", "initials": "A"}, {"family": "Mi\u0161kec", "given": "Karlo", "initials": "K"}, {"family": "Nostaeva", "given": "Arina", "initials": "A"}, {"family": "Sharapov", "given": "Sodbo Z", "initials": "SZ"}, {"family": "Landini", "given": "Arianna", "initials": "A"}, {"family": "Haller", "given": "Toomas", "initials": "T"}, {"family": "Akker", "given": "Erik van den", "initials": "EVD"}, {"family": "Sharma", "given": "Sapna", "initials": "S"}, {"family": "Cuadrat", "given": "Rafael R C", "initials": "RRC"}, {"family": "Mangino", "given": "Massimo", "initials": "M"}, {"family": "Li", "given": "Yong", "initials": "Y"}, {"family": "Keser", "given": "Toma", "initials": "T"}, {"family": "Rudman", "given": "Najda", "initials": "N"}, {"family": "\u0160tambuk", "given": "Tamara", "initials": "T"}, {"family": "Pu\u010di\u0107-Bakovi\u0107", "given": "Maja", "initials": "M"}, {"family": "Trbojevi\u0107-Akma\u010di\u0107", "given": "Irena", "initials": "I"}, {"family": "Gudelj", "given": "Ivan", "initials": "I"}, {"family": "\u0160tambuk", "given": "Jerko", "initials": "J"}, {"family": "Pribi\u0107", "given": "Tea", "initials": "T"}, {"family": "Radovani", "given": "Barbara", "initials": "B"}, {"family": "Tominac", "given": "Petra", "initials": "P"}, {"family": "Fischer", "given": "Krista", "initials": "K"}, {"family": "Beekman", "given": "Marian", "initials": "M"}, {"family": "Wuhrer", "given": "Manfred", "initials": "M"}, {"family": "Gieger", "given": "Christian", "initials": "C"}, {"family": "Schulze", "given": "Matthias B", "initials": "MB", "orcid": "0000-0002-0830-5277", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/853ded2c43b64f26a8b47da7ea7b79c0.json"}}, {"family": "Wittenbecher", "given": "Clemens", "initials": "C", "orcid": "0000-0001-7792-877X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2f7d2c289b3c47d5a79d23bd48a3225a.json"}}, {"family": "Polasek", "given": "Ozren", "initials": "O"}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "Wilson", "given": "James F", "initials": "JF"}, {"family": "Spector", "given": "Tim D", "initials": "TD"}, {"family": "K\u00f6ttgen", "given": "Anna", "initials": "A"}, {"family": "Vu\u010dkovi\u0107", "given": "Frano", "initials": "F"}, {"family": "Aulchenko", "given": "Yurii S", "initials": "YS"}, {"family": "Vojta", "given": "Aleksandar", "initials": "A"}, {"family": "Kri\u0161ti\u0107", "given": "Jasminka", "initials": "J"}, {"family": "Klari\u0107", "given": "Lucija", "initials": "L"}, {"family": "Zoldo\u0161", "given": "Vlatka", "initials": "V"}, {"family": "Lauc", "given": "Gordan", "initials": "G"}], "type": "journal article", "published": "2023-12-26", "journal": {"title": "Aging (Albany NY)", "issn": "1945-4589", "volume": "15", "issue": "24", "pages": "14509-14552", "issn-l": null}, "abstract": "Glycans are an essential structural component of immunoglobulin G (IgG) that modulate its structure and function. However, regulatory mechanisms behind this complex posttranslational modification are not well known. Previous genome-wide association studies (GWAS) identified 29 genomic regions involved in regulation of IgG glycosylation, but only a few were functionally validated. One of the key functional features of IgG glycosylation is the addition of galactose (galactosylation), a trait which was shown to be associated with ageing. We performed GWAS of IgG galactosylation (N=13,705) and identified 16 significantly associated loci, indicating that IgG galactosylation is regulated by a complex network of genes that extends beyond the galactosyltransferase enzyme that adds galactose to IgG glycans. Gene prioritization identified 37 candidate genes. Using a recently developed CRISPR/dCas9 system we manipulated gene expression of candidate genes in the in vitro IgG expression system. Upregulation of three genes, EEF1A1, MANBA and TNFRSF13B, changed the IgG glycome composition, which confirmed that these three genes are involved in IgG galactosylation in this in vitro expression system.", "doi": "10.18632/aging.205106", "pmid": "38149987", "labels": {"Clemens Wittenbecher": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC10781487"}, {"db": "pii", "key": "205106"}], "notes": [], "created": "2025-03-19T08:18:46.846Z", "modified": "2026-09-23T11:25:46.188Z"}, {"entity": "publication", "iuid": "4fd036fbbd514647b7a29b9d956b34fd", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4fd036fbbd514647b7a29b9d956b34fd.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4fd036fbbd514647b7a29b9d956b34fd"}}, "title": "A community-curated, global atlas of Bacillus cereus sensu lato genomes for epidemiological surveillance", "authors": [{"family": "Ramnath", "given": "Vignesh", "initials": "V"}, {"family": "Larralde", "given": "Martin", "initials": "M"}, {"family": "Menchik", "given": "Pedro", "initials": "P", "orcid": "0000-0001-6240-0198", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/77eb0b9012264fd58458eaa91fe02148.json"}}, {"family": "Buehler", "given": "Ariel J", "initials": "AJ"}, {"family": "Harrand", "given": "Anna Sophia", "initials": "AS"}, {"family": "Chung", "given": "Taejung", "initials": "T", "orcid": "0000-0003-4783-6473", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7a7b898b08a84a1ab602619308a98cb8.json"}}, {"family": "Wei", "given": "Xiaoyuan", "initials": "X"}, {"family": "Raghuram", "given": "Vishnu", "initials": "V", "orcid": "0000-0002-7435-6435", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ff2d5f765134ecd921c708747629965.json"}}, {"family": "Gourl\u00e9", "given": "Hadrien", "initials": "H", "orcid": "0000-0001-9807-1082", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d5485a48dfde4e53b14d39c54f2b2483.json"}}, {"family": "Pierneef", "given": "Rian", "initials": "R", "orcid": "0000-0002-0619-0058", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8fc4cd2ef72c419fb5012a7fdd59e456.json"}}, {"family": "Matle", "given": "Itumeleng", "initials": "I", "orcid": "0000-0002-1495-357X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dd13d91d769e49738063ce04919c589f.json"}}, {"family": "Aspholm", "given": "Marina", "initials": "M", "orcid": "0000-0003-3175-6022", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/621f705f3e244848a361061acaa7b21b.json"}}, {"family": "Andersson", "given": "Magnus", "initials": "M", "orcid": "0000-0002-9835-3263", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/72fda843704b4af7a182a06d2ad83153.json"}}, {"family": "Cheng", "given": "Rachel A", "initials": "RA", "orcid": "0000-0002-5932-7011", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c4b1b7638c9c4ec7bad01d1ad6497b6a.json"}}, {"family": "Kovac", "given": "Jasna", "initials": "J", "orcid": "0000-0002-9465-4552", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d18e6f5bd24644e18030b59391d1a755.json"}}, {"family": "Henriksson", "given": "Johan", "initials": "J", "orcid": "0000-0002-7745-2844", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/598b7031d1c9448a91de58d8544af7fa.json"}}, {"family": "Carroll", "given": "Laura M", "initials": "LM", "orcid": "0000-0002-3677-0192", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02112eccb0664819af916a3c3dc79daa.json"}}], "type": "posted-content", "published": "2023-12-21", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2023.12.20.572685", "pmid": null, "labels": {"Laura Carroll": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2025-03-18T17:33:20.837Z", "modified": "2026-09-23T13:53:12.872Z"}, {"entity": "publication", "iuid": "82fd50632a9145269d144fc0e833fab9", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/82fd50632a9145269d144fc0e833fab9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/82fd50632a9145269d144fc0e833fab9"}}, "title": "Undiscovered bird extinctions obscure the true magnitude of human-driven extinction waves.", "authors": [{"family": "Cooke", "given": "Rob", "initials": "R", "orcid": "0000-0003-0601-8888", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2a2e0e2acd86409f9ab6ef39b71fd471.json"}}, {"family": "Sayol", "given": "Ferran", "initials": "F"}, {"family": "Andermann", "given": "Tobias", "initials": "T", "orcid": "0000-0002-0932-1623", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dfff478dfcfc43ddbd40bb1bafbcb0a7.json"}}, {"family": "Blackburn", "given": "Tim M", "initials": "TM", "orcid": "0000-0003-0152-2663", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ab42f43c627742f398a1f5c0f427dcf3.json"}}, {"family": "Steinbauer", "given": "Manuel J", "initials": "MJ", "orcid": "0000-0002-7142-9272", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f9ea30844daa4cc29397ce1726044737.json"}}, {"family": "Antonelli", "given": "Alexandre", "initials": "A", "orcid": "0000-0003-1842-9297", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1de98df1bb2140fc9666507cb2fb5614.json"}}, {"family": "Faurby", "given": "S\u00f8ren", "initials": "S", "orcid": "0000-0002-2974-2628", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e9be75db97d64624a90e272c14ac7f5b.json"}}], "type": "journal article", "published": "2023-12-19", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "8116", "issn-l": "2041-1723"}, "abstract": "Birds are among the best-studied animal groups, but their prehistoric diversity is poorly known due to low fossilization potential. Hence, while many human-driven bird extinctions (i.e., extinctions caused directly by human activities such as hunting, as well as indirectly through human-associated impacts such as land use change, fire, and the introduction of invasive species) have been recorded, the true number is likely much larger. Here, by combining recorded extinctions with model estimates based on the completeness of the fossil record, we suggest that at least ~1300-1500 bird species (~12% of the total) have gone extinct since the Late Pleistocene, with 55% of these extinctions undiscovered (not yet discovered or left no trace). We estimate that the Pacific accounts for 61% of total bird extinctions. Bird extinction rate varied through time with an intense episode ~1300 CE, which likely represents the largest human-driven vertebrate extinction wave ever, and a rate 80 (60-95) times the background extinction rate. Thus, humans have already driven more than one in nine bird species to extinction, with likely severe, and potentially irreversible, ecological and evolutionary consequences.", "doi": "10.1038/s41467-023-43445-2", "pmid": "38114469", "labels": {"Tobias Andermann": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC10730700"}, {"db": "pii", "key": "10.1038/s41467-023-43445-2"}, {"db": "Dryad", "key": "10.5061/dryad.s1rn8pk66"}], "notes": [], "created": "2025-03-18T16:01:34.544Z", "modified": "2026-09-23T08:41:28.768Z"}, {"entity": "publication", "iuid": "2d3fe81551fa4460aa2a48d466dba3e2", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/2d3fe81551fa4460aa2a48d466dba3e2.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/2d3fe81551fa4460aa2a48d466dba3e2"}}, "title": "Metagenomic assemblies tend to break around antibiotic resistance genes", "authors": [{"family": "Abramova", "given": "Anna", "initials": "A", "orcid": "0000-0002-0493-7808", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dd75cbcc659c4ca398eb678fad1dc498.json"}}, {"family": "Karkman", "given": "Antti", "initials": "A", "orcid": "0000-0003-0983-3319", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/51ba670092f8496d8ebedcb07d0b6e62.json"}}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J", "orcid": "0000-0002-6528-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c666068e9d34939b0252a627007cec7.json"}}], "type": "posted-content", "published": "2023-12-14", "journal": {"title": "bioRxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2023.12.13.571436", "pmid": null, "labels": {"DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2026-08-20T10:51:00.058Z", "modified": "2026-10-05T08:51:21.808Z"}, {"entity": "publication", "iuid": "3d9db77345be4f35a5c808e67bf118ea", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3d9db77345be4f35a5c808e67bf118ea.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3d9db77345be4f35a5c808e67bf118ea"}}, "title": "Seeing the Membrane from Both Sides Now: Lipid Asymmetry and Its Strange Consequences.", "authors": [{"family": "Doktorova", "given": "Milka", "initials": "M", "orcid": "0000-0003-4366-2242", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/791384c319f04584bac8ffb21df7271f.json"}}, {"family": "Levental", "given": "Ilya", "initials": "I", "orcid": "0000-0002-1206-9545", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7fe40c2b810348cab78616402d4d1f1f.json"}}, {"family": "Heberle", "given": "Frederick A", "initials": "FA", "orcid": "0000-0002-0424-3240", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2557f5621a0b4c87b5f4702fbc7b6bdb.json"}}], "type": "journal article", "published": "2023-12-01", "journal": {"title": "Cold Spring Harbor Perspectives in Biology", "issn": "1943-0264", "issn-l": "1943-0264", "volume": "15", "issue": "12", "pages": null}, "abstract": "Almost all biomembranes are constructed as lipid bilayers and, in almost all of these, the two opposing monolayers (leaflets) have distinct lipid compositions. This lipid asymmetry arises through the concerted action of a suite of energy-dependent enzymes that maintain living bilayers in a far-from-equilibrium steady-state. Recent discoveries reveal that lipid compositional asymmetry imparts biophysical asymmetries and that this dualistic organization may have major consequences for cellular physiology. Importantly, while transbilayer asymmetry appears to be an essential, near-ubiquitous characteristic of biological membranes, it has been challenging to reproduce in reconstituted or synthetic systems. Although recent methodological developments have overcome some critical challenges, it remains difficult to extrapolate results from available models to biological systems. Concurrently, there are few experimental approaches for targeted, controlled manipulation of lipid asymmetry in living cells. Thus, the biophysical and functional consequences of membrane asymmetry remain almost wholly unexplored. This perspective summarizes the current state of knowledge and highlights emerging themes that are beginning to make inroads into the fundamental question of why life tends toward asymmetry in its bilayers.", "doi": "10.1101/cshperspect.a041393", "pmid": "37604588", "labels": {"Milka Doktorova": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC10691478"}, {"db": "pii", "key": "cshperspect.a041393"}], "notes": [], "created": "2024-11-27T12:20:17.089Z", "modified": "2024-11-29T10:55:27.362Z"}, {"entity": "publication", "iuid": "4abbe65ef51444dca548fd02a35c843d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4abbe65ef51444dca548fd02a35c843d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4abbe65ef51444dca548fd02a35c843d"}}, "title": "Deep lipidomics profiling captures the impact of improved dietary fat quality on cardiometabolic risk and provides potential tools for precision nutrition approaches", "authors": [{"family": "Wittenbecher", "given": "Clemens", "initials": "C", "orcid": "0000-0001-7792-877X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2f7d2c289b3c47d5a79d23bd48a3225a.json"}}, {"family": "Eichelmann", "given": "Fabian", "initials": "F", "orcid": "0000-0002-3975-5596", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4f6083a259c6440ab3201d53f44a0d55.json"}}, {"family": "Schulze", "given": "Matthias", "initials": "M", "orcid": "0000-0002-0830-5277", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/853ded2c43b64f26a8b47da7ea7b79c0.json"}}, {"family": "Prada", "given": "Marcela", "initials": "M"}, {"family": "Lovegrove", "given": "Julie", "initials": "J"}, {"family": "Jackson", "given": "Kim", "initials": "K"}, {"family": "Sellem", "given": "Laury", "initials": "L"}, {"family": "Salas-Salvado", "given": "Jordi", "initials": "J", "orcid": "0000-0003-2700-7459", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/49e886d4d7e346e1a65f949699f620a4.json"}}, {"family": "Razquin", "given": "Cristina", "initials": "C", "orcid": "0000-0003-3480-2645", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f0f5c529e0a647528ca99b42fe8a9e8b.json"}}, {"family": "Mart\u00ednez-Gonz\u00e1lez", "given": "Miguel", "initials": "M", "orcid": "0000-0002-3917-9808", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7852fa98fe3a4da285d79f04e09cbd34.json"}}, {"family": "Estruch", "given": "Ramon", "initials": "R", "orcid": "0000-0003-1260-4445", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/122cb01329f24931ae77ae5ac5a05059.json"}}, {"family": "Rexrode", "given": "Kathryn", "initials": "K", "orcid": "0000-0003-3387-8429", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a3600b145b304aa7959c0f85fa198192.json"}}, {"family": "Guasch-Ferr\u00e9", "given": "Marta", "initials": "M"}, {"family": "Sun", "given": "Qi", "initials": "Q", "orcid": "0000-0002-8480-1563", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4a65407257ac4518ac5cb19317ee3b32.json"}}, {"family": "Willett", "given": "Walter", "initials": "W"}, {"family": "Hu", "given": "Frank", "initials": "F"}], "type": "posted-content", "published": "2023-11-29", "journal": {"issn-l": null}, "abstract": null, "doi": "10.21203/rs.3.rs-3653633/v1", "pmid": null, "labels": {"Clemens Wittenbecher": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2025-12-09T13:32:37.682Z", "modified": "2025-12-09T13:33:00.679Z"}, {"entity": "publication", "iuid": "88d46598d38049e49334326bc3a3c0bc", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/88d46598d38049e49334326bc3a3c0bc.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/88d46598d38049e49334326bc3a3c0bc"}}, "title": "Author Correction: Elevated plasma complement factor H related 5 protein is associated with venous thromboembolism.", "authors": [{"family": "Iglesias", "given": "Maria Jesus", "initials": "MJ"}, {"family": "Sanchez-Rivera", "given": "Laura", "initials": "L"}, {"family": "Ibrahim-Kosta", "given": "Manal", "initials": "M"}, {"family": "Naudin", "given": "Cl\u00e9ment", "initials": "C", "orcid": "0000-0002-6777-9587", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f89e25cd7fcc4617ab5299c72fd17e0c.json"}}, {"family": "Munsch", "given": "Ga\u00eblle", "initials": "G", "orcid": "0000-0003-1564-9825", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ed62bf6aa35643f283511d68d2aa4b01.json"}}, {"family": "Goumidi", "given": "Louisa", "initials": "L", "orcid": "0000-0003-4164-8471", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7d3df066e5e54e32bb99110289ab8a45.json"}}, {"family": "Farm", "given": "Maria", "initials": "M"}, {"family": "Smith", "given": "Philip M", "initials": "PM"}, {"family": "Thibord", "given": "Florian", "initials": "F"}, {"family": "Kral-Pointner", "given": "Julia Barbara", "initials": "JB"}, {"family": "Hong", "given": "Mun-Gwan", "initials": "MG", "orcid": "0000-0001-8603-8293", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d12504acae5c4f31b83f75c3d7786cd4.json"}}, {"family": "Suchon", "given": "Pierre", "initials": "P"}, {"family": "Germain", "given": "Marine", "initials": "M"}, {"family": "Schrottmaier", "given": "Waltraud", "initials": "W", "orcid": "0000-0003-0550-4120", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0ab65a615b9e477aa6206677e57025b0.json"}}, {"family": "Dusart", "given": "Philip", "initials": "P", "orcid": "0000-0003-2747-3214", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/26cf50c230954da190746c16b5ac2b7d.json"}}, {"family": "Boland", "given": "Anne", "initials": "A"}, {"family": "Kotol", "given": "David", "initials": "D", "orcid": "0000-0002-5388-3826", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c41f8f491c474e6bba2047b5d04b4af5.json"}}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e213b04f8984c8eb00c68f5bc2f6a36.json"}}, {"family": "Koprulu", "given": "Mine", "initials": "M", "orcid": "0000-0001-6870-4539", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e8fa2ddd2cfa4bbeb9c0b043513a6701.json"}}, {"family": "Pietzner", "given": "Maik", "initials": "M", "orcid": "0000-0003-3437-9963", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3304844cece945168cbec0b5e3d9a9cf.json"}}, {"family": "Langenberg", "given": "Claudia", "initials": "C", "orcid": "0000-0002-5017-7344", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f287f3248cc24c6cbfc100c249b87418.json"}}, {"family": "Damrauer", "given": "Scott M", "initials": "SM", "orcid": "0000-0001-8009-1632", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f35b78d4384d41f2bfae2639b23b1e82.json"}}, {"family": "Johnson", "given": "Andrew D", "initials": "AD", "orcid": "0000-0001-6369-5178", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8b268f8da3f247ba90dc37ea73d93c2f.json"}}, {"family": "Klarin", "given": "Derek M", "initials": "DM", "orcid": "0000-0002-4636-5780", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0b81fbf037ec4b4b8ac0013544539f00.json"}}, {"family": "Smith", "given": "Nicholas L", "initials": "NL"}, {"family": "Smadja", "given": "David M", "initials": "DM"}, {"family": "Holmstr\u00f6m", "given": "Margareta", "initials": "M"}, {"family": "Magnusson", "given": "Maria", "initials": "M"}, {"family": "Silveira", "given": "Angela", "initials": "A", "orcid": "0000-0003-2063-4935", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2d8cbafcc7f04ac3adda984af7d85a16.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ea446aa574042a295d5f69437402f76.json"}}, {"family": "Renn\u00e9", "given": "Thomas", "initials": "T"}, {"family": "Martinez-Perez", "given": "Angel", "initials": "A", "orcid": "0000-0002-5934-1454", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0fa8f32fb99f46dcb16d3a64643dbbfa.json"}}, {"family": "Emmerich", "given": "Joseph", "initials": "J"}, {"family": "Deleuze", "given": "Jean-Francois", "initials": "JF", "orcid": "0000-0002-5358-4463", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/33bb50dc6b8045bd9dbbde4423f66129.json"}}, {"family": "Antovic", "given": "Jovan", "initials": "J"}, {"family": "Soria Fernandez", "given": "Jose Manuel", "initials": "JM"}, {"family": "Assinger", "given": "Alice", "initials": "A", "orcid": "0000-0002-5670-5910", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ccb6bb03693c4c799f4cbb53e6ff7049.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/022e140799b6466ea123319c3d70c76e.json"}}, {"family": "Souto Andres", "given": "Joan Carles", "initials": "JC", "orcid": "0000-0003-2092-5142", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/164af41db2204f2591c719a8b024d32a.json"}}, {"family": "Morange", "given": "Pierre-Emmanuel", "initials": "PE", "orcid": "0000-0002-9065-722X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/50bca11c313740c299901843e86e5d48.json"}}, {"family": "Butler", "given": "Lynn Marie", "initials": "LM", "orcid": "0000-0002-2352-8217", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca98647aea15499485d755977bd0869a.json"}}, {"family": "Tr\u00e9gou\u00ebt", "given": "David-Alexandre", "initials": "DA", "orcid": "0000-0001-9084-7800", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/74ca463a0d804b1ab97dac4750563220.json"}}, {"family": "Odeberg", "given": "Jacob", "initials": "J", "orcid": "0000-0003-0996-1644", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d6abb3fc822a4cacbf1d45224f2442f5.json"}}], "type": "published erratum", "published": "2023-11-27", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "7752", "issn-l": "2041-1723"}, "abstract": null, "doi": "10.1038/s41467-023-43764-4", "pmid": "38012230", "labels": {"Fredrik Edfors": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC10682365"}, {"db": "pii", "key": "10.1038/s41467-023-43764-4"}], "notes": [], "created": "2026-08-20T08:53:02.011Z", "modified": "2026-09-23T14:27:47.656Z"}, {"entity": "publication", "iuid": "34d9e94ed881436a930c8d9337cfeefe", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/34d9e94ed881436a930c8d9337cfeefe.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/34d9e94ed881436a930c8d9337cfeefe"}}, "title": "CCR5 promoter region polymorphisms in systemic lupus erythematosus.", "authors": [{"family": "Schauren", "given": "Juliana da Silveira", "initials": "JDS", "orcid": "0000-0002-1920-1369", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c87cdcfc9e2b4b54a3d6ae94ade5c754.json"}}, {"family": "de Oliveira", "given": "Amanda Henrique", "initials": "AH", "orcid": "0000-0002-1733-2840", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/23b294638e1d4129be3ac380ee332751.json"}}, {"family": "Consiglio", "given": "Camila Rosat", "initials": "CR", "orcid": "0000-0002-8901-2328", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a786e29de11b41dd9da2b680ad5b351f.json"}}, {"family": "Monticielo", "given": "Odirlei Andr\u00e9", "initials": "OA", "orcid": "0000-0003-0720-2097", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d180f3159ec84ee1b8bf56cb0b5ed59e.json"}}, {"family": "Xavier", "given": "Ricardo Machado", "initials": "RM", "orcid": "0000-0001-6570-4533", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/acd8e531146749a39e9b84acea8e7caa.json"}}, {"family": "Nunes", "given": "Nat\u00e1lia Schneider", "initials": "NS", "orcid": "0000-0003-1950-4391", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a20ef3611f2240ef99ede1a764824530.json"}}, {"family": "Ellwanger", "given": "Joel Henrique", "initials": "JH", "orcid": "0000-0002-1040-2738", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/612d3bfd4c04448ca05803ac7be97c63.json"}}, {"family": "Chies", "given": "Jos\u00e9 Artur Bogo", "initials": "JAB", "orcid": "0000-0001-7025-0660", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fc7e836e395a483998d071cc9deab43f.json"}}], "type": "journal article", "published": "2023-11-20", "journal": {"title": "Int J Immunogenet", "issn": "1744-313X", "issn-l": null}, "abstract": "This study investigated the impacts of CCR5 promoter region polymorphisms on the development of systemic lupus erythematosus (SLE) by comparing CCR5 genotypes and haplotypes from SLE patients with ethnically matched controls. A total of 382 SLE patients (289 European-derived and 93 African-derived) and 375 controls (243 European-derived and 132 African-derived) were genotyped for the CCR2-64I G > A (rs1799864), CCR5-59353 C > T (rs1799988), CCR5-59356 C > T (rs41469351), CCR5-59402 A > G (rs1800023) and CCR5-59653 C > T (rs1800024) polymorphisms through polymerase chain reaction-restriction fragment length polymorphism and direct sequencing. Previous data from CCR5\u039432 analysis was included in the study to infer the CCR5 haplotypes and as a possible confounding factor in the binary logistic regression. European-derived patients showed a higher frequency of CCR5 wild-type genotype (conversely, a reduced frequency of \u039432 allele) and a reduced frequency of the HHG*2 haplotype compared to controls; both factors significantly affecting disease risk [p = .003 (OR 3.5, 95%CI 1.6-7.5) and 2.0% vs. 7.2% (residual p = 2.9E - 5), respectively]. Additionally, the HHA/HHB, HHC and HHG*2 haplotype frequencies differed between African-derived patients and controls [10% vs. 20.5% (residual p = .003), 29.4% vs. 17.4% (residual p = .003) and 3.9% vs. 0.8% (residual p = .023), respectively]. Considering the clinical manifestations of the disease, the CCR5\u039432 presence was confirmed as a susceptibility factor to class IV nephritis in the African-derived group and when all patients were grouped for comparison [pcorrected = .012 (OR 3.0; 95%CI 3.0-333.3) and pcorrected = .0006 (OR 6.8; 95%CI 1.9-24.8), respectively]. In conclusion, this study indicates that CCR5 promoter polymorphisms are important disease modifiers in SLE. Present data reinforces the CCR5\u039432 polymorphism as a protective factor for the development of the disease in European-derived patients and as a susceptibility factor for class IV nephritis in African-derived patients. Furthermore, we also described a reduced frequency of HHA/HHB and an increased frequency of HHC and HHG*2 haplotypes in African-derived patients, which could modify the CCR5 protein expression in specific cell subsets.", "doi": "10.1111/iji.12646", "pmid": "37984413", "labels": {"Camila Consiglio": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2023-11-22T09:17:29.694Z", "modified": "2023-11-22T09:17:30.085Z"}, {"entity": "publication", "iuid": "88fc94697e8f4ea2adceb6767b20da34", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/88fc94697e8f4ea2adceb6767b20da34.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/88fc94697e8f4ea2adceb6767b20da34"}}, "title": "Between but Not Within-Species Variation in the Distribution of Fitness Effects.", "authors": [{"family": "James", "given": "Jennifer", "initials": "J", "orcid": "0000-0003-0518-6783", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4b807f7ab8f46f8a5e927e1b090d662.json"}}, {"family": "Kastally", "given": "Chedly", "initials": "C", "orcid": "0000-0002-1820-4752", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f074636c47854f66a0287fb7382a1462.json"}}, {"family": "Budde", "given": "Katharina B", "initials": "KB", "orcid": "0000-0002-5361-2815", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb5427d15ddc46b0a0afaed44aea0cf0.json"}}, {"family": "Gonz\u00e1lez-Mart\u00ednez", "given": "Santiago C", "initials": "SC", "orcid": "0000-0002-4534-3766", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eac16e91ca6a49c18fb4206b5349cfff.json"}}, {"family": "Milesi", "given": "Pascal", "initials": "P"}, {"family": "Pyh\u00e4j\u00e4rvi", "given": "Tanja", "initials": "T", "orcid": "0000-0001-6958-5172", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7256c4910788401f873272cf29fedf91.json"}}, {"family": "Lascoux", "given": "Martin", "initials": "M", "orcid": "0000-0003-1699-9042", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0730d0f9c2524eb19383640612924701.json"}}, {"family": "GenTree Consortium", "given": "", "initials": ""}], "type": "journal article", "published": "2023-11-03", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "issn-l": "0737-4038", "volume": "40", "issue": "11", "pages": null}, "abstract": "New mutations provide the raw material for evolution and adaptation. The distribution of fitness effects (DFE) describes the spectrum of effects of new mutations that can occur along a genome, and is, therefore, of vital interest in evolutionary biology. Recent work has uncovered striking similarities in the DFE between closely related species, prompting us to ask whether there is variation in the DFE among populations of the same species, or among species with different degrees of divergence, that is whether there is variation in the DFE at different levels of evolution. Using exome capture data from six tree species sampled across Europe we characterized the DFE for multiple species, and for each species, multiple populations, and investigated the factors potentially influencing the DFE, such as demography, population divergence, and genetic background. We find statistical support for the presence of variation in the DFE at the species level, even among relatively closely related species. However, we find very little difference at the population level, suggesting that differences in the DFE are primarily driven by deep features of species biology, and those evolutionarily recent events, such as demographic changes and local adaptation, have little impact.", "doi": "10.1093/molbev/msad228", "pmid": "37832225", "labels": {"Jennifer James": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC10630145"}, {"db": "pii", "key": "7313554"}], "notes": [], "created": "2023-12-04T08:37:18.774Z", "modified": "2026-09-23T11:07:15.154Z"}, {"entity": "publication", "iuid": "7d942355294b4b20a4b2ab4bfe5c98ab", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/7d942355294b4b20a4b2ab4bfe5c98ab.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/7d942355294b4b20a4b2ab4bfe5c98ab"}}, "title": "SRCAP mutations drive clonal hematopoiesis through epigenetic and DNA repair dysregulation.", "authors": [{"family": "Chen", "given": "Chun-Wei", "initials": "CW"}, {"family": "Zhang", "given": "Linda", "initials": "L", "orcid": "0000-0001-9552-3848", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/92213aa004e349f09baf5440c791897e.json"}}, {"family": "Dutta", "given": "Ravi", "initials": "R"}, {"family": "Niroula", "given": "Abhishek", "initials": "A", "orcid": "0000-0002-5904-0635", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/05df7afc7a494ba5af8a378e5ffa53f0.json"}}, {"family": "Miller", "given": "Peter G", "initials": "PG", "orcid": "0000-0002-6797-9335", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0abfb0f5d3fb419dbcfc03afa2885d41.json"}}, {"family": "Gibson", "given": "Christopher J", "initials": "CJ", "orcid": "0000-0002-3700-5310", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/71ce9f64755e483496f8c28a76a2a1ff.json"}}, {"family": "Bick", "given": "Alexander G", "initials": "AG", "orcid": "0000-0001-5824-9595", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d2da5a35a4984921b19dfafe64cea2de.json"}}, {"family": "Reyes", "given": "Jaime M", "initials": "JM"}, {"family": "Lee", "given": "Yi-Tang", "initials": "YT"}, {"family": "Tovy", "given": "Ayala", "initials": "A"}, {"family": "Gu", "given": "Tianpeng", "initials": "T"}, {"family": "Waldvogel", "given": "Sarah", "initials": "S"}, {"family": "Chen", "given": "Yi-Hung", "initials": "YH"}, {"family": "Venters", "given": "Bryan J", "initials": "BJ"}, {"family": "Est\u00e8ve", "given": "Pierre-Olivier", "initials": "PO"}, {"family": "Pradhan", "given": "Sriharsa", "initials": "S"}, {"family": "Keogh", "given": "Michael-Christopher", "initials": "MC"}, {"family": "Natarajan", "given": "Pradeep", "initials": "P", "orcid": "0000-0001-8402-7435", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fe8bd48c61c047cd8e61c35d9e9ac650.json"}}, {"family": "Takahashi", "given": "Koichi", "initials": "K"}, {"family": "Sperling", "given": "Adam S", "initials": "AS", "orcid": "0000-0002-9369-4413", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b8fef41b72dd464f9f0e46ddcd0a2434.json"}}, {"family": "Goodell", "given": "Margaret A", "initials": "MA"}], "type": "journal article", "published": "2023-11-02", "journal": {"title": "Cell Stem Cell", "issn": "1875-9777", "volume": "30", "issue": "11", "pages": "1503-1519.e8", "issn-l": null}, "abstract": "Somatic mutations accumulate in all cells with age and can confer a selective advantage, leading to clonal expansion over time. In hematopoietic cells, mutations in a subset of genes regulating DNA repair or epigenetics frequently lead to clonal hematopoiesis (CH). Here, we describe the context and mechanisms that lead to enrichment of hematopoietic stem cells (HSCs) with mutations in SRCAP, which encodes a chromatin remodeler that also influences DNA repair. We show that SRCAP mutations confer a selective advantage in human cells and in mice upon treatment with the anthracycline-class chemotherapeutic doxorubicin and bone marrow transplantation. Furthermore, Srcap mutations lead to a lymphoid-biased expansion, driven by loss of SRCAP-regulated H2A.Z deposition and increased DNA repair. Altogether, we demonstrate that SRCAP operates at the intersection of multiple pathways in stem and progenitor cells, offering a new perspective on the functional impact of genetic variants that promote stem cell competition in the hematopoietic system.", "doi": "10.1016/j.stem.2023.09.011", "pmid": "37863054", "labels": {"Abhishek Niroula": null, "DDLS Fellow": null}, "xrefs": [{"db": "pii", "key": "S1934-5909(23)00358-2"}], "notes": [], "created": "2023-11-20T11:39:42.101Z", "modified": "2025-04-11T07:24:15.568Z"}, {"entity": "publication", "iuid": "08fa1459a350410ba363f0fd630ae6d5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/08fa1459a350410ba363f0fd630ae6d5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/08fa1459a350410ba363f0fd630ae6d5"}}, "title": "Host Phylogeny Structures the Gut Bacterial Community Within Galerucella Leaf Beetles.", "authors": [{"family": "An", "given": "Yueqing", "initials": "Y"}, {"family": "Braga", "given": "Mariana P", "initials": "MP"}, {"family": "Garcia", "given": "Sarahi L", "initials": "SL"}, {"family": "Grudzinska-Sterno", "given": "Magdalena", "initials": "M"}, {"family": "Hamb\u00e4ck", "given": "Peter A", "initials": "PA"}], "type": "journal article", "published": "2023-11-00", "journal": {"title": "Microb. Ecol.", "issn": "1432-184X", "volume": "86", "issue": "4", "pages": "2477-2487", "issn-l": "0095-3628"}, "abstract": "Gut microbes play important roles for their hosts. Previous studies suggest that host-microbial systems can form long-term associations over evolutionary time and the dynamic changes of the intestinal system may represent major driving forces and contribute to insect dietary diversification and speciation. Our study system includes a set of six closely related leaf beetle species (Galerucella spp.) and our study aims to separate the roles of host phylogeny and ecology in determining the gut microbial community and to identify eventual relationship between host insects and gut bacteria. We collected adult beetles from their respective host plants and quantified their microbial community using 16S rRNA sequencing. The results showed that the gut bacteria community composition was structured by host beetle phylogeny, where more or less host-specific gut bacteria interact with the different Galerucella species. For example, the endosymbiotic bacteria Wolbachia was found almost exclusively in G. nymphaea and G. sagittariae. Diversity indicators also suggested that \u03b1- and \u03b2-diversities of gut bacteria communities varied among host beetle species. Overall, our results suggest a phylogenetically controlled co-occurrence pattern between the six closely related Galerucella beetles and their gut bacteria, indicating the potential of co-evolutionary processes occurring between hosts and their gut bacterial communities.", "doi": "10.1007/s00248-023-02251-5", "pmid": "37314477", "labels": {"SciLifeLab Fellow": "", "Sarahi Garcia": "", "Mariana Pires Braga": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC10640405"}, {"db": "pii", "key": "10.1007/s00248-023-02251-5"}], "notes": [], "created": "2023-11-01T07:09:08.860Z", "modified": "2026-09-23T12:12:01.096Z"}, {"entity": "publication", "iuid": "824c14ef7ba444bbba442e1e23032c40", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/824c14ef7ba444bbba442e1e23032c40.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/824c14ef7ba444bbba442e1e23032c40"}}, "title": "Functional and molecular profiling of hematopoietic stem cells during regeneration.", "authors": [{"family": "Rydstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Grahn", "given": "Tan H M", "initials": "THM", "orcid": "0000-0002-4737-4320", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2dd4d05a5728436bb7347e2d94df7469.json"}}, {"family": "Niroula", "given": "Abhishek", "initials": "A", "orcid": "0000-0002-5904-0635", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/05df7afc7a494ba5af8a378e5ffa53f0.json"}}, {"family": "Mansell", "given": "Els", "initials": "E"}, {"family": "van der Garde", "given": "Mark", "initials": "M"}, {"family": "Pertesi", "given": "Maroulio", "initials": "M", "orcid": "0000-0002-4869-8925", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1395ddcc49604bc1a05ea52f7b1ad79a.json"}}, {"family": "Subramaniam", "given": "Agatheeswaran", "initials": "A"}, {"family": "Soneji", "given": "Shamit", "initials": "S"}, {"family": "Zubarev", "given": "Roman", "initials": "R"}, {"family": "Enver", "given": "Tariq", "initials": "T"}, {"family": "Nilsson", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-5542-0254", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2e9df5bbe6f948b196a65176963748c8.json"}}, {"family": "Miharada", "given": "Kenichi", "initials": "K"}, {"family": "Larsson", "given": "Jonas", "initials": "J"}, {"family": "Karlsson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-2353-2531", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/78905b5834b44e8982484b2a910f476d.json"}}], "type": "journal article", "published": "2023-11-00", "journal": {"title": "Exp. Hematol.", "issn": "1873-2399", "volume": "127", "pages": "40-51", "issn-l": "0301-472X"}, "abstract": "Hematopoietic stem cells (HSCs) enable hematopoietic stem cell transplantation (HCT) through their ability to replenish the entire blood system. Proliferation of HSCs is linked to decreased reconstitution potential, and a precise regulation of actively dividing HSCs is thus essential to ensure long-term functionality. This regulation becomes important in the transplantation setting where HSCs undergo proliferation followed by a gradual transition to quiescence and homeostasis. Although mouse HSCs have been well studied under homeostatic conditions, the mechanisms regulating HSC activation under stress remain unclear. Here, we analyzed the different phases of regeneration after transplantation. We isolated bone marrow from mice at 8 time points after transplantation and examined the reconstitution dynamics and transcriptional profiles of stem and progenitor populations. We found that regenerating HSCs initially produced rapidly expanding progenitors and displayed distinct changes in fatty acid metabolism and glycolysis. Moreover, we observed molecular changes in cell cycle, MYC and mTOR signaling in both HSCs, and progenitor subsets. We used a decay rate model to fit the temporal transcription profiles of regenerating HSCs and identified genes with progressively decreased or increased expression after transplantation. These genes overlapped to a large extent with published gene sets associated with key aspects of HSC function, demonstrating the potential of this data set as a resource for identification of novel HSC regulators. Taken together, our study provides a detailed functional and molecular characterization of HSCs at different phases of regeneration and identifies a gene set associated with the transition from proliferation to quiescence.", "doi": "10.1016/j.exphem.2023.08.010", "pmid": "37666355", "labels": {"Abhishek Niroula": null, "DDLS Fellow": null}, "xrefs": [{"db": "pii", "key": "S0301-472X(23)01700-9"}], "notes": [], "created": "2023-11-20T11:39:40.893Z", "modified": "2025-04-11T07:24:56.095Z"}, {"entity": "publication", "iuid": "f7bf0dc0c9004aa49322742f07c120d5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f7bf0dc0c9004aa49322742f07c120d5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f7bf0dc0c9004aa49322742f07c120d5"}}, "title": "Artificial intelligence for natural product drug discovery.", "authors": [{"family": "Mullowney", "given": "Michael W", "initials": "MW", "orcid": "0000-0002-2884-4307", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8476ba2bc9314aad807a40d831242b75.json"}}, {"family": "Duncan", "given": "Katherine R", "initials": "KR", "orcid": "0000-0002-3670-4849", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d2e9739747a4491a95fbed8d68ce40fc.json"}}, {"family": "Elsayed", "given": "Somayah S", "initials": "SS", "orcid": "0000-0003-3837-6137", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1f561b9b107b4795a3c172909b70bca2.json"}}, {"family": "Garg", "given": "Neha", "initials": "N", "orcid": "0000-0002-2760-7123", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c0a283a6f9c04dfa98f0649b0f85051d.json"}}, {"family": "van der Hooft", "given": "Justin J J", "initials": "JJJ", "orcid": "0000-0002-9340-5511", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5c3918b083fe4b31bfe49c2e2e7fcd07.json"}}, {"family": "Martin", "given": "Nathaniel I", "initials": "NI", "orcid": "0000-0001-8246-3006", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ac5e6d2689244197a3f3c3e38bff0d34.json"}}, {"family": "Meijer", "given": "David", "initials": "D", "orcid": "0000-0001-6406-4394", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3bb3234e29e24d93847698b8e911b0c5.json"}}, {"family": "Terlouw", "given": "Barbara R", "initials": "BR", "orcid": "0000-0002-4058-6718", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fb81ee96959d4808a7d3ba3806b18c0b.json"}}, {"family": "Biermann", "given": "Friederike", "initials": "F", "orcid": "0000-0002-9152-2562", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/108a3b323641477293ff28c5525afad8.json"}}, {"family": "Blin", "given": "Kai", "initials": "K", "orcid": "0000-0003-3764-6051", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f23a8d665db44e6a8acf61b0fd5b2fbe.json"}}, {"family": "Durairaj", "given": "Janani", "initials": "J", "orcid": "0000-0002-1698-4556", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bbc37e3024a34e18b93c50bd7ce6c3a7.json"}}, {"family": "Gorostiola Gonz\u00e1lez", "given": "Marina", "initials": "M", "orcid": "0000-0003-1568-0881", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/88e4e7a563dd4687ad099c0b7708fd11.json"}}, {"family": "Helfrich", "given": "Eric J N", "initials": "EJN", "orcid": "0000-0001-8751-3279", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a4f09854b1ec488e8b2ef6dfda71e25b.json"}}, {"family": "Huber", "given": "Florian", "initials": "F", "orcid": "0000-0002-3535-9406", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e7c22c2954074f2da5fcaa7fc9f0a699.json"}}, {"family": "Leopold-Messer", "given": "Stefan", "initials": "S", "orcid": "0000-0003-3490-3550", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7a1b54ff23ae4c579fed531ff72ce940.json"}}, {"family": "Rajan", "given": "Kohulan", "initials": "K", "orcid": "0000-0003-1066-7792", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/98a81c8d47dc4e8a9ae1a85105705e39.json"}}, {"family": "de Rond", "given": "Tristan", "initials": "T", "orcid": "0000-0002-5203-4662", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f4bcb3518fd9488d8df8a867dcb63526.json"}}, {"family": "van Santen", "given": "Jeffrey A", "initials": "JA"}, {"family": "Sorokina", "given": "Maria", "initials": "M", "orcid": "0000-0001-9359-7149", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cfb01cbc08b34f219caa9dab8150f3b0.json"}}, {"family": "Balunas", "given": "Marcy J", "initials": "MJ", "orcid": "0000-0003-2374-4048", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8c79210140b548b38bf9645e0f188c8b.json"}}, {"family": "Beniddir", "given": "Mehdi A", "initials": "MA", "orcid": "0000-0003-2153-4290", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7c75378915464d5cac9e27ca3b6da03a.json"}}, {"family": "van Bergeijk", "given": "Doris A", "initials": "DA", "orcid": "0000-0002-2316-920X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/75fe47dab34b48ed904dc6c1c34bded8.json"}}, {"family": "Carroll", "given": "Laura M", "initials": "LM", "orcid": "0000-0002-3677-0192", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02112eccb0664819af916a3c3dc79daa.json"}}, {"family": "Clark", "given": "Chase M", "initials": "CM", "orcid": "0000-0001-6439-9397", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/298f837e473d401a8e251f1d98c14365.json"}}, {"family": "Clevert", "given": "Djork-Arn\u00e9", "initials": "DA", "orcid": "0000-0003-4191-2156", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b2776b6cae0a4cdca185f32d38b7ee15.json"}}, {"family": "Dejong", "given": "Chris A", "initials": "CA"}, {"family": "Du", "given": "Chao", "initials": "C"}, {"family": "Ferrinho", "given": "Scarlet", "initials": "S", "orcid": "0000-0002-9621-848X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e98ba36db9a44567a4b3dedab1e21848.json"}}, {"family": "Grisoni", "given": "Francesca", "initials": "F", "orcid": "0000-0001-8552-6615", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/08cbe22fd6e54fd299b4b75fbf43234f.json"}}, {"family": "Hofstetter", "given": "Albert", "initials": "A"}, {"family": "Jespers", "given": "Willem", "initials": "W"}, {"family": "Kalinina", "given": "Olga V", "initials": "OV", "orcid": "0000-0002-9445-477X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/180c720541634ea89321400f525e3a98.json"}}, {"family": "Kautsar", "given": "Satria A", "initials": "SA"}, {"family": "Kim", "given": "Hyunwoo", "initials": "H", "orcid": "0000-0003-2473-8360", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e89727ab51434f5eb83ddd4c4442a243.json"}}, {"family": "Leao", "given": "Tiago F", "initials": "TF"}, {"family": "Masschelein", "given": "Joleen", "initials": "J", "orcid": "0000-0003-4366-3675", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/68757738a6db412e9c760724170692ad.json"}}, {"family": "Rees", "given": "Evan R", "initials": "ER"}, {"family": "Reher", "given": "Raphael", "initials": "R", "orcid": "0000-0002-5858-1173", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cc11dc4aedfd4bf4a0583a48f1e1df4b.json"}}, {"family": "Reker", "given": "Daniel", "initials": "D", "orcid": "0000-0003-4789-7380", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/05b760d4547d4dedbe9e5a831201fc51.json"}}, {"family": "Schwaller", "given": "Philippe", "initials": "P"}, {"family": "Segler", "given": "Marwin", "initials": "M"}, {"family": "Skinnider", "given": "Michael A", "initials": "MA", "orcid": "0000-0002-2168-1621", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7b079f1236994be9885ad7f4a63b3af6.json"}}, {"family": "Walker", "given": "Allison S", "initials": "AS"}, {"family": "Willighagen", "given": "Egon L", "initials": "EL", "orcid": "0000-0001-7542-0286", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f6af0a094c4a4ac1ab7fa07c7363ee21.json"}}, {"family": "Zdrazil", "given": "Barbara", "initials": "B", "orcid": "0000-0001-9395-1515", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3ac81e512aaf49b984436e937493c700.json"}}, {"family": "Ziemert", "given": "Nadine", "initials": "N"}, {"family": "Goss", "given": "Rebecca J M", "initials": "RJM", "orcid": "0000-0001-9869-8205", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dd29853db52140e882865026de922027.json"}}, {"family": "Guyomard", "given": "Pierre", "initials": "P", "orcid": "0000-0003-3130-2258", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/424fcafc98354278b73bc0354b8ef328.json"}}, {"family": "Volkamer", "given": "Andrea", "initials": "A"}, {"family": "Gerwick", "given": "William H", "initials": "WH"}, {"family": "Kim", "given": "Hyun Uk", "initials": "HU", "orcid": "0000-0001-7224-642X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/238c901ce2094f32903057b5a528c3a9.json"}}, {"family": "M\u00fcller", "given": "Rolf", "initials": "R", "orcid": "0000-0002-1042-5665", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/692f22b3ace7461da94881ca5829e8ab.json"}}, {"family": "van Wezel", "given": "Gilles P", "initials": "GP", "orcid": "0000-0003-0341-1561", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a5e3130ec34449cfbe63f74d618c2c0e.json"}}, {"family": "van Westen", "given": "Gerard J P", "initials": "GJP", "orcid": "0000-0003-0717-1817", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b487ce42d3ad4be795b97d3d41f95357.json"}}, {"family": "Hirsch", "given": "Anna K H", "initials": "AKH", "orcid": "0000-0001-8734-4663", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b306c036449c450c9fc51e8667544a2f.json"}}, {"family": "Linington", "given": "Roger G", "initials": "RG", "orcid": "0000-0003-1818-4971", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5c7ec1488df44dde8ae1df59459a7120.json"}}, {"family": "Robinson", "given": "Serina L", "initials": "SL", "orcid": "0000-0001-6947-7913", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/258518282d5f43268420a8bf71ddccd8.json"}}, {"family": "Medema", "given": "Marnix H", "initials": "MH", "orcid": "0000-0002-2191-2821", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/162de2f7977b43d89c6686361daa4fc4.json"}}], "type": "journal article", "published": "2023-11-00", "journal": {"title": "Nat Rev Drug Discov", "issn": "1474-1784", "volume": "22", "issue": "11", "pages": "895-916", "issn-l": "1474-1776"}, "abstract": "Developments in computational omics technologies have provided new means to access the hidden diversity of natural products, unearthing new potential for drug discovery. In parallel, artificial intelligence approaches such as machine learning have led to exciting developments in the computational drug design field, facilitating biological activity prediction and de novo drug design for molecular targets of interest. Here, we describe current and future synergies between these developments to effectively identify drug candidates from the plethora of molecules produced by nature. We also discuss how to address key challenges in realizing the potential of these synergies, such as the need for high-quality datasets to train deep learning algorithms and appropriate strategies for algorithm validation.", "doi": "10.1038/s41573-023-00774-7", "pmid": "37697042", "labels": {"Laura Carroll": null, "DDLS Fellow": null}, "xrefs": [{"db": "pii", "key": "10.1038/s41573-023-00774-7"}], "notes": [], "created": "2025-03-18T17:31:25.070Z", "modified": "2025-03-18T17:31:26.821Z"}, {"entity": "publication", "iuid": "8e1ca614783248468e5af9a7c8525f3c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8e1ca614783248468e5af9a7c8525f3c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8e1ca614783248468e5af9a7c8525f3c"}}, "title": "A data-driven framework to model the organism-environment system.", "authors": [{"family": "Milocco", "given": "Lisandro", "initials": "L", "orcid": "0000-0003-3953-0407", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/74f9e4dfff0e4b008c46b75e3d319673.json"}}, {"family": "Uller", "given": "Tobias", "initials": "T", "orcid": "0000-0003-1293-5842", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/63799fa606284069a4ccf960795749e8.json"}}], "type": "journal article", "published": "2023-11-00", "journal": {"title": "Evol Dev", "issn": "1525-142X", "volume": "25", "issue": "6", "pages": "439-450", "issn-l": null}, "abstract": "Organisms modify their development and function in response to the environment. At the same time, the environment is modified by the activities of the organism. Despite the ubiquity of such dynamical interactions in nature, it remains challenging to develop models that accurately represent them, and that can be fitted using data. These features are desirable when modeling phenomena such as phenotypic plasticity, to generate quantitative predictions of how the system will respond to environmental signals of different magnitude or at different times, for example, during ontogeny. Here, we explain a modeling framework that represents the organism and environment as a single coupled dynamical system in terms of inputs and outputs. Inputs are external signals, and outputs are measurements of the system in time. The framework uses time-series data of inputs and outputs to fit a nonlinear black-box model that allows to predict how the system will respond to novel input signals. The framework has three key properties: it captures the dynamical nature of the organism-environment system, it can be fitted with data, and it can be applied without detailed knowledge of the system. We study phenotypic plasticity using in silico experiments and demonstrate that the framework predicts the response to novel environmental signals. The framework allows us to model plasticity as a dynamical property that changes in time during ontogeny, reflecting the well-known fact that organisms are more or less plastic at different developmental stages.", "doi": "10.1111/ede.12449", "pmid": "37277921", "labels": {"DDLS Fellow": null, "Lisandro Milocco": null}, "xrefs": [], "notes": [], "created": "2025-11-28T14:28:29.457Z", "modified": "2025-11-28T14:29:07.061Z"}, {"entity": "publication", "iuid": "7472b08ff92e401f907b54144ee97ed0", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/7472b08ff92e401f907b54144ee97ed0.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/7472b08ff92e401f907b54144ee97ed0"}}, "title": "Circulation of enterotoxigenic Escherichia coli (ETEC) isolates expressing CS23 from the environment to clinical settings.", "authors": [{"family": "Calderon Toledo", "given": "Carla", "initials": "C", "orcid": "0000-0001-9483-9891", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b8c67b3b7435453396d0fd62636838e3.json"}}, {"family": "von Mentzer", "given": "Astrid", "initials": "A", "orcid": "0000-0002-2167-1394", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/36cefe255ba14d8684826fae58598036.json"}}, {"family": "Agramont", "given": "Jorge", "initials": "J"}, {"family": "Thorell", "given": "Kaisa", "initials": "K", "orcid": "0000-0002-4447-8968", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/789d4029a5c14d3c83df7c47b3b514c7.json"}}, {"family": "Zhou", "given": "Yingshun", "initials": "Y"}, {"family": "Szab\u00f3", "given": "Mikl\u00f3s", "initials": "M"}, {"family": "Colque", "given": "Patricia", "initials": "P"}, {"family": "Kuhn", "given": "Inger", "initials": "I"}, {"family": "Guti\u00e9rrez-Cortez", "given": "Sergio", "initials": "S", "orcid": "0000-0001-6181-6554", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4ef7d00721e143df9ae40299cb131fff.json"}}, {"family": "Joffr\u00e9", "given": "Enrique", "initials": "E", "orcid": "0000-0003-0328-518X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d0a7d88da85f4dbfab455ac2df10a8de.json"}}], "type": "journal article", "published": "2023-10-26", "journal": {"title": "mSystems", "issn": "2379-5077", "volume": "8", "issue": "5", "pages": "e0014123", "issn-l": "2379-5077"}, "abstract": "The importance of clean water cannot be overstated. It is a vital resource for maintaining health and well-being. Unfortunately, water sources contaminated with fecal discharges from animal and human origin due to a lack of wastewater management pose a significant risk to communities, as they can become a means of transmission of pathogenic bacteria like enterotoxigenic E. coli (ETEC). ETEC is frequently found in polluted water in countries with a high prevalence of diarrheal diseases, such as Bolivia. This study provides novel insights into the circulation of ETEC between diarrheal cases and polluted water sources in areas with high rates of diarrheal disease. These findings highlight the Choqueyapu River as a potential reservoir for emerging pathogens carrying antibiotic-resistance genes, making it a crucial area for monitoring and intervention. Furthermore, the results demonstrate the feasibility of a low-cost, high-throughput method for tracking bacterial pathogens in low- and middle-income countries, making it a valuable tool for One Health monitoring efforts.", "doi": "10.1128/msystems.00141-23", "pmid": "37681982", "labels": {"Astrid von Mentzer": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC10654058"}], "notes": [], "created": "2025-12-02T15:47:10.590Z", "modified": "2025-12-02T15:47:10.700Z"}, {"entity": "publication", "iuid": "85647eabbe644ebf93336f6e2534b98b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/85647eabbe644ebf93336f6e2534b98b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/85647eabbe644ebf93336f6e2534b98b"}}, "title": "Peptide binder design with inverse folding and protein structure prediction.", "authors": [{"family": "Bryant", "given": "Patrick", "initials": "P", "orcid": "0000-0003-3439-1866", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a683bcf98234ff09b2398976583b66f.json"}}, {"family": "Elofsson", "given": "Arne", "initials": "A", "orcid": "0000-0002-7115-9751", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/248e70e81bd64f31a5f83e6e329bba95.json"}}], "type": "journal article", "published": "2023-10-25", "journal": {"title": "Commun Chem", "issn": "2399-3669", "volume": "6", "issue": "1", "pages": "229", "issn-l": null}, "abstract": "The computational design of peptide binders towards a specific protein interface can aid diagnostic and therapeutic efforts. Here, we design peptide binders by combining the known structural space searched with Foldseek, the protein design method ESM-IF1, and AlphaFold2 (AF) in a joint framework. Foldseek generates backbone seeds for a modified version of ESM-IF1 adapted to protein complexes. The resulting sequences are evaluated with AF using an MSA representation for the receptor structure and a single sequence for the binder. We show that AF can accurately evaluate protein binders and that our bind score can select these (ROC AUC = 0.96 for the heterodimeric case). We find that designs created from seeds with more contacts per residue are more successful and tend to be short. There is a relationship between the sequence recovery in interface positions and the plDDT of the designs, where designs with \u226580% recovery have an average plDDT of 84 compared to 55 at 0%. Designed sequences have 60% higher median plDDT values towards intended receptors than non-intended ones. Successful binders (predicted interface RMSD \u2264 2 \u00c5) are designed towards 185 (6.5%) heteromeric and 42 (3.6%) homomeric protein interfaces with ESM-IF1 compared with 18 (1.5%) using ProteinMPNN from 100 samples.", "doi": "10.1038/s42004-023-01029-7", "pmid": "37880344", "labels": {"Patrick Bryant": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC10600234"}, {"db": "pii", "key": "10.1038/s42004-023-01029-7"}], "notes": [], "created": "2026-08-20T09:25:36.744Z", "modified": "2026-09-23T08:54:48.010Z"}, {"entity": "publication", "iuid": "f5e0c130e1784f818079a60a79ae857f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f5e0c130e1784f818079a60a79ae857f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f5e0c130e1784f818079a60a79ae857f"}}, "title": "aMeta: an accurate and memory-efficient ancient metagenomic profiling workflow.", "authors": [{"family": "Pochon", "given": "Zo\u00e9", "initials": "Z", "orcid": "0000-0001-7981-5795", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/86bda59888834d6889a108f8abbdb0fa.json"}}, {"family": "Bergfeldt", "given": "Nora", "initials": "N", "orcid": "0000-0003-2767-8156", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9141014a18c54129b99af1006ff76f9b.json"}}, {"family": "K\u0131rd\u00f6k", "given": "Emrah", "initials": "E", "orcid": "0000-0003-0500-1208", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3a60c96525a642b4be97e15a53de250b.json"}}, {"family": "Vicente", "given": "M\u00e1rio", "initials": "M", "orcid": "0000-0002-9122-4530", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/70f79b138afe4df99b780eb97ebdbc13.json"}}, {"family": "Naidoo", "given": "Thijessen", "initials": "T"}, {"family": "van der Valk", "given": "Tom", "initials": "T", "orcid": "0000-0001-6582-3452", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/aa0dba3cc12143cba213f7f3a052216c.json"}}, {"family": "Alt\u0131n\u0131\u015f\u0131k", "given": "N Ezgi", "initials": "NE", "orcid": "0000-0003-0653-4292", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f06df27a24874d5e9b11db34a31730d1.json"}}, {"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M", "orcid": "0000-0002-6702-8724", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02faff0c060a4c25a13a9c7556dd30c3.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6ff87fd5aabe4a38954dd96d8e6c261d.json"}}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-8579-1304", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0c4e61575ab14fe3aa59190a82521921.json"}}, {"family": "Mirabello", "given": "Claudio", "initials": "C", "orcid": "0000-0001-7868-034X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f4ca88bb3cf24e2591c447ec929502e6.json"}}, {"family": "Unneberg", "given": "Per", "initials": "P", "orcid": "0000-0001-5735-3315", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/47dae455224d4af4a35865907088f0b1.json"}}, {"family": "Oskolkov", "given": "Nikolay", "initials": "N", "orcid": "0000-0001-5326-8893", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3c448f1b878442c687d58549f90ba4e9.json"}}], "type": "journal article", "published": "2023-10-23", "journal": {"title": "Genome Biol.", "issn": "1474-760X", "issn-l": "1474-7596", "volume": "24", "issue": "1", "pages": "242"}, "abstract": "Analysis of microbial data from archaeological samples is a growing field with great potential for understanding ancient environments, lifestyles, and diseases. However, high error rates have been a challenge in ancient metagenomics, and the availability of computational frameworks that meet the demands of the field is limited. Here, we propose aMeta, an accurate metagenomic profiling workflow for ancient DNA designed to minimize the amount of false discoveries and computer memory requirements. Using simulated data, we benchmark aMeta against a current state-of-the-art workflow and demonstrate its superiority in microbial detection and authentication, as well as substantially lower usage of computer memory.", "doi": "10.1186/s13059-023-03083-9", "pmid": "37872569", "labels": {"Tom van der Valk": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC10591440"}, {"db": "pii", "key": "10.1186/s13059-023-03083-9"}], "notes": [], "created": "2022-12-02T13:45:21.283Z", "modified": "2026-09-23T08:42:42.775Z"}, {"entity": "publication", "iuid": "50762128607b4f2ca31bdaec4929010e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/50762128607b4f2ca31bdaec4929010e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/50762128607b4f2ca31bdaec4929010e"}}, "title": "Inference of drug off-target effects on cellular signaling using Interactome-Based Deep Learning", "authors": [{"family": "Meimetis", "given": "Nikolaos", "initials": "N", "orcid": "0000-0003-2333-0187", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e0e968cb5cc44b52818647cea77762d9.json"}}, {"family": "Lauffenburger", "given": "Douglas A", "initials": "DA"}, {"family": "Nilsson", "given": "Avlant", "initials": "A", "orcid": "0000-0002-9476-4516", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f2e21dbc1c624f6a841c59e959e948e4.json"}}], "type": "posted-content", "published": "2023-10-10", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2023.10.08.561429", "pmid": null, "labels": {"Avlant Nilsson": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T10:48:20.517Z", "modified": "2026-09-23T15:29:43.371Z"}, {"entity": "publication", "iuid": "8a10bbd111a14f20ba4904d7c4592166", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8a10bbd111a14f20ba4904d7c4592166.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8a10bbd111a14f20ba4904d7c4592166"}}, "title": "Sex-Specific Associations between Adiponectin and Leptin Signaling and Pancreatic Cancer Survival.", "authors": [{"family": "Babic", "given": "Ana", "initials": "A", "orcid": "0000-0003-1199-5958", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a3b7f71f0bf4058a8aed3acc297e34c.json"}}, {"family": "Wang", "given": "Qiao-Li", "initials": "QL", "orcid": "0000-0003-4152-7821", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/357edb3116b64ad5aa929dcb7d07a1be.json"}}, {"family": "Lee", "given": "Alice A", "initials": "AA", "orcid": "0000-0002-5241-1878", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bd79d5f5ddba4406b54cdc2bbb81a288.json"}}, {"family": "Yuan", "given": "Chen", "initials": "C", "orcid": "0000-0002-0708-9648", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cd3904c835394e0d89bba633a0b74c54.json"}}, {"family": "Rifai", "given": "Nader", "initials": "N", "orcid": "0000-0003-0706-2477", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ab4f3063ee7445fc86878f1216702ca4.json"}}, {"family": "Luo", "given": "Juhua", "initials": "J", "orcid": "0000-0002-8901-4462", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/73e0c8ed86ed4e80956e97e9f77c79b9.json"}}, {"family": "Tabung", "given": "Fred K", "initials": "FK", "orcid": "0000-0001-8193-7150", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8ff9aff2493d4cd7918706ac46f32c52.json"}}, {"family": "Shadyab", "given": "Aladdin H", "initials": "AH", "orcid": "0000-0002-9693-0522", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/72d783e4f9dd445a81a6d3eac3731c5d.json"}}, {"family": "Wactawski-Wende", "given": "Jean", "initials": "J", "orcid": "0000-0003-3096-9595", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b129d0b9a9654fc5be2db957c5bb5f0b.json"}}, {"family": "Saquib", "given": "Nazmus", "initials": "N", "orcid": "0000-0002-2819-2839", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b28abaf966da46e392081d9e103b11c1.json"}}, {"family": "Kim", "given": "Jihye", "initials": "J", "orcid": "0000-0001-7096-820X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2eba24e7e4f74a2daab62926a94fa485.json"}}, {"family": "Kraft", "given": "Peter", "initials": "P", "orcid": "0000-0002-4472-8103", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d44ae97bc78b4ce2aec4bee2432b70c6.json"}}, {"family": "Sesso", "given": "Howard D", "initials": "HD", "orcid": "0000-0002-9698-9954", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/16b49d081cba4870b59b6c7a9230b77d.json"}}, {"family": "Buring", "given": "Julie E", "initials": "JE", "orcid": "0000-0003-2648-8692", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8efad4a60f5e4567950fd64338329561.json"}}, {"family": "Giovannucci", "given": "Edward L", "initials": "EL", "orcid": "0000-0002-6123-0219", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4958abe8f85b417cae3009a782e9f69d.json"}}, {"family": "Manson", "given": "JoAnn E", "initials": "JE", "orcid": "0000-0002-9426-7595", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6e39f122c5fd4f0ea0dcf2353ed4a274.json"}}, {"family": "Stampfer", "given": "Meir J", "initials": "MJ", "orcid": "0000-0001-8865-935X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8c7bbba94f5c43fd897f20001faa7a18.json"}}, {"family": "Ng", "given": "Kimmie", "initials": "K", "orcid": "0000-0003-0631-1494", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/00bc0d97cfc44e9398c9bf1db5783402.json"}}, {"family": "Fuchs", "given": "Charles S", "initials": "CS", "orcid": "0000-0003-1582-9842", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4dd3b36e3b444d5b890959320a879830.json"}}, {"family": "Wolpin", "given": "Brian M", "initials": "BM", "orcid": "0000-0002-0455-1032", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/90c86221350a45c1a398d089855e7dac.json"}}], "type": "journal article", "published": "2023-10-02", "journal": {"title": "Cancer Epidemiol Biomarkers Prev", "issn": "1538-7755", "volume": "32", "issue": "10", "pages": "1458-1469", "issn-l": null}, "abstract": "Circulating adiponectin and leptin have been associated with risk of pancreatic cancer. However, the relationship between long-term exposure to these adipokines in the prediagnostic period with patient survival has not been investigated.\n\nAdipokine levels were measured in prospectively collected samples from 472 patients with pancreatic cancer. Because of sex-specific differences in adipokine levels, associations were evaluated separately for men and women. In a subset of 415 patients, we genotyped 23 SNPs in adiponectin receptor genes (ADIPOR1 and ADIPOR2) and 30 SNPs in the leptin receptor gene (LEPR).\n\nAdiponectin levels were inversely associated with survival in women [HR, 1.71; 95% confidence interval (CI), 1.15-2.54]; comparing top with bottom quartile but not in men (HR, 0.89; 95% CI, 0.46-1.70). The SNPs rs10753929 and rs1418445 in ADIPOR1 were associated with survival in the combined population (per minor allele HR, 0.66; 95% CI, 0.51-0.84, and HR, 1.33; 95% CI, 1.12-1.58, respectively). Among SNPs in LEPR, rs12025906, rs3790431, and rs17127601 were associated with survival in the combined population [HRs, 1.54 (95% CI, 1.25-1.90), 0.72 (95% CI, 0.59-0.88), and 0.70 (95% CI, 0.56-0.89), respectively], whereas rs11585329 was associated with survival in men only (HR, 0.39; 95% CI, 0.23-0.66; Pinteraction = 0.0002).\n\nHigh levels of adiponectin in the prediagnostic period were associated with shorter survival among women, but not among men with pancreatic cancer. Several polymorphisms in ADIPOR1 and LEPR are associated with patient survival.\n\nOur findings reveal the association between adipokine signaling and pancreatic cancer survival and demonstrate the importance of examining obesity-associated pathways in relation to pancreatic cancer in a sex-specific manner.", "doi": "10.1158/1055-9965.EPI-23-0505", "pmid": "37555827", "labels": {"DDLS Fellow": null, "Qiaoli Wang": null}, "xrefs": [{"db": "mid", "key": "NIHMS1925329"}, {"db": "pmc", "key": "PMC10592159"}, {"db": "pii", "key": "728394"}], "notes": [], "created": "2025-11-28T12:22:59.238Z", "modified": "2025-11-28T12:22:59.759Z"}, {"entity": "publication", "iuid": "244e55a1fe3f4cc689483a2f4bbe8d29", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/244e55a1fe3f4cc689483a2f4bbe8d29.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/244e55a1fe3f4cc689483a2f4bbe8d29"}}, "title": "Connectome-based modelling of neurodegenerative diseases: towards precision medicine and mechanistic insight.", "authors": [{"family": "Vogel", "given": "Jacob W", "initials": "JW"}, {"family": "Corriveau-Lecavalier", "given": "Nick", "initials": "N", "orcid": "0000-0002-6561-9870", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/61f1bca2c0d64bc4927b2d7ed4f75139.json"}}, {"family": "Franzmeier", "given": "Nicolai", "initials": "N", "orcid": "0000-0001-9736-2283", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/55b52b106c0c45ea8da2d14f52588fb3.json"}}, {"family": "Pereira", "given": "Joana B", "initials": "JB"}, {"family": "Brown", "given": "Jesse A", "initials": "JA"}, {"family": "Maass", "given": "Anne", "initials": "A"}, {"family": "Botha", "given": "Hugo", "initials": "H"}, {"family": "Seeley", "given": "William W", "initials": "WW"}, {"family": "Bassett", "given": "Dani S", "initials": "DS", "orcid": "0000-0002-6183-4493", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1df60e7e90a942ffb8e97713221f7f5e.json"}}, {"family": "Jones", "given": "David T", "initials": "DT", "orcid": "0000-0002-4807-9833", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dcc287a740324b4cbe89fdcd0c6dba04.json"}}, {"family": "Ewers", "given": "Michael", "initials": "M", "orcid": "0000-0001-5231-1714", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d2368c66c8ea44e4a04f798487a6242a.json"}}], "type": "journal article", "published": "2023-10-00", "journal": {"title": "Nat Rev Neurosci", "issn": "1471-0048", "issn-l": null, "volume": "24", "issue": "10", "pages": "620-639"}, "abstract": "Neurodegenerative diseases are the most common cause of dementia. Although their underlying molecular pathologies have been identified, there is substantial heterogeneity in the patterns of progressive brain alterations across and within these diseases. Recent advances in neuroimaging methods have revealed that pathological proteins accumulate along specific macroscale brain networks, implicating the network architecture of the brain in the system-level pathophysiology of neurodegenerative diseases. However, the extent to which 'network-based neurodegeneration' applies across the wide range of neurodegenerative disorders remains unclear. Here, we discuss the state-of-the-art of neuroimaging-based connectomics for the mapping and prediction of neurodegenerative processes. We review findings supporting brain networks as passive conduits through which pathological proteins spread. As an alternative view, we also discuss complementary work suggesting that network alterations actively modulate the spreading of pathological proteins between connected brain regions. We conclude this Perspective by proposing an integrative framework in which connectome-based models can be advanced along three dimensions of innovation: incorporating parameters that modulate propagation behaviour on the basis of measurable biological features; building patient-tailored models that use individual-level information and allowing model parameters to interact dynamically over time. We discuss promises and pitfalls of these strategies for improving disease insights and moving towards precision medicine.", "doi": "10.1038/s41583-023-00731-8", "pmid": "37620599", "labels": {"Jacob W Vogel": null, "DDLS Fellow": null}, "xrefs": [{"db": "pii", "key": "10.1038/s41583-023-00731-8"}], "notes": [], "created": "2023-10-25T16:52:17.842Z", "modified": "2023-11-29T06:41:38.564Z"}, {"entity": "publication", "iuid": "fd9b20839e3749cb9467bdb4a7da178f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/fd9b20839e3749cb9467bdb4a7da178f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/fd9b20839e3749cb9467bdb4a7da178f"}}, "title": "Blood Proteins are Associated with Aneurysm Growth in Men with Screening Detected Abdominal Aortic Aneurysm", "authors": [{"family": "Siika", "given": "Antti", "initials": "A"}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Obeberg", "given": "Jacob", "initials": "J"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Hultgren", "given": "Rebecka", "initials": "R"}, {"family": "Roy", "given": "Joy", "initials": "J"}], "type": "journal-article", "published": "2023-10-00", "journal": {"title": "Aorta (Stamford)", "issn": "2325-4637", "volume": "11", "issue": "05", "pages": "1-18", "issn-l": null}, "abstract": null, "doi": "10.1055/s-0044-1787936", "pmid": null, "labels": {"Fredrik Edfors": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T09:28:51.740Z", "modified": "2026-09-23T15:39:31.872Z"}, {"entity": "publication", "iuid": "464fe0b0bf2d4fa398acd5bbeef2b698", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/464fe0b0bf2d4fa398acd5bbeef2b698.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/464fe0b0bf2d4fa398acd5bbeef2b698"}}, "title": "Absolute Quantification of Pan-Cancer Plasma Proteomes Reveals Unique Signature in Multiple Myeloma.", "authors": [{"family": "Kotol", "given": "David", "initials": "D", "orcid": "0000-0002-5388-3826", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c41f8f491c474e6bba2047b5d04b4af5.json"}}, {"family": "Woessmann", "given": "Jakob", "initials": "J", "orcid": "0000-0002-2283-7237", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8a4b10f5f96244b98122eddcee694ec0.json"}}, {"family": "Hober", "given": "Andreas", "initials": "A"}, {"family": "\u00c1lvez", "given": "Mar\u00eda Bueno", "initials": "MB", "orcid": "0000-0002-2669-7796", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a7d09e4780a445b9b432d494c76d07e8.json"}}, {"family": "Tran Minh", "given": "Khue Hua", "initials": "KH"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/abbbf8193d5a4376a5c726768d039439.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e213b04f8984c8eb00c68f5bc2f6a36.json"}}], "type": "journal article", "published": "2023-09-28", "journal": {"title": "Cancers (Basel)", "issn": "2072-6694", "volume": "15", "issue": "19", "issn-l": "2072-6694"}, "abstract": "Mass spectrometry based on data-independent acquisition (DIA) has developed into a powerful quantitative tool with a variety of implications, including precision medicine. Combined with stable isotope recombinant protein standards, this strategy provides confident protein identification and precise quantification on an absolute scale. Here, we describe a comprehensive targeted proteomics approach to profile a pan-cancer cohort consisting of 1800 blood plasma samples representing 15 different cancer types. We successfully performed an absolute quantification of 253 proteins in multiplex. The assay had low intra-assay variability with a coefficient of variation below 20% (CV = 17.2%) for a total of 1013 peptides quantified across almost two thousand injections. This study identified a potential biomarker panel of seven protein targets for the diagnosis of multiple myeloma patients using differential expression analysis and machine learning. The combination of markers, including the complement C1 complex, JCHAIN, and CD5L, resulted in a prediction model with an AUC of 0.96 for the identification of multiple myeloma patients across various cancer patients. All these proteins are known to interact with immunoglobulins.", "doi": "10.3390/cancers15194764", "pmid": "37835457", "labels": {"DDLS Fellow": "", "Fredrik Edfors": ""}, "xrefs": [{"db": "pmc", "key": "PMC10571728"}, {"db": "pii", "key": "cancers15194764"}], "notes": [], "created": "2026-08-21T13:01:57.098Z", "modified": "2026-10-01T08:27:55.537Z"}, {"entity": "publication", "iuid": "aa4086879ab245d38e9508c4b112bd8d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/aa4086879ab245d38e9508c4b112bd8d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/aa4086879ab245d38e9508c4b112bd8d"}}, "title": "Historical Pathogen-Driven Selection May Contribute to Contemporary Ethnic Difference in Bladder Cancer Susceptibility.", "authors": [{"family": "Meng", "given": "Xiang-Yu", "initials": "XY"}, {"family": "Wang", "given": "Qiao-Li", "initials": "QL"}, {"family": "Shi", "given": "Ming-Jun", "initials": "MJ"}, {"family": "Zhang", "given": "Hong-Yu", "initials": "HY"}], "type": "journal article", "published": "2023-09-25", "journal": {"title": "Bladder Cancer", "issn": "2352-3735", "volume": "9", "issue": "3", "pages": "211-216", "issn-l": null}, "abstract": "The rationale for ethnic differences in bladder cancer (BCa) susceptibility is an important open question. In this study, we raised the hypothesis that the APOBEC3-rs1014971 variant associated with BCa risk and APOBEC-mutagenesis probably contribute to ethnic differences.\n\nWe calculated the ethnicity-stratified 5-year age-adjusted incidence rates of BCa using the US SEER database. We performed somatic mutational-signature analyses and compared the APOBEC-related mutational contribution across BCa tumors in patients of different ethnicities. We analyzed the allele frequency distribution of APOBEC3-related rs1014971 in contemporary populations of different ethnicities and in ancient human genomes. We also analyzed the natural selection profiles and ages of the investigated SNPs.\n\nWe validated the ethnic difference in BCa risk using US SEER data, revealing Caucasians to be at >2-fold greater risk than Asians / Pacific islanders. In contemporary populations, we observed a coherent ethnic distribution in terms not only of the allele frequency of APOBEC3-related rs1014971, but also the mutational contribution of APOBEC-mediated mutagenesis in BCa tumors. Population genetics and ancient genome analyses further suggested that the diverse ethnic distribution of rs1014971 could be rooted in human evolution.\n\nIt is possible that APOBEC3-related rs1014971 is involved in the different BCa incidence across ethnic groups, and this difference is potentially derived from human evolution. Our findings suggested an evolutionary link between contemporary population-level variations in malignancy susceptibility and pathogen-driven selection in the past, not unlike previously reported cases of certain autoimmune and metabolic disorders.", "doi": "10.3233/BLC-230010", "pmid": "38993187", "labels": {"DDLS Fellow": null, "Qiaoli Wang": null}, "xrefs": [{"db": "pmc", "key": "PMC11181760"}, {"db": "pii", "key": "BLC230010"}], "notes": [], "created": "2025-11-28T12:22:57.992Z", "modified": "2025-11-28T12:22:58.101Z"}, {"entity": "publication", "iuid": "b0b2b27d131d474d863f0a7f04296de1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b0b2b27d131d474d863f0a7f04296de1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b0b2b27d131d474d863f0a7f04296de1"}}, "title": "Building the next generation of virtual cells to understand cellular biology.", "authors": [{"family": "Johnson", "given": "Graham T", "initials": "GT"}, {"family": "Agmon", "given": "Eran", "initials": "E"}, {"family": "Akamatsu", "given": "Matthew", "initials": "M"}, {"family": "Lundberg", "given": "Emma", "initials": "E"}, {"family": "Lyons", "given": "Blair", "initials": "B"}, {"family": "Ouyang", "given": "Wei", "initials": "W"}, {"family": "Quintero-Carmona", "given": "Omar A", "initials": "OA"}, {"family": "Riel-Mehan", "given": "Megan", "initials": "M"}, {"family": "Rafelski", "given": "Susanne", "initials": "S"}, {"family": "Horwitz", "given": "Rick", "initials": "R"}], "type": "journal article", "published": "2023-09-19", "journal": {"title": "Biophys. J.", "issn": "1542-0086", "volume": "122", "issue": "18", "pages": "3560-3569", "issn-l": "0006-3495"}, "abstract": "Cell science has made significant progress by focusing on understanding individual cellular processes through reductionist approaches. However, the sheer volume of knowledge collected presents challenges in integrating this information across different scales of space and time to comprehend cellular behaviors, as well as making the data and methods more accessible for the community to tackle complex biological questions. This perspective proposes the creation of next-generation virtual cells, which are dynamic 3D models that integrate information from diverse sources, including simulations, biophysical models, image-based models, and evidence-based knowledge graphs. These virtual cells would provide statistically accurate and holistic views of real cells, bridging the gap between theoretical concepts and experimental data, and facilitating productive new collaborations among researchers across related fields.", "doi": "10.1016/j.bpj.2023.04.006", "pmid": "37050874", "labels": {"DDLS Fellow": "", "Wei Ouyang": ""}, "xrefs": [{"db": "pmc", "key": "PMC10541477"}, {"db": "pii", "key": "S0006-3495(23)00236-9"}], "notes": [], "created": "2026-08-20T06:44:58.948Z", "modified": "2026-09-23T08:54:08.813Z"}, {"entity": "publication", "iuid": "8cd9028a4df04b1ea0d961df50c35df0", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8cd9028a4df04b1ea0d961df50c35df0.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8cd9028a4df04b1ea0d961df50c35df0"}}, "title": "Metabolite interactions in the bacterial Calvin cycle and implications for flux regulation.", "authors": [{"family": "Sporre", "given": "Emil", "initials": "E"}, {"family": "Karlsen", "given": "Jan", "initials": "J"}, {"family": "Schriever", "given": "Karen", "initials": "K", "orcid": "0000-0002-3677-5508", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/282cce0f6c054fd8a7858977be549b24.json"}}, {"family": "Asplund-Samuelsson", "given": "Johannes", "initials": "J"}, {"family": "Janasch", "given": "Markus", "initials": "M"}, {"family": "Strandberg", "given": "Linn\u00e9a", "initials": "L"}, {"family": "Karlsson", "given": "Anna", "initials": "A"}, {"family": "Kotol", "given": "David", "initials": "D", "orcid": "0000-0002-5388-3826", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c41f8f491c474e6bba2047b5d04b4af5.json"}}, {"family": "Zeckey", "given": "Luise", "initials": "L"}, {"family": "Piazza", "given": "Ilaria", "initials": "I"}, {"family": "Syr\u00e9n", "given": "Per-Olof", "initials": "PO"}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Hudson", "given": "Elton P", "initials": "EP", "orcid": "0000-0003-1899-7649", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3b1c894d4c8b48569b9879d0342b91dd.json"}}], "type": "journal article", "published": "2023-09-18", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "6", "issue": "1", "pages": "947", "issn-l": "2399-3642"}, "abstract": "Metabolite-level regulation of enzyme activity is important for microbes to cope with environmental shifts. Knowledge of such regulations can also guide strain engineering for biotechnology. Here we apply limited proteolysis-small molecule mapping (LiP-SMap) to identify and compare metabolite-protein interactions in the proteomes of two cyanobacteria and two lithoautotrophic bacteria that fix CO2 using the Calvin cycle. Clustering analysis of the hundreds of detected interactions shows that some metabolites interact in a species-specific manner. We estimate that approximately 35% of interacting metabolites affect enzyme activity in vitro, and the effect is often minor. Using LiP-SMap data as a guide, we find that the Calvin cycle intermediate glyceraldehyde-3-phosphate enhances activity of fructose-1,6/sedoheptulose-1,7-bisphosphatase (F/SBPase) from Synechocystis sp. PCC 6803 and Cupriavidus necator in reducing conditions, suggesting a convergent feed-forward activation of the cycle. In oxidizing conditions, glyceraldehyde-3-phosphate inhibits Synechocystis F/SBPase by promoting enzyme aggregation. In contrast, the glycolytic intermediate glucose-6-phosphate activates F/SBPase from Cupriavidus necator but not F/SBPase from Synechocystis. Thus, metabolite-level regulation of the Calvin cycle is more prevalent than previously appreciated.", "doi": "10.1038/s42003-023-05318-8", "pmid": "37723200", "labels": {"Paul Hudson": "", "SciLifeLab Fellow": "", "Fredrik Edfors": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC10507043"}, {"db": "pii", "key": "10.1038/s42003-023-05318-8"}], "notes": [], "created": "2026-08-20T09:25:15.821Z", "modified": "2026-09-23T10:38:17.292Z"}, {"entity": "publication", "iuid": "b5a0d61a6cfc4bf6b3a3f14279b5d87e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b5a0d61a6cfc4bf6b3a3f14279b5d87e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b5a0d61a6cfc4bf6b3a3f14279b5d87e"}}, "title": "Plasma metabolomic profiles associated with mortality and longevity in a prospective analysis of 13,512 individuals.", "authors": [{"family": "Wang", "given": "Fenglei", "initials": "F", "orcid": "0000-0002-3850-2482", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/41a725cb032d4e2097b2c75a5b18e937.json"}}, {"family": "Tessier", "given": "Anne-Julie", "initials": "AJ", "orcid": "0000-0003-4551-1640", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/79588c2979634d5590d2545afef7bbbe.json"}}, {"family": "Liang", "given": "Liming", "initials": "L", "orcid": "0000-0001-8261-3174", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7da355304cad4309ab4dee783a341611.json"}}, {"family": "Wittenbecher", "given": "Clemens", "initials": "C"}, {"family": "Haslam", "given": "Danielle E", "initials": "DE"}, {"family": "Fern\u00e1ndez-Duval", "given": "Gonzalo", "initials": "G", "orcid": "0000-0003-0495-4437", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2c1f501068d54664aea7a909a33e8a40.json"}}, {"family": "Heather Eliassen", "given": "A", "initials": "A", "orcid": "0000-0002-3961-6609", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f288e05e7e6449be856ad8955b546ad2.json"}}, {"family": "Rexrode", "given": "Kathryn M", "initials": "KM", "orcid": "0000-0003-3387-8429", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a3600b145b304aa7959c0f85fa198192.json"}}, {"family": "Tobias", "given": "Deirdre K", "initials": "DK"}, {"family": "Li", "given": "Jun", "initials": "J", "orcid": "0000-0003-3519-8638", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/77d0c8cac07b47228b383aa851382852.json"}}, {"family": "Zeleznik", "given": "Oana", "initials": "O", "orcid": "0000-0002-8705-1163", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f6b162661d75438880a6a3248645c8ee.json"}}, {"family": "Grodstein", "given": "Francine", "initials": "F"}, {"family": "Mart\u00ednez-Gonz\u00e1lez", "given": "Miguel A", "initials": "MA"}, {"family": "Salas-Salvad\u00f3", "given": "Jordi", "initials": "J", "orcid": "0000-0003-2700-7459", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/49e886d4d7e346e1a65f949699f620a4.json"}}, {"family": "Clish", "given": "Clary", "initials": "C", "orcid": "0000-0001-8259-9245", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/25b862e77efe474ca91bce1bd96fd366.json"}}, {"family": "Lee", "given": "Kyu Ha", "initials": "KH"}, {"family": "Sun", "given": "Qi", "initials": "Q", "orcid": "0000-0002-8480-1563", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4a65407257ac4518ac5cb19317ee3b32.json"}}, {"family": "Stampfer", "given": "Meir J", "initials": "MJ"}, {"family": "Hu", "given": "Frank B", "initials": "FB"}, {"family": "Guasch-Ferr\u00e9", "given": "Marta", "initials": "M", "orcid": "0000-0001-8525-1404", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2d1a49f5df124e96a9285b43d628cee9.json"}}], "type": "journal article", "published": "2023-09-16", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "5744", "issn-l": "2041-1723"}, "abstract": "Experimental studies reported biochemical actions underpinning aging processes and mortality, but the relevant metabolic alterations in humans are not well understood. Here we examine the associations of 243 plasma metabolites with mortality and longevity (attaining age 85 years) in 11,634 US (median follow-up of 22.6 years, with 4288 deaths) and 1878 Spanish participants (median follow-up of 14.5 years, with 525 deaths). We find that, higher levels of N2,N2-dimethylguanosine, pseudouridine, N4-acetylcytidine, 4-acetamidobutanoic acid, N1-acetylspermidine, and lipids with fewer double bonds are associated with increased risk of all-cause mortality and reduced odds of longevity; whereas L-serine and lipids with more double bonds are associated with lower mortality risk and a higher likelihood of longevity. We further develop a multi-metabolite profile score that is associated with higher mortality risk. Our findings suggest that differences in levels of nucleosides, amino acids, and several lipid subclasses can predict mortality. The underlying mechanisms remain to be determined.", "doi": "10.1038/s41467-023-41515-z", "pmid": "37717037", "labels": {"Clemens Wittenbecher": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC10505179"}, {"db": "pii", "key": "10.1038/s41467-023-41515-z"}], "notes": [], "created": "2025-03-19T08:18:50.034Z", "modified": "2026-09-23T08:34:06.474Z"}, {"entity": "publication", "iuid": "cad35a21593644b9852021cda586dd3e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/cad35a21593644b9852021cda586dd3e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/cad35a21593644b9852021cda586dd3e"}}, "title": "Genetic modification of inflammation- and clonal hematopoiesis-associated cardiovascular risk.", "authors": [{"family": "Yu", "given": "Zhi", "initials": "Z", "orcid": "0000-0003-4810-3474", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4b810efe02244148b701c1468543ea3.json"}}, {"family": "Fidler", "given": "Trevor P", "initials": "TP"}, {"family": "Ruan", "given": "Yunfeng", "initials": "Y", "orcid": "0000-0002-3213-8309", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/13398a8656e64d88b858b22f59eeeb48.json"}}, {"family": "Vlasschaert", "given": "Caitlyn", "initials": "C"}, {"family": "Nakao", "given": "Tetsushi", "initials": "T", "orcid": "0000-0001-9979-2682", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7e818cd4544c41c2a7fa91dbce13429e.json"}}, {"family": "Uddin", "given": "Md Mesbah", "initials": "MM", "orcid": "0000-0003-1846-0411", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/42f1ac7010c34ba997a3fd9e56c6a56a.json"}}, {"family": "Mack", "given": "Taralynn", "initials": "T", "orcid": "0000-0003-1043-2950", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b126c40c737b4b06a8702801ee227b04.json"}}, {"family": "Niroula", "given": "Abhishek", "initials": "A", "orcid": "0000-0002-5904-0635", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/05df7afc7a494ba5af8a378e5ffa53f0.json"}}, {"family": "Heimlich", "given": "J Brett", "initials": "JB", "orcid": "0000-0003-2812-5326", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/57e0bced1405484b94ce062052f498c0.json"}}, {"family": "Zekavat", "given": "Seyedeh M", "initials": "SM", "orcid": "0000-0003-4026-8944", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6234b31f08e442a9b71a711ec7b1147a.json"}}, {"family": "Gibson", "given": "Christopher J", "initials": "CJ", "orcid": "0000-0002-3700-5310", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/71ce9f64755e483496f8c28a76a2a1ff.json"}}, {"family": "Griffin", "given": "Gabriel K", "initials": "GK"}, {"family": "Wang", "given": "Yuxuan", "initials": "Y"}, {"family": "Peloso", "given": "Gina M", "initials": "GM", "orcid": "0000-0002-5355-8636", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b1478b88eafd41d09194cf8967e8ea5f.json"}}, {"family": "Heard-Costa", "given": "Nancy", "initials": "N"}, {"family": "Levy", "given": "Daniel", "initials": "D", "orcid": "0000-0003-1843-8724", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/57605ba755d44792ab87cf14114ec757.json"}}, {"family": "Vasan", "given": "Ramachandran S", "initials": "RS", "orcid": "0000-0001-7357-5970", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/22de41f77ce541d09a9b04aa59de33f7.json"}}, {"family": "Aguet", "given": "Fran\u00e7ois", "initials": "F"}, {"family": "Ardlie", "given": "Kristin G", "initials": "KG"}, {"family": "Taylor", "given": "Kent D", "initials": "KD"}, {"family": "Rich", "given": "Stephen S", "initials": "SS", "orcid": "0000-0003-3872-7793", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b55061262f4541c1b28d3081e4001833.json"}}, {"family": "Rotter", "given": "Jerome I", "initials": "JI", "orcid": "0000-0001-7191-1723", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/50edc25b80cc48b699db367e372fded5.json"}}, {"family": "Libby", "given": "Peter", "initials": "P", "orcid": "0000-0002-1502-502X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/39fb20acff0442bd92fc7931d3ee6cf9.json"}}, {"family": "Jaiswal", "given": "Siddhartha", "initials": "S", "orcid": "0000-0002-9597-0477", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a1901e08f989434fb01dfa17b0a85470.json"}}, {"family": "Ebert", "given": "Benjamin L", "initials": "BL", "orcid": "0000-0003-0197-5451", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56e4f1c53a4348e2b0ceb44a38850a17.json"}}, {"family": "Bick", "given": "Alexander G", "initials": "AG", "orcid": "0000-0001-5824-9595", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d2da5a35a4984921b19dfafe64cea2de.json"}}, {"family": "Tall", "given": "Alan R", "initials": "AR"}, {"family": "Natarajan", "given": "Pradeep", "initials": "P", "orcid": "0000-0001-8402-7435", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fe8bd48c61c047cd8e61c35d9e9ac650.json"}}], "type": "journal article", "published": "2023-09-15", "journal": {"title": "J. Clin. Invest.", "issn": "1558-8238", "volume": "133", "issue": "18", "issn-l": "0021-9738"}, "abstract": "Clonal hematopoiesis of indeterminate potential (CHIP) is associated with an increased risk of cardiovascular diseases (CVDs), putatively via inflammasome activation. We pursued an inflammatory gene modifier scan for CHIP-associated CVD risk among 424,651 UK Biobank participants. We identified CHIP using whole-exome sequencing data of blood DNA and modeled as a composite, considering all driver genes together, as well as separately for common drivers (DNMT3A, TET2, ASXL1, and JAK2). We developed predicted gene expression scores for 26 inflammasome-related genes and assessed how they modify CHIP-associated CVD risk. We identified IL1RAP as a potential key molecule for CHIP-associated CVD risk across genes and increased AIM2 gene expression leading to heightened JAK2- and ASXL1-associated CVD risk. We show that CRISPR-induced Asxl1-mutated murine macrophages had a particularly heightened inflammatory response to AIM2 agonism, associated with an increased DNA damage response, as well as increased IL-10 secretion, mirroring a CVD-protective effect of IL10 expression in ASXL1 CHIP. Our study supports the role of inflammasomes in CHIP-associated CVD and provides evidence to support gene-specific strategies to address CHIP-associated CVD risk.", "doi": "10.1172/JCI168597", "pmid": "37498674", "labels": {"Abhishek Niroula": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC10503804"}, {"db": "pii", "key": "168597"}], "notes": [], "created": "2023-11-20T11:39:39.730Z", "modified": "2025-04-11T07:26:34.477Z"}, {"entity": "publication", "iuid": "b425a447d0f7479f9b5db768890b886b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b425a447d0f7479f9b5db768890b886b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b425a447d0f7479f9b5db768890b886b"}}, "title": "Identification of essential genes associated with SARS-CoV-2 infection as potential drug target candidates with machine learning algorithms.", "authors": [{"family": "Taheri", "given": "Golnaz", "initials": "G", "orcid": "0000-0002-2741-0355", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/014c217121d346b2b371bbc1c2fede57.json"}}, {"family": "Habibi", "given": "Mahnaz", "initials": "M", "orcid": "0000-0002-8969-2706", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f04af4e059814b78bfb107c3a5782f70.json"}}], "type": "journal article", "published": "2023-09-13", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "13", "issue": "1", "pages": "15141"}, "abstract": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) requires the fast discovery of effective treatments to fight this worldwide concern. Several genes associated with the SARS-CoV-2, which are essential for its functionality, pathogenesis, and survival, have been identified. These genes, which play crucial roles in SARS-CoV-2 infection, are considered potential therapeutic targets. Developing drugs against these essential genes to inhibit their regular functions could be a good approach for COVID-19 treatment. Artificial intelligence and machine learning methods provide powerful infrastructures for interpreting and understanding the available data and can assist in finding fast explanations and cures. We propose a method to highlight the essential genes that play crucial roles in SARS-CoV-2 pathogenesis. For this purpose, we define eleven informative topological and biological features for the biological and PPI networks constructed on gene sets that correspond to COVID-19. Then, we use three different unsupervised learning algorithms with different approaches to rank the important genes with respect to our defined informative features. Finally, we present a set of 18 important genes related to COVID-19. Materials and implementations are available at: https://github.com/MahnazHabibi/Gene_analysis .", "doi": "10.1038/s41598-023-42127-9", "pmid": "37704748", "labels": {"Golnaz Taheri": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC10499814"}, {"db": "pii", "key": "10.1038/s41598-023-42127-9"}], "notes": [], "created": "2025-03-21T09:08:32.053Z", "modified": "2026-09-23T11:11:45.619Z"}, {"entity": "publication", "iuid": "d4b90b5fde534237997540b64d92ca3d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d4b90b5fde534237997540b64d92ca3d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d4b90b5fde534237997540b64d92ca3d"}}, "title": "Assessing the Role of Trypsin in Quantitative Plasma and Single-Cell Proteomics toward Clinical Application.", "authors": [{"family": "Woessmann", "given": "Jakob", "initials": "J", "orcid": "0000-0002-2283-7237", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8a4b10f5f96244b98122eddcee694ec0.json"}}, {"family": "Petrosius", "given": "Valdemaras", "initials": "V"}, {"family": "\u00dcresin", "given": "Nil", "initials": "N"}, {"family": "Kotol", "given": "David", "initials": "D", "orcid": "0000-0002-5388-3826", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c41f8f491c474e6bba2047b5d04b4af5.json"}}, {"family": "Aragon-Fernandez", "given": "Pedro", "initials": "P"}, {"family": "Hober", "given": "Andreas", "initials": "A", "orcid": "0000-0001-8947-2562", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/06cbc187628340278395a00ab9dd6c89.json"}}, {"family": "Auf dem Keller", "given": "Ulrich", "initials": "U", "orcid": "0000-0002-3431-7415", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4396aa490c374a8b8b3f8ac564dc2d05.json"}}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Schoof", "given": "Erwin M", "initials": "EM", "orcid": "0000-0002-3117-7832", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3cdcc7198f5f4cf9b13f55639fc8c9f9.json"}}], "type": "journal article", "published": "2023-09-12", "journal": {"title": "Anal. Chem.", "issn": "1520-6882", "volume": "95", "issue": "36", "pages": "13649-13658", "issn-l": "0003-2700"}, "abstract": "Mass spectrometry-based bottom-up proteomics is rapidly evolving and routinely applied in large-scale biomedical studies. Proteases are a central component of every bottom-up proteomics experiment, digesting proteins into peptides. Trypsin has been the most widely applied protease in proteomics due to its characteristics. With ever-larger cohort sizes and possible future clinical application of mass spectrometry-based proteomics, the technical impact of trypsin becomes increasingly relevant. To assess possible biases introduced by trypsin digestion, we evaluated the impact of eight commercially available trypsins in a variety of bottom-up proteomics experiments and across a range of protease concentrations and storage times. To investigate the universal impact of these technical attributes, we included bulk HeLa cell lysate, human plasma, and single HEK293 cells, which were analyzed over a range of selected reaction monitoring (SRM), data-independent acquisition (DIA), and data-dependent acquisition (DDA) instrument methods on three LC-MS instruments. The quantification methods employed encompassed both label-free approaches and absolute quantification utilizing spike-in heavy-labeled recombinant protein fragment standards. Based on this extensive data set, we report variations between commercial trypsins, their source, and their concentration. Furthermore, we provide suggestions on the handling of trypsin in large-scale studies.", "doi": "10.1021/acs.analchem.3c02543", "pmid": "37639361", "labels": {"Fredrik Edfors": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC10500548"}], "notes": [], "created": "2026-08-20T08:08:39.556Z", "modified": "2026-09-23T11:04:24.316Z"}, {"entity": "publication", "iuid": "3ed377b358b24d68849cbe2a6a2e40df", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3ed377b358b24d68849cbe2a6a2e40df.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3ed377b358b24d68849cbe2a6a2e40df"}}, "title": "Risk of estrogen receptor-specific breast cancer by family history of estrogen receptor subtypes and other cancers.", "authors": [{"family": "Wang", "given": "Qiao-Li", "initials": "QL"}, {"family": "Zhang", "given": "Yuqi", "initials": "Y", "orcid": "0000-0002-3656-5383", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ed4a997f34964bd882903c156573a1f7.json"}}, {"family": "Zeng", "given": "Erwei", "initials": "E"}, {"family": "Grassmann", "given": "Felix", "initials": "F", "orcid": "0000-0003-1390-7528", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b6fea6013a4047e08d0e6b2f1d3b8c8c.json"}}, {"family": "He", "given": "Wei", "initials": "W", "orcid": "0000-0003-0161-3274", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b15b923113274ff0a659a05fab5e2f51.json"}}, {"family": "Czene", "given": "Kamila", "initials": "K", "orcid": "0000-0002-3233-5695", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c5637c3ce2214ecbb0df2fd10ad6e4c2.json"}}], "type": "journal article", "published": "2023-09-07", "journal": {"title": "J. Natl. Cancer Inst.", "issn": "1460-2105", "volume": "115", "issue": "9", "pages": "1020-1028", "issn-l": "0027-8874"}, "abstract": "The extent to which the risk of estrogen receptor (ER)-specific breast cancer is associated with ER status of breast cancer and other cancers among first-degree relatives is unclear.\n\nThis population-based cohort included 464 707 cancer-free women in Stockholm, Sweden, during 1978-2019. For ER-negative and ER-positive breast cancers, we estimated hazard ratios (HRs) associated with ER status of female first-degree relatives with breast cancer and of other cancers in all first-degree relatives. Associations between ER-negative and ER-positive status by family cancer history were estimated using logistic regression in a case-only design.\n\nWomen with familial ER-positive breast cancer had 1.87 times (95% confidence interval [CI] = 1.77 to 1.97) higher risk of ER-positive subtype, whereas the corresponding hazard ratio for ER-negative was 2.54 (95% CI = 2.08 to 3.10) when having familial ER-negative breast cancer. The risk increased with an increasing number of female first-degree relatives having concordant subtypes and younger age at diagnosis (Ptrend <.001 for both). Nonbreast cancers among first-degree relatives were associated with both ER-positive (HR = 1.14, 95% CI = 1.10 to 1.17) and ER-negative (HR = 1.08, 95% CI = 1.01 to 1.16) breast cancers. Compared with women with ER-positive breast cancer, women with ER-negative breast cancer were more likely to have family history of liver (odds ratio [OR] = 1.33, 95% CI = 1.05 to 1.67), ovary (OR = 1.28, 95% CI = 1.01 to 1.61), and testicle cancer (OR = 1.79, 95% CI = 1.01 to 3.16) but less likely to have family history of endometrial cancer (OR = 0.77, 95% CI = 0.60 to 1.00) and leukemia (OR = 0.72, 95% CI = 0.56 to 0.91).\n\nRisk of ER-specific breast cancer differs according to ER status of female first-degree relatives with breast cancer and some other cancers of first-degree relatives. This family history information should be considered in the individual risk prediction for ER subtypes.", "doi": "10.1093/jnci/djad104", "pmid": "37243749", "labels": {"DDLS Fellow": null, "Qiaoli Wang": null}, "xrefs": [{"db": "pmc", "key": "PMC10483332"}, {"db": "pii", "key": "7181281"}], "notes": [], "created": "2025-11-28T12:23:01.912Z", "modified": "2025-11-28T12:23:02.037Z"}, {"entity": "publication", "iuid": "b72d4d04b8af4104a4153ae2480c45bf", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b72d4d04b8af4104a4153ae2480c45bf.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b72d4d04b8af4104a4153ae2480c45bf"}}, "title": "Long-term longitudinal analysis of 4,187 participants reveals new insights into determinants of incident clonal hematopoiesis.", "authors": [{"family": "Uddin", "given": "Md Mesbah", "initials": "MM"}, {"family": "Saadatagah", "given": "Seyedmohammad", "initials": "S"}, {"family": "Niroula", "given": "Abhishek", "initials": "A"}, {"family": "Yu", "given": "Bing", "initials": "B"}, {"family": "Hornsby", "given": "Whitney", "initials": "W"}, {"family": "Ganesh", "given": "Shriienidhie", "initials": "S"}, {"family": "Lannery", "given": "Kim", "initials": "K"}, {"family": "Shuermans", "given": "Art", "initials": "A"}, {"family": "Honigberg", "given": "Michael C", "initials": "MC"}, {"family": "Bick", "given": "Alexander G", "initials": "AG"}, {"family": "Libby", "given": "Peter", "initials": "P"}, {"family": "Ebert", "given": "Benjamin L", "initials": "BL"}, {"family": "Ballantyne", "given": "Christie M", "initials": "CM"}, {"family": "Natarajan", "given": "Pradeep", "initials": "P"}], "type": "preprint", "published": "2023-09-07", "journal": {"title": "medRxiv", "issn-l": null}, "abstract": "Clonal hematopoiesis (CH), characterized by blood cells predominantly originating from a single mutated hematopoietic stem cell, is linked to diverse aging-related diseases, including hematologic malignancy and atherosclerotic cardiovascular disease (ASCVD). While CH is common among older adults, the underlying factors driving its development are largely unknown. To address this, we performed whole-exome sequencing on 8,374 blood DNA samples collected from 4,187 Atherosclerosis Risk in Communities Study (ARIC) participants over a median follow-up of 21 years. During this period, 735 participants developed incident CH. We found that age at baseline, sex, and dyslipidemia significantly influence the incidence of CH, while ASCVD and other traditional risk factors for ASCVD did not exhibit such associations. Our study also revealed associations between germline genetic variants and incident CH, prioritizing genes in CH development. Our comprehensive longitudinal assessment yields novel insights into the factors contributing to incident CH in older adults.", "doi": "10.1101/2023.09.05.23295093", "pmid": "37732181", "labels": {"DDLS Fellow": "", "Abhishek Niroula": ""}, "xrefs": [{"db": "pmc", "key": "PMC10508802"}, {"db": "pii", "key": "2023.09.05.23295093"}], "notes": [], "created": "2026-08-20T10:47:44.338Z", "modified": "2026-09-23T14:17:23.680Z"}, {"entity": "publication", "iuid": "d6f97413fcc64401be69c49a50119362", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d6f97413fcc64401be69c49a50119362.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d6f97413fcc64401be69c49a50119362"}}, "title": "Structure-based virtual screening discovers potent and selective adenosine A1 receptor antagonists.", "authors": [{"family": "Matricon", "given": "Pierre", "initials": "P", "orcid": "0000-0001-9350-896X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/19dcd180ddc54eb48269a1638d83ece1.json"}}, {"family": "Nguyen", "given": "Anh Tn", "initials": "AT"}, {"family": "Vo", "given": "Duc Duy", "initials": "DD"}, {"family": "Baltos", "given": "Jo-Anne", "initials": "JA"}, {"family": "Jaiteh", "given": "Mariama", "initials": "M", "orcid": "0000-0002-9229-5314", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dc99e1f36efa4efb8400c13d361ae17f.json"}}, {"family": "Luttens", "given": "Andreas", "initials": "A", "orcid": "0000-0003-2915-7901", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d2944edc47eb4b639f1c61ae7b94b60a.json"}}, {"family": "Kampen", "given": "Stefanie", "initials": "S"}, {"family": "Christopoulos", "given": "Arthur", "initials": "A", "orcid": "0000-0003-4442-3294", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7569b7081884421e9afecc122663834e.json"}}, {"family": "Kihlberg", "given": "Jan", "initials": "J", "orcid": "0000-0002-4205-6040", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7edb4dfa7c4b4d6c8c4cf0282a9c9a1a.json"}}, {"family": "May", "given": "Lauren Therese", "initials": "LT"}, {"family": "Carlsson", "given": "Jens", "initials": "J", "orcid": "0000-0003-4623-2977", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/792c1cd4aca248dc94b967115ffa82df.json"}}], "type": "journal article", "published": "2023-09-05", "journal": {"title": "Eur J Med Chem", "issn": "1768-3254", "volume": "257", "pages": "115419", "issn-l": "0223-5234"}, "abstract": "Development of subtype-selective leads is essential in drug discovery campaigns targeting G protein-coupled receptors (GPCRs). Herein, a structure-based virtual screening approach to rationally design subtype-selective ligands was applied to the A1 and A2A adenosine receptors (A1R and A2AR). Crystal structures of these closely related subtypes revealed a non-conserved subpocket in the binding sites that could be exploited to identify A1R selective ligands. A library of 4.6 million compounds was screened computationally against both receptors using molecular docking and 20 A1R selective ligands were predicted. Of these, seven antagonized the A1R with micromolar activities and several compounds displayed slight selectivity for this subtype. Twenty-seven analogs of two discovered scaffolds were designed, resulting in antagonists with nanomolar potency and up to 76-fold A1R-selectivity. Our results show the potential of structure-based virtual screening to guide discovery and optimization of subtype-selective ligands, which could facilitate the development of safer drugs.", "doi": "10.1016/j.ejmech.2023.115419", "pmid": "37301076", "labels": {"Jens Carlsson": "", "SciLifeLab Fellow": "", "Andreas Luttens": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pii", "key": "S0223-5234(23)00385-9"}], "notes": [], "created": "2023-11-27T19:57:12.187Z", "modified": "2026-09-23T11:09:06.207Z"}, {"entity": "publication", "iuid": "5fc47a4102964480960ca7e6f1d5a6d4", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5fc47a4102964480960ca7e6f1d5a6d4.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5fc47a4102964480960ca7e6f1d5a6d4"}}, "title": "OME-Zarr: a cloud-optimized bioimaging file format with international community support.", "authors": [{"family": "Moore", "given": "Josh", "initials": "J", "orcid": "0000-0003-4028-811X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d1ffe6a8671646ac9e75ec4a6b5a26de.json"}}, {"family": "Basurto-Lozada", "given": "Daniela", "initials": "D", "orcid": "0000-0003-3943-8424", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/43bc2250ca1e4f7d81a1887f2cfb5ed1.json"}}, {"family": "Besson", "given": "S\u00e9bastien", "initials": "S", "orcid": "0000-0001-8783-1429", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ce1fb03b0bc44c4a8c6580d727ac75d5.json"}}, {"family": "Bogovic", "given": "John", "initials": "J", "orcid": "0000-0002-4829-9457", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3bcdd7e4893c4c15b5aea0be49ee4a18.json"}}, {"family": "Bragantini", "given": "Jord\u00e3o", "initials": "J", "orcid": "0000-0001-7652-2735", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d127ca6fd51945819d6ad49008a348f3.json"}}, {"family": "Brown", "given": "Eva M", "initials": "EM", "orcid": "0000-0003-2564-0373", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a5d1620cef0c4def883a3bc85768bee8.json"}}, {"family": "Burel", "given": "Jean-Marie", "initials": "JM", "orcid": "0000-0002-1789-1861", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/66a815a758ee45f7bbf34bb603ee57d6.json"}}, {"family": "Casas Moreno", "given": "Xavier", "initials": "X", "orcid": "0000-0002-9583-9022", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/26b876b7f5094fe6a03880bea27ee0ed.json"}}, {"family": "de Medeiros", "given": "Gustavo", "initials": "G", "orcid": "0000-0001-5877-3012", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/29db632b56e4425a9e784fa2394a78de.json"}}, {"family": "Diel", "given": "Erin E", "initials": "EE", "orcid": "0000-0003-2526-3512", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ee08390e07864723b9458986f0ab2325.json"}}, {"family": "Gault", "given": "David", "initials": "D"}, {"family": "Ghosh", "given": "Satrajit S", "initials": "SS", "orcid": "0000-0002-5312-6729", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca3dd3bab0dd46e69837c94b06cb6fee.json"}}, {"family": "Gold", "given": "Ilan", "initials": "I", "orcid": "0000-0002-5823-1026", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cbe9f7bb98f54b0aadbf4ba3d8afae31.json"}}, {"family": "Halchenko", "given": "Yaroslav O", "initials": "YO", "orcid": "0000-0003-3456-2493", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bd58d0aada0945eda973af6e7a5ffd18.json"}}, {"family": "Hartley", "given": "Matthew", "initials": "M", "orcid": "0000-0001-6178-2884", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/891c0d850b244c209d1852b74d2a532f.json"}}, {"family": "Horsfall", "given": "Dave", "initials": "D", "orcid": "0000-0002-8086-812X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8c44045f7b7245d2b64de62cbe4efc31.json"}}, {"family": "Keller", "given": "Mark S", "initials": "MS", "orcid": "0000-0003-3003-874X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d636b357587a4ffaae79625adbf053f8.json"}}, {"family": "Kittisopikul", "given": "Mark", "initials": "M", "orcid": "0000-0002-9558-6248", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/58f9954605874bcd9596c0de56450af6.json"}}, {"family": "Kovacs", "given": "Gabor", "initials": "G", "orcid": "0000-0003-1779-775X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e38029f20f84ded8ad485c61b6a2814.json"}}, {"family": "K\u00fcpc\u00fc Yolda\u015f", "given": "Ayb\u00fcke", "initials": "A", "orcid": "0000-0001-6191-5069", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/17c95f8e0c74460ab11d1b74b365110c.json"}}, {"family": "Kyoda", "given": "Koji", "initials": "K", "orcid": "0000-0001-9455-2153", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9bb67ecdd0b34cd9a8dbcf94b3cfd141.json"}}, {"family": "le Tournoulx de la Villegeorges", "given": "Albane", "initials": "A", "orcid": "0000-0001-7394-8941", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e46b049ef8f244e1bec66513463ee7e5.json"}}, {"family": "Li", "given": "Tong", "initials": "T", "orcid": "0000-0002-8240-4476", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ae704a6309244a11ac7e54a4d9b0b639.json"}}, {"family": "Liberali", "given": "Prisca", "initials": "P", "orcid": "0000-0003-0695-6081", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/89699b18aa704608b816550f396412a0.json"}}, {"family": "Lindner", "given": "Dominik", "initials": "D", "orcid": "0000-0001-8038-1250", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b868f60d7204453cb4034881e4144434.json"}}, {"family": "Linkert", "given": "Melissa", "initials": "M"}, {"family": "L\u00fcthi", "given": "Joel", "initials": "J", "orcid": "0000-0003-3023-170X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1cbd5796debc4ab9a2d6c2b7e14dd185.json"}}, {"family": "Maitin-Shepard", "given": "Jeremy", "initials": "J", "orcid": "0000-0001-8453-7961", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3ab733cfcb7540c09bb496c3ddff83b3.json"}}, {"family": "Manz", "given": "Trevor", "initials": "T", "orcid": "0000-0001-7694-5164", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/96fe4296510d42449be0fbd5e61aa5fa.json"}}, {"family": "Marconato", "given": "Luca", "initials": "L", "orcid": "0000-0003-3198-1326", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/74ad9bcf847c45c58a5f143f158782a0.json"}}, {"family": "McCormick", "given": "Matthew", "initials": "M", "orcid": "0000-0001-9475-3756", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8beaeb2777ad484794a28dc2015ec637.json"}}, {"family": "Lange", "given": "Merlin", "initials": "M", "orcid": "0000-0003-0534-4374", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7bccf38df438403d93fdeba0f5d4ad7a.json"}}, {"family": "Mohamed", "given": "Khaled", "initials": "K", "orcid": "0000-0003-1480-8695", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1c7cbc60aad6446ea70bdf252e3ef87c.json"}}, {"family": "Moore", "given": "William", "initials": "W", "orcid": "0000-0002-7264-8338", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/75eb8663f03c468bb651c14fc895287b.json"}}, {"family": "Norlin", "given": "Nils", "initials": "N", "orcid": "0000-0003-1970-3198", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d44ba4bdcb59424782a9be2753cc1a54.json"}}, {"family": "Ouyang", "given": "Wei", "initials": "W", "orcid": "0000-0002-0291-926X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56f601e1d1c6448aab0c3a1e3cffdbfc.json"}}, {"family": "\u00d6zdemir", "given": "Bugra", "initials": "B", "orcid": "0000-0001-9823-0581", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/07b061f4b9424e70924efbfcecaefa5a.json"}}, {"family": "Palla", "given": "Giovanni", "initials": "G", "orcid": "0000-0002-8004-4462", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e87add202a7b4520be57b5beaa24155c.json"}}, {"family": "Pape", "given": "Constantin", "initials": "C", "orcid": "0000-0001-6562-7187", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a92d98129eff4ea38ab084287ec20155.json"}}, {"family": "Pelkmans", "given": "Lucas", "initials": "L", "orcid": "0000-0002-6754-9730", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7bee0de97a7047cc9b5d7091ab5620ec.json"}}, {"family": "Pietzsch", "given": "Tobias", "initials": "T", "orcid": "0000-0002-9477-3957", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cc19b653f96d47658e84bef25c2d5a5f.json"}}, {"family": "Preibisch", "given": "Stephan", "initials": "S", "orcid": "0000-0002-0276-494X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c4064680bfd344b090e97878014c6f84.json"}}, {"family": "Prete", "given": "Martin", "initials": "M", "orcid": "0000-0002-5946-821X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3e3176eeed6d417cb9a00dedf7c2db55.json"}}, {"family": "Rzepka", "given": "Norman", "initials": "N", "orcid": "0000-0002-8168-7929", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a9819240522b415d9716d8c5f930520a.json"}}, {"family": "Samee", "given": "Sameeul", "initials": "S", "orcid": "0009-0006-9305-7146", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/41df55fbc7d244eca5769e6ef5439a37.json"}}, {"family": "Schaub", "given": "Nicholas", "initials": "N", "orcid": "0000-0001-6581-7191", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bcc511dcc6904085935eb98fd6bba01c.json"}}, {"family": "Sidky", "given": "Hythem", "initials": "H", "orcid": "0000-0003-3532-4809", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8e860cace62644a9afa304db2ad3cf1f.json"}}, {"family": "Solak", "given": "Ahmet Can", "initials": "AC", "orcid": "0000-0002-1381-8309", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cee3282706ac435b91b32af2b2392552.json"}}, {"family": "Stirling", "given": "David R", "initials": "DR", "orcid": "0000-0001-6802-4103", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8908ee21e7d04b3ab9dc304a14780137.json"}}, {"family": "Striebel", "given": "Jonathan", "initials": "J", "orcid": "0000-0002-5547-5973", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/22eec49863f742888f9317c6ef51400b.json"}}, {"family": "Tischer", "given": "Christian", "initials": "C", "orcid": "0000-0003-4105-1990", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fcd2fb2d08e44af8bd9444fba9ed8048.json"}}, {"family": "Toloudis", "given": "Daniel", "initials": "D", "orcid": "0000-0003-2620-1233", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bd8ccbb97ead4d19ba1ee627fece561c.json"}}, {"family": "Virshup", "given": "Isaac", "initials": "I", "orcid": "0000-0002-1710-8945", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/20af345b3aaa4283a448cf927dabd79f.json"}}, {"family": "Walczysko", "given": "Petr", "initials": "P", "orcid": "0000-0003-0302-8247", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3e20ef6c9b3a4c368955607988dc8867.json"}}, {"family": "Watson", "given": "Alan M", "initials": "AM", "orcid": "0000-0003-0632-8296", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b6d50dfa37074c08895aada511e7a64a.json"}}, {"family": "Weisbart", "given": "Erin", "initials": "E", "orcid": "0000-0002-6437-2458", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8ca1a2568e694532a5ce703221a9f488.json"}}, {"family": "Wong", "given": "Frances", "initials": "F", "orcid": "0000-0001-7397-8251", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8b6b47be1ed34add9d98f3729812d552.json"}}, {"family": "Yamauchi", "given": "Kevin A", "initials": "KA", "orcid": "0000-0002-7818-1388", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f1fa42ae4afb4a89a684754b7075f1c0.json"}}, {"family": "Bayraktar", "given": "Omer", "initials": "O", "orcid": "0000-0001-6055-277X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c33c0dfa62cc46318b16be449da80e31.json"}}, {"family": "Cimini", "given": "Beth A", "initials": "BA", "orcid": "0000-0001-9640-9318", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cbe15524bb604092be6daf433faa9610.json"}}, {"family": "Gehlenborg", "given": "Nils", "initials": "N", "orcid": "0000-0003-0327-8297", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/83f7f88927584d80b6b5a5447b20dfdb.json"}}, {"family": "Haniffa", "given": "Muzlifah", "initials": "M", "orcid": "0000-0002-3927-2084", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0702147e80fd42358ad19a66451e2442.json"}}, {"family": "Hotaling", "given": "Nathan", "initials": "N", "orcid": "0000-0001-8423-6464", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e526892854084fe5ab16081f86d38d22.json"}}, {"family": "Onami", "given": "Shuichi", "initials": "S", "orcid": "0000-0002-8255-1724", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/83ea9aff97ad4f03ac4982160b20365f.json"}}, {"family": "Royer", "given": "Loic A", "initials": "LA", "orcid": "0000-0002-9991-9724", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/38277bc865f047df8c4523ebf0f1261c.json"}}, {"family": "Saalfeld", "given": "Stephan", "initials": "S", "orcid": "0000-0002-4106-1761", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/11e2453103c0410581737e66c33afec9.json"}}, {"family": "Stegle", "given": "Oliver", "initials": "O", "orcid": "0000-0002-8818-7193", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/73e53d349cfa48458444d75b18cf6d75.json"}}, {"family": "Theis", "given": "Fabian J", "initials": "FJ", "orcid": "0000-0002-2419-1943", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8969d033a36f40aab191ad1b3960114d.json"}}, {"family": "Swedlow", "given": "Jason R", "initials": "JR", "orcid": "0000-0002-2198-1958", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/919be1b6ecf34615a2c3e2a05f6c01de.json"}}], "type": "journal article", "published": "2023-09-00", "journal": {"title": "Histochem Cell Biol", "issn": "1432-119X", "volume": "160", "issue": "3", "pages": "223-251", "issn-l": null}, "abstract": "A growing community is constructing a next-generation file format (NGFF) for bioimaging to overcome problems of scalability and heterogeneity. Organized by the Open Microscopy Environment (OME), individuals and institutes across diverse modalities facing these problems have designed a format specification process (OME-NGFF) to address these needs. This paper brings together a wide range of those community members to describe the cloud-optimized format itself-OME-Zarr-along with tools and data resources available today to increase FAIR access and remove barriers in the scientific process. The current momentum offers an opportunity to unify a key component of the bioimaging domain-the file format that underlies so many personal, institutional, and global data management and analysis tasks.", "doi": "10.1007/s00418-023-02209-1", "pmid": "37428210", "labels": {"DDLS Fellow": "", "Wei Ouyang": ""}, "xrefs": [{"db": "pmc", "key": "PMC10492740"}, {"db": "pii", "key": "10.1007/s00418-023-02209-1"}], "notes": [], "created": "2026-08-20T06:39:48.671Z", "modified": "2026-09-23T07:33:11.456Z"}, {"entity": "publication", "iuid": "8265a3efebde4ad694da7086335d0ca6", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8265a3efebde4ad694da7086335d0ca6.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8265a3efebde4ad694da7086335d0ca6"}}, "title": "Immune system adaptation during gender-affirming testosterone treatment", "authors": [{"family": "Consiglio", "given": "Camila", "initials": "C"}, {"family": "Tadepally", "given": "Lakshmikanth", "initials": "L"}, {"family": "Sardh", "given": "Fabian", "initials": "F"}, {"family": "Forlin", "given": "Rikard", "initials": "R"}, {"family": "Wang", "given": "Jun", "initials": "J"}, {"family": "Tan", "given": "Ziyang", "initials": "Z"}, {"family": "Barcenilla", "given": "Hugo", "initials": "H"}, {"family": "Rodriguez", "given": "Lucie", "initials": "L"}, {"family": "Sugrue", "given": "Jamie", "initials": "J"}, {"family": "Noori", "given": "Peri", "initials": "P"}, {"family": "P\u00e1ez", "given": "Laura P", "initials": "LP"}, {"family": "Gonzalez", "given": "Laura", "initials": "L"}, {"family": "Mugabo", "given": "Constantin H", "initials": "CH"}, {"family": "Johnsson", "given": "Annette", "initials": "A"}, {"family": "Hallgren", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Pou", "given": "Christian", "initials": "C"}, {"family": "Chen", "given": "Yang", "initials": "Y"}, {"family": "Mike\u0161", "given": "Jarom\u00edr", "initials": "J"}, {"family": "James", "given": "Anna", "initials": "A"}, {"family": "Dahlqvist", "given": "Per", "initials": "P"}, {"family": "Wahlberg", "given": "Jeanette", "initials": "J"}, {"family": "Hagelin", "given": "Anders", "initials": "A"}, {"family": "Holmberg", "given": "Mats", "initials": "M"}, {"family": "Degerblad", "given": "Marie", "initials": "M"}, {"family": "Isaksson", "given": "Magnus", "initials": "M"}, {"family": "Duffy", "given": "Darragh", "initials": "D"}, {"family": "K\u00e4mpe", "given": "Olle", "initials": "O"}, {"family": "Landegren", "given": "Nils", "initials": "N"}, {"family": "Brodin", "given": "Petter", "initials": "P"}], "type": "journal-article", "published": "2023-09-00", "journal": {"title": "Journal of Reproductive Immunology", "issn": "0165-0378", "volume": "159", "pages": "104065", "issn-l": null}, "abstract": null, "doi": "10.1016/j.jri.2023.104065", "pmid": null, "labels": {"Camila Consiglio": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T08:00:05.053Z", "modified": "2026-09-23T12:28:50.520Z"}, {"entity": "publication", "iuid": "e10a46376db74caba7746d411faa4302", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e10a46376db74caba7746d411faa4302.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e10a46376db74caba7746d411faa4302"}}, "title": "Ghost admixture in eastern gorillas.", "authors": [{"family": "Pawar", "given": "Harvinder", "initials": "H"}, {"family": "Rymbekova", "given": "Aigerim", "initials": "A", "orcid": "0009-0001-5461-5161", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d8c43ad5829f4ad28597d45d65260729.json"}}, {"family": "Cuadros-Espinoza", "given": "Sebastian", "initials": "S"}, {"family": "Huang", "given": "Xin", "initials": "X", "orcid": "0000-0002-9918-9602", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/27a6d482c13b437a8ba45a652135aef7.json"}}, {"family": "de Manuel", "given": "Marc", "initials": "M"}, {"family": "van der Valk", "given": "Tom", "initials": "T"}, {"family": "Lobon", "given": "Irene", "initials": "I", "orcid": "0000-0003-1170-9915", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0c162d3810c048afb25925af6ff5ea86.json"}}, {"family": "Alvarez-Estape", "given": "Marina", "initials": "M"}, {"family": "Haber", "given": "Marc", "initials": "M"}, {"family": "Dolgova", "given": "Olga", "initials": "O"}, {"family": "Han", "given": "Sojung", "initials": "S", "orcid": "0000-0002-6113-1042", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ec6576ca2d1a480e8e5aec022199bcb5.json"}}, {"family": "Esteller-Cucala", "given": "Paula", "initials": "P", "orcid": "0000-0003-3048-4280", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/610f0a88c36a4acd80c59acbca72cc8a.json"}}, {"family": "Juan", "given": "David", "initials": "D", "orcid": "0000-0003-1912-9667", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/027154f54530486eac69b942138bc07f.json"}}, {"family": "Ayub", "given": "Qasim", "initials": "Q", "orcid": "0000-0003-3291-0917", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56fe9f679c2d442290a454dd4a38f92e.json"}}, {"family": "Bautista", "given": "Ruben", "initials": "R", "orcid": "0009-0007-0059-4178", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cc84c095e1114b8aa8381712203baa80.json"}}, {"family": "Kelley", "given": "Joanna L", "initials": "JL", "orcid": "0000-0002-7731-605X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a2809ef2164f4fd2bb01ac7e65a13fe9.json"}}, {"family": "Cornejo", "given": "Omar E", "initials": "OE", "orcid": "0000-0003-4076-4227", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2ed9d28368d84181a1d971b651a8f909.json"}}, {"family": "Lao", "given": "Oscar", "initials": "O"}, {"family": "Andr\u00e9s", "given": "Aida M", "initials": "AM"}, {"family": "Guschanski", "given": "Katerina", "initials": "K", "orcid": "0000-0002-8493-5457", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4e062373c6bc46b98e56215d3ec89eeb.json"}}, {"family": "Ssebide", "given": "Benard", "initials": "B"}, {"family": "Cranfield", "given": "Mike", "initials": "M"}, {"family": "Tyler-Smith", "given": "Chris", "initials": "C"}, {"family": "Xue", "given": "Yali", "initials": "Y"}, {"family": "Prado-Martinez", "given": "Javier", "initials": "J"}, {"family": "Marques-Bonet", "given": "Tomas", "initials": "T", "orcid": "0000-0002-5597-3075", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1091cb5bfe394d459969d24bb1c22c66.json"}}, {"family": "Kuhlwilm", "given": "Martin", "initials": "M", "orcid": "0000-0002-0115-1797", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c21afe591ec14eeab27425b903e4db99.json"}}], "type": "journal article", "published": "2023-09-00", "journal": {"title": "Nat Ecol Evol", "issn": "2397-334X", "volume": "7", "issue": "9", "pages": "1503-1514", "issn-l": "2397-334X"}, "abstract": "Archaic admixture has had a substantial impact on human evolution with multiple events across different clades, including from extinct hominins such as Neanderthals and Denisovans into modern humans. In great apes, archaic admixture has been identified in chimpanzees and bonobos but the possibility of such events has not been explored in other species. Here, we address this question using high-coverage whole-genome sequences from all four extant gorilla subspecies, including six newly sequenced eastern gorillas from previously unsampled geographic regions. Using approximate Bayesian computation with neural networks to model the demographic history of gorillas, we find a signature of admixture from an archaic 'ghost' lineage into the common ancestor of eastern gorillas but not western gorillas. We infer that up to 3% of the genome of these individuals is introgressed from an archaic lineage that diverged more than 3 million years ago from the common ancestor of all extant gorillas. This introgression event took place before the split of mountain and eastern lowland gorillas, probably more than 40 thousand years ago and may have influenced perception of bitter taste in eastern gorillas. When comparing the introgression landscapes of gorillas, humans and bonobos, we find a consistent depletion of introgressed fragments on the X chromosome across these species. However, depletion in protein-coding content is not detectable in eastern gorillas, possibly as a consequence of stronger genetic drift in this species.", "doi": "10.1038/s41559-023-02145-2", "pmid": "37500909", "labels": {"DDLS Fellow": "", "Tom van der Valk": ""}, "xrefs": [{"db": "pmc", "key": "PMC10482688"}, {"db": "pii", "key": "10.1038/s41559-023-02145-2"}], "notes": [], "created": "2026-08-20T08:55:12.210Z", "modified": "2026-09-23T08:53:42.068Z"}, {"entity": "publication", "iuid": "36212ac7310c4b549ce72c41f2cced1f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/36212ac7310c4b549ce72c41f2cced1f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/36212ac7310c4b549ce72c41f2cced1f"}}, "title": "A Multi-Stain Breast Cancer Histological Whole-Slide-Image Data Set from Routine Diagnostics.", "authors": [{"family": "Weitz", "given": "Philippe", "initials": "P", "orcid": "0000-0002-1788-0716", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a70939bc05a04f87b9a61e7d98448e09.json"}}, {"family": "Valkonen", "given": "Masi", "initials": "M", "orcid": "0000-0003-3091-2484", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ae4841e8a4124dc79c921b3af09096fe.json"}}, {"family": "Solorzano", "given": "Leslie", "initials": "L", "orcid": "0000-0001-8658-6417", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f5c33a5b8cef4cad8b9f57b4510fb0c2.json"}}, {"family": "Carr", "given": "Circe", "initials": "C"}, {"family": "Kartasalo", "given": "Kimmo", "initials": "K", "orcid": "0000-0002-9470-4783", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7c6fc97c06ed456c8bdd1f03db8a9b72.json"}}, {"family": "Boissin", "given": "Constance", "initials": "C"}, {"family": "Koivukoski", "given": "Sonja", "initials": "S", "orcid": "0000-0002-4909-3522", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1889b0f9c9f943609f51e8d8d15041f1.json"}}, {"family": "Kuusela", "given": "Aino", "initials": "A"}, {"family": "Rasic", "given": "Dusan", "initials": "D", "orcid": "0000-0003-4610-5265", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/42ddfdb3b820417197cedfd1b96ab172.json"}}, {"family": "Feng", "given": "Yanbo", "initials": "Y"}, {"family": "Sinius Pouplier", "given": "Sandra", "initials": "S", "orcid": "0000-0002-2625-7440", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/190eef15655e4ea6b8eaa15ccddfb7a0.json"}}, {"family": "Sharma", "given": "Abhinav", "initials": "A"}, {"family": "Ledesma Eriksson", "given": "Kajsa", "initials": "K"}, {"family": "Latonen", "given": "Leena", "initials": "L", "orcid": "0000-0003-4502-2193", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f85efd5db6e74874acdb8d14237ae732.json"}}, {"family": "Laenkholm", "given": "Anne-Vibeke", "initials": "A"}, {"family": "Hartman", "given": "Johan", "initials": "J", "orcid": "0000-0002-6500-8527", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d62d622200d443b7b5be34ff3c0945be.json"}}, {"family": "Ruusuvuori", "given": "Pekka", "initials": "P", "orcid": "0000-0001-9086-9591", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb947cd395e84612a53569f4a39abd19.json"}}, {"family": "Rantalainen", "given": "Mattias", "initials": "M"}], "type": "dataset", "published": "2023-08-24", "journal": {"title": "Sci Data", "issn": "2052-4463", "issn-l": "2052-4463", "volume": "10", "issue": "1", "pages": "562"}, "abstract": "The analysis of FFPE tissue sections stained with haematoxylin and eosin (H&E) or immunohistochemistry (IHC) is essential for the pathologic assessment of surgically resected breast cancer specimens. IHC staining has been broadly adopted into diagnostic guidelines and routine workflows to assess the status of several established biomarkers, including ER, PGR, HER2 and KI67. Biomarker assessment can also be facilitated by computational pathology image analysis methods, which have made numerous substantial advances recently, often based on publicly available whole slide image (WSI) data sets. However, the field is still considerably limited by the sparsity of public data sets. In particular, there are no large, high quality publicly available data sets with WSIs of matching IHC and H&E-stained tissue sections from the same tumour. Here, we publish the currently largest publicly available data set of WSIs of tissue sections from surgical resection specimens from female primary breast cancer patients with matched WSIs of corresponding H&E and IHC-stained tissue, consisting of 4,212 WSIs from 1,153 patients.", "doi": "10.1038/s41597-023-02422-6", "pmid": "37620357", "labels": {"Kimmo Kartasalo": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC10449765"}, {"db": "pii", "key": "10.1038/s41597-023-02422-6"}], "notes": [], "created": "2024-11-05T16:10:24.038Z", "modified": "2024-11-29T09:28:40.734Z"}, {"entity": "publication", "iuid": "3e38ecde6ec649f38fef945dec76119f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3e38ecde6ec649f38fef945dec76119f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3e38ecde6ec649f38fef945dec76119f"}}, "title": "Complex Polyploids: Origins, Genomic Composition, and Role of Introgressed Alleles", "authors": [{"family": "Leal", "given": "J Luis", "initials": "JL", "orcid": "0000-0003-0731-7329", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5c8ad8376a7f483ebe91ed2d15d9147a.json"}}, {"family": "Milesi", "given": "Pascal", "initials": "P"}, {"family": "Hodkov\u00e1", "given": "Eva", "initials": "E"}, {"family": "Zhou", "given": "Qiujie", "initials": "Q"}, {"family": "James", "given": "Jennifer", "initials": "J"}, {"family": "Eklund", "given": "D Magnus", "initials": "DM", "orcid": "0000-0002-0576-7636", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ef55918b907d440ca73f6d250e9f5751.json"}}, {"family": "Pyh\u00e4j\u00e4rvi", "given": "Tanja", "initials": "T", "orcid": "0000-0001-6958-5172", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7256c4910788401f873272cf29fedf91.json"}}, {"family": "Saloj\u00e4rvi", "given": "Jarkko", "initials": "J", "orcid": "0000-0002-4096-6278", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dacfe7893125487cb615161b04034a99.json"}}, {"family": "Lascoux", "given": "Martin", "initials": "M", "orcid": "0000-0003-1699-9042", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0730d0f9c2524eb19383640612924701.json"}}], "type": "posted-content", "published": "2023-08-23", "journal": {"title": "bioRxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2023.08.23.553805", "pmid": null, "labels": {"SciLifeLab Fellow": null, "Pascal Milesi": null, "DDLS Fellow": null, "Jennifer James": null}, "xrefs": [], "notes": [], "created": "2026-08-20T10:47:36.378Z", "modified": "2026-10-05T08:50:56.428Z"}, {"entity": "publication", "iuid": "5fef08eda5114edea2d9e41d5d5c3d56", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5fef08eda5114edea2d9e41d5d5c3d56.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5fef08eda5114edea2d9e41d5d5c3d56"}}, "title": "Prevalence of the human papillomavirus (HPV) types among cervical dysplasia women attending a gynaecological clinic in Sweden.", "authors": [{"family": "Garc\u00eda", "given": "Fabricio Romero", "initials": "FR"}, {"family": "Norenhag", "given": "Johanna", "initials": "J"}, {"family": "Edfeldt", "given": "Gabriella", "initials": "G"}, {"family": "Cheng", "given": "Liqin", "initials": "L"}, {"family": "Hugerth", "given": "Luisa Warchavchik", "initials": "LW"}, {"family": "Pennhag", "given": "Alexandra A L", "initials": "AAL"}, {"family": "Schuppe-Koistinen", "given": "Ina", "initials": "I"}, {"family": "Engstrand", "given": "Lars", "initials": "L"}, {"family": "Olovsson", "given": "Matts", "initials": "M"}, {"family": "Du", "given": "Juan", "initials": "J"}], "type": "journal article", "published": "2023-08-22", "journal": {"title": "BJC Rep", "issn": "2731-9377", "volume": "1", "issue": "1", "pages": "11", "issn-l": null}, "abstract": "Human papillomavirus (HPV) is the main cause of cervical cancer. HPV-vaccines have led to a significant decrease in HPV-infections and related cancer cases. The estimation of the current HPV-prevalence and distribution of different HPV-types among women with cervical dysplasia is important for the future vaccination strategy.\n\nBy using a multiplexed bead-based immunoassay, we revealed the prevalence of 27 HPV-types in 168 dysplasia women aged 21-70 from Uppsala University hospital, Sweden.\n\nThe prevalence of HPV in low-and high-grade squamous intraepithelial lesions (LSIL and HSIL, respectively) were 56.3% and 76.7%, respectively. The oncogenic HPV-types constituted 80.0%, and 97.1% among the HPV-positive LSIL and HSIL-groups, respectively, with HPV16 as the most prevalent type. We found a reduction in oncogenic HPV-types covered by the bi- and quadrivalent vaccines in the vaccinated HSIL-group, suggesting the effectiveness of the HPV-vaccine in preventing dysplasia caused by the covered HPV-types. Oncogenic HPV-types 39 and 59, not covered by any current vaccine have an important prevalence among patients with cervical dysplasia.\n\nOncogenic-HPV-types are highly prevalent among women with HSIL. The current vaccine presents effectiveness for reducing the covered HPV-types among dysplasia patients.", "doi": "10.1038/s44276-023-00012-y", "pmid": "39516656", "labels": {"DDLS Fellow": "", "Luisa Hugerth": ""}, "xrefs": [{"db": "pmc", "key": "PMC11524002"}, {"db": "pii", "key": "10.1038/s44276-023-00012-y"}], "notes": [], "created": "2026-08-20T09:26:34.298Z", "modified": "2026-09-23T12:16:21.342Z"}, {"entity": "publication", "iuid": "ef8f2fd33af64e0e8de4681bea630167", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ef8f2fd33af64e0e8de4681bea630167.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ef8f2fd33af64e0e8de4681bea630167"}}, "title": "Broadcasters, receivers, functional groups of metabolites and the link to heart failure progression using polygenic factors.", "authors": [{"family": "Yazdani", "given": "Azam", "initials": "A"}, {"family": "Mendez-Giraldez", "given": "Raul", "initials": "R"}, {"family": "Yazdani", "given": "Akram", "initials": "A"}, {"family": "Schaid", "given": "Daniel", "initials": "D"}, {"family": "Won Kong", "given": "Sek", "initials": "S", "orcid": "0000-0003-4877-7567", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d55f2a433f9b4f808a3443a8f0d12df1.json"}}, {"family": "Hadi", "given": "Mohamad", "initials": "M"}, {"family": "Samiei", "given": "Ahmad", "initials": "A"}, {"family": "Wittenbecher", "given": "Clemens", "initials": "C"}, {"family": "Lasky-Su", "given": "Jessica", "initials": "J"}, {"family": "Clish", "given": "Clary", "initials": "C", "orcid": "0000-0001-8259-9245", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/25b862e77efe474ca91bce1bd96fd366.json"}}, {"family": "Marotta", "given": "Francesco", "initials": "F"}, {"family": "Kosorok", "given": "Michael", "initials": "M"}, {"family": "Mora", "given": "Samia", "initials": "S", "orcid": "0000-0001-6283-0980", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e1189d5d8e634514b0272b8aad38641f.json"}}, {"family": "Muehlschlegel", "given": "Jochen", "initials": "J"}, {"family": "Chasman", "given": "Daniel", "initials": "D"}, {"family": "Larson", "given": "Martin", "initials": "M"}, {"family": "Elsea", "given": "Sarah", "initials": "S", "orcid": "0000-0002-1400-8519", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3d5390fa40c240b4a6171d2264fd495e.json"}}], "type": "preprint", "published": "2023-08-18", "journal": {"title": "Res Sq", "issn": "2693-5015", "issn-l": null}, "abstract": "In a prospective study with records of heart failure (HF) incidence, we present metabolite profiling data from individuals without HF at baseline. We uncovered the interconnectivity of metabolites using data-driven and causal networks augmented with polygenic factors. Exploring the networks, we identified metabolite broadcasters, receivers, mediators, and subnetworks corresponding to functional classes of metabolites, and provided insights into the link between metabolomic architecture and regulation in health. We incorporated the network structure into the identification of metabolites associated with HF to control the effect of confounding metabolites. We identified metabolites associated with higher or lower risk of HF incidence, the associations that were not confounded by the other metabolites, such as glycine, ureidopropionic and glycocholic acids, and LPC 18:2. We revealed the underlying relationships of the findings. For example, asparagine directly influenced glycine, and both were inversely associated with HF. These two metabolites were influenced by polygenic factors and only essential amino acids which are not synthesized in the human body and come directly from the diet. Metabolites may play a critical role in linking genetic background and lifestyle factors to HF progression. Revealing the underlying connectivity of metabolites associated with HF strengthens the findings and facilitates a mechanistic understanding of HF progression.", "doi": "10.21203/rs.3.rs-3246406/v1", "pmid": "37645766", "labels": {"Clemens Wittenbecher": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC10462252"}, {"db": "pii", "key": "rs.3.rs-3246406"}], "notes": [], "created": "2025-03-19T08:18:51.573Z", "modified": "2025-03-19T08:18:51.755Z"}, {"entity": "publication", "iuid": "1eef9842024d48a08f179b42bd814715", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1eef9842024d48a08f179b42bd814715.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1eef9842024d48a08f179b42bd814715"}}, "title": "Association of the human gut microbiota with vascular stiffness.", "authors": [{"family": "Cuadrat", "given": "Rafael R C", "initials": "RRC"}, {"family": "Goris", "given": "Tobias", "initials": "T"}, {"family": "Birukov", "given": "Anna", "initials": "A"}, {"family": "Eichelmann", "given": "Fabian", "initials": "F"}, {"family": "Andrade", "given": "Bruno G N", "initials": "BGN"}, {"family": "Bang", "given": "Corinna", "initials": "C"}, {"family": "Franke", "given": "Andre", "initials": "A"}, {"family": "Wittenbecher", "given": "Clemens", "initials": "C"}, {"family": "Schulze", "given": "Matthias B", "initials": "MB"}], "type": "journal article", "published": "2023-08-16", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "13", "issue": "1", "pages": "13348", "issn-l": "2045-2322"}, "abstract": "Gut microbiota metabolites have been mechanistically linked to inflammatory pathway activation and atherosclerosis, which are major causes of vascular stiffness (VS). Aiming to investigate if the gut microbiome might be involved in VS development, we performed a cross-sectional study (n = 3,087), nested within the population-based European Prospective Investigations into Cancer and Nutrition (EPIC) Potsdam. We investigated the correlation of the gut microbiota (alpha diversity and taxa abundance) with 3 vascular stiffness measures: carotid-femoral (PWV), aortic augmentation index (AIX) and ankle-brachial index (ABI). Shannon index was not significantly associated with VS but the number of observed Amplicon Sequence Variants (ASV) was positively associated with PWV and AIX. We found a total of 19 ASVs significantly associated with at least one VS measure in multivariable-adjusted models. One ASV (classified as Sutterella wadsworthensis) was associated with 2 VS measures, AIX (- 0.11 \u00b1 0.04) and PWV (-0.14 \u00b1 0.03). Other examples of ASVs associated with VS were Collinsella aerofaciens, previously reported to be affected by diet and Bacteroides uniformis, commercially available as probiotics. In conclusion, our study suggests a potential role of individual components of the gut microbiota in the aetiology of VS.", "doi": "10.1038/s41598-023-40178-6", "pmid": "37587126", "labels": {"Clemens Wittenbecher": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC10432492"}, {"db": "pii", "key": "10.1038/s41598-023-40178-6"}], "notes": [], "created": "2025-03-19T08:18:52.885Z", "modified": "2025-12-09T13:32:54.216Z"}, {"entity": "publication", "iuid": "566d0bcd091c4efb9a0c8621c74affb7", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/566d0bcd091c4efb9a0c8621c74affb7.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/566d0bcd091c4efb9a0c8621c74affb7"}}, "title": "The Genomic and Epigenomic Landscape of Double-Negative Metastatic Prostate Cancer.", "authors": [{"family": "Lundberg", "given": "Arian", "initials": "A", "orcid": "0000-0002-6630-2787", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/baa2c7c8963840bfb6a22d7c5cfe35f9.json"}}, {"family": "Zhang", "given": "Meng", "initials": "M", "orcid": "0000-0003-1042-6294", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3d24c6c51c024ac0b27a5162c4c2fa91.json"}}, {"family": "Aggarwal", "given": "Rahul", "initials": "R", "orcid": "0000-0001-7003-7982", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dc6eb510bedd42bbb6f57e03e724efba.json"}}, {"family": "Li", "given": "Haolong", "initials": "H", "orcid": "0000-0002-8628-9698", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fbc2d2abba854008b56d417e6083614c.json"}}, {"family": "Zhang", "given": "Li", "initials": "L", "orcid": "0000-0002-3617-2627", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4a197e422e644bd38f0d69f33e653ac7.json"}}, {"family": "Foye", "given": "Adam", "initials": "A", "orcid": "0000-0002-9910-9836", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/74c8c402b4a243ab95b9d20ecc43d4b9.json"}}, {"family": "Sj\u00f6str\u00f6m", "given": "Martin", "initials": "M", "orcid": "0000-0002-2629-9966", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b42d7aeedc844018bbe28980b73cb6c6.json"}}, {"family": "Chou", "given": "Jonathan", "initials": "J", "orcid": "0000-0003-1258-0391", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c4a72f7d3b2d4f72a8ebfc23f36f3714.json"}}, {"family": "Chang", "given": "Kevin", "initials": "K", "orcid": "0000-0001-6227-6430", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/703469ab773341ae86aa8c0a44968b2f.json"}}, {"family": "Moreno-Rodriguez", "given": "Thaidy", "initials": "T", "orcid": "0000-0003-3588-3889", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/be9adfae1d354f85a76d66de8bc08cba.json"}}, {"family": "Shrestha", "given": "Raunak", "initials": "R", "orcid": "0000-0002-1144-1413", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1ee8056667cd46ecbec79e2789ae8029.json"}}, {"family": "Baskin", "given": "Avi", "initials": "A", "orcid": "0000-0002-1016-2025", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d74a04ff676b4051b905f344e90a00ac.json"}}, {"family": "Zhu", "given": "Xiaolin", "initials": "X", "orcid": "0000-0002-3221-595X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/30d1c66f02ef4b5abc414a110705ccf9.json"}}, {"family": "Weinstein", "given": "Alana S", "initials": "AS", "orcid": "0000-0002-1563-9072", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e16ba4d459704a96adc34a85197bab05.json"}}, {"family": "Younger", "given": "Noah", "initials": "N", "orcid": "0000-0001-5536-6999", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0ef8306568e64bd0935d6ecaad78cf89.json"}}, {"family": "Alumkal", "given": "Joshi J", "initials": "JJ", "orcid": "0000-0003-1278-0166", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/92169d39d28f4819959b032eff1b1b80.json"}}, {"family": "Beer", "given": "Tomasz M", "initials": "TM", "orcid": "0000-0001-5600-9993", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c828b8adf0944e72aaacab129733f181.json"}}, {"family": "Chi", "given": "Kim N", "initials": "KN", "orcid": "0000-0002-3782-7226", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6ee7573962f6411688894c17260e1095.json"}}, {"family": "Evans", "given": "Christopher P", "initials": "CP", "orcid": "0000-0001-5626-8901", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a8a9ee6f18f94c9ea82f34401edc3467.json"}}, {"family": "Gleave", "given": "Martin", "initials": "M", "orcid": "0000-0003-4235-0167", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f3a7aa50e3874927b1db062aa35b415d.json"}}, {"family": "Lara", "given": "Primo N", "initials": "PN", "orcid": "0000-0001-9512-0002", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a9baabb4a6be4dfd9dad6ab7bcb8319d.json"}}, {"family": "Reiter", "given": "Rob E", "initials": "RE", "orcid": "0000-0002-7962-3985", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a81ac4aa295d40d6825364129548f95d.json"}}, {"family": "Rettig", "given": "Matthew B", "initials": "MB", "orcid": "0000-0002-7394-3056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/df1dd288962643beb53cce332f615144.json"}}, {"family": "Witte", "given": "Owen N", "initials": "ON", "orcid": "0000-0003-4461-4533", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/435dcbfb32af474a9027576c7dc49ec6.json"}}, {"family": "Wyatt", "given": "Alexander W", "initials": "AW", "orcid": "0000-0003-2399-0329", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/41e8ef800a344c68be341f0691438260.json"}}, {"family": "Feng", "given": "Felix Y", "initials": "FY", "orcid": "0000-0002-0963-7687", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c5af5c0e774941ac97890f17640a339e.json"}}, {"family": "Small", "given": "Eric J", "initials": "EJ", "orcid": "0000-0003-3191-6268", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a5a6d3bacede42059d6bf0f2cbfe0fec.json"}}, {"family": "Quigley", "given": "David A", "initials": "DA", "orcid": "0000-0002-4726-1473", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a7672a24a905407c8b5f9d1e28deea02.json"}}], "type": "journal article", "published": "2023-08-15", "journal": {"title": "Cancer Res.", "issn": "1538-7445", "volume": "83", "issue": "16", "pages": "2763-2774", "issn-l": "0008-5472"}, "abstract": "Systemic targeted therapy in prostate cancer is primarily focused on ablating androgen signaling. Androgen deprivation therapy and second-generation androgen receptor (AR)-targeted therapy selectively favor the development of treatment-resistant subtypes of metastatic castration-resistant prostate cancer (mCRPC), defined by AR and neuroendocrine (NE) markers. Molecular drivers of double-negative (AR-/NE-) mCRPC are poorly defined. In this study, we comprehensively characterized treatment-emergent mCRPC by integrating matched RNA sequencing, whole-genome sequencing, and whole-genome bisulfite sequencing from 210 tumors. AR-/NE- tumors were clinically and molecularly distinct from other mCRPC subtypes, with the shortest survival, amplification of the chromatin remodeler CHD7, and PTEN loss. Methylation changes in CHD7 candidate enhancers were linked to elevated CHD7 expression in AR-/NE+ tumors. Genome-wide methylation analysis nominated Kr\u00fcppel-like factor 5 (KLF5) as a driver of the AR-/NE- phenotype, and KLF5 activity was linked to RB1 loss. These observations reveal the aggressiveness of AR-/NE- mCRPC and could facilitate the identification of therapeutic targets in this highly aggressive disease.\n\nComprehensive characterization of the five subtypes of metastatic castration-resistant prostate cancer identified transcription factors that drive each subtype and showed that the double-negative subtype has the worst prognosis.", "doi": "10.1158/0008-5472.CAN-23-0593", "pmid": "37289025", "labels": {"DDLS Fellow": null, "Arian Lundberg": null}, "xrefs": [{"db": "pmc", "key": "PMC10425725"}, {"db": "pii", "key": "727214"}], "notes": [], "created": "2025-11-14T07:50:04.624Z", "modified": "2025-11-14T07:50:05.101Z"}, {"entity": "publication", "iuid": "a2c8fd6258fc41fc9057fd1d0f79b690", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a2c8fd6258fc41fc9057fd1d0f79b690.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a2c8fd6258fc41fc9057fd1d0f79b690"}}, "title": "Towards monitoring of antimicrobial resistance in the environment: For what reasons, how to implement it, and what are the data needs?", "authors": [{"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Abramova", "given": "Anna", "initials": "A"}, {"family": "Berendonk", "given": "Thomas U", "initials": "TU"}, {"family": "Coelho", "given": "Luis Pedro", "initials": "LP"}, {"family": "Forslund", "given": "Sofia K", "initials": "SK"}, {"family": "Gschwind", "given": "R\u00e9mi", "initials": "R"}, {"family": "Heikinheimo", "given": "Annamari", "initials": "A"}, {"family": "Jarqu\u00edn-D\u00edaz", "given": "V\u00edctor Hugo", "initials": "VH"}, {"family": "Khan", "given": "Ayaz Ali", "initials": "AA"}, {"family": "Kl\u00fcmper", "given": "Uli", "initials": "U"}, {"family": "L\u00f6ber", "given": "Ulrike", "initials": "U"}, {"family": "Nekoro", "given": "Marmar", "initials": "M"}, {"family": "Osi\u0144ska", "given": "Adriana D", "initials": "AD"}, {"family": "Ugarcina Perovic", "given": "Svetlana", "initials": "S"}, {"family": "Pitk\u00e4nen", "given": "Tarja", "initials": "T"}, {"family": "R\u00f8dland", "given": "Ernst Kristian", "initials": "EK"}, {"family": "Rupp\u00e9", "given": "Etienne", "initials": "E"}, {"family": "Wasteson", "given": "Yngvild", "initials": "Y"}, {"family": "Wester", "given": "Astrid Louise", "initials": "AL"}, {"family": "Zahra", "given": "Rabaab", "initials": "R"}], "type": "journal article", "published": "2023-08-00", "journal": {"title": "Environ Int", "issn": "1873-6750", "volume": "178", "pages": "108089", "issn-l": "0160-4120"}, "abstract": "Antimicrobial resistance (AMR) is a global threat to human and animal health and well-being. To understand AMR dynamics, it is important to monitor resistant bacteria and resistance genes in all relevant settings. However, while monitoring of AMR has been implemented in clinical and veterinary settings, comprehensive monitoring of AMR in the environment is almost completely lacking. Yet, the environmental dimension of AMR is critical for understanding the dissemination routes and selection of resistant microorganisms, as well as the human health risks related to environmental AMR. Here, we outline important knowledge gaps that impede implementation of environmental AMR monitoring. These include lack of knowledge of the 'normal' background levels of environmental AMR, definition of high-risk environments for transmission, and a poor understanding of the concentrations of antibiotics and other chemical agents that promote resistance selection. Furthermore, there is a lack of methods to detect resistance genes that are not already circulating among pathogens. We conclude that these knowledge gaps need to be addressed before routine monitoring for AMR in the environment can be implemented on a large scale. Yet, AMR monitoring data bridging different sectors is needed in order to fill these knowledge gaps, which means that some level of national, regional and global AMR surveillance in the environment must happen even without all scientific questions answered. With the possibilities opened up by rapidly advancing technologies, it is time to fill these knowledge gaps. Doing so will allow for specific actions against environmental AMR development and spread to pathogens and thereby safeguard the health and wellbeing of humans and animals.", "doi": "10.1016/j.envint.2023.108089", "pmid": "37441817", "labels": {"DDLS Fellow": ""}, "xrefs": [{"db": "pii", "key": "S0160-4120(23)00362-8"}], "notes": [], "created": "2024-11-18T11:42:56.329Z", "modified": "2026-09-23T06:46:23.866Z"}, {"entity": "publication", "iuid": "1dd5448da4264efab44a0f27d42fad69", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1dd5448da4264efab44a0f27d42fad69.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1dd5448da4264efab44a0f27d42fad69"}}, "title": "A global baseline for qPCR-determined antimicrobial resistance gene prevalence across environments.", "authors": [{"family": "Abramova", "given": "Anna", "initials": "A", "orcid": "0000-0002-0493-7808", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dd75cbcc659c4ca398eb678fad1dc498.json"}}, {"family": "Berendonk", "given": "Thomas U", "initials": "TU", "orcid": "0000-0002-9301-1803", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c66286f83a8430f954fbc5c52db10c5.json"}}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J", "orcid": "0000-0002-6528-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c666068e9d34939b0252a627007cec7.json"}}], "type": "review", "published": "2023-08-00", "journal": {"title": "Environ Int", "issn": "1873-6750", "issn-l": "0160-4120", "volume": "178", "issue": null, "pages": "108084"}, "abstract": "The environment is an important component in the emergence and transmission of antimicrobial resistance (AMR). Despite that, little effort has been made to monitor AMR outside of clinical and veterinary settings. Partially, this is caused by a lack of comprehensive reference data for the vast majority of environments. To enable monitoring to detect deviations from the normal background resistance levels in the environment, it is necessary to establish a baseline of AMR in a variety of settings. In an attempt to establish this baseline level, we here performed a comprehensive literature survey, identifying 150 scientific papers containing relevant qPCR data on antimicrobial resistance genes (ARGs) in environments associated with potential routes for AMR dissemination. The collected data included 1594 samples distributed across 30 different countries and 12 sample types, in a time span from 2001 to 2020. We found that for most ARGs, the typically reported abundances in human impacted environments fell in an interval from 10-5 to 10-3 copies per 16S rRNA, roughly corresponding to one ARG copy in a thousand bacteria. Altogether these data represent a comprehensive overview of the occurrence and levels of ARGs in different environments, providing background data for risk assessment models within current and future AMR monitoring frameworks.", "doi": "10.1016/j.envint.2023.108084", "pmid": "37421899", "labels": {"DDLS Fellow": ""}, "xrefs": [{"db": "pii", "key": "S0160-4120(23)00357-4"}], "notes": [], "created": "2022-11-08T09:31:13.181Z", "modified": "2026-09-23T07:46:30.567Z"}, {"entity": "publication", "iuid": "15bee8eb34a0438a9b7c764bc2631381", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/15bee8eb34a0438a9b7c764bc2631381.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/15bee8eb34a0438a9b7c764bc2631381"}}, "title": "A new codon adaptation metric predicts vertebrate body size and tendency to protein disorder", "authors": [{"family": "Weibel", "given": "Catherine A", "initials": "CA", "orcid": "0000-0003-1837-5209", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/54d6dc2af7084fc58d9ab18aa72423e7.json"}}, {"family": "Wheeler", "given": "Andrew L", "initials": "AL", "orcid": "0000-0002-5347-5419", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d5be19398f37475282b6d184b7e77cfe.json"}}, {"family": "James", "given": "Jennifer E", "initials": "JE", "orcid": "0000-0003-0518-6783", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4b807f7ab8f46f8a5e927e1b090d662.json"}}, {"family": "Willis", "given": "Sara M", "initials": "SM", "orcid": "0000-0002-1605-6426", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6316b06885844b32a451c3b8ab502060.json"}}, {"family": "Masel", "given": "Joanna", "initials": "J", "orcid": "0000-0002-7398-2127", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eed69f257e574f4aa53f59349c3ff384.json"}}], "type": "posted-content", "published": "2023-07-26", "journal": {"title": null, "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.7554/elife.87335.1", "pmid": null, "labels": {"Jennifer James": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2024-11-27T09:25:31.199Z", "modified": "2024-11-29T09:34:33.892Z"}, {"entity": "publication", "iuid": "6c145a5f700f4bedaeff29e6b88fa46d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/6c145a5f700f4bedaeff29e6b88fa46d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/6c145a5f700f4bedaeff29e6b88fa46d"}}, "title": "Moving beyond the desktop: prospects for practical bioimage analysis via the web.", "authors": [{"family": "Ouyang", "given": "Wei", "initials": "W"}, {"family": "Eliceiri", "given": "Kevin W", "initials": "KW"}, {"family": "Cimini", "given": "Beth A", "initials": "BA"}], "type": "journal article", "published": "2023-07-25", "journal": {"title": "Front Bioinform", "issn": "2673-7647", "volume": "3", "pages": "1233748", "issn-l": null}, "abstract": "As biological imaging continues to rapidly advance, it results in increasingly complex image data, necessitating a reevaluation of conventional bioimage analysis methods and their accessibility. This perspective underscores our belief that a transition from desktop-based tools to web-based bioimage analysis could unlock immense opportunities for improved accessibility, enhanced collaboration, and streamlined workflows. We outline the potential benefits, such as reduced local computational demands and solutions to common challenges, including software installation issues and limited reproducibility. Furthermore, we explore the present state of web-based tools, hurdles in implementation, and the significance of collective involvement from the scientific community in driving this transition. In acknowledging the potential roadblocks and complexity of data management, we suggest a combined approach of selective prototyping and large-scale workflow application for optimal usage. Embracing web-based bioimage analysis could pave the way for the life sciences community to accelerate biological research, offering a robust platform for a more collaborative, efficient, and democratized science.", "doi": "10.3389/fbinf.2023.1233748", "pmid": "37560357", "labels": {"DDLS Fellow": "", "Wei Ouyang": ""}, "xrefs": [{"db": "pmc", "key": "PMC10409478"}, {"db": "pii", "key": "1233748"}], "notes": [], "created": "2026-08-20T13:05:21.721Z", "modified": "2026-09-23T12:56:30.929Z"}, {"entity": "publication", "iuid": "dd820619d0bd4ca29c27b758dfd69742", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/dd820619d0bd4ca29c27b758dfd69742.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/dd820619d0bd4ca29c27b758dfd69742"}}, "title": "Genus-wide genomic characterization of Macrococcus: insights into evolution, population structure, and functional potential.", "authors": [{"family": "Carroll", "given": "Laura M", "initials": "LM"}, {"family": "Pierneef", "given": "Rian", "initials": "R"}, {"family": "Mafuna", "given": "Thendo", "initials": "T"}, {"family": "Magwedere", "given": "Kudakwashe", "initials": "K"}, {"family": "Matle", "given": "Itumeleng", "initials": "I"}], "type": "journal article", "published": "2023-07-20", "journal": {"title": "Front Microbiol", "issn": "1664-302X", "volume": "14", "pages": "1181376", "issn-l": "1664-302X"}, "abstract": "Macrococcus species have been isolated from a range of mammals and mammal-derived food products. While they are largely considered to be animal commensals, Macrococcus spp. can be opportunistic pathogens in both veterinary and human clinical settings. This study aimed to provide insight into the evolution, population structure, and functional potential of the Macrococcus genus, with an emphasis on antimicrobial resistance (AMR) and virulence potential.\n\nAll high-quality, publicly available Macrococcus genomes (n = 104, accessed 27 August 2022), plus six South African genomes sequenced here (two strains from bovine clinical mastitis cases and four strains from beef products), underwent taxonomic assignment (using four different approaches), AMR determinant detection (via AMRFinderPlus), and virulence factor detection (using DIAMOND and the core Virulence Factor Database).\n\nOverall, the 110 Macrococcus genomes were of animal commensal, veterinary clinical, food-associated (including food spoilage), and environmental origins; five genomes (4.5%) originated from human clinical cases. Notably, none of the taxonomic assignment methods produced identical results, highlighting the potential for Macrococcus species misidentifications. The most common predicted antimicrobial classes associated with AMR determinants identified across Macrococcus included macrolides, beta-lactams, and aminoglycosides (n = 81, 61, and 44 of 110 genomes; 73.6, 55.5, and 40.0%, respectively). Genes showing homology to Staphylococcus aureus exoenzyme aureolysin were detected across multiple species (using 90% coverage, n = 40 and 77 genomes harboring aureolysin-like genes at 60 and 40% amino acid [AA] identity, respectively). S. aureus Panton-Valentine leucocidin toxin-associated lukF-PV and lukS-PV homologs were identified in eight M. canis genomes (\u226540% AA identity, >85% coverage). Using a method that delineates populations using recent gene flow (PopCOGenT), two species (M. caseolyticus and M. armenti) were composed of multiple within-species populations. Notably, M. armenti was partitioned into two populations, which differed in functional potential (e.g., one harbored beta-lactamase family, type II toxin-antitoxin system, and stress response proteins, while the other possessed a Type VII secretion system; PopCOGenT p < 0.05).\n\nOverall, this study leverages all publicly available Macrococcus genomes in addition to newly sequenced genomes from South Africa to identify genomic elements associated with AMR or virulence potential, which can be queried in future experiments.", "doi": "10.3389/fmicb.2023.1181376", "pmid": "37547688", "labels": {"Laura Carroll": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC10400458"}], "notes": [], "created": "2025-03-18T17:31:08.329Z", "modified": "2026-09-23T11:09:14.773Z"}, {"entity": "publication", "iuid": "ec2cc1f2f82349ebad78c1e7c3f76984", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ec2cc1f2f82349ebad78c1e7c3f76984.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ec2cc1f2f82349ebad78c1e7c3f76984"}}, "title": "Next generation pan-cancer blood proteome profiling using proximity extension assay.", "authors": [{"family": "\u00c1lvez", "given": "Mar\u00eda Bueno", "initials": "MB", "orcid": "0000-0002-2669-7796", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a7d09e4780a445b9b432d494c76d07e8.json"}}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e213b04f8984c8eb00c68f5bc2f6a36.json"}}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K", "orcid": "0000-0002-0257-7554", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f4c4545bd2324b7d9b6696dab5bcb7dd.json"}}, {"family": "Zwahlen", "given": "Martin", "initials": "M", "orcid": "0000-0002-0064-4776", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/456805fa3f4f47328f3923b78bf66996.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca58bf2d214047e0ae5e38a42a0f2808.json"}}, {"family": "Edqvist", "given": "Per-Henrik", "initials": "PH", "orcid": "0000-0002-8330-0134", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5219527c2dc6480da474f3c47dff9318.json"}}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T", "orcid": "0000-0001-6668-4140", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/851b95a56b3244fb9bc7cec8294e7ae7.json"}}, {"family": "Lundin", "given": "Emma", "initials": "E", "orcid": "0009-0000-7711-1962", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c300121409e64e4c9a99f59d8b2a07c1.json"}}, {"family": "Rameika", "given": "Natallia", "initials": "N", "orcid": "0000-0002-7835-4357", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c9ea2e7b3c3f4df8aab2f25ac4f9923b.json"}}, {"family": "Enblad", "given": "Gunilla", "initials": "G", "orcid": "0000-0002-0594-724X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2a285fb437854e2c998356b1a3124416.json"}}, {"family": "Lindman", "given": "Henrik", "initials": "H"}, {"family": "H\u00f6glund", "given": "Martin", "initials": "M", "orcid": "0000-0003-2468-0226", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b04dde8160944595a255121a2571d2da.json"}}, {"family": "Hesselager", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0001-9613-1344", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/84c0500c4312423ca21366265e4aa4dc.json"}}, {"family": "St\u00e5lberg", "given": "Karin", "initials": "K", "orcid": "0000-0001-5527-8796", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ca801fe1aba4d04a06eaf9f6e3407dd.json"}}, {"family": "Enblad", "given": "Malin", "initials": "M", "orcid": "0000-0001-5900-0900", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bd2f8ad89196420584d0f79ad24575d3.json"}}, {"family": "Simonson", "given": "Oscar E", "initials": "OE", "orcid": "0000-0002-3552-5558", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f721cc39cb13464b964a10eba1045a04.json"}}, {"family": "H\u00e4ggman", "given": "Michael", "initials": "M"}, {"family": "Axelsson", "given": "Tomas", "initials": "T"}, {"family": "\u00c5berg", "given": "Mikael", "initials": "M", "orcid": "0000-0002-7858-8233", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a08650cb00404b6dba35959f3cb0a53c.json"}}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/27ee07e408e24eefa23105dcc6aa252b.json"}}, {"family": "Zhong", "given": "Wen", "initials": "W", "orcid": "0000-0002-7422-6104", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d6ffb1140aaa42c5ac63fe76653fc63b.json"}}, {"family": "Karlsson", "given": "Max", "initials": "M", "orcid": "0000-0002-7000-4416", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b93284f942e44f1086616357d77267c3.json"}}, {"family": "Gyllensten", "given": "Ulf", "initials": "U", "orcid": "0000-0002-6316-3355", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eacfdf2095e947e99ac45fe994261b72.json"}}, {"family": "Ponten", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9f5294424542413c9ba4432c839c2b63.json"}}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/abbbf8193d5a4376a5c726768d039439.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ea446aa574042a295d5f69437402f76.json"}}], "type": "journal article", "published": "2023-07-18", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "4308", "issn-l": "2041-1723"}, "abstract": "A comprehensive characterization of blood proteome profiles in cancer patients can contribute to a better understanding of the disease etiology, resulting in earlier diagnosis, risk stratification and better monitoring of the different cancer subtypes. Here, we describe the use of next generation protein profiling to explore the proteome signature in blood across patients representing many of the major cancer types. Plasma profiles of 1463 proteins from more than 1400 cancer patients are measured in minute amounts of blood collected at the time of diagnosis and before treatment. An open access Disease Blood Atlas resource allows the exploration of the individual protein profiles in blood collected from the individual cancer patients. We also present studies in which classification models based on machine learning have been used for the identification of a set of proteins associated with each of the analyzed cancers. The implication for cancer precision medicine of next generation plasma profiling is discussed.", "doi": "10.1038/s41467-023-39765-y", "pmid": "37463882", "labels": {"Adil Mardinoglu": "", "SciLifeLab Fellow": "", "Fredrik Edfors": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC10354027"}, {"db": "pii", "key": "10.1038/s41467-023-39765-y"}], "notes": [], "created": "2023-12-04T14:49:43.596Z", "modified": "2026-09-23T08:29:19.964Z"}, {"entity": "publication", "iuid": "3378a871f18a4148aae6068891b260e8", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3378a871f18a4148aae6068891b260e8.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3378a871f18a4148aae6068891b260e8"}}, "title": "Adipose tissue and skeletal muscle wasting precede clinical diagnosis of pancreatic cancer.", "authors": [{"family": "Babic", "given": "Ana", "initials": "A", "orcid": "0000-0003-1199-5958", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a3b7f71f0bf4058a8aed3acc297e34c.json"}}, {"family": "Rosenthal", "given": "Michael H", "initials": "MH", "orcid": "0000-0002-5085-3904", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fc9283f8577440f48d79357f384904c0.json"}}, {"family": "Sundaresan", "given": "Tilak K", "initials": "TK"}, {"family": "Khalaf", "given": "Natalia", "initials": "N"}, {"family": "Lee", "given": "Valerie", "initials": "V"}, {"family": "Brais", "given": "Lauren K", "initials": "LK"}, {"family": "Loftus", "given": "Maureen", "initials": "M"}, {"family": "Caplan", "given": "Leah", "initials": "L", "orcid": "0000-0002-6594-1608", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8809f219a2764b8888f7e1cb3831f77e.json"}}, {"family": "Denning", "given": "Sarah", "initials": "S"}, {"family": "Gurung", "given": "Anamol", "initials": "A"}, {"family": "Harrod", "given": "Joanna", "initials": "J"}, {"family": "Schawkat", "given": "Khoschy", "initials": "K"}, {"family": "Yuan", "given": "Chen", "initials": "C"}, {"family": "Wang", "given": "Qiao-Li", "initials": "QL"}, {"family": "Lee", "given": "Alice A", "initials": "AA"}, {"family": "Biller", "given": "Leah H", "initials": "LH"}, {"family": "Yurgelun", "given": "Matthew B", "initials": "MB", "orcid": "0000-0002-6184-9273", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/601bf1b5f39a4be39c0e022be87e96c7.json"}}, {"family": "Ng", "given": "Kimmie", "initials": "K", "orcid": "0000-0003-0631-1494", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/00bc0d97cfc44e9398c9bf1db5783402.json"}}, {"family": "Nowak", "given": "Jonathan A", "initials": "JA"}, {"family": "Aguirre", "given": "Andrew J", "initials": "AJ", "orcid": "0000-0002-0701-6203", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0854cc8538a64679bd3f4ed7c2ddfa56.json"}}, {"family": "Bhatia", "given": "Sangeeta N", "initials": "SN", "orcid": "0000-0002-1293-2097", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0cd662b291c94b04bc9b6ddc30d3f251.json"}}, {"family": "Vander Heiden", "given": "Matthew G", "initials": "MG", "orcid": "0000-0002-6702-4192", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/94f86a2c5cbd412e82fa431c97e70d3d.json"}}, {"family": "Van Den Eeden", "given": "Stephen K", "initials": "SK", "orcid": "0000-0002-5599-8387", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/622928482be5479981a77cf50721027a.json"}}, {"family": "Caan", "given": "Bette J", "initials": "BJ"}, {"family": "Wolpin", "given": "Brian M", "initials": "BM", "orcid": "0000-0002-0455-1032", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/90c86221350a45c1a398d089855e7dac.json"}}], "type": "journal article", "published": "2023-07-18", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "4317", "issn-l": "2041-1723"}, "abstract": "Patients with pancreatic cancer commonly develop weight loss and muscle wasting. Whether adipose tissue and skeletal muscle losses begin before diagnosis and the potential utility of such losses for earlier cancer detection are not well understood. We quantify skeletal muscle and adipose tissue areas from computed tomography (CT) imaging obtained 2 months to 5 years before cancer diagnosis in 714 pancreatic cancer cases and 1748 matched controls. Adipose tissue loss is identified up to 6 months, and skeletal muscle wasting is identified up to 18 months before the clinical diagnosis of pancreatic cancer and is not present in the matched control population. Tissue losses are of similar magnitude in cases diagnosed with localized compared with metastatic disease and are not correlated with at-diagnosis circulating levels of CA19-9. Skeletal muscle wasting occurs in the 1-2 years before pancreatic cancer diagnosis and may signal an upcoming diagnosis of pancreatic cancer.", "doi": "10.1038/s41467-023-40024-3", "pmid": "37463915", "labels": {"DDLS Fellow": null, "Qiaoli Wang": null}, "xrefs": [{"db": "pmc", "key": "PMC10354105"}, {"db": "pii", "key": "10.1038/s41467-023-40024-3"}], "notes": [], "created": "2025-11-28T12:23:08.754Z", "modified": "2025-11-28T12:23:09.015Z"}, {"entity": "publication", "iuid": "9194f47a06d344d39b20f1b699515268", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9194f47a06d344d39b20f1b699515268.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9194f47a06d344d39b20f1b699515268"}}, "title": "Plasma 25-Hydroxyvitamin D Levels and Survival in Stage III Colon Cancer: Findings from CALGB/SWOG 80702 (Alliance).", "authors": [{"family": "Wang", "given": "Qiao-Li", "initials": "QL", "orcid": "0000-0003-4152-7821", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/357edb3116b64ad5aa929dcb7d07a1be.json"}}, {"family": "Ma", "given": "Chao", "initials": "C", "orcid": "0000-0001-7741-818X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/332d015449d74d488c597a2a1cd76639.json"}}, {"family": "Yuan", "given": "Chen", "initials": "C", "orcid": "0000-0002-0708-9648", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cd3904c835394e0d89bba633a0b74c54.json"}}, {"family": "Shi", "given": "Qian", "initials": "Q", "orcid": "0000-0002-4640-8832", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a3d059b019db4c0db503b05effe1b0fb.json"}}, {"family": "Wolpin", "given": "Brian M", "initials": "BM", "orcid": "0000-0002-0455-1032", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/90c86221350a45c1a398d089855e7dac.json"}}, {"family": "Zhang", "given": "Yin", "initials": "Y", "orcid": "0000-0001-6367-6583", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/86a19de667ad4273ac7552cd7d79982a.json"}}, {"family": "Fuchs", "given": "Charles S", "initials": "CS", "orcid": "0000-0003-1582-9842", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4dd3b36e3b444d5b890959320a879830.json"}}, {"family": "Meyer", "given": "Jeffrey", "initials": "J", "orcid": "0000-0003-2203-0756", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ddb0d7f1c6f746e484945d0ec05a5867.json"}}, {"family": "Zemla", "given": "Tyler", "initials": "T", "orcid": "0009-0005-2390-3557", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1982f707bc7b42718e1b7804552803ae.json"}}, {"family": "Cheng", "given": "En", "initials": "E", "orcid": "0000-0001-9523-9310", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8ef2f8a6aa4b4dfeac720ca7c71e95f0.json"}}, {"family": "Kumthekar", "given": "Priya", "initials": "P", "orcid": "0000-0001-5923-0677", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fec7f9019685481c86d031cffea9f0f8.json"}}, {"family": "Guthrie", "given": "Katherine A", "initials": "KA", "orcid": "0000-0001-7257-8280", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3548ee4b704c40eabd445a477836f977.json"}}, {"family": "Couture", "given": "Felix", "initials": "F", "orcid": "0009-0002-0190-1938", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6d3aa6f80d47431db31ff04773d57ba9.json"}}, {"family": "Kuebler", "given": "Philip", "initials": "P", "orcid": "0009-0004-0964-2971", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/80c029af5bc64a6f92ab2d5e0e3e4ae6.json"}}, {"family": "Kumar", "given": "Pankaj", "initials": "P", "orcid": "0000-0003-4284-6787", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6eca99c6b2524a6894a3bf2a439a9d90.json"}}, {"family": "Tan", "given": "Benjamin", "initials": "B", "orcid": "0000-0003-1838-1182", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dd6902fd49ba490a9ce7ca3b4afebc34.json"}}, {"family": "Krishnamurthi", "given": "Smitha", "initials": "S", "orcid": "0000-0003-2411-3504", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bd2be584227d434ba9cac88c9c968939.json"}}, {"family": "Goldberg", "given": "Richard M", "initials": "RM", "orcid": "0000-0003-0308-8223", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5d00914d17d64006ad1d16c6c05c7f58.json"}}, {"family": "Venook", "given": "Alan", "initials": "A", "orcid": "0000-0001-9749-6548", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3a154c75c8b44f1ca15077178b7c79d7.json"}}, {"family": "Blanke", "given": "Charles", "initials": "C", "orcid": "0000-0002-6493-7834", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3839fb3ba48247aba32bca94ce506770.json"}}, {"family": "Shields", "given": "Anthony F", "initials": "AF", "orcid": "0000-0002-9122-1014", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c3075458d988442d99f01f04d304aab2.json"}}, {"family": "O'Reilly", "given": "Eileen M", "initials": "EM", "orcid": "0000-0002-8076-9199", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/41c42f62e33a4e9b91405d4f861943a2.json"}}, {"family": "Meyerhardt", "given": "Jeffrey A", "initials": "JA", "orcid": "0000-0002-1120-0898", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1be03d64e6674271953b194ddaac4f29.json"}}, {"family": "Ng", "given": "Kimmie", "initials": "K", "orcid": "0000-0003-0631-1494", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/00bc0d97cfc44e9398c9bf1db5783402.json"}}], "type": "randomized controlled trial", "published": "2023-07-14", "journal": {"title": "Clin. Cancer Res.", "issn": "1557-3265", "volume": "29", "issue": "14", "pages": "2621-2630", "issn-l": "1078-0432"}, "abstract": "To assess whether higher plasma 25-hydroxyvitamin D [25(OH)D] is associated with improved outcomes in colon cancer and whether circulating inflammatory cytokines mediate such association.\n\nPlasma samples were collected from 1,437 patients with stage III colon cancer enrolled in a phase III randomized clinical trial (CALGB/SWOG 80702) from 2010 to 2015, who were followed until 2020. Cox regressions were used to examine associations between plasma 25(OH)D and disease-free survival (DFS), overall survival (OS), and time to recurrence (TTR). Mediation analysis was performed for circulating inflammatory biomarkers of C-reactive protein (CRP), IL6, and soluble TNF receptor 2 (sTNF-R2).\n\nVitamin D deficiency [25(OH)D <12 ng/mL] was present in 13% of total patients at baseline and in 32% of Black patients. Compared with deficiency, nondeficient vitamin D status (\u226512 ng/mL) was significantly associated with improved DFS, OS, and TTR (all Plog-rank<0.05), with multivariable-adjusted HRs of 0.68 (95% confidence interval, 0.51-0.92) for DFS, 0.57 (0.40-0.80) for OS, and 0.71 (0.52-0.98) for TTR. A U-shaped dose-response pattern was observed for DFS and OS (both Pnonlinearity<0.05). The proportion of the association with survival that was mediated by sTNF-R2 was 10.6% (Pmediation = 0.04) for DFS and 11.8% (Pmediation = 0.05) for OS, whereas CRP and IL6 were not shown to be mediators. Plasma 25(OH)D was not associated with the occurrence of \u2265 grade 2 adverse events.\n\nNondeficient vitamin D is associated with improved outcomes in patients with stage III colon cancer, largely independent of circulation inflammations. A randomized trial is warranted to elucidate whether adjuvant vitamin D supplementation improves patient outcomes.", "doi": "10.1158/1078-0432.CCR-23-0447", "pmid": "37289007", "labels": {"DDLS Fellow": null, "Qiaoli Wang": null}, "xrefs": [{"db": "mid", "key": "NIHMS1901788"}, {"db": "pmc", "key": "PMC10524689"}, {"db": "pii", "key": "727221"}], "notes": [], "created": "2025-11-28T12:23:04.229Z", "modified": "2025-11-28T12:23:05.247Z"}, {"entity": "publication", "iuid": "0740518bfbe543128aa1cd363b3509f8", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0740518bfbe543128aa1cd363b3509f8.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0740518bfbe543128aa1cd363b3509f8"}}, "title": "A data-driven study of Alzheimer's disease related amyloid and tau pathology progression.", "authors": [{"family": "Aksman", "given": "Leon M", "initials": "LM", "orcid": "0000-0003-2342-0780", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/215408c0a9f9472ca3ff3ec8e53cf4d6.json"}}, {"family": "Oxtoby", "given": "Neil P", "initials": "NP", "orcid": "0000-0003-0203-3909", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2408e58de5794533979e1f8f15ba217d.json"}}, {"family": "Scelsi", "given": "Marzia A", "initials": "MA"}, {"family": "Wijeratne", "given": "Peter A", "initials": "PA", "orcid": "0000-0002-4885-6241", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6567732a74d64c9d93d0e691ab3e0a8e.json"}}, {"family": "Young", "given": "Alexandra L", "initials": "AL", "orcid": "0000-0002-7772-781X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d8a71365a32a4f4da1a29a925e5334c3.json"}}, {"family": "Lopes Alves", "given": "Isadora", "initials": "I"}, {"family": "Collij", "given": "Lyduine E", "initials": "LE", "orcid": "0000-0001-6263-1762", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6612222d48fd4bdcaa7c091d38efcc2b.json"}}, {"family": "Vogel", "given": "Jacob W", "initials": "JW", "orcid": "0000-0001-6394-9940", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d2ad5af780c245da9b59a8c80a0b00ff.json"}}, {"family": "Barkhof", "given": "Frederik", "initials": "F"}, {"family": "Alexander", "given": "Daniel C", "initials": "DC"}, {"family": "Altmann", "given": "Andre", "initials": "A", "orcid": "0000-0002-9265-2393", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c629171e9c0749e39088eeee9272eea4.json"}}, {"family": "ADNI", "given": "", "initials": ""}], "type": "journal article", "published": "2023-07-11", "journal": {"title": "Brain", "issn": "1460-2156", "issn-l": "0006-8950", "volume": null, "issue": null, "pages": null}, "abstract": "Amyloid-beta is thought to facilitate the spread of tau throughout the neocortex in Alzheimer's disease, though how this occurs is not well understood. This is because of the spatial discordance between amyloid-beta, which accumulates in the neocortex, and tau, which accumulates in the medial temporal lobe during aging. There is evidence that in some cases amyloid-beta-independent tau spreads beyond the medial temporal lobe where it may interact with neocortical amyloid-beta. This suggests that there may be multiple distinct spatiotemporal subtypes of Alzheimer's-related protein aggregation, with potentially different demographic and genetic risk profiles. We investigated this hypothesis, applying data-driven disease progression subtyping models to post-mortem neuropathology and in vivo PET based measures from two large observational studies: the Alzheimer's Disease Neuroimaging Initiative and the Religious Orders Study and Rush Memory and Aging Project. We consistently identified 'amyloid-first' and 'tau-first' subtypes using cross-sectional information from both studies. In the amyloid-first subtype, extensive neocortical amyloid-beta precedes the spread of tau beyond the medial temporal lobe, while in the tau-first subtype mild tau accumulates in medial temporal and neocortical areas prior to interacting with amyloid-beta. As expected, we found a higher prevalence of the amyloid-first subtype among apolipoprotein E (APOE) \u03b54 allele carriers while the tau-first subtype was more common among APOE \u03b54 non-carriers. Within tau-first APOE \u03b54 carriers, we found an increased rate of amyloid-beta accumulation (via longitudinal amyloid PET), suggesting that this rare group may belong within the Alzheimer's disease continuum. We also found that tau-first APOE \u03b54 carriers had several fewer years of education than other groups, suggesting a role for modifiable risk factors in facilitating amyloid-beta-independent tau. Tau-first APOE \u03b54 non-carriers, in contrast, recapitulated many of the features of Primary Age-related Tauopathy. The rate of longitudinal amyloid-beta and tau accumulation (both measured via PET) within this group did not differ from normal aging, supporting the distinction of Primary Age-related Tauopathy from Alzheimer's disease. We also found reduced longitudinal subtype consistency within tau-first APOE \u03b54 non-carriers, suggesting additional heterogeneity within this group. Our findings support the idea that amyloid-beta and tau may begin as independent processes in spatially disconnected regions, with widespread neocortical tau resulting from the local interaction of amyloid-beta and tau. The site of this interaction may be subtype-dependent: medial temporal lobe in amyloid-first, neocortex in tau-first. These insights into the dynamics of amyloid-beta and tau may inform research and clinical trials that target these pathologies.", "doi": "10.1093/brain/awad232", "pmid": "37433038", "labels": {"Jacob W Vogel": null, "DDLS Fellow": null}, "xrefs": [{"db": "pii", "key": "7222857"}], "notes": [], "created": "2023-10-25T16:52:13.310Z", "modified": "2023-11-29T06:41:22.561Z"}, {"entity": "publication", "iuid": "477d12db1eb84e9a9cca913d8eb48c4e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/477d12db1eb84e9a9cca913d8eb48c4e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/477d12db1eb84e9a9cca913d8eb48c4e"}}, "title": "MOBILE pipeline enables identification of context-specific networks and regulatory mechanisms.", "authors": [{"family": "Erdem", "given": "Cemal", "initials": "C", "orcid": "0000-0003-3663-3646", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f71b5af589264614a52eefa8baba3132.json"}}, {"family": "Gross", "given": "Sean M", "initials": "SM"}, {"family": "Heiser", "given": "Laura M", "initials": "LM", "orcid": "0000-0003-3330-0950", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ce0d380df324afcbbaa1971aa8472cc.json"}}, {"family": "Birtwistle", "given": "Marc R", "initials": "MR", "orcid": "0000-0002-0341-0705", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/df52e09a2f984f10833bda7b554b1a22.json"}}], "type": "journal article", "published": "2023-07-06", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "3991", "issn-l": "2041-1723"}, "abstract": "Robust identification of context-specific network features that control cellular phenotypes remains a challenge. We here introduce MOBILE (Multi-Omics Binary Integration via Lasso Ensembles) to nominate molecular features associated with cellular phenotypes and pathways. First, we use MOBILE to nominate mechanisms of interferon-\u03b3 (IFN\u03b3) regulated PD-L1 expression. Our analyses suggest that IFN\u03b3-controlled PD-L1 expression involves BST2, CLIC2, FAM83D, ACSL5, and HIST2H2AA3 genes, which were supported by prior literature. We also compare networks activated by related family members transforming growth factor-beta 1 (TGF\u03b21) and bone morphogenetic protein 2 (BMP2) and find that differences in ligand-induced changes in cell size and clustering properties are related to differences in laminin/collagen pathway activity. Finally, we demonstrate the broad applicability and adaptability of MOBILE by analyzing publicly available molecular datasets to investigate breast cancer subtype specific networks. Given the ever-growing availability of multi-omics datasets, we envision that MOBILE will be broadly useful for identification of context-specific molecular features and pathways.", "doi": "10.1038/s41467-023-39729-2", "pmid": "37414767", "labels": {"DDLS Fellow": null, "Cemal Erdem": null}, "xrefs": [{"db": "pmc", "key": "PMC10326020"}, {"db": "pii", "key": "10.1038/s41467-023-39729-2"}], "notes": [], "created": "2023-10-27T08:53:28.475Z", "modified": "2023-10-27T08:53:28.873Z"}, {"entity": "publication", "iuid": "1ec4aea248e54794acb926703e7b5385", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1ec4aea248e54794acb926703e7b5385.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1ec4aea248e54794acb926703e7b5385"}}, "title": "Cardiomyocyte-specific PCSK9 deficiency compromises mitochondrial bioenergetics and heart function.", "authors": [{"family": "Laudette", "given": "Marion", "initials": "M"}, {"family": "Lindbom", "given": "Malin", "initials": "M"}, {"family": "Arif", "given": "Muhammad", "initials": "M", "orcid": "0000-0003-2261-0881", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c8ffc9889ace44e3b992816601b817e2.json"}}, {"family": "Cinato", "given": "Mathieu", "initials": "M", "orcid": "0000-0002-8490-4335", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5b2d3790356a446e85061a007b50bb28.json"}}, {"family": "Ruiz", "given": "Mario", "initials": "M"}, {"family": "Doran", "given": "Stephen", "initials": "S", "orcid": "0000-0002-9236-5407", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/836142c593f64f98a4c5a5ea20663485.json"}}, {"family": "Miljanovic", "given": "Azra", "initials": "A"}, {"family": "Rutberg", "given": "Mikael", "initials": "M"}, {"family": "Andersson", "given": "Linda", "initials": "L"}, {"family": "Klevstig", "given": "Martina", "initials": "M"}, {"family": "Henricsson", "given": "Marcus", "initials": "M", "orcid": "0000-0002-4202-0339", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e0fbd663456e4767acbfbe87f79a930b.json"}}, {"family": "Bergh", "given": "Per-Olof", "initials": "PO"}, {"family": "Bollano", "given": "Entela", "initials": "E"}, {"family": "Aung", "given": "Nay", "initials": "N", "orcid": "0000-0001-5095-1611", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/741c9417ac1d451c8f6fcd4adfa7b78a.json"}}, {"family": "Gustav Smith", "given": "J", "initials": "J"}, {"family": "Pilon", "given": "Marc", "initials": "M"}, {"family": "Hy\u00f6tyl\u00e4inen", "given": "Tuulia", "initials": "T", "orcid": "0000-0002-1389-8302", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fc08a199297b42afa85e07adc381a8f4.json"}}, {"family": "Ore\u0161i\u010d", "given": "Matej", "initials": "M"}, {"family": "Perkins", "given": "Rosie", "initials": "R"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Levin", "given": "Malin C", "initials": "MC"}, {"family": "Bor\u00e9n", "given": "Jan", "initials": "J", "orcid": "0000-0003-0786-8091", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/73a770eb9e614448a046b8e9199052e9.json"}}], "type": "journal article", "published": "2023-07-04", "journal": {"title": "Cardiovasc Res", "issn": "1755-3245", "volume": "119", "issue": "7", "pages": "1537-1552", "issn-l": null}, "abstract": "Pro-protein convertase subtilisin-kexin type 9 (PCSK9), which is expressed mainly in the liver and at low levels in the heart, regulates cholesterol levels by directing low-density lipoprotein receptors to degradation. Studies to determine the role of PCSK9 in the heart are complicated by the close link between cardiac function and systemic lipid metabolism. Here, we sought to elucidate the function of PCSK9 specifically in the heart by generating and analysing mice with cardiomyocyte-specific Pcsk9 deficiency (CM-Pcsk9-/- mice) and by silencing Pcsk9 acutely in a cell culture model of adult cardiomyocyte-like cells.\n\nMice with cardiomyocyte-specific deletion of Pcsk9 had reduced contractile capacity, impaired cardiac function, and left ventricular dilatation at 28 weeks of age and died prematurely. Transcriptomic analyses revealed alterations of signalling pathways linked to cardiomyopathy and energy metabolism in hearts from CM-Pcsk9-/- mice vs. wild-type littermates. In agreement, levels of genes and proteins involved in mitochondrial metabolism were reduced in CM-Pcsk9-/- hearts. By using a Seahorse flux analyser, we showed that mitochondrial but not glycolytic function was impaired in cardiomyocytes from CM-Pcsk9-/- mice. We further showed that assembly and activity of electron transport chain (ETC) complexes were altered in isolated mitochondria from CM-Pcsk9-/- mice. Circulating lipid levels were unchanged in CM-Pcsk9-/- mice, but the lipid composition of mitochondrial membranes was altered. In addition, cardiomyocytes from CM-Pcsk9-/- mice had an increased number of mitochondria-endoplasmic reticulum contacts and alterations in the morphology of cristae, the physical location of the ETC complexes. We also showed that acute Pcsk9 silencing in adult cardiomyocyte-like cells reduced the activity of ETC complexes and impaired mitochondrial metabolism.\n\nPCSK9, despite its low expression in cardiomyocytes, contributes to cardiac metabolic function, and PCSK9 deficiency in cardiomyocytes is linked to cardiomyopathy, impaired heart function, and compromised energy production.", "doi": "10.1093/cvr/cvad041", "pmid": "36880401", "labels": {"Adil Mardinoglu": "", "SciLifeLab Fellow": "", "DDLS Fellow": "", "Muhammad Arif": ""}, "xrefs": [{"db": "pmc", "key": "PMC10318396"}, {"db": "pii", "key": "7070420"}], "notes": [], "created": "2023-12-04T14:52:58.422Z", "modified": "2026-09-23T11:06:27.783Z"}, {"entity": "publication", "iuid": "85bf3bb87581432991d192142246ef86", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/85bf3bb87581432991d192142246ef86.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/85bf3bb87581432991d192142246ef86"}}, "title": "Birth Weight Is Associated With Clonal Hematopoiesis of Indeterminate Potential and Cardiovascular Outcomes in Adulthood.", "authors": [{"family": "Schuermans", "given": "Art", "initials": "A", "orcid": "0000-0001-8146-9692", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/af284c3bd9304f54ac7b8c9970ce56be.json"}}, {"family": "Nakao", "given": "Tetsushi", "initials": "T"}, {"family": "Ruan", "given": "Yunfeng", "initials": "Y", "orcid": "0000-0002-3213-8309", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/13398a8656e64d88b858b22f59eeeb48.json"}}, {"family": "Koyama", "given": "Satoshi", "initials": "S", "orcid": "0000-0002-9286-0360", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8e79637c05b54d7089b1d23155db2b3a.json"}}, {"family": "Yu", "given": "Zhi", "initials": "Z", "orcid": "0000-0003-4810-3474", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4b810efe02244148b701c1468543ea3.json"}}, {"family": "Uddin", "given": "Md Mesbah", "initials": "MM", "orcid": "0000-0003-1846-0411", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/42f1ac7010c34ba997a3fd9e56c6a56a.json"}}, {"family": "Haidermota", "given": "Sara", "initials": "S"}, {"family": "Hornsby", "given": "Whitney", "initials": "W"}, {"family": "Lewandowski", "given": "Adam J", "initials": "AJ", "orcid": "0000-0002-4978-8965", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/65eb58c27af94d23bca04b670f94b12a.json"}}, {"family": "Bick", "given": "Alexander G", "initials": "AG", "orcid": "0000-0001-5824-9595", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d2da5a35a4984921b19dfafe64cea2de.json"}}, {"family": "Niroula", "given": "Abhishek", "initials": "A", "orcid": "0000-0002-5904-0635", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/05df7afc7a494ba5af8a378e5ffa53f0.json"}}, {"family": "Jaiswal", "given": "Siddhartha", "initials": "S", "orcid": "0000-0002-9597-0477", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a1901e08f989434fb01dfa17b0a85470.json"}}, {"family": "Ebert", "given": "Benjamin L", "initials": "BL", "orcid": "0000-0003-0197-5451", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56e4f1c53a4348e2b0ceb44a38850a17.json"}}, {"family": "Natarajan", "given": "Pradeep", "initials": "P", "orcid": "0000-0001-8402-7435", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fe8bd48c61c047cd8e61c35d9e9ac650.json"}}, {"family": "Honigberg", "given": "Michael C", "initials": "MC", "orcid": "0000-0001-8630-5021", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c541cd0864c947a6bafa7ad6e78bfe49.json"}}], "type": "journal article", "published": "2023-07-04", "journal": {"title": "J Am Heart Assoc", "issn": "2047-9980", "volume": "12", "issue": "13", "pages": "e030220", "issn-l": "2047-9980"}, "abstract": "Background High and low birth weight are independently associated with increased cardiovascular disease risk in adulthood. Clonal hematopoiesis of indeterminate potential (CHIP), the age-related clonal expansion of hematopoietic cells with preleukemic somatic mutations, predicts incident cardiovascular disease independent of traditional cardiovascular risk factors. Whether birth weight predicts development of CHIP later in life is unknown. Methods and Results A total of 221 047 adults enrolled in the UK Biobank with whole exome sequences and self-reported birth weight were analyzed. Of those, 22 030 (11.5%) had low (<2.5 kg) and 29 292 (14.7%) high birth weight (>4.0 kg). CHIP prevalence was higher among participants with low (6.0%, P=0.049) and high (6.3%, P<0.001) versus normal birth weight (5.7%, ref.). Multivariable-adjusted logistic regression analyses demonstrated that each 1-kg increase in birth weight was associated with a 3% increased risk of CHIP (odds ratio, 1.03 [95% CI, 1.00-1.06]; P=0.04), driven by a stronger association observed between birth weight and DNMT3A CHIP (odds ratio, 1.04 per 1-kg increase [95% CI, 1.01-1.08]; P=0.02). Mendelian randomization analyses supported a causal relationship of longer gestational age at delivery with DNMT3A CHIP. Multivariable Cox regression demonstrated that CHIP was independently and additively associated with incident cardiovascular disease or death across birth weight groups, with highest absolute risks in those with CHIP plus high or low birth weight. Conclusions Higher birth weight is associated with increased risk of developing CHIP in midlife, especially DNMT3A CHIP. These findings identify a novel risk factor for CHIP and provide insights into the relationships among early-life environment, CHIP, cancer, and cardiovascular disease.", "doi": "10.1161/JAHA.123.030220", "pmid": "37345823", "labels": {"Abhishek Niroula": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC10356089"}], "notes": [], "created": "2023-11-20T11:39:36.856Z", "modified": "2023-11-20T11:39:37.072Z"}, {"entity": "publication", "iuid": "9b0aa1fc4e2d408eb1d4658b1d4b81ff", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9b0aa1fc4e2d408eb1d4658b1d4b81ff.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9b0aa1fc4e2d408eb1d4658b1d4b81ff"}}, "title": "Diabetes, metformin use, and survival in esophageal cancer: a population-based cohort study.", "authors": [{"family": "Wang", "given": "Qiao-Li", "initials": "QL", "orcid": "0000-0003-4152-7821", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/357edb3116b64ad5aa929dcb7d07a1be.json"}}, {"family": "Santoni", "given": "Giola", "initials": "G"}, {"family": "Lagergren", "given": "Jesper", "initials": "J", "orcid": "0000-0002-5143-5448", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/22af2b7bdbc64885a7853f684001735b.json"}}], "type": "journal article", "published": "2023-07-03", "journal": {"title": "JNCI Cancer Spectr", "issn": "2515-5091", "volume": "7", "issue": "4", "issn-l": null}, "abstract": "It is unclear how diabetes and metformin use is associated with survival of esophageal cancer.\n\nThis population-based cohort study included new cases of esophageal cancer reported in Sweden from 2006 to 2018 with follow-up through 2019. Diabetes status and metformin use were analyzed in relation to all-cause and disease-specific mortality using multivariable Cox regression. The hazard ratios (HRs) with 95% confidence intervals (CIs) were adjusted for age, sex, calendar year, obesity, comorbidity, and use of nonsteroidal anti-inflammatory drugs or statins. For comparison reasons, 3 other antidiabetic medications were also analyzed (ie, sulfonylureas, insulin, and thiazolidinedione).\n\nAmong 4851 esophageal cancer patients (8404 person-years), 4072 (84%) died during follow-up. Compared with esophageal cancer patients with diabetes but not using metformin, decreased all-cause mortality was indicated among nondiabetic patients (without metformin) (HR = 0.86, 95% CI = 0.77 to 0.96) and diabetic patients who used metformin (HR = 0.86, 95% CI = 0.75 to 1.00). The hazard ratios of all-cause mortality decreased with a higher daily dose of metformin (Ptrend = .04). The corresponding hazard ratios for disease-specific mortality were similar but slightly attenuated. The results were also similar in separate analyses of esophageal cancer patients with adenocarcinoma or squamous cell carcinoma, with tumor stage I-II or III-IV, and in those who had or had not undergone surgery. No associations with mortality outcomes were found for use of sulfonylureas, insulin, or thiazolidinedione.\n\nDiabetes was associated with an increased all-cause mortality, whereas metformin use was associated with decreased all-cause mortality among esophageal cancer patients. More research is needed to determine if metformin affects survival in esophageal cancer.", "doi": "10.1093/jncics/pkad043", "pmid": "37314979", "labels": {"DDLS Fellow": null, "Qiaoli Wang": null}, "xrefs": [{"db": "pmc", "key": "PMC10322653"}, {"db": "pii", "key": "7197818"}], "notes": [], "created": "2025-11-28T12:23:00.767Z", "modified": "2025-11-28T12:23:00.850Z"}, {"entity": "publication", "iuid": "b0be7a934a6540319c3d8ec40ca0436a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b0be7a934a6540319c3d8ec40ca0436a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b0be7a934a6540319c3d8ec40ca0436a"}}, "title": "Sex and gender in infection and immunity: addressing the bottlenecks from basic science to public health and clinical applications.", "authors": [{"family": "Pasin", "given": "Chlo\u00e9", "initials": "C", "orcid": "0000-0001-8730-790X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ba77746459b24894bb5cc2229cd56e95.json"}}, {"family": "Consiglio", "given": "Camila R", "initials": "CR", "orcid": "0000-0002-8901-2328", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a786e29de11b41dd9da2b680ad5b351f.json"}}, {"family": "Huisman", "given": "Jana S", "initials": "JS", "orcid": "0000-0002-1782-8109", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0b855a6c7cb54933a4db0316b6bc6e18.json"}}, {"family": "de Lange", "given": "Ann-Marie G", "initials": "AG", "orcid": "0000-0002-5150-6656", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3ffea7a54a014d2195c230aa0578521f.json"}}, {"family": "Peckham", "given": "Hannah", "initials": "H", "orcid": "0000-0002-9668-4683", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/195f477c302f40c199f9b9f78aeb3f83.json"}}, {"family": "Vallejo-Yag\u00fce", "given": "Enriqueta", "initials": "E", "orcid": "0000-0002-5911-2037", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c44f0a9cdee24c1e8186ccf9b01c6383.json"}}, {"family": "Abela", "given": "Irene A", "initials": "IA", "orcid": "0000-0002-5566-8628", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ac1a5173ee2548d2aac5bd45f05fbb72.json"}}, {"family": "Islander", "given": "Ulrika", "initials": "U", "orcid": "0000-0002-8493-1739", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/344771532a2b4cb080d8451e5c9e5c72.json"}}, {"family": "Neuner-Jehle", "given": "Nadia", "initials": "N"}, {"family": "Pujantell", "given": "Maria", "initials": "M", "orcid": "0000-0002-9471-5853", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b589243fce9a4089bf98ffe69b305f19.json"}}, {"family": "Roth", "given": "Olivia", "initials": "O", "orcid": "0000-0002-7349-7797", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0015e7a49e08423990f7a243cc2fc559.json"}}, {"family": "Schirmer", "given": "Melanie", "initials": "M", "orcid": "0000-0001-6456-3679", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/112b441fb60743598eb4046727b0eaf4.json"}}, {"family": "Tepekule", "given": "Burcu", "initials": "B", "orcid": "0000-0001-6936-9138", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/152e5caffe444060879728c29b008edb.json"}}, {"family": "Zeeb", "given": "Marius", "initials": "M", "orcid": "0000-0001-6822-1473", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7aacc58a2a7d46deaeaad7c30793e639.json"}}, {"family": "Hachfeld", "given": "Anna", "initials": "A", "orcid": "0000-0001-9308-7130", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/88755305df914029ac189b419dfe627c.json"}}, {"family": "Aebi-Popp", "given": "Karoline", "initials": "K", "orcid": "0000-0002-9337-900X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/db59df7e68ec4a21a779037f06d731d8.json"}}, {"family": "Kouyos", "given": "Roger D", "initials": "RD", "orcid": "0000-0002-9220-8348", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/34c4714df88b4291b9a15d4b49ed76c8.json"}}, {"family": "Bonhoeffer", "given": "Sebastian", "initials": "S", "orcid": "0000-0001-8052-3925", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/086e218b0c854ce8b1fd4a244aede566.json"}}], "type": "journal article", "published": "2023-07-00", "journal": {"title": "R Soc Open Sci", "issn": "2054-5703", "volume": "10", "issue": "7", "pages": "221628", "issn-l": "2054-5703"}, "abstract": "Although sex and gender are recognized as major determinants of health and immunity, their role is rarely considered in clinical practice and public health. We identified six bottlenecks preventing the inclusion of sex and gender considerations from basic science to clinical practice, precision medicine and public health policies. (i) A terminology-related bottleneck, linked to the definitions of sex and gender themselves, and the lack of consensus on how to evaluate gender. (ii) A data-related bottleneck, due to gaps in sex-disaggregated data, data on trans/non-binary people and gender identity. (iii) A translational bottleneck, limited by animal models and the underrepresentation of gender minorities in biomedical studies. (iv) A statistical bottleneck, with inappropriate statistical analyses and results interpretation. (v) An ethical bottleneck posed by the underrepresentation of pregnant people and gender minorities in clinical studies. (vi) A structural bottleneck, as systemic bias and discriminations affect not only academic research but also decision makers. We specify guidelines for researchers, scientific journals, funding agencies and academic institutions to address these bottlenecks. Following such guidelines will support the development of more efficient and equitable care strategies for all.", "doi": "10.1098/rsos.221628", "pmid": "37416827", "labels": {"Camila Consiglio": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC10320357"}, {"db": "pii", "key": "rsos221628"}], "notes": [], "created": "2023-11-22T09:17:23.544Z", "modified": "2026-09-23T11:06:39.869Z"}, {"entity": "publication", "iuid": "740dad026c3b49f9a3c9e9e17773b369", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/740dad026c3b49f9a3c9e9e17773b369.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/740dad026c3b49f9a3c9e9e17773b369"}}, "title": "HLA Class I Genotype Is Associated with Relapse Risk after Allogeneic Stem Cell Transplantation for NPM1-Mutated Acute Myeloid Leukemia.", "authors": [{"family": "Narayan", "given": "Rupa", "initials": "R"}, {"family": "Niroula", "given": "Abhishek", "initials": "A"}, {"family": "Wang", "given": "Tao", "initials": "T"}, {"family": "Kuxhausen", "given": "Michelle", "initials": "M"}, {"family": "He", "given": "Meilun", "initials": "M"}, {"family": "Meyer", "given": "Everett", "initials": "E"}, {"family": "Chen", "given": "Yi-Bin", "initials": "YB"}, {"family": "Bhatt", "given": "Vijaya Raj", "initials": "VR"}, {"family": "Beitinjaneh", "given": "Amer", "initials": "A"}, {"family": "Nishihori", "given": "Taiga", "initials": "T"}, {"family": "Sharma", "given": "Akshay", "initials": "A"}, {"family": "Brown", "given": "Valerie I", "initials": "VI"}, {"family": "Kamoun", "given": "Malek", "initials": "M"}, {"family": "Diaz", "given": "Miguel A", "initials": "MA"}, {"family": "Abid", "given": "Muhammad Bilal", "initials": "MB"}, {"family": "Askar", "given": "Medhat", "initials": "M"}, {"family": "Kanakry", "given": "Christopher G", "initials": "CG"}, {"family": "Gragert", "given": "Loren", "initials": "L"}, {"family": "Bolon", "given": "Yung-Tsi", "initials": "YT"}, {"family": "Marsh", "given": "Steven G E", "initials": "SGE"}, {"family": "Gadalla", "given": "Shahinaz M", "initials": "SM"}, {"family": "Paczesny", "given": "Sophie", "initials": "S"}, {"family": "Spellman", "given": "Stephen", "initials": "S"}, {"family": "Lee", "given": "Stephanie J", "initials": "SJ"}], "type": "journal article", "published": "2023-07-00", "journal": {"title": "Transplant Cell Ther", "issn": "2666-6367", "volume": "29", "issue": "7", "pages": "452.e1-452.e11", "issn-l": null}, "abstract": "Mutation-bearing peptide ligands from mutated nucleophosmin-1 (NPM1) protein have been empirically found to be presented by HLA class I in acute myeloid leukemia (AML). We hypothesized that HLA genotype may impact allogeneic hematopoietic stem cell transplantation (allo-HCT) outcomes in NPM1-mutated AML owing to differences in antigen presentation. We evaluated the effect of the variable of predicted strong binding to mutated NPM1 peptides using HLA class I genotypes from matched donor-recipient pairs on transplant recipients' overall survival (OS) and disease-free survival (DFS) as part of the primary objectives and cumulative incidence of relapse and nonrelapse mortality (NRM) as part of secondary objectives. Baseline and outcome data reported to the Center for International Blood and Marrow Transplant Research from a study cohort of adult patients (n = 1020) with NPM1-mutated de novo AML in first (71%) or second (29%) complete remission undergoing 8/8 matched related (18%) or matched unrelated (82%) allo-HCT were analyzed retrospectively. Class I alleles from donor-recipient pairs were analyzed for predicted strong HLA binding to mutated NPM1 using netMHCpan 4.0. A total of 429 (42%) donor-recipient pairs were classified as having predicted strong-binding HLA alleles (SBHAs) to mutated NPM1. In multivariable analyses adjusting for clinical covariates, the presence of predicted SBHAs was associated with a lower risk of relapse (hazard ratio [HR], .72; 95% confidence interval [CI], .55 to .94; P = .015). OS (HR, .81; 95% CI, .67 to .98; P = .028) and DFS (HR, .84; 95% CI, .69 to 1.01; P = .070) showed a suggestion of better outcomes if predicted SBHAs were present but did not meet the prespecified P value of <.025. NRM did not differ (HR, 1.04; P = .740). These hypothesis-generating data support further exploration of HLA genotype-neoantigen interactions in the allo-HCT context.", "doi": "10.1016/j.jtct.2023.03.027", "pmid": "36997024", "labels": {"Abhishek Niroula": null, "DDLS Fellow": null}, "xrefs": [{"db": "mid", "key": "NIHMS1899184"}, {"db": "pmc", "key": "PMC10330307"}, {"db": "pii", "key": "S2666-6367(23)01204-6"}], "notes": [], "created": "2023-11-20T11:36:28.286Z", "modified": "2023-11-20T11:36:28.336Z"}, {"entity": "publication", "iuid": "a8fa7a7e41e14c9f868233e3b29ce60c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a8fa7a7e41e14c9f868233e3b29ce60c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a8fa7a7e41e14c9f868233e3b29ce60c"}}, "title": "Esr1+ hypothalamic-habenula neurons shape aversive states.", "authors": [{"family": "Calvigioni", "given": "Daniela", "initials": "D"}, {"family": "Fuzik", "given": "Janos", "initials": "J", "orcid": "0000-0002-5408-4882", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb41e780c4244ded84b6c6740d971efa.json"}}, {"family": "Le Merre", "given": "Pierre", "initials": "P", "orcid": "0000-0003-4205-7411", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3ebebeabbd3a4bc89ea05d00cc47013a.json"}}, {"family": "Slashcheva", "given": "Marina", "initials": "M"}, {"family": "Jung", "given": "Felix", "initials": "F", "orcid": "0000-0002-7565-977X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/482ed1ec940c4b09aaf24e71403ac324.json"}}, {"family": "Ortiz", "given": "Cantin", "initials": "C"}, {"family": "Lentini", "given": "Antonio", "initials": "A", "orcid": "0000-0003-1239-5495", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c5042d3005814ad0a2d1eaeee5d2de3b.json"}}, {"family": "Csillag", "given": "Veronika", "initials": "V"}, {"family": "Graziano", "given": "Marta", "initials": "M"}, {"family": "Nikolakopoulou", "given": "Ifigeneia", "initials": "I"}, {"family": "Weglage", "given": "Moritz", "initials": "M", "orcid": "0000-0002-9173-7459", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f0e6c7066d05464aa7270b87f9a08f51.json"}}, {"family": "Lazaridis", "given": "Iakovos", "initials": "I", "orcid": "0000-0002-4578-2347", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a5db088903a0452181c145009d6eace8.json"}}, {"family": "Kim", "given": "Hoseok", "initials": "H"}, {"family": "Lenzi", "given": "Irene", "initials": "I", "orcid": "0000-0002-9229-7301", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ce77429076541e98927c8000ff1d2ae.json"}}, {"family": "Park", "given": "Hyunsoo", "initials": "H", "orcid": "0000-0001-5754-9617", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/216293b628d44f22a52c691d888adfd3.json"}}, {"family": "Reinius", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0002-7021-5248", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a7c1abacc8d446bf8855254246b8d899.json"}}, {"family": "Carl\u00e9n", "given": "Marie", "initials": "M", "orcid": "0000-0003-1658-1631", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a5bb1bfff3214cca8753a75f5a251b93.json"}}, {"family": "Meletis", "given": "Konstantinos", "initials": "K", "orcid": "0000-0001-5665-4781", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/314d93feac4048799b81ca9cb04fc078.json"}}], "type": "journal article", "published": "2023-07-00", "journal": {"title": "Nat. Neurosci.", "issn": "1546-1726", "volume": "26", "issue": "7", "pages": "1245-1255", "issn-l": "1097-6256"}, "abstract": "Excitatory projections from the lateral hypothalamic area (LHA) to the lateral habenula (LHb) drive aversive responses. We used patch-sequencing (Patch-seq) guided multimodal classification to define the structural and functional heterogeneity of the LHA-LHb pathway. Our classification identified six glutamatergic neuron types with unique electrophysiological properties, molecular profiles and projection patterns. We found that genetically defined LHA-LHb neurons signal distinct aspects of emotional or naturalistic behaviors, such as estrogen receptor 1-expressing (Esr1+) LHA-LHb neurons induce aversion, whereas neuropeptide Y-expressing (Npy+) LHA-LHb neurons control rearing behavior. Repeated optogenetic drive of Esr1+ LHA-LHb neurons induces a behaviorally persistent aversive state, and large-scale recordings showed a region-specific neural representation of the aversive signals in the prelimbic region of the prefrontal cortex. We further found that exposure to unpredictable mild shocks induced a sex-specific sensitivity to develop a stress state in female mice, which was associated with a specific shift in the intrinsic properties of bursting-type Esr1+ LHA-LHb neurons. In summary, we describe the diversity of LHA-LHb neuron types and provide evidence for the role of Esr1+ neurons in aversion and sexually dimorphic stress sensitivity.", "doi": "10.1038/s41593-023-01367-8", "pmid": "37349481", "labels": {"Antonio Lentini": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC10322719"}, {"db": "pii", "key": "10.1038/s41593-023-01367-8"}], "notes": [], "created": "2025-03-28T07:09:46.854Z", "modified": "2025-03-28T07:09:47.130Z"}, {"entity": "publication", "iuid": "28e1ca10e215410dbd1a91a886e8dbd6", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/28e1ca10e215410dbd1a91a886e8dbd6.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/28e1ca10e215410dbd1a91a886e8dbd6"}}, "title": "A multidrug-resistant Salmonella enterica Typhimurium DT104 complex lineage circulating among humans and cattle in the USA lost the ability to produce pertussis-like toxin ArtAB.", "authors": [{"family": "Carroll", "given": "Laura M", "initials": "LM"}, {"family": "Piacenza", "given": "Nicolo", "initials": "N"}, {"family": "Cheng", "given": "Rachel A", "initials": "RA"}, {"family": "Wiedmann", "given": "Martin", "initials": "M"}, {"family": "Guldimann", "given": "Claudia", "initials": "C"}], "type": "journal article", "published": "2023-07-00", "journal": {"title": "Microb Genom", "issn": "2057-5858", "volume": "9", "issue": "7", "issn-l": null}, "abstract": "Salmonella enterica subsp. enterica serotype Typhimurium definitive type 104 (DT104) can infect both humans and animals and is often multidrug-resistant (MDR). Previous studies have indicated that, unlike most S. Typhimurium, the overwhelming majority of DT104 strains produce pertussis-like toxin ArtAB via prophage-encoded genes artAB. However, DT104 that lack artAB have been described on occasion. Here, we identify an MDR DT104 complex lineage circulating among humans and cattle in the USA, which lacks artAB (i.e. the \u2018U.S. artAB-negative major clade\u2019; n=42 genomes). Unlike most other bovine- and human-associated DT104 complex strains from the USA (n=230 total genomes), which harbour artAB on prophage Gifsy-1 (n=177), members of the U.S. artAB-negative major clade lack Gifsy-1, as well as anti-inflammatory effector gogB. The U.S. artAB-negative major clade encompasses human- and cattle-associated strains isolated from \u226511 USA states over a 20-year period. The clade was predicted to have lost artAB, Gifsy-1 and gogB circa 1985\u20131987 (95 % highest posterior density interval 1979.0\u20131992.1). When compared to DT104 genomes from other regions of the world (n=752 total genomes), several additional, sporadic artAB, Gifsy-1 and/or gogB loss events among clades encompassing five or fewer genomes were observed. Using phenotypic assays that simulate conditions encountered during human and/or bovine digestion, members of the U.S. artAB-negative major clade did not differ from closely related Gifsy-1/artAB/gogB-harbouring U.S. DT104 complex strains (ANOVA raw P>0.05); thus, future research is needed to elucidate the roles that artAB, gogB and Gifsy-1 play in DT104 virulence in humans and animals.", "doi": "10.1099/mgen.0.001050", "pmid": "37402177", "labels": {"Laura Carroll": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC10438809"}, {"db": "figshare", "key": "10.6084/m9.figshare.22194385.v1"}], "notes": [], "created": "2025-03-18T17:30:51.699Z", "modified": "2026-09-23T13:28:15.003Z"}, {"entity": "publication", "iuid": "3d4bda3882c643729212886f1c463afe", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3d4bda3882c643729212886f1c463afe.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3d4bda3882c643729212886f1c463afe"}}, "title": "Building Asymmetric Lipid Bilayers for Molecular Dynamics Simulations: What Methods Exist and How to Choose One?", "authors": [{"family": "Chaisson", "given": "Emily H", "initials": "EH"}, {"family": "Heberle", "given": "Frederick A", "initials": "FA", "orcid": "0000-0002-0424-3240", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2557f5621a0b4c87b5f4702fbc7b6bdb.json"}}, {"family": "Doktorova", "given": "Milka", "initials": "M", "orcid": "0000-0003-4366-2242", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/791384c319f04584bac8ffb21df7271f.json"}}], "type": "journal article", "published": "2023-06-29", "journal": {"title": "Membranes (Basel)", "issn": "2077-0375", "issn-l": "2077-0375", "volume": "13", "issue": "7", "pages": null}, "abstract": "The compositional asymmetry of biological membranes has attracted significant attention over the last decade. Harboring more differences from symmetric membranes than previously appreciated, asymmetric bilayers have proven quite challenging to study with familiar concepts and techniques, leaving many unanswered questions about the reach of the asymmetry effects. One particular area of active research is the computational investigation of composition- and number-asymmetric lipid bilayers with molecular dynamics (MD) simulations. Offering a high level of detail into the organization and properties of the simulated systems, MD has emerged as an indispensable tool in the study of membrane asymmetry. However, the realization that results depend heavily on the protocol used for constructing the asymmetric bilayer models has sparked an ongoing debate about how to choose the most appropriate approach. Here we discuss the underlying source of the discrepant results and review the existing methods for creating asymmetric bilayers for MD simulations. Considering the available data, we argue that each method is well suited for specific applications and hence there is no single best approach. Instead, the choice of a construction protocol-and consequently, its perceived accuracy-must be based primarily on the scientific question that the simulations are designed to address.", "doi": "10.3390/membranes13070629", "pmid": "37504995", "labels": {"Milka Doktorova": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC10384462"}, {"db": "pii", "key": "membranes13070629"}], "notes": [], "created": "2024-11-27T12:20:11.334Z", "modified": "2024-11-29T10:52:52.701Z"}, {"entity": "publication", "iuid": "8b39eb28d48f45bfa2aec273673208f2", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8b39eb28d48f45bfa2aec273673208f2.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8b39eb28d48f45bfa2aec273673208f2"}}, "title": "Orthogonal proteomics methods warrant the development of Duchenne muscular dystrophy biomarkers.", "authors": [{"family": "Johansson", "given": "Camilla", "initials": "C"}, {"family": "Hunt", "given": "Helian", "initials": "H"}, {"family": "Signorelli", "given": "Mirko", "initials": "M"}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Hober", "given": "Andreas", "initials": "A"}, {"family": "Svensson", "given": "Anne-Sophie", "initials": "AS"}, {"family": "Tegel", "given": "Hanna", "initials": "H"}, {"family": "Forststr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Aartsma-Rus", "given": "Annemieke", "initials": "A"}, {"family": "Niks", "given": "Erik", "initials": "E"}, {"family": "Spitali", "given": "Pietro", "initials": "P"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Szigyarto", "given": "Cristina Al-Khalili", "initials": "CA"}], "type": "journal article", "published": "2023-06-12", "journal": {"title": "Clin Proteomics", "issn": "1542-6416", "volume": "20", "issue": "1", "pages": "23", "issn-l": null}, "abstract": "Molecular components in blood, such as proteins, are used as biomarkers to detect or predict disease states, guide clinical interventions and aid in the development of therapies. While multiplexing proteomics methods promote discovery of such biomarkers, their translation to clinical use is difficult due to the lack of substantial evidence regarding their reliability as quantifiable indicators of disease state or outcome. To overcome this challenge, a novel orthogonal strategy was developed and used to assess the reliability of biomarkers and analytically corroborate already identified serum biomarkers for Duchenne muscular dystrophy (DMD). DMD is a monogenic incurable disease characterized by progressive muscle damage that currently lacks reliable and specific disease monitoring tools.\n\nTwo technological platforms are used to detect and quantify the biomarkers in 72 longitudinally collected serum samples from DMD patients at 3 to 5 timepoints. Quantification of the biomarkers is achieved by detection of the same biomarker fragment either through interaction with validated antibodies in immuno-assays or through quantification of peptides by Parallel Reaction Monitoring Mass Spectrometry assay (PRM-MS).\n\nFive, out of ten biomarkers previously identified by affinity-based proteomics methods, were confirmed to be associated with DMD using the mass spectrometry-based method. Two biomarkers, carbonic anhydrase III and lactate dehydrogenase B, were quantified with two independent methods, sandwich immunoassays and PRM-MS, with Pearson correlations of 0.92 and 0.946 respectively. The median concentrations of CA3 and LDHB in DMD patients was elevated in comparison to those in healthy individuals by 35- and 3-fold, respectively. Levels of CA3 vary between 10.26 and 0.36 ng/ml in DMD patients whereas those of LDHB vary between 15.1 and 0.8 ng/ml.\n\nThese results demonstrate that orthogonal assays can be used to assess the analytical reliability of biomarker quantification assays, providing a means to facilitate the translation of biomarkers to clinical practice. This strategy also warrants the development of the most relevant biomarkers, markers that can be reliably quantified with different proteomics methods.", "doi": "10.1186/s12014-023-09412-1", "pmid": "37308827", "labels": {"Fredrik Edfors": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC10258980"}, {"db": "pii", "key": "10.1186/s12014-023-09412-1"}], "notes": [], "created": "2026-08-20T12:19:15.965Z", "modified": "2026-09-23T12:11:59.059Z"}, {"entity": "publication", "iuid": "19e635d203f04a55a0f80bdc96d6d64f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/19e635d203f04a55a0f80bdc96d6d64f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/19e635d203f04a55a0f80bdc96d6d64f"}}, "title": "Autoencoder Model for Translating Omics Signatures", "authors": [{"family": "Meimetis", "given": "Nikolaos", "initials": "N", "orcid": "0000-0003-2333-0187", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e0e968cb5cc44b52818647cea77762d9.json"}}, {"family": "Pullen", "given": "Krista M", "initials": "KM", "orcid": "0000-0002-4857-8907", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6930c9935ef740479a3052b4796d7d6d.json"}}, {"family": "Zhu", "given": "Daniel Y", "initials": "DY"}, {"family": "Nilsson", "given": "Avlant", "initials": "A", "orcid": "0000-0002-9476-4516", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f2e21dbc1c624f6a841c59e959e948e4.json"}}, {"family": "Hoang", "given": "Trong Nghia", "initials": "TN"}, {"family": "Magliacane", "given": "Sara", "initials": "S"}, {"family": "Lauffenburger", "given": "Douglas A", "initials": "DA", "orcid": "0000-0002-0050-989X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ac0a09cb7c9c49de95b660756a4e5464.json"}}], "type": "posted-content", "published": "2023-06-11", "journal": {"title": null, "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2023.06.08.544243", "pmid": null, "labels": {"Avlant Nilsson": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2025-03-20T11:10:27.535Z", "modified": "2025-03-21T10:37:20.777Z"}, {"entity": "publication", "iuid": "6e484729d5094c33a361aa9f8fe226e4", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/6e484729d5094c33a361aa9f8fe226e4.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/6e484729d5094c33a361aa9f8fe226e4"}}, "title": "More than mcr: canonical plasmid- and transposon-encoded mobilized colistin resistance genes represent a subset of phosphoethanolamine transferases.", "authors": [{"family": "Gaballa", "given": "Ahmed", "initials": "A"}, {"family": "Wiedmann", "given": "Martin", "initials": "M"}, {"family": "Carroll", "given": "Laura M", "initials": "LM"}], "type": "journal article", "published": "2023-06-08", "journal": {"title": "Front. Cell. Infect. Microbiol.", "issn": "2235-2988", "volume": "13", "pages": "1060519", "issn-l": "2235-2988"}, "abstract": "Mobilized colistin resistance genes (mcr) may confer resistance to the last-resort antimicrobial colistin and can often be transmitted horizontally. mcr encode phosphoethanolamine transferases (PET), which are closely related to chromosomally encoded, intrinsic lipid modification PET (i-PET; e.g., EptA, EptB, CptA). To gain insight into the evolution of mcr within the context of i-PET, we identified 69,814 MCR-like proteins present across 256 bacterial genera (obtained by querying known MCR family representatives against the National Center for Biotechnology Information [NCBI] non-redundant protein database via protein BLAST). We subsequently identified 125 putative novel mcr-like genes, which were located on the same contig as (i) \u22651 plasmid replicon and (ii) \u22651 additional antimicrobial resistance gene (obtained by querying the PlasmidFinder database and NCBI's National Database of Antibiotic Resistant Organisms, respectively, via nucleotide BLAST). At 80% amino acid identity, these putative novel MCR-like proteins formed 13 clusters, five of which represented putative novel MCR families. Sequence similarity and a maximum likelihood phylogeny of mcr, putative novel mcr-like, and ipet genes indicated that sequence similarity was insufficient to discriminate mcr from ipet genes. A mixed-effect model of evolution (MEME) indicated that site- and branch-specific positive selection played a role in the evolution of alleles within the mcr-2 and mcr-9 families. MEME suggested that positive selection played a role in the diversification of several residues in structurally important regions, including (i) a bridging region that connects the membrane-bound and catalytic periplasmic domains, and (ii) a periplasmic loop juxtaposing the substrate entry tunnel. Moreover, eptA and mcr were localized within different genomic contexts. Canonical eptA genes were typically chromosomally encoded in an operon with a two-component regulatory system or adjacent to a TetR-type regulator. Conversely, mcr were represented by single-gene operons or adjacent to pap2 and dgkA, which encode a PAP2 family lipid A phosphatase and diacylglycerol kinase, respectively. Our data suggest that eptA can give rise to \"colistin resistance genes\" through various mechanisms, including mobilization, selection, and diversification of genomic context and regulatory pathways. These mechanisms likely altered gene expression levels and enzyme activity, allowing bona fide eptA to evolve to function in colistin resistance.", "doi": "10.3389/fcimb.2023.1060519", "pmid": "37360531", "labels": {"Laura Carroll": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC10285318"}], "notes": [], "created": "2025-03-18T17:30:30.075Z", "modified": "2026-09-23T10:51:19.146Z"}, {"entity": "publication", "iuid": "3eab6f40adba4a1eaa807ee583bf2a28", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3eab6f40adba4a1eaa807ee583bf2a28.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3eab6f40adba4a1eaa807ee583bf2a28"}}, "title": "Elevated plasma complement factor H related 5 protein is associated with venous thromboembolism.", "authors": [{"family": "Iglesias", "given": "Maria Jesus", "initials": "MJ"}, {"family": "Sanchez-Rivera", "given": "Laura", "initials": "L"}, {"family": "Ibrahim-Kosta", "given": "Manal", "initials": "M"}, {"family": "Naudin", "given": "Cl\u00e9ment", "initials": "C", "orcid": "0000-0002-6777-9587", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f89e25cd7fcc4617ab5299c72fd17e0c.json"}}, {"family": "Munsch", "given": "Ga\u00eblle", "initials": "G", "orcid": "0000-0003-1564-9825", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ed62bf6aa35643f283511d68d2aa4b01.json"}}, {"family": "Goumidi", "given": "Louisa", "initials": "L", "orcid": "0000-0003-4164-8471", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7d3df066e5e54e32bb99110289ab8a45.json"}}, {"family": "Farm", "given": "Maria", "initials": "M"}, {"family": "Smith", "given": "Philip M", "initials": "PM"}, {"family": "Thibord", "given": "Florian", "initials": "F"}, {"family": "Kral-Pointner", "given": "Julia Barbara", "initials": "JB"}, {"family": "Hong", "given": "Mun-Gwan", "initials": "MG", "orcid": "0000-0001-8603-8293", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d12504acae5c4f31b83f75c3d7786cd4.json"}}, {"family": "Suchon", "given": "Pierre", "initials": "P"}, {"family": "Germain", "given": "Marine", "initials": "M"}, {"family": "Schrottmaier", "given": "Waltraud", "initials": "W", "orcid": "0000-0003-0550-4120", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0ab65a615b9e477aa6206677e57025b0.json"}}, {"family": "Dusart", "given": "Philip", "initials": "P", "orcid": "0000-0003-2747-3214", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/26cf50c230954da190746c16b5ac2b7d.json"}}, {"family": "Boland", "given": "Anne", "initials": "A"}, {"family": "Kotol", "given": "David", "initials": "D", "orcid": "0000-0002-5388-3826", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c41f8f491c474e6bba2047b5d04b4af5.json"}}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e213b04f8984c8eb00c68f5bc2f6a36.json"}}, {"family": "Koprulu", "given": "Mine", "initials": "M", "orcid": "0000-0001-6870-4539", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e8fa2ddd2cfa4bbeb9c0b043513a6701.json"}}, {"family": "Pietzner", "given": "Maik", "initials": "M", "orcid": "0000-0003-3437-9963", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3304844cece945168cbec0b5e3d9a9cf.json"}}, {"family": "Langenberg", "given": "Claudia", "initials": "C", "orcid": "0000-0002-5017-7344", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f287f3248cc24c6cbfc100c249b87418.json"}}, {"family": "Damrauer", "given": "Scott M", "initials": "SM", "orcid": "0000-0001-8009-1632", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f35b78d4384d41f2bfae2639b23b1e82.json"}}, {"family": "Johnson", "given": "Andrew D", "initials": "AD", "orcid": "0000-0001-6369-5178", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8b268f8da3f247ba90dc37ea73d93c2f.json"}}, {"family": "Klarin", "given": "Derek M", "initials": "DM", "orcid": "0000-0002-4636-5780", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0b81fbf037ec4b4b8ac0013544539f00.json"}}, {"family": "Smith", "given": "Nicholas L", "initials": "NL"}, {"family": "Smadja", "given": "David M", "initials": "DM"}, {"family": "Holmstr\u00f6m", "given": "Margareta", "initials": "M"}, {"family": "Magnusson", "given": "Maria", "initials": "M"}, {"family": "Silveira", "given": "Angela", "initials": "A", "orcid": "0000-0003-2063-4935", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2d8cbafcc7f04ac3adda984af7d85a16.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ea446aa574042a295d5f69437402f76.json"}}, {"family": "Renn\u00e9", "given": "Thomas", "initials": "T"}, {"family": "Martinez-Perez", "given": "Angel", "initials": "A", "orcid": "0000-0002-5934-1454", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0fa8f32fb99f46dcb16d3a64643dbbfa.json"}}, {"family": "Emmerich", "given": "Joseph", "initials": "J"}, {"family": "Deleuze", "given": "Jean-Francois", "initials": "JF", "orcid": "0000-0002-5358-4463", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/33bb50dc6b8045bd9dbbde4423f66129.json"}}, {"family": "Antovic", "given": "Jovan", "initials": "J"}, {"family": "Soria Fernandez", "given": "Jose Manuel", "initials": "JM"}, {"family": "Assinger", "given": "Alice", "initials": "A", "orcid": "0000-0002-5670-5910", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ccb6bb03693c4c799f4cbb53e6ff7049.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/022e140799b6466ea123319c3d70c76e.json"}}, {"family": "Souto Andres", "given": "Joan Carles", "initials": "JC", "orcid": "0000-0003-2092-5142", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/164af41db2204f2591c719a8b024d32a.json"}}, {"family": "Morange", "given": "Pierre-Emmanuel", "initials": "PE", "orcid": "0000-0002-9065-722X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/50bca11c313740c299901843e86e5d48.json"}}, {"family": "Butler", "given": "Lynn Marie", "initials": "LM", "orcid": "0000-0002-2352-8217", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca98647aea15499485d755977bd0869a.json"}}, {"family": "Tr\u00e9gou\u00ebt", "given": "David-Alexandre", "initials": "DA", "orcid": "0000-0001-9084-7800", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/74ca463a0d804b1ab97dac4750563220.json"}}, {"family": "Odeberg", "given": "Jacob", "initials": "J", "orcid": "0000-0003-0996-1644", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d6abb3fc822a4cacbf1d45224f2442f5.json"}}], "type": "journal article", "published": "2023-06-07", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "3280", "issn-l": "2041-1723"}, "abstract": "Venous thromboembolism (VTE) is a common, multi-causal disease with potentially serious short- and long-term complications. In clinical practice, there is a need for improved plasma biomarker-based tools for VTE diagnosis and risk prediction. Here we show, using proteomics profiling to screen plasma from patients with suspected acute VTE, and several case-control studies for VTE, how Complement Factor H Related 5 protein (CFHR5), a regulator of the alternative pathway of complement activation, is a VTE-associated plasma biomarker. In plasma, higher CFHR5 levels are associated with increased thrombin generation potential and recombinant CFHR5 enhanced platelet activation in vitro. GWAS analysis of ~52,000 participants identifies six loci associated with CFHR5 plasma levels, but Mendelian randomization do not demonstrate causality between CFHR5 and VTE. Our results indicate an important role for the regulation of the alternative pathway of complement activation in VTE and that CFHR5 represents a potential diagnostic and/or risk predictive plasma biomarker.", "doi": "10.1038/s41467-023-38383-y", "pmid": "37286573", "labels": {"Fredrik Edfors": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC10247781"}, {"db": "pii", "key": "10.1038/s41467-023-38383-y"}], "notes": [], "created": "2026-08-20T08:52:37.351Z", "modified": "2026-09-23T08:54:10.824Z"}, {"entity": "publication", "iuid": "f1bcf52cf254477b83b5b518a3c36ed0", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f1bcf52cf254477b83b5b518a3c36ed0.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f1bcf52cf254477b83b5b518a3c36ed0"}}, "title": "RegiSTORM: channel registration for multi-color stochastic optical reconstruction microscopy.", "authors": [{"family": "\u00d8vreb\u00f8", "given": "\u00d8ystein", "initials": "\u00d8"}, {"family": "Ojansivu", "given": "Miina", "initials": "M"}, {"family": "Kartasalo", "given": "Kimmo", "initials": "K"}, {"family": "Barriga", "given": "Hanna M G", "initials": "HMG"}, {"family": "Ranefall", "given": "Petter", "initials": "P"}, {"family": "Holme", "given": "Margaret N", "initials": "MN"}, {"family": "Stevens", "given": "Molly M", "initials": "MM"}], "type": "journal article", "published": "2023-06-05", "journal": {"title": "BMC Bioinformatics", "issn": "1471-2105", "issn-l": "1471-2105", "volume": "24", "issue": "1", "pages": "237"}, "abstract": "Stochastic optical reconstruction microscopy (STORM), a super-resolution microscopy technique based on single-molecule localizations, has become popular to characterize sub-diffraction limit targets. However, due to lengthy image acquisition, STORM recordings are prone to sample drift. Existing cross-correlation or fiducial marker-based algorithms allow correcting the drift within each channel, but misalignment between channels remains due to interchannel drift accumulating during sequential channel acquisition. This is a major drawback in multi-color STORM, a technique of utmost importance for the characterization of various biological interactions.\n\nWe developed RegiSTORM, a software for reducing channel misalignment by accurately registering STORM channels utilizing fiducial markers in the sample. RegiSTORM identifies fiducials from the STORM localization data based on their non-blinking nature and uses them as landmarks for channel registration. We first demonstrated accurate registration on recordings of fiducials only, as evidenced by significantly reduced target registration error with all the tested channel combinations. Next, we validated the performance in a more practically relevant setup on cells multi-stained for tubulin. Finally, we showed that RegiSTORM successfully registers two-color STORM recordings of cargo-loaded lipid nanoparticles without fiducials, demonstrating the broader applicability of this software.\n\nThe developed RegiSTORM software was demonstrated to be able to accurately register multiple STORM channels and is freely available as open-source (MIT license) at https://github.com/oystein676/RegiSTORM.git and https://doi.org/10.5281/zenodo.5509861 (archived), and runs as a standalone executable (Windows) or via Python (Mac OS, Linux).", "doi": "10.1186/s12859-023-05320-1", "pmid": "37277712", "labels": {"Kimmo Kartasalo": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC10242778"}, {"db": "pii", "key": "10.1186/s12859-023-05320-1"}], "notes": [], "created": "2024-11-05T16:10:22.926Z", "modified": "2026-09-23T12:26:17.210Z"}, {"entity": "publication", "iuid": "f86eaba3b2c94b8da2af804bc648fda9", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f86eaba3b2c94b8da2af804bc648fda9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f86eaba3b2c94b8da2af804bc648fda9"}}, "title": "Defining Vaginal Community Dynamics: daily microbiome transitions, the role of menstruation, bacteriophages and bacterial genes", "authors": [{"family": "Hugerth", "given": "Luisa W", "initials": "LW", "orcid": "0000-0001-5432-1764", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/246ed7b405dd4c3f9ec5e7ff9f1d3ade.json"}}, {"family": "Krog", "given": "Maria Christine", "initials": "MC", "orcid": "0000-0002-2110-0479", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bdd65c5105f4480692383dae8d4ac986.json"}}, {"family": "Vomstein", "given": "Kilian", "initials": "K", "orcid": "0000-0003-2981-4211", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/de8dcc493f994095b2bb66bbf7e5624a.json"}}, {"family": "Du", "given": "Juan", "initials": "J", "orcid": "0000-0001-7649-9571", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f67834a614ca4cd4aff026e5e9a1a1e4.json"}}, {"family": "Bashir", "given": "Zahra", "initials": "Z", "orcid": "0000-0002-2497-282X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2d15fce497fe4cdabd82e994e7cd83ad.json"}}, {"family": "Kaldhusdal", "given": "Vilde", "initials": "V", "orcid": "0000-0002-2485-5156", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c81e47a6defb4e2288b252ee3a651d46.json"}}, {"family": "Fransson", "given": "Emma", "initials": "E", "orcid": "0000-0001-9010-8522", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8c05290187ec426b8804eefc3d954971.json"}}, {"family": "Engstrand", "given": "Lars", "initials": "L", "orcid": "0000-0002-7713-2373", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02d8684df81e42169e613de803446fbf.json"}}, {"family": "Nielsen", "given": "Henriette Svarre", "initials": "HS", "orcid": "0000-0003-2106-8103", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9a99fa7ebb204c618ed70f29be0085b3.json"}}, {"family": "Schuppe-Koistinen", "given": "Ina", "initials": "I", "orcid": "0000-0002-1423-3089", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/659fb04e6a1a430cbd707b8a50d500a3.json"}}], "type": "posted-content", "published": "2023-06-02", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2023.06.02.543379", "pmid": null, "labels": {"DDLS Fellow": "", "Luisa Hugerth": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T10:46:20.098Z", "modified": "2026-09-23T14:48:44.868Z"}, {"entity": "publication", "iuid": "923555aa39b248c2addd35124b4f7067", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/923555aa39b248c2addd35124b4f7067.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/923555aa39b248c2addd35124b4f7067"}}, "title": "Obesity-induced inflammation exacerbates clonal hematopoiesis.", "authors": [{"family": "Pasupuleti", "given": "Santhosh Kumar", "initials": "SK"}, {"family": "Ramdas", "given": "Baskar", "initials": "B"}, {"family": "Burns", "given": "Sarah S", "initials": "SS"}, {"family": "Palam", "given": "Lakshmi Reddy", "initials": "LR"}, {"family": "Kanumuri", "given": "Rahul", "initials": "R"}, {"family": "Kumar", "given": "Ramesh", "initials": "R"}, {"family": "Pandhiri", "given": "Taruni Reddy", "initials": "TR"}, {"family": "Dave", "given": "Utpal P", "initials": "UP"}, {"family": "Yellapu", "given": "Nanda Kumar", "initials": "NK"}, {"family": "Zhou", "given": "Xinyu", "initials": "X"}, {"family": "Zhang", "given": "Chi", "initials": "C"}, {"family": "Sandusky", "given": "George E", "initials": "GE"}, {"family": "Yu", "given": "Zhi", "initials": "Z"}, {"family": "Honigberg", "given": "Michael C", "initials": "MC"}, {"family": "Bick", "given": "Alexander G", "initials": "AG"}, {"family": "Griffin", "given": "Gabriel K", "initials": "GK"}, {"family": "Niroula", "given": "Abhishek", "initials": "A"}, {"family": "Ebert", "given": "Benjamin L", "initials": "BL"}, {"family": "Paczesny", "given": "Sophie", "initials": "S"}, {"family": "Natarajan", "given": "Pradeep", "initials": "P"}, {"family": "Kapur", "given": "Reuben", "initials": "R"}], "type": "journal article", "published": "2023-06-01", "journal": {"title": "J. Clin. Invest.", "issn": "1558-8238", "volume": "133", "issue": "11", "issn-l": "0021-9738"}, "abstract": "Characterized by the accumulation of somatic mutations in blood cell lineages, clonal hematopoiesis of indeterminate potential (CHIP) is frequent in aging and involves the expansion of mutated hematopoietic stem and progenitor cells (HSC/Ps) that leads to an increased risk of hematologic malignancy. However, the risk factors that contribute to CHIP-associated clonal hematopoiesis (CH) are poorly understood. Obesity induces a proinflammatory state and fatty bone marrow (FBM), which may influence CHIP-associated pathologies. We analyzed exome sequencing and clinical data for 47,466 individuals with validated CHIP in the UK Biobank. CHIP was present in 5.8% of the study population and was associated with a significant increase in the waist-to-hip ratio (WHR). Mouse models of obesity and CHIP driven by heterozygosity of Tet2, Dnmt3a, Asxl1, and Jak2 resulted in exacerbated expansion of mutant HSC/Ps due in part to excessive inflammation. Our results show that obesity is highly associated with CHIP and that a proinflammatory state could potentiate the progression of CHIP to more significant hematologic neoplasia. The calcium channel blockers nifedipine and SKF-96365, either alone or in combination with metformin, MCC950, or anakinra (IL-1 receptor antagonist), suppressed the growth of mutant CHIP cells and partially restored normal hematopoiesis. Targeting CHIP-mutant cells with these drugs could be a potential therapeutic approach to treat CH and its associated abnormalities in individuals with obesity.", "doi": "10.1172/JCI163968", "pmid": "37071471", "labels": {"Abhishek Niroula": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC10231999"}, {"db": "pii", "key": "163968"}], "notes": [], "created": "2023-11-20T11:39:34.146Z", "modified": "2023-11-20T11:39:34.150Z"}, {"entity": "publication", "iuid": "c2c2e79baef2498db9896b801a207426", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c2c2e79baef2498db9896b801a207426.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c2c2e79baef2498db9896b801a207426"}}, "title": "Analysis of Breast Cancer Family History, Estrogen Receptor Status, and Breast Cancer Outcomes in Sweden.", "authors": [{"family": "Zhang", "given": "Yuqi", "initials": "Y"}, {"family": "Wang", "given": "Qiao-Li", "initials": "QL"}, {"family": "Zeng", "given": "Erwei", "initials": "E"}, {"family": "He", "given": "Wei", "initials": "W"}, {"family": "Czene", "given": "Kamila", "initials": "K"}], "type": "journal article", "published": "2023-06-01", "journal": {"title": "JAMA Netw Open", "issn": "2574-3805", "volume": "6", "issue": "6", "pages": "e2318053", "issn-l": null}, "abstract": "Breast cancer (BC), the most prevalent cancer among women globally, is a heterogeneous disease, with prognosis differing by estrogen receptor (ER) status. Having a family history of BC increases the risk of BC; however, it is unclear whether family history is associated with the prognosis of overall and ER-specific BC.\n\nTo assess whether a family history of BC is associated with the prognosis of overall and ER-specific BC.\n\nThis cohort study was based on data from several national registers in Sweden. All female residents of Stockholm who were born after 1932; had their first BC diagnosis between January 1, 1991, and December 31, 2019; and had at least 1 identified female first-degree relative (FDR) were included. Women who were diagnosed with other types of cancer before their BC diagnosis, were older than 75 years at diagnosis, or had distant metastasis at diagnosis were excluded. A total of 28 649 women were included. Data were analyzed from January 10, 2022, to December 20, 2022.\n\nFamily history of BC, defined as 1 or more female FDRs diagnosed with BC.\n\nPatients were followed up until BC-specific death, censoring, or end of follow-up on December 31, 2019. The role of family history in BC-specific mortality was investigated using flexible parametric survival models among the full cohort, ER-positive subgroup, and ER-negative subgroup, adjusting for demographic characteristics, tumor characteristics, and treatments received.\n\nAmong 28 649 patients, the mean (SD) age at BC diagnosis was 55.7 (10.4) years; 19 545 (68.2%) had ER-positive BC, and 4078 (14.2%) had ER-negative BC. Overall, 5081 patients (17.7%) had at least 1 female FDR diagnosed with BC, while 384 (1.3%) had a family history of early-onset BC (FDR diagnosed before age 40 years). During the follow-up period (median [IQR], 8.7 [4.1-15.1] years), 2748 patients (9.6%) died of BC. Multivariable analyses revealed that having a family history of BC was associated with a lower risk of BC-specific death among the full cohort (hazard ratio [HR], 0.78; 95% CI, 0.65-0.95) and the ER-negative subgroup (HR, 0.57; 95% CI, 0.40-0.82) in the first 5 years, after which no association was observed. However, having an early-onset family history was associated with a higher risk of BC-specific death (HR, 1.41; 95% CI, 1.03-2.34).\n\nIn this study, patients with a family history of BC did not necessarily have a worse prognosis. Those with ER-negative status and a family history of BC had more favorable outcomes in the first 5 years after diagnosis, possibly due to enhanced motivation to receive and adhere to treatment. However, patients with a family history of early-onset BC had worse survival, suggesting that genetic testing of newly diagnosed patients with early-onset family history may provide useful information to aid treatment and future research.", "doi": "10.1001/jamanetworkopen.2023.18053", "pmid": "37310740", "labels": {"DDLS Fellow": null, "Qiaoli Wang": null}, "xrefs": [{"db": "pmc", "key": "PMC10265300"}, {"db": "pii", "key": "2805967"}], "notes": [], "created": "2025-11-28T12:23:03.096Z", "modified": "2025-11-28T12:23:03.114Z"}, {"entity": "publication", "iuid": "0d560d9b6d9e4640b985feda5d992d55", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0d560d9b6d9e4640b985feda5d992d55.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0d560d9b6d9e4640b985feda5d992d55"}}, "title": "Replacement of dietary saturated with unsaturated fatty acids is associated with beneficial effects on lipidome metabolites: a secondary analysis of a randomized trial.", "authors": [{"family": "Sellem", "given": "Laury", "initials": "L"}, {"family": "Eichelmann", "given": "Fabian", "initials": "F"}, {"family": "Jackson", "given": "Kim G", "initials": "KG"}, {"family": "Wittenbecher", "given": "Clemens", "initials": "C"}, {"family": "Schulze", "given": "Matthias B", "initials": "MB"}, {"family": "Lovegrove", "given": "Julie A", "initials": "JA"}], "type": "randomized controlled trial", "published": "2023-06-00", "journal": {"title": "Am. J. Clin. Nutr.", "issn": "1938-3207", "volume": "117", "issue": "6", "pages": "1248-1261", "issn-l": "0002-9165"}, "abstract": "The effects of replacing dietary saturated fatty acids (SFAs) with monounsaturated fatty acids (MUFAs) and/or polyunsaturated fatty acids (PUFAs) on the plasma lipidome in relation to the cardiometabolic disease (CMD) risk is poorly understood.\n\nWe aimed to assess the impact of substituting dietary SFAs with unsaturated fatty acids (UFAs) on the plasma lipidome and examine the relationship between lipid metabolites modulated by diet and CMD risk.\n\nPlasma fatty acid (FA) concentrations among 16 lipid classes (within-class FAs) were measured in a subgroup from the Dietary Intervention and VAScular function (DIVAS) parallel randomized controlled trial (n = 113/195), which consisted of three 16-wk diets enriched in SFAs (target SFA:MUFA:n-6PUFA ratio = 17:11:4% total energy [TE]), MUFAs (9:19:4% TE), or a MUFA/PUFA mixture (9:13:10% TE). Similar lipidomics analyses were conducted in the European Prospective Investigation into Cancer and Nutrition (EPIC)-Potsdam study (specific case/cohorts: n = 775/1886 for type 2 diabetes [T2D], n = 551/1671 for cardiovascular disease [CVD]). Multiple linear regression and multivariable Cox models identified within-class FAs sensitive to replacement of dietary SFA with UFA in DIVAS and their association with CMD risk in EPIC-Potsdam. Elastic-net regression models identified within-class FAs associated with changes in CMD risk markers post-DIVAS interventions.\n\nDIVAS high-UFA interventions reduced plasma within-class FAs associated with a higher CVD risk in EPIC-Potsdam, especially SFA-containing glycerolipids and sphingolipids (e.g., diacylglycerol (20:0) z-score = -1.08; SE = 0.17; P value < 10-8), whereas they increased those inversely associated with CVD risk. The results on T2D were less clear. Specific sphingolipids and phospholipids were associated with changes in markers of endothelial function and ambulatory blood pressure, whereas higher low-density lipoprotein cholesterol concentrations were characterized by higher plasma glycerolipids containing lauric and stearic acids.\n\nThese results suggest a mediating role of plasma lipid metabolites in the association between dietary fat and CMD risk. Future research combining interventional and observational findings will further our understanding of the role of dietary fat in CMD etiology. This trial was registered in ClinicalTrials.gov as NCT01478958.", "doi": "10.1016/j.ajcnut.2023.03.024", "pmid": "37062359", "labels": {"Clemens Wittenbecher": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC10315407"}, {"db": "pii", "key": "S0002-9165(23)46314-9"}, {"db": "ClinicalTrials.gov", "key": "NCT01478958"}], "notes": [], "created": "2025-03-19T08:20:46.954Z", "modified": "2025-12-09T13:38:46.050Z"}, {"entity": "publication", "iuid": "8e776ae9f3404abda636d84ddb8576f7", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8e776ae9f3404abda636d84ddb8576f7.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8e776ae9f3404abda636d84ddb8576f7"}}, "title": "Development of early life gut resistome and mobilome across gestational ages and microbiota-modifying treatments.", "authors": [{"family": "Bargheet", "given": "Ahmed", "initials": "A"}, {"family": "Klingenberg", "given": "Claus", "initials": "C"}, {"family": "Esaiassen", "given": "Eirin", "initials": "E"}, {"family": "Hjerde", "given": "Erik", "initials": "E"}, {"family": "Cavanagh", "given": "Jorunn Pauline", "initials": "JP"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J", "orcid": "0000-0002-6528-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c666068e9d34939b0252a627007cec7.json"}}, {"family": "Pettersen", "given": "Veronika Kucha\u0159ov\u00e1", "initials": "VK"}], "type": "observational study", "published": "2023-06-00", "journal": {"title": "EBioMedicine", "issn": "2352-3964", "volume": "92", "pages": "104613", "issn-l": "2352-3964"}, "abstract": "Gestational age (GA) and associated level of gastrointestinal tract maturation are major factors driving the initial gut microbiota composition in preterm infants. Besides, compared to term infants, premature infants often receive antibiotics to treat infections and probiotics to restore optimal gut microbiota. How GA, antibiotics, and probiotics modulate the microbiota's core characteristics, gut resistome and mobilome, remains nascent.\n\nWe analysed metagenomic data from a longitudinal observational study in six Norwegian neonatal intensive care units to describe the bacterial microbiota of infants of varying GA and receiving different treatments. The cohort consisted of probiotic-supplemented and antibiotic-exposed extremely preterm infants (n = 29), antibiotic-exposed very preterm (n = 25), antibiotic-unexposed very preterm (n = 8), and antibiotic-unexposed full-term (n = 10) infants. The stool samples were collected on days of life 7, 28, 120, and 365, and DNA extraction was followed by shotgun metagenome sequencing and bioinformatical analysis.\n\nThe top predictors of microbiota maturation were hospitalisation length and GA. Probiotic administration rendered the gut microbiota and resistome of extremely preterm infants more alike to term infants on day 7 and ameliorated GA-driven loss of microbiota interconnectivity and stability. GA, hospitalisation, and both microbiota-modifying treatments (antibiotics and probiotics) contributed to an elevated carriage of mobile genetic elements in preterm infants compared to term controls. Finally, Escherichia coli was associated with the highest number of antibiotic-resistance genes, followed by Klebsiella pneumoniae and Klebsiella aerogenes.\n\nProlonged hospitalisation, antibiotics, and probiotic intervention contribute to dynamic alterations in resistome and mobilome, gut microbiota characteristics relevant to infection risk.\n\nOdd-Berg Group, Northern Norway Regional Health Authority.", "doi": "10.1016/j.ebiom.2023.104613", "pmid": "37187112", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pmc", "key": "PMC10192547"}, {"db": "pii", "key": "S2352-3964(23)00178-0"}], "notes": [], "created": "2024-11-18T11:42:51.648Z", "modified": "2024-11-19T07:24:11.774Z"}, {"entity": "publication", "iuid": "cb6c678f978d42dca45e0d35ec0d3482", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/cb6c678f978d42dca45e0d35ec0d3482.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/cb6c678f978d42dca45e0d35ec0d3482"}}, "title": "Assessing the role of trypsin in quantitative plasma- and single-cell proteomics towards clinical application", "authors": [{"family": "Woessmann", "given": "Jakob", "initials": "J", "orcid": "0000-0002-2283-7237", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8a4b10f5f96244b98122eddcee694ec0.json"}}, {"family": "Petrosius", "given": "Valdemaras", "initials": "V", "orcid": "0000-0003-3814-9583", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c8f8c38ac466400a947fc09edff4d755.json"}}, {"family": "\u00dcresin", "given": "Nil", "initials": "N", "orcid": "0000-0002-8530-1675", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f18ae177792c489e89f25018cf084828.json"}}, {"family": "Kotol", "given": "David", "initials": "D", "orcid": "0000-0002-5388-3826", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c41f8f491c474e6bba2047b5d04b4af5.json"}}, {"family": "Aragon-Fernandez", "given": "Pedro", "initials": "P"}, {"family": "Hober", "given": "Andreas", "initials": "A", "orcid": "0000-0001-8947-2562", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/06cbc187628340278395a00ab9dd6c89.json"}}, {"family": "Keller", "given": "Ulrich auf dem", "initials": "Uad", "orcid": "0000-0002-3431-7415", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4396aa490c374a8b8b3f8ac564dc2d05.json"}}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e213b04f8984c8eb00c68f5bc2f6a36.json"}}, {"family": "Schoof", "given": "Erwin M", "initials": "EM"}], "type": "posted-content", "published": "2023-05-26", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2023.05.26.542422", "pmid": null, "labels": {"Fredrik Edfors": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T10:46:16.015Z", "modified": "2026-09-23T15:27:03.176Z"}, {"entity": "publication", "iuid": "198a7d8355314c54bd80630db07047c6", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/198a7d8355314c54bd80630db07047c6.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/198a7d8355314c54bd80630db07047c6"}}, "title": "Clonal Hematopoiesis of Indeterminate Potential Predicts Adverse Outcomes in Patients With Atherosclerotic Cardiovascular Disease.", "authors": [{"family": "Gumuser", "given": "Esra D", "initials": "ED"}, {"family": "Schuermans", "given": "Art", "initials": "A"}, {"family": "Cho", "given": "So Mi Jemma", "initials": "SMJ"}, {"family": "Sporn", "given": "Zachary A", "initials": "ZA"}, {"family": "Uddin", "given": "Md Mesbah", "initials": "MM"}, {"family": "Paruchuri", "given": "Kaavya", "initials": "K"}, {"family": "Nakao", "given": "Tetsushi", "initials": "T"}, {"family": "Yu", "given": "Zhi", "initials": "Z"}, {"family": "Haidermota", "given": "Sara", "initials": "S"}, {"family": "Hornsby", "given": "Whitney", "initials": "W"}, {"family": "Weeks", "given": "Lachelle D", "initials": "LD"}, {"family": "Niroula", "given": "Abhishek", "initials": "A"}, {"family": "Jaiswal", "given": "Siddhartha", "initials": "S"}, {"family": "Libby", "given": "Peter", "initials": "P"}, {"family": "Ebert", "given": "Benjamin L", "initials": "BL"}, {"family": "Bick", "given": "Alexander G", "initials": "AG"}, {"family": "Natarajan", "given": "Pradeep", "initials": "P"}, {"family": "Honigberg", "given": "Michael C", "initials": "MC"}], "type": "journal article", "published": "2023-05-23", "journal": {"title": "J. Am. Coll. Cardiol.", "issn": "1558-3597", "volume": "81", "issue": "20", "pages": "1996-2009", "issn-l": "0735-1097"}, "abstract": "Clonal hematopoiesis of indeterminate potential (CHIP)-the age-related clonal expansion of blood stem cells with leukemia-associated mutations-is a novel cardiovascular risk factor. Whether CHIP remains prognostic in individuals with established atherosclerotic cardiovascular disease (ASCVD) is less clear.\n\nThis study tested whether CHIP predicts adverse outcomes in individuals with established ASCVD.\n\nIndividuals aged 40 to 70 years from the UK Biobank with established ASCVD and available whole-exome sequences were analyzed. The primary outcome was a composite of ASCVD events and all-cause mortality. Associations of any CHIP (variant allele fraction \u22652%), large CHIP clones (variant allele fraction \u226510%), and the most commonly mutated driver genes (DNMT3A, TET2, ASXL1, JAK2, PPM1D/TP53 [DNA damage repair genes], and SF3B1/SRSF2/U2AF1 [spliceosome genes]) with incident outcomes were compared using unadjusted and multivariable-adjusted Cox regression.\n\nOf 13,129 individuals (median age: 63 years) included, 665 (5.1%) had CHIP. Over a median follow-up of 10.8 years, any CHIP and large CHIP at baseline were associated with adjusted HRs of 1.23 (95% CI: 1.10-1.38; P < 0.001) and 1.34 (95% CI: 1.17-1.53; P < 0.001), respectively, for the primary outcome. TET2 and spliceosome CHIP, especially large clones, were most strongly associated with adverse outcomes (large TET2 CHIP: HR: 1.89; 95% CI: 1.40-2.55; P <0.001; large spliceosome CHIP: HR: 3.02; 95% CI: 1.95-4.70; P < 0.001).\n\nCHIP is independently associated with adverse outcomes in individuals with established ASCVD, with especially high risks observed in TET2 and SF3B1/SRSF2/U2AF1 CHIP.", "doi": "10.1016/j.jacc.2023.03.401", "pmid": "37197843", "labels": {"Abhishek Niroula": null, "DDLS Fellow": null}, "xrefs": [{"db": "mid", "key": "NIHMS1902366"}, {"db": "pmc", "key": "PMC10249057"}, {"db": "pii", "key": "S0735-1097(23)05158-6"}], "notes": [], "created": "2023-11-20T11:39:35.549Z", "modified": "2023-11-20T11:39:35.553Z"}, {"entity": "publication", "iuid": "3e1ff6d5cd75418a86f774150d804a20", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3e1ff6d5cd75418a86f774150d804a20.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3e1ff6d5cd75418a86f774150d804a20"}}, "title": "Design of Drug Efficacy Guided by Free Energy Simulations of the \u03b22 -Adrenoceptor.", "authors": [{"family": "Panel", "given": "Nicolas", "initials": "N", "orcid": "0000-0001-8782-0586", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/09000aac395d45c7820a49e03164f80c.json"}}, {"family": "Vo", "given": "Duc Duy", "initials": "DD"}, {"family": "Kahlous", "given": "Nour Aldin", "initials": "NA", "orcid": "0000-0002-7744-1491", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ed14cfbd31384338928150f4a97aee16.json"}}, {"family": "H\u00fcbner", "given": "Harald", "initials": "H", "orcid": "0000-0002-7892-599X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/786b2b0e9a8f47f7a66ba38700da5510.json"}}, {"family": "Tiedt", "given": "Stephanie", "initials": "S"}, {"family": "Matricon", "given": "Pierre", "initials": "P"}, {"family": "Pacalon", "given": "Jody", "initials": "J"}, {"family": "Fleetwood", "given": "Oliver", "initials": "O"}, {"family": "Kampen", "given": "Stefanie", "initials": "S"}, {"family": "Luttens", "given": "Andreas", "initials": "A"}, {"family": "Delemotte", "given": "Lucie", "initials": "L"}, {"family": "Kihlberg", "given": "Jan", "initials": "J"}, {"family": "Gmeiner", "given": "Peter", "initials": "P", "orcid": "0000-0002-4127-197X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1f9c6990db94493f902488530f54636c.json"}}, {"family": "Carlsson", "given": "Jens", "initials": "J", "orcid": "0000-0003-4623-2977", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/792c1cd4aca248dc94b967115ffa82df.json"}}], "type": "journal article", "published": "2023-05-22", "journal": {"title": "Angew. Chem. Int. Ed. Engl.", "issn": "1521-3773", "volume": "62", "issue": "22", "pages": "e202218959", "issn-l": "1433-7851"}, "abstract": "G-protein-coupled receptors (GPCRs) play important roles in physiological processes and are modulated by drugs that either activate or block signaling. Rational design of the pharmacological efficacy profiles of GPCR ligands could enable the development of more efficient drugs, but is challenging even if high-resolution receptor structures are available. We performed molecular dynamics simulations of the \u03b22 adrenergic receptor in active and inactive conformations to assess if binding free energy calculations can predict differences in ligand efficacy for closely related compounds. Previously identified ligands were successfully classified into groups with comparable efficacy profiles based on the calculated shift in ligand affinity upon activation. A series of ligands were then predicted and synthesized, leading to the discovery of partial agonists with nanomolar potencies and novel scaffolds. Our results demonstrate that free energy simulations enable design of ligand efficacy and the same approach can be applied to other GPCR drug targets.", "doi": "10.1002/anie.202218959", "pmid": "36914577", "labels": {"Lucie Delemotte": "", "SciLifeLab Fellow": "", "Jens Carlsson": "", "Andreas Luttens": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2023-05-15T08:02:59.542Z", "modified": "2026-09-23T10:51:09.652Z"}, {"entity": "publication", "iuid": "d96f2f2adb0743329d178d0efc44f244", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d96f2f2adb0743329d178d0efc44f244.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d96f2f2adb0743329d178d0efc44f244"}}, "title": "Design of Drug Efficacy Guided by Free Energy Simulations of the \u03b2 2 \u2010Adrenoceptor", "authors": [{"family": "Panel", "given": "Nicolas", "initials": "N", "orcid": "0000-0001-8782-0586", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/09000aac395d45c7820a49e03164f80c.json"}}, {"family": "Vo", "given": "Duc Duy", "initials": "DD"}, {"family": "Kahlous", "given": "Nour Aldin", "initials": "NA", "orcid": "0000-0002-7744-1491", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ed14cfbd31384338928150f4a97aee16.json"}}, {"family": "H\u00fcbner", "given": "Harald", "initials": "H", "orcid": "0000-0002-7892-599X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/786b2b0e9a8f47f7a66ba38700da5510.json"}}, {"family": "Tiedt", "given": "Stephanie", "initials": "S"}, {"family": "Matricon", "given": "Pierre", "initials": "P"}, {"family": "Pacalon", "given": "Jody", "initials": "J"}, {"family": "Fleetwood", "given": "Oliver", "initials": "O"}, {"family": "Kampen", "given": "Stefanie", "initials": "S"}, {"family": "Luttens", "given": "Andreas", "initials": "A"}, {"family": "Delemotte", "given": "Lucie", "initials": "L"}, {"family": "Kihlberg", "given": "Jan", "initials": "J"}, {"family": "Gmeiner", "given": "Peter", "initials": "P", "orcid": "0000-0002-4127-197X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1f9c6990db94493f902488530f54636c.json"}}, {"family": "Carlsson", "given": "Jens", "initials": "J", "orcid": "0000-0003-4623-2977", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/792c1cd4aca248dc94b967115ffa82df.json"}}], "type": "journal-article", "published": "2023-05-22", "journal": {"title": "Angewandte Chemie", "issn": "0044-8249", "volume": "135", "issue": "22", "issn-l": null}, "abstract": null, "doi": "10.1002/ange.202218959", "pmid": null, "labels": {"SciLifeLab Fellow": "", "Jens Carlsson": "", "Andreas Luttens": "", "DDLS Fellow": "", "Lucie Delemotte": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T06:29:40.773Z", "modified": "2026-09-23T13:19:44.344Z"}, {"entity": "publication", "iuid": "7cb0ede3c925473894b7806a11e787fd", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/7cb0ede3c925473894b7806a11e787fd.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/7cb0ede3c925473894b7806a11e787fd"}}, "title": "Rapid Traversal of Ultralarge Chemical Space using Machine Learning Guided Docking Screens", "authors": [{"family": "Luttens", "given": "Andreas", "initials": "A", "orcid": "0000-0003-2915-7901", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d2944edc47eb4b639f1c61ae7b94b60a.json"}}, {"family": "Cabeza de Vaca", "given": "Israel", "initials": "I"}, {"family": "Sparring", "given": "Leonard", "initials": "L"}, {"family": "Norinder", "given": "Ulf", "initials": "U"}, {"family": "Carlsson", "given": "Jens", "initials": "J"}], "type": "posted-content", "published": "2023-05-10", "journal": {"issn-l": null}, "abstract": null, "doi": "10.26434/chemrxiv-2023-w3x36", "pmid": null, "labels": {"SciLifeLab Fellow": "", "Jens Carlsson": "", "Andreas Luttens": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T13:03:29.980Z", "modified": "2026-09-23T14:09:01.284Z"}, {"entity": "publication", "iuid": "ab017fadede24f978c242b554911532b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ab017fadede24f978c242b554911532b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ab017fadede24f978c242b554911532b"}}, "title": "Genomics of adaptive evolution in the woolly mammoth.", "authors": [{"family": "D\u00edez-Del-Molino", "given": "David", "initials": "D"}, {"family": "Dehasque", "given": "Marianne", "initials": "M"}, {"family": "Chac\u00f3n-Duque", "given": "J Camilo", "initials": "JC"}, {"family": "Pe\u010dnerov\u00e1", "given": "Patr\u00edcia", "initials": "P"}, {"family": "Tikhonov", "given": "Alexei", "initials": "A"}, {"family": "Protopopov", "given": "Albert", "initials": "A"}, {"family": "Plotnikov", "given": "Valeri", "initials": "V"}, {"family": "Kanellidou", "given": "Foteini", "initials": "F"}, {"family": "Nikolskiy", "given": "Pavel", "initials": "P"}, {"family": "Mortensen", "given": "Peter", "initials": "P"}, {"family": "Danilov", "given": "Gleb K", "initials": "GK"}, {"family": "Vartanyan", "given": "Sergey", "initials": "S"}, {"family": "Gilbert", "given": "M Thomas P", "initials": "MTP"}, {"family": "Lister", "given": "Adrian M", "initials": "AM"}, {"family": "Heintzman", "given": "Peter D", "initials": "PD"}, {"family": "van der Valk", "given": "Tom", "initials": "T"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L"}], "type": "journal article", "published": "2023-05-08", "journal": {"title": "Curr. Biol.", "issn": "1879-0445", "volume": "33", "issue": "9", "pages": "1753-1764.e4", "issn-l": "0960-9822"}, "abstract": "Ancient genomes provide a tool to investigate the genetic basis of adaptations in extinct organisms. However, the identification of species-specific fixed genetic variants requires the analysis of genomes from multiple individuals. Moreover, the long-term scale of adaptive evolution coupled with the short-term nature of traditional time series data has made it difficult to assess when different adaptations evolved. Here, we analyze 23 woolly mammoth genomes, including one of the oldest known specimens at 700,000 years old, to identify fixed derived non-synonymous mutations unique to the species and to obtain estimates of when these mutations evolved. We find that at the time of its origin, the woolly mammoth had already acquired a broad spectrum of positively selected genes, including ones associated with hair and skin development, fat storage and metabolism, and immune system function. Our results also suggest that these phenotypes continued to evolve during the last 700,000 years, but through positive selection on different sets of genes. Finally, we also identify additional genes that underwent comparatively recent positive selection, including multiple genes related to skeletal morphology and body size, as well as one gene that may have contributed to the small ear size in Late Quaternary woolly mammoths.", "doi": "10.1016/j.cub.2023.03.084", "pmid": "37030294", "labels": {"DDLS Fellow": "", "Tom van der Valk": ""}, "xrefs": [{"db": "pii", "key": "S0960-9822(23)00404-9"}], "notes": [], "created": "2026-09-23T08:52:38.416Z", "modified": "2026-09-23T08:52:38.430Z"}, {"entity": "publication", "iuid": "01aae6b1f7e847ee8e8e86a74f5eaf87", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/01aae6b1f7e847ee8e8e86a74f5eaf87.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/01aae6b1f7e847ee8e8e86a74f5eaf87"}}, "title": "Data-driven neuropathological staging and subtyping of TDP-43 proteinopathies.", "authors": [{"family": "Young", "given": "Alexandra L", "initials": "AL", "orcid": "0000-0002-7772-781X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d8a71365a32a4f4da1a29a925e5334c3.json"}}, {"family": "Vogel", "given": "Jacob W", "initials": "JW", "orcid": "0000-0001-6394-9940", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d2ad5af780c245da9b59a8c80a0b00ff.json"}}, {"family": "Robinson", "given": "John L", "initials": "JL"}, {"family": "McMillan", "given": "Corey T", "initials": "CT"}, {"family": "Ossenkoppele", "given": "Rik", "initials": "R"}, {"family": "Wolk", "given": "David A", "initials": "DA"}, {"family": "Irwin", "given": "David J", "initials": "DJ", "orcid": "0000-0002-5599-5098", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e2ac606ce8ca46acae68b7c212c35809.json"}}, {"family": "Elman", "given": "Lauren", "initials": "L"}, {"family": "Grossman", "given": "Murray", "initials": "M"}, {"family": "Lee", "given": "Virginia M-Y", "initials": "VM"}, {"family": "Lee", "given": "Edward B", "initials": "EB", "orcid": "0000-0002-4589-1180", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/65cf7239c7b4486f9dc47215d82fc5ae.json"}}, {"family": "Hansson", "given": "Oskar", "initials": "O", "orcid": "0000-0001-8467-7286", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9292115deece4d9fafc8a02d4a430707.json"}}], "type": "journal article", "published": "2023-05-08", "journal": {"title": "Brain", "issn": "1460-2156", "issn-l": "0006-8950", "volume": null, "issue": null, "pages": null}, "abstract": "TAR DNA-binding protein-43 (TDP-43) accumulation is the primary pathology underlying several neurodegenerative diseases. Charting the progression and heterogeneity of TDP-43 accumulation is necessary to better characterise TDP-43 proteinopathies, but current TDP-43 staging systems are heuristic and assume each syndrome is homogeneous. Here, we use data-driven disease progression modelling to derive a fine-grained empirical staging system for the classification and differentiation of frontotemporal lobar degeneration due to TDP-43 (FTLD-TDP, n=126), amyotrophic lateral sclerosis (ALS, n=141) and limbic-predominant age-related TDP-43 encephalopathy neuropathologic change (LATE-NC) with and without Alzheimer's disease (n=304). The data-driven staging of ALS and FTLD-TDP complement and extend previously described human-defined staging schema for ALS and behavioural variant frontotemporal dementia. In LATE-NC individuals, progression along data-driven stages was positively associated with age, but negatively associated with age in individuals with FTLD-TDP. Using only regional TDP-43 severity, our data driven model distinguished individuals diagnosed with ALS, FTLD-TDP or LATE-NC with a cross-validated accuracy of 85.9%, with misclassifications associated with mixed pathological diagnosis, age and genetic mutations. Adding age and SuStaIn stage to this model increased accuracy to 92.3%. Our model differentiates LATE-NC from FTLD-TDP, though some overlap was observed between late-stage LATE-NC and early-stage FTLD-TDP. We further tested for the presence of subtypes with distinct regional TDP-43 progression patterns within each diagnostic group, identifying two distinct cortical-predominant and brainstem-predominant subtypes within FTLD-TDP and a further two subcortical-predominant and corticolimbic-predominant subtypes within ALS. The FTLD-TDP subtypes exhibited differing proportions of TDP-43 type, while there was a trend for age differing between ALS subtypes. Interestingly, a negative relationship between age and SuStaIn stage was seen in the brainstem/subcortical-predominant subtype of each proteinopathy. No subtypes were observed for the LATE-NC group, despite aggregating individuals with and without Alzheimer's disease and a larger sample size for this group. Overall, we provide an empirical pathological TDP-43 staging system for ALS, FTLD-TDP and LATE-NC, which yielded accurate classification. We further demonstrate that there is substantial heterogeneity amongst ALS and FTLD-TDP progression patterns that warrants further investigation in larger cross-cohort studies.", "doi": "10.1093/brain/awad145", "pmid": "37150879", "labels": {"Jacob W Vogel": null, "DDLS Fellow": null}, "xrefs": [{"db": "pii", "key": "7156599"}], "notes": [], "created": "2023-05-24T14:13:34.812Z", "modified": "2023-11-29T06:41:10.111Z"}, {"entity": "publication", "iuid": "6d24f615699f4b0eab7ada8945fb0f6a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/6d24f615699f4b0eab7ada8945fb0f6a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/6d24f615699f4b0eab7ada8945fb0f6a"}}, "title": "Comparison of Group-Level and Individualized Brain Regions for Measuring Change in Longitudinal Tau Positron Emission Tomography in Alzheimer Disease.", "authors": [{"family": "Leuzy", "given": "Antoine", "initials": "A"}, {"family": "Binette", "given": "Alexa Pichet", "initials": "AP"}, {"family": "Vogel", "given": "Jacob W", "initials": "JW"}, {"family": "Klein", "given": "Gregory", "initials": "G"}, {"family": "Borroni", "given": "Edilio", "initials": "E"}, {"family": "Tonietto", "given": "Matteo", "initials": "M"}, {"family": "Strandberg", "given": "Olof", "initials": "O"}, {"family": "Mattsson-Carlgren", "given": "Niklas", "initials": "N"}, {"family": "Palmqvist", "given": "Sebastian", "initials": "S"}, {"family": "Pontecorvo", "given": "Michael J", "initials": "MJ"}, {"family": "Iaccarino", "given": "Leonardo", "initials": "L"}, {"family": "Stomrud", "given": "Erik", "initials": "E"}, {"family": "Ossenkoppele", "given": "Rik", "initials": "R"}, {"family": "Smith", "given": "Ruben", "initials": "R"}, {"family": "Hansson", "given": "Oskar", "initials": "O"}, {"family": "Alzheimer\u2019s Disease Neuroimaging Initiative", "given": "", "initials": ""}], "type": "journal article", "published": "2023-05-08", "journal": {"title": "JAMA Neurol", "issn": "2168-6157", "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": "Longitudinal tau positron emission tomography (PET) is a relevant outcome in clinical trials evaluating disease-modifying therapies in Alzheimer disease (AD). A key unanswered question is whether the use of participant-specific (individualized) regions of interest (ROIs) is superior to conventional approaches where the same ROI (group-level) is used for each participant.\r\n\r\nTo compare group- and participant-level ROIs in participants at different stages of the AD clinical continuum in terms of annual percentage change in tau-PET standardized uptake value ratio (SUVR) and sample size requirements.\r\n\r\nThis was a longitudinal cohort study with consecutive participant enrollment between September 18, 2017, and November 15, 2021. Included in the analysis were participants with mild cognitive impairment and AD dementia from the prospective and longitudinal Swedish Biomarkers For Identifying Neurodegenerative Disorders Early and Reliably 2 (BioFINDER-2) study; in addition, a validation sample (the AVID 05e, Expedition-3, Alzheimer's Disease Neuroimaging Initiative [ADNI], and BioFINDER-1 study cohorts) was also included.\r\n\r\nTau PET (BioFINDER-2, [18F]RO948; validation sample, [18F]flortaucipir), 7 group-level (5 data-driven stages, meta-temporal, whole brain), and 5 individualized ROIs.\r\n\r\nAnnual percentage change in tau-PET SUVR across ROIs. Sample size requirements in simulated clinical trials using tau PET as an outcome were also calculated.\r\n\r\nA total of 215 participants (mean [SD] age, 71.4 (7.5) years; 111 male [51.6%]) from the BioFINDER-2 study were included in this analysis: 97 amyloid-\u03b2 (A\u03b2)-positive cognitively unimpaired (CU) individuals, 77 with A\u03b2-positive mild cognitive impairment (MCI), and 41 with AD dementia. In the validation sample were 137 A\u03b2-positive CU participants, 144 with A\u03b2-positive MCI, and 125 with AD dementia. Mean (SD) follow-up time was 1.8 (0.3) years. Using group-level ROIs, the largest annual percentage increase in tau-PET SUVR in A\u03b2-positive CU individuals was seen in a composite ROI combining the entorhinal cortex, hippocampus, and amygdala (4.29%; 95% CI, 3.42%-5.16%). In individuals with A\u03b2-positive MCI, the greatest change was seen in the temporal cortical regions (5.82%; 95% CI, 4.67%-6.97%), whereas in those with AD dementia, the greatest change was seen in the parietal regions (5.22%; 95% CI, 3.95%-6.49%). Significantly higher estimates of annual percentage change were found using several of the participant-specific ROIs. Importantly, the simplest participant-specific approach, where change in tau PET was calculated in an ROI that best matched the participant's data-driven disease stage, performed best in all 3 subgroups. For the power analysis, sample size reductions for the participant-specific ROIs ranged from 15.94% (95% CI, 8.14%-23.74%) to 72.10% (95% CI, 67.10%-77.20%) compared with the best-performing group-level ROIs. Findings were replicated using [18F]flortaucipir.\r\n\r\nFinding suggest that certain individualized ROIs carry an advantage over group-level ROIs for assessing longitudinal tau changes and increase the power to detect treatment effects in AD clinical trials using longitudinal tau PET as an outcome.", "doi": "10.1001/jamaneurol.2023.1067", "pmid": "37155176", "labels": {"Jacob W Vogel": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC10167602"}, {"db": "pii", "key": "2804754"}], "notes": [], "created": "2023-05-28T17:50:22.736Z", "modified": "2023-11-29T06:40:54.137Z"}, {"entity": "publication", "iuid": "1c7447d86c504d7abceb68914defaf42", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1c7447d86c504d7abceb68914defaf42.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1c7447d86c504d7abceb68914defaf42"}}, "title": "OME-Zarr: a cloud-optimized bioimaging file format with international community support.", "authors": [{"family": "Moore", "given": "Josh", "initials": "J", "orcid": "0000-0003-4028-811X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d1ffe6a8671646ac9e75ec4a6b5a26de.json"}}, {"family": "Basurto-Lozada", "given": "Daniela", "initials": "D", "orcid": "0000-0003-3943-8424", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/43bc2250ca1e4f7d81a1887f2cfb5ed1.json"}}, {"family": "Besson", "given": "S\u00e9bastien", "initials": "S", "orcid": "0000-0001-8783-1429", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ce1fb03b0bc44c4a8c6580d727ac75d5.json"}}, {"family": "Bogovic", "given": "John", "initials": "J", "orcid": "0000-0002-4829-9457", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3bcdd7e4893c4c15b5aea0be49ee4a18.json"}}, {"family": "Bragantini", "given": "Jord\u00e3o", "initials": "J", "orcid": "0000-0001-7652-2735", "researcher": 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"initials": "N", "orcid": "0000-0003-0327-8297", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/83f7f88927584d80b6b5a5447b20dfdb.json"}}, {"family": "Haniffa", "given": "Muzlifah", "initials": "M", "orcid": "0000-0002-3927-2084", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0702147e80fd42358ad19a66451e2442.json"}}, {"family": "Hotaling", "given": "Nathan", "initials": "N", "orcid": "0000-0001-8423-6464", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e526892854084fe5ab16081f86d38d22.json"}}, {"family": "Onami", "given": "Shuichi", "initials": "S", "orcid": "0000-0002-8255-1724", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/83ea9aff97ad4f03ac4982160b20365f.json"}}, {"family": "Royer", "given": "Loic A", "initials": "LA", "orcid": "0000-0002-9991-9724", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/38277bc865f047df8c4523ebf0f1261c.json"}}, {"family": "Saalfeld", "given": "Stephan", "initials": "S", "orcid": "0000-0002-4106-1761", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/11e2453103c0410581737e66c33afec9.json"}}, {"family": "Stegle", "given": "Oliver", "initials": "O", "orcid": "0000-0002-8818-7193", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/73e53d349cfa48458444d75b18cf6d75.json"}}, {"family": "Theis", "given": "Fabian J", "initials": "FJ", "orcid": "0000-0002-2419-1943", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8969d033a36f40aab191ad1b3960114d.json"}}, {"family": "Swedlow", "given": "Jason R", "initials": "JR", "orcid": "0000-0002-2198-1958", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/919be1b6ecf34615a2c3e2a05f6c01de.json"}}], "type": "preprint", "published": "2023-05-07", "journal": {"title": "bioRxiv", "issn": "2692-8205", "issn-l": null}, "abstract": "A growing community is constructing a next-generation file format (NGFF) for bioimaging to overcome problems of scalability and heterogeneity. Organized by the Open Microscopy Environment (OME), individuals and institutes across diverse modalities facing these problems have designed a format specification process (OME-NGFF) to address these needs. This paper brings together a wide range of those community members to describe the cloud-optimized format itself -- OME-Zarr -- along with tools and data resources available today to increase FAIR access and remove barriers in the scientific process. The current momentum offers an opportunity to unify a key component of the bioimaging domain -- the file format that underlies so many personal, institutional, and global data management and analysis tasks.", "doi": "10.1101/2023.02.17.528834", "pmid": "36865282", "labels": {"DDLS Fellow": "", "Wei Ouyang": ""}, "xrefs": [{"db": "pmc", "key": "PMC9980008"}, {"db": "pii", "key": "2023.02.17.528834"}], "notes": [], "created": "2026-08-20T10:43:56.007Z", "modified": "2026-09-23T13:45:34.054Z"}, {"entity": "publication", "iuid": "75a909d34d6845308290d0cc98b716b8", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/75a909d34d6845308290d0cc98b716b8.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/75a909d34d6845308290d0cc98b716b8"}}, "title": "A practical approach to curate clonal hematopoiesis of indeterminate potential in human genetic data sets.", "authors": [{"family": "Vlasschaert", "given": "Caitlyn", "initials": "C"}, {"family": "Mack", "given": "Taralynn", "initials": "T", "orcid": "0000-0003-1043-2950", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b126c40c737b4b06a8702801ee227b04.json"}}, {"family": "Heimlich", "given": "J Brett", "initials": "JB", "orcid": "0000-0003-2812-5326", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/57e0bced1405484b94ce062052f498c0.json"}}, {"family": "Niroula", "given": "Abhishek", "initials": "A"}, {"family": "Uddin", "given": "Md Mesbah", "initials": "MM", "orcid": "0000-0003-1846-0411", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/42f1ac7010c34ba997a3fd9e56c6a56a.json"}}, {"family": "Weinstock", "given": "Joshua", "initials": "J", "orcid": "0000-0001-7013-1899", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2501ed5d8a4e43d488e7267e58ad68cd.json"}}, {"family": "Sharber", "given": "Brian", "initials": "B"}, {"family": "Silver", "given": "Alexander J", "initials": "AJ", "orcid": "0000-0001-8255-3140", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/207d0026e724498f86d32cfd69c78209.json"}}, {"family": "Xu", "given": "Yaomin", "initials": "Y", "orcid": "0000-0002-3752-4006", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7f974a0eac8b482696f97e7e579298ab.json"}}, {"family": "Savona", "given": "Michael", "initials": "M"}, {"family": "Gibson", "given": "Christopher", "initials": "C"}, {"family": "Lanktree", "given": "Matthew B", "initials": "MB", "orcid": "0000-0002-5750-6286", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0e941f0c76354792a451f2f5d8632e29.json"}}, {"family": "Rauh", "given": "Michael J", "initials": "MJ", "orcid": "0000-0002-8346-5537", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/908769b86132425e885a742ac04d3642.json"}}, {"family": "Ebert", "given": "Benjamin L", "initials": "BL", "orcid": "0000-0003-0197-5451", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56e4f1c53a4348e2b0ceb44a38850a17.json"}}, {"family": "Natarajan", "given": "Pradeep", "initials": "P", "orcid": "0000-0001-8402-7435", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fe8bd48c61c047cd8e61c35d9e9ac650.json"}}, {"family": "Jaiswal", "given": "Siddhartha", "initials": "S", "orcid": "0000-0002-9597-0477", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a1901e08f989434fb01dfa17b0a85470.json"}}, {"family": "Bick", "given": "Alexander G", "initials": "AG"}], "type": "journal article", "published": "2023-05-04", "journal": {"title": "Blood", "issn": "1528-0020", "volume": "141", "issue": "18", "pages": "2214-2223", "issn-l": "0006-4971"}, "abstract": "Clonal hematopoiesis of indeterminate potential (CHIP) is a common form of age-related somatic mosaicism that is associated with significant morbidity and mortality. CHIP mutations can be identified in peripheral blood samples that are sequenced using approaches that cover the whole genome, the whole exome, or targeted genetic regions; however, differentiating true CHIP mutations from sequencing artifacts and germ line variants is a considerable bioinformatic challenge. We present a stepwise method that combines filtering based on sequencing metrics, variant annotation, and population-based associations to increase the accuracy of CHIP calls. We apply this approach to ascertain CHIP in \u223c550 000 individuals in the UK Biobank complete whole exome cohort and the All of Us Research Program initial whole genome release cohort. CHIP ascertainment on this scale unmasks recurrent artifactual variants and highlights the importance of specialized filtering approaches for several genes, including TET2 and ASXL1. We show how small changes in filtering parameters can considerably increase CHIP misclassification and reduce the effect size of epidemiological associations. Our high-fidelity call set refines previous population-based associations of CHIP with incident outcomes. For example, the annualized incidence of myeloid malignancy in individuals with small CHIP clones is 0.03% per year, which increases to 0.5% per year among individuals with very large CHIP clones. We also find a significantly lower prevalence of CHIP in individuals of self-reported Latino or Hispanic ethnicity in All of Us, highlighting the importance of including diverse populations. The standardization of CHIP calling will increase the fidelity of CHIP epidemiological work and is required for clinical CHIP diagnostic assays.", "doi": "10.1182/blood.2022018825", "pmid": "36652671", "labels": {"Abhishek Niroula": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC10273159"}, {"db": "pii", "key": "S0006-4971(23)00143-X"}], "notes": [], "created": "2023-11-20T11:36:24.658Z", "modified": "2023-11-20T11:36:24.991Z"}, {"entity": "publication", "iuid": "c821d77769bb4f73bc35652bdab972d9", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c821d77769bb4f73bc35652bdab972d9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c821d77769bb4f73bc35652bdab972d9"}}, "title": "Helicobacter pylori Seropositivity, ABO Blood Type, and Pancreatic Cancer Risk From 5 Prospective Cohorts.", "authors": [{"family": "Lee", "given": "Alice A", "initials": "AA", "orcid": "0000-0002-5241-1878", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bd79d5f5ddba4406b54cdc2bbb81a288.json"}}, {"family": "Wang", "given": "Qiao-Li", "initials": "QL"}, {"family": "Kim", "given": "Jihye", "initials": "J"}, {"family": "Babic", "given": "Ana", "initials": "A"}, {"family": "Zhang", "given": "Xuehong", "initials": "X"}, {"family": "Perez", "given": "Kimberly", "initials": "K"}, {"family": "Ng", "given": "Kimmie", "initials": "K"}, {"family": "Nowak", "given": "Jonathan", "initials": "J"}, {"family": "Rifai", "given": "Nader", "initials": "N"}, {"family": "Sesso", "given": "Howard D", "initials": "HD"}, {"family": "Buring", "given": "Julie E", "initials": "JE"}, {"family": "Anderson", "given": "Garnet L", "initials": "GL"}, {"family": "Wactawski-Wende", "given": "Jean", "initials": "J"}, {"family": "Wallace", "given": "Robert", "initials": "R"}, {"family": "Manson", "given": "JoAnn E", "initials": "JE"}, {"family": "Giovannucci", "given": "Edward L", "initials": "EL"}, {"family": "Stampfer", "given": "Meir J", "initials": "MJ"}, {"family": "Kraft", "given": "Peter", "initials": "P"}, {"family": "Fuchs", "given": "Charles S", "initials": "CS"}, {"family": "Yuan", "given": "Chen", "initials": "C"}, {"family": "Wolpin", "given": "Brian M", "initials": "BM"}], "type": "journal article", "published": "2023-05-01", "journal": {"title": "Clin Transl Gastroenterol", "issn": "2155-384X", "volume": "14", "issue": "5", "pages": "e00573", "issn-l": null}, "abstract": "Helicobacter pylori infection may be a risk factor for pancreatic cancer, particularly infection by strains without the cytotoxin-associated gene A (CagA) virulence factor. Non-O blood type is a known risk factor for pancreatic cancer, and H. pylori gastric colonization occurs largely from bacterial adhesins binding to blood group antigens on gastric mucosa.\n\nWe included 485 pancreatic cancer cases and 1,122 matched controls from 5 U.S. prospective cohorts. Prediagnostic plasma samples were assessed for H. pylori and CagA antibody titers. Conditional logistic regression was used to estimate odds ratios (ORs) and 95% confidence intervals (CIs) for pancreatic cancer. ABO blood type was assessed using genetic polymorphisms at the ABO gene locus or self-report.\n\nCompared with H. pylori -seronegative participants, those who were seropositive did not demonstrate an increased risk of pancreatic cancer (OR 0.83, 95% CI 0.65-1.06). This lack of association was similar among CagA-seropositive (OR 0.75, 95% CI 0.53-1.04) and -seronegative (OR 0.89, 95% CI 0.65-1.20) participants. The association was also similar when stratified by time between blood collection and cancer diagnosis ( P -interaction = 0.80). Consistent with previous studies, non-O blood type was associated with increased pancreatic cancer risk, but this increase in risk was similar regardless of H. pylori seropositivity ( P -interaction = 0.51).\n\nIn this nested case-control study, history of H. pylori infection as determined by H. pylori antibody serology was not associated with pancreatic cancer risk, regardless of CagA virulence factor status. The elevated risk associated with non-O blood type was consistent in those with or without H. pylori seropositivity.", "doi": "10.14309/ctg.0000000000000573", "pmid": "36854058", "labels": {"DDLS Fellow": null, "Qiaoli Wang": null}, "xrefs": [{"db": "pmc", "key": "PMC10208692"}, {"db": "pii", "key": "01720094-202305000-00006"}], "notes": [], "created": "2025-11-28T12:23:06.403Z", "modified": "2025-11-28T12:23:06.437Z"}, {"entity": "publication", "iuid": "bc9e27b680c94219a8657e18efeaefab", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/bc9e27b680c94219a8657e18efeaefab.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/bc9e27b680c94219a8657e18efeaefab"}}, "title": "Prediction of risk for myeloid malignancy in clonal hematopoiesis.", "authors": [{"family": "Weeks", "given": "Lachelle D", "initials": "LD"}, {"family": "Niroula", "given": "Abhishek", "initials": "A"}, {"family": "Neuberg", "given": "Donna", "initials": "D"}, {"family": "Wong", "given": "Waihay", "initials": "W"}, {"family": "Lindsley", "given": "R Coleman", "initials": "RC"}, {"family": "Luskin", "given": "Marlise", "initials": "M"}, {"family": "Berliner", "given": "Nancy", "initials": "N"}, {"family": "Stone", "given": "Richard M", "initials": "RM"}, {"family": "DeAngelo", "given": "Daniel J", "initials": "DJ"}, {"family": "Soiffer", "given": "Robert", "initials": "R"}, {"family": "Uddin", "given": "Md Mesbah", "initials": "MM"}, {"family": "Griffin", "given": "Gabriel", "initials": "G"}, {"family": "Vlasschaert", "given": "Caitlyn", "initials": "C"}, {"family": "Gibson", "given": "Christopher J", "initials": "CJ"}, {"family": "Jaiswal", "given": "Siddhartha", "initials": "S"}, {"family": "Bick", "given": "Alexander G", "initials": "AG"}, {"family": "Malcovati", "given": "Luca", "initials": "L"}, {"family": "Natarajan", "given": "Pradeep", "initials": "P"}, {"family": "Ebert", "given": "Benjamin L", "initials": "BL"}], "type": "journal article", "published": "2023-05-00", "journal": {"title": "NEJM Evid", "issn": "2766-5526", "volume": "2", "issue": "5", "issn-l": null}, "abstract": "Clonal hematopoiesis of indeterminate potential (CHIP) and clonal cytopenia of undetermined significance (CCUS) are defined by somatic mutations in genes associated with myeloid neoplasms (MN) at a variant allele fraction (VAF) \u2265 0.02, in the absence and presence of cytopenia, respectively. CHIP/CCUS is highly prevalent in adults and defining predictors of MN risk would aid clinical management and research.\n\nWe analyzed sequenced exomes of healthy UK Biobank (UKB) participants (n = 438,890) in separate derivation and validation cohorts. Genetic mutations, laboratory values, and MN outcomes were used in conditional probability-based recursive partitioning and Cox regression to determine predictors of incident MN. Combined statistical weights defined a clonal hematopoiesis risk score (CHRS). Independent CHIP/CCUS patient cohorts were used to test prognostic capability of the CHRS in the clinical setting.\n\nRecursive partitioning distinguished CHIP/CCUS cases with 10-year probabilities of MN ranging from 0.0078 - 0.85. Multivariable analysis validated partitioning variables as predictors of MN. Key features, including single DNMT3A mutations, high risk mutations, \u2265 2 mutations, VAF \u2265 0.2, age \u2265 65 years, CCUS vs CHIP and red blood cell indices, influenced MN risk in variable direction. The CHRS defined low risk (n = 10018, 88.4%), intermediate risk (n = 1196, 10.5%), and high risk (n = 123, 1.1%) groups. In clinical cohorts, most MN events occurred in high risk CHIP/CCUS patients.\n\nThe CHRS provides simple prognostic framework for CHIP/CCUS, distinguishing a high risk minority from the majority of CHIP/CCUS which has minimal risk for progression to MN.", "doi": "10.1056/evidoa2200310", "pmid": "37483562", "labels": {"Abhishek Niroula": null, "DDLS Fellow": null}, "xrefs": [{"db": "mid", "key": "NIHMS1911751"}, {"db": "pmc", "key": "PMC10361696"}], "notes": [], "created": "2023-11-20T11:39:38.381Z", "modified": "2023-11-20T11:39:38.418Z"}, {"entity": "publication", "iuid": "4615294af5ba457b98b4d58ae432100b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4615294af5ba457b98b4d58ae432100b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4615294af5ba457b98b4d58ae432100b"}}, "title": "Plasma lipidome and risk of atrial fibrillation: results from the PREDIMED trial.", "authors": [{"family": "Toledo", "given": "Estefania", "initials": "E", "orcid": "0000-0002-6263-4434", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d04ea61c7230463ab64e537f97fb07fe.json"}}, {"family": "Wittenbecher", "given": "Clemens", "initials": "C"}, {"family": "Razquin", "given": "Cristina", "initials": "C"}, {"family": "Ruiz-Canela", "given": "Miguel", "initials": "M"}, {"family": "Clish", "given": "Clary B", "initials": "CB"}, {"family": "Liang", "given": "Liming", "initials": "L"}, {"family": "Alonso", "given": "Alvaro", "initials": "A"}, {"family": "Hern\u00e1ndez-Alonso", "given": "Pablo", "initials": "P"}, {"family": "Becerra-Tom\u00e1s", "given": "Nerea", "initials": "N"}, {"family": "Ar\u00f3s-Borau", "given": "Fernando", "initials": "F"}, {"family": "Corella", "given": "Dolores", "initials": "D"}, {"family": "Ros", "given": "Emilio", "initials": "E"}, {"family": "Estruch", "given": "Ram\u00f3n", "initials": "R"}, {"family": "Garc\u00eda-Rodr\u00edguez", "given": "Antonio", "initials": "A"}, {"family": "Fit\u00f3", "given": "Montserrat", "initials": "M"}, {"family": "Lapetra", "given": "Jos\u00e9", "initials": "J"}, {"family": "Fiol", "given": "Miquel", "initials": "M"}, {"family": "Alonso-Gomez", "given": "\u00c1ngel M", "initials": "\u00c1M"}, {"family": "Serra-Majem", "given": "Luis", "initials": "L"}, {"family": "Deik", "given": "Amy", "initials": "A"}, {"family": "Salas-Salvad\u00f3", "given": "Jordi", "initials": "J"}, {"family": "Hu", "given": "Frank B", "initials": "FB"}, {"family": "Mart\u00ednez-Gonz\u00e1lez", "given": "Miguel A", "initials": "MA"}], "type": "journal article", "published": "2023-05-00", "journal": {"title": "J Physiol Biochem", "issn": "1877-8755", "volume": "79", "issue": "2", "pages": "355-364", "issn-l": null}, "abstract": "The potential role of the lipidome in atrial fibrillation (AF) development is still widely unknown. We aimed to assess the association between lipidome profiles of the Prevenci\u00f3n con Dieta Mediterr\u00e1nea (PREDIMED) trial participants and incidence of AF. We conducted a nested case-control study (512 incident centrally adjudicated AF cases and 735 controls matched by age, sex, and center). Baseline plasma lipids were profiled using a Nexera X2 U-HPLC system coupled to an Exactive Plus orbitrap mass spectrometer. We estimated the association between 216 individual lipids and AF using multivariable conditional logistic regression and adjusted the p values for multiple testing. We also examined the joint association of lipid clusters with AF incidence. Hitherto, we estimated the lipidomics network, used machine learning to select important network-clusters and AF-predictive lipid patterns, and summarized the joint association of these lipid patterns weighted scores. Finally, we addressed the possible interaction by the randomized dietary intervention.Forty-one individual lipids were associated with AF at the nominal level (p < 0.05), but no longer after adjustment for multiple-testing. However, the network-based score identified with a robust data-driven lipid network showed a multivariable-adjusted ORper+1SD of 1.32 (95% confidence interval: 1.16-1.51; p < 0.001). The score included PC plasmalogens and PE plasmalogens, palmitoyl-EA, cholesterol, CE 16:0, PC 36:4;O, and TG 53:3. No interaction with the dietary intervention was found. A multilipid score, primarily made up of plasmalogens, was associated with an increased risk of AF. Future studies are needed to get further insights into the lipidome role on AF.Current Controlled Trials number, ISRCTN35739639.", "doi": "10.1007/s13105-023-00958-0", "pmid": "37004634", "labels": {"Clemens Wittenbecher": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC10300169"}, {"db": "pii", "key": "10.1007/s13105-023-00958-0"}], "notes": [], "created": "2025-03-19T08:20:48.093Z", "modified": "2026-09-23T12:56:21.326Z"}, {"entity": "publication", "iuid": "f85fb3bc915e4840a3e68620ac3d82e6", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f85fb3bc915e4840a3e68620ac3d82e6.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f85fb3bc915e4840a3e68620ac3d82e6"}}, "title": "Interobserver reproducibility of cribriform cancer in prostate needle biopsies and validation of International Society of Urological Pathology criteria.", "authors": [{"family": "Egevad", "given": "Lars", "initials": "L", "orcid": "0000-0001-8531-222X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a7d46f1f5fc047dc8edb910eb4f0645c.json"}}, {"family": "Delahunt", "given": "Brett", "initials": "B", "orcid": "0000-0002-5398-0300", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/433a3f884f95451383cc746925d9a08c.json"}}, {"family": "Iczkowski", "given": "Kenneth A", "initials": "KA"}, {"family": "van der Kwast", "given": "Theo", "initials": "T"}, {"family": "van Leenders", "given": "Geert J L H", "initials": "GJLH", "orcid": "0000-0003-2176-9102", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/06fb563d1d3243ffb42d4dbfb495eccf.json"}}, {"family": "Leite", "given": "Katia R M", "initials": "KRM", "orcid": "0000-0002-2615-7730", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5186bb78617340128628091c878daeda.json"}}, {"family": "Pan", "given": "Chin-Chen", "initials": "C"}, {"family": "Samaratunga", "given": "Hemamali", "initials": "H"}, {"family": "Tsuzuki", "given": "Toyonori", "initials": "T", "orcid": "0000-0002-4855-4366", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/42c993c2c0ab4b50afa03134f70118d9.json"}}, {"family": "Mulliqi", "given": "Nita", "initials": "N"}, {"family": "Ji", "given": "Xiaoyi", "initials": "X"}, {"family": "Olsson", "given": "Henrik", "initials": "H"}, {"family": "Valkonen", "given": "Masi", "initials": "M"}, {"family": "Ruusuvuori", "given": "Pekka", "initials": "P"}, {"family": "Eklund", "given": "Martin", "initials": "M"}, {"family": "Kartasalo", "given": "Kimmo", "initials": "K"}], "type": "journal article", "published": "2023-05-00", "journal": {"title": "Histopathology", "issn": "1365-2559", "issn-l": "0309-0167", "volume": "82", "issue": "6", "pages": "837-845"}, "abstract": "There is strong evidence that cribriform morphology indicates a worse prognosis of prostatic adenocarcinoma. Our aim was to investigate its interobserver reproducibility in prostate needle biopsies.\r\n\r\nA panel of nine prostate pathology experts from five continents independently reviewed 304 digitised biopsies for cribriform cancer according to recent International Society of Urological Pathology criteria. The biopsies were collected from a series of 702 biopsies that were reviewed by one of the panellists for enrichment of high-grade cancer and potentially cribriform structures. A 2/3 consensus diagnosis of cribriform and noncribriform cancer was reached in 90% (272/304) of the biopsies with a mean kappa value of 0.56 (95% confidence interval 0.52-0.61). The prevalence of consensus cribriform cancers was estimated to 4%, 12%, 21%, and 20% of Gleason scores 7 (3 + 4), 7 (4 + 3), 8, and 9-10, respectively. More than two cribriform structures per level or a largest cribriform mass with \u22659 lumina or a diameter of \u22650.5 mm predicted a consensus diagnosis of cribriform cancer in 88% (70/80), 84% (87/103), and 90% (56/62), respectively, and noncribriform cancer in 3% (2/80), 5% (5/103), and 2% (1/62), respectively (all P < 0.01).\r\n\r\nCribriform prostate cancer was seen in a minority of needle biopsies with high-grade cancer. Stringent diagnostic criteria enabled the identification of cribriform patterns and the generation of a large set of consensus cases for standardisation.", "doi": "10.1111/his.14867", "pmid": "36645163", "labels": {"Kimmo Kartasalo": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2024-11-05T16:10:21.528Z", "modified": "2024-11-29T10:41:30.167Z"}, {"entity": "publication", "iuid": "abc5a6e9aabb4c538b17d1ec56d381c6", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/abc5a6e9aabb4c538b17d1ec56d381c6.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/abc5a6e9aabb4c538b17d1ec56d381c6"}}, "title": "Pancreatic cancer is associated with medication changes prior to clinical diagnosis.", "authors": [{"family": "Zhang", "given": "Yin", "initials": "Y", "orcid": "0000-0001-6367-6583", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/86a19de667ad4273ac7552cd7d79982a.json"}}, {"family": "Wang", "given": "Qiao-Li", "initials": "QL"}, {"family": "Yuan", "given": "Chen", "initials": "C"}, {"family": "Lee", "given": "Alice A", "initials": "AA", "orcid": "0000-0002-5241-1878", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bd79d5f5ddba4406b54cdc2bbb81a288.json"}}, {"family": "Babic", "given": "Ana", "initials": "A"}, {"family": "Ng", "given": "Kimmie", "initials": "K", "orcid": "0000-0003-0631-1494", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/00bc0d97cfc44e9398c9bf1db5783402.json"}}, {"family": "Perez", "given": "Kimberly", "initials": "K"}, {"family": "Nowak", "given": "Jonathan A", "initials": "JA"}, {"family": "Lagergren", "given": "Jesper", "initials": "J"}, {"family": "Stampfer", "given": "Meir J", "initials": "MJ"}, {"family": "Giovannucci", "given": "Edward L", "initials": "EL"}, {"family": "Sander", "given": "Chris", "initials": "C"}, {"family": "Rosenthal", "given": "Michael H", "initials": "MH"}, {"family": "Kraft", "given": "Peter", "initials": "P", "orcid": "0000-0002-4472-8103", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d44ae97bc78b4ce2aec4bee2432b70c6.json"}}, {"family": "Wolpin", "given": "Brian M", "initials": "BM", "orcid": "0000-0002-0455-1032", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/90c86221350a45c1a398d089855e7dac.json"}}], "type": "journal article", "published": "2023-04-28", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "2437", "issn-l": "2041-1723"}, "abstract": "Patients with pancreatic ductal adenocarcinoma (PDAC) commonly develop symptoms and signs in the 1-2 years before diagnosis that can result in changes to medications. We investigate recent medication changes and PDAC diagnosis in Nurses' Health Study (NHS; females) and Health Professionals Follow-up Study (HPFS; males), including up to 148,973 U.S. participants followed for 2,994,057 person-years and 991 incident PDAC cases. Here we show recent initiation of antidiabetic (NHS) or anticoagulant (NHS, HFS) medications and cessation of antihypertensive medications (NHS, HPFS) are associated with pancreatic cancer diagnosis in the next 2 years. Two-year PDAC risk increases as number of relevant medication changes increases (P-trend <1 \u00d7 10-5), with participants who recently start antidiabetic and stop antihypertensive medications having multivariable-adjusted hazard ratio of 4.86 (95%CI, 1.74-13.6). These changes are not associated with diagnosis of other digestive system cancers. Recent medication changes should be considered as candidate features in multi-factor risk models for PDAC, though they are not causally implicated in development of PDAC.", "doi": "10.1038/s41467-023-38088-2", "pmid": "37117188", "labels": {"DDLS Fellow": null, "Qiaoli Wang": null}, "xrefs": [{"db": "pmc", "key": "PMC10147931"}, {"db": "pii", "key": "10.1038/s41467-023-38088-2"}], "notes": [], "created": "2025-11-28T12:23:07.503Z", "modified": "2025-11-28T12:23:07.559Z"}, {"entity": "publication", "iuid": "49ae51f0bd934e61a19d0d79070fc767", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/49ae51f0bd934e61a19d0d79070fc767.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/49ae51f0bd934e61a19d0d79070fc767"}}, "title": "Mapping of the gene network that regulates glycan clock of ageing", "authors": [{"family": "Frkatovi\u0107-Hod\u017ei\u0107", "given": "Azra", "initials": "A", "orcid": "0000-0002-0751-4421", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8d9c561305c24ca088101edc1bb1971a.json"}}, {"family": "Mi\u0161kec", "given": "Karlo", "initials": "K"}, {"family": "Mijakovac", "given": "Anika", "initials": "A"}, {"family": "Nostaeva", "given": "Arina", "initials": "A"}, {"family": "Sharapov", "given": "Sodbo Z", "initials": "SZ"}, {"family": "Landini", "given": "Arianna", "initials": "A"}, {"family": "Haller", "given": "Toomas", "initials": "T"}, {"family": "van den Akker", "given": "Erik", "initials": "E"}, {"family": "Sharma", "given": "Sapna", "initials": "S"}, {"family": "Cuadrat", "given": "Rafael R C", "initials": "RRC"}, {"family": "Mangino", "given": "Massimo", "initials": "M"}, {"family": "Li", "given": "Yong", "initials": "Y"}, {"family": "Keser", "given": "Toma", "initials": "T"}, {"family": "Rudman", "given": "Najda", "initials": "N"}, {"family": "\u0160tambuk", "given": "Tamara", "initials": "T"}, {"family": "Pu\u010di\u0107-Bakovi\u0107", "given": "Maja", "initials": "M"}, {"family": "Trbojevi\u0107-Akma\u010di\u0107", "given": "Irena", "initials": "I"}, {"family": "Gudelj", "given": "Ivan", "initials": "I"}, {"family": "\u0160tambuk", "given": "Jerko", "initials": "J"}, {"family": "Pribi\u0107", "given": "Tea", "initials": "T"}, {"family": "Radovani", "given": "Barbara", "initials": "B"}, {"family": "Tominac", "given": "Petra", "initials": "P"}, {"family": "Fischer", "given": "Krista", "initials": "K"}, {"family": "Beekman", "given": "Marian", "initials": "M"}, {"family": "Wuhrer", "given": "Manfred", "initials": "M"}, {"family": "Gieger", "given": "Christian", "initials": "C"}, {"family": "Schulze", "given": "Matthias B", "initials": "MB"}, {"family": "Wittenbecher", "given": "Clemens", "initials": "C"}, {"family": "Polasek", "given": "Ozren", "initials": "O"}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "Wilson", "given": "James F", "initials": "JF"}, {"family": "Spector", "given": "Tim D", "initials": "TD"}, {"family": "K\u00f6ttgen", "given": "Anna", "initials": "A"}, {"family": "Vu\u010dkovi\u0107", "given": "Frano", "initials": "F"}, {"family": "Aulchenko", "given": "Yurii S", "initials": "YS"}, {"family": "Vojta", "given": "Aleksandar", "initials": "A"}, {"family": "Kri\u0161ti\u0107", "given": "Jasminka", "initials": "J"}, {"family": "Klari\u0107", "given": "Lucija", "initials": "L"}, {"family": "Zoldo\u0161", "given": "Vlatka", "initials": "V"}, {"family": "Lauc", "given": "Gordan", "initials": "G"}], "type": "posted-content", "published": "2023-04-27", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2023.04.25.23289027", "pmid": null, "labels": {"DDLS Fellow": "", "Clemens Wittenbecher": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T10:45:18.791Z", "modified": "2026-09-23T14:21:32.948Z"}, {"entity": "publication", "iuid": "09e5480ec42446e9b3e43ec972405797", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/09e5480ec42446e9b3e43ec972405797.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/09e5480ec42446e9b3e43ec972405797"}}, "title": "Antibodies against the Ebola virus soluble glycoprotein are associated with long-term vaccine-mediated protection of non-human primates.", "authors": [{"family": "Gunn", "given": "Bronwyn M", "initials": "BM"}, {"family": "McNamara", "given": "Ryan P", "initials": "RP"}, {"family": "Wood", "given": "Lianna", "initials": "L"}, {"family": "Taylor", "given": "Sabian", "initials": "S"}, {"family": "Devadhasan", "given": "Anush", "initials": "A"}, {"family": "Guo", "given": "Wenyu", "initials": "W"}, {"family": "Das", "given": "Jishnu", "initials": "J"}, {"family": "Nilsson", "given": "Avlant", "initials": "A", "orcid": "0000-0002-9476-4516", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f2e21dbc1c624f6a841c59e959e948e4.json"}}, {"family": "Shurtleff", "given": "Amy", "initials": "A"}, {"family": "Dubey", "given": "Sheri", "initials": "S"}, {"family": "Eichberg", "given": "Michael", "initials": "M"}, {"family": "Suscovich", "given": "Todd J", "initials": "TJ"}, {"family": "Saphire", "given": "Erica Ollmann", "initials": "EO"}, {"family": "Lauffenburger", "given": "Douglas", "initials": "D", "orcid": "0000-0002-0050-989X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ac0a09cb7c9c49de95b660756a4e5464.json"}}, {"family": "Coller", "given": "Beth-Ann", "initials": "B"}, {"family": "Simon", "given": "Jakub K", "initials": "JK"}, {"family": "Alter", "given": "Galit", "initials": "G"}], "type": "journal article", "published": "2023-04-25", "journal": {"title": "Cell Reports", "issn": "2211-1247", "issn-l": null, "volume": "42", "issue": "4", "pages": "112402"}, "abstract": "The 2013 Ebola epidemic in Central and West Africa heralded the emergence of wide-spread, highly pathogenic viruses. The successful recombinant vector vaccine against Ebola (rVSV\u0394G-ZEBOV-GP) will limit future outbreaks, but identifying mechanisms of protection is essential to protect the most vulnerable. Vaccine-induced antibodies are key determinants of vaccine efficacy, yet the mechanism by which vaccine-induced antibodies prevent Ebola infection remains elusive. Here, we exploit a break in long-term vaccine efficacy in non-human primates to identify predictors of protection. Using unbiased humoral profiling that captures neutralization and Fc-mediated functions, we find that antibodies specific for soluble glycoprotein (sGP) drive neutrophil-mediated phagocytosis and predict vaccine-mediated protection. Similarly, we show that protective sGP-specific monoclonal antibodies have elevated neutrophil-mediated phagocytic activity compared with non-protective antibodies, highlighting the importance of sGP in vaccine protection and monoclonal antibody therapeutics against Ebola virus.", "doi": "10.1016/j.celrep.2023.112402", "pmid": "37061918", "labels": {"Avlant Nilsson": null, "DDLS Fellow": null}, "xrefs": [{"db": "mid", "key": "NIHMS1897948"}, {"db": "pmc", "key": "PMC10576837"}, {"db": "pii", "key": "S2211-1247(23)00413-8"}], "notes": [], "created": "2025-03-20T11:10:25.614Z", "modified": "2025-03-21T10:37:39.686Z"}, {"entity": "publication", "iuid": "db45a1cf1cf5478db787c92fc8e56bb5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/db45a1cf1cf5478db787c92fc8e56bb5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/db45a1cf1cf5478db787c92fc8e56bb5"}}, "title": "Development of top-down cortical propagations in youth.", "authors": [{"family": "Pines", "given": "Adam", "initials": "A"}, {"family": "Keller", "given": "Arielle S", "initials": "AS"}, {"family": "Larsen", "given": "Bart", "initials": "B"}, {"family": "Bertolero", "given": "Maxwell", "initials": "M"}, {"family": "Ashourvan", "given": "Arian", "initials": "A"}, {"family": "Bassett", "given": "Dani S", "initials": "DS"}, {"family": "Cieslak", "given": "Matthew", "initials": "M"}, {"family": "Covitz", "given": "Sydney", "initials": "S"}, {"family": "Fan", "given": "Yong", "initials": "Y"}, {"family": "Feczko", "given": "Eric", "initials": "E"}, {"family": "Houghton", "given": "Audrey", "initials": "A"}, {"family": "Rueter", "given": "Amanda R", "initials": "AR"}, {"family": "Saggar", "given": "Manish", "initials": "M"}, {"family": "Shafiei", "given": "Golia", "initials": "G"}, {"family": "Tapera", "given": "Tinashe M", "initials": "TM"}, {"family": "Vogel", "given": "Jacob", "initials": "J"}, {"family": "Weinstein", "given": "Sarah M", "initials": "SM"}, {"family": "Shinohara", "given": "Russell T", "initials": "RT"}, {"family": "Williams", "given": "Leanne M", "initials": "LM"}, {"family": "Fair", "given": "Damien A", "initials": "DA"}, {"family": "Satterthwaite", "given": "Theodore D", "initials": "TD"}], "type": "journal article", "published": "2023-04-19", "journal": {"title": "Neuron", "issn": "1097-4199", "issn-l": "0896-6273", "volume": "111", "issue": "8", "pages": "1316-1330.e5"}, "abstract": "Hierarchical processing requires activity propagating between higher- and lower-order cortical areas. However, functional neuroimaging studies have chiefly quantified fluctuations within regions over time rather than propagations occurring over space. Here, we leverage advances in neuroimaging and computer vision to track cortical activity propagations in a large sample of youth (n = 388). We delineate cortical propagations that systematically ascend and descend a cortical hierarchy in all individuals in our developmental cohort, as well as in an independent dataset of densely sampled adults. Further, we demonstrate that top-down, descending hierarchical propagations become more prevalent with greater demands for cognitive control as well as with development in youth. These findings emphasize that hierarchical processing is reflected in the directionality of propagating cortical activity and suggest top-down propagations as a potential mechanism of neurocognitive maturation in youth.", "doi": "10.1016/j.neuron.2023.01.014", "pmid": "36803653", "labels": {"Jacob W Vogel": null, "DDLS Fellow": null}, "xrefs": [{"db": "mid", "key": "NIHMS1869726"}, {"db": "pmc", "key": "PMC10121821"}, {"db": "pii", "key": "S0896-6273(23)00038-7"}], "notes": [], "created": "2023-05-28T17:53:59.951Z", "modified": "2023-11-29T06:40:41.918Z"}, {"entity": "publication", "iuid": "4f4ce83594914a62b938092ec4567560", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4f4ce83594914a62b938092ec4567560.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4f4ce83594914a62b938092ec4567560"}}, "title": "Molecular profiling of high-level athlete skeletal muscle after acute exercise \u2013 a systems biology approach", "authors": [{"family": "Reitzner", "given": "Stefan M", "initials": "SM", "orcid": "0000-0003-0151-2780", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f1d32bad414e49569ede9d7c80e2bf6f.json"}}, {"family": "Emanuelsson", "given": "Eric B", "initials": "EB", "orcid": "0000-0002-2746-8581", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5e6f00426a2c4aa8b65497f25bce9fd3.json"}}, {"family": "Arif", "given": "Muhammad", "initials": "M", "orcid": "0000-0003-2261-0881", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c8ffc9889ace44e3b992816601b817e2.json"}}, {"family": "Kaczkowski", "given": "Bogumil", "initials": "B", "orcid": "0000-0001-6554-5608", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/aa7757730ee344698d0bc47e68f6a353.json"}}, {"family": "Kwon", "given": "Andrew TJ", "initials": "AT", "orcid": "0000-0001-5019-8156", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6ca67d3235084dc493e5bb43cfd191d0.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca58bf2d214047e0ae5e38a42a0f2808.json"}}, {"family": "Arner", "given": "Erik", "initials": "E", "orcid": "0000-0003-1225-4908", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a3d57fe1bc44f24bc2a5079f024719d.json"}}, {"family": "Chapman", "given": "Mark A", "initials": "MA", "orcid": "0000-0001-9905-4022", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/71c4b747b8794745a547d635953c9960.json"}}, {"family": "Sundberg", "given": "Carl Johan", "initials": "CJ", "orcid": "0000-0002-7000-466X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7ed337b1089b4b3ca6e7787c2228326d.json"}}], "type": "posted-content", "published": "2023-04-11", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2023.04.11.535671", "pmid": null, "labels": {"SciLifeLab Fellow": "", "DDLS Fellow": "", "Adil Mardinoglu": "", "Muhammad Arif": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T10:45:12.765Z", "modified": "2026-09-23T14:48:29.627Z"}, {"entity": "publication", "iuid": "5ee01ddf5e5944ec80351b70a0ebf8c1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5ee01ddf5e5944ec80351b70a0ebf8c1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5ee01ddf5e5944ec80351b70a0ebf8c1"}}, "title": "Differential Retention of Pfam Domains Contributes to Long-term Evolutionary Trends.", "authors": [{"family": "James", "given": "Jennifer E", "initials": "JE", "orcid": "0000-0003-0518-6783", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4b807f7ab8f46f8a5e927e1b090d662.json"}}, {"family": "Nelson", "given": "Paul G", "initials": "PG", "orcid": "0000-0003-4453-9895", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/90045bdb5a234df4b5448db1ed4a5ff3.json"}}, {"family": "Masel", "given": "Joanna", "initials": "J", "orcid": "0000-0002-7398-2127", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eed69f257e574f4aa53f59349c3ff384.json"}}], "type": "journal article", "published": "2023-04-04", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "issn-l": "0737-4038", "volume": "40", "issue": "4", "pages": null}, "abstract": "Protein domains that emerged more recently in evolution have a higher structural disorder and greater clustering of hydrophobic residues along the primary sequence. It is hard to explain how selection acting via descent with modification could act so slowly as not to saturate over the extraordinarily long timescales over which these trends persist. Here, we hypothesize that the trends were created by a higher level of selection that differentially affects the retention probabilities of protein domains with different properties. This hypothesis predicts that loss rates should depend on disorder and clustering trait values. To test this, we inferred loss rates via maximum likelihood for animal Pfam domains, after first performing a set of stringent quality control methods to reduce annotation errors. Intermediate trait values, matching those of ancient domains, are associated with the lowest loss rates, making our results difficult to explain with reference to previously described homology detection biases. Simulations confirm that effect sizes are of the right magnitude to produce the observed long-term trends. Our results support the hypothesis that differential domain loss slowly weeds out those protein domains that have nonoptimal levels of disorder and clustering. The same preferences also shape the differential diversification of Pfam domains, thereby further impacting proteome composition.", "doi": "10.1093/molbev/msad073", "pmid": "36947137", "labels": {"Jennifer James": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC10089649"}, {"db": "pii", "key": "7083726"}], "notes": [], "created": "2024-11-27T09:25:33.221Z", "modified": "2024-11-29T09:36:28.003Z"}, {"entity": "publication", "iuid": "225b4f7dfa6640918214472b03260d0f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/225b4f7dfa6640918214472b03260d0f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/225b4f7dfa6640918214472b03260d0f"}}, "title": "Plasma Lipidomic n-6 Polyunsaturated Fatty Acids and Type 2 Diabetes Risk in the EPIC-Potsdam Prospective Cohort Study.", "authors": [{"family": "Prada", "given": "Marcela", "initials": "M"}, {"family": "Eichelmann", "given": "Fabian", "initials": "F"}, {"family": "Wittenbecher", "given": "Clemens", "initials": "C"}, {"family": "Kuxhaus", "given": "Olga", "initials": "O"}, {"family": "Schulze", "given": "Matthias B", "initials": "MB", "orcid": "0000-0002-0830-5277", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/853ded2c43b64f26a8b47da7ea7b79c0.json"}}], "type": "journal article", "published": "2023-04-01", "journal": {"title": "Diabetes Care", "issn": "1935-5548", "volume": "46", "issue": "4", "pages": "836-844", "issn-l": null}, "abstract": "Evidence on plasma n-6 polyunsaturated fatty acids (PUFAs) and type 2 diabetes risk is inconsistent. We examined the associations of lipid class-specific PUFA concentrations with type 2 diabetes risk.\n\nIn the prospective European Prospective Investigation into Cancer and Nutrition (EPIC)-Potsdam cohort (nested case-cohort study: subcohort 1,084 participants, 536 participants with type 2 diabetes, median follow-up 6.5 years), we measured plasma 18:2, 20:3, and 20:4 concentrations in 12 lipid (sub)classes, likely reflecting the plasma concentrations of linoleic acid (18:2n-6), dihomo-\u03b3-linolenic acid (20:3n-6), and arachidonic acid (20:4n-6). The \u0394-5 desaturase (D5D) activity was estimated as the 20:4/20:3 ratio. Associations with diabetes were estimated with Cox proportional hazards models.\n\nHigher concentrations of 18:2 were inversely associated with type 2 diabetes risk, particularly in lysophosphatidylcholines (hazard ratio [HR] per 1 SD 0.53; 95% CI 0.23-1.26) and monoacylglycerols (HR 0.59; 0.38-0.92). Higher concentrations of 20:3 in phospholipid classes phosphatidylcholines (HR 1.63; 1.23-2.14), phosphatidylethanolamines (HR 1.87; 1.32-2.65), and phosphatidylinositol (HR 1.40; 1.05-1.87); free fatty acids (HR 1.44; 1.10-1.90); and cholesteryl esters (HR 1.47; 1.09-1.98) were linked to higher type 2 diabetes incidence, and these associations remained statistically significant after correction for multiple testing. Higher 20:4 concentrations were not associated with risk. The estimated D5D activity in phospholipids and cholesteryl esters was associated with lower type 2 diabetes risk. Single nucleotide polymorphisms in the D5D-encoding FADS genes explained relatively high proportions of variation of estimated D5D activity in those lipid classes.\n\nPlasma n-6 PUFAs were associated differently with type 2 diabetes, depending on fatty acid and the lipid class.", "doi": "10.2337/dc22-1435", "pmid": "36787959", "labels": {"Clemens Wittenbecher": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC10090908"}, {"db": "pii", "key": "148425"}], "notes": [], "created": "2025-03-19T08:20:49.332Z", "modified": "2025-03-19T08:21:01.136Z"}, {"entity": "publication", "iuid": "b0289a0d97364f01994b12b7aebbe7fe", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b0289a0d97364f01994b12b7aebbe7fe.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b0289a0d97364f01994b12b7aebbe7fe"}}, "title": "Low-Carbohydrate Diet Scores and Mortality Among Adults With Incident Type 2 Diabetes.", "authors": [{"family": "Hu", "given": "Yang", "initials": "Y", "orcid": "0000-0002-0200-5951", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/03db056e0c8d457b96111b6d13a1422f.json"}}, {"family": "Liu", "given": "Gang", "initials": "G"}, {"family": "Yu", "given": "Edward", "initials": "E"}, {"family": "Wang", "given": "Biqi", "initials": "B"}, {"family": "Wittenbecher", "given": "Clemens", "initials": "C"}, {"family": "Manson", "given": "JoAnn E", "initials": "JE"}, {"family": "Rimm", "given": "Eric B", "initials": "EB"}, {"family": "Liang", "given": "Liming", "initials": "L"}, {"family": "Rexrode", "given": "Kathryn", "initials": "K"}, {"family": "Willett", "given": "Walter C", "initials": "WC"}, {"family": "Hu", "given": "Frank B", "initials": "FB"}, {"family": "Sun", "given": "Qi", "initials": "Q", "orcid": "0000-0002-8480-1563", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4a65407257ac4518ac5cb19317ee3b32.json"}}], "type": "journal article", "published": "2023-04-01", "journal": {"title": "Diabetes Care", "issn": "1935-5548", "volume": "46", "issue": "4", "pages": "874-884", "issn-l": null}, "abstract": "The current study aims to prospectively examine the association between postdiagnosis low-carbohydrate diet (LCD) patterns and mortality among individuals with type 2 diabetes (T2D).\n\nAmong participants with incident diabetes identified in the Nurses' Health Study and Health Professionals Follow-up Study, an overall total LCD score (TLCDS) was calculated based on the percentage of energy as total carbohydrates. In addition, vegetable (VLCDS), animal (ALCDS), healthy (HLCDS), and unhealthy (ULCDS) LCDS were further derived that emphasized different sources and quality of macronutrients. Multivariable-adjusted Cox models were used to assess the association between the LCDS and mortality.\n\nAmong 10,101 incident T2D cases contributing 139,407 person-years during follow-up, we documented 4,595 deaths of which 1,389 cases were attributed to cardiovascular disease (CVD) and 881 to cancer. The pooled multivariable-adjusted hazard ratios (HRs, 95% CIs) of total mortality per 10-point increment of postdiagnosis LCDS were 0.87 (0.82, 0.92) for TLCDS, 0.76 (0.71, 0.82) for VLCDS, and 0.78 (0.73, 0.84) for HLCDS. Both VLCDS and HLCDS were also associated with significantly lower CVD and cancer mortality. Each 10-point increase of TLCDS, VLCDS, and HLCDS from prediagnosis to postdiagnosis period was associated with 12% (7%, 17%), 25% (19%, 30%), and 25% (19%, 30%) lower total mortality, respectively. No significant associations were observed for ALCDS and ULCDS.\n\nAmong people with T2D, greater adherence to LCD patterns that emphasize high-quality sources of macronutrients was significantly associated with lower total, cardiovascular, and cancer mortality.", "doi": "10.2337/dc22-2310", "pmid": "36787923", "labels": {"Clemens Wittenbecher": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC10090909"}, {"db": "pii", "key": "148449"}], "notes": [], "created": "2025-03-19T08:20:50.554Z", "modified": "2025-03-19T08:21:02.265Z"}, {"entity": "publication", "iuid": "fd6c2aced6d8418098e17a687693a49b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/fd6c2aced6d8418098e17a687693a49b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/fd6c2aced6d8418098e17a687693a49b"}}, "title": "Gray matter hypoperfusion is a late pathological event in the course of Alzheimer's disease.", "authors": [{"family": "Ahmadi", "given": "Khazar", "initials": "K", "orcid": "0000-0002-3371-6211", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5295cea5ead34b96a887d4055ccd659b.json"}}, {"family": "Pereira", "given": "Joana B", "initials": "JB"}, {"family": "Berron", "given": "David", "initials": "D"}, {"family": "Vogel", "given": "Jacob", "initials": "J"}, {"family": "Ingala", "given": "Silvia", "initials": "S"}, {"family": "Strandberg", "given": "Olof T", "initials": "OT"}, {"family": "Janelidze", "given": "Shorena", "initials": "S"}, {"family": "Barkhof", "given": "Frederik", "initials": "F"}, {"family": "Pfeuffer", "given": "Josef", "initials": "J", "orcid": "0000-0001-9887-0458", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/68ada20f4e5b4740aa57148d9e3356a7.json"}}, {"family": "Knutsson", "given": "Linda", "initials": "L", "orcid": "0000-0002-4263-113X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a434aaf67332472dbcb8d1aed36b27e0.json"}}, {"family": "van Westen", "given": "Danielle", "initials": "D"}, {"family": "Palmqvist", "given": "Sebastian", "initials": "S"}, {"family": "Mutsaerts", "given": "Henk Jmm", "initials": "HJ", "orcid": "0000-0003-0894-0307", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/00d0bad3d5dc4b0799da545ab3b95e06.json"}}, {"family": "Hansson", "given": "Oskar", "initials": "O"}], "type": "journal article", "published": "2023-04-00", "journal": {"title": "J. Cereb. Blood Flow Metab.", "issn": "1559-7016", "issn-l": "0271-678X", "volume": "43", "issue": "4", "pages": "565-580"}, "abstract": "Several studies have shown decreased cerebral blood flow (CBF) in Alzheimer's disease (AD). However, the role of hypoperfusion in the disease pathogenesis remains unclear. Combining arterial spin labeling MRI, PET, and CSF biomarkers, we investigated the associations between gray matter (GM)-CBF and the key mechanisms in AD including amyloid-\u03b2 (A\u03b2) and tau pathology, synaptic and axonal degeneration. Further, we applied a disease progression modeling to characterize the temporal sequence of different AD biomarkers. Lower perfusion was observed in temporo-occipito-parietal cortex in the A\u03b2-positive cognitively impaired compared to both A\u03b2-negative and A\u03b2-positive cognitively unimpaired individuals. In participants along the AD spectrum, GM-CBF was associated with tau, synaptic and axonal dysfunction, but not A\u03b2 in similar cortical regions. Axonal degeneration was further associated with hypoperfusion in cognitively unimpaired individuals. Disease progression modeling revealed that GM-CBF disruption Followed the abnormality of biomarkers of A\u03b2, tau and brain atrophy. These findings indicate that tau tangles and neurodegeneration are more closely connected with GM-CBF changes than A\u03b2 pathology. Although subjected to the sensitivity of the employed neuroimaging techniques and the modeling approach, these findings suggest that hypoperfusion might not be an early event associated with the build-up of A\u03b2 in preclinical phase of AD.", "doi": "10.1177/0271678X221141139", "pmid": "36412244", "labels": {"Jacob W Vogel": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC10063832"}], "notes": [], "created": "2023-05-28T17:58:13.613Z", "modified": "2023-11-29T06:40:28.606Z"}, {"entity": "publication", "iuid": "310edab64fbe4438bd9861d29899ebc9", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/310edab64fbe4438bd9861d29899ebc9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/310edab64fbe4438bd9861d29899ebc9"}}, "title": "Dietary intake of total, heme and non-heme iron and the risk of colorectal cancer in a European prospective cohort study.", "authors": [{"family": "Aglago", "given": "Elom K", "initials": "EK", "orcid": "0000-0002-0442-3284", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0058cc3c02944cf4bf78ed9c503f4569.json"}}, {"family": "Cross", "given": "Amanda J", "initials": "AJ"}, {"family": "Riboli", "given": "Elio", "initials": "E", "orcid": "0000-0001-6795-6080", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9adbccffd7fd47fabc95e684054b8ec1.json"}}, {"family": "Fedirko", "given": "Veronika", "initials": "V"}, {"family": "Hughes", "given": "David J", "initials": "DJ"}, {"family": "Fournier", "given": "Agnes", "initials": "A"}, {"family": "Jakszyn", "given": "Paula", "initials": "P"}, {"family": "Freisling", "given": "Heinz", "initials": "H", "orcid": "0000-0001-8648-4998", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1fbe42aec4c844f98d1551887e5dcb38.json"}}, {"family": "Gunter", "given": "Marc J", "initials": "MJ"}, {"family": "Dahm", "given": "Christina C", "initials": "CC", "orcid": "0000-0003-0481-2893", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/64083e92104a41d0a3a89d9c757857fa.json"}}, {"family": "Overvad", "given": "Kim", "initials": "K"}, {"family": "Tj\u00f8nneland", "given": "Anne", "initials": "A"}, {"family": "Kyr\u00f8", "given": "Cecilie", "initials": "C"}, {"family": "Boutron-Ruault", "given": "Marie-Christine", "initials": "MC"}, {"family": "Rothwell", "given": "Joseph A", "initials": "JA"}, {"family": "Severi", "given": "Gianluca", "initials": "G"}, {"family": "Katzke", "given": "Verena", "initials": "V"}, {"family": "Srour", "given": "Bernard", "initials": "B"}, {"family": "Schulze", "given": "Matthias B", "initials": "MB"}, {"family": "Wittenbecher", "given": "Clemens", "initials": "C"}, {"family": "Palli", "given": "Domenico", "initials": "D", "orcid": "0000-0002-5558-2437", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d6ce0a934eb244da8719e3bfca616e96.json"}}, {"family": "Sieri", "given": "Sabina", "initials": "S"}, {"family": "Pasanisi", "given": "Fabrizio", "initials": "F"}, {"family": "Tumino", "given": "Rosario", "initials": "R", "orcid": "0000-0003-2666-414X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fca52195ea344dd7a1ce61afbf04a242.json"}}, {"family": "Ricceri", "given": "Fulvio", "initials": "F", "orcid": "0000-0001-8749-9737", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dd4ad819a55a4185aa2751299848a7a4.json"}}, {"family": "Bueno-de-Mesquita", "given": "Bas", "initials": "B"}, {"family": "Derksen", "given": "Jeroen W G", "initials": "JWG"}, {"family": "Skeie", "given": "Guri", "initials": "G"}, {"family": "Jensen", "given": "Torill Enget", "initials": "TE"}, {"family": "Lukic", "given": "Marko", "initials": "M"}, {"family": "S\u00e1nchez", "given": "Maria-Jose", "initials": "MJ"}, {"family": "Amiano", "given": "Pilar", "initials": "P"}, {"family": "Colorado-Yohar", "given": "Sandra", "initials": "S"}, {"family": "Barricarte", "given": "Aurelio", "initials": "A"}, {"family": "Ericson", "given": "Ulrika", "initials": "U"}, {"family": "van Guelpen", "given": "Bethany", "initials": "B"}, {"family": "Papier", "given": "Keren", "initials": "K"}, {"family": "Knuppel", "given": "Anika", "initials": "A"}, {"family": "Casagrande", "given": "Corinne", "initials": "C"}, {"family": "Huybrechts", "given": "Inge", "initials": "I", "orcid": "0000-0003-3838-855X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/794776b7254046d8a0398ea6d104df51.json"}}, {"family": "Heath", "given": "Alicia K", "initials": "AK", "orcid": "0000-0001-6517-1300", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b153bfb01b424c22aa0b351f203534e4.json"}}, {"family": "Tsilidis", "given": "Konstantinos K", "initials": "KK", "orcid": "0000-0002-8452-8472", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1aedb8ced973427dae1948739a431d71.json"}}, {"family": "Jenab", "given": "Mazda", "initials": "M", "orcid": "0000-0002-0573-1852", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/134c7c03768b431e8903090fa1163287.json"}}], "type": "journal article", "published": "2023-04-00", "journal": {"title": "Br. J. Cancer", "issn": "1532-1827", "volume": "128", "issue": "8", "pages": "1529-1540", "issn-l": "0007-0920"}, "abstract": "Iron is an essential micronutrient with differing intake patterns and metabolism between men and women. Epidemiologic evidence on the association of dietary iron and its heme and non-heme components with colorectal cancer (CRC) development is inconclusive.\n\nWe examined baseline dietary questionnaire-assessed intakes of total, heme, and non-heme iron and CRC risk in the EPIC cohort. Sex-specific multivariable-adjusted hazard ratios (HRs) and 95% confidence intervals (CIs) were computed using Cox regression. We modelled substitution of a 1 mg/day of heme iron intake with non-heme iron using the leave one-out method.\n\nOf 450,105 participants (318,680 women) followed for 14.2 \u00b1 4.0 years, 6162 (3511 women) developed CRC. In men, total iron intake was not associated with CRC risk (highest vs. lowest quintile, HRQ5vs.Q1:0.88; 95%CI:0.73, 1.06). An inverse association was observed for non-heme iron (HRQ5vs.Q1:0.80, 95%CI:0.67, 0.96) whereas heme iron showed a non-significant association (HRQ5vs.Q1:1.10; 95%CI:0.96, 1.27). In women, CRC risk was not associated with intakes of total (HRQ5vs.Q1:1.11, 95%CI:0.94, 1.31), heme (HRQ5vs.Q1:0.95; 95%CI:0.84, 1.07) or non-heme iron (HRQ5vs.Q1:1.03, 95%CI:0.88, 1.20). Substitution of heme with non-heme iron demonstrated lower CRC risk in men (HR:0.94; 95%CI: 0.89, 0.99).\n\nOur findings suggest potential sex-specific CRC risk associations for higher iron consumption that may differ by dietary sources.", "doi": "10.1038/s41416-023-02164-7", "pmid": "36759722", "labels": {"Clemens Wittenbecher": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC10070394"}, {"db": "pii", "key": "10.1038/s41416-023-02164-7"}], "notes": [], "created": "2025-03-19T08:20:51.793Z", "modified": "2025-12-09T13:33:02.870Z"}, {"entity": "publication", "iuid": "231cf1cf478e4e7bada16e3877f65ba0", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/231cf1cf478e4e7bada16e3877f65ba0.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/231cf1cf478e4e7bada16e3877f65ba0"}}, "title": "Deep learning for protein complex structure prediction.", "authors": [{"family": "Bryant", "given": "Patrick", "initials": "P"}], "type": "journal article", "published": "2023-04-00", "journal": {"title": "Curr. Opin. Struct. Biol.", "issn": "1879-033X", "volume": "79", "pages": "102529", "issn-l": "0959-440X"}, "abstract": "Recent developments in the structure prediction of protein complexes have resulted in accuracies rivalling experimental methods in many cases. The high accuracy is mainly observed in dimeric complexes and other problems such as protein disorder and predicting the structure of host-pathogen interactions remain. This review highlights the foundation for current accurate structure prediction of protein complexes and possible ways to address the remaining limitations.", "doi": "10.1016/j.sbi.2023.102529", "pmid": "36731337", "labels": {"Patrick Bryant": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pii", "key": "S0959-440X(23)00003-9"}], "notes": [], "created": "2026-08-20T08:04:17.914Z", "modified": "2026-09-23T08:38:41.004Z"}, {"entity": "publication", "iuid": "ec7c5372a6954d0186cb4fa27ef713d9", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ec7c5372a6954d0186cb4fa27ef713d9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ec7c5372a6954d0186cb4fa27ef713d9"}}, "title": "Clonal haematopoiesis and risk of chronic liver disease.", "authors": [{"family": "Wong", "given": "Waihay J", "initials": "WJ", "orcid": "0000-0003-2023-6590", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3a4e1a5be5c54646ab5881bc338bf6cd.json"}}, {"family": "Emdin", "given": "Connor", "initials": "C"}, {"family": "Bick", "given": "Alexander G", "initials": "AG"}, {"family": "Zekavat", "given": "Seyedeh M", "initials": "SM", "orcid": "0000-0003-4026-8944", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6234b31f08e442a9b71a711ec7b1147a.json"}}, {"family": "Niroula", "given": "Abhishek", "initials": "A"}, {"family": "Pirruccello", "given": "James P", "initials": "JP", "orcid": "0000-0001-6088-4037", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/60d2e9f23cce41f5b1f40ce0f010e9d9.json"}}, {"family": "Dichtel", "given": "Laura", "initials": "L"}, {"family": "Griffin", "given": "Gabriel", "initials": "G"}, {"family": "Uddin", "given": "Md Mesbah", "initials": "MM", "orcid": "0000-0003-1846-0411", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/42f1ac7010c34ba997a3fd9e56c6a56a.json"}}, {"family": "Gibson", "given": "Christopher J", "initials": "CJ", "orcid": "0000-0002-3700-5310", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/71ce9f64755e483496f8c28a76a2a1ff.json"}}, {"family": "Kovalcik", "given": "Veronica", "initials": "V"}, {"family": "Lin", "given": "Amy E", "initials": "AE"}, {"family": "McConkey", "given": "Marie E", "initials": "ME"}, {"family": "Vromman", "given": "Amelie", "initials": "A", "orcid": "0000-0002-1724-2095", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c5297e9d22b24ac7beaab07f94c6d1f7.json"}}, {"family": "Sellar", "given": "Rob S", "initials": "RS"}, {"family": "Kim", "given": "Peter G", "initials": "PG", "orcid": "0000-0002-8716-8759", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bab07a767447416fa8e4004c6cbe7b7f.json"}}, {"family": "Agrawal", "given": "Mridul", "initials": "M"}, {"family": "Weinstock", "given": "Joshua", "initials": "J", "orcid": "0000-0001-7013-1899", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2501ed5d8a4e43d488e7267e58ad68cd.json"}}, {"family": "Long", "given": "Michelle T", "initials": "MT", "orcid": "0000-0001-6131-3981", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e3d2425beb9d4716a378684bbf3817f3.json"}}, {"family": "Yu", "given": "Bing", "initials": "B"}, {"family": "Banerjee", "given": "Rajarshi", "initials": "R"}, {"family": "Nicholls", "given": "Rowan C", "initials": "RC", "orcid": "0000-0002-3311-4974", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a9861d98d104414aa96c7646418b04e7.json"}}, {"family": "Dennis", "given": "Andrea", "initials": "A"}, {"family": "Kelly", "given": "Matt", "initials": "M", "orcid": "0000-0002-5834-635X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e1f150673cd0427ea54c82ecadd62a15.json"}}, {"family": "Loh", "given": "Po-Ru", "initials": "PR", "orcid": "0000-0001-5542-9064", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ace35329adf34fc6a3ea3d31c880d5c2.json"}}, {"family": "McCarroll", "given": "Steve", "initials": "S", "orcid": "0000-0002-6954-8184", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bde6c6c1092647c090d29dae413b2073.json"}}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Vasan", "given": "Ramachandran S", "initials": "RS", "orcid": "0000-0001-7357-5970", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/22de41f77ce541d09a9b04aa59de33f7.json"}}, {"family": "Jaiswal", "given": "Siddhartha", "initials": "S", "orcid": "0000-0002-9597-0477", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a1901e08f989434fb01dfa17b0a85470.json"}}, {"family": "Johnson", "given": "Andrew D", "initials": "AD", "orcid": "0000-0001-6369-5178", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8b268f8da3f247ba90dc37ea73d93c2f.json"}}, {"family": "Chung", "given": "Raymond T", "initials": "RT"}, {"family": "Corey", "given": "Kathleen", "initials": "K"}, {"family": "Levy", "given": "Daniel", "initials": "D", "orcid": "0000-0003-1843-8724", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/57605ba755d44792ab87cf14114ec757.json"}}, {"family": "Ballantyne", "given": "Christie", "initials": "C", "orcid": "0000-0002-6432-1730", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/27dc5297c262410bad3bbb66a488d4b4.json"}}, {"family": "NHLBI TOPMed Hematology Working Group", "given": "", "initials": ""}, {"family": "Ebert", "given": "Benjamin L", "initials": "BL", "orcid": "0000-0003-0197-5451", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56e4f1c53a4348e2b0ceb44a38850a17.json"}}, {"family": "Natarajan", "given": "Pradeep", "initials": "P", "orcid": "0000-0001-8402-7435", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fe8bd48c61c047cd8e61c35d9e9ac650.json"}}], "type": "journal article", "published": "2023-04-00", "journal": {"title": "Nature", "issn": "1476-4687", "volume": "616", "issue": "7958", "pages": "747-754", "issn-l": "0028-0836"}, "abstract": "Chronic liver disease is a major public health burden worldwide1. Although different aetiologies and mechanisms of liver injury exist, progression of chronic liver disease follows a common pathway of liver inflammation, injury and fibrosis2. Here we examined the association between clonal haematopoiesis of indeterminate potential (CHIP) and chronic liver disease in 214,563 individuals from 4 independent cohorts with whole-exome sequencing data (Framingham Heart Study, Atherosclerosis Risk in Communities Study, UK Biobank and Mass General Brigham Biobank). CHIP was associated with an increased risk of prevalent and incident chronic liver disease (odds ratio = 2.01, 95% confidence interval (95% CI) [1.46, 2.79]; P < 0.001). Individuals with CHIP were more likely to demonstrate liver inflammation and fibrosis detectable by magnetic resonance imaging compared to those without CHIP (odds ratio = 1.74, 95% CI [1.16, 2.60]; P = 0.007). To assess potential causality, Mendelian randomization analyses showed that genetic predisposition to CHIP was associated with a greater risk of chronic liver disease (odds ratio = 2.37, 95% CI [1.57, 3.6]; P < 0.001). In a dietary model of non-alcoholic steatohepatitis, mice transplanted with Tet2-deficient haematopoietic cells demonstrated more severe liver inflammation and fibrosis. These effects were mediated by the NLRP3 inflammasome and increased levels of expression of downstream inflammatory cytokines in Tet2-deficient macrophages. In summary, clonal haematopoiesis is associated with an elevated risk of liver inflammation and chronic liver disease progression through an aberrant inflammatory response.", "doi": "10.1038/s41586-023-05857-4", "pmid": "37046084", "labels": {"Abhishek Niroula": null, "DDLS Fellow": null}, "xrefs": [{"db": "mid", "key": "NIHMS1912281"}, {"db": "pmc", "key": "PMC10405350"}, {"db": "pii", "key": "10.1038/s41586-023-05857-4"}], "notes": [], "created": "2023-11-20T11:39:32.404Z", "modified": "2023-11-20T11:39:32.756Z"}, {"entity": "publication", "iuid": "717022265f074bd6998670aa2f225090", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/717022265f074bd6998670aa2f225090.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/717022265f074bd6998670aa2f225090"}}, "title": "Diverticulosis is not associated with altered gut microbiota nor is it predictive of future diverticulitis: a population-based colonoscopy study.", "authors": [{"family": "Alexandersson", "given": "Bjarki T", "initials": "BT"}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW"}, {"family": "Hedin", "given": "Charlotte", "initials": "C"}, {"family": "Forsberg", "given": "Anna", "initials": "A"}, {"family": "Talley", "given": "Nicholas J", "initials": "NJ"}, {"family": "Agreus", "given": "Lars", "initials": "L"}, {"family": "J\u00e4rbrink-Sehgal", "given": "Ellionore", "initials": "E"}, {"family": "Engstrand", "given": "Lars", "initials": "L"}, {"family": "Andreasson", "given": "Anna", "initials": "A", "orcid": "0000-0003-0203-7977", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ee0ba3e533b6411eb61bdfad641ef474.json"}}, {"family": "Schmidt", "given": "Peter T", "initials": "PT", "orcid": "0000-0001-8338-5468", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e891fe37f73f49c798aa7ccc39e35417.json"}}], "type": "journal article", "published": "2023-03-29", "journal": {"title": "Scand. J. Gastroenterol.", "issn": "1502-7708", "pages": "1131-1138", "volume": "58", "issue": "10", "issn-l": "0036-5521"}, "abstract": "The etiopathogenesis of diverticular disease is unknown.\n\nTo compare the fecal and mucosa-associated microbiota between participants with and without diverticulosis and participants who later developed diverticulitis versus those that did not from a population-based study.\n\nThe PopCol study, conducted in Stockholm, Sweden, invited a random sample of 3556 adults to participate, of which 745 underwent colonoscopy. Overall, 130 participants (17.5%) had diverticulosis. 16S rRNA gene sequencing was conducted on available sigmoid biopsy samples from 529 and fecal samples from 251 individuals. We identified individuals who subsequently developed acute diverticulitis up to 13 years after sample collection. In a case-control design matching for gender, age (+/-5 years), smoking and antibiotic exposure, we compared taxonomic composition, richness and diversity of the microbiota between participants with or without diverticulosis, and between participants who later developed acute diverticulitis versus those who did not.\n\nNo differences in microbiota richness or diversity were observed between participants with or without diverticulosis, nor for those who developed diverticulitis compared with those who did not. No bacterial taxa were significantly different between participants with diverticulosis compared with those without diverticulosis. Individuals who later developed acute diverticulitis (2.8%) had a higher abundance of genus Comamonas than those who did not (p = .027).\n\nIn a population-based cohort study the only significant difference was that those who later develop diverticulitis had more abundance of genus Comamonas. The significance of Comamonas is unclear, suggesting a limited role for the gut microbiota in the etiopathogenesis of diverticular disease.", "doi": "10.1080/00365521.2023.2194010", "pmid": "36987880", "labels": {"DDLS Fellow": "", "Luisa Hugerth": ""}, "xrefs": [], "notes": [], "created": "2023-05-12T13:19:58.189Z", "modified": "2026-09-23T11:15:48.298Z"}, {"entity": "publication", "iuid": "98d7e4300da14cf997ff302f19322b47", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/98d7e4300da14cf997ff302f19322b47.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/98d7e4300da14cf997ff302f19322b47"}}, "title": "Computational speed-up of large-scale, single-cell model simulations via a fully integrated SBML-based format.", "authors": [{"family": "Mutsuddy", "given": "Arnab", "initials": "A", "orcid": "0000-0001-6488-7067", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8e14f7a9dc804ab1bccf030cc31a121b.json"}}, {"family": "Erdem", "given": "Cemal", "initials": "C", "orcid": "0000-0003-3663-3646", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f71b5af589264614a52eefa8baba3132.json"}}, {"family": "Huggins", "given": "Jonah R", "initials": "JR"}, {"family": "Salim", "given": "Misha", "initials": "M"}, {"family": "Cook", "given": "Daniel", "initials": "D"}, {"family": "Hobbs", "given": "Nicole", "initials": "N"}, {"family": "Feltus", "given": "F Alex", "initials": "FA"}, {"family": "Birtwistle", "given": "Marc R", "initials": "MR", "orcid": "0000-0002-0341-0705", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/df52e09a2f984f10833bda7b554b1a22.json"}}], "type": "journal article", "published": "2023-03-23", "journal": {"title": "Bioinform Adv", "issn": "2635-0041", "volume": "3", "issue": "1", "pages": "vbad039", "issn-l": null}, "abstract": "Large-scale and whole-cell modeling has multiple challenges, including scalable model building and module communication bottlenecks (e.g. between metabolism, gene expression, signaling, etc.). We previously developed an open-source, scalable format for a large-scale mechanistic model of proliferation and death signaling dynamics, but communication bottlenecks between gene expression and protein biochemistry modules remained. Here, we developed two solutions to communication bottlenecks that speed-up simulation by \u223c4-fold for hybrid stochastic-deterministic simulations and by over 100-fold for fully deterministic simulations. Fully deterministic speed-up facilitates model initialization, parameter estimation and sensitivity analysis tasks.\n\nSource code is freely available at https://github.com/birtwistlelab/SPARCED/releases/tag/v1.3.0 implemented in python, and supported on Linux, Windows and MacOS (via Docker).", "doi": "10.1093/bioadv/vbad039", "pmid": "37020976", "labels": {"DDLS Fellow": null, "Cemal Erdem": null}, "xrefs": [{"db": "pmc", "key": "PMC10070034"}, {"db": "pii", "key": "vbad039"}], "notes": [], "created": "2023-10-27T08:53:34.543Z", "modified": "2023-10-27T08:53:34.667Z"}, {"entity": "publication", "iuid": "f778f58e35674bcab0ca941b6b8ec473", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f778f58e35674bcab0ca941b6b8ec473.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f778f58e35674bcab0ca941b6b8ec473"}}, "title": "Molecular simulations and NMR reveal how lipid fluctuations affect membrane mechanics.", "authors": [{"family": "Doktorova", "given": "Milka", "initials": "M", "orcid": "0000-0003-4366-2242", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/791384c319f04584bac8ffb21df7271f.json"}}, {"family": "Khelashvili", "given": "George", "initials": "G", "orcid": "0000-0001-7235-8579", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/49b73bce7f8541fd8c959b5117bbe668.json"}}, {"family": "Ashkar", "given": "Rana", "initials": "R", "orcid": "0000-0003-4075-2330", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b0cebcd6caec4fae986f23a3669ea406.json"}}, {"family": "Brown", "given": "Michael F", "initials": "MF", "orcid": "0000-0003-4154-0241", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b57572fcc90e4033b1c705a9c030e7eb.json"}}], "type": "journal article", "published": "2023-03-21", "journal": {"title": "Biophys. J.", "issn": "1542-0086", "issn-l": "0006-3495", "volume": "122", "issue": "6", "pages": "984-1002"}, "abstract": "Lipid bilayers form the main matrix of functional cell membranes, and their dynamics underlie a host of physical and biological processes. Here we show that elastic membrane properties and collective molecular dynamics (MD) are related by the mean-square amplitudes (order parameters) and relaxation rates (correlation times) of lipid acyl chain motions. We performed all-atom MD simulations of liquid-crystalline bilayers that allow direct comparison with carbon-hydrogen (CH) bond relaxations measured with NMR spectroscopy. Previous computational and theoretical approaches have assumed isotropic relaxation, which yields inaccurate description of lipid chain dynamics and incorrect data interpretation. Instead, the new framework includes a fixed bilayer normal (director axis) and restricted anisotropic motion of the CH bonds in accord with their segmental order parameters, enabling robust validation of lipid force fields. Simulated spectral densities of thermally excited CH bond fluctuations exhibited well-defined spin-lattice (Zeeman) relaxations analogous to those in NMR measurements. Their frequency signature could be fit to a simple power-law function, indicative of nematic-like collective dynamics. Moreover, calculated relaxation rates scaled as the squared order parameters yielding an apparent \u03baC modulus for bilayer bending. Our results show a strong correlation with \u03baC values obtained from solid-state NMR studies of bilayers without and with cholesterol as validated by neutron spin-echo measurements of membrane elasticity. The simulations uncover a critical role of interleaflet coupling in membrane mechanics and thus provide important insights into molecular sites of emerging elastic properties within lipid bilayers.", "doi": "10.1016/j.bpj.2022.12.007", "pmid": "36474442", "labels": {"Milka Doktorova": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC10111610"}, {"db": "pii", "key": "S0006-3495(22)03895-4"}], "notes": [], "created": "2024-11-27T12:19:24.456Z", "modified": "2024-11-29T10:49:02.527Z"}, {"entity": "publication", "iuid": "545401c7e945475d895003be2e4625fd", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/545401c7e945475d895003be2e4625fd.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/545401c7e945475d895003be2e4625fd"}}, "title": "MEMMAL: A tool for expanding large-scale mechanistic models with machine learned associations and big datasets", "authors": [{"family": "Erdem", "given": "Cemal", "initials": "C", "orcid": "0000-0003-3663-3646", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f71b5af589264614a52eefa8baba3132.json"}}, {"family": "Birtwistle", "given": "Marc R", "initials": "MR", "orcid": "0000-0002-0341-0705", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/df52e09a2f984f10833bda7b554b1a22.json"}}], "type": "journal-article", "published": "2023-03-09", "journal": {"title": "Front. Syst. Biol.", "issn": "2674-0702", "volume": "3", "issn-l": null}, "abstract": "Computational models that can explain and predict complex sub-cellular, cellular, and tissue-level drug response mechanisms could speed drug discovery and prioritize patient-specific treatments (i.e., precision medicine). Some models are mechanistic with detailed equations describing known (or supposed) physicochemical processes, while some are statistical or machine learning-based approaches, that explain datasets but have no mechanistic or causal guarantees. These two types of modeling are rarely combined, missing the opportunity to explore possibly causal but data-driven new knowledge while explaining what is already known. Here, we explore combining machine learned associations with mechanistic models to develop computational models that could more fully represent cellular behavior. In this proposed MEMMAL (MEchanistic Modeling with MAchine Learning) framework, machine learning/statistical models built using omics datasets provide predictions for new interactions between genes and proteins where there is physicochemical uncertainty. These interactions are used as a basis for new reactions in mechanistic models. As a test case, we focused on incorporating novel IFN\u03b3/PD-L1 related associations into a large-scale mechanistic model for cell proliferation and death to better recapitulate the recently released NIH LINCS Consortium MCF10A dataset and enable description of the cellular response to checkpoint inhibitor immunotherapies. This work is a template for combining big-data-inferred interactions with mechanistic models, which could be more broadly applicable for building multi-scale precision medicine and whole cell models.", "doi": "10.3389/fsysb.2023.1099413", "pmid": "38269333", "labels": {"DDLS Fellow": null, "Cemal Erdem": null}, "xrefs": [{"db": "mid", "key": "NIHMS1959801"}, {"db": "pmc", "key": "PMC10807051"}, {"db": "pii", "key": "1099413"}], "notes": [], "created": "2023-10-27T08:53:31.274Z", "modified": "2025-12-04T16:55:14.628Z"}, {"entity": "publication", "iuid": "2ae997665fba4d6786d40b6faf1df374", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/2ae997665fba4d6786d40b6faf1df374.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/2ae997665fba4d6786d40b6faf1df374"}}, "title": "Pre-pregnancy complications - associated factors and wellbeing in early pregnancy: a Swedish cohort study.", "authors": [{"family": "Gudnadottir", "given": "Unnur", "initials": "U"}, {"family": "Du", "given": "Juan", "initials": "J"}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW"}, {"family": "Engstrand", "given": "Lars", "initials": "L"}, {"family": "Schuppe-Koistinen", "given": "Ina", "initials": "I"}, {"family": "Wiberg Itzel", "given": "Eva", "initials": "E"}, {"family": "Fransson", "given": "Emma", "initials": "E"}, {"family": "Brusselaers", "given": "Nele", "initials": "N"}], "type": "journal article", "published": "2023-03-08", "journal": {"title": "BMC Pregnancy Childbirth", "issn": "1471-2393", "volume": "23", "issue": "1", "pages": "153", "issn-l": "1471-2393"}, "abstract": "Many couples experience difficulties to become pregnant or carry a pregnancy to term due to unknown causes. Here we define pre-pregnancy complications as having prior recurrent pregnancy loss, prior late miscarriages, time to pregnancy more than one year, or the use of artificial reproductive technologies. We aim to identify factors associated with pre-pregnancy complications and poor well-being in early pregnancy.\n\nOnline questionnaire data from 5330 unique pregnancies in Sweden were collected from November 2017 - February 2021. Multivariable logistic regression modelling was used to investigate potential risk factors for pre-pregnancy complications and differences in early pregnancy symptoms.\n\nPre-pregnancy complications were identified in 1142 participants (21%). Risk factors included diagnosed endometriosis, thyroid medication, opioids and other strong pain medication, body mass index > 25 kg/m2 and age over 35 years. Different subgroups of pre-pregnancy complications had unique risk factors. The groups also experienced different pregnancy symptoms in early pregnancy, where women that had experienced recurrent pregnancy loss were at higher risk of depression in their current pregnancy.\n\nWe report one of the largest pregnancy cohorts with high frequency of pre-pregnancy complications compared to the Swedish population. Prescribed drug use and body weight were the top potentially modifiable risk factors in all groups. Participants that experienced pre-pregnancy complications also had higher risk of depression and pregnancy problems in early pregnancy.", "doi": "10.1186/s12884-023-05479-8", "pmid": "36890460", "labels": {"DDLS Fellow": "", "Luisa Hugerth": ""}, "xrefs": [{"db": "pmc", "key": "PMC9993650"}, {"db": "pii", "key": "10.1186/s12884-023-05479-8"}], "notes": [], "created": "2023-05-12T13:20:00.388Z", "modified": "2026-09-23T12:54:32.183Z"}, {"entity": "publication", "iuid": "8495f35a8b6243688a5302fecccdf9b7", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8495f35a8b6243688a5302fecccdf9b7.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8495f35a8b6243688a5302fecccdf9b7"}}, "title": "Latent antibiotic resistance genes are abundant, diverse, and mobile in human, animal, and environmental microbiomes.", "authors": [{"family": "Inda-D\u00edaz", "given": "Juan Salvador", "initials": "JS"}, {"family": "Lund", "given": "David", "initials": "D"}, {"family": "Parras-Molt\u00f3", "given": "Marcos", "initials": "M"}, {"family": "Johnning", "given": "Anna", "initials": "A"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Kristiansson", "given": "Erik", "initials": "E"}], "type": "video-audio media", "published": "2023-03-08", "journal": {"title": "Microbiome", "issn": "2049-2618", "volume": "11", "issue": "1", "pages": "44", "issn-l": "2049-2618"}, "abstract": "Bacterial communities in humans, animals, and the external environment maintain a large collection of antibiotic resistance genes (ARGs). However, few of these ARGs are well-characterized and thus established in existing resistance gene databases. In contrast, the remaining latent ARGs are typically unknown and overlooked in most sequencing-based studies. Our view of the resistome and its diversity is therefore incomplete, which hampers our ability to assess risk for promotion and spread of yet undiscovered resistance determinants.\n\nA reference database consisting of both established and latent ARGs (ARGs not present in current resistance gene repositories) was created. By analyzing more than 10,000 metagenomic samples, we showed that latent ARGs were more abundant and diverse than established ARGs in all studied environments, including the human- and animal-associated microbiomes. The pan-resistomes, i.e., all ARGs present in an environment, were heavily dominated by latent ARGs. In comparison, the core-resistome, i.e., ARGs that were commonly encountered, comprised both latent and established ARGs. We identified several latent ARGs shared between environments and/or present in human pathogens. Context analysis of these genes showed that they were located on mobile genetic elements, including conjugative elements. We, furthermore, identified that wastewater microbiomes had a surprisingly large pan- and core-resistome, which makes it a potentially high-risk environment for the mobilization and promotion of latent ARGs.\n\nOur results show that latent ARGs are ubiquitously present in all environments and constitute a diverse reservoir from which new resistance determinants can be recruited to pathogens. Several latent ARGs already had high mobile potential and were present in human pathogens, suggesting that they may constitute emerging threats to human health. We conclude that the full resistome-including both latent and established ARGs-needs to be considered to properly assess the risks associated with antibiotic selection pressures. Video Abstract.", "doi": "10.1186/s40168-023-01479-0", "pmid": "36882798", "labels": {"DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC9993715"}, {"db": "pii", "key": "10.1186/s40168-023-01479-0"}], "notes": [], "created": "2024-11-18T11:42:49.594Z", "modified": "2026-09-23T07:28:47.974Z"}, {"entity": "publication", "iuid": "3c4309bca065470aacebfbf802e0ef8b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3c4309bca065470aacebfbf802e0ef8b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3c4309bca065470aacebfbf802e0ef8b"}}, "title": "Exome sequencing in a Swedish family with PMS2 mutation with varying penetrance of colorectal cancer: investigating the presence of genetic risk modifiers in colorectal cancer risk.", "authors": [{"family": "Bryant", "given": "Patrick", "initials": "P"}, {"family": "Walton Bernstedt", "given": "Sophie", "initials": "S"}, {"family": "Thutkawkorapin", "given": "Jessada", "initials": "J"}, {"family": "Backman", "given": "Ann-Sofie", "initials": "AS"}, {"family": "Lindblom", "given": "Annika", "initials": "A"}, {"family": "Lagerstedt-Robinson", "given": "Kristina", "initials": "K"}], "type": "journal article", "published": "2023-03-01", "journal": {"title": "Eur J Cancer Prev", "issn": "1473-5709", "volume": "32", "issue": "2", "pages": "113-118", "issn-l": null}, "abstract": "Lynch syndrome is caused by germline mutations in the mismatch repair (MMR) genes, such as the PMS2 gene, and is characterised by a familial accumulation of colorectal cancer. The penetrance of cancer in PMS2 carriers is still not fully elucidated as a colorectal cancer risk has been shown to vary between PMS2 carriers, suggesting the presence of risk modifiers.\n\nWhole exome sequencing was performed in a Swedish family carrying a PMS2 missense mutation [c.2113G>A, p.(Glu705Lys)]. Thirteen genetic sequence variants were further selected and analysed in a case-control study (724 cases and 711 controls).\n\nThe most interesting variant was an 18 bp deletion in gene BAG1. BAG1 has been linked to colorectal tumour progression with poor prognosis and is thought to promote colorectal tumour cell survival through increased NF-\u03baB activity.\n\nWe conclude the genetic architecture behind the incomplete penetrance of PMS2 is complicated and must be assessed in a genome wide manner using large families and multifactorial analysis.", "doi": "10.1097/CEJ.0000000000000769", "pmid": "36134613", "labels": {"Patrick Bryant": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pii", "key": "00008469-202303000-00003"}], "notes": [], "created": "2026-08-20T09:52:38.575Z", "modified": "2026-09-23T13:11:38.667Z"}, {"entity": "publication", "iuid": "367da52594d24257b0893c583572611c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/367da52594d24257b0893c583572611c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/367da52594d24257b0893c583572611c"}}, "title": "Clonal Hematopoiesis and Risk of Incident Lung Cancer.", "authors": [{"family": "Tian", "given": "Ruiyi", "initials": "R", "orcid": "0000-0001-5024-6832", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1a2cc8a38bbe41649a441405def87345.json"}}, {"family": "Wiley", "given": "Brian", "initials": "B"}, {"family": "Liu", "given": "Jie", "initials": "J", "orcid": "0000-0001-6365-1888", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ddad30666cdd405aa37bb60d42f29348.json"}}, {"family": "Zong", "given": "Xiaoyu", "initials": "X", "orcid": "0000-0001-5646-710X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f1250f735b6b4cd2a6873a9208e862a8.json"}}, {"family": "Truong", "given": "Buu", "initials": "B", "orcid": "0000-0003-0043-0812", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/24e9ec70c1f74fdfa182de3d7d9e21fa.json"}}, {"family": "Zhao", "given": "Stephanie", "initials": "S", "orcid": "0000-0001-6637-1486", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e8551483c0f5406b864d2353e8978add.json"}}, {"family": "Uddin", "given": "Md Mesbah", "initials": "MM", "orcid": "0000-0003-1846-0411", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/42f1ac7010c34ba997a3fd9e56c6a56a.json"}}, {"family": "Niroula", "given": "Abhishek", "initials": "A", "orcid": "0000-0002-5904-0635", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/05df7afc7a494ba5af8a378e5ffa53f0.json"}}, {"family": "Miller", "given": "Christopher A", "initials": "CA", "orcid": "0000-0003-4266-6700", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/80d153aa89554327b42354faae946064.json"}}, {"family": "Mukherjee", "given": "Semanti", "initials": "S", "orcid": "0000-0002-1843-9359", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7fe7a9badb944aa5998031b33a6d43cc.json"}}, {"family": "Heiden", "given": "Brendan T", "initials": "BT", "orcid": "0000-0002-0116-7377", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9fa032b03f8b4b9cab62d43a2d4fc7ac.json"}}, {"family": "Luo", "given": "Jingqin", "initials": "J", "orcid": "0000-0003-2759-3072", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/767ef98656bb42149d14aebb4618059e.json"}}, {"family": "Puri", "given": "Varun", "initials": "V"}, {"family": "Kozower", "given": "Benjamin D", "initials": "BD"}, {"family": "Walter", "given": "Matthew J", "initials": "MJ", "orcid": "0000-0002-7753-1091", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/055099b1d98c4b43bf1163a4553c1f34.json"}}, {"family": "Ding", "given": "Li", "initials": "L"}, {"family": "Link", "given": "Daniel C", "initials": "DC"}, {"family": "Amos", "given": "Christopher I", "initials": "CI", "orcid": "0000-0002-8540-7023", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dc5439b0cf4b4619a56d6d361fc12210.json"}}, {"family": "Ebert", "given": "Benjamin L", "initials": "BL", "orcid": "0000-0003-0197-5451", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56e4f1c53a4348e2b0ceb44a38850a17.json"}}, {"family": "Govindan", "given": "Ramaswamy", "initials": "R", "orcid": "0000-0002-6964-9612", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f0d884b2cbfb41af8df1101ba9d7f7d0.json"}}, {"family": "Natarajan", "given": "Pradeep", "initials": "P", "orcid": "0000-0001-8402-7435", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fe8bd48c61c047cd8e61c35d9e9ac650.json"}}, {"family": "Bolton", "given": "Kelly L", "initials": "KL", "orcid": "0000-0001-6584-3357", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/74eb7c71cebc4e8c888ff2b7426b4438.json"}}, {"family": "Cao", "given": "Yin", "initials": "Y", "orcid": "0000-0001-9835-7662", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a34eb276a5514342adb104aa5df642c9.json"}}], "type": "journal article", "published": "2023-03-01", "journal": {"title": "J Clin Oncol", "issn": "1527-7755", "volume": "41", "issue": "7", "pages": "1423-1433", "issn-l": "0732-183X"}, "abstract": "To prospectively examine the association between clonal hematopoiesis (CH) and subsequent risk of lung cancer.\n\nAmong 200,629 UK Biobank (UKBB) participants with whole-exome sequencing, CH was identified in a nested case-control study of 832 incident lung cancer cases and 3,951 controls (2006-2019) matched on age and year at blood draw, sex, race, and smoking status. A similar nested case-control study (141 cases/652 controls) was conducted among 27,975 participants with whole-exome sequencing in the Mass General Brigham Biobank (MGBB, 2010-2021). In parallel, we compared CH frequency in published data from 5,003 patients with solid tumor (2,279 lung cancer) who had pretreatment blood sequencing performed through Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets.\n\nIn UKBB, the presence of CH was associated with increased risk of lung cancer (cases: 12.5% v controls: 8.7%; multivariable-adjusted odds ratio [OR], 1.36; 95% CI, 1.06 to 1.74). The association remained robust after excluding participants with chronic obstructive pulmonary disease. No significant interactions with known risk factors, including polygenic risk score and C-reactive protein, were identified. In MGBB, we observed similar enrichment of CH in lung cancer (cases: 15.6% v controls: 12.7%). The meta-analyzed OR (95% CI) of UKBB and MGBB was 1.35 (1.08 to 1.68) for CH overall and 1.61 (1.19 to 2.18) for variant allele frequencies \u2265 10%. In Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets, CH with a variant allele frequency \u2265 10% was enriched in pretreatment lung cancer compared with other tumors after adjusting for age, sex, and smoking (OR for lung v breast cancer: 1.61; 95% CI, 1.03 to 2.53).\n\nIndependent of known risk factors, CH is associated with increased risk of lung cancer.", "doi": "10.1200/JCO.22.00857", "pmid": "36480766", "labels": {"Abhishek Niroula": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC9995101"}], "notes": [], "created": "2023-11-20T11:36:22.458Z", "modified": "2023-11-20T11:36:23.254Z"}, {"entity": "publication", "iuid": "172a8b31921f49d1b8de69c4d0a85213", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/172a8b31921f49d1b8de69c4d0a85213.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/172a8b31921f49d1b8de69c4d0a85213"}}, "title": "A Swedish Familial Genome-Wide Haplotype Analysis Identified Five Novel Breast Cancer Susceptibility Loci on 9p24.3, 11q22.3, 15q11.2, 16q24.1 and Xq21.31.", "authors": [{"family": "Barnekow", "given": "Elin", "initials": "E", "orcid": "0000-0002-4960-664X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4d1565675a50453db71ed36cf1a90eb1.json"}}, {"family": "Hasslow", "given": "Johan", "initials": "J"}, {"family": "Liu", "given": "Wen", "initials": "W"}, {"family": "Bryant", "given": "Patrick", "initials": "P"}, {"family": "Thutkawkorapin", "given": "Jessada", "initials": "J"}, {"family": "Wendt", "given": "Camilla", "initials": "C"}, {"family": "Czene", "given": "Kamila", "initials": "K"}, {"family": "Hall", "given": "Per", "initials": "P"}, {"family": "Margolin", "given": "Sara", "initials": "S"}, {"family": "Lindblom", "given": "Annika", "initials": "A"}], "type": "journal article", "published": "2023-02-24", "journal": {"title": "Int J Mol Sci", "issn": "1422-0067", "volume": "24", "issue": "5", "issn-l": null}, "abstract": "Most breast cancer heritability is unexplained. We hypothesized that analysis of unrelated familial cases in a GWAS context could enable the identification of novel susceptibility loci. In order to examine the association of a haplotype with breast cancer risk, we performed a genome-wide haplotype association study using a sliding window analysis of window sizes 1-25 SNPs in 650 familial invasive breast cancer cases and 5021 controls. We identified five novel risk loci on 9p24.3 (OR 3.4; p 4.9 \u00d7 10-11), 11q22.3 (OR 2.4; p 5.2 \u00d7 10-9), 15q11.2 (OR 3.6; p 2.3 \u00d7 10-8), 16q24.1 (OR 3; p 3 \u00d7 10-8) and Xq21.31 (OR 3.3; p 1.7 \u00d7 10-8) and confirmed three well-known loci on 10q25.13, 11q13.3, and 16q12.1. In total, 1593 significant risk haplotypes and 39 risk SNPs were distributed on the eight loci. In comparison with unselected breast cancer cases from a previous study, the OR was increased in the familial analysis in all eight loci. Analyzing familial cancer cases and controls enabled the identification of novel breast cancer susceptibility loci.", "doi": "10.3390/ijms24054468", "pmid": "36901898", "labels": {"Patrick Bryant": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC10003706"}, {"db": "pii", "key": "ijms24054468"}], "notes": [], "created": "2026-08-20T13:41:38.330Z", "modified": "2026-09-23T12:54:30.095Z"}, {"entity": "publication", "iuid": "4bc155f82d0c4e57ab67cbb059dcbc5c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4bc155f82d0c4e57ab67cbb059dcbc5c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4bc155f82d0c4e57ab67cbb059dcbc5c"}}, "title": "Targeted proteomics using stable isotope labeled protein fragments enables precise and robust determination of total apolipoprotein(a) in human plasma.", "authors": [{"family": "Hober", "given": "Andreas", "initials": "A", "orcid": "0000-0001-8947-2562", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/06cbc187628340278395a00ab9dd6c89.json"}}, {"family": "Rekanovic", "given": "Mirela", "initials": "M"}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Hansson", "given": "Sara", "initials": "S"}, {"family": "Kotol", "given": "David", "initials": "D"}, {"family": "Percy", "given": "Andrew J", "initials": "AJ"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Oscarsson", "given": "Jan", "initials": "J"}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Miliotis", "given": "Tasso", "initials": "T", "orcid": "0000-0003-4917-0724", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a0d5ba9b546949db95c9b8597bd1fe7e.json"}}], "type": "journal article", "published": "2023-02-15", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "18", "issue": "2", "pages": "e0281772", "issn-l": "1932-6203"}, "abstract": "Lipoprotein(a), also known as Lp(a), is an LDL-like particle composed of apolipoprotein(a) (apo(a)) bound covalently to apolipoprotein B100. Plasma concentrations of Lp(a) are highly heritable and vary widely between individuals. Elevated plasma concentration of Lp(a) is considered as an independent, causal risk factor of cardiovascular disease (CVD). Targeted mass spectrometry (LC-SRM/MS) combined with stable isotope-labeled recombinant proteins provides robust and precise quantification of proteins in the blood, making LC-SRM/MS assays appealing for monitoring plasma proteins for clinical implications. This study presents a novel quantitative approach, based on proteotypic peptides, to determine the absolute concentration of apo(a) from two microliters of plasma and qualified according to guideline requirements for targeted proteomics assays. After optimization, assay parameters such as linearity, lower limits of quantification (LLOQ), intra-assay variability (CV: 4.7%) and inter-assay repeatability (CV: 7.8%) were determined and the LC-SRM/MS results were benchmarked against a commercially available immunoassay. In summary, the measurements of an apo(a) single copy specific peptide and a kringle 4 specific peptide allow for the determination of molar concentration and relative size of apo(a) in individuals.", "doi": "10.1371/journal.pone.0281772", "pmid": "36791076", "labels": {"Fredrik Edfors": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC9931122"}, {"db": "pii", "key": "PONE-D-22-14035"}], "notes": [], "created": "2026-08-20T12:44:20.753Z", "modified": "2026-09-23T12:26:13.247Z"}, {"entity": "publication", "iuid": "063de44677c94a4ead25f18e471b3e7c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/063de44677c94a4ead25f18e471b3e7c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/063de44677c94a4ead25f18e471b3e7c"}}, "title": "Larval transcriptomes reflect the evolutionary history of plant-insect associations.", "authors": [{"family": "de la Paz Celorio-Mancera", "given": "Maria", "initials": "M", "orcid": "0000-0003-0296-0577", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/309ef007cfc249e69905c8b23b05bc03.json"}}, {"family": "Steward", "given": "Rachel A", "initials": "RA", "orcid": "0000-0001-8610-334X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f47144d62760484b87623f2c0b3f6a88.json"}}, {"family": "Pruisscher", "given": "Peter", "initials": "P"}, {"family": "Smialowska", "given": "Agata", "initials": "A"}, {"family": "Pires Braga", "given": "Mariana", "initials": "M", "orcid": "0000-0002-1253-2536", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4f9064ed501545dca268c351c993aa26.json"}}, {"family": "Janz", "given": "Niklas", "initials": "N"}, {"family": "Wheat", "given": "Christopher W", "initials": "CW", "orcid": "0000-0003-1863-2340", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/77b0fc9157fe4852b14f55a804f5f13c.json"}}, {"family": "Nylin", "given": "S\u00f6ren", "initials": "S"}], "type": "journal article", "published": "2023-02-04", "journal": {"title": "Evolution", "issn": "1558-5646", "volume": "77", "issue": "2", "pages": "519-533", "issn-l": "0014-3820"}, "abstract": "In this study, we investigated whether patterns of gene expression in larvae feeding on different plants can explain important aspects of the evolution of insect-plant associations, such as phylogenetic conservatism of host use and re-colonization of ancestral hosts that have been lost from the host repertoire. To this end, we performed a phylogenetically informed study comparing the transcriptomes of 4 nymphalid butterfly species in Polygonia and the closely related genus Nymphalis. Larvae were reared on Urtica dioica, Salix spp., and Ribes spp. Plant-specific gene expression was found to be similar across butterfly species, even in the case of host plants that are no longer used by two of the butterfly species. These results suggest that plant-specific transcriptomes can be robust over evolutionary time. We propose that adaptations to particular larval food plants can profitably be understood as an evolved set of modules of co-expressed genes, promoting conservatism in host use and facilitating re-colonization. Moreover, we speculate that the degree of overlap between plant-specific transcriptomes may correlate with the strength of trade-offs between plants as resources and hence to the probability of colonizing hosts and complete host shifts.", "doi": "10.1093/evolut/qpac049", "pmid": "36625474", "labels": {"Mariana Pires Braga": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pii", "key": "6881564"}], "notes": [], "created": "2026-09-23T12:52:38.070Z", "modified": "2026-09-23T12:52:38.166Z"}, {"entity": "publication", "iuid": "05fb67bb44f442af81957f2ad2f226a5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/05fb67bb44f442af81957f2ad2f226a5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/05fb67bb44f442af81957f2ad2f226a5"}}, "title": "Combined metabolic activators improve metabolic functions in the animal models of neurodegenerative diseases.", "authors": [{"family": "Turkez", "given": "Hasan", "initials": "H"}, {"family": "Altay", "given": "Ozlem", "initials": "O"}, {"family": "Yildirim", "given": "Serkan", "initials": "S"}, {"family": "Li", "given": "Xiangyu", "initials": "X"}, {"family": "Yang", "given": "Hong", "initials": "H"}, {"family": "Bayram", "given": "Cemil", "initials": "C"}, {"family": "Bolat", "given": "Ismail", "initials": "I"}, {"family": "Oner", "given": "Sena", "initials": "S"}, {"family": "Tozlu", "given": "Ozlem Ozdemir", "initials": "OO"}, {"family": "Arslan", "given": "Mehmet Enes", "initials": "ME"}, {"family": "Arif", "given": "Muhammad", "initials": "M"}, {"family": "Yulug", "given": "Burak", "initials": "B"}, {"family": "Hanoglu", "given": "Lutfu", "initials": "L"}, {"family": "Cankaya", "given": "Seyda", "initials": "S"}, {"family": "Lam", "given": "Simon", "initials": "S"}, {"family": "Velioglu", "given": "Halil Aziz", "initials": "HA"}, {"family": "Coskun", "given": "Ebru", "initials": "E"}, {"family": "Idil", "given": "Ezgi", "initials": "E"}, {"family": "Nogaylar", "given": "Rahim", "initials": "R"}, {"family": "Ozsimsek", "given": "Ahmet", "initials": "A"}, {"family": "Hacimuftuoglu", "given": "Ahmet", "initials": "A"}, {"family": "Shoaie", "given": "Saeed", "initials": "S"}, {"family": "Zhang", "given": "Cheng", "initials": "C"}, {"family": "Nielsen", "given": "Jens", "initials": "J"}, {"family": "Bor\u00e9n", "given": "Jan", "initials": "J"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}], "type": "journal article", "published": "2023-02-01", "journal": {"title": "Life Sci", "issn": "1879-0631", "volume": "314", "pages": "121325", "issn-l": null}, "abstract": "Neurodegenerative diseases (NDDs), including Alzheimer's disease (AD) and Parkinson's disease (PD), are associated with metabolic abnormalities. Integrative analysis of human clinical data and animal studies have contributed to a better understanding of the molecular and cellular pathways involved in the progression of NDDs. Previously, we have reported that the combined metabolic activators (CMA), which include the precursors of nicotinamide adenine dinucleotide and glutathione can be utilized to alleviate metabolic disorders by activating mitochondrial metabolism.\n\nWe first analysed the brain transcriptomics data from AD patients and controls using a brain-specific genome-scale metabolic model (GEM). Then, we investigated the effect of CMA administration in animal models of AD and PD. We evaluated pathological and immunohistochemical findings of brain and liver tissues. Moreover, PD rats were tested for locomotor activity and apomorphine-induced rotation.\n\nAnalysis of transcriptomics data with GEM revealed that mitochondrial dysfunction is involved in the underlying molecular pathways of AD. In animal models of AD and PD, we showed significant damage in the high-fat diet groups' brain and liver tissues compared to the chow diet. The histological analyses revealed that hyperemia, degeneration and necrosis in neurons were improved by CMA administration in both AD and PD animal models. These findings were supported by immunohistochemical evidence of decreased immunoreactivity in neurons. In parallel to the improvement in the brain, we also observed dramatic metabolic improvement in the liver tissue. CMA administration also showed a beneficial effect on behavioural functions in PD rats.\n\nOverall, we showed that CMA administration significantly improved behavioural scores in parallel with the neurohistological outcomes in the AD and PD animal models and is a promising treatment for improving the metabolic parameters and brain functions in NDDs.", "doi": "10.1016/j.lfs.2022.121325", "pmid": "36581096", "labels": {"Adil Mardinoglu": "", "SciLifeLab Fellow": "", "Saeed Shoaie": "", "DDLS Fellow": "", "Muhammad Arif": ""}, "xrefs": [{"db": "pii", "key": "S0024-3205(22)01025-6"}], "notes": [], "created": "2023-12-04T14:53:05.727Z", "modified": "2026-10-01T08:27:49.978Z"}, {"entity": "publication", "iuid": "7a190019b7f04814bc65ca0fb5f89942", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/7a190019b7f04814bc65ca0fb5f89942.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/7a190019b7f04814bc65ca0fb5f89942"}}, "title": "Towards a structurally resolved human protein interaction network.", "authors": [{"family": "Burke", "given": "David F", "initials": "DF", "orcid": "0000-0001-8830-3951", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0ae9a94abf5e47778d59e4f3c9d8e62e.json"}}, {"family": "Bryant", "given": "Patrick", "initials": "P", "orcid": "0000-0003-3439-1866", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a683bcf98234ff09b2398976583b66f.json"}}, {"family": "Barrio-Hernandez", "given": "Inigo", "initials": "I", "orcid": "0000-0002-5686-0451", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/59ccf621e75c48868e9c215b04dcf787.json"}}, {"family": "Memon", "given": "Danish", "initials": "D", "orcid": "0000-0002-1365-0710", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0f9e1ae20abe4f7f94af1f6856d026bc.json"}}, {"family": "Pozzati", "given": "Gabriele", "initials": "G", "orcid": "0000-0002-4303-9939", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/94129216debe4e22ab3f3b74c33f9ab9.json"}}, {"family": "Shenoy", "given": "Aditi", "initials": "A", "orcid": "0000-0001-7748-2501", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/35bef00b985a45d59602675316e3d706.json"}}, {"family": "Zhu", "given": "Wensi", "initials": "W"}, {"family": "Dunham", "given": "Alistair S", "initials": "AS", "orcid": "0000-0001-9076-3025", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/41348047cf374b149851ea1b9bca2014.json"}}, {"family": "Albanese", "given": "Pascal", "initials": "P"}, {"family": "Keller", "given": "Andrew", "initials": "A"}, {"family": "Scheltema", "given": "Richard A", "initials": "RA", "orcid": "0000-0002-1668-0253", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/de6c6b9b87574d7eb67d48a73ab5f230.json"}}, {"family": "Bruce", "given": "James E", "initials": "JE", "orcid": "0000-0001-6441-6089", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/66c3622f73ef4c62a4100d87ab6aeded.json"}}, {"family": "Leitner", "given": "Alexander", "initials": "A", "orcid": "0000-0003-4126-0725", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca32a3af642745ea9d26f0e7f1413b6a.json"}}, {"family": "Kundrotas", "given": "Petras", "initials": "P", "orcid": "0000-0001-5080-1664", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e645003f2000464c9e289ccd3b92ce68.json"}}, {"family": "Beltrao", "given": "Pedro", "initials": "P", "orcid": "0000-0002-2724-7703", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/952eba119d2e4d4b89e14b294c5c6885.json"}}, {"family": "Elofsson", "given": "Arne", "initials": "A", "orcid": "0000-0002-7115-9751", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/248e70e81bd64f31a5f83e6e329bba95.json"}}], "type": "journal article", "published": "2023-02-00", "journal": {"title": "Nat. Struct. Mol. Biol.", "issn": "1545-9985", "volume": "30", "issue": "2", "pages": "216-225", "issn-l": "1545-9985"}, "abstract": "Cellular functions are governed by molecular machines that assemble through protein-protein interactions. Their atomic details are critical to studying their molecular mechanisms. However, fewer than 5% of hundreds of thousands of human protein interactions have been structurally characterized. Here we test the potential and limitations of recent progress in deep-learning methods using AlphaFold2 to predict structures for 65,484 human protein interactions. We show that experiments can orthogonally confirm higher-confidence models. We identify 3,137 high-confidence models, of which 1,371 have no homology to a known structure. We identify interface residues harboring disease mutations, suggesting potential mechanisms for pathogenic variants. Groups of interface phosphorylation sites show patterns of co-regulation across conditions, suggestive of coordinated tuning of multiple protein interactions as signaling responses. Finally, we provide examples of how the predicted binary complexes can be used to build larger assemblies helping to expand our understanding of human cell biology.", "doi": "10.1038/s41594-022-00910-8", "pmid": "36690744", "labels": {"Patrick Bryant": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC9935395"}, {"db": "pii", "key": "10.1038/s41594-022-00910-8"}], "notes": [], "created": "2026-08-20T09:03:53.064Z", "modified": "2026-09-23T06:39:30.749Z"}, {"entity": "publication", "iuid": "ecf6cba2f3624f6ea03c9e737cfcf94a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ecf6cba2f3624f6ea03c9e737cfcf94a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ecf6cba2f3624f6ea03c9e737cfcf94a"}}, "title": "Combined metabolic activators improve cognitive functions in Alzheimer's disease patients: a randomised, double-blinded, placebo-controlled phase-II trial.", "authors": [{"family": "Yulug", "given": "Burak", "initials": "B"}, {"family": "Altay", "given": "Ozlem", "initials": "O"}, {"family": "Li", "given": "Xiangyu", "initials": "X"}, {"family": "Hanoglu", "given": "Lutfu", "initials": "L"}, {"family": "Cankaya", "given": "Seyda", "initials": "S"}, {"family": "Lam", "given": "Simon", "initials": "S"}, {"family": "Velioglu", "given": "Halil Aziz", "initials": "HA"}, {"family": "Yang", "given": "Hong", "initials": "H"}, {"family": "Coskun", "given": "Ebru", "initials": "E"}, {"family": "Idil", "given": "Ezgi", "initials": "E"}, {"family": "Nogaylar", "given": "Rahim", "initials": "R"}, {"family": "Ozsimsek", "given": "Ahmet", "initials": "A"}, {"family": "Bayram", "given": "Cemil", "initials": "C"}, {"family": "Bolat", "given": "Ismail", "initials": "I"}, {"family": "Oner", "given": "Sena", "initials": "S"}, {"family": "Tozlu", "given": "Ozlem Ozdemir", "initials": "OO"}, {"family": "Arslan", "given": "Mehmet Enes", "initials": "ME"}, {"family": "Hacimuftuoglu", "given": "Ahmet", "initials": "A"}, {"family": "Yildirim", "given": "Serkan", "initials": "S"}, {"family": "Arif", "given": "Muhammad", "initials": "M"}, {"family": "Shoaie", "given": "Saeed", "initials": "S"}, {"family": "Zhang", "given": "Cheng", "initials": "C"}, {"family": "Nielsen", "given": "Jens", "initials": "J"}, {"family": "Turkez", "given": "Hasan", "initials": "H"}, {"family": "Bor\u00e9n", "given": "Jan", "initials": "J"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}], "type": "clinical trial, phase ii", "published": "2023-01-26", "journal": {"title": "Transl Neurodegener", "issn": "2047-9158", "volume": "12", "issue": "1", "pages": "4", "issn-l": null}, "abstract": "Alzheimer's disease (AD) is associated with metabolic abnormalities linked to critical elements of neurodegeneration. We recently administered combined metabolic activators (CMA) to the AD rat model and observed that CMA improves the AD-associated histological parameters in the animals. CMA promotes mitochondrial fatty acid uptake from the cytosol, facilitates fatty acid oxidation in the mitochondria, and alleviates oxidative stress.\n\nHere, we designed a randomised, double-blinded, placebo-controlled phase-II clinical trial and studied the effect of CMA administration on the global metabolism of AD patients. One-dose CMA included 12.35 g L-serine (61.75%), 1 g nicotinamide riboside (5%), 2.55 g N-acetyl-L-cysteine (12.75%), and 3.73 g L-carnitine tartrate (18.65%). AD patients received one dose of CMA or placebo daily during the first 28 days and twice daily between day 28 and day 84. The primary endpoint was the difference in the cognitive function and daily living activity scores between the placebo and the treatment arms. The secondary aim of this study was to evaluate the safety and tolerability of CMA. A comprehensive plasma metabolome and proteome analysis was also performed to evaluate the efficacy of the CMA in AD patients.\n\nWe showed a significant decrease of AD Assessment Scale-cognitive subscale (ADAS-Cog) score on day 84 vs day 0 (P = 0.00001, 29% improvement) in the CMA group. Moreover, there was a significant decline (P = 0.0073) in ADAS-Cog scores (improvement of cognitive functions) in the CMA compared to the placebo group in patients with higher ADAS-Cog scores. Improved cognitive functions in AD patients were supported by the relevant alterations in the hippocampal volumes and cortical thickness based on imaging analysis. Moreover, the plasma levels of proteins and metabolites associated with NAD + and glutathione metabolism were significantly improved after CMA treatment.\n\nOur results indicate that treatment of AD patients with CMA can lead to enhanced cognitive functions and improved clinical parameters associated with phenomics, metabolomics, proteomics and imaging analysis. Trial registration ClinicalTrials.gov NCT04044131 Registered 17 July 2019, https://clinicaltrials.gov/ct2/show/NCT04044131.", "doi": "10.1186/s40035-023-00336-2", "pmid": "36703196", "labels": {"Adil Mardinoglu": "", "SciLifeLab Fellow": "", "Saeed Shoaie": "", "DDLS Fellow": "", "Muhammad Arif": ""}, "xrefs": [{"db": "pmc", "key": "PMC9879258"}, {"db": "pii", "key": "10.1186/s40035-023-00336-2"}, {"db": "ClinicalTrials.gov", "key": "NCT04044131"}], "notes": [], "created": "2023-12-04T14:53:02.918Z", "modified": "2026-09-23T08:30:31.134Z"}, {"entity": "publication", "iuid": "57eb18cb932542d0bb38c2a2767d25fd", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/57eb18cb932542d0bb38c2a2767d25fd.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/57eb18cb932542d0bb38c2a2767d25fd"}}, "title": "TP53-mediated clonal hematopoiesis confers increased risk for incident atherosclerotic disease.", "authors": [{"family": "Zekavat", "given": "Seyedeh M", "initials": "SM"}, {"family": "Viana-Huete", "given": "Vanesa", "initials": "V"}, {"family": "Matesanz", "given": "Nuria", "initials": "N"}, {"family": "Jorshery", "given": "Saman Doroodgar", "initials": "SD"}, {"family": "Zuriaga", "given": "Mar\u00eda A", "initials": "MA"}, {"family": "Uddin", "given": "Md Mesbah", "initials": "MM"}, {"family": "Trinder", "given": "Mark", "initials": "M"}, {"family": "Paruchuri", "given": "Kaavya", "initials": "K"}, {"family": "Zorita", "given": "Virginia", "initials": "V"}, {"family": "Ferrer-P\u00e9rez", "given": "Alba", "initials": "A"}, {"family": "Amor\u00f3s-P\u00e9rez", "given": "Marta", "initials": "M"}, {"family": "Kunderfranco", "given": "Paolo", "initials": "P"}, {"family": "Carriero", "given": "Roberta", "initials": "R"}, {"family": "Greco", "given": "Carolina M", "initials": "CM"}, {"family": "Aroca-Crevillen", "given": "Alejandra", "initials": "A"}, {"family": "Hidalgo", "given": "Andr\u00e9s", "initials": "A"}, {"family": "Damrauer", "given": "Scott M", "initials": "SM"}, {"family": "Ballantyne", "given": "Christie M", "initials": "CM"}, {"family": "Niroula", "given": "Abhishek", "initials": "A"}, {"family": "Gibson", "given": "Christopher J", "initials": "CJ"}, {"family": "Pirruccello", "given": "James", "initials": "J"}, {"family": "Griffin", "given": "Gabriel", "initials": "G"}, {"family": "Ebert", "given": "Benjamin L", "initials": "BL"}, {"family": "Libby", "given": "Peter", "initials": "P"}, {"family": "Fuster", "given": "Valent\u00edn", "initials": "V"}, {"family": "Zhao", "given": "Hongyu", "initials": "H"}, {"family": "Ghassemi", "given": "Marzyeh", "initials": "M"}, {"family": "Natarajan", "given": "Pradeep", "initials": "P"}, {"family": "Bick", "given": "Alexander G", "initials": "AG"}, {"family": "Fuster", "given": "Jos\u00e9 J", "initials": "JJ", "orcid": "0000-0002-5970-629X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6f051a754bdc49f0b7b6b23893d9600d.json"}}, {"family": "Klarin", "given": "Derek", "initials": "D", "orcid": "0000-0002-4636-5780", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0b81fbf037ec4b4b8ac0013544539f00.json"}}], "type": "journal article", "published": "2023-01-16", "journal": {"title": "Nat Cardiovasc Res", "issn": "2731-0590", "volume": "2", "pages": "144-158", "issn-l": null}, "abstract": "Somatic mutations in blood indicative of clonal hematopoiesis of indeterminate potential (CHIP) are associated with an increased risk of hematologic malignancy, coronary artery disease, and all-cause mortality. Here we analyze the relation between CHIP status and incident peripheral artery disease (PAD) and atherosclerosis, using whole-exome sequencing and clinical data from the UK Biobank and Mass General Brigham Biobank. CHIP associated with incident PAD and atherosclerotic disease across multiple beds, with increased risk among individuals with CHIP driven by mutation in DNA Damage Repair (DDR) genes such as TP53 and PPM1D. To model the effects of DDR-induced CHIP on atherosclerosis, we used a competitive bone marrow transplantation strategy, and generated atherosclerosis-prone Ldlr-/- chimeric mice carrying 20% p53-deficient hematopoietic cells. The chimeric mice were analyzed 13-weeks post-grafting and showed increased aortic plaque size and accumulation of macrophages within the plaque, driven by increased proliferation of p53-deficient plaque macrophages. In summary, our findings highlight the role of CHIP as a broad driver of atherosclerosis across the entire arterial system beyond the coronary arteries, and provide genetic and experimental support for a direct causal contribution of TP53-mutant CHIP to atherosclerosis.", "doi": "10.1038/s44161-022-00206-6", "pmid": "36949957", "labels": {"Abhishek Niroula": null, "DDLS Fellow": null}, "xrefs": [{"db": "mid", "key": "NIHMS1875484"}, {"db": "pmc", "key": "PMC10026701"}], "notes": [], "created": "2023-11-20T11:36:26.520Z", "modified": "2023-11-20T11:36:26.670Z"}, {"entity": "publication", "iuid": "dd280f98746a48d0b721e6644c08c0fc", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/dd280f98746a48d0b721e6644c08c0fc.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/dd280f98746a48d0b721e6644c08c0fc"}}, "title": "EvoBind: peptide binder design with inverse folding and protein structure prediction", "authors": [{"family": "Bryant", "given": "Patrick", "initials": "P", "orcid": "0000-0003-3439-1866", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a683bcf98234ff09b2398976583b66f.json"}}, {"family": "Elofsson", "given": "Arne", "initials": "A", "orcid": "0000-0002-7115-9751", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/248e70e81bd64f31a5f83e6e329bba95.json"}}], "type": "posted-content", "published": "2023-01-10", "journal": {"issn-l": null}, "abstract": null, "doi": "10.21203/rs.3.rs-2385835/v1", "pmid": null, "labels": {"Patrick Bryant": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T12:58:49.978Z", "modified": "2026-09-23T15:23:44.744Z"}, {"entity": "publication", "iuid": "469d934487b34bb48106dac1fcb698a2", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/469d934487b34bb48106dac1fcb698a2.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/469d934487b34bb48106dac1fcb698a2"}}, "title": "Genome-Wide Annotation of the Human Protein-Coding Genes Using Co-Expression Clustering", "authors": [{"family": "Bueno \u00c1lvez", "given": "Mar\u00eda", "initials": "M"}, {"family": "Karlsson", "given": "Max", "initials": "M"}, {"family": "Shi", "given": "Mengnan", "initials": "M"}, {"family": "Tj\u00f6rnhammar", "given": "Richard", "initials": "R"}, {"family": "M\u00e9ar", "given": "Loren", "initials": "L"}, {"family": "Digre", "given": "Andreas", "initials": "A"}, {"family": "Schutten", "given": "Rutger", "initials": "R"}, {"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E"}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Oksvold", "given": "Per", "initials": "P"}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K"}, {"family": "Zwahlen", "given": "Martin", "initials": "M"}, {"family": "Forsberg", "given": "Mattias", "initials": "M"}, {"family": "Johansson", "given": "Fredric", "initials": "F"}, {"family": "Butler", "given": "Lynn", "initials": "L"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Ponten", "given": "Fredrik", "initials": "F"}, {"family": "Zhang", "given": "Cheng", "initials": "C"}, {"family": "Sivertsson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Uhlen", "given": "Mathias", "initials": "M"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Lindskog", "given": "Cecilia", "initials": "C"}], "type": "posted-content", "published": "2023-00-00", "journal": {"issn-l": null}, "abstract": null, "doi": "10.2139/ssrn.4647291", "pmid": null, "labels": {"SciLifeLab Fellow": "", "Fredrik Edfors": "", "DDLS Fellow": "", "Adil Mardinoglu": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T13:01:41.304Z", "modified": "2026-09-23T15:30:37.522Z"}, {"entity": "publication", "iuid": "de619dacc5e54886a5910d8354b1a07b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/de619dacc5e54886a5910d8354b1a07b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/de619dacc5e54886a5910d8354b1a07b"}}, "title": "A Risk Management Framework for Emergence of Novel Antibiotic Resistance Determinants", "authors": [{"family": "He\u00df", "given": "Stefanie", "initials": "S"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}], "type": "posted-content", "published": "2023-00-00", "journal": {"issn-l": null}, "abstract": null, "doi": "10.2139/ssrn.4615467", "pmid": null, "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [], "notes": [], "created": "2024-11-18T11:45:35.573Z", "modified": "2024-11-18T11:45:35.573Z"}, {"entity": "publication", "iuid": "b8349fd78cda45e6993ca5beb0064a09", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b8349fd78cda45e6993ca5beb0064a09.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b8349fd78cda45e6993ca5beb0064a09"}}, "title": "ISG15-modification of the Arp2/3 complex restricts pathogen spread", "authors": [{"family": "Zhang", "given": "Yifeng", "initials": "Y", "orcid": "0000-0002-7348-0223", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4796ef3abda242d5a50071733314b37d.json"}}, {"family": "Ripley", "given": "Brittany", "initials": "B", "orcid": "0000-0001-5909-8864", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4e641be6308d458796de07040465df34.json"}}, {"family": "Ouyang", "given": "Wei", "initials": "W", "orcid": "0000-0002-0291-926X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56f601e1d1c6448aab0c3a1e3cffdbfc.json"}}, {"family": "Sturtz", "given": "Miranda", "initials": "M", "orcid": "0000-0002-1195-8973", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9fb74c08c51a438fa2d40c8abb1445d6.json"}}, {"family": "Upton", "given": "Ellen", "initials": "E", "orcid": "0000-0002-7028-2061", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9a36af7e77d1449887f15fb91e7af705.json"}}, {"family": "Luhmann", "given": "Emma", "initials": "E", "orcid": "0000-0002-4017-9805", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/94c2e31d000c477787061aaa967aa507.json"}}, {"family": "Vessely", "given": "Madeleine", "initials": "M"}, {"family": "Coloma", "given": "Rocio", "initials": "R", "orcid": "0000-0003-0365-1565", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/326a8e2c06334a58bd1220848f20b83c.json"}}, {"family": "Schwery", "given": "Nathan", "initials": "N"}, {"family": "Anthony", "given": "Scott M", "initials": "SM"}, {"family": "Goeken", "given": "Adam", "initials": "A"}, {"family": "Moninger", "given": "Thomas O", "initials": "TO"}, {"family": "Harty", "given": "John T", "initials": "JT"}, {"family": "Klingelhutz", "given": "Aloysius", "initials": "A", "orcid": "0000-0003-4258-5046", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2ac39e9239f74969b03683c6dd63b27a.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb07e6d0122c4528a927c1fe922e3bc8.json"}}, {"family": "Meyerholz", "given": "David K", "initials": "DK", "orcid": "0000-0003-1552-3253", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/47a10bdf687848119c7503cc1fd8828a.json"}}, {"family": "Manicassamy", "given": "Balaji", "initials": "B", "orcid": "0000-0003-1964-0967", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ab3143d19b6148ae98682010d34f1de1.json"}}, {"family": "Stipp", "given": "Christopher", "initials": "C"}, {"family": "Guerra", "given": "Susana", "initials": "S"}, {"family": "Radoshevich", "given": "Lilliana", "initials": "L", "orcid": "0000-0003-0294-9300", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/353744452b2a4eb2b767592dd3a99a97.json"}}], "type": "posted-content", "published": "2022-12-27", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2022.12.27.522022", "pmid": null, "labels": {"DDLS Fellow": "", "Wei Ouyang": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T10:43:10.027Z", "modified": "2026-09-23T15:23:23.333Z"}, {"entity": "publication", "iuid": "89aa86cc2a3641b590a172e3f40d7354", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/89aa86cc2a3641b590a172e3f40d7354.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/89aa86cc2a3641b590a172e3f40d7354"}}, "title": "Obesity-Associated Neurodegeneration Pattern Mimics Alzheimer's Disease in an Observational Cohort Study.", "authors": [{"family": "Morys", "given": "Filip", "initials": "F"}, {"family": "Potvin", "given": "Olivier", "initials": "O"}, {"family": "Zeighami", "given": "Yashar", "initials": "Y"}, {"family": "Vogel", "given": "Jacob", "initials": "J", "orcid": "0000-0001-6394-9940", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d2ad5af780c245da9b59a8c80a0b00ff.json"}}, {"family": "Lamontagne-Caron", "given": "R\u00e9mi", "initials": "R"}, {"family": "Duchesne", "given": "Simon", "initials": "S"}, {"family": "Dagher", "given": "Alain", "initials": "A", "orcid": "0000-0002-0945-5779", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/642c0c268b8a447784b84ad589d0ba7f.json"}}, {"family": "Alzheimer\u2019s Disease Neuroimaging Initiative", "given": "", "initials": ""}], "type": "observational study", "published": "2022-12-25", "journal": {"title": "J. Alzheimers Dis.", "issn": "1875-8908", "issn-l": "1387-2877", "volume": "91", "issue": "3", "pages": "1059-1071"}, "abstract": "Excess weight in adulthood leads to health complications such as diabetes, hypertension, or dyslipidemia. Recently, excess weight has also been related to brain atrophy and cognitive decline. Reports show that obesity is linked with Alzheimer's disease (AD)-related changes, such as cerebrovascular damage or amyloid-\u03b2 accumulation. However, to date no research has conducted a direct comparison between brain atrophy patterns in AD and obesity.\r\n\r\nHere, we compared patterns of brain atrophy and amyloid-\u03b2/tau protein accumulation in obesity and AD using a sample of over 1,300 individuals from four groups: AD patients, healthy controls, obese otherwise healthy individuals, and lean individuals.\r\n\r\nWe age- and sex-matched all groups to the AD-patients group and created cortical thickness maps of AD and obesity. This was done by comparing AD patients with healthy controls, and obese individuals with lean individuals. We then compared the AD and obesity maps using correlation analyses and permutation-based tests that account for spatial autocorrelation. Similarly, we compared obesity brain maps with amyloid-\u03b2 and tau protein maps from other studies.\r\n\r\nObesity maps were highly correlated with AD maps but were not correlated with amyloid-\u03b2/tau protein maps. This effect was not accounted for by the presence of obesity in the AD group.\r\n\r\nOur research confirms that obesity-related grey matter atrophy resembles that of AD. Excess weight management could lead to improved health outcomes, slow down cognitive decline in aging, and lower the risk for AD.", "doi": "10.3233/JAD-220535", "pmid": "36565111", "labels": {"Jacob W Vogel": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC9912737"}, {"db": "pii", "key": "JAD220535"}], "notes": [], "created": "2023-05-28T17:54:04.481Z", "modified": "2025-04-29T07:07:00.679Z"}, {"entity": "publication", "iuid": "9ae1f98b03044d66b1ad0fcd9f0b93ed", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9ae1f98b03044d66b1ad0fcd9f0b93ed.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9ae1f98b03044d66b1ad0fcd9f0b93ed"}}, "title": "Circulating Amino Acids and Risk of Peripheral Artery Disease in the PREDIMED Trial.", "authors": [{"family": "Razquin", "given": "Cristina", "initials": "C", "orcid": "0000-0003-3480-2645", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f0f5c529e0a647528ca99b42fe8a9e8b.json"}}, {"family": "Ruiz-Canela", "given": "Miguel", "initials": "M", "orcid": "0000-0002-7684-2787", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4f947f7399034daeb6778d0781b6e789.json"}}, {"family": "Toledo", "given": "Estefania", "initials": "E", "orcid": "0000-0002-6263-4434", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d04ea61c7230463ab64e537f97fb07fe.json"}}, {"family": "Clish", "given": "Clary B", "initials": "CB"}, {"family": "Guasch-Ferr\u00e9", "given": "Marta", "initials": "M", "orcid": "0000-0001-8525-1404", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2d1a49f5df124e96a9285b43d628cee9.json"}}, {"family": "Garc\u00eda-Gavil\u00e1n", "given": "Jes\u00fas F", "initials": "JF", "orcid": "0000-0002-3707-5255", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/89296f9aee3146208cddcb8485c9e116.json"}}, {"family": "Wittenbecher", "given": "Clemens", "initials": "C"}, {"family": "Alonso-G\u00f3mez", "given": "Angel", "initials": "A", "orcid": "0000-0003-2945-7509", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4fb0647407d44a0398631dadbf3340ca.json"}}, {"family": "Fit\u00f3", "given": "Montse", "initials": "M"}, {"family": "Liang", "given": "Liming", "initials": "L"}, {"family": "Corella", "given": "Dolores", "initials": "D", "orcid": "0000-0002-2366-4104", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5b2b00c374df498794b8623cfbd6cc30.json"}}, {"family": "G\u00f3mez-Gracia", "given": "Enrique", "initials": "E"}, {"family": "Estruch", "given": "Ramon", "initials": "R", "orcid": "0000-0003-1260-4445", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/122cb01329f24931ae77ae5ac5a05059.json"}}, {"family": "Fiol", "given": "Miquel", "initials": "M"}, {"family": "Santos-Lozano", "given": "Jose M", "initials": "JM"}, {"family": "Serra-Majem", "given": "Luis", "initials": "L", "orcid": "0000-0002-9658-9061", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/17c5739ca7c34721a8fe2696b8350eea.json"}}, {"family": "Ros", "given": "Emilio", "initials": "E"}, {"family": "Aros", "given": "Fernando", "initials": "F", "orcid": "0000-0001-8337-7185", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bafd2db45467474c9f6896ada491e747.json"}}, {"family": "Salas-Salvad\u00f3", "given": "Jordi", "initials": "J", "orcid": "0000-0003-2700-7459", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/49e886d4d7e346e1a65f949699f620a4.json"}}, {"family": "Hu", "given": "Frank B", "initials": "FB"}, {"family": "Mart\u00ednez-Gonz\u00e1lez", "given": "Miguel A", "initials": "MA", "orcid": "0000-0002-3917-9808", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7852fa98fe3a4da285d79f04e09cbd34.json"}}], "type": "randomized controlled trial", "published": "2022-12-23", "journal": {"title": "Int J Mol Sci", "issn": "1422-0067", "volume": "24", "issue": "1", "issn-l": null}, "abstract": "Effective prevention and risk prediction are important for peripheral artery disease (PAD) due to its poor prognosis and the huge disease burden it produces. Circulating amino acids (AA) and their metabolites may serve as biomarkers of PAD risk, but they have been scarcely investigated. The objective was to prospectively analyze the associations of baseline levels of plasma AA (and their pathways) with subsequent risk of PAD and the potential effect modification by a nutritional intervention with the Mediterranean diet (MedDiet). A matched case-control study was nested in the PREDIMED trial, in which participants were randomized to three arms: MedDiet with tree nut supplementation group, MedDiet with extra-virgin olive oil (EVOO) supplementation group or control group (low-fat diet). One hundred and sixty-seven PAD cases were matched with 250 controls. Plasma AA was measured with liquid chromatography/mass spectrometry at the Broad Institute. Baseline tryptophan, serine and threonine were inversely associated with PAD (ORfor 1 SD increase = 0.78 (0.61-0.99); 0.67 (0.51-0.86) and 0.75 (0.59-0.95), respectively) in a multivariable-adjusted conditional logistic regression model. The kynurenine/tryptophan ratio was directly associated with PAD (ORfor 1 SD increase = 1.50 (1.14-1.98)). The nutritional intervention with the MedDiet+nuts modified the association between threonine and PAD (p-value interaction = 0.018) compared with the control group. However, subjects allocated to the MedDiet+EVOO group were protected against PAD independently of baseline threonine. Plasma tryptophan, kynurenine/tryptophan ratio, serine and threonine might serve as early biomarkers of future PAD in subjects at a high risk of cardiovascular disease. The MedDiet supplemented with EVOO exerted a protective effect, regardless of baseline levels of threonine.", "doi": "10.3390/ijms24010270", "pmid": "36613713", "labels": {"Clemens Wittenbecher": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC9820556"}, {"db": "pii", "key": "ijms24010270"}], "notes": [], "created": "2025-03-19T08:20:53.455Z", "modified": "2026-09-23T11:01:45.733Z"}, {"entity": "publication", "iuid": "05f038f754da4f4781f21a4937cf7db3", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/05f038f754da4f4781f21a4937cf7db3.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/05f038f754da4f4781f21a4937cf7db3"}}, "title": "Ghost admixture in eastern gorillas", "authors": [{"family": "Pawar", "given": "Harvinder", "initials": "H", "orcid": "0000-0002-3852-4999", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1eab80604aac428f880af679461e32ac.json"}}, {"family": "Rymbekova", "given": "Aigerim", "initials": "A"}, {"family": "Cuadros", "given": "Sebastian", "initials": "S", "orcid": "0000-0002-6240-281X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a56b2cee5df84075abf3a87573937347.json"}}, {"family": "Huang", "given": "Xin", "initials": "X", "orcid": "0000-0002-9918-9602", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/27a6d482c13b437a8ba45a652135aef7.json"}}, {"family": "de Manuel", "given": "Marc", "initials": "M", "orcid": "0000-0002-1245-0127", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/32a9a768dceb47d682d91f91799b35fa.json"}}, {"family": "van der Valk", "given": "Tom", "initials": "T", "orcid": "0000-0001-6582-3452", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/aa0dba3cc12143cba213f7f3a052216c.json"}}, {"family": "Lobon", "given": "Irene", "initials": "I"}, {"family": "Alvarez-Estape", "given": "Marina", "initials": "M", "orcid": "0000-0001-8242-1092", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/92207dc6de3d4bfaa8614bcdb3738cfb.json"}}, {"family": "Haber", "given": "Marc", "initials": "M", "orcid": "0000-0003-1000-1448", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f33d7d7019084d4c9973df74a53b58da.json"}}, {"family": "Dolgova", "given": "Olga", "initials": "O", "orcid": "0000-0001-5231-9388", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/51a65f7fb8544946b506f69b37b414b0.json"}}, {"family": "Han", "given": "Sojung", "initials": "S", "orcid": "0000-0002-6113-1042", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ec6576ca2d1a480e8e5aec022199bcb5.json"}}, {"family": "Esteller-Cucala", "given": "Paula", "initials": "P", "orcid": "0000-0003-3048-4280", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/610f0a88c36a4acd80c59acbca72cc8a.json"}}, {"family": "Juan", "given": "David", "initials": "D", "orcid": "0000-0003-1912-9667", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/027154f54530486eac69b942138bc07f.json"}}, {"family": "Ayub", "given": "Qasim", "initials": "Q"}, {"family": "Bautista", "given": "Ruben", "initials": "R"}, {"family": "Kelley", "given": "Joanna L", "initials": "JL"}, {"family": "Cornejo", "given": "Omar E", "initials": "OE"}, {"family": "Lao", "given": "Oscar", "initials": "O", "orcid": "0000-0002-8525-9649", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f3a9334fa5dd44198f1cde45246d8480.json"}}, {"family": "Andr\u00e9s", "given": "Aida M", "initials": "AM", "orcid": "0000-0002-8590-9672", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/58f57f8eb741498a95bcb05b3c9c7dd6.json"}}, {"family": "Guschanski", "given": "Katerina", "initials": "K", "orcid": "0000-0002-8493-5457", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4e062373c6bc46b98e56215d3ec89eeb.json"}}, {"family": "Ssebide", "given": "Benard", "initials": "B"}, {"family": "Cranfield", "given": "Mike", "initials": "M"}, {"family": "Tyler-Smith", "given": "Chris", "initials": "C", "orcid": "0000-0002-6492-5403", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d9c0139811de45f9bf0f31b69b31e846.json"}}, {"family": "Xue", "given": "Yali", "initials": "Y", "orcid": "0000-0002-4501-6909", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/367981d027d44ff9ba2c8ad927ca15e4.json"}}, {"family": "Prado-Martinez", "given": "Javier", "initials": "J", "orcid": "0000-0001-5402-2721", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/43966b07053e4841948de2d54d41b2f3.json"}}, {"family": "Marques-Bonet", "given": "Tomas", "initials": "T", "orcid": "0000-0002-5597-3075", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1091cb5bfe394d459969d24bb1c22c66.json"}}, {"family": "Kuhlwilm", "given": "Martin", "initials": "M", "orcid": "0000-0002-0115-1797", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c21afe591ec14eeab27425b903e4db99.json"}}], "type": "posted-content", "published": "2022-12-19", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2022.12.19.521012", "pmid": null, "labels": {"DDLS Fellow": "", "Tom van der Valk": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T10:43:03.727Z", "modified": "2026-09-23T15:23:41.228Z"}, {"entity": "publication", "iuid": "97cbd36549c9406d956368d8d636336e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/97cbd36549c9406d956368d8d636336e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/97cbd36549c9406d956368d8d636336e"}}, "title": "Linking Individual Differences in Personalized Functional Network Topography to Psychopathology in Youth.", "authors": [{"family": "Cui", "given": "Zaixu", "initials": "Z"}, {"family": "Pines", "given": "Adam R", "initials": "AR"}, {"family": "Larsen", "given": "Bart", "initials": "B", "orcid": "0000-0002-6169-2317", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5f1c48a4f8b34cf6935b967ddff43b90.json"}}, {"family": "Sydnor", "given": "Valerie J", "initials": "VJ"}, {"family": "Li", "given": "Hongming", "initials": "H", "orcid": "0000-0002-8628-9698", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fbc2d2abba854008b56d417e6083614c.json"}}, {"family": "Adebimpe", "given": "Azeez", "initials": "A"}, {"family": "Alexander-Bloch", "given": "Aaron F", "initials": "AF", "orcid": "0000-0001-6554-1893", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d96b7bb3399c4a0f8cd66be01f00b02c.json"}}, {"family": "Bassett", "given": "Dani S", "initials": "DS", "orcid": "0000-0002-6183-4493", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1df60e7e90a942ffb8e97713221f7f5e.json"}}, {"family": "Bertolero", "given": "Max", "initials": "M"}, {"family": "Calkins", "given": "Monica E", "initials": "ME"}, {"family": "Davatzikos", "given": "Christos", "initials": "C"}, {"family": "Fair", "given": "Damien A", "initials": "DA"}, {"family": "Gur", "given": "Ruben C", "initials": "RC"}, {"family": "Gur", "given": "Raquel E", "initials": "RE"}, {"family": "Moore", "given": "Tyler M", "initials": "TM"}, {"family": "Shanmugan", "given": "Sheila", "initials": "S"}, {"family": "Shinohara", "given": "Russell T", "initials": "RT"}, {"family": "Vogel", "given": "Jacob W", "initials": "JW", "orcid": "0000-0001-6394-9940", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d2ad5af780c245da9b59a8c80a0b00ff.json"}}, {"family": "Xia", "given": "Cedric H", "initials": "CH"}, {"family": "Fan", "given": "Yong", "initials": "Y"}, {"family": "Satterthwaite", "given": "Theodore D", "initials": "TD", "orcid": "0000-0001-7072-9399", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/461c3637946f4ed8956764658711fca7.json"}}], "type": "journal article", "published": "2022-12-15", "journal": {"title": "Biol. Psychiatry", "issn": "1873-2402", "issn-l": "0006-3223", "volume": "92", "issue": "12", "pages": "973-983"}, "abstract": "The spatial layout of large-scale functional brain networks differs between individuals and is particularly variable in the association cortex, implicated in a broad range of psychiatric disorders. However, it remains unknown whether this variation in functional topography is related to major dimensions of psychopathology in youth.\r\n\r\nThe authors studied 790 youths ages 8 to 23 years who had 27 minutes of high-quality functional magnetic resonance imaging data as part of the Philadelphia Neurodevelopmental Cohort. Four correlated dimensions were estimated using a confirmatory correlated traits factor analysis on 112 item-level clinical symptoms, and one overall psychopathology factor with 4 orthogonal dimensions were extracted using a confirmatory factor analysis. Spatially regularized nonnegative matrix factorization was used to identify 17 individual-specific functional networks for each participant. Partial least square regression with split-half cross-validation was conducted to evaluate to what extent the topography of personalized functional networks encodes major dimensions of psychopathology.\r\n\r\nPersonalized functional network topography significantly predicted unseen individuals' major dimensions of psychopathology, including fear, psychosis, externalizing, and anxious-misery. Reduced representation of association networks was among the most important features for the prediction of all 4 dimensions. Further analysis revealed that personalized functional network topography predicted overall psychopathology (r = 0.16, permutation testing p < .001), which drove prediction of the 4 correlated dimensions.\r\n\r\nThese results suggest that individual differences in functional network topography in association networks is related to overall psychopathology in youth. Such results underscore the importance of considering functional neuroanatomy for personalized diagnostics and therapeutics in psychiatry.", "doi": "10.1016/j.biopsych.2022.05.014", "pmid": "35927072", "labels": {"Jacob W Vogel": null, "DDLS Fellow": null}, "xrefs": [{"db": "mid", "key": "NIHMS1880507"}, {"db": "pmc", "key": "PMC10040299"}, {"db": "pii", "key": "S0006-3223(22)01251-3"}], "notes": [], "created": "2023-05-28T17:54:06.966Z", "modified": "2025-04-29T07:06:48.984Z"}, {"entity": "publication", "iuid": "f6fa8d20bb97447395117dfa447db2c5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f6fa8d20bb97447395117dfa447db2c5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f6fa8d20bb97447395117dfa447db2c5"}}, "title": "Intrinsic Molecular Subtypes of Metastatic Castration-Resistant Prostate Cancer.", "authors": [{"family": "Feng", "given": "Eric", "initials": "E", "orcid": "0000-0002-0906-0558", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fc1adaa53615451bbe7b019a16bcd5ff.json"}}, {"family": "Rydzewski", "given": "Nicholas R", "initials": "NR", "orcid": "0000-0002-9465-9441", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2274f0d17a124161ae74c957a1cfef07.json"}}, {"family": "Zhang", "given": "Meng", "initials": "M", "orcid": "0000-0003-1042-6294", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3d24c6c51c024ac0b27a5162c4c2fa91.json"}}, {"family": "Lundberg", "given": "Arian", "initials": "A", "orcid": "0000-0002-6630-2787", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/baa2c7c8963840bfb6a22d7c5cfe35f9.json"}}, {"family": "Bootsma", "given": "Matthew", "initials": "M", "orcid": "0000-0003-0879-5066", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e05e082928c444a6b7750cf5476f3953.json"}}, {"family": "Helzer", "given": "Kyle T", "initials": "KT", "orcid": "0000-0003-3853-5564", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7011e2b72c254794baf945f716d3372d.json"}}, {"family": "Lang", "given": "Joshua M", "initials": "JM", "orcid": "0000-0002-0943-8872", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d37a2599fa044894abc8642baa80e00b.json"}}, {"family": "Aggarwal", "given": "Rahul", "initials": "R", "orcid": "0000-0001-7003-7982", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dc6eb510bedd42bbb6f57e03e724efba.json"}}, {"family": "Small", "given": "Eric J", "initials": "EJ", "orcid": "0000-0003-3191-6268", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a5a6d3bacede42059d6bf0f2cbfe0fec.json"}}, {"family": "Quigley", "given": "David A", "initials": "DA", "orcid": "0000-0002-4726-1473", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a7672a24a905407c8b5f9d1e28deea02.json"}}, {"family": "Sj\u00f6str\u00f6m", "given": "Martin", "initials": "M", "orcid": "0000-0002-2629-9966", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b42d7aeedc844018bbe28980b73cb6c6.json"}}, {"family": "Zhao", "given": "Shuang G", "initials": "SG", "orcid": "0000-0002-9166-6507", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c7d9e7e456be4376adb63a3e5ab895a7.json"}}], "type": "journal article", "published": "2022-12-15", "journal": {"title": "Clin. Cancer Res.", "issn": "1557-3265", "volume": "28", "issue": "24", "pages": "5396-5404", "issn-l": "1078-0432"}, "abstract": "Although numerous biology-driven subtypes have been described previously in metastatic castration-resistant prostate cancer (mCRPC), unsupervised molecular subtyping based on gene expression has been less studied, especially using large cohorts. Thus, we sought to identify the intrinsic molecular subtypes of mCRPC and assess molecular and clinical correlates in the largest combined cohort of mCRPC samples with gene expression data available to date.\n\nWe combined and batch-effect corrected gene expression data from four mCRPC cohorts from the Fred Hutchinson Cancer Research Center (N = 157), a small-cell neuroendocrine (NE) prostate cancer (SCNC)-enriched cohort from Weill Cornell Medicine (N = 49), and cohorts from the Stand Up 2 Cancer/Prostate Cancer Foundation East Coast Dream Team (N = 266) and the West Coast Dream Team (N = 162).\n\nHierarchical clustering of RNA-sequencing data from these 634 mCRPC samples identified two distinct adenocarcinoma subtypes, one of which (adeno-immune) was characterized by higher gene expression of immune pathways, higher CIBERSORTx immune scores, diminished ASI benefit, and non-lymph node metastasis tropism compared with an adeno-classic subtype. We also identified two distinct subtypes with enrichment for an NE phenotype, including an NE-liver subgroup characterized by liver metastasis tropism, PTEN loss, and APC and SPOP mutations compared with an NE-classic subgroup.\n\nOur results emphasize the heterogeneity of mCRPC beyond currently accepted molecular phenotypes, and suggest that future studies should consider incorporating transcriptome-wide profiling to better understand how these differences impact treatment responses and outcomes.", "doi": "10.1158/1078-0432.CCR-22-2567", "pmid": "36260524", "labels": {"DDLS Fellow": null, "Arian Lundberg": null}, "xrefs": [{"db": "mid", "key": "NIHMS1845221"}, {"db": "pmc", "key": "PMC9890931"}, {"db": "pii", "key": "709863"}], "notes": [], "created": "2025-11-14T07:50:06.218Z", "modified": "2025-11-14T07:51:43.990Z"}, {"entity": "publication", "iuid": "34dd4118753048eab5325f80ccac79e7", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/34dd4118753048eab5325f80ccac79e7.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/34dd4118753048eab5325f80ccac79e7"}}, "title": "Estimating diagnostic uncertainty in artificial intelligence assisted pathology using conformal prediction.", "authors": [{"family": "Olsson", "given": "Henrik", "initials": "H", "orcid": "0000-0002-2270-2017", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/da0547e978264d9c88fc6a222dcbfd5f.json"}}, {"family": "Kartasalo", "given": "Kimmo", "initials": "K", "orcid": "0000-0002-9470-4783", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7c6fc97c06ed456c8bdd1f03db8a9b72.json"}}, {"family": "Mulliqi", "given": "Nita", "initials": "N"}, {"family": "Capuccini", "given": "Marco", "initials": "M"}, {"family": "Ruusuvuori", "given": "Pekka", "initials": "P", "orcid": "0000-0001-9086-9591", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb947cd395e84612a53569f4a39abd19.json"}}, {"family": "Samaratunga", "given": "Hemamali", "initials": "H"}, {"family": "Delahunt", "given": "Brett", "initials": "B", "orcid": "0000-0002-5398-0300", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/433a3f884f95451383cc746925d9a08c.json"}}, {"family": "Lindskog", "given": "Cecilia", "initials": "C", "orcid": "0000-0001-5611-1015", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/21610a810a87459c962d6da3f2ad38ad.json"}}, {"family": "Janssen", "given": "Emiel A M", "initials": "EAM"}, {"family": "Blilie", "given": "Anders", "initials": "A"}, {"family": "ISUP Prostate Imagebase Expert Panel", "given": "", "initials": ""}, {"family": "Egevad", "given": "Lars", "initials": "L", "orcid": "0000-0001-8531-222X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a7d46f1f5fc047dc8edb910eb4f0645c.json"}}, {"family": "Spjuth", "given": "Ola", "initials": "O", "orcid": "0000-0002-8083-2864", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2c192389f99d4801b91f3350e07dfb9e.json"}}, {"family": "Eklund", "given": "Martin", "initials": "M", "orcid": "0000-0001-5032-5266", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/06721510ebc8462386e0e6fc6c84315b.json"}}], "type": "journal article", "published": "2022-12-15", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "13", "issue": "1", "pages": "7761"}, "abstract": "Unreliable predictions can occur when an artificial intelligence (AI) system is presented with data it has not been exposed to during training. We demonstrate the use of conformal prediction to detect unreliable predictions, using histopathological diagnosis and grading of prostate biopsies as example. We digitized 7788 prostate biopsies from 1192 men in the STHLM3 diagnostic study, used for training, and 3059 biopsies from 676 men used for testing. With conformal prediction, 1 in 794 (0.1%) predictions is incorrect for cancer diagnosis (compared to 14 errors [2%] without conformal prediction) while 175 (22%) of the predictions are flagged as unreliable when the AI-system is presented with new data from the same lab and scanner that it was trained on. Conformal prediction could with small samples (N = 49 for external scanner, N = 10 for external lab and scanner, and N = 12 for external lab, scanner and pathology assessment) detect systematic differences in external data leading to worse predictive performance. The AI-system with conformal prediction commits 3 (2%) errors for cancer detection in cases of atypical prostate tissue compared to 44 (25%) without conformal prediction, while the system flags 143 (80%) unreliable predictions. We conclude that conformal prediction can increase patient safety of AI-systems.", "doi": "10.1038/s41467-022-34945-8", "pmid": "36522311", "labels": {"Kimmo Kartasalo": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC9755280"}, {"db": "pii", "key": "10.1038/s41467-022-34945-8"}], "notes": [], "created": "2024-11-05T16:10:20.350Z", "modified": "2024-11-29T09:28:59.239Z"}, {"entity": "publication", "iuid": "7cebd93ef4254e08ae9d0ca81d7271fd", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/7cebd93ef4254e08ae9d0ca81d7271fd.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/7cebd93ef4254e08ae9d0ca81d7271fd"}}, "title": "Orthogonal proteomics methods warrants development of Duchenne Muscular Dystrophy biomarkers", "authors": [{"family": "Johansson", "given": "Camilla", "initials": "C"}, {"family": "Hunt", "given": "Helian", "initials": "H"}, {"family": "Signorelli", "given": "Mirko", "initials": "M"}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Hober", "given": "Andreas", "initials": "A"}, {"family": "Svensson", "given": "Anne Sophie", "initials": "AS"}, {"family": "Tegel", "given": "Hanna", "initials": "H"}, {"family": "Forststr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Aartsma-Rus", "given": "Annemieke", "initials": "A"}, {"family": "Niks", "given": "Erik", "initials": "E"}, {"family": "Spitali", "given": "Pietro", "initials": "P"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Szigyarto", "given": "Cristina Al Khalili", "initials": "CAK"}], "type": "posted-content", "published": "2022-12-05", "journal": {"issn-l": null}, "abstract": null, "doi": "10.21203/rs.3.rs-2285032/v1", "pmid": null, "labels": {"Fredrik Edfors": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T12:58:40.540Z", "modified": "2026-09-23T15:22:47.264Z"}, {"entity": "publication", "iuid": "0077a5a770054c2ba093eaec1bfd19cb", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0077a5a770054c2ba093eaec1bfd19cb.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0077a5a770054c2ba093eaec1bfd19cb"}}, "title": "Madagascar's extraordinary biodiversity: Threats and opportunities.", "authors": [{"family": "Ralimanana", "given": "H\u00e9l\u00e8ne", "initials": "H", "orcid": "0000-0002-7963-5644", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e50b104bc8964dd1b7501697190b49dd.json"}}, {"family": "Perrigo", "given": "Allison L", "initials": "AL", "orcid": "0000-0002-6565-6305", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6b717e90aede450c822d31f23b2206a4.json"}}, {"family": "Smith", "given": "Rhian J", "initials": "RJ", "orcid": "0000-0003-2836-0246", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cac6b43a59fe45b8a6bdc806b04586b3.json"}}, {"family": "Borrell", "given": "James S", "initials": "JS", "orcid": "0000-0001-9902-7681", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e02f3ac4129044e6b1de4edb01ce9e21.json"}}, {"family": "Faurby", "given": "S\u00f8ren", "initials": "S", "orcid": "0000-0002-2974-2628", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e9be75db97d64624a90e272c14ac7f5b.json"}}, {"family": "Rajaonah", "given": "Mamy Tiana", "initials": "MT", "orcid": "0000-0002-3117-4180", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0a2925867af84b45a4544975880042bc.json"}}, {"family": "Randriamboavonjy", "given": "Tianjanahary", "initials": "T", "orcid": "0000-0001-5767-3992", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5c9bd2b565a24d75895b6def899e22a8.json"}}, {"family": "Vorontsova", "given": "Maria S", "initials": "MS", "orcid": "0000-0003-0899-1120", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/658bd52a89af4667bf9fc6bfa6f14b39.json"}}, {"family": "Cooke", "given": "Robert S C", "initials": "RSC", "orcid": "0000-0003-0601-8888", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2a2e0e2acd86409f9ab6ef39b71fd471.json"}}, {"family": "Phelps", "given": "Leanne N", "initials": "LN", "orcid": "0000-0002-7385-3907", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9bdc38406efd41a1868e6b73df5da116.json"}}, {"family": "Sayol", "given": "Ferran", "initials": "F", "orcid": "0000-0003-3540-7487", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/29fc435dab2048309355a53700cd56df.json"}}, {"family": "Andela", "given": "Niels", "initials": "N"}, {"family": "Andermann", "given": "Tobias", "initials": "T", "orcid": "0000-0002-0932-1623", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dfff478dfcfc43ddbd40bb1bafbcb0a7.json"}}, {"family": "Andriamanohera", "given": "Andotiana M", "initials": "AM", "orcid": "0000-0001-9853-0613", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/207aa3b4891c4a04bb8e1c1c0662b48c.json"}}, {"family": "Andriambololonera", "given": "Sylvie", "initials": "S"}, {"family": "Bachman", "given": "Steven P", "initials": "SP", "orcid": "0000-0003-1085-6075", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d148ff68ba004c58baeeb9bcfb7b79f9.json"}}, {"family": "Bacon", "given": "Christine D", "initials": "CD", "orcid": "0000-0003-2341-2705", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/659f1ab881cf4890b80ebbdf23188ebc.json"}}, {"family": "Baker", "given": "William J", "initials": "WJ", "orcid": "0000-0001-6727-1831", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cb94076c4bb446acaf1183208ba7e98f.json"}}, {"family": "Belluardo", "given": "Francesco", "initials": "F", "orcid": "0000-0002-3967-2686", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/84f309d8ecd84d16bf3cabf558703847.json"}}, {"family": "Birkinshaw", "given": "Chris", "initials": "C"}, {"family": "Cable", "given": "Stuart", "initials": "S", "orcid": "0000-0001-7119-9844", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2a0627a8c201402f98bbc56738c13802.json"}}, {"family": "Canales", "given": "Nataly A", "initials": "NA", "orcid": "0000-0003-3241-8607", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/593ec63fe13b423a9898d92bdfa6491b.json"}}, {"family": "Carrillo", "given": "Juan D", "initials": "JD", "orcid": "0000-0003-2475-3341", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2d06bdba7aad4eee9478823d8ac44e40.json"}}, {"family": "Clegg", "given": "Rosie", "initials": "R", "orcid": "0000-0002-7073-2093", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/115c7407afa94aa3ad8ef240b2fc9416.json"}}, {"family": "Clubbe", "given": "Colin", "initials": "C", "orcid": "0000-0002-0532-1722", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1557bff6241242979e5f51adb2dfc12e.json"}}, {"family": "Crottini", "given": "Angelica", "initials": "A", "orcid": "0000-0002-8505-3050", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/808578f9edf74cbcbba10ad1447bcdb0.json"}}, {"family": "Damasco", "given": "Gabriel", "initials": "G"}, {"family": "Dhanda", "given": "Sonia", "initials": "S", "orcid": "0000-0002-5440-9229", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e6db69f9afca424e9213c5237f838755.json"}}, {"family": "Edler", "given": "Daniel", "initials": "D", "orcid": "0000-0001-5420-0591", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/10c85cb53c3e4b6e9eb2d2d1764b8ef5.json"}}, {"family": "Farooq", "given": "Harith", "initials": "H", "orcid": "0000-0001-9031-2785", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2df4a4a86585457792924c2c58738407.json"}}, {"family": "de Lima Ferreira", "given": "Paola", "initials": "P", "orcid": "0000-0002-6957-4243", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bfe90aac74ee4ce6a42335499787c705.json"}}, {"family": "Fisher", "given": "Brian L", "initials": "BL", "orcid": "0000-0002-4653-3270", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b8bec3ecbfe9443489d4f0ac5a37496f.json"}}, {"family": "Forest", "given": 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{"family": "Rakotoarinivo", "given": "Mijoro", "initials": "M", "orcid": "0000-0001-6644-5107", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b6e237293ed8495383a6a64a04b8a9a0.json"}}, {"family": "Rakotoarisoa", "given": "Am\u00e9d\u00e9e A", "initials": "AA"}, {"family": "Rakotoarisoa", "given": "Solofo E", "initials": "SE"}, {"family": "Rakotomalala", "given": "Herizo N", "initials": "HN"}, {"family": "Rakotonasolo", "given": "Franck", "initials": "F"}, {"family": "Ralaiveloarisoa", "given": "Berthe A", "initials": "BA", "orcid": "0000-0002-4046-9028", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d8423142782e412a9f09aeaeec275a48.json"}}, {"family": "Ramirez-Herranz", "given": "Myriam", "initials": "M", "orcid": "0000-0002-4715-9372", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e5faee8184b4411bff2658ef005d89e.json"}}, {"family": "Randriamamonjy", "given": "Jean Emmanuel N", "initials": "JEN"}, {"family": "Randrianasolo", "given": "Vonona", "initials": "V"}, {"family": "Rasolohery", "given": "Andriambolantsoa", "initials": "A", "orcid": "0000-0002-9686-262X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e8f44376bd7b4a58812f60090f3806e0.json"}}, {"family": "Ratsifandrihamanana", "given": "Anitry N", "initials": "AN"}, {"family": "Ravololomanana", "given": "Noro", "initials": "N"}, {"family": "Razafiniary", "given": "Velosoa", "initials": "V"}, {"family": "Razanajatovo", "given": "Henintsoa", "initials": "H", "orcid": "0000-0001-8084-6791", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/147568f11ec9408ca6927409476fb651.json"}}, {"family": "Razanatsoa", "given": "Estelle", "initials": "E", "orcid": "0000-0002-7219-1411", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6af21892343b4c95bd50d9d1ea4d16ad.json"}}, {"family": "Rivers", "given": "Malin", "initials": "M", "orcid": "0000-0001-9690-1353", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/683c1aaedb8e4960ae5a1a07464f3104.json"}}, {"family": "Silvestro", "given": "Daniele", "initials": "D", "orcid": "0000-0003-0100-0961", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4870742190514c5b83450c567c11398a.json"}}, {"family": "Testo", "given": "Weston", "initials": "W", "orcid": "0000-0003-3194-5763", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0f9f8e35ceed47919e27083e781b4f35.json"}}, {"family": "Torres Jim\u00e9nez", "given": "Maria F", "initials": "MF", "orcid": "0000-0002-7177-4164", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2a153e26e4344406a910f4cea7b41a4d.json"}}, {"family": "Walker", "given": "Kim", "initials": "K", "orcid": "0000-0002-2617-4768", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/06c1381411864d049ce72790afc18553.json"}}, {"family": "Walker", "given": "Barnaby E", "initials": "BE", "orcid": "0000-0002-3884-671X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b509b9abc063438282593246a14cf6c7.json"}}, {"family": "Wilkin", "given": "Paul", "initials": "P", "orcid": "0000-0003-4982-7175", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e8c5ed8b406145669ee7f737bf2355c8.json"}}, {"family": "Williams", "given": "Jenny", "initials": "J", "orcid": "0000-0003-3392-0738", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/99de79e2ac2c482f931f0a258390a6e9.json"}}, {"family": "Ziegler", "given": "Thomas", "initials": "T", "orcid": "0000-0002-4797-609X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2c4bb2d31756432b96e412f439210080.json"}}, {"family": "Zizka", "given": "Alexander", "initials": "A", "orcid": "0000-0002-1680-9192", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c62a905324e94d869ccd715ebbc98828.json"}}, {"family": "Antonelli", "given": "Alexandre", "initials": "A", "orcid": "0000-0003-1842-9297", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1de98df1bb2140fc9666507cb2fb5614.json"}}], "type": "journal article", "published": "2022-12-02", "journal": {"title": "Science (New York, N.Y.)", "issn": "1095-9203", "volume": "378", "issue": "6623", "pages": "eadf1466", "issn-l": "0036-8075"}, "abstract": "Madagascar's unique biota is heavily affected by human activity and is under intense threat. Here, we review the current state of knowledge on the conservation status of Madagascar's terrestrial and freshwater biodiversity by presenting data and analyses on documented and predicted species-level conservation statuses, the most prevalent and relevant threats, ex situ collections and programs, and the coverage and comprehensiveness of protected areas. The existing terrestrial protected area network in Madagascar covers 10.4% of its land area and includes at least part of the range of the majority of described native species of vertebrates with known distributions (97.1% of freshwater fishes, amphibians, reptiles, birds, and mammals combined) and plants (67.7%). The overall figures are higher for threatened species (97.7% of threatened vertebrates and 79.6% of threatened plants occurring within at least one protected area). International Union for Conservation of Nature (IUCN) Red List assessments and Bayesian neural network analyses for plants identify overexploitation of biological resources and unsustainable agriculture as the most prominent threats to biodiversity. We highlight five opportunities for action at multiple levels to ensure that conservation and ecological restoration objectives, programs, and activities take account of complex underlying and interacting factors and produce tangible benefits for the biodiversity and people of Madagascar.", "doi": "10.1126/science.adf1466", "pmid": "36454830", "labels": {"DDLS Fellow": "", "Tobias Andermann": ""}, "xrefs": [], "notes": [], "created": "2022-12-02T17:57:31.515Z", "modified": "2026-09-23T07:25:27.253Z"}, {"entity": "publication", "iuid": "3f057beec9e34be39b0df10b7d84c6e4", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3f057beec9e34be39b0df10b7d84c6e4.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3f057beec9e34be39b0df10b7d84c6e4"}}, "title": "Madagascar's extraordinary biodiversity: Evolution, distribution, and use.", "authors": [{"family": "Antonelli", "given": "Alexandre", "initials": "A", "orcid": "0000-0003-1842-9297", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1de98df1bb2140fc9666507cb2fb5614.json"}}, {"family": "Smith", "given": "Rhian J", "initials": "RJ", "orcid": "0000-0003-2836-0246", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cac6b43a59fe45b8a6bdc806b04586b3.json"}}, {"family": "Perrigo", "given": "Allison L", "initials": "AL", "orcid": "0000-0002-6565-6305", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6b717e90aede450c822d31f23b2206a4.json"}}, {"family": "Crottini", "given": "Angelica", "initials": "A", "orcid": "0000-0002-8505-3050", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/808578f9edf74cbcbba10ad1447bcdb0.json"}}, {"family": "Hackel", "given": "Jan", "initials": "J", "orcid": "0000-0002-9657-5372", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b0474875c79f4955bfc9e5bda7736ba8.json"}}, {"family": "Testo", "given": "Weston", "initials": "W", "orcid": "0000-0003-3194-5763", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0f9f8e35ceed47919e27083e781b4f35.json"}}, {"family": "Farooq", "given": "Harith", "initials": "H", "orcid": "0000-0001-9031-2785", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2df4a4a86585457792924c2c58738407.json"}}, {"family": "Torres Jim\u00e9nez", "given": "Maria F", "initials": "MF", "orcid": "0000-0002-7177-4164", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2a153e26e4344406a910f4cea7b41a4d.json"}}, {"family": "Andela", "given": "Niels", "initials": "N", "orcid": "0000-0002-8241-6143", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6ca9bd004b9447bbb68a6e7211871c4c.json"}}, {"family": "Andermann", "given": "Tobias", "initials": "T", "orcid": "0000-0002-0932-1623", "researcher": {"href": 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"orcid": "0000-0002-8937-7626", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1cb7282d7ec9420e85d9ef50ffef16e4.json"}}, {"family": "Przelomska", "given": "Natalia A S", "initials": "NAS", "orcid": "0000-0001-9207-4565", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5bc74028cc88468a9363cdd4fb8c09c8.json"}}, {"family": "Rabarimanarivo", "given": "Marina", "initials": "M", "orcid": "0000-0001-5049-9151", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ad109269b03e4a8daa1ebdb4f6153520.json"}}, {"family": "Rabehevitra", "given": "David", "initials": "D", "orcid": "0000-0003-2763-5754", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ded88fddcc424ff7b0c0992c5f015a6f.json"}}, {"family": "Raharimampionona", "given": "Jeannie", "initials": "J"}, {"family": "Rajaonah", "given": "Mamy Tiana", "initials": "MT", "orcid": "0000-0002-3117-4180", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0a2925867af84b45a4544975880042bc.json"}}, {"family": "Rajaonary", "given": "Fano", "initials": "F"}, {"family": "Rajaovelona", "given": "Landy R", "initials": "LR"}, {"family": "Rakotoarinivo", "given": "Mijoro", "initials": "M", "orcid": "0000-0001-6644-5107", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b6e237293ed8495383a6a64a04b8a9a0.json"}}, {"family": "Rakotoarisoa", "given": "Am\u00e9d\u00e9e A", "initials": "AA"}, {"family": "Rakotoarisoa", "given": "Solofo E", "initials": "SE"}, {"family": "Rakotomalala", "given": "Herizo N", "initials": "HN"}, {"family": "Rakotonasolo", "given": "Franck", "initials": "F"}, {"family": "Ralaiveloarisoa", "given": "Berthe A", "initials": "BA", "orcid": "0000-0002-4046-9028", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d8423142782e412a9f09aeaeec275a48.json"}}, {"family": "Ramirez-Herranz", "given": "Myriam", "initials": "M", "orcid": "0000-0002-4715-9372", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e5faee8184b4411bff2658ef005d89e.json"}}, {"family": "Randriamamonjy", "given": "Jean Emmanuel N", "initials": "JEN"}, {"family": "Randriamboavonjy", "given": "Tianjanahary", "initials": "T", "orcid": "0000-0001-5767-3992", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5c9bd2b565a24d75895b6def899e22a8.json"}}, {"family": "Randrianasolo", "given": "Vonona", "initials": "V"}, {"family": "Rasolohery", "given": "Andriambolantsoa", "initials": "A", "orcid": "0000-0002-9686-262X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e8f44376bd7b4a58812f60090f3806e0.json"}}, {"family": "Ratsifandrihamanana", "given": "Anitry N", "initials": "AN"}, {"family": "Ravololomanana", "given": "Noro", "initials": "N"}, {"family": "Razafiniary", "given": "Velosoa", "initials": "V"}, {"family": "Razanajatovo", "given": "Henintsoa", "initials": "H", "orcid": "0000-0001-8084-6791", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/147568f11ec9408ca6927409476fb651.json"}}, {"family": "Razanatsoa", "given": "Estelle", "initials": "E", "orcid": "0000-0002-7219-1411", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6af21892343b4c95bd50d9d1ea4d16ad.json"}}, {"family": "Rivers", "given": "Malin", "initials": "M", "orcid": "0000-0001-9690-1353", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/683c1aaedb8e4960ae5a1a07464f3104.json"}}, {"family": "Sayol", "given": "Ferran", "initials": "F", "orcid": "0000-0003-3540-7487", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/29fc435dab2048309355a53700cd56df.json"}}, {"family": "Silvestro", "given": "Daniele", "initials": "D", "orcid": "0000-0003-0100-0961", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4870742190514c5b83450c567c11398a.json"}}, {"family": "Vorontsova", "given": "Maria S", "initials": "MS", "orcid": "0000-0003-0899-1120", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/658bd52a89af4667bf9fc6bfa6f14b39.json"}}, {"family": "Walker", "given": "Kim", "initials": "K", "orcid": "0000-0002-2617-4768", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/06c1381411864d049ce72790afc18553.json"}}, {"family": "Walker", "given": "Barnaby E", "initials": "BE", "orcid": "0000-0002-3884-671X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b509b9abc063438282593246a14cf6c7.json"}}, {"family": "Wilkin", "given": "Paul", "initials": "P", "orcid": "0000-0003-4982-7175", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e8c5ed8b406145669ee7f737bf2355c8.json"}}, {"family": "Williams", "given": "Jenny", "initials": "J", "orcid": "0000-0003-3392-0738", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/99de79e2ac2c482f931f0a258390a6e9.json"}}, {"family": "Ziegler", "given": "Thomas", "initials": "T", "orcid": "0000-0002-4797-609X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2c4bb2d31756432b96e412f439210080.json"}}, {"family": "Zizka", "given": "Alexander", "initials": "A", "orcid": "0000-0002-1680-9192", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c62a905324e94d869ccd715ebbc98828.json"}}, {"family": "Ralimanana", "given": "H\u00e9l\u00e8ne", "initials": "H", "orcid": "0000-0002-7963-5644", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e50b104bc8964dd1b7501697190b49dd.json"}}], "type": "journal article", "published": "2022-12-02", "journal": {"title": "Science (New York, N.Y.)", "issn": "1095-9203", "volume": "378", "issue": "6623", "pages": "eabf0869", "issn-l": "0036-8075"}, "abstract": "Madagascar's biota is hyperdiverse and includes exceptional levels of endemicity. We review the current state of knowledge on Madagascar's past and current terrestrial and freshwater biodiversity by compiling and presenting comprehensive data on species diversity, endemism, and rates of species description and human uses, in addition to presenting an updated and simplified map of vegetation types. We report a substantial increase of records and species new to science in recent years; however, the diversity and evolution of many groups remain practically unknown (e.g., fungi and most invertebrates). Digitization efforts are increasing the resolution of species richness patterns and we highlight the crucial role of field- and collections-based research for advancing biodiversity knowledge and identifying gaps in our understanding, particularly as species richness corresponds closely to collection effort. Phylogenetic diversity patterns mirror that of species richness and endemism in most of the analyzed groups. We highlight humid forests as centers of diversity and endemism because of their role as refugia and centers of recent and rapid radiations. However, the distinct endemism of other areas, such as the grassland-woodland mosaic of the Central Highlands and the spiny forest of the southwest, is also biologically important despite lower species richness. The documented uses of Malagasy biodiversity are manifold, with much potential for the uncovering of new useful traits for food, medicine, and climate mitigation. The data presented here showcase Madagascar as a unique \"living laboratory\" for our understanding of evolution and the complex interactions between people and nature. The gathering and analysis of biodiversity data must continue and accelerate if we are to fully understand and safeguard this unique subset of Earth's biodiversity.", "doi": "10.1126/science.abf0869", "pmid": "36454829", "labels": {"DDLS Fellow": "", "Tobias Andermann": ""}, "xrefs": [], "notes": [], "created": "2022-12-02T17:57:27.364Z", "modified": "2026-09-23T07:26:50.601Z"}, {"entity": "publication", "iuid": "4d857ba23c74469eb4dd384ceaff5fea", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4d857ba23c74469eb4dd384ceaff5fea.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4d857ba23c74469eb4dd384ceaff5fea"}}, "title": "Plasma Metabolite Profiles Associated with the Amount and Source of Meat and Fish Consumption and the Risk of Type 2 Diabetes.", "authors": [{"family": "Garc\u00eda-Gavil\u00e1n", "given": "Jes\u00fas", "initials": "J", "orcid": "0000-0002-3707-5255", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/89296f9aee3146208cddcb8485c9e116.json"}}, {"family": "Nishi", "given": "Stephanie K", "initials": "SK", "orcid": "0000-0002-7878-5368", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e432e1d202814120b92893eaad656845.json"}}, {"family": "Paz-Graniel", "given": "Indira", "initials": "I"}, {"family": "Guasch-Ferr\u00e9", "given": "Marta", "initials": "M", "orcid": "0000-0001-8525-1404", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2d1a49f5df124e96a9285b43d628cee9.json"}}, {"family": "Razquin", "given": "Cristina", "initials": "C"}, {"family": "Clish", "given": "Clary B", "initials": "CB"}, {"family": "Toledo", "given": "Estefan\u00eda", "initials": "E"}, {"family": "Ruiz-Canela", "given": "Miguel", "initials": "M", "orcid": "0000-0002-7684-2787", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4f947f7399034daeb6778d0781b6e789.json"}}, {"family": "Corella", "given": "Dolores", "initials": "D"}, {"family": "Deik", "given": "Amy", "initials": "A"}, {"family": "Drouin-Chartier", "given": "Jean-Philippe", "initials": "JP"}, {"family": "Wittenbecher", "given": "Clemens", "initials": "C"}, {"family": "Babio", "given": "Nancy", "initials": "N"}, {"family": "Estruch", "given": "Ramon", "initials": "R"}, {"family": "Ros", "given": "Emilio", "initials": "E"}, {"family": "Fit\u00f3", "given": "Montserrat", "initials": "M"}, {"family": "Ar\u00f3s", "given": "Fernando", "initials": "F"}, {"family": "Fiol", "given": "Miquel", "initials": "M"}, {"family": "Serra-Majem", "given": "Llu\u00eds", "initials": "L"}, {"family": "Liang", "given": "Liming", "initials": "L"}, {"family": "Mart\u00ednez-Gonz\u00e1lez", "given": "Miguel A", "initials": "MA"}, {"family": "Hu", "given": "Frank B", "initials": "FB"}, {"family": "Salas-Salvad\u00f3", "given": "Jordi", "initials": "J", "orcid": "0000-0003-2700-7459", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/49e886d4d7e346e1a65f949699f620a4.json"}}], "type": "journal article", "published": "2022-12-00", "journal": {"title": "Mol Nutr Food Res", "issn": "1613-4133", "volume": "66", "issue": "23", "pages": "e2200145", "issn-l": null}, "abstract": "Consumption of meat has been associated with a higher risk of type 2 diabetes (T2D), but if plasma metabolite profiles associated with these foods reflect this relationship is unknown. The objective is to identify a metabolite signature of consumption of total meat (TM), red meat (RM), processed red meat (PRM), and fish and examine if they are associated with T2D risk.\n\nThe discovery population includes 1833 participants from the PREDIMED trial. The internal validation sample includes 1522 participants with available 1-year follow-up metabolomic data. Associations between metabolites and TM, RM, PRM, and fish are evaluated with elastic net regression. Associations between the profiles and incident T2D are estimated using Cox regressions. The profiles included 72 metabolites for TM, 69 for RM, 74 for PRM, and 66 for fish. After adjusting for T2D risk factors, only profiles of TM (Hazard Ratio (HR): 1.25, 95% CI: 1.06-1.49), RM (HR: 1.27, 95% CI: 1.07-1.52), and PRM (HR: 1.27, 95% CI: 1.07-1.51) are associated with T2D.\n\nThe consumption of TM, its subtypes, and fish is associated with different metabolites, some of which have been previously associated with T2D. Scores based on the identified metabolites for TM, RM, and PRM show a significant association with T2D risk.", "doi": "10.1002/mnfr.202200145", "pmid": "36214069", "labels": {"Clemens Wittenbecher": null, "DDLS Fellow": null}, "xrefs": [{"db": "mid", "key": "NIHMS1842078"}, {"db": "pmc", "key": "PMC9722604"}], "notes": [], "created": "2025-03-19T08:20:54.895Z", "modified": "2025-03-19T08:21:05.880Z"}, {"entity": "publication", "iuid": "1ea481b2eda848ba8b5b32273d7f0922", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1ea481b2eda848ba8b5b32273d7f0922.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1ea481b2eda848ba8b5b32273d7f0922"}}, "title": "Salmonella enterica serovar Cerro displays a phylogenetic structure and genomic features consistent with virulence attenuation and adaptation to cattle.", "authors": [{"family": "Cohn", "given": "Alexa R", "initials": "AR"}, {"family": "Orsi", "given": "Renato H", "initials": "RH", "orcid": "0000-0003-4933-9817", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/faa4bd30679547898c7bd57690ba18bf.json"}}, {"family": "Carroll", "given": "Laura M", "initials": "LM", "orcid": "0000-0002-3677-0192", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02112eccb0664819af916a3c3dc79daa.json"}}, {"family": "Liao", "given": "Jingqiu", "initials": "J", "orcid": "0000-0002-2579-8157", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ac812840b9814e919ed1dca12a484c87.json"}}, {"family": "Wiedmann", "given": "Martin", "initials": "M", "orcid": "0000-0002-4168-5662", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ff5ceeea60684abeb83951c53f7b6e31.json"}}, {"family": "Cheng", "given": "Rachel A", "initials": "RA", "orcid": "0000-0002-5932-7011", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c4b1b7638c9c4ec7bad01d1ad6497b6a.json"}}], "type": "journal article", "published": "2022-11-30", "journal": {"title": "Front Microbiol", "issn": "1664-302X", "volume": "13", "pages": "1005215", "issn-l": "1664-302X"}, "abstract": "Salmonella enterica subsp. enterica (S.) serovar Cerro is rarely isolated from human clinical cases of salmonellosis but represents the most common serovar isolated from cattle without clinical signs of illness in the United States. In this study, using a large, diverse set of 316 isolates, we utilized genomic methods to further elucidate the evolutionary history of S. Cerro and to identify genomic features associated with its apparent virulence attenuation in humans. Phylogenetic analyses showed that within this polyphyletic serovar, 98.4% of isolates (311/316) represent a monophyletic clade within section Typhi and the remaining 1.6% of isolates (5/316) form a monophyletic clade within subspecies enterica Clade A1. Of the section Typhi S. Cerro isolates, 93.2% of isolates (290/311) clustered into a large clonal clade comprised of predominantly sequence type (ST) 367 cattle and environmental isolates, while the remaining 6.8% of isolates (21/311), primarily from human clinical sources, clustered outside of this clonal clade. A tip-dated phylogeny of S. Cerro ST367 identified two major clades (I and II), one of which overwhelmingly consisted of cattle isolates that share a most recent common ancestor that existed circa 1975. Gene presence/absence and rarefaction curve analyses suggested that the pangenome of section Typhi S. Cerro is open, potentially reflecting the gain/loss of prophage; human isolates contained the most open pangenome, while cattle isolates had the least open pangenome. Hypothetically disrupted coding sequences (HDCs) displayed clade-specific losses of intact speC and sopA virulence genes within the large clonal S. Cerro clade, while loss of intact vgrG, araH, and vapC occurred in all section Typhi S. Cerro isolates. Further phenotypic analysis suggested that the presence of a premature stop codon in speC does not abolish ornithine decarboxylase activity in S. Cerro, likely due to the activity of the second ornithine decarboxylase encoded by speF, which remained intact in all isolates. Overall, our study identifies specific genomic features associated with S. Cerro's infrequent isolation from humans and its apparent adaptation to cattle, which has broader implications for informing our understanding of the evolutionary events facilitating host adaptation in Salmonella.", "doi": "10.3389/fmicb.2022.1005215", "pmid": "36532462", "labels": {"DDLS Fellow": null, "Laura Carroll": null}, "xrefs": [{"db": "pmc", "key": "PMC9748477"}], "notes": [], "created": "2023-05-13T11:52:27.912Z", "modified": "2025-04-29T07:05:49.849Z"}, {"entity": "publication", "iuid": "7371edd9de8342c6980325e1b5be34d5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/7371edd9de8342c6980325e1b5be34d5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/7371edd9de8342c6980325e1b5be34d5"}}, "title": "A Novel Machine Learning Method for Mutational Analysis to Identifying Driver Genes in Breast Cancer", "authors": [{"family": "Taheri", "given": "Golnaz", "initials": "G", "orcid": "0000-0002-2741-0355", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/014c217121d346b2b371bbc1c2fede57.json"}}, {"family": "Habibi", "given": "Mahnaz", "initials": "M", "orcid": "0000-0002-8969-2706", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f04af4e059814b78bfb107c3a5782f70.json"}}], "type": "posted-content", "published": "2022-11-22", "journal": {"title": null, "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2022.11.20.517205", "pmid": null, "labels": {"Golnaz Taheri": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2025-03-21T09:08:34.048Z", "modified": "2026-09-23T14:26:52.547Z"}, {"entity": "publication", "iuid": "15cde7dd73754026b68cf4db2e796dc1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/15cde7dd73754026b68cf4db2e796dc1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/15cde7dd73754026b68cf4db2e796dc1"}}, "title": "Temporal Association of Total Serum Cholesterol and Pancreatic Cancer Incidence.", "authors": [{"family": "Wang", "given": "Qiao-Li", "initials": "QL", "orcid": "0000-0003-4152-7821", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/357edb3116b64ad5aa929dcb7d07a1be.json"}}, {"family": "Khil", "given": "Jaewon", "initials": "J"}, {"family": "Hong", "given": "SungEun", "initials": "S", "orcid": "0000-0003-3030-2061", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d0a1660c4cfa4a968b7c724304d639dd.json"}}, {"family": "Lee", "given": "Dong Hoon", "initials": "DH", "orcid": "0000-0003-1329-4637", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/43e0e71f4ccd4f5290a0909ba3a1b7ce.json"}}, {"family": "Ha", "given": "Kyoung Hwa", "initials": "KH", "orcid": "0000-0002-3408-7568", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6ecff50fa2e942f4bdd5300c9b2c91d4.json"}}, {"family": "Keum", "given": "NaNa", "initials": "N"}, {"family": "Kim", "given": "Hyeon Chang", "initials": "HC", "orcid": "0000-0001-7867-1240", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/501a0652887a4622a15436c1a9bd8896.json"}}, {"family": "Giovannucci", "given": "Edward L", "initials": "EL"}], "type": "journal article", "published": "2022-11-21", "journal": {"title": "Nutrients", "issn": "2072-6643", "volume": "14", "issue": "22", "issn-l": "2072-6643"}, "abstract": "Previous studies have suggested a \u201ccholesterol-lowering effect\u201d of preclinical pancreatic cancer, suggesting lower total cholesterol as a potential diagnostic marker. Leveraging repeated measurements of total cholesterol, this study aims to examine the temporal association of total cholesterol and pancreatic cancer incidence. We conducted a nested case-control study based on a Korean National Health Insurance Service\u2212Health Screening Cohort, including 215 pancreatic cancer cases and 645 controls matched on age and sex. Conditional logistic regression was applied to estimate the odds ratio (OR) and 95% confidence interval (CI) for the associations of pancreatic cancer incidence with total cholesterol levels across different time windows over 11 years before pancreatic cancer diagnosis (recent, mid, distant). We found that, compared to participants with total cholesterol < 200 mg/dL in the recent 3 years prior to diagnosis, those having total cholesterol \u2265 240 mg/dL showed a significantly lower pancreatic cancer incidence (OR = 0.50 (0.27\u22120.93)). No significant association was found in relation to total cholesterol measured in the mid and distant past. When changes in total cholesterol over the three time periods were analyzed, compared with those with total cholesterol levels consistently below 240 mg/dL over the entire period, the OR of pancreatic cancer was 0.45 (0.20\u22121.03) for participants with recent-onset hypercholesterolemia, 1.89 (0.95\u22123.75) for recent-resolved hypercholesterolemia, and 0.71 (0.30\u22121.66) for consistent hypercholesterolemia. In conclusion, while high total cholesterol in the recent past may indicate a lower pancreatic cancer incidence, a recent decrease in total cholesterol may suggest an elevated incidence of pancreatic cancer.", "doi": "10.3390/nu14224938", "pmid": "36432624", "labels": {"DDLS Fellow": null, "Qiaoli Wang": null}, "xrefs": [{"db": "pmc", "key": "PMC9696583"}, {"db": "pii", "key": "nu14224938"}], "notes": [], "created": "2025-11-27T18:53:41.095Z", "modified": "2025-11-27T18:53:41.256Z"}, {"entity": "publication", "iuid": "83596194452742659a225044f49b5c0d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/83596194452742659a225044f49b5c0d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/83596194452742659a225044f49b5c0d"}}, "title": "The global groundwater resistome: core antibiotic resistance genes, their dynamics and drivers", "authors": [{"family": "Kampouris", "given": "Ioannis D", "initials": "ID", "orcid": "0000-0003-2093-5930", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2a58d348ca1f496d8c3915e23c411a6c.json"}}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J", "orcid": "0000-0002-6528-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c666068e9d34939b0252a627007cec7.json"}}, {"family": "Babin", "given": "Doreen", "initials": "D", "orcid": "0000-0001-7144-8898", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/08f37fc331864001bf591275055c77a0.json"}}, {"family": "Gallego", "given": "Sara", "initials": "S", "orcid": "0000-0002-4521-5879", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ed3f2793013a43df9a4343a086bf9344.json"}}, {"family": "Li", "given": "Bing", "initials": "B"}, {"family": "Smalla", "given": "Kornelia", "initials": "K", "orcid": "0000-0001-6980-729X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8b633d4578e0468aa449a427329d4182.json"}}, {"family": "Berendonk", "given": "Thomas U", "initials": "TU", "orcid": "0000-0002-9301-1803", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c66286f83a8430f954fbc5c52db10c5.json"}}, {"family": "Kl\u00fcmper", "given": "Uli", "initials": "U", "orcid": "0000-0002-4169-6548", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7d8605cdbfc14403b607a3b5ace7249d.json"}}], "type": "posted-content", "published": "2022-11-15", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2022.11.14.516424", "pmid": null, "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [], "notes": [], "created": "2024-11-18T11:45:41.639Z", "modified": "2024-11-18T11:45:41.872Z"}, {"entity": "publication", "iuid": "df4795e44b4949ed85aa1a9c3a966746", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/df4795e44b4949ed85aa1a9c3a966746.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/df4795e44b4949ed85aa1a9c3a966746"}}, "title": "Genomic trajectories of a near-extinction event in the Chatham Island black robin.", "authors": [{"family": "von Seth", "given": "Johanna", "initials": "J"}, {"family": "van der Valk", "given": "Tom", "initials": "T", "orcid": "0000-0001-6582-3452", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/aa0dba3cc12143cba213f7f3a052216c.json"}}, {"family": "Lord", "given": "Edana", "initials": "E"}, {"family": "Sigeman", "given": "Hanna", "initials": "H"}, {"family": "Olsen", "given": "Remi-Andr\u00e9", "initials": "RA"}, {"family": "Knapp", "given": "Michael", "initials": "M"}, {"family": "Kardailsky", "given": "Olga", "initials": "O"}, {"family": "Robertson", "given": "Fiona", "initials": "F"}, {"family": "Hale", "given": "Marie", "initials": "M"}, {"family": "Houston", "given": "Dave", "initials": "D"}, {"family": "Kennedy", "given": "Euan", "initials": "E"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L"}, {"family": "Nor\u00e9n", "given": "Karin", "initials": "K"}, {"family": "Massaro", "given": "Melanie", "initials": "M"}, {"family": "Robertson", "given": "Bruce C", "initials": "BC"}, {"family": "Dussex", "given": "Nicolas", "initials": "N"}], "type": "journal article", "published": "2022-11-10", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "23", "issue": "1", "pages": "747", "issn-l": "1471-2164"}, "abstract": "Understanding the micro--evolutionary response of populations to demographic declines is a major goal in evolutionary and conservation biology. In small populations, genetic drift can lead to an accumulation of deleterious mutations, which will increase the risk of extinction. However, demographic recovery can still occur after extreme declines, suggesting that natural selection may purge deleterious mutations, even in extremely small populations. The Chatham Island black robin (Petroica traversi) is arguably the most inbred bird species in the world. It avoided imminent extinction in the early 1980s and after a remarkable recovery from a single pair, a second population was established and the two extant populations have evolved in complete isolation since then. Here, we analysed 52 modern and historical genomes to examine the genomic consequences of this extreme bottleneck and the subsequent translocation.\n\nWe found evidence for two-fold decline in heterozygosity and three- to four-fold increase in inbreeding in modern genomes. Moreover, there was partial support for temporal reduction in total load for detrimental variation. In contrast, compared to historical genomes, modern genomes showed a significantly higher realised load, reflecting the temporal increase in inbreeding. Furthermore, the translocation induced only small changes in the frequency of deleterious alleles, with the majority of detrimental variation being shared between the two populations.\n\nOur results highlight the dynamics of mutational load in a species that recovered from the brink of extinction, and show rather limited temporal changes in mutational load. We hypothesise that ancestral purging may have been facilitated by population fragmentation and isolation on several islands for thousands of generations and may have already reduced much of the highly deleterious load well before human arrival and introduction of pests to the archipelago. The majority of fixed deleterious variation was shared between the modern populations, but translocation of individuals with low mutational load could possibly mitigate further fixation of high-frequency deleterious variation.", "doi": "10.1186/s12864-022-08963-1", "pmid": "36357860", "labels": {"Tom van der Valk": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC9647977"}, {"db": "pii", "key": "10.1186/s12864-022-08963-1"}], "notes": [], "created": "2022-12-02T13:45:19.103Z", "modified": "2026-09-23T08:54:04.399Z"}, {"entity": "publication", "iuid": "e888cf20161f4732abcb28375b838cdf", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e888cf20161f4732abcb28375b838cdf.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e888cf20161f4732abcb28375b838cdf"}}, "title": "Uncovering molecular grammars of intrinsically disordered regions that organize nucleolar fibrillar centers", "authors": [{"family": "King", "given": "Matthew R", "initials": "MR", "orcid": "0000-0002-8533-3589", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bc6782b6eb7c416da33c49ce1196cb78.json"}}, {"family": "Lin", "given": "Andrew Z", "initials": "AZ"}, {"family": "Ruff", "given": "Kiersten M", "initials": "KM", "orcid": "0000-0003-3240-1856", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3a823d8dfee14668bae7cc380359a755.json"}}, {"family": "Farag", "given": "Mina", "initials": "M"}, {"family": "Ouyang", "given": "Wei", "initials": "W"}, {"family": "Vahey", "given": "Michael D", "initials": "MD", "orcid": "0000-0001-9453-4860", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3da41d34343b44c58810320084b9eb56.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb07e6d0122c4528a927c1fe922e3bc8.json"}}, {"family": "Pappu", "given": "Rohit V", "initials": "RV", "orcid": "0000-0003-2568-1378", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e573db4519524951a4d5975a45c7291d.json"}}], "type": "posted-content", "published": "2022-11-05", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2022.11.05.515292", "pmid": null, "labels": {"DDLS Fellow": "", "Wei Ouyang": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T10:42:04.128Z", "modified": "2026-09-23T13:50:44.641Z"}, {"entity": "publication", "iuid": "995c9d0360cd4a8697f31e6faee4eef6", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/995c9d0360cd4a8697f31e6faee4eef6.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/995c9d0360cd4a8697f31e6faee4eef6"}}, "title": "The 5-Hydroxymethylcytosine Landscape of Prostate Cancer.", "authors": [{"family": "Sj\u00f6str\u00f6m", "given": "Martin", "initials": "M", "orcid": "0000-0002-2629-9966", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b42d7aeedc844018bbe28980b73cb6c6.json"}}, {"family": "Zhao", "given": "Shuang G", "initials": "SG"}, {"family": "Levy", "given": "Samuel", "initials": "S", "orcid": "0000-0002-4444-5103", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d205805d1cfb4e71ace25822afb039cb.json"}}, {"family": "Zhang", "given": "Meng", "initials": "M", "orcid": "0000-0003-1042-6294", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3d24c6c51c024ac0b27a5162c4c2fa91.json"}}, {"family": "Ning", "given": "Yuhong", "initials": "Y"}, {"family": "Shrestha", "given": "Raunak", "initials": "R", "orcid": "0000-0002-1144-1413", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1ee8056667cd46ecbec79e2789ae8029.json"}}, {"family": "Lundberg", "given": "Arian", "initials": "A", "orcid": "0000-0002-6630-2787", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/baa2c7c8963840bfb6a22d7c5cfe35f9.json"}}, {"family": "Herberts", "given": "Cameron", "initials": "C", "orcid": "0000-0002-9929-8374", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/951e9991fa8a46708c499649d1b6da59.json"}}, {"family": "Foye", "given": "Adam", "initials": "A", "orcid": "0000-0002-9910-9836", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/74c8c402b4a243ab95b9d20ecc43d4b9.json"}}, {"family": "Aggarwal", "given": "Rahul", "initials": "R", "orcid": "0000-0001-7003-7982", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dc6eb510bedd42bbb6f57e03e724efba.json"}}, {"family": "Hua", "given": "Junjie T", "initials": "JT", "orcid": "0000-0002-1197-1174", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ac6c246ec5104f86a2eae545eb2a8155.json"}}, {"family": "Li", "given": "Haolong", "initials": "H"}, {"family": "Bergamaschi", "given": "Anna", "initials": "A", "orcid": "0000-0001-8709-1766", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0e4bf75e08ef47cda746d7ef8d563b78.json"}}, {"family": "Maurice-Dror", "given": "Corinne", "initials": "C", "orcid": "0000-0003-4455-4497", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e527b177e77f42188e783b702851d298.json"}}, {"family": "Maheshwari", "given": "Ashutosh", "initials": "A"}, {"family": "Chen", "given": "Sujun", "initials": "S"}, {"family": "Ng", "given": "Sarah W S", "initials": "SWS", "orcid": "0000-0002-7647-6940", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7d889d4ea89443ef9898994e886fab85.json"}}, {"family": "Ye", "given": "Wenbin", "initials": "W", "orcid": "0000-0002-9303-9363", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9b717fa60edd4b7aa6e7dc899bff0767.json"}}, {"family": "Petricca", "given": "Jessica", "initials": "J"}, {"family": "Fraser", "given": "Michael", "initials": "M"}, {"family": "Chesner", "given": "Lisa", "initials": "L"}, {"family": "Perry", "given": "Marc D", "initials": "MD", "orcid": "0000-0001-6476-2942", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/78f79ccc14c042b49c4b223887c717ed.json"}}, {"family": "Moreno-Rodriguez", "given": "Thaidy", "initials": "T", "orcid": "0000-0003-3588-3889", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/be9adfae1d354f85a76d66de8bc08cba.json"}}, {"family": "Chen", "given": "William S", "initials": "WS"}, {"family": "Alumkal", "given": "Joshi J", "initials": "JJ", "orcid": "0000-0003-1278-0166", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/92169d39d28f4819959b032eff1b1b80.json"}}, {"family": "Chou", "given": "Jonathan", "initials": "J", "orcid": "0000-0003-1258-0391", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c4a72f7d3b2d4f72a8ebfc23f36f3714.json"}}, {"family": "Morgans", "given": "Alicia K", "initials": "AK"}, {"family": "Beer", "given": "Tomasz M", "initials": "TM", "orcid": "0000-0001-5600-9993", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c828b8adf0944e72aaacab129733f181.json"}}, {"family": "Thomas", "given": "George V", "initials": "GV"}, {"family": "Gleave", "given": "Martin", "initials": "M"}, {"family": "Lloyd", "given": "Paul", "initials": "P", "orcid": "0000-0003-3508-5553", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/96da8d6dbf344cf9a2e36a864ad8ab57.json"}}, {"family": "Phillips", "given": "Tierney", "initials": "T"}, {"family": "McCarthy", "given": "Erin", "initials": "E", "orcid": "0000-0002-3845-4142", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/122a0753d84d47649be4060eb51e8a4d.json"}}, {"family": "Haffner", "given": "Michael C", "initials": "MC", "orcid": "0000-0003-0809-6425", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cce395fe9a8b4fcdaec08d5d1cb37dde.json"}}, {"family": "Zoubeidi", "given": "Amina", "initials": "A", "orcid": "0000-0002-0498-142X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a96ebc9e3f464db8b25305742981ed8d.json"}}, {"family": "Annala", "given": "Matti", "initials": "M"}, {"family": "Reiter", "given": "Robert E", "initials": "RE", "orcid": "0000-0002-7962-3985", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a81ac4aa295d40d6825364129548f95d.json"}}, {"family": "Rettig", "given": "Matthew B", "initials": "MB", "orcid": "0000-0002-7394-3056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/df1dd288962643beb53cce332f615144.json"}}, {"family": "Witte", "given": "Owen N", "initials": "ON", "orcid": "0000-0003-4461-4533", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/435dcbfb32af474a9027576c7dc49ec6.json"}}, {"family": "Fong", "given": "Lawrence", "initials": "L", "orcid": "0000-0002-6428-428X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0124854879b543d8b9653fd99cce332c.json"}}, {"family": "Bose", "given": "Rohit", "initials": "R", "orcid": "0000-0002-6785-0697", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/af6c55d3791a4419813918497eef18b3.json"}}, {"family": "Huang", "given": "Franklin W", "initials": "FW"}, {"family": "Luo", "given": "Jianhua", "initials": "J", "orcid": "0000-0002-0943-8872", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d37a2599fa044894abc8642baa80e00b.json"}}, {"family": "Bjartell", "given": "Anders", "initials": "A"}, {"family": "Lang", "given": "Joshua M", "initials": "JM", "orcid": "0000-0002-0943-8872", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d37a2599fa044894abc8642baa80e00b.json"}}, {"family": "Mahajan", "given": "Nupam P", "initials": "NP", "orcid": "0000-0002-4150-602X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d7e3a532024d413585c0b943b37de3e5.json"}}, {"family": "Lara", "given": "Primo N", "initials": "PN"}, {"family": "Evans", "given": "Christopher P", "initials": "CP", "orcid": "0000-0001-5626-8901", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a8a9ee6f18f94c9ea82f34401edc3467.json"}}, {"family": "Tran", "given": "Phuoc T", "initials": "PT", "orcid": "0000-0002-0147-0376", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fa2bdba7d34d48b89dd173cd0af631f1.json"}}, {"family": "Posadas", "given": "Edwin M", "initials": "EM", "orcid": "0000-0001-8649-1346", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/50ac1885a27d499b863843697d82d870.json"}}, {"family": "He", "given": "Chuan", "initials": "C"}, {"family": "Cui", "given": "Xiao-Long", "initials": "XL"}, {"family": "Huang", "given": "Jiaoti", "initials": "J"}, {"family": "Zwart", "given": "Wilbert", "initials": "W", "orcid": "0000-0002-9823-7289", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/014603af06df4629b83fb3e7aa17710a.json"}}, {"family": "Gilbert", "given": "Luke A", "initials": "LA"}, {"family": "Maher", "given": "Christopher A", "initials": "CA", "orcid": "0000-0002-9035-603X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6d6e57151d8f42b3af517e57cd09baa0.json"}}, {"family": "Boutros", "given": "Paul C", "initials": "PC", "orcid": "0000-0003-0553-7520", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8dbb2a0bed664b03b96b34bd73d65993.json"}}, {"family": "Chi", "given": "Kim N", "initials": "KN", "orcid": "0000-0002-3782-7226", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6ee7573962f6411688894c17260e1095.json"}}, {"family": "Ashworth", "given": "Alan", "initials": "A", "orcid": "0000-0003-1446-7878", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/217e8097b1a14deba9247b30c1b978a7.json"}}, {"family": "Small", "given": "Eric J", "initials": "EJ"}, {"family": "He", "given": "Housheng H", "initials": "HH", "orcid": "0000-0003-2898-3363", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/487cb044249647b2a1608be1a33dff98.json"}}, {"family": "Wyatt", "given": "Alexander W", "initials": "AW", "orcid": "0000-0003-2399-0329", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/41e8ef800a344c68be341f0691438260.json"}}, {"family": "Quigley", "given": "David A", "initials": "DA", "orcid": "0000-0002-4726-1473", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a7672a24a905407c8b5f9d1e28deea02.json"}}, {"family": "Feng", "given": "Felix Y", "initials": "FY", "orcid": "0000-0002-0963-7687", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c5af5c0e774941ac97890f17640a339e.json"}}], "type": "journal article", "published": "2022-11-02", "journal": {"title": "Cancer Res.", "issn": "1538-7445", "volume": "82", "issue": "21", "pages": "3888-3902", "issn-l": "0008-5472"}, "abstract": "Analysis of DNA methylation is a valuable tool to understand disease progression and is increasingly being used to create diagnostic and prognostic clinical biomarkers. While conversion of cytosine to 5-methylcytosine (5mC) commonly results in transcriptional repression, further conversion to 5-hydroxymethylcytosine (5hmC) is associated with transcriptional activation. Here we perform the first study integrating whole-genome 5hmC with DNA, 5mC, and transcriptome sequencing in clinical samples of benign, localized, and advanced prostate cancer. 5hmC is shown to mark activation of cancer drivers and downstream targets. Furthermore, 5hmC sequencing revealed profoundly altered cell states throughout the disease course, characterized by increased proliferation, oncogenic signaling, dedifferentiation, and lineage plasticity to neuroendocrine and gastrointestinal lineages. Finally, 5hmC sequencing of cell-free DNA from patients with metastatic disease proved useful as a prognostic biomarker able to identify an aggressive subtype of prostate cancer using the genes TOP2A and EZH2, previously only detectable by transcriptomic analysis of solid tumor biopsies. Overall, these findings reveal that 5hmC marks epigenomic activation in prostate cancer and identify hallmarks of prostate cancer progression with potential as biomarkers of aggressive disease.\n\nIn prostate cancer, 5-hydroxymethylcytosine delineates oncogene activation and stage-specific cell states and can be analyzed in liquid biopsies to detect cancer phenotypes. See related article by Wu and Attard, p. 3880.", "doi": "10.1158/0008-5472.CAN-22-1123", "pmid": "36251389", "labels": {"DDLS Fellow": null, "Arian Lundberg": null}, "xrefs": [{"db": "pmc", "key": "PMC9627125"}, {"db": "pii", "key": "709960"}], "notes": [], "created": "2025-11-14T07:51:45.135Z", "modified": "2025-11-14T07:51:46.107Z"}, {"entity": "publication", "iuid": "5bc10062f1ca4c4d98979da98b2f5a3c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5bc10062f1ca4c4d98979da98b2f5a3c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5bc10062f1ca4c4d98979da98b2f5a3c"}}, "title": "Next generation pan-cancer blood proteome profiling using proximity extension assay", "authors": [{"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ea446aa574042a295d5f69437402f76.json"}}, {"family": "\u00c1lvez", "given": "Mar\u00eda Bueno", "initials": "MB", "orcid": "0000-0002-2669-7796", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a7d09e4780a445b9b432d494c76d07e8.json"}}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e213b04f8984c8eb00c68f5bc2f6a36.json"}}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K"}, {"family": "Zwahlen", "given": "Martin", "initials": "M"}, {"family": "mardinoglu", "given": "adil", "initials": "a"}, {"family": "Edqvist", "given": "Per Henrik", "initials": "PH", "orcid": "0000-0002-8330-0134", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5219527c2dc6480da474f3c47dff9318.json"}}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T", "orcid": "0000-0001-6668-4140", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/851b95a56b3244fb9bc7cec8294e7ae7.json"}}, {"family": "Lundin", "given": "Emma", "initials": "E"}, {"family": "Rameika", "given": "Natallia", "initials": "N"}, {"family": "Axelsson", "given": "Tomas", "initials": "T"}, {"family": "\u00c5berg", "given": "Mikael", "initials": "M"}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/27ee07e408e24eefa23105dcc6aa252b.json"}}, {"family": "Zhong", "given": "Wen", "initials": "W", "orcid": "0000-0002-7422-6104", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d6ffb1140aaa42c5ac63fe76653fc63b.json"}}, {"family": "Karlsson", "given": "Max", "initials": "M", "orcid": "0000-0002-7000-4416", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b93284f942e44f1086616357d77267c3.json"}}, {"family": "Gyllensten", "given": "Ulf", "initials": "U", "orcid": "0000-0002-6316-3355", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eacfdf2095e947e99ac45fe994261b72.json"}}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9f5294424542413c9ba4432c839c2b63.json"}}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/abbbf8193d5a4376a5c726768d039439.json"}}], "type": "posted-content", "published": "2022-11-01", "journal": {"issn-l": null}, "abstract": null, "doi": "10.21203/rs.3.rs-2025767/v1", "pmid": null, "labels": {"SciLifeLab Fellow": "", "Fredrik Edfors": "", "DDLS Fellow": "", "Adil Mardinoglu": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T12:58:29.979Z", "modified": "2026-09-23T14:21:06.709Z"}, {"entity": "publication", "iuid": "6e0f70f55dc34f738fcddf705fe6152e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/6e0f70f55dc34f738fcddf705fe6152e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/6e0f70f55dc34f738fcddf705fe6152e"}}, "title": "Immunoglobulin G N-Glycosylation Signatures in Incident Type 2 Diabetes and Cardiovascular Disease.", "authors": [{"family": "Birukov", "given": "Anna", "initials": "A", "orcid": "0000-0002-8306-3351", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0485c5a948c343d78bd63652195e7253.json"}}, {"family": "Plav\u0161a", "given": "Branimir", "initials": "B"}, {"family": "Eichelmann", "given": "Fabian", "initials": "F", "orcid": "0000-0002-3975-5596", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4f6083a259c6440ab3201d53f44a0d55.json"}}, {"family": "Kuxhaus", "given": "Olga", "initials": "O"}, {"family": "Hoshi", "given": "Rosangela Akemi", "initials": "RA"}, {"family": "Rudman", "given": "Najda", "initials": "N"}, {"family": "\u0160tambuk", "given": "Tamara", "initials": "T"}, {"family": "Trbojevi\u0107-Akma\u010di\u0107", "given": "Irena", "initials": "I"}, {"family": "Schiborn", "given": "Catarina", "initials": "C", "orcid": "0000-0002-9556-4540", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e47026eec7f4544893d442b8f81d424.json"}}, {"family": "Morze", "given": "Jakub", "initials": "J"}, {"family": "Mihel\u010di\u0107", "given": "Matea", "initials": "M"}, {"family": "Cindri\u0107", "given": "Ana", "initials": "A"}, {"family": "Liu", "given": "Yanyan", "initials": "Y"}, {"family": "Demler", "given": "Olga", "initials": "O"}, {"family": "Perola", "given": "Markus", "initials": "M"}, {"family": "Mora", "given": "Samia", "initials": "S", "orcid": "0000-0001-6283-0980", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e1189d5d8e634514b0272b8aad38641f.json"}}, {"family": "Schulze", "given": "Matthias B", "initials": "MB", "orcid": "0000-0002-0830-5277", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/853ded2c43b64f26a8b47da7ea7b79c0.json"}}, {"family": "Lauc", "given": "Gordan", "initials": "G"}, {"family": "Wittenbecher", "given": "Clemens", "initials": "C", "orcid": "0000-0001-7792-877X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2f7d2c289b3c47d5a79d23bd48a3225a.json"}}], "type": "journal article", "published": "2022-11-01", "journal": {"title": "Diabetes Care", "issn": "1935-5548", "volume": "45", "issue": "11", "pages": "2729-2736", "issn-l": null}, "abstract": "N-glycosylation is a functional posttranslational modification of immunoglobulins (Igs). We hypothesized that specific IgG N-glycans are associated with incident type 2 diabetes and cardiovascular disease (CVD).\n\nWe performed case-cohort studies within the population-based European Prospective Investigation into Cancer and Nutrition (EPIC)-Potsdam cohort (2,127 in the type 2 diabetes subcohort [741 incident cases]; 2,175 in the CVD subcohort [417 myocardial infarction and stroke cases]). Relative abundances of 24 IgG N-glycan peaks (IgG-GPs) were measured by ultraperformance liquid chromatography, and eight glycosylation traits were derived based on structural similarity. End point-associated IgG-GPs were preselected with fractional polynomials, and prospective associations were estimated in confounder-adjusted Cox models. Diabetes risk associations were validated in three independent studies.\n\nAfter adjustment for confounders and multiple testing correction, IgG-GP7, IgG-GP8, IgG-GP9, IgG-GP11, and IgG-GP19 were associated with type 2 diabetes risk. A score based on these IgG-GPs was associated with a higher diabetes risk in EPIC-Potsdam and independent validation studies (843 total cases, 3,149 total non-cases, pooled estimate per SD increase 1.50 [95% CI 1.37-1.64]). Associations of IgG-GPs with CVD risk differed between men and women. In women, IgG-GP9 was inversely associated with CVD risk (hazard ratio [HR] per SD 0.80 [95% CI 0.65-0.98]). In men, a weighted score based on IgG-GP19 and IgG-GP23 was associated with higher CVD risk (HR per SD 1.47 [95% CI 1.20-1.80]). In addition, several derived traits were associated with cardiometabolic disease incidence.\n\nSelected IgG N-glycans are associated with cardiometabolic risk beyond classic risk factors, including clinical biomarkers.", "doi": "10.2337/dc22-0833", "pmid": "36174116", "labels": {"Clemens Wittenbecher": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC9679264"}, {"db": "pii", "key": "147697"}], "notes": [], "created": "2025-03-19T08:20:56.132Z", "modified": "2026-09-23T08:40:01.923Z"}, {"entity": "publication", "iuid": "402bed4e8127484e8b8044064cbe0645", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/402bed4e8127484e8b8044064cbe0645.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/402bed4e8127484e8b8044064cbe0645"}}, "title": "ShareLoc - an open platform for sharing localization microscopy data.", "authors": [{"family": "Ouyang", "given": "Wei", "initials": "W", "orcid": "0000-0002-0291-926X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56f601e1d1c6448aab0c3a1e3cffdbfc.json"}}, {"family": "Bai", "given": "Jiachuan", "initials": "J", "orcid": "0000-0001-5087-0344", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/688a92f42bd24cf2814e3f89c8cb4995.json"}}, {"family": "Singh", "given": "Manish Kumar", "initials": "MK"}, {"family": "Leterrier", "given": "Christophe", "initials": "C", "orcid": "0000-0002-2957-2032", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c65543128972480b8339028632ed9c58.json"}}, {"family": "Barthelemy", "given": "Paul", "initials": "P"}, {"family": "Barnett", "given": "Samuel F H", "initials": "SFH", "orcid": "0000-0002-3696-3509", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8b9798ae424d45ed8828f714458a4831.json"}}, {"family": "Klein", "given": "Teresa", "initials": "T"}, {"family": "Sauer", "given": "Markus", "initials": "M", "orcid": "0000-0002-1692-3219", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d97dea1b7ddd4f659735c19d60e5baad.json"}}, {"family": "Kanchanawong", "given": "Pakorn", "initials": "P", "orcid": "0000-0001-8765-3861", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/21127c5c91a34a03bc34b8c143fe4051.json"}}, {"family": "Bourg", "given": "Nicolas", "initials": "N", "orcid": "0000-0002-0640-2241", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8711ebee580d4e2ba5942d55f121c849.json"}}, {"family": "Cohen", "given": "Mickael M", "initials": "MM"}, {"family": "Lelandais", "given": "Beno\u00eet", "initials": "B", "orcid": "0000-0003-0321-4015", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/67246de8e2f549ffb9431820e1d76229.json"}}, {"family": "Zimmer", "given": "Christophe", "initials": "C", "orcid": "0000-0001-9910-1589", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ab6793e6696c4f8eb149afa2be603687.json"}}], "type": "letter", "published": "2022-11-00", "journal": {"title": "Nat. Methods", "issn": "1548-7105", "volume": "19", "issue": "11", "pages": "1331-1333", "issn-l": "1548-7091"}, "abstract": null, "doi": "10.1038/s41592-022-01659-0", "pmid": "36271059", "labels": {"DDLS Fellow": "", "Wei Ouyang": ""}, "xrefs": [{"db": "pii", "key": "10.1038/s41592-022-01659-0"}], "notes": [], "created": "2026-08-21T11:52:19.856Z", "modified": "2026-10-01T08:25:52.044Z"}, {"entity": "publication", "iuid": "3a682c29429c4b4da6c8a7e604617169", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3a682c29429c4b4da6c8a7e604617169.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3a682c29429c4b4da6c8a7e604617169"}}, "title": "Curation of BIDS (CuBIDS): A workflow and software package for streamlining reproducible curation of large BIDS datasets.", "authors": [{"family": "Covitz", "given": "Sydney", "initials": "S"}, {"family": "Tapera", "given": "Tinashe M", "initials": "TM"}, {"family": "Adebimpe", "given": "Azeez", "initials": "A"}, {"family": "Alexander-Bloch", "given": "Aaron F", "initials": "AF", "orcid": "0000-0001-6554-1893", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d96b7bb3399c4a0f8cd66be01f00b02c.json"}}, {"family": "Bertolero", "given": "Maxwell A", "initials": "MA"}, {"family": "Feczko", "given": "Eric", "initials": "E"}, {"family": "Franco", "given": "Alexandre R", "initials": "AR"}, {"family": "Gur", "given": "Raquel E", "initials": "RE"}, {"family": "Gur", "given": "Ruben C", "initials": "RC"}, {"family": "Hendrickson", "given": "Timothy", "initials": "T"}, {"family": "Houghton", "given": "Audrey", "initials": "A"}, {"family": "Mehta", "given": "Kahini", "initials": "K"}, {"family": "Murtha", "given": "Kristin", "initials": "K"}, {"family": "Perrone", "given": "Anders J", "initials": "AJ"}, {"family": "Robert-Fitzgerald", "given": "Tim", "initials": "T"}, {"family": "Schabdach", "given": "Jenna M", "initials": "JM"}, {"family": "Shinohara", "given": "Russell T", "initials": "RT"}, {"family": "Vogel", "given": "Jacob W", "initials": "JW", "orcid": "0000-0001-6394-9940", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d2ad5af780c245da9b59a8c80a0b00ff.json"}}, {"family": "Zhao", "given": "Chenying", "initials": "C"}, {"family": "Fair", "given": "Damien A", "initials": "DA"}, {"family": "Milham", "given": "Michael P", "initials": "MP"}, {"family": "Cieslak", "given": "Matthew", "initials": "M", "orcid": "0000-0002-1931-4734", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cb84822ea2c34c73bba1786bfb3dc2d3.json"}}, {"family": "Satterthwaite", "given": "Theodore D", "initials": "TD", "orcid": "0000-0001-7072-9399", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/461c3637946f4ed8956764658711fca7.json"}}], "type": "journal article", "published": "2022-11-00", "journal": {"title": "NeuroImage", "issn": "1095-9572", "issn-l": "1053-8119", "volume": "263", "issue": null, "pages": "119609"}, "abstract": "The Brain Imaging Data Structure (BIDS) is a specification accompanied by a software ecosystem that was designed to create reproducible and automated workflows for processing neuroimaging data. BIDS Apps flexibly build workflows based on the metadata detected in a dataset. However, even BIDS valid metadata can include incorrect values or omissions that result in inconsistent processing across sessions. Additionally, in large-scale, heterogeneous neuroimaging datasets, hidden variability in metadata is difficult to detect and classify. To address these challenges, we created a Python-based software package titled \"Curation of BIDS\" (CuBIDS), which provides an intuitive workflow that helps users validate and manage the curation of their neuroimaging datasets. CuBIDS includes a robust implementation of BIDS validation that scales to large samples and incorporates DataLad--a version control software package for data--as an optional dependency to ensure reproducibility and provenance tracking throughout the entire curation process. CuBIDS provides tools to help users perform quality control on their images' metadata and identify unique combinations of imaging parameters. Users can then execute BIDS Apps on a subset of participants that represent the full range of acquisition parameters that are present, accelerating pipeline testing on large datasets.", "doi": "10.1016/j.neuroimage.2022.119609", "pmid": "36064140", "labels": {"Jacob W Vogel": null, "DDLS Fellow": null}, "xrefs": [{"db": "mid", "key": "NIHMS1850027"}, {"db": "pmc", "key": "PMC9981813"}, {"db": "pii", "key": "S1053-8119(22)00724-8"}], "notes": [], "created": "2023-05-28T17:54:11.881Z", "modified": "2025-04-29T07:07:42.943Z"}, {"entity": "publication", "iuid": "76136dad3c65455eb4dd2347eafd3b24", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/76136dad3c65455eb4dd2347eafd3b24.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/76136dad3c65455eb4dd2347eafd3b24"}}, "title": "A structural biology community assessment of AlphaFold2 applications.", "authors": [{"family": "Akdel", "given": "Mehmet", "initials": "M"}, {"family": "Pires", "given": "Douglas E V", "initials": "DEV"}, {"family": "Pardo", "given": "Eduard Porta", "initials": "EP"}, {"family": "J\u00e4nes", "given": "J\u00fcrgen", "initials": "J", "orcid": "0000-0002-2540-1236", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/59c4858a6ab9448695b233e09ff58698.json"}}, {"family": "Zalevsky", "given": "Arthur O", "initials": "AO", "orcid": "0000-0001-6987-8119", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7fdb6c4d5c9b4feb83952a3674708a12.json"}}, {"family": "M\u00e9sz\u00e1ros", "given": "B\u00e1lint", "initials": "B"}, {"family": "Bryant", "given": "Patrick", "initials": "P", "orcid": "0000-0003-3439-1866", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a683bcf98234ff09b2398976583b66f.json"}}, {"family": "Good", "given": "Lydia L", "initials": "LL", "orcid": "0000-0001-5308-8542", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6b413593ce63451b9e3a3e79cbd20a53.json"}}, {"family": "Laskowski", "given": "Roman A", "initials": "RA", "orcid": "0000-0001-5528-0087", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1b0e4268b73b406d823b6b66059f2a53.json"}}, {"family": "Pozzati", "given": "Gabriele", "initials": "G", "orcid": "0000-0002-4303-9939", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/94129216debe4e22ab3f3b74c33f9ab9.json"}}, {"family": "Shenoy", "given": "Aditi", "initials": "A", "orcid": "0000-0001-7748-2501", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/35bef00b985a45d59602675316e3d706.json"}}, {"family": "Zhu", "given": "Wensi", "initials": "W"}, {"family": "Kundrotas", "given": "Petras", "initials": "P"}, {"family": "Serra", "given": "Victoria Ruiz", "initials": "VR", "orcid": "0000-0003-3991-0514", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0e03258443954d6d978ce8efb02a37b6.json"}}, {"family": "Rodrigues", "given": "Carlos H M", "initials": "CHM", "orcid": "0000-0002-4420-6401", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/642dc0c5ff09491d8e1e55449e251b80.json"}}, {"family": "Dunham", "given": "Alistair S", "initials": "AS", "orcid": "0000-0001-9076-3025", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/41348047cf374b149851ea1b9bca2014.json"}}, {"family": "Burke", "given": "David", "initials": "D", "orcid": "0000-0001-8830-3951", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0ae9a94abf5e47778d59e4f3c9d8e62e.json"}}, {"family": "Borkakoti", "given": "Neera", "initials": "N"}, {"family": "Velankar", "given": "Sameer", "initials": "S", "orcid": "0000-0002-8439-5964", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/30f88888429c46d698e49f80e79c3083.json"}}, {"family": "Frost", "given": "Adam", "initials": "A", "orcid": "0000-0003-2231-2577", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2b31e4961e0c457c85f8b0729a492a57.json"}}, {"family": "Basquin", "given": "J\u00e9r\u00f4me", "initials": "J"}, {"family": "Lindorff-Larsen", "given": "Kresten", "initials": "K", "orcid": "0000-0002-4750-6039", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2cd1f0559c6d4d58a1459dd38f851c93.json"}}, {"family": "Bateman", "given": "Alex", "initials": "A", "orcid": "0000-0002-6982-4660", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/01e1775e560147c2b7c40e1ba7d95a4e.json"}}, {"family": "Kajava", "given": "Andrey V", "initials": "AV", "orcid": "0000-0002-2342-6886", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5dfbae9ca6144d0381bf58f16029dcfe.json"}}, {"family": "Valencia", "given": "Alfonso", "initials": "A", "orcid": "0000-0002-8937-6789", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/80973e7b48094490adf93726d44c49b1.json"}}, {"family": "Ovchinnikov", "given": "Sergey", "initials": "S", "orcid": "0000-0003-2774-2744", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9c1c152b72314d178a2f01630d3ebbb7.json"}}, {"family": "Durairaj", "given": "Janani", "initials": "J", "orcid": "0000-0002-1698-4556", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bbc37e3024a34e18b93c50bd7ce6c3a7.json"}}, {"family": "Ascher", "given": "David B", "initials": "DB", "orcid": "0000-0003-2948-2413", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d141d7d1cbad4e87aef2a8878a845872.json"}}, {"family": "Thornton", "given": "Janet M", "initials": "JM", "orcid": "0000-0003-0824-4096", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/af0a3c9c4f12412d9709e6065c8d0813.json"}}, {"family": "Davey", "given": "Norman E", "initials": "NE", "orcid": "0000-0001-6988-4850", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dbb4780925604932b0853a1f8ad75145.json"}}, {"family": "Stein", "given": "Amelie", "initials": "A", "orcid": "0000-0002-5862-1681", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b99e2fc33a714b929e442e312f7513f1.json"}}, {"family": "Elofsson", "given": "Arne", "initials": "A", "orcid": "0000-0002-7115-9751", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/248e70e81bd64f31a5f83e6e329bba95.json"}}, {"family": "Croll", "given": "Tristan I", "initials": "TI", "orcid": "0000-0002-3514-8377", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/71c79d83429041ee8f4f47e6e4fa55f9.json"}}, {"family": "Beltrao", "given": "Pedro", "initials": "P", "orcid": "0000-0002-2724-7703", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/952eba119d2e4d4b89e14b294c5c6885.json"}}], "type": "journal article", "published": "2022-11-00", "journal": {"title": "Nat. Struct. Mol. Biol.", "issn": "1545-9985", "volume": "29", "issue": "11", "pages": "1056-1067", "issn-l": "1545-9985"}, "abstract": "Most proteins fold into 3D structures that determine how they function and orchestrate the biological processes of the cell. Recent developments in computational methods for protein structure predictions have reached the accuracy of experimentally determined models. Although this has been independently verified, the implementation of these methods across structural-biology applications remains to be tested. Here, we evaluate the use of AlphaFold2 (AF2) predictions in the study of characteristic structural elements; the impact of missense variants; function and ligand binding site predictions; modeling of interactions; and modeling of experimental structural data. For 11 proteomes, an average of 25% additional residues can be confidently modeled when compared with homology modeling, identifying structural features rarely seen in the Protein Data Bank. AF2-based predictions of protein disorder and complexes surpass dedicated tools, and AF2 models can be used across diverse applications equally well compared with experimentally determined structures, when the confidence metrics are critically considered. In summary, we find that these advances are likely to have a transformative impact in structural biology and broader life-science research.", "doi": "10.1038/s41594-022-00849-w", "pmid": "36344848", "labels": {"Patrick Bryant": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC9663297"}, {"db": "pii", "key": "10.1038/s41594-022-00849-w"}], "notes": [], "created": "2026-08-20T09:03:48.315Z", "modified": "2026-09-23T06:30:46.478Z"}, {"entity": "publication", "iuid": "5970c195b01949debfadbc434dc3a450", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5970c195b01949debfadbc434dc3a450.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5970c195b01949debfadbc434dc3a450"}}, "title": "Cohort profile: the Swedish Maternal Microbiome project (SweMaMi) - assessing the dynamic associations between the microbiome and maternal and neonatal adverse events.", "authors": [{"family": "Fransson", "given": "Emma", "initials": "E", "orcid": "0000-0001-9010-8522", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8c05290187ec426b8804eefc3d954971.json"}}, {"family": "Gudnadottir", "given": "Unnur", "initials": "U", "orcid": "0000-0002-4663-9921", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8702d95608284348b837ebbe275cc6af.json"}}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW"}, {"family": "Itzel", "given": "Eva Wiberg", "initials": "EW"}, {"family": "Hamsten", "given": "Marica", "initials": "M"}, {"family": "Boulund", "given": "Fredrik", "initials": "F"}, {"family": "Pennhag", "given": "Alexandra", "initials": "A"}, {"family": "Du", "given": "Juan", "initials": "J"}, {"family": "Schuppe-Koistinen", "given": "Ina", "initials": "I"}, {"family": "Brusselaers", "given": "Nele", "initials": "N", "orcid": "0000-0003-0137-447X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/70d0a6a2f4eb4272be4865e7e369c0e9.json"}}, {"family": "Engstrand", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2022-10-26", "journal": {"title": "BMJ Open", "issn": "2044-6055", "volume": "12", "issue": "10", "pages": "e065825", "issn-l": "2044-6055"}, "abstract": "The Swedish Maternal Microbiome (SweMaMi) project was initiated to better understand the dynamics of the microbiome in pregnancy, with longitudinal microbiome sampling, shotgun metagenomics, extensive questionnaires and health registry linkage.\n\nPregnant women were recruited before the 20th gestational week during 2017-2021 in Sweden. In total, 5439 pregnancies (5193 unique women) were included. For 3973 pregnancies (73%), samples were provided at baseline, and for 3141 (58%) at all three timepoints (second and third trimester and postpartum). In total, 38 591 maternal microbiome samples (vaginal, faecal and saliva) and 3109 infant faecal samples were collected. Questionnaires were used to collect information on general, reproductive and mental health, diet and lifestyle, complemented by linkage to the nationwide health registries, also used to follow up the health of the offspring (up to age 10).\n\nThe cohort is fairly representative for the total Swedish pregnant population (data from 2019), with 41% first-time mothers. Women with university level education, born in Sweden, with normal body mass index, not using tobacco-products and aged 30-34 years were slightly over-represented.\n\nThe sample and data collection were finalised in November 2021. The next steps are the characterisation of the microbial DNA and linkage to the health and demographic information from the questionnaires and registries. The role of the microbiome on maternal and neonatal outcomes and early-childhood diseases will be explored (including preterm birth, miscarriage) and the role and interaction of other risk factors and confounders (including endometriosis, polycystic ovarian syndrome, diet, drug use). This is currently among the largest pregnancy cohorts in the world with longitudinal design and detailed and standardised microbiome sampling enabling follow-up of both mothers and children. The findings are expected to contribute greatly to the field of reproductive health focusing on pregnancy and neonatal outcomes.", "doi": "10.1136/bmjopen-2022-065825", "pmid": "36288838", "labels": {"DDLS Fellow": "", "Luisa Hugerth": ""}, "xrefs": [{"db": "pmc", "key": "PMC9615996"}, {"db": "pii", "key": "bmjopen-2022-065825"}], "notes": [], "created": "2023-05-12T13:20:02.412Z", "modified": "2026-09-23T11:11:16.260Z"}, {"entity": "publication", "iuid": "1c4fd28f42be4dfab7823bc044fb70ea", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1c4fd28f42be4dfab7823bc044fb70ea.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1c4fd28f42be4dfab7823bc044fb70ea"}}, "title": "Draft Genome Sequence of an Enterotoxigenic Escherichia coli Strain Carrying Genes for Colonization Surface Antigen 13 and a Heat-Labile Toxin.", "authors": [{"family": "Njoroge", "given": "Samuel M", "initials": "SM", "orcid": "0000-0001-6965-3681", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5f5fb995ffd1436eaad3f617e3babca7.json"}}, {"family": "Mad\u00e9", "given": "Laure F", "initials": "LF"}, {"family": "von Mentzer", "given": "Astrid", "initials": "A", "orcid": "0000-0002-2167-1394", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/36cefe255ba14d8684826fae58598036.json"}}, {"family": "Kulohoma", "given": "Benard W", "initials": "BW", "orcid": "0000-0001-6825-1832", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/33f39d8e14324968ba3a8fdbacf4fb98.json"}}, {"family": "Kamanu", "given": "Timothy K", "initials": "TK", "orcid": "0000-0002-3842-9502", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e7cd9ed92621424a922b6ff8456ac80c.json"}}, {"family": "Ouko", "given": "Tom T", "initials": "TT"}, {"family": "Kiiru", "given": "John", "initials": "J"}, {"family": "Ward", "given": "Melissa J", "initials": "MJ"}, {"family": "Thomson", "given": "Nicholas R", "initials": "NR", "orcid": "0000-0002-4432-8505", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f79fd0f3dd3f4ac29de70a188710ac62.json"}}, {"family": "F\u00e8vre", "given": "Eric M", "initials": "EM", "orcid": "0000-0001-8931-4986", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/30fe04f11e2643fe8bb5d6a00a801f5d.json"}}, {"family": "Woolhouse", "given": "Mark", "initials": "M", "orcid": "0000-0003-3765-8167", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a4251084181b42fa84c86f4459e278dc.json"}}, {"family": "Kariuki", "given": "Samuel", "initials": "S"}], "type": "journal article", "published": "2022-10-20", "journal": {"title": "Microbiol Resour Announc", "issn": "2576-098X", "volume": "11", "issue": "10", "pages": "e0041622", "issn-l": null}, "abstract": "Here, we report the draft genome of ESEI_597, an enterotoxigenic Escherichia coli (ETEC) strain harboring genes encoding colonization surface antigen 13 (CS13) and a heat-labile toxin. The ESEI_597 strain was isolated from an 8-month-old child living in Korogocho, Kenya, in 2013.", "doi": "10.1128/mra.00416-22", "pmid": "36094211", "labels": {"Astrid von Mentzer": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC9583797"}], "notes": [], "created": "2025-12-02T15:48:43.547Z", "modified": "2025-12-02T15:48:43.751Z"}, {"entity": "publication", "iuid": "e7936e54cc944f8cb2fb74f8209cf94f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e7936e54cc944f8cb2fb74f8209cf94f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e7936e54cc944f8cb2fb74f8209cf94f"}}, "title": "Cholesterol's balancing act: Defying the status quo.", "authors": [{"family": "Doktorova", "given": "Milka", "initials": "M", "orcid": "0000-0003-4366-2242", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/791384c319f04584bac8ffb21df7271f.json"}}, {"family": "Levental", "given": "Ilya", "initials": "I", "orcid": "0000-0002-1206-9545", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7fe40c2b810348cab78616402d4d1f1f.json"}}], "type": "journal article", "published": "2022-10-18", "journal": {"title": "Biophys. J.", "issn": "1542-0086", "issn-l": "0006-3495", "volume": "121", "issue": "20", "pages": "3771-3773"}, "abstract": null, "doi": "10.1016/j.bpj.2022.08.036", "pmid": "36084632", "labels": {"Milka Doktorova": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC9674974"}, {"db": "pii", "key": "S0006-3495(22)00696-8"}], "notes": [], "created": "2024-11-27T12:20:15.974Z", "modified": "2025-04-29T07:09:59.476Z"}, {"entity": "publication", "iuid": "742f8e9ffe22495b83683c9efa073fe8", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/742f8e9ffe22495b83683c9efa073fe8.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/742f8e9ffe22495b83683c9efa073fe8"}}, "title": "Predicting the structure of large protein complexes using AlphaFold and Monte Carlo tree search.", "authors": [{"family": "Bryant", "given": "Patrick", "initials": "P", "orcid": "0000-0003-3439-1866", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a683bcf98234ff09b2398976583b66f.json"}}, {"family": "Pozzati", "given": "Gabriele", "initials": "G", "orcid": "0000-0002-4303-9939", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/94129216debe4e22ab3f3b74c33f9ab9.json"}}, {"family": "Zhu", "given": "Wensi", "initials": "W"}, {"family": "Shenoy", "given": "Aditi", "initials": "A", "orcid": "0000-0001-7748-2501", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/35bef00b985a45d59602675316e3d706.json"}}, {"family": "Kundrotas", "given": "Petras", "initials": "P"}, {"family": "Elofsson", "given": "Arne", "initials": "A", "orcid": "0000-0002-7115-9751", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/248e70e81bd64f31a5f83e6e329bba95.json"}}], "type": "journal article", "published": "2022-10-12", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "13", "issue": "1", "pages": "6028", "issn-l": "2041-1723"}, "abstract": "AlphaFold can predict the structure of single- and multiple-chain proteins with very high accuracy. However, the accuracy decreases with the number of chains, and the available GPU memory limits the size of protein complexes which can be predicted. Here we show that one can predict the structure of large complexes starting from predictions of subcomponents. We assemble 91 out of 175 complexes with 10-30 chains from predicted subcomponents using Monte Carlo tree search, with a median TM-score of 0.51. There are 30 highly accurate complexes (TM-score \u22650.8, 33% of complete assemblies). We create a scoring function, mpDockQ, that can distinguish if assemblies are complete and predict their accuracy. We find that complexes containing symmetry are accurately assembled, while asymmetrical complexes remain challenging. The method is freely available and accesible as a Colab notebook https://colab.research.google.com/github/patrickbryant1/MoLPC/blob/master/MoLPC.ipynb .", "doi": "10.1038/s41467-022-33729-4", "pmid": "36224222", "labels": {"Patrick Bryant": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC9556563"}, {"db": "pii", "key": "10.1038/s41467-022-33729-4"}], "notes": [], "created": "2026-08-20T08:52:21.196Z", "modified": "2026-09-23T06:42:56.668Z"}, {"entity": "publication", "iuid": "1cf2e7ddba514861ae0233ed0b1bac07", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1cf2e7ddba514861ae0233ed0b1bac07.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1cf2e7ddba514861ae0233ed0b1bac07"}}, "title": "Addressing the Protease Bias in Quantitative Proteomics.", "authors": [{"family": "Woessmann", "given": "Jakob", "initials": "J", "orcid": "0000-0002-2283-7237", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8a4b10f5f96244b98122eddcee694ec0.json"}}, {"family": "Kotol", "given": "David", "initials": "D", "orcid": "0000-0002-5388-3826", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c41f8f491c474e6bba2047b5d04b4af5.json"}}, {"family": "Hober", "given": "Andreas", "initials": "A", "orcid": "0000-0001-8947-2562", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/06cbc187628340278395a00ab9dd6c89.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e213b04f8984c8eb00c68f5bc2f6a36.json"}}], "type": "journal article", "published": "2022-10-07", "journal": {"title": "J. Proteome Res.", "issn": "1535-3907", "volume": "21", "issue": "10", "pages": "2526-2534", "issn-l": "1535-3893"}, "abstract": "Protein quantification strategies using multiple proteases have been shown to deliver poor interprotease accuracy in label-free mass spectrometry experiments. By utilizing six different proteases with different cleavage sites, this study explores the protease bias and its effect on accuracy and precision by using recombinant protein standards. We established 557 SRM assays, using a recombinant protein standard resource, toward 10 proteins in human plasma and determined their concentration with multiple proteases. The quantified peptides of these plasma proteins spanned 3 orders of magnitude (0.02-70 \u03bcM). In total, 60 peptides were used for absolute quantification and the majority of the peptides showed high robustness. The retained reproducibility was achieved by quantifying plasma proteins using spiked stable isotope standard recombinant proteins in a targeted proteomics workflow.", "doi": "10.1021/acs.jproteome.2c00491", "pmid": "36044728", "labels": {"Fredrik Edfors": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC9552229"}], "notes": [], "created": "2026-08-20T08:11:40.340Z", "modified": "2026-09-23T12:05:43.703Z"}, {"entity": "publication", "iuid": "b6c0845a4aea452aab28b70877869834", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b6c0845a4aea452aab28b70877869834.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b6c0845a4aea452aab28b70877869834"}}, "title": "A multi-omic analysis of MCF10A cells provides a resource for integrative assessment of ligand-mediated molecular and phenotypic responses.", "authors": [{"family": "Gross", "given": "Sean M", "initials": "SM"}, {"family": "Dane", "given": "Mark A", "initials": "MA", "orcid": "0000-0003-3742-9866", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/49681b28b1454254b580cf27882f81f2.json"}}, {"family": "Smith", "given": "Rebecca L", "initials": "RL"}, {"family": "Devlin", "given": "Kaylyn L", "initials": "KL"}, {"family": "McLean", "given": "Ian C", "initials": "IC", "orcid": "0000-0003-2741-7941", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/76a38d39e69347508aaf8fc1932b0cb6.json"}}, {"family": "Derrick", "given": "Daniel S", "initials": "DS"}, {"family": "Mills", "given": "Caitlin E", "initials": "CE", "orcid": "0000-0002-2608-4084", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5dbe516477294dd08e4404bedd3e0ce0.json"}}, {"family": "Subramanian", "given": "Kartik", "initials": "K"}, {"family": "London", "given": "Alexandra B", "initials": "AB"}, {"family": "Torre", "given": "Denis", "initials": "D"}, {"family": "Evangelista", "given": "John Erol", "initials": "JE"}, {"family": "Clarke", "given": "Daniel J B", "initials": "DJB"}, {"family": "Xie", "given": "Zhuorui", "initials": "Z"}, {"family": "Erdem", "given": "Cemal", "initials": "C", "orcid": "0000-0003-3663-3646", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f71b5af589264614a52eefa8baba3132.json"}}, {"family": "Lyons", "given": "Nicholas", "initials": "N"}, {"family": "Natoli", "given": "Ted", "initials": "T"}, {"family": "Pessa", "given": "Sarah", "initials": "S"}, {"family": "Lu", "given": "Xiaodong", "initials": "X"}, {"family": "Mullahoo", "given": "James", "initials": "J"}, {"family": "Li", "given": "Jonathan", "initials": "J", "orcid": "0000-0003-3519-8638", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/77d0c8cac07b47228b383aa851382852.json"}}, {"family": "Adam", "given": "Miriam", "initials": "M"}, {"family": "Wassie", "given": "Brook", "initials": "B"}, {"family": "Liu", "given": "Moqing", "initials": "M"}, {"family": "Kilburn", "given": "David F", "initials": "DF"}, {"family": "Liby", "given": "Tiera A", "initials": "TA"}, {"family": "Bucher", "given": "Elmar", "initials": "E", "orcid": "0000-0002-2929-2460", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1602ed968b5b4b4a8841834d98a861f2.json"}}, {"family": "Sanchez-Aguila", "given": "Crystal", "initials": "C"}, {"family": "Daily", "given": "Kenneth", "initials": "K"}, {"family": "Omberg", "given": "Larsson", "initials": "L"}, {"family": "Wang", "given": "Yunguan", "initials": "Y"}, {"family": "Jacobson", "given": "Connor", "initials": "C"}, {"family": "Yapp", "given": "Clarence", "initials": "C"}, {"family": "Chung", "given": "Mirra", "initials": "M"}, {"family": "Vidovic", "given": "Dusica", "initials": "D"}, {"family": "Lu", "given": "Yiling", "initials": "Y"}, {"family": "Schurer", "given": "Stephan", "initials": "S", "orcid": "0000-0001-7180-0978", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5d44cae6b7434241bb9d26dd8c441d55.json"}}, {"family": "Lee", "given": "Albert", "initials": "A", "orcid": "0000-0001-9917-514X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1cd097a0d7e6445b90061cc59a9c3c91.json"}}, {"family": "Pillai", "given": "Ajay", "initials": "A"}, {"family": "Subramanian", "given": "Aravind", "initials": "A"}, {"family": "Papanastasiou", "given": "Malvina", "initials": "M", "orcid": "0000-0003-3378-6612", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/459809dbb4304431885efdf57f83bd0d.json"}}, {"family": "Fraenkel", "given": "Ernest", "initials": "E", "orcid": "0000-0001-9249-8181", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c4a3be6fa84346b08b91eacba40a98a0.json"}}, {"family": "Feiler", "given": "Heidi S", "initials": "HS", "orcid": "0000-0002-6580-3547", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56596e02cda4441dbe0deaea48fc6aef.json"}}, {"family": "Mills", "given": "Gordon B", "initials": "GB"}, {"family": "Jaffe", "given": "Jake D", "initials": "JD", "orcid": "0000-0001-9845-1210", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5c01e6b4a88645378c52425c7c3bdd36.json"}}, {"family": "Ma'ayan", "given": "Avi", "initials": "A"}, {"family": "Birtwistle", "given": "Marc R", "initials": "MR", "orcid": "0000-0002-0341-0705", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/df52e09a2f984f10833bda7b554b1a22.json"}}, {"family": "Sorger", "given": "Peter K", "initials": "PK", "orcid": "0000-0002-3364-1838", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/833b610a34424918827421ae3c8dc8c3.json"}}, {"family": "Korkola", "given": "James E", "initials": "JE"}, {"family": "Gray", "given": "Joe W", "initials": "JW"}, {"family": "Heiser", "given": "Laura M", "initials": "LM", "orcid": "0000-0003-3330-0950", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ce0d380df324afcbbaa1971aa8472cc.json"}}], "type": "journal article", "published": "2022-10-07", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "5", "issue": "1", "pages": "1066", "issn-l": "2399-3642"}, "abstract": "The phenotype of a cell and its underlying molecular state is strongly influenced by extracellular signals, including growth factors, hormones, and extracellular matrix proteins. While these signals are normally tightly controlled, their dysregulation leads to phenotypic and molecular states associated with diverse diseases. To develop a detailed understanding of the linkage between molecular and phenotypic changes, we generated a comprehensive dataset that catalogs the transcriptional, proteomic, epigenomic and phenotypic responses of MCF10A mammary epithelial cells after exposure to the ligands EGF, HGF, OSM, IFNG, TGFB and BMP2. Systematic assessment of the molecular and cellular phenotypes induced by these ligands comprise the LINCS Microenvironment (ME) perturbation dataset, which has been curated and made publicly available for community-wide analysis and development of novel computational methods ( synapse.org/LINCS_MCF10A ). In illustrative analyses, we demonstrate how this dataset can be used to discover functionally related molecular features linked to specific cellular phenotypes. Beyond these analyses, this dataset will serve as a resource for the broader scientific community to mine for biological insights, to compare signals carried across distinct molecular modalities, and to develop new computational methods for integrative data analysis.", "doi": "10.1038/s42003-022-03975-9", "pmid": "36207580", "labels": {"DDLS Fellow": null, "Cemal Erdem": null}, "xrefs": [{"db": "pmc", "key": "PMC9546880"}, {"db": "pii", "key": "10.1038/s42003-022-03975-9"}], "notes": [], "created": "2023-10-27T08:53:37.687Z", "modified": "2025-04-29T07:09:50.939Z"}, {"entity": "publication", "iuid": "76358c9d2a394794ad8a06a269f1bca3", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/76358c9d2a394794ad8a06a269f1bca3.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/76358c9d2a394794ad8a06a269f1bca3"}}, "title": "aMeta: an accurate and memory-efficient ancient Metagenomic profiling workflow", "authors": [{"family": "Pochon", "given": "Zo\u00e9", "initials": "Z", "orcid": "0000-0001-7981-5795", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/86bda59888834d6889a108f8abbdb0fa.json"}}, {"family": "Bergfeldt", "given": "Nora", "initials": "N", "orcid": "0000-0003-2767-8156", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9141014a18c54129b99af1006ff76f9b.json"}}, {"family": "K\u0131rd\u00f6k", "given": "Emrah", "initials": "E", "orcid": "0000-0003-0500-1208", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3a60c96525a642b4be97e15a53de250b.json"}}, {"family": "Vicente", "given": "M\u00e1rio", "initials": "M", "orcid": "0000-0002-9122-4530", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/70f79b138afe4df99b780eb97ebdbc13.json"}}, {"family": "Naidoo", "given": "Thijessen", "initials": "T"}, {"family": "van der Valk", "given": "Tom", "initials": "T", "orcid": "0000-0001-6582-3452", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/aa0dba3cc12143cba213f7f3a052216c.json"}}, {"family": "Alt\u0131n\u0131\u015f\u0131k", "given": "N Ezgi", "initials": "NE", "orcid": "0000-0003-0653-4292", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f06df27a24874d5e9b11db34a31730d1.json"}}, {"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M", "orcid": "0000-0002-6702-8724", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02faff0c060a4c25a13a9c7556dd30c3.json"}}, {"family": "Dalen", "given": "Love", "initials": "L", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6ff87fd5aabe4a38954dd96d8e6c261d.json"}}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-8579-1304", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0c4e61575ab14fe3aa59190a82521921.json"}}, {"family": "Mirabello", "given": "Claudio", "initials": "C", "orcid": "0000-0001-7868-034X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f4ca88bb3cf24e2591c447ec929502e6.json"}}, {"family": "Unneberg", "given": "Per", "initials": "P", "orcid": "0000-0001-5735-3315", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/47dae455224d4af4a35865907088f0b1.json"}}, {"family": "Oskolkov", "given": "Nikolay", "initials": "N", "orcid": "0000-0001-5326-8893", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3c448f1b878442c687d58549f90ba4e9.json"}}], "type": "posted-content", "published": "2022-10-05", "journal": {"title": "bioRxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2022.10.03.510579", "pmid": null, "labels": {"DDLS Fellow": null, "Tom van der Valk": null}, "xrefs": [], "notes": [], "created": "2026-08-20T10:41:14.984Z", "modified": "2026-10-05T08:24:10.787Z"}, {"entity": "publication", "iuid": "3278c59c61e340e486c23565f6981adb", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3278c59c61e340e486c23565f6981adb.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3278c59c61e340e486c23565f6981adb"}}, "title": "Elevation and plant species identity jointly shape a diverse arbuscular mycorrhizal fungal community in the High Arctic.", "authors": [{"family": "Rasmussen", "given": "Pil U", "initials": "PU", "orcid": "0000-0003-0607-4230", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/80035ea7380843aa9d2c58a3ebfa3d4b.json"}}, {"family": "Abrego", "given": "Nerea", "initials": "N", "orcid": "0000-0001-6347-6127", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/224552896bb04ea6a2cf695729ea94f7.json"}}, {"family": "Roslin", "given": "Tomas", "initials": "T", "orcid": "0000-0002-2957-4791", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4b6e491ae382479b8e92eda9a11cabae.json"}}, {"family": "\u00d6pik", "given": "Maarja", "initials": "M", "orcid": "0000-0001-8025-7460", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d4aa2839065c4a0f86a008d9c6a8bb57.json"}}, {"family": "Sepp", "given": "Siim-Kaarel", "initials": "SK", "orcid": "0000-0003-2906-4609", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/76351ce330da4f2eaf2c12948882dfbb.json"}}, {"family": "Blanchet", "given": "F Guillaume", "initials": "FG", "orcid": "0000-0001-5149-2488", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5332dbed91464890b63acd68c6770254.json"}}, {"family": "Huotari", "given": "Tea", "initials": "T"}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW", "orcid": "0000-0001-5432-1764", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/246ed7b405dd4c3f9ec5e7ff9f1d3ade.json"}}, {"family": "Tack", "given": "Ayco J M", "initials": "AJM", "orcid": "0000-0002-3550-1070", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/20531f32048b4cd498311138500cc6bc.json"}}], "type": "journal article", "published": "2022-10-00", "journal": {"title": "New Phytol.", "issn": "1469-8137", "volume": "236", "issue": "2", "pages": "671-683", "issn-l": "0028-646X"}, "abstract": "Knowledge about the distribution and local diversity patterns of arbuscular mycorrhizal (AM) fungi are limited for extreme environments such as the Arctic, where most studies have focused on spore morphology or root colonization. We here studied the joint effects of plant species identity and elevation on AM fungal distribution and diversity. We sampled roots of 19 plant species in 18 locations in Northeast Greenland, using next generation sequencing to identify AM fungi. We studied the joint effect of plant species, elevation and selected abiotic conditions on AM fungal presence, richness and composition. We identified 29 AM fungal virtual taxa (VT), of which six represent putatively new VT. Arbuscular mycorrhizal fungal presence increased with elevation, and as vegetation cover and the active soil layer decreased. Arbuscular mycorrhizal fungal composition was shaped jointly by elevation and plant species identity. We demonstrate that the Arctic harbours a relatively species-rich and nonrandomly distributed diversity of AM fungi. Given the high diversity and general lack of knowledge exposed herein, we encourage further research into the diversity, drivers and functional role of AM fungi in the Arctic. Such insight is urgently needed for an area with some of the globally highest rates of climate change.", "doi": "10.1111/nph.18342", "pmid": "35751540", "labels": {"DDLS Fellow": "", "Luisa Hugerth": ""}, "xrefs": [{"db": "pmc", "key": "PMC9796444"}, {"db": "RefSeq", "key": "PRJEB40490"}], "notes": [], "created": "2023-05-12T13:20:04.309Z", "modified": "2026-09-23T10:58:48.583Z"}, {"entity": "publication", "iuid": "0c212ea4e16c4ec4a972c543606725d9", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0c212ea4e16c4ec4a972c543606725d9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0c212ea4e16c4ec4a972c543606725d9"}}, "title": "Comprehensive analysis of pathways in Coronavirus 2019 (COVID-19) using an unsupervised machine learning method.", "authors": [{"family": "Taheri", "given": "Golnaz", "initials": "G", "orcid": "0000-0002-2741-0355", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/014c217121d346b2b371bbc1c2fede57.json"}}, {"family": "Habibi", "given": "Mahnaz", "initials": "M", "orcid": "0000-0002-8969-2706", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f04af4e059814b78bfb107c3a5782f70.json"}}], "type": "journal article", "published": "2022-10-00", "journal": {"title": "Appl Soft Comput", "issn": "1568-4946", "issn-l": null, "volume": "128", "issue": null, "pages": "109510"}, "abstract": "The World Health Organization (WHO) introduced \"Coronavirus disease 19\" or \"COVID-19\" as a novel coronavirus in March 2020. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) requires the fast discovery of effective treatments to fight this worldwide crisis. Artificial intelligence and bioinformatics analysis pipelines can assist with finding biomarkers, explanations, and cures. Artificial intelligence and machine learning methods provide powerful infrastructures for interpreting and understanding the available data. On the other hand, pathway enrichment analysis, as a dominant tool, could help researchers discover potential key targets present in biological pathways of host cells that are targeted by SARS-CoV-2. In this work, we propose a two-stage machine learning approach for pathway analysis. During the first stage, four informative gene sets that can represent important COVID-19 related pathways are selected. These \"representative genes\" are associated with the COVID-19 pathology. Then, two distinctive networks were constructed for COVID-19 related signaling and disease pathways. In the second stage, the pathways of each network are ranked with respect to some unsupervised scorning method based on our defined informative features. Finally, we present a comprehensive analysis of the top important pathways in both networks. Materials and implementations are available at: https://github.com/MahnazHabibi/Pathway.", "doi": "10.1016/j.asoc.2022.109510", "pmid": "35992221", "labels": {"Golnaz Taheri": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC9384336"}, {"db": "pii", "key": "S1568-4946(22)00596-8"}], "notes": [], "created": "2025-03-21T09:08:38.399Z", "modified": "2026-09-23T10:56:04.318Z"}, {"entity": "publication", "iuid": "82fcc044a9424abea9804a6b4242c8a5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/82fcc044a9424abea9804a6b4242c8a5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/82fcc044a9424abea9804a6b4242c8a5"}}, "title": "Analysis of the Human Protein Atlas Weakly Supervised Single-Cell Classification competition.", "authors": [{"family": "Le", "given": "Trang", "initials": "T"}, {"family": "Winsnes", "given": "Casper F", "initials": "CF", "orcid": "0000-0002-0028-5865", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/edeb3bc6c95d4185bf2098bf1e4a5e3c.json"}}, {"family": "Axelsson", "given": "Ulrika", "initials": "U", "orcid": "0000-0002-0273-9306", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5c60c73df0c445b38aabb5e91a118a2b.json"}}, {"family": "Xu", "given": "Hao", "initials": "H"}, {"family": "Mohanakrishnan Kaimal", "given": "Jayasankar", "initials": "J"}, {"family": "Mahdessian", "given": "Diana", "initials": "D"}, {"family": "Dai", "given": "Shubin", "initials": "S", "orcid": "0000-0001-6680-0500", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7f4835d5b16a400b9dd9aaff8a8d49f7.json"}}, {"family": "Makarov", "given": "Ilya S", "initials": "IS"}, {"family": "Ostankovich", "given": "Vladislav", "initials": "V", "orcid": "0000-0001-7020-8825", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b3a24a4ce6254b1aa5ee0ffc987b3b45.json"}}, {"family": "Xu", "given": "Yang", "initials": "Y"}, {"family": "Benhamou", "given": "Eric", "initials": "E"}, {"family": "Henkel", "given": "Christof", "initials": "C", "orcid": "0000-0002-2913-3662", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2560edfc894b48b4849f28173e580861.json"}}, {"family": "Solovyev", "given": "Roman A", "initials": "RA", "orcid": "0000-0003-0312-452X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6aee06b530294a58b87b0e0c40aa316d.json"}}, {"family": "Bani\u0107", "given": "Nikola", "initials": "N"}, {"family": "Bo\u0161njak", "given": "Vito", "initials": "V", "orcid": "0000-0003-3786-0592", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/14fb5bfa316e4fb48cb6afc00ccbb2dc.json"}}, {"family": "Bo\u0161njak", "given": "Ana", "initials": "A", "orcid": "0000-0002-3425-8363", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/58a2bdb9d5b94686a57238eddc685730.json"}}, {"family": "Mili\u010devi\u0107", "given": "Andrija", "initials": "A", "orcid": "0000-0001-7148-7651", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ffd8bc851170484c85db3c7699c3c49d.json"}}, {"family": "Ouyang", "given": "Wei", "initials": "W", "orcid": "0000-0002-0291-926X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56f601e1d1c6448aab0c3a1e3cffdbfc.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb07e6d0122c4528a927c1fe922e3bc8.json"}}], "type": "journal article", "published": "2022-10-00", "journal": {"title": "Nat. Methods", "issn": "1548-7105", "volume": "19", "issue": "10", "pages": "1221-1229", "issn-l": "1548-7091"}, "abstract": "While spatial proteomics by fluorescence imaging has quickly become an essential discovery tool for researchers, fast and scalable methods to classify and embed single-cell protein distributions in such images are lacking. Here, we present the design and analysis of the results from the competition Human Protein Atlas - Single-Cell Classification hosted on the Kaggle platform. This represents a crowd-sourced competition to develop machine learning models trained on limited annotations to label single-cell protein patterns in fluorescent images. The particular challenges of this competition include class imbalance, weak labels and multi-label classification, prompting competitors to apply a wide range of approaches in their solutions. The winning models serve as the first subcellular omics tools that can annotate single-cell locations, extract single-cell features and capture cellular dynamics.", "doi": "10.1038/s41592-022-01606-z", "pmid": "36175767", "labels": {"DDLS Fellow": "", "Wei Ouyang": ""}, "xrefs": [{"db": "pmc", "key": "PMC9550622"}, {"db": "pii", "key": "10.1038/s41592-022-01606-z"}], "notes": [], "created": "2026-08-20T09:02:51.438Z", "modified": "2026-09-23T08:52:27.380Z"}, {"entity": "publication", "iuid": "2924ee4928cd43a69d0bf07ec37fe41b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/2924ee4928cd43a69d0bf07ec37fe41b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/2924ee4928cd43a69d0bf07ec37fe41b"}}, "title": "A new machine learning method for cancer mutation analysis.", "authors": [{"family": "Habibi", "given": "Mahnaz", "initials": "M", "orcid": "0000-0002-8969-2706", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f04af4e059814b78bfb107c3a5782f70.json"}}, {"family": "Taheri", "given": "Golnaz", "initials": "G", "orcid": "0000-0002-2741-0355", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/014c217121d346b2b371bbc1c2fede57.json"}}], "type": "journal article", "published": "2022-10-00", "journal": {"title": "PLoS Comput Biol", "issn": "1553-7358", "issn-l": "1553-734X", "volume": "18", "issue": "10", "pages": "e1010332"}, "abstract": "It is complicated to identify cancer-causing mutations. The recurrence of a mutation in patients remains one of the most reliable features of mutation driver status. However, some mutations are more likely to happen than others for various reasons. Different sequencing analysis has revealed that cancer driver genes operate across complex pathways and networks, with mutations often arising in a mutually exclusive pattern. Genes with low-frequency mutations are understudied as cancer-related genes, especially in the context of networks. Here we propose a machine learning method to study the functionality of mutually exclusive genes in the networks derived from mutation associations, gene-gene interactions, and graph clustering. These networks have indicated critical biological components in the essential pathways, especially those mutated at low frequency. Studying the network and not just the impact of a single gene significantly increases the statistical power of clinical analysis. The proposed method identified important driver genes with different frequencies. We studied the function and the associated pathways in which the candidate driver genes participate. By introducing lower-frequency genes, we recognized less studied cancer-related pathways. We also proposed a novel clustering method to specify driver modules. We evaluated each driver module with different criteria, including the terms of biological processes and the number of simultaneous mutations in each cancer. Materials and implementations are available at: https://github.com/MahnazHabibi/MutationAnalysis.", "doi": "10.1371/journal.pcbi.1010332", "pmid": "36251702", "labels": {"Golnaz Taheri": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC9612828"}, {"db": "pii", "key": "PCOMPBIOL-D-22-00959"}], "notes": [], "created": "2025-03-21T09:08:36.278Z", "modified": "2026-09-23T11:11:13.445Z"}, {"entity": "publication", "iuid": "7b8eda6059a74744a616b74fb5745541", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/7b8eda6059a74744a616b74fb5745541.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/7b8eda6059a74744a616b74fb5745541"}}, "title": "Barcode-free prediction of cell lineages from scRNA-seq datasets", "authors": [{"family": "Eisele", "given": "A S", "initials": "AS"}, {"family": "Tarbier", "given": "M", "initials": "M"}, {"family": "Dormann", "given": "A A", "initials": "AA"}, {"family": "Pelechano", "given": "V", "initials": "V", "orcid": "0000-0002-9415-788X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e893b93b7654d10b4072e1b5de0bd71.json"}}, {"family": "Suter", "given": "D M", "initials": "DM", "orcid": "0000-0001-5644-4899", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3a3dd88c76314449ad1823ac1f067db7.json"}}], "type": "posted-content", "published": "2022-09-20", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2022.09.20.508646", "pmid": null, "labels": {"SciLifeLab Fellow": "", "DDLS Fellow": "", "Marcel Tarbier": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T10:14:22.144Z", "modified": "2026-09-23T14:11:31.110Z"}, {"entity": "publication", "iuid": "5a90568ccd944b2f8919a5b987cd77e9", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5a90568ccd944b2f8919a5b987cd77e9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5a90568ccd944b2f8919a5b987cd77e9"}}, "title": "Retinol and Retinol Binding Protein 4 Levels and Cardiometabolic Disease Risk.", "authors": [{"family": "Schiborn", "given": "Catarina", "initials": "C", "orcid": "0000-0002-9556-4540", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e47026eec7f4544893d442b8f81d424.json"}}, {"family": "Weber", "given": "Daniela", "initials": "D", "orcid": "0000-0002-2054-6233", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/727ef7e223eb44b09323bb6603d4c679.json"}}, {"family": "Grune", "given": "Tilman", "initials": "T", "orcid": "0000-0003-4775-9973", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/01678fe6bf964fe596a641349dfd1bba.json"}}, {"family": "Biemann", "given": "Ronald", "initials": "R"}, {"family": "J\u00e4ger", "given": "Susanne", "initials": "S"}, {"family": "Neu", "given": "Natascha", "initials": "N"}, {"family": "M\u00fcller von Blumencron", "given": "Marie", "initials": "M"}, {"family": "Fritsche", "given": "Andreas", "initials": "A"}, {"family": "Weikert", "given": "Cornelia", "initials": "C"}, {"family": "Schulze", "given": "Matthias B", "initials": "MB", "orcid": "0000-0002-0830-5277", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/853ded2c43b64f26a8b47da7ea7b79c0.json"}}, {"family": "Wittenbecher", "given": "Clemens", "initials": "C", "orcid": "0000-0001-7792-877X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2f7d2c289b3c47d5a79d23bd48a3225a.json"}}], "type": "journal article", "published": "2022-09-16", "journal": {"title": "Circ. Res.", "issn": "1524-4571", "volume": "131", "issue": "7", "pages": "637-649", "issn-l": "0009-7330"}, "abstract": "Despite mechanistic studies linking retinol and RBP4 (retinol binding protein 4) to the pathogenesis of cardiovascular diseases (CVD) and type 2 diabetes (T2D), epidemiological evidence is still conflicting. We investigated whether conflicting results of previous studies may be explained by differences in the association of retinol and RBP4 with cardiometabolic risk across subgroups with distinct sex, hypertension state, liver, or kidney function.\n\nWe used case-cohorts nested in the EPIC (European Prospective Investigation Into Cancer and Nutrition)-Potsdam cohort (N=27 548) comprising a random sample of participants (n=2500) and all physician-verified cases of incident CVD (n=508, median follow-up time 8.2 years) and T2D (n=820, median follow-up time 6.3 years). We estimated nonlinear and linear multivariable-adjusted associations between the biomarkers and cardiometabolic diseases by restricted cubic splines and Cox regression, respectively, testing potential interactions with hypertension, liver, and kidney function. Additionally, we performed 2-sample Mendelian Randomization analyses in publicly available data.\n\nThe association of retinol with cardiometabolic risk was modified by hypertension state (P interaction CVD<0.001; P interaction T2D<0.001). Retinol was associated with lower cardiometabolic risk in participants with treated hypertension (hazard ratioper SD [95% CI]: CVD, 0.71 [0.56-0.90]; T2D, 0.81 [0.70-0.94]) but with higher cardiometabolic risk in normotensive participants (CVD, 1.32 [1.06-1.64]; T2D, 1.15 [0.98-1.36]). Our analyses also indicated a significant interaction between RBP4 and hypertension on CVD risk (P interaction=0.04). Regarding T2D risk, we observed a u-shaped association with RBP4 in women (P nonlinearity=0.01, P effect=0.02) and no statistically significant association in men. The biomarkers' interactions with liver or kidney function were not statistically significant. Hypertension state-specific associations for retinol concentrations with cardiovascular mortality risk were replicated in National Health and Nutrition Examination Survey III.\n\nOur findings suggest a hypertension-dependent relationship between plasma retinol and cardiometabolic risk and complex interactions of RBP4 with sex and hypertension on cardiometabolic risk.", "doi": "10.1161/CIRCRESAHA.122.321295", "pmid": "36017698", "labels": {"Clemens Wittenbecher": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC9473720"}], "notes": [], "created": "2025-03-19T08:20:57.424Z", "modified": "2025-03-19T08:21:08.177Z"}, {"entity": "publication", "iuid": "008ab3f4e36c42e5864a4c7a99715784", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/008ab3f4e36c42e5864a4c7a99715784.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/008ab3f4e36c42e5864a4c7a99715784"}}, "title": "Monitoring of the SARS-CoV-2 Omicron BA.1/BA.2 lineage transition in the Swedish population reveals increased viral RNA levels in BA.2 cases.", "authors": [{"family": "Lentini", "given": "Antonio", "initials": "A"}, {"family": "Pereira", "given": "Antonio", "initials": "A"}, {"family": "Winqvist", "given": "Ola", "initials": "O"}, {"family": "Reinius", "given": "Bj\u00f6rn", "initials": "B"}], "type": "case reports", "published": "2022-09-09", "journal": {"title": "Med", "issn": "2666-6340", "volume": "3", "issue": "9", "pages": "636-643.e4", "issn-l": null}, "abstract": "Throughout the SARS-CoV-2 pandemic, multiple waves of variants of concern have swept across populations, leading to a chain of new and yet more contagious variants dominating COVID-19 cases. Here, we tracked the remarkably rapid shift from Omicron BA.1 to BA.2 sublineage dominance in the Swedish population in early 2022 at a day-by-day basis.\n\nUsing a custom SARS-CoV-2 Omicron BA.1 lineage-typing RT-PCR assay, we analyzed 174,933 clinical upper airway samples collected during January to March 2022.\n\nOur study demonstrates the feasibility and reliability of parallel lineage assignment of select variants at population scale, tracking the dominant sublineage transition from BA.1 to BA.2 at day-to-day resolution and uncovering nearly 2-fold higher levels of viral RNA in cases infected with Omicron BA.2 relative to BA.1.\n\nOur data provide unique insights into the Omicron BA.1 to BA.2 transition that occurred in Sweden during early 2022, and later, across the world. This may help to understand the increased transmissibility of the BA.2 variant.", "doi": "10.1016/j.medj.2022.07.007", "pmid": "35981541", "labels": {"Antonio Lentini": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC9359497"}, {"db": "pii", "key": "S2666-6340(22)00317-8"}], "notes": [], "created": "2025-03-28T07:09:49.547Z", "modified": "2025-03-28T07:09:49.565Z"}, {"entity": "publication", "iuid": "2a03ef9ebe88444eb1262850a45b7daa", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/2a03ef9ebe88444eb1262850a45b7daa.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/2a03ef9ebe88444eb1262850a45b7daa"}}, "title": "TET2-mutant clonal hematopoiesis and risk of gout.", "authors": [{"family": "Agrawal", "given": "Mridul", "initials": "M"}, {"family": "Niroula", "given": "Abhishek", "initials": "A"}, {"family": "Cunin", "given": "Pierre", "initials": "P", "orcid": "0000-0001-8550-2306", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/363ef392810f4098843bf0c40ec53a0d.json"}}, {"family": "McConkey", "given": "Marie", "initials": "M"}, {"family": "Shkolnik", "given": "Veronica", "initials": "V"}, {"family": "Kim", "given": "Peter G", "initials": "PG"}, {"family": "Wong", "given": "Waihay J", "initials": "WJ", "orcid": "0000-0003-2023-6590", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3a4e1a5be5c54646ab5881bc338bf6cd.json"}}, {"family": "Weeks", "given": "Lachelle D", "initials": "LD", "orcid": "0000-0001-8726-6212", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ec1c3cd65e44fdb9f5cc2c2bf09bbc1.json"}}, {"family": "Lin", "given": "Amy E", "initials": "AE", "orcid": "0000-0002-0554-2832", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca94bff0b2bf49fda6fd77a16e6ef0fd.json"}}, {"family": "Miller", "given": "Peter G", "initials": "PG", "orcid": "0000-0002-6797-9335", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0abfb0f5d3fb419dbcfc03afa2885d41.json"}}, {"family": "Gibson", "given": "Christopher J", "initials": "CJ"}, {"family": "Sekar", "given": "Aswin", "initials": "A"}, {"family": "Schaefer", "given": "Inga-Marie", "initials": "IM", "orcid": "0000-0001-9710-5500", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8a87f32d6ccf4bfd8947b7ed9531aed7.json"}}, {"family": "Neuberg", "given": "Donna", "initials": "D"}, {"family": "Stone", "given": "Richard M", "initials": "RM"}, {"family": "Bick", "given": "Alexander G", "initials": "AG"}, {"family": "Uddin", "given": "Md Mesbah", "initials": "MM", "orcid": "0000-0003-1846-0411", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/42f1ac7010c34ba997a3fd9e56c6a56a.json"}}, {"family": "Griffin", "given": "Gabriel K", "initials": "GK"}, {"family": "Jaiswal", "given": "Siddhartha", "initials": "S", "orcid": "0000-0002-9597-0477", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a1901e08f989434fb01dfa17b0a85470.json"}}, {"family": "Natarajan", "given": "Pradeep", "initials": "P", "orcid": "0000-0001-8402-7435", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fe8bd48c61c047cd8e61c35d9e9ac650.json"}}, {"family": "Nigrovic", "given": "Peter A", "initials": "PA", "orcid": "0000-0002-2126-3702", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/06a54c6610794e30a29945f032c4c6bb.json"}}, {"family": "Rao", "given": "Deepak A", "initials": "DA", "orcid": "0000-0001-9672-7746", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/769f937bc2864984abc0718f548f6265.json"}}, {"family": "Ebert", "given": "Benjamin L", "initials": "BL", "orcid": "0000-0003-0197-5451", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56e4f1c53a4348e2b0ceb44a38850a17.json"}}], "type": "journal article", "published": "2022-09-08", "journal": {"title": "Blood", "issn": "1528-0020", "volume": "140", "issue": "10", "pages": "1094-1103", "issn-l": "0006-4971"}, "abstract": "Gout is a common inflammatory arthritis caused by precipitation of monosodium urate (MSU) crystals in individuals with hyperuricemia. Acute flares are accompanied by secretion of proinflammatory cytokines, including interleukin-1\u03b2 (IL-1\u03b2). Clonal hematopoiesis of indeterminate potential (CHIP) is an age-related condition predisposing to hematologic cancers and cardiovascular disease. CHIP is associated with elevated IL-1\u03b2, thus we investigated CHIP as a risk factor for gout. To test the clinical association between CHIP and gout, we analyzed whole exome sequencing data from 177 824 individuals in the MGB Biobank (MGBB) and UK Biobank (UKB). In both cohorts, the frequency of gout was higher among individuals with CHIP than without CHIP (MGBB, CHIP with variant allele fraction [VAF] \u22652%: odds ratio [OR], 1.69; 95% CI, 1.09-2.61; P = .0189; UKB, CHIP with VAF \u226510%: OR, 1.25; 95% CI, 1.05-1.50; P = .0133). Moreover, individuals with CHIP and a VAF \u226510% had an increased risk of incident gout (UKB: hazard ratio [HR], 1.28; 95% CI, 1.06-1.55; P = .0107). In murine models of gout pathogenesis, animals with Tet2 knockout hematopoietic cells had exaggerated IL-1\u03b2 secretion and paw edema upon administration of MSU crystals. Tet2 knockout macrophages elaborated higher levels of IL-1\u03b2 in response to MSU crystals in vitro, which was ameliorated through genetic and pharmacologic Nlrp3 inflammasome inhibition. These studies show that TET2-mutant CHIP is associated with an increased risk of gout in humans and that MSU crystals lead to elevated IL-1\u03b2 levels in Tet2 knockout murine models. We identify CHIP as an amplifier of NLRP3-dependent inflammatory responses to MSU crystals in patients with gout.", "doi": "10.1182/blood.2022015384", "pmid": "35714308", "labels": {"Abhishek Niroula": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC9461470"}, {"db": "pii", "key": "S0006-4971(22)00804-7"}], "notes": [], "created": "2023-11-20T11:36:20.793Z", "modified": "2023-11-20T11:36:21.146Z"}, {"entity": "publication", "iuid": "ce5cd7274182457aad1e78b0d07a906c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ce5cd7274182457aad1e78b0d07a906c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ce5cd7274182457aad1e78b0d07a906c"}}, "title": "Arginine catabolism metabolites and atrial fibrillation or heart failure risk: 2 case-control studies within the Prevenci\u00f3n con Dieta Mediterr\u00e1nea (PREDIMED) trial.", "authors": [{"family": "Goni", "given": "Leticia", "initials": "L", "orcid": "0000-0002-5479-2045", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3da50ff1e8524021aa309722c93e25ae.json"}}, {"family": "Razquin", "given": "Cristina", "initials": "C"}, {"family": "Toledo", "given": "Estefan\u00eda", "initials": "E", "orcid": "0000-0002-6263-4434", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d04ea61c7230463ab64e537f97fb07fe.json"}}, {"family": "Guasch-Ferr\u00e9", "given": "Marta", "initials": "M", "orcid": "0000-0001-8525-1404", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2d1a49f5df124e96a9285b43d628cee9.json"}}, {"family": "Clish", "given": "Clary B", "initials": "CB"}, {"family": "Babio", "given": "Nancy", "initials": "N", "orcid": "0000-0003-3527-5277", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d0277dede92a4923b41087d900dff1c5.json"}}, {"family": "Wittenbecher", "given": "Clemens", "initials": "C"}, {"family": "Atzeni", "given": "Alessandro", "initials": "A"}, {"family": "Li", "given": "Jun", "initials": "J", "orcid": "0000-0003-3519-8638", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/77d0c8cac07b47228b383aa851382852.json"}}, {"family": "Liang", "given": "Liming", "initials": "L"}, {"family": "Dennis", "given": "Courtney", "initials": "C"}, {"family": "Alonso-G\u00f3mez", "given": "\u00c1ngel", "initials": "\u00c1"}, {"family": "Fit\u00f3", "given": "Montserrat", "initials": "M"}, {"family": "Corella", "given": "Dolores", "initials": "D"}, {"family": "G\u00f3mez-Gracia", "given": "Enrique", "initials": "E"}, {"family": "Estruch", "given": "Ram\u00f3n", "initials": "R"}, {"family": "Fiol", "given": "Miquel", "initials": "M", "orcid": "0000-0002-5370-1391", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a818c11a8ce9483ab18d73ec27bb248b.json"}}, {"family": "Lapetra", "given": "Jose", "initials": "J"}, {"family": "Serra-Majem", "given": "Lluis", "initials": "L"}, {"family": "Ros", "given": "Emilio", "initials": "E"}, {"family": "Ar\u00f3s", "given": "Fernando", "initials": "F"}, {"family": "Salas-Salvad\u00f3", "given": "Jordi", "initials": "J"}, {"family": "Hu", "given": "Frank B", "initials": "FB"}, {"family": "Mart\u00ednez-Gonz\u00e1lez", "given": "Miguel A", "initials": "MA"}, {"family": "Ruiz-Canela", "given": "Miguel", "initials": "M", "orcid": "0000-0002-7684-2787", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4f947f7399034daeb6778d0781b6e789.json"}}], "type": "journal article", "published": "2022-09-02", "journal": {"title": "Am. J. Clin. Nutr.", "issn": "1938-3207", "volume": "116", "issue": "3", "pages": "653-662", "issn-l": "0002-9165"}, "abstract": "Arginine-derived metabolites are involved in oxidative and inflammatory processes related to endothelial functions and cardiovascular risks.\n\nWe prospectively examined the associations of arginine catabolism metabolites with the risks of atrial fibrillation (AF) or heart failure (HF), and evaluated the potential modifications of these associations through Mediterranean diet (MedDiet) interventions in a large, primary-prevention trial.\n\nTwo nested, matched, case-control studies were designed within the Prevenci\u00f3n con Dieta Mediterr\u00e1nea (PREDIMED) trial. We selected 509 incident cases and 547 matched controls for the AF case-control study and 326 cases and 402 matched controls for the HF case-control study using incidence density sampling. Fasting blood samples were collected at baseline and arginine catabolism metabolites were measured using LC-tandem MS. Multivariable conditional logistic regression models were applied to test the associations between the metabolites and incident AF or HF. Interactions between metabolites and intervention groups (MedDiet groups compared with control group) were analyzed with the likelihood ratio test.\n\nInverse association with incident AF was observed for arginine (OR per 1 SD, 0.83; 95% CI: 0.73-0.94), whereas a positive association was found for N1-acetylspermidine (OR for Q4 compared with Q1 1.58; 95% CI: 1.13-2.25). For HF, inverse associations were found for arginine (OR per 1 SD, 0.82; 95% CI: 0.69-0.97) and homoarginine (OR per 1 SD, 0.81; 95% CI: 0.68-0.96), and positive associations were found for the asymmetric dimethylarginine (ADMA) and symmetric dimethlyarginine (SDMA) ratio (OR per 1 SD, 1.19; 95% CI: 1.02-1.41), N1-acetylspermidine (OR per 1 SD, 1.34; 95% CI: 1.12-1.60), and diacetylspermine (OR per 1 SD, 1.20; 95% CI: 1.02-1.41). In the stratified analysis according to the dietary intervention, the lower HF risk associated with arginine was restricted to participants in the MedDiet groups (P-interaction = 0.044).\n\nOur results suggest that arginine catabolism metabolites could be involved in AF and HF. Interventions with the MedDiet may contribute to strengthen the inverse association between arginine and the risk of HF. This trial was registered at controlled-trials.com as ISRCTN35739639.", "doi": "10.1093/ajcn/nqac139", "pmid": "35575609", "labels": {"Clemens Wittenbecher": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC9437981"}, {"db": "pii", "key": "S0002-9165(22)00082-X"}], "notes": [], "created": "2025-12-09T13:38:48.076Z", "modified": "2025-12-09T13:38:48.206Z"}, {"entity": "publication", "iuid": "8d1b10d91a224dc490c59a7955057476", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8d1b10d91a224dc490c59a7955057476.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8d1b10d91a224dc490c59a7955057476"}}, "title": "Of problems and opportunities-How to treat and how to not treat crystallographic fragment screening data.", "authors": [{"family": "Weiss", "given": "Manfred S", "initials": "MS", "orcid": "0000-0002-2362-7047", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eb2742d32bf7458b8903369a87c99607.json"}}, {"family": "Wollenhaupt", "given": "Jan", "initials": "J", "orcid": "0000-0002-3418-5213", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/008145e5b0e4416cb338418005b271ae.json"}}, {"family": "Correy", "given": "Galen J", "initials": "GJ", "orcid": "0000-0001-5155-7325", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/31d07fbdc0de4b66a483c9863ac83845.json"}}, {"family": "Fraser", "given": "James S", "initials": "JS", "orcid": "0000-0002-5080-2859", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c95b7a3dcf1545ff87da0c64abdd0f68.json"}}, {"family": "Heine", "given": "Andreas", "initials": "A", "orcid": "0000-0002-5285-4089", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4b6546eddfa248f1a9d67c4f3db5a9f6.json"}}, {"family": "Klebe", "given": "Gerhard", "initials": "G", "orcid": "0000-0002-4913-390X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4d98355820a041dca9521a5db321f3e3.json"}}, {"family": "Krojer", "given": "Tobias", "initials": "T", "orcid": "0000-0003-0661-0814", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/82e5150348ba4db6b9c07b7167532ab7.json"}}, {"family": "Thunissen", "given": "Marjolein", "initials": "M"}, {"family": "Pearce", "given": "Nicholas M", "initials": "NM", "orcid": "0000-0002-6693-8603", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/07d6d5de91cc4120b2bf996ca578a13e.json"}}], "type": "letter", "published": "2022-09-00", "journal": {"title": "Protein Sci.", "issn": "1469-896X", "volume": "31", "issue": "9", "pages": "e4391", "issn-l": "0961-8368"}, "abstract": "In their recent commentary in Protein Science, Jaskolski et al. analyzed three randomly picked diffraction data sets from fragment-screening group depositions from the PDB and, based on that, they claimed that such data are principally problematic. We demonstrate here that if such data are treated properly, none of the proclaimed criticisms persist.", "doi": "10.1002/pro.4391", "pmid": "36040268", "labels": {"Nicholas Pearce": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC9424839"}], "notes": [], "created": "2022-12-05T19:30:45.795Z", "modified": "2022-12-05T19:30:45.970Z"}, {"entity": "publication", "iuid": "e46844fa329545d6be2ff7af18cfbd15", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e46844fa329545d6be2ff7af18cfbd15.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e46844fa329545d6be2ff7af18cfbd15"}}, "title": "Microbial and human transcriptome in vaginal fluid at midgestation: Association with spontaneous preterm delivery.", "authors": [{"family": "Wikstr\u00f6m", "given": "Tove", "initials": "T", "orcid": "0000-0002-4208-8667", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b7afe54efbd4414b8de112df092e5e74.json"}}, {"family": "Abrahamsson", "given": "Sanna", "initials": "S"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Ek", "given": "Joakim", "initials": "J"}, {"family": "Kuusela", "given": "Pihla", "initials": "P"}, {"family": "Rekabdar", "given": "Elham", "initials": "E"}, {"family": "Lindgren", "given": "Peter", "initials": "P"}, {"family": "Wennerholm", "given": "Ulla-Britt", "initials": "UB"}, {"family": "Jacobsson", "given": "Bo", "initials": "B"}, {"family": "Valentin", "given": "Lil", "initials": "L"}, {"family": "Hagberg", "given": "Henrik", "initials": "H"}], "type": "journal article", "published": "2022-09-00", "journal": {"title": "Clin Transl Med", "issn": "2001-1326", "volume": "12", "issue": "9", "pages": "e1023", "issn-l": null}, "abstract": "Intrauterine infection and inflammation caused by microbial transfer from the vagina are believed to be important factors causing spontaneous preterm delivery (PTD). Multiple studies have examined the relationship between the cervicovaginal microbiome and spontaneous PTD with divergent results. Most studies have applied a DNA-based assessment, providing information on the microbial composition but not transcriptional activity. A transcriptomic approach was applied to investigate differences in the active vaginal microbiome and human transcriptome at midgestation between women delivering spontaneously preterm versus those delivering at term.\n\nVaginal swabs were collected in women with a singleton pregnancy at 18 + 0 to 20 + 6 gestational weeks. For each case of spontaneous PTD (delivery <37 + 0 weeks) two term controls were randomized (39 + 0 to 40 + 6 weeks). Vaginal specimens were subject to sequencing of both human and microbial RNA. Microbial reads were taxonomically classified using Kraken2 and RefSeq as a reference. Statistical analyses were performed using DESeq2. GSEA and HUMAnN3 were used for pathway analyses.\n\nWe found 17 human genes to be differentially expressed (false discovery rate, FDR < 0.05) in the preterm group (n = 48) compared to the term group (n = 96). Gene expression of kallikrein-2 (KLK2), KLK3 and four isoforms of metallothioneins 1 (MT1s) was higher in the preterm group (FDR < 0.05). We found 11 individual bacterial species to be differentially expressed (FDR < 0.05), most with a low occurrence. No statistically significant differences in bacterial load, diversity or microbial community state types were found between the groups.\n\nIn our mainly white population, primarily bacterial species of low occurrence were differentially expressed at midgestation in women who delivered preterm versus at term. However, the expression of specific human transcripts including KLK2, KLK3 and several isoforms of MT1s was higher in preterm cases. This is of interest, because these genes may be involved in critical inflammatory pathways associated with spontaneous PTD.", "doi": "10.1002/ctm2.1023", "pmid": "36103557", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pmc", "key": "PMC9473488"}], "notes": [], "created": "2022-11-08T09:24:46.370Z", "modified": "2022-11-08T09:26:55.355Z"}, {"entity": "publication", "iuid": "d3ee01de6c5148f580fcdb20128618a5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d3ee01de6c5148f580fcdb20128618a5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d3ee01de6c5148f580fcdb20128618a5"}}, "title": "Laboratory Misidentifications Resulting from Taxonomic Changes to Bacillus cereus Group Species, 2018-2022.", "authors": [{"family": "Carroll", "given": "Laura M", "initials": "LM"}, {"family": "Matle", "given": "Itumeleng", "initials": "I"}, {"family": "Kovac", "given": "Jasna", "initials": "J"}, {"family": "Cheng", "given": "Rachel A", "initials": "RA"}, {"family": "Wiedmann", "given": "Martin", "initials": "M"}], "type": "journal article", "published": "2022-09-00", "journal": {"title": "Emerg Infect Dis", "issn": "1080-6059", "volume": "28", "issue": "9", "pages": "1877-1881", "issn-l": null}, "abstract": "Whole-genome sequencing (WGS) is being applied increasingly to Bacillus cereus group species; however, misinterpretation of WGS results may have severe consequences. We report 3 cases, 1 of which was an outbreak, in which misinterpretation of B. cereus group WGS results hindered communication within public health and industrial laboratories.", "doi": "10.3201/eid2809.220293", "pmid": "35997597", "labels": {"DDLS Fellow": null, "Laura Carroll": null}, "xrefs": [{"db": "pmc", "key": "PMC9423903"}], "notes": [], "created": "2023-05-13T11:52:30.376Z", "modified": "2025-03-18T17:29:47.579Z"}, {"entity": "publication", "iuid": "be8d7ba75691414f8d21e79057012597", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/be8d7ba75691414f8d21e79057012597.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/be8d7ba75691414f8d21e79057012597"}}, "title": "Discovery of therapeutic agents targeting PKLR for NAFLD using drug repositioning.", "authors": [{"family": "Zhang", "given": "Cheng", "initials": "C"}, {"family": "Shi", "given": "Mengnan", "initials": "M"}, {"family": "Kim", "given": "Woonghee", "initials": "W"}, {"family": "Arif", "given": "Muhammad", "initials": "M"}, {"family": "Klevstig", "given": "Martina", "initials": "M"}, {"family": "Li", "given": "Xiangyu", "initials": "X"}, {"family": "Yang", "given": "Hong", "initials": "H"}, {"family": "Bayram", "given": "Cemil", "initials": "C"}, {"family": "Bolat", "given": "Ismail", "initials": "I"}, {"family": "Tozlu", "given": "\u00d6zlem \u00d6zdemir", "initials": "\u00d6\u00d6"}, {"family": "Hac\u0131muftuoglu", "given": "Ahmet", "initials": "A"}, {"family": "Y\u0131ld\u0131r\u0131m", "given": "Serkan", "initials": "S"}, {"family": "Sebhaoui", "given": "Jihad", "initials": "J"}, {"family": "Iqbal", "given": "Shazia", "initials": "S"}, {"family": "Wei", "given": "Yongjun", "initials": "Y"}, {"family": "Shi", "given": "Xiaojing", "initials": "X"}, {"family": "Nielsen", "given": "Jens", "initials": "J"}, {"family": "Turkez", "given": "Hasan", "initials": "H"}, {"family": "Uhlen", "given": "Mathias", "initials": "M"}, {"family": "Boren", "given": "Jan", "initials": "J"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}], "type": "journal article", "published": "2022-09-00", "journal": {"title": "EBioMedicine", "issn": "2352-3964", "volume": "83", "pages": "104214", "issn-l": "2352-3964"}, "abstract": "Non-alcoholic fatty liver disease (NAFLD) encompasses a wide spectrum of liver pathologies. However, no medical treatment has been approved for the treatment of NAFLD. In our previous study, we found that PKLR could be a potential target for treatment of NALFD. Here, we investigated the effect of PKLR in in vivo model and performed drug repositioning to identify a drug candidate for treatment of NAFLD.\n\nTissue samples from liver, muscle, white adipose and heart were obtained from control and PKLR knockout mice fed with chow and high sucrose diets. Lipidomics as well as transcriptomics analyses were conducted using these tissue samples. In addition, a computational drug repositioning analysis was performed and drug candidates were identified. The drug candidates were both tested in in vitro and in vivo models to evaluate their toxicity and efficacy.\n\nThe Pklr KO reversed the increased hepatic triglyceride level in mice fed with high sucrose diet and partly recovered the transcriptomic changes in the liver as well as in other three tissues. Both liver and white adipose tissues exhibited dysregulated circadian transcriptomic profiles, and these dysregulations were reversed by hepatic knockout of Pklr. In addition, 10 small molecule drug candidates were identified as potential inhibitor of PKLR using our drug repositioning pipeline, and two of them significantly inhibited both the PKLR expression and triglyceride level in in vitro model. Finally, the two selected small molecule drugs were evaluated in in vivo rat models and we found that these drugs attenuate the hepatic steatosis without side effect on other tissues.\n\nIn conclusion, our study provided biological insights about the critical role of PKLR in NAFLD progression and proposed a treatment strategy for NAFLD patients, which has been validated in preclinical studies.\n\nScandiEdge Therapeutics and Knut and Alice Wallenberg Foundation.", "doi": "10.1016/j.ebiom.2022.104214", "pmid": "35988463", "labels": {"Adil Mardinoglu": "", "SciLifeLab Fellow": "", "DDLS Fellow": "", "Muhammad Arif": ""}, "xrefs": [{"db": "pmc", "key": "PMC9420484"}, {"db": "pii", "key": "S2352-3964(22)00396-6"}], "notes": [], "created": "2023-12-04T14:58:13.747Z", "modified": "2026-09-23T10:35:34.609Z"}, {"entity": "publication", "iuid": "db6047a9398b4cb1abeed3e8c81c9fc1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/db6047a9398b4cb1abeed3e8c81c9fc1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/db6047a9398b4cb1abeed3e8c81c9fc1"}}, "title": "Mesowestern Blot: Simultaneous Analysis of Hundreds of Submicroliter Lysates.", "authors": [{"family": "Zadeh", "given": "Cameron O", "initials": "CO"}, {"family": "Huggins", "given": "Jonah R", "initials": "JR", "orcid": "0000-0001-7468-4626", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7cba794166d94144af105b8894423e35.json"}}, {"family": "Sarmah", "given": "Deepraj", "initials": "D"}, {"family": "Westbury", "given": "Baylee C", "initials": "BC"}, {"family": "Interiano", "given": "William R", "initials": "WR"}, {"family": "Jordan", "given": "Micah C", "initials": "MC"}, {"family": "Phillips", "given": "S Ashley", "initials": "SA"}, {"family": "Dodd", "given": "William B", "initials": "WB"}, {"family": "Meredith", "given": "Wesley O", "initials": "WO"}, {"family": "Harold", "given": "Nicholas J", "initials": "NJ"}, {"family": "Erdem", "given": "Cemal", "initials": "C", "orcid": "0000-0003-3663-3646", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f71b5af589264614a52eefa8baba3132.json"}}, {"family": "Birtwistle", "given": "Marc R", "initials": "MR", "orcid": "0000-0002-0341-0705", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/df52e09a2f984f10833bda7b554b1a22.json"}}], "type": "journal article", "published": "2022-08-23", "journal": {"title": "ACS Omega", "issn": "2470-1343", "volume": "7", "issue": "33", "pages": "28912-28923", "issn-l": "2470-1343"}, "abstract": "Western blotting is a widely used technique for molecular-weight-resolved analysis of proteins and their posttranslational modifications, but high-throughput implementations of the standard slab gel arrangement are scarce. The previously developed Microwestern requires a piezoelectric pipetting instrument, which is not available for many labs. Here, we report the Mesowestern blot, which uses a 3D-printable gel casting mold to enable high-throughput Western blotting without piezoelectric pipetting and is compatible with the standard sample preparation and small (\u223c1 \u03bcL) sample sizes. The main tradeoffs are reduced molecular weight resolution and higher sample-to-sample CV, making it suitable for qualitative screening applications. The casted polyacrylamide gel contains 336, \u223c0.5 \u03bcL micropipette-loadable sample wells arranged within a standard microplate footprint. Polyacrylamide % can be altered to change molecular weight resolution profiles. Proof-of-concept experiments using both infrared-fluorescent molecular weight protein ladder and cell lysate (RIPA buffer) demonstrate that the protein loaded in Mesowestern gels is amenable to the standard Western blotting steps. The main difference between Mesowestern and traditional Western is that semidry horizontal instead of immersed vertical gel electrophoresis is used. The linear range of detection is at least 32-fold, and at least \u223c500 attomols of \u03b2-actin can be detected (\u223c29 ng of total protein from mammalian cell lysates: \u223c100-300 cells). Because the gel mold is 3D-printable, users with access to additive manufacturing cores have significant design freedom for custom layouts. We expect that the technique could be easily adopted by any typical cell and molecular biology laboratory already performing Western blots.", "doi": "10.1021/acsomega.2c02201", "pmid": "36033686", "labels": {"DDLS Fellow": null, "Cemal Erdem": null}, "xrefs": [{"db": "pmc", "key": "PMC9404195"}], "notes": [], "created": "2023-10-27T08:53:44.872Z", "modified": "2023-10-27T08:53:44.987Z"}, {"entity": "publication", "iuid": "8143db0e550e4134b2ef07c0a4e06d6a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8143db0e550e4134b2ef07c0a4e06d6a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8143db0e550e4134b2ef07c0a4e06d6a"}}, "title": "Reclassifying tumour cell cycle activity in terms of its tissue of origin.", "authors": [{"family": "Lundberg", "given": "Arian", "initials": "A", "orcid": "0000-0002-6630-2787", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/baa2c7c8963840bfb6a22d7c5cfe35f9.json"}}, {"family": "Yi", "given": "Joan Jong Jing", "initials": "JJJ", "orcid": "0000-0002-4735-301X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6e2eda77a9e04bef8400ddb96fdba325.json"}}, {"family": "Lindstr\u00f6m", "given": "Linda S", "initials": "LS"}, {"family": "Tobin", "given": "Nicholas P", "initials": "NP", "orcid": "0000-0003-2343-9772", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b9aa223903694c8399b89adc231facce.json"}}], "type": "journal article", "published": "2022-08-20", "journal": {"title": "NPJ Precis Oncol", "issn": "2397-768X", "volume": "6", "issue": "1", "pages": "59", "issn-l": null}, "abstract": "Genomic alterations resulting in loss of control over the cell cycle is a fundamental hallmark of human malignancies. Whilst pan-cancer studies have broadly assessed tumour genomics and their impact on oncogenic pathways, analyses taking the baseline signalling levels in normal tissue into account are lacking. To this end, we aimed to reclassify the cell cycle activity of tumours in terms of their tissue of origin and determine if any common DNA mutations, chromosome arm-level changes or signalling pathways contribute to an increase in baseline corrected cell cycle activity. Combining normal tissue and pan-cancer data from over 13,000 samples we demonstrate that tumours of gynaecological origin show the highest levels of corrected cell cycle activity, partially owing to hormonal signalling and gene expression changes. We also show that normal and tumour tissues can be separated into groups (quadrants) of low/high cell cycle activity and propose the hypothesis of an upper limit on these activity levels in tumours.", "doi": "10.1038/s41698-022-00302-7", "pmid": "35987928", "labels": {"DDLS Fellow": null, "Arian Lundberg": null}, "xrefs": [{"db": "pmc", "key": "PMC9392789"}, {"db": "pii", "key": "10.1038/s41698-022-00302-7"}], "notes": [], "created": "2025-11-14T07:51:47.320Z", "modified": "2026-01-03T12:21:55.200Z"}, {"entity": "publication", "iuid": "bd81d8a30a474e5baf75fe9ed2d55fca", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/bd81d8a30a474e5baf75fe9ed2d55fca.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/bd81d8a30a474e5baf75fe9ed2d55fca"}}, "title": "Evolutionary consequences of genomic deletions and insertions in the woolly mammoth genome.", "authors": [{"family": "van der Valk", "given": "Tom", "initials": "T"}, {"family": "Dehasque", "given": "Marianne", "initials": "M"}, {"family": "Chac\u00f3n-Duque", "given": "J Camilo", "initials": "JC"}, {"family": "Oskolkov", "given": "Nikolay", "initials": "N"}, {"family": "Vartanyan", "given": "Sergey", "initials": "S"}, {"family": "Heintzman", "given": "Peter D", "initials": "PD"}, {"family": "Pe\u010dnerov\u00e1", "given": "Patr\u00edcia", "initials": "P"}, {"family": "D\u00edez-Del-Molino", "given": "David", "initials": "D"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L"}], "type": "journal article", "published": "2022-08-19", "journal": {"title": "iScience", "issn": "2589-0042", "volume": "25", "issue": "8", "pages": "104826", "issn-l": null}, "abstract": "Woolly mammoths had a set of adaptations that enabled them to thrive in the Arctic environment. Many mammoth-specific single nucleotide polymorphisms (SNPs) responsible for unique mammoth traits have been previously identified from ancient genomes. However, a multitude of other genetic variants likely contributed to woolly mammoth evolution. In this study, we sequenced two woolly mammoth genomes and combined these with previously sequenced mammoth and elephant genomes to conduct a survey of mammoth-specific deletions and indels. We find that deletions are highly enriched in non-coding regions, suggesting selection against structural variants that affect protein sequences. Nonetheless, at least 87 woolly mammoth genes contain deletions or indels that modify the coding sequence, including genes involved in skeletal morphology and hair growth. These results suggest that deletions and indels contributed to the unique phenotypic adaptations of the woolly mammoth, and were potentially critical to surviving in its natural environment.", "doi": "10.1016/j.isci.2022.104826", "pmid": "35992080", "labels": {"Tom van der Valk": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC9382235"}, {"db": "pii", "key": "S2589-0042(22)01098-7"}], "notes": [], "created": "2022-12-02T13:45:14.097Z", "modified": "2026-09-23T11:17:31.261Z"}, {"entity": "publication", "iuid": "7ec5addeba634921b8f8fd88bc2b6a8f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/7ec5addeba634921b8f8fd88bc2b6a8f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/7ec5addeba634921b8f8fd88bc2b6a8f"}}, "title": "The origin and evolution of open habitats in North America inferred by Bayesian deep learning models.", "authors": [{"family": "Andermann", "given": "Tobias", "initials": "T", "orcid": "0000-0002-0932-1623", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dfff478dfcfc43ddbd40bb1bafbcb0a7.json"}}, {"family": "Str\u00f6mberg", "given": "Caroline A E", "initials": "CAE"}, {"family": "Antonelli", "given": "Alexandre", "initials": "A", "orcid": "0000-0003-1842-9297", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1de98df1bb2140fc9666507cb2fb5614.json"}}, {"family": "Silvestro", "given": "Daniele", "initials": "D", "orcid": "0000-0003-0100-0961", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4870742190514c5b83450c567c11398a.json"}}], "type": "journal article", "published": "2022-08-17", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "13", "issue": "1", "pages": "4833", "issn-l": "2041-1723"}, "abstract": "Some of the most extensive terrestrial biomes today consist of open vegetation, including temperate grasslands and tropical savannas. These biomes originated relatively recently in Earth's history, likely replacing forested habitats in the second half of the Cenozoic. However, the timing of their origination and expansion remains disputed. Here, we present a Bayesian deep learning model that utilizes information from fossil evidence, geologic models, and paleoclimatic proxies to reconstruct paleovegetation, placing the emergence of open habitats in North America at around 23 million years ago. By the time of the onset of the Quaternary glacial cycles, open habitats were covering more than 30% of North America and were expanding at peak rates, to eventually become the most prominent natural vegetation type today. Our entirely data-driven approach demonstrates how deep learning can harness unexplored signals from complex data sets to provide insights into the evolution of Earth's biomes in time and space.", "doi": "10.1038/s41467-022-32300-5", "pmid": "35977931", "labels": {"Tobias Andermann": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC9385654"}, {"db": "pii", "key": "10.1038/s41467-022-32300-5"}], "notes": [], "created": "2022-11-11T09:08:46.701Z", "modified": "2026-09-23T10:40:27.754Z"}, {"entity": "publication", "iuid": "cf107b51cc954216b3016222042265e8", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/cf107b51cc954216b3016222042265e8.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/cf107b51cc954216b3016222042265e8"}}, "title": "Multi-omics personalized network analyses highlight progressive disruption of central metabolism associated with COVID-19 severity.", "authors": [{"family": "Ambikan", "given": "Anoop T", "initials": "AT"}, {"family": "Yang", "given": "Hong", "initials": "H"}, {"family": "Krishnan", "given": "Shuba", "initials": "S"}, {"family": "Svensson Akusj\u00e4rvi", "given": "Sara", "initials": "S"}, {"family": "Gupta", "given": "Soham", "initials": "S"}, {"family": "Lourda", "given": "Magda", "initials": "M"}, {"family": "Sperk", "given": "Maike", "initials": "M"}, {"family": "Arif", "given": "Muhammad", "initials": "M"}, {"family": "Zhang", "given": "Cheng", "initials": "C"}, {"family": "Nordqvist", "given": "Hampus", "initials": "H"}, {"family": "Ponnan", "given": "Sivasankaran Munusamy", "initials": "SM"}, {"family": "S\u00f6nnerborg", "given": "Anders", "initials": "A"}, {"family": "Treutiger", "given": "Carl Johan", "initials": "CJ"}, {"family": "O'Mahony", "given": "Liam", "initials": "L"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Benfeitas", "given": "Rui", "initials": "R"}, {"family": "Neogi", "given": "Ujjwal", "initials": "U"}], "type": "journal article", "published": "2022-08-17", "journal": {"title": "Cell Syst", "issn": "2405-4720", "volume": "13", "issue": "8", "pages": "665-681.e4", "issn-l": null}, "abstract": "The clinical outcome and disease severity in coronavirus disease 2019 (COVID-19) are heterogeneous, and the progression or fatality of the disease cannot be explained by a single factor like age or comorbidities. In this study, we used system-wide network-based system biology analysis using whole blood RNA sequencing, immunophenotyping by flow cytometry, plasma metabolomics, and single-cell-type metabolomics of monocytes to identify the potential determinants of COVID-19 severity at personalized and group levels. Digital cell quantification and immunophenotyping of the mononuclear phagocytes indicated a substantial role in coordinating the immune cells that mediate COVID-19 severity. Stratum-specific and personalized genome-scale metabolic modeling indicated monocarboxylate transporter family genes (e.g., SLC16A6), nucleoside transporter genes (e.g., SLC29A1), and metabolites such as \u03b1-ketoglutarate, succinate, malate, and butyrate could play a crucial role in COVID-19 severity. Metabolic perturbations targeting the central metabolic pathway (TCA cycle) can be an alternate treatment strategy in severe COVID-19.", "doi": "10.1016/j.cels.2022.06.006", "pmid": "35933992", "labels": {"Adil Mardinoglu": "", "SciLifeLab Fellow": "", "DDLS Fellow": "", "Muhammad Arif": ""}, "xrefs": [{"db": "pmc", "key": "PMC9263811"}, {"db": "pii", "key": "S2405-4712(22)00276-9"}], "notes": [], "created": "2023-12-04T14:58:16.554Z", "modified": "2026-09-23T08:45:52.035Z"}, {"entity": "publication", "iuid": "6494c4cad1f14a19a28472a8355a7586", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/6494c4cad1f14a19a28472a8355a7586.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/6494c4cad1f14a19a28472a8355a7586"}}, "title": "nQMaker: Estimating Time Nonreversible Amino Acid Substitution Models.", "authors": [{"family": "Dang", "given": "Cuong Cao", "initials": "CC"}, {"family": "Minh", "given": "Bui Quang", "initials": "BQ", "orcid": "0000-0002-5535-6560", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e410aeb274c244cebec7c2aac20a4050.json"}}, {"family": "McShea", "given": "Hanon", "initials": "H"}, {"family": "Masel", "given": "Joanna", "initials": "J", "orcid": "0000-0002-7398-2127", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eed69f257e574f4aa53f59349c3ff384.json"}}, {"family": "James", "given": "Jennifer Eleanor", "initials": "JE"}, {"family": "Vinh", "given": "Le Sy", "initials": "LS"}, {"family": "Lanfear", "given": "Robert", "initials": "R"}], "type": "journal article", "published": "2022-08-10", "journal": {"title": "Syst. Biol.", "issn": "1076-836X", "issn-l": "1063-5157", "volume": "71", "issue": "5", "pages": "1110-1123"}, "abstract": "Amino acid substitution models are a key component in phylogenetic analyses of protein sequences. All commonly used amino acid models available to date are time-reversible, an assumption designed for computational convenience but not for biological reality. Another significant downside to time-reversible models is that they do not allow inference of rooted trees without outgroups. In this article, we introduce a maximum likelihood approach nQMaker, an extension of the recently published QMaker method, that allows the estimation of time nonreversible amino acid substitution models and rooted phylogenetic trees from a set of protein sequence alignments. We show that the nonreversible models estimated with nQMaker are a much better fit to empirical alignments than pre-existing reversible models, across a wide range of data sets including mammals, birds, plants, fungi, and other taxa, and that the improvements in model fit scale with the size of the data set. Notably, for the recently published plant and bird trees, these nonreversible models correctly recovered the commonly estimated root placements with very high-statistical support without the need to use an outgroup. We provide nQMaker as an easy-to-use feature in the IQ-TREE software (http://www.iqtree.org), allowing users to estimate nonreversible models and rooted phylogenies from their own protein data sets. The data sets and scripts used in this article are available at https://doi.org/10.5061/dryad.3tx95x6hx. [amino acid sequence analyses; amino acid substitution models; maximum likelihood model estimation; nonreversible models; phylogenetic inference; reversible models.].", "doi": "10.1093/sysbio/syac007", "pmid": "35139203", "labels": {"Jennifer James": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC9366462"}, {"db": "pii", "key": "6525257"}, {"db": "Dryad", "key": "10.5061/dryad.3tx95x6hx"}], "notes": [], "created": "2024-11-27T09:25:35.329Z", "modified": "2024-11-29T10:50:48.619Z"}, {"entity": "publication", "iuid": "da88b1480524423180d0c9690442bf3a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/da88b1480524423180d0c9690442bf3a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/da88b1480524423180d0c9690442bf3a"}}, "title": "Local molecular and global connectomic contributions to cross-disorder cortical abnormalities.", "authors": [{"family": "Hansen", "given": "Justine Y", "initials": "JY", "orcid": "0000-0003-3142-7480", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cb0fa058a43d40329e061d621d305b06.json"}}, {"family": "Shafiei", "given": "Golia", "initials": "G", "orcid": "0000-0002-2036-5571", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2a248c7067e0487e90ef72448bb7fd1c.json"}}, {"family": "Vogel", "given": "Jacob W", "initials": "JW", "orcid": "0000-0001-6394-9940", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d2ad5af780c245da9b59a8c80a0b00ff.json"}}, {"family": "Smart", "given": "Kelly", "initials": "K", "orcid": "0000-0002-4775-6943", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fcc8495ae5c34c0f8b5be2b2e36ca5c0.json"}}, {"family": "Bearden", "given": "Carrie E", "initials": "CE", "orcid": "0000-0002-8516-923X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/747391903b0148f39f23a2a106995a1c.json"}}, {"family": "Hoogman", "given": "Martine", "initials": "M"}, {"family": "Franke", "given": "Barbara", "initials": "B"}, {"family": "van Rooij", "given": "Daan", "initials": "D"}, {"family": "Buitelaar", "given": "Jan", "initials": "J", "orcid": "0000-0001-8288-7757", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8abc7e5901ea43ccb4f02dd516fab810.json"}}, {"family": "McDonald", "given": "Carrie R", "initials": "CR"}, {"family": "Sisodiya", "given": "Sanjay M", "initials": "SM"}, {"family": "Schmaal", "given": "Lianne", "initials": "L", "orcid": "0000-0001-9822-048X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/601a457b9ac94b1eadefc9e611e0dbc2.json"}}, {"family": "Veltman", "given": "Dick J", "initials": "DJ"}, {"family": "van den Heuvel", "given": "Odile A", "initials": "OA"}, {"family": "Stein", "given": "Dan J", "initials": "DJ", "orcid": "0000-0001-7218-7810", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/25e779a8905d45518b4440bfbb1e8050.json"}}, {"family": "van Erp", "given": "Theo G M", "initials": "TGM", "orcid": "0000-0002-2465-2797", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/496d84f2b39f425aa01f9b68c6cdeacd.json"}}, {"family": "Ching", "given": "Christopher R K", "initials": "CRK"}, {"family": "Andreassen", "given": "Ole A", "initials": "OA"}, {"family": "Hajek", "given": "Tomas", "initials": "T"}, {"family": "Opel", "given": "Nils", "initials": "N"}, {"family": "Modinos", "given": "Gemma", "initials": "G"}, {"family": "Aleman", "given": "Andr\u00e9", "initials": "A"}, {"family": "van der Werf", "given": "Ysbrand", "initials": "Y", "orcid": "0000-0003-2370-9584", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1eb787a7390646228564dfdf834a2f53.json"}}, {"family": "Jahanshad", "given": "Neda", "initials": "N"}, {"family": "Thomopoulos", "given": "Sophia I", "initials": "SI"}, {"family": "Thompson", "given": "Paul M", "initials": "PM"}, {"family": "Carson", "given": "Richard E", "initials": "RE", "orcid": "0000-0002-9338-7966", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ce09a469dbc42feb9631e513a23c19d.json"}}, {"family": "Dagher", "given": "Alain", "initials": "A", "orcid": "0000-0002-0945-5779", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/642c0c268b8a447784b84ad589d0ba7f.json"}}, {"family": "Misic", "given": "Bratislav", "initials": "B", "orcid": "0000-0003-0307-2862", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b6cba1b095bd43b2b9a44cbd57fac573.json"}}], "type": "journal article", "published": "2022-08-10", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "13", "issue": "1", "pages": "4682"}, "abstract": "Numerous brain disorders demonstrate structural brain abnormalities, which are thought to arise from molecular perturbations or connectome miswiring. The unique and shared contributions of these molecular and connectomic vulnerabilities to brain disorders remain unknown, and has yet to be studied in a single multi-disorder framework. Using MRI morphometry from the ENIGMA consortium, we construct maps of cortical abnormalities for thirteen neurodevelopmental, neurological, and psychiatric disorders from N = 21,000 participants and N = 26,000 controls, collected using a harmonised processing protocol. We systematically compare cortical maps to multiple micro-architectural measures, including gene expression, neurotransmitter density, metabolism, and myelination (molecular vulnerability), as well as global connectomic measures including number of connections, centrality, and connection diversity (connectomic vulnerability). We find a relationship between molecular vulnerability and white-matter architecture that drives cortical disorder profiles. Local attributes, particularly neurotransmitter receptor profiles, constitute the best predictors of both disorder-specific cortical morphology and cross-disorder similarity. Finally, we find that cross-disorder abnormalities are consistently subtended by a small subset of network epicentres in bilateral sensory-motor, inferior temporal lobe, precuneus, and superior parietal cortex. Collectively, our results highlight how local molecular attributes and global connectivity jointly shape cross-disorder cortical abnormalities.", "doi": "10.1038/s41467-022-32420-y", "pmid": "35948562", "labels": {"Jacob W Vogel": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC9365855"}, {"db": "pii", "key": "10.1038/s41467-022-32420-y"}], "notes": [], "created": "2023-05-28T17:54:14.361Z", "modified": "2023-11-29T06:39:44.700Z"}, {"entity": "publication", "iuid": "5f5c21f7e3234bf48653afca410eb85f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5f5c21f7e3234bf48653afca410eb85f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5f5c21f7e3234bf48653afca410eb85f"}}, "title": "Genome-wide single cell annotation of the human protein-coding genes", "authors": [{"family": "Karlsson", "given": "Max", "initials": "M", "orcid": "0000-0002-7000-4416", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b93284f942e44f1086616357d77267c3.json"}}, {"family": "\u00c1lvez", "given": "Mar\u00eda Bueno", "initials": "MB", "orcid": "0000-0002-2669-7796", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a7d09e4780a445b9b432d494c76d07e8.json"}}, {"family": "Shi", "given": "Mengnan", "initials": "M", "orcid": "0000-0001-8643-5846", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/642e9296ea7645848f1a28f619447231.json"}}, {"family": "M\u00e9ar", "given": "Loren", "initials": "L", "orcid": "0000-0001-9333-0110", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0dcfbca8ff5446ef9d6d219f23480e0c.json"}}, {"family": "Schutten", "given": "Rutger", "initials": "R", "orcid": "0000-0001-8787-8868", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/770756518b8d49d58ce15957b07c8b46.json"}}, {"family": "Hikmet", "given": "Feria", "initials": "F", "orcid": "0000-0002-3750-9308", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0193c8f793be4446827f92db9871e2a7.json"}}, {"family": "Digre", "given": "Andreas", "initials": "A", "orcid": "0000-0003-1145-6700", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3deb03dd3c21410282f4a414d6c394be.json"}}, {"family": "Katona", "given": "Borbala", "initials": "B", "orcid": "0000-0003-2431-5288", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/19828108d9bf441ba5ba99e3e00327c1.json"}}, {"family": "Vuu", "given": "Jimmy", "initials": "J"}, {"family": "Bosic", "given": "Martina", "initials": "M", "orcid": "0000-0001-7113-2834", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5d1642462dcc43469933afe00c81305b.json"}}, {"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E", "orcid": "0000-0002-0327-7377", "researcher": {"href": 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"initials": "M"}, {"family": "Johansson", "given": "Fredric", "initials": "F", "orcid": "0000-0001-5160-9543", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/88e81d055b6f4c23852dfa7768e62c99.json"}}, {"family": "Mulder", "given": "Jan", "initials": "J", "orcid": "0000-0003-3717-5018", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/40ed8170792444b491519e499d51c434.json"}}, {"family": "H\u00f6kfelt", "given": "Tomas", "initials": "T", "orcid": "0000-0002-3587-0116", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3c3a72e637e24e79abaf263ce5a23821.json"}}, {"family": "Luo", "given": "Younglun", "initials": "Y", "orcid": "0000-0002-0007-7759", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f0283cb6c284428f906b0d03fda62a1e.json"}}, {"family": "Butler", "given": "Lynn", "initials": "L", "orcid": "0000-0002-2352-8217", "researcher": {"href": 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"initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f46e4161be08458994efddb75ed75874.json"}}, {"family": "Lindskog", "given": "Cecilia", "initials": "C", "orcid": "0000-0001-5611-1015", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/21610a810a87459c962d6da3f2ad38ad.json"}}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/abbbf8193d5a4376a5c726768d039439.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ea446aa574042a295d5f69437402f76.json"}}], "type": "posted-content", "published": "2022-08-04", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2022.08.03.502627", "pmid": null, "labels": {"SciLifeLab Fellow": "", "Fredrik Edfors": "", "DDLS Fellow": "", "Adil Mardinoglu": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T10:12:50.664Z", "modified": "2026-09-23T14:34:07.318Z"}, {"entity": "publication", "iuid": "09ce71f3c3984e3da160fbdb914547d7", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/09ce71f3c3984e3da160fbdb914547d7.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/09ce71f3c3984e3da160fbdb914547d7"}}, "title": "Recent and local diversification of Central American understorey palms", "authors": [{"family": "Cano", "given": "\u00c1ngela", "initials": "\u00c1", "orcid": "0000-0002-5090-7730", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/879568c65e434f65a288a6df9c7f6865.json"}}, {"family": "Stauffer", "given": "Fred W", "initials": "FW"}, {"family": "Andermann", "given": "Tobias", "initials": "T", "orcid": "0000-0002-0932-1623", "researcher": {"href": 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"0000-0003-2021-114X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6e64434c1ab84d8da6225a71a8c59548.json"}}, {"family": "Antonelli", "given": "Alexandre", "initials": "A", "orcid": "0000-0003-1842-9297", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1de98df1bb2140fc9666507cb2fb5614.json"}}], "type": "journal-article", "published": "2022-08-00", "journal": {"title": "Global Ecol. Biogeogr.", "issn": "1466-822X", "volume": "31", "issue": "8", "pages": "1513-1525", "issn-l": null}, "abstract": null, "doi": "10.1111/geb.13521", "pmid": null, "labels": {"Tobias Andermann": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2022-11-11T09:10:42.303Z", "modified": "2025-12-04T16:58:22.484Z"}, {"entity": "publication", "iuid": "df293d53882b4896bf5c0e2b9fc40e8a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/df293d53882b4896bf5c0e2b9fc40e8a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/df293d53882b4896bf5c0e2b9fc40e8a"}}, "title": "Author Correction: Spatiotemporal dissection of the cell cycle with single-cell proteogenomics.", "authors": [{"family": "Mahdessian", "given": "Diana", "initials": "D"}, {"family": "Cesnik", "given": "Anthony J", "initials": "AJ", "orcid": "0000-0002-5326-7134", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0fda549f3795457fb60ec3372b98e2d5.json"}}, {"family": "Gnann", "given": "Christian", "initials": "C"}, {"family": "Danielsson", "given": "Frida", "initials": "F"}, {"family": "Stenstr\u00f6m", "given": "Lovisa", "initials": "L"}, {"family": "Arif", "given": "Muhammad", "initials": "M", "orcid": "0000-0003-2261-0881", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c8ffc9889ace44e3b992816601b817e2.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f46e4161be08458994efddb75ed75874.json"}}, {"family": "Le", "given": "Trang", "initials": "T"}, {"family": "Johansson", "given": "Fredric", "initials": "F", "orcid": "0000-0001-5160-9543", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/88e81d055b6f4c23852dfa7768e62c99.json"}}, {"family": "Schutten", "given": "Rutger", "initials": "R"}, {"family": "B\u00e4ckstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Axelsson", "given": "Ulrika", "initials": "U"}, {"family": "Thul", "given": "Peter", "initials": "P", "orcid": "0000-0002-6107-1465", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/af9dad977d4649bbbb883a9836dade94.json"}}, {"family": "Cho", "given": "Nathan H", "initials": "NH"}, {"family": "Carja", "given": "Oana", "initials": "O"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ea446aa574042a295d5f69437402f76.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Stadler", "given": "Charlotte", "initials": "C"}, {"family": "Lindskog", "given": "Cecilia", "initials": "C", "orcid": "0000-0001-5611-1015", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/21610a810a87459c962d6da3f2ad38ad.json"}}, {"family": "Ayoglu", "given": "Burcu", "initials": "B", "orcid": "0000-0001-7843-2960", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4d75c3ce33814d2b961aef643f0d7f0c.json"}}, {"family": "Leonetti", "given": "Manuel D", "initials": "MD"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9f5294424542413c9ba4432c839c2b63.json"}}, {"family": "Sullivan", "given": "Devin P", "initials": "DP"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb07e6d0122c4528a927c1fe922e3bc8.json"}}], "type": "published erratum", "published": "2022-08-00", "journal": {"title": "Nature", "issn": "1476-4687", "volume": "608", "issue": "7924", "pages": "E32", "issn-l": "0028-0836"}, "abstract": null, "doi": "10.1038/s41586-022-05180-4", "pmid": "35931766", "labels": {"Adil Mardinoglu": "", "SciLifeLab Fellow": "", "DDLS Fellow": "", "Muhammad Arif": ""}, "xrefs": [{"db": "pii", "key": "10.1038/s41586-022-05180-4"}], "notes": [], "created": "2023-12-04T14:58:17.819Z", "modified": "2026-09-23T14:46:27.941Z"}, {"entity": "publication", "iuid": "2646bb2aa5b44951a4c1e84944d4efa5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/2646bb2aa5b44951a4c1e84944d4efa5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/2646bb2aa5b44951a4c1e84944d4efa5"}}, "title": "Strains Associated with Two 2020 Welder Anthrax Cases in the United States Belong to Separate Lineages within Bacillus cereus sensu lato.", "authors": [{"family": "Carroll", "given": "Laura M", "initials": "LM"}, {"family": "Marston", "given": "Chung K", "initials": "CK"}, {"family": "Kolton", "given": "Cari B", "initials": "CB"}, {"family": "Gulvik", "given": "Christopher A", "initials": "CA"}, {"family": "Gee", "given": "Jay E", "initials": "JE", "orcid": "0000-0003-4308-1659", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7dfdb82a97f64e8480e7fc6d5f1b790b.json"}}, {"family": "Weiner", "given": "Zachary P", "initials": "ZP"}, {"family": "Kovac", "given": "Jasna", "initials": "J", "orcid": "0000-0002-9465-4552", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d18e6f5bd24644e18030b59391d1a755.json"}}], "type": "journal article", "published": "2022-07-29", "journal": {"title": "Pathogens", "issn": "2076-0817", "volume": "11", "issue": "8", "issn-l": null}, "abstract": "Anthrax-causing members of Bacillus cereus sensu lato (s.l.) pose a serious threat to public health. While most anthrax-causing strains resemble B. anthracis phenotypically, rare cases of anthrax-like illness caused by strains resembling \"B. cereus\" have been reported. Here, whole-genome sequencing was used to characterize three B. cereus s.l. isolates associated with two 2020 welder anthrax cases in the United States, which resembled \"B. cereus\" phenotypically. Comparison of the three genomes sequenced here to all publicly available, high-quality B. cereus s.l. genomes (n = 2890 total genomes) demonstrated that genomes associated with each case effectively belonged to separate species at the conventional 95% average nucleotide identity prokaryotic species threshold. Two PubMLST sequence type 78 (ST78) genomes affiliated with a case in Louisiana were most closely related to B. tropicus and possessed genes encoding the Bps exopolysaccharide capsule, as well as hemolysin BL (Hbl) and cytotoxin K (CytK). Comparatively, a ST108 genome associated with a case in Texas was most closely related to B. anthracis; however, like other anthrax-causing strains most closely related to B. anthracis, this genome did not possess Bps-, Hbl-, or CytK-encoding genes. Overall, results presented here provide insights into the evolution of anthrax-causing B. cereus s.l.", "doi": "10.3390/pathogens11080856", "pmid": "36014977", "labels": {"DDLS Fellow": null, "Laura Carroll": null}, "xrefs": [{"db": "pmc", "key": "PMC9413466"}, {"db": "pii", "key": "pathogens11080856"}], "notes": [], "created": "2023-05-13T11:52:32.866Z", "modified": "2025-03-18T17:29:32.652Z"}, {"entity": "publication", "iuid": "fe628affc8944824b57b88e27c29539f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/fe628affc8944824b57b88e27c29539f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/fe628affc8944824b57b88e27c29539f"}}, "title": "Predicting the structure of large protein complexes using AlphaFold and Monte Carlo tree search.", "authors": [{"family": "Elofsson", "given": "Arne", "initials": "A", "orcid": "0000-0002-7115-9751", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/248e70e81bd64f31a5f83e6e329bba95.json"}}, {"family": "Bryant", "given": "Patrick", "initials": "P", "orcid": "0000-0003-3439-1866", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a683bcf98234ff09b2398976583b66f.json"}}, {"family": "Pozzati", "given": "Gabriele", "initials": "G", "orcid": "0000-0002-4303-9939", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/94129216debe4e22ab3f3b74c33f9ab9.json"}}, {"family": "Zhu", "given": "Wensi", "initials": "W"}, {"family": "Shenoy", "given": "Aditi", "initials": "A", "orcid": "0000-0001-7748-2501", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/35bef00b985a45d59602675316e3d706.json"}}, {"family": "Kundrotas", "given": "Petras", "initials": "P"}], "type": "posted-content", "published": "2022-07-27", "journal": {"issn-l": null}, "abstract": null, "doi": "10.21203/rs.3.rs-1870813/v1", "pmid": null, "labels": {"Patrick Bryant": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T12:58:17.863Z", "modified": "2026-09-23T15:20:20.552Z"}, {"entity": "publication", "iuid": "681396db2a484a029d9c472926a2eb84", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/681396db2a484a029d9c472926a2eb84.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/681396db2a484a029d9c472926a2eb84"}}, "title": "Issues and recommendations for the residual approach to quantifying cognitive resilience and reserve.", "authors": [{"family": "Elman", "given": "Jeremy A", "initials": "JA"}, {"family": "Vogel", "given": "Jacob W", "initials": "JW"}, {"family": "Bocancea", "given": "Diana I", "initials": "DI"}, {"family": "Ossenkoppele", "given": "Rik", "initials": "R"}, {"family": "van Loenhoud", "given": "Anna C", "initials": "AC"}, {"family": "Tu", "given": "Xin M", "initials": "XM"}, {"family": "Kremen", "given": "William S", "initials": "WS"}, {"family": "Alzheimer\u2019s Disease Neuroimaging Initiative", "given": "", "initials": ""}], "type": "journal article", "published": "2022-07-25", "journal": {"title": "Alzheimers Res Ther", "issn": "1758-9193", "issn-l": null, "volume": "14", "issue": "1", "pages": "102"}, "abstract": "Cognitive reserve and resilience are terms used to explain interindividual variability in maintenance of cognitive health in response to adverse factors, such as brain pathology in the context of aging or neurodegenerative disorders. There is substantial interest in identifying tractable substrates of resilience to potentially leverage this phenomenon into intervention strategies. One way of operationalizing cognitive resilience that has gained popularity is the residual method: regressing cognition on an adverse factor and using the residual as a measure of resilience. This method is attractive because it provides a statistical approach that is an intuitive match to the reserve/resilience conceptual framework. However, due to statistical properties of the regression equation, the residual approach has qualities that complicate its interpretation as an index of resilience and make it statistically inappropriate in certain circumstances.\r\n\r\nWe describe statistical properties of the regression equation to illustrate why the residual is highly correlated with the cognitive score from which it was derived. Using both simulations and real data, we model common applications of the approach by creating a residual score (global cognition residualized for hippocampal volume) in individuals along the AD spectrum. We demonstrate that in most real-life scenarios, the residual measure of cognitive resilience is highly correlated with cognition, and the degree of this correlation depends on the initial relationship between the adverse factor and cognition. Subsequently, any association between this resilience metric and an external variable may actually be driven by cognition, rather than by an operationalized measure of resilience. We then assess several strategies proposed as potential solutions to this problem, such as including both the residual and original cognitive measure in a model. However, we conclude these solutions may be insufficient, and we instead recommend against \"pre-regression\" strategies altogether in favor of using statistical moderation (e.g., interactions) to quantify resilience.\r\n\r\nCaution should be taken in the use and interpretation of the residual-based method of cognitive resilience. Rather than identifying resilient individuals, we encourage building more complete models of cognition to better identify the specific adverse and protective factors that influence cognitive decline.", "doi": "10.1186/s13195-022-01049-w", "pmid": "35879736", "labels": {"Jacob W Vogel": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC9310423"}, {"db": "pii", "key": "10.1186/s13195-022-01049-w"}], "notes": [], "created": "2023-05-28T17:54:09.409Z", "modified": "2023-11-29T06:39:32.622Z"}, {"entity": "publication", "iuid": "b4b73434a62b4cfa9abd9f9b67afda17", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b4b73434a62b4cfa9abd9f9b67afda17.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b4b73434a62b4cfa9abd9f9b67afda17"}}, "title": "EvoBind: in silico directed evolution of peptide binders with AlphaFold", "authors": [{"family": "Bryant", "given": "Patrick", "initials": "P", "orcid": "0000-0003-3439-1866", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a683bcf98234ff09b2398976583b66f.json"}}, {"family": "Elofsson", "given": "Arne", "initials": "A", "orcid": "0000-0002-7115-9751", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/248e70e81bd64f31a5f83e6e329bba95.json"}}], "type": "posted-content", "published": "2022-07-23", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2022.07.23.501214", "pmid": null, "labels": {"Patrick Bryant": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T10:12:46.396Z", "modified": "2026-09-23T13:43:49.873Z"}, {"entity": "publication", "iuid": "356495fd20e04cf2bb9395e13f941c83", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/356495fd20e04cf2bb9395e13f941c83.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/356495fd20e04cf2bb9395e13f941c83"}}, "title": "Neoadjuvant Chemoradiotherapy and Surgery for Esophageal Squamous Cell Carcinoma Versus Definitive Chemoradiotherapy With Salvage Surgery as Needed: The Study Protocol for the Randomized Controlled NEEDS Trial.", "authors": [{"family": "Nilsson", "given": "Magnus", "initials": "M"}, {"family": "Olafsdottir", "given": "Halla", "initials": "H"}, {"family": "Alexandersson von D\u00f6beln", "given": "Gabriella", "initials": "G"}, {"family": "Villegas", "given": "Fernanda", "initials": "F"}, {"family": "Gagliardi", "given": "Giovanna", "initials": "G"}, {"family": "Hellstr\u00f6m", "given": "Mats", "initials": "M"}, {"family": "Wang", "given": "Qiao-Li", "initials": "QL"}, {"family": "Johansson", "given": "Hemming", "initials": "H"}, {"family": "Gebski", "given": "Val", "initials": "V"}, {"family": "Hedberg", "given": "Jakob", "initials": "J"}, {"family": "Klevebro", "given": "Fredrik", "initials": "F"}, {"family": "Markar", "given": "Sheraz", "initials": "S"}, {"family": "Smyth", "given": "Elizabeth", "initials": "E"}, {"family": "Lagergren", "given": "Pernilla", "initials": "P"}, {"family": "Al-Haidari", "given": "Ghazwan", "initials": "G"}, {"family": "Rekstad", "given": "Lars Cato", "initials": "LC"}, {"family": "Aahlin", "given": "Eirik Kjus", "initials": "EK"}, {"family": "Wallner", "given": "Bengt", "initials": "B"}, {"family": "Edholm", "given": "David", "initials": "D"}, {"family": "Johansson", "given": "Jan", "initials": "J"}, {"family": "Szabo", "given": "Eva", "initials": "E"}, {"family": "Reynolds", "given": "John V", "initials": "JV"}, {"family": "Pramesh", "given": "C S", "initials": "CS"}, {"family": "Mummudi", "given": "Naveen", "initials": "N"}, {"family": "Joshi", "given": "Amit", "initials": "A"}, {"family": "Ferri", "given": "Lorenzo", "initials": "L"}, {"family": "Wong", "given": "Rebecca Ks", "initials": "RK"}, {"family": "O'Callaghan", "given": "Chris", "initials": "C"}, {"family": "Lukovic", "given": "Jelena", "initials": "J"}, {"family": "Chan", "given": "Kelvin Kw", "initials": "KK"}, {"family": "Leong", "given": "Trevor", "initials": "T"}, {"family": "Barbour", "given": "Andrew", "initials": "A"}, {"family": "Smithers", "given": "Mark", "initials": "M"}, {"family": "Li", "given": "Yin", "initials": "Y"}, {"family": "Kang", "given": "Xiaozheng", "initials": "X"}, {"family": "Kong", "given": "Feng-Ming", "initials": "FM"}, {"family": "Chao", "given": "Yin-Kai", "initials": "YK"}, {"family": "Crosby", "given": "Tom", "initials": "T"}, {"family": "Bruns", "given": "Christiane", "initials": "C"}, {"family": "van Laarhoven", "given": "Hanneke", "initials": "H"}, {"family": "van Berge Henegouwen", "given": "Mark", "initials": "M"}, {"family": "van Hillegersberg", "given": "Richard", "initials": "R"}, {"family": "Rosati", "given": "Riccardo", "initials": "R"}, {"family": "Piessen", "given": "Guillaume", "initials": "G"}, {"family": "de Manzoni", "given": "Giovanni", "initials": "G"}, {"family": "Lordick", "given": "Florian", "initials": "F"}], "type": "journal article", "published": "2022-07-13", "journal": {"title": "Front Oncol", "issn": "2234-943X", "volume": "12", "pages": "917961", "issn-l": "2234-943X"}, "abstract": "The globally dominant treatment with curative intent for locally advanced esophageal squamous cell carcinoma (ESCC) is neoadjuvant chemoradiotherapy (nCRT) with subsequent esophagectomy. This multimodal treatment leads to around 60% overall 5-year survival, yet with impaired post-surgical quality of life. Observational studies indicate that curatively intended chemoradiotherapy, so-called definitive chemoradiotherapy (dCRT) followed by surveillance of the primary tumor site and regional lymph node stations and surgery only when needed to ensure local tumor control, may lead to similar survival as nCRT with surgery, but with considerably less impairment of quality of life. This trial aims to demonstrate that dCRT, with selectively performed salvage esophagectomy only when needed to achieve locoregional tumor control, is non-inferior regarding overall survival, and superior regarding health-related quality of life (HRQOL), compared to nCRT followed by mandatory surgery, in patients with operable, locally advanced ESCC.\n\nThis is a pragmatic open-label, randomized controlled phase III, multicenter trial with non-inferiority design with regard to the primary endpoint overall survival and a superiority hypothesis for the experimental intervention dCRT with regard to the main secondary endpoint global HRQOL one year after randomization. The control intervention is nCRT followed by preplanned surgery and the experimental intervention is dCRT followed by surveillance and salvage esophagectomy only when needed to secure local tumor control. A target sample size of 1200 randomized patients is planned in order to reach 462 events (deaths) during follow-up.\n\nwww.ClinicalTrials.gov, identifier: NCT04460352.", "doi": "10.3389/fonc.2022.917961", "pmid": "35912196", "labels": {"DDLS Fellow": null, "Qiaoli Wang": null}, "xrefs": [{"db": "pmc", "key": "PMC9326032"}, {"db": "ClinicalTrials.gov", "key": "NCT04460352"}], "notes": [], "created": "2025-11-27T18:53:39.957Z", "modified": "2025-11-27T18:53:39.974Z"}, {"entity": "publication", "iuid": "8adefbcc09204715af853a48f861e45c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8adefbcc09204715af853a48f861e45c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8adefbcc09204715af853a48f861e45c"}}, "title": "A method to predict the response to directional selection using a Kalman filter.", "authors": [{"family": "Milocco", "given": "Lisandro", "initials": "L", "orcid": "0000-0003-3953-0407", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/74f9e4dfff0e4b008c46b75e3d319673.json"}}, {"family": "Salazar-Ciudad", "given": "Isaac", "initials": "I"}], "type": "journal article", "published": "2022-07-12", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "119", "issue": "28", "pages": "e2117916119", "issn-l": "0027-8424"}, "abstract": "Predicting evolution remains challenging. The field of quantitative genetics provides predictions for the response to directional selection through the breeder's equation, but these predictions can have errors. The sources of these errors include omission of traits under selection, inaccurate estimates of genetic variance, and nonlinearities in the relationship between genetic and phenotypic variation. Previous research showed that the expected value of these prediction errors is often not zero, so predictions are systematically biased. Here, we propose that this bias, rather than being a nuisance, can be used to improve the predictions. We use this to develop a method to predict evolution, which is built on three key innovations. First, the method predicts change as the breeder's equation plus a bias term. Second, the method combines information from the breeder's equation and from the record of past changes in the mean to predict change using a Kalman filter. Third, the parameters of the filter are fitted in each generation using a learning algorithm on the record of past changes. We compare the method to the breeder's equation in two artificial selection experiments, one using the wing of the fruit fly and another using simulations that include a complex mapping of genotypes to phenotypes. The proposed method outperforms the breeder's equation, particularly when traits under selection are omitted from the analysis, when data are noisy, and when additive genetic variance is estimated inaccurately or not estimated at all. The proposed method is easy to apply, requiring only the trait means over past generations.", "doi": "10.1073/pnas.2117916119", "pmid": "35867739", "labels": {"DDLS Fellow": null, "Lisandro Milocco": null}, "xrefs": [{"db": "pmc", "key": "PMC9282428"}], "notes": [], "created": "2025-11-28T14:28:27.492Z", "modified": "2025-11-28T14:29:05.074Z"}, {"entity": "publication", "iuid": "4cc13510b72040c8bb9cde89ff668173", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4cc13510b72040c8bb9cde89ff668173.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4cc13510b72040c8bb9cde89ff668173"}}, "title": "Deep Lipidomics in Human Plasma: Cardiometabolic Disease Risk and Effect of Dietary Fat Modulation.", "authors": [{"family": "Eichelmann", "given": "Fabian", "initials": "F", "orcid": "0000-0002-3975-5596", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4f6083a259c6440ab3201d53f44a0d55.json"}}, {"family": "Sellem", "given": "Laury", "initials": "L", "orcid": "0000-0002-2697-997X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b57881c0e91f4c8d89f516f9eb6fc734.json"}}, {"family": "Wittenbecher", "given": "Clemens", "initials": "C", "orcid": "0000-0001-7792-877X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2f7d2c289b3c47d5a79d23bd48a3225a.json"}}, {"family": "J\u00e4ger", "given": "Susanne", "initials": "S", "orcid": "0000-0001-6619-0861", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/28dce9f2224f4278bd7cd44639793f8d.json"}}, {"family": "Kuxhaus", "given": "Olga", "initials": "O"}, {"family": "Prada", "given": "Marcela", "initials": "M", "orcid": "0000-0002-1159-417X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/61b493b46a934273a4bfaaaa81106987.json"}}, {"family": "Cuadrat", "given": "Rafael", "initials": "R"}, {"family": "Jackson", "given": "Kim G", "initials": "KG"}, {"family": "Lovegrove", "given": "Julie A", "initials": "JA", "orcid": "0000-0001-7633-9455", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a3da45ee27d40349f54306b4cb77b09.json"}}, {"family": "Schulze", "given": "Matthias B", "initials": "MB", "orcid": "0000-0002-0830-5277", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/853ded2c43b64f26a8b47da7ea7b79c0.json"}}], "type": "journal article", "published": "2022-07-05", "journal": {"title": "Circulation", "issn": "1524-4539", "volume": "146", "issue": "1", "pages": "21-35", "issn-l": "0009-7322"}, "abstract": "In blood and tissues, dietary and endogenously generated fatty acids (FAs) occur in free form or as part of complex lipid molecules that collectively represent the lipidome of the respective tissue. We assessed associations of plasma lipids derived from high-resolution lipidomics with incident cardiometabolic diseases and subsequently tested if the identified risk-associated lipids were sensitive to dietary fat modification.\n\nThe EPIC Potsdam cohort study (European Prospective Investigation into Cancer and Nutrition) comprises 27 548 participants recruited within an age range of 35 to 65 years from the general population around Potsdam, Germany. We generated 2 disease-specific case cohorts on the basis of a fixed random subsample (n=1262) and all respective cohort-wide identified incident primary cardiovascular disease (composite of fatal and nonfatal myocardial infarction and stroke; n=551) and type 2 diabetes (n=775) cases. We estimated the associations of baseline plasma concentrations of 282 class-specific FA abundances (calculated from 940 distinct molecular species across 15 lipid classes) with the outcomes in multivariable-adjusted Cox models. We tested the effect of an isoenergetic dietary fat modification on risk-associated lipids in the DIVAS randomized controlled trial (Dietary Intervention and Vascular Function; n=113). Participants consumed either a diet rich in saturated FAs (control), monounsaturated FAs, or a mixture of monounsaturated and n-6 polyunsaturated FAs for 16 weeks.\n\nSixty-nine lipids associated (false discovery rate<0.05) with at least 1 outcome (both, 8; only cardiovascular disease, 49; only type 2 diabetes, 12). In brief, several monoacylglycerols and FA16:0 and FA18:0 in diacylglycerols were associated with both outcomes; cholesteryl esters, free fatty acids, and sphingolipids were largely cardiovascular disease specific; and several (glycero)phospholipids were type 2 diabetes specific. In addition, 19 risk-associated lipids were affected (false discovery rate<0.05) by the diets rich in unsaturated dietary FAs compared with the saturated fat diet (17 in a direction consistent with a potential beneficial effect on long-term cardiometabolic risk). For example, the monounsaturated FA-rich diet decreased diacylglycerol(FA16:0) by 0.4 (95% CI, 0.5-0.3) SD units and increased triacylglycerol(FA22:1) by 0.5 (95% CI, 0.4-0.7) SD units.\n\nWe identified several lipids associated with cardiometabolic disease risk. A subset was beneficially altered by a dietary fat intervention that supports the substitution of dietary saturated FAs with unsaturated FAs as a potential tool for primary disease prevention.", "doi": "10.1161/CIRCULATIONAHA.121.056805", "pmid": "35422138", "labels": {"Clemens Wittenbecher": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC9241667"}], "notes": [], "created": "2025-12-09T13:38:54.335Z", "modified": "2025-12-09T13:38:54.506Z"}, {"entity": "publication", "iuid": "7e11472b12be4af5a92c1c67c65c45a8", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/7e11472b12be4af5a92c1c67c65c45a8.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/7e11472b12be4af5a92c1c67c65c45a8"}}, "title": "A new machine learning method for cancer mutation analysis", "authors": [{"family": "Habibi", "given": "Mahnaz", "initials": "M"}, {"family": "Taheri", "given": "Golnaz", "initials": "G", "orcid": "0000-0002-2741-0355", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/014c217121d346b2b371bbc1c2fede57.json"}}], "type": "posted-content", "published": "2022-07-02", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2022.06.29.498062", "pmid": null, "labels": {"Golnaz Taheri": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T10:12:24.062Z", "modified": "2026-09-23T14:46:07.666Z"}, {"entity": "publication", "iuid": "d32f1a8dd5f547edb0127591d585d9c3", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d32f1a8dd5f547edb0127591d585d9c3.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d32f1a8dd5f547edb0127591d585d9c3"}}, "title": "The age-dependent association of risk factors with pancreatic cancer.", "authors": [{"family": "Yuan", "given": "C", "initials": "C"}, {"family": "Kim", "given": "J", "initials": "J"}, {"family": "Wang", "given": "Q L", "initials": "QL"}, {"family": "Lee", "given": "A A", "initials": "AA"}, {"family": "Babic", "given": "A", "initials": "A"}, {"family": "PanScan/PanC4 I-III Consortium", "given": "", "initials": ""}, {"family": "Amundadottir", "given": "L T", "initials": "LT"}, {"family": "Klein", "given": "A P", "initials": "AP"}, {"family": "Li", "given": "D", "initials": "D"}, {"family": "McCullough", "given": "M L", "initials": "ML"}, {"family": "Petersen", "given": "G M", "initials": "GM"}, {"family": "Risch", "given": "H A", "initials": "HA"}, {"family": "Stolzenberg-Solomon", "given": "R Z", "initials": "RZ"}, {"family": "Perez", "given": "K", "initials": "K"}, {"family": "Ng", "given": "K", "initials": "K"}, {"family": "Giovannucci", "given": "E L", "initials": "EL"}, {"family": "Stampfer", "given": "M J", "initials": "MJ"}, {"family": "Kraft", "given": "P", "initials": "P"}, {"family": "Wolpin", "given": "B M", "initials": "BM"}], "type": "journal article", "published": "2022-07-00", "journal": {"title": "Ann. Oncol.", "issn": "1569-8041", "volume": "33", "issue": "7", "pages": "693-701", "issn-l": "0923-7534"}, "abstract": "Pancreatic cancer presents as advanced disease in >80% of patients; yet, appropriate ages to consider prevention and early detection strategies are poorly defined. We investigated age-specific associations and attributable risks of pancreatic cancer for established modifiable and non-modifiable risk factors.\n\nWe included 167 483 participants from two prospective US cohort studies with 1190 incident cases of pancreatic cancer during >30 years of follow-up; 5107 pancreatic cancer cases and 8845 control participants of European ancestry from a completed multicenter genome-wide association study (GWAS); and 248 893 pancreatic cancer cases documented in the US Surveillance, Epidemiology, and End Results (SEER) Program. Across different age categories, we investigated cigarette smoking, obesity, diabetes, height, and non-O blood group in the prospective cohorts; weighted polygenic risk score of 22 previously identified single nucleotide polymorphisms in the GWAS; and male sex and black race in the SEER Program.\n\nIn the prospective cohorts, all five risk factors were more strongly associated with pancreatic cancer risk among younger participants, with associations attenuated among those aged >70 years. The hazard ratios comparing participants with three to five risk factors with those with no risk factors were 9.24 [95% confidence interval (CI) 4.11-20.77] among those aged \u226460 years, 3.00 (95% CI 1.85-4.86) among those aged 61-70 years, and 1.46 (95% CI 1.10-1.94) among those aged >70 years (Pheterogeneity = 3\u00d710-5). These factors together were related to 65.6%, 49.7%, and 17.2% of incident pancreatic cancers in these age groups, respectively. In the GWAS and the SEER Program, the associations with the polygenic risk score, male sex, and black race were all stronger among younger individuals (Pheterogeneity \u22640.01).\n\nEstablished risk factors are more strongly associated with earlier-onset pancreatic cancer, emphasizing the importance of age at initiation for cancer prevention and control programs targeting this highly lethal malignancy.", "doi": "10.1016/j.annonc.2022.03.276", "pmid": "35398288", "labels": {"DDLS Fellow": null, "Qiaoli Wang": null}, "xrefs": [{"db": "mid", "key": "NIHMS1796471"}, {"db": "pmc", "key": "PMC9233063"}, {"db": "pii", "key": "S0923-7534(22)00672-X"}], "notes": [], "created": "2025-11-27T18:53:38.594Z", "modified": "2025-11-27T18:53:38.615Z"}, {"entity": "publication", "iuid": "1e23011f8a6b46d8a172430d4c29e1c3", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1e23011f8a6b46d8a172430d4c29e1c3.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1e23011f8a6b46d8a172430d4c29e1c3"}}, "title": "MRI characterization of skeletal muscle size and fatty infiltration in long-term trained and untrained individuals.", "authors": [{"family": "Emanuelsson", "given": "Eric B", "initials": "EB"}, {"family": "Berry", "given": "David B", "initials": "DB"}, {"family": "Reitzner", "given": "Stefan M", "initials": "SM", "orcid": "0000-0003-0151-2780", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f1d32bad414e49569ede9d7c80e2bf6f.json"}}, {"family": "Arif", "given": "Muhammad", "initials": "M"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Gustafsson", "given": "Thomas", "initials": "T"}, {"family": "Ward", "given": "Samuel R", "initials": "SR"}, {"family": "Sundberg", "given": "Carl Johan", "initials": "CJ"}, {"family": "Chapman", "given": "Mark A", "initials": "MA", "orcid": "0000-0001-9905-4022", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/71c4b747b8794745a547d635953c9960.json"}}], "type": "journal article", "published": "2022-07-00", "journal": {"title": "Physiol Rep", "issn": "2051-817X", "volume": "10", "issue": "14", "pages": "e15398", "issn-l": null}, "abstract": "This study investigated body composition measures in highly trained and untrained individuals using whole-body magnetic resonance imaging (MRI). Additionally, correlations between these measures and skeletal muscle gene expression were performed. Thirty-six individuals were included: endurance-trained males (ME, n = 8) and females (FE, n = 7), strength-trained males (MS, n = 7), and untrained control males (MC, n = 8) and females (FC, n = 6). MRI scans were performed, and resting M. vastus lateralis (VL) biopsies were subjected to RNA sequencing. Liver fat fraction, visceral adipose tissue volume (VAT), total body fat, and total lean tissue were measured from MRI data. Additionally, cross-sectional area (CSA) and fat signal fraction (FSF) were calculated from Mm. pectoralis, M. erector spinae and M. multifidus combined, Mm. quadriceps, and Mm. triceps surae (TS). Liver fat fraction, VAT, and total body fat relative to body weight were lower in ME and FE compared with corresponding controls. MS had a larger CSA across all four muscle groups and lower FSF in all muscles apart from TS compared with MC. ME had a lower FSF across all muscle groups and a larger CSA in all muscles except TS than MC. FE athletes showed a higher CSA in Mm. pectoralis and Mm. quadriceps and a lower CSA in TS than FC with no CSA differences found in the back muscles investigated. Surprisingly, the only difference in FSF between FE and FC was found in Mm. pectoralis. Lastly, correlations between VL gene expression and VL CSA as well as FSF showed that genes positively correlated with CSA revealed an enrichment of the oxidative phosphorylation and thermogenesis pathways, while the genes positively correlated with FSF showed significant enrichment of the spliceosome pathway. Although limited differences were found with training in females, our study suggests that both regular endurance and resistance training are useful in maintaining muscle mass, reducing adipose tissue deposits, and reducing muscle fat content in males.", "doi": "10.14814/phy2.15398", "pmid": "35854646", "labels": {"Adil Mardinoglu": "", "SciLifeLab Fellow": "", "DDLS Fellow": "", "Muhammad Arif": ""}, "xrefs": [{"db": "pmc", "key": "PMC9296904"}], "notes": [], "created": "2023-12-04T15:02:02.496Z", "modified": "2026-09-23T11:13:33.456Z"}, {"entity": "publication", "iuid": "a262c24ffd2e4b568f79c6a4399bc8be", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a262c24ffd2e4b568f79c6a4399bc8be.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a262c24ffd2e4b568f79c6a4399bc8be"}}, "title": "Harnessing secretory pathway differences between HEK293 and CHO to rescue production of difficult to express proteins.", "authors": [{"family": "Malm", "given": "Magdalena", "initials": "M"}, {"family": "Kuo", "given": "Chih-Chung", "initials": "CC"}, {"family": "Barzadd", "given": "Mona Moradi", "initials": "MM"}, {"family": "Mebrahtu", "given": "Aman", "initials": "A"}, {"family": "Wistbacka", "given": "Num", "initials": "N"}, {"family": "Razavi", "given": "Ronia", "initials": "R"}, {"family": "Volk", "given": "Anna-Luisa", "initials": "AL"}, {"family": "Lundqvist", "given": "Magnus", "initials": "M"}, {"family": "Kotol", "given": "David", "initials": "D"}, {"family": "Tegel", "given": "Hanna", "initials": "H"}, {"family": "Hober", "given": "Sophia", "initials": "S"}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Gr\u00e4slund", "given": "Torbj\u00f6rn", "initials": "T"}, {"family": "Chotteau", "given": "Veronique", "initials": "V"}, {"family": "Field", "given": "Ray", "initials": "R"}, {"family": "Varley", "given": "Paul G", "initials": "PG"}, {"family": "Roth", "given": "Robert G", "initials": "RG"}, {"family": "Lewis", "given": "Nathan E", "initials": "NE"}, {"family": "Hatton", "given": "Diane", "initials": "D"}, {"family": "Rockberg", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2022-07-00", "journal": {"title": "Metab. Eng.", "issn": "1096-7184", "volume": "72", "pages": "171-187", "issn-l": "1096-7176"}, "abstract": "Biologics represent the fastest growing group of therapeutics, but many advanced recombinant protein moieties remain difficult to produce. Here, we identify metabolic engineering targets limiting expression of recombinant human proteins through a systems biology analysis of the transcriptomes of CHO and HEK293 during recombinant expression. In an expression comparison of 24 difficult to express proteins, one third of the challenging human proteins displayed improved secretion upon host cell swapping from CHO to HEK293. Guided by a comprehensive transcriptomics comparison between cell lines, especially highlighting differences in secretory pathway utilization, a co-expression screening of 21 secretory pathway components validated ATF4, SRP9, JUN, PDIA3 and HSPA8 as productivity boosters in CHO. Moreover, more heavily glycosylated products benefitted more from the elevated activities of the N- and O-glycosyltransferases found in HEK293. Collectively, our results demonstrate the utilization of HEK293 for expression rescue of human proteins and suggest a methodology for identification of secretory pathway components for metabolic engineering of HEK293 and CHO.", "doi": "10.1016/j.ymben.2022.03.009", "pmid": "35301123", "labels": {"Fredrik Edfors": "", "DDLS Fellow": ""}, "xrefs": [{"db": "mid", "key": "NIHMS1801357"}, {"db": "pmc", "key": "PMC9189052"}, {"db": "pii", "key": "S1096-7176(22)00044-1"}], "notes": [], "created": "2026-08-20T08:07:11.071Z", "modified": "2026-09-23T08:48:13.423Z"}, {"entity": "publication", "iuid": "a9d473ca72164e18a3db61d78fef3d7a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a9d473ca72164e18a3db61d78fef3d7a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a9d473ca72164e18a3db61d78fef3d7a"}}, "title": "Detection of perineural invasion in prostate needle biopsies with deep neural networks.", "authors": [{"family": "Kartasalo", "given": "Kimmo", "initials": "K", "orcid": "0000-0002-9470-4783", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7c6fc97c06ed456c8bdd1f03db8a9b72.json"}}, {"family": "Str\u00f6m", "given": "Peter", "initials": "P", "orcid": "0000-0002-1631-806X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2798ea6ef2ed4ae88b78dd04d2f14437.json"}}, {"family": "Ruusuvuori", "given": "Pekka", "initials": "P", "orcid": "0000-0001-9086-9591", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb947cd395e84612a53569f4a39abd19.json"}}, {"family": "Samaratunga", "given": "Hemamali", "initials": "H"}, {"family": "Delahunt", "given": "Brett", "initials": "B", "orcid": "0000-0002-5398-0300", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/433a3f884f95451383cc746925d9a08c.json"}}, {"family": "Tsuzuki", "given": "Toyonori", "initials": "T", "orcid": "0000-0002-4855-4366", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/42c993c2c0ab4b50afa03134f70118d9.json"}}, {"family": "Eklund", "given": "Martin", "initials": "M", "orcid": "0000-0001-5032-5266", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/06721510ebc8462386e0e6fc6c84315b.json"}}, {"family": "Egevad", "given": "Lars", "initials": "L", "orcid": "0000-0001-8531-222X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a7d46f1f5fc047dc8edb910eb4f0645c.json"}}], "type": "journal article", "published": "2022-07-00", "journal": {"title": "Virchows Arch.", "issn": "1432-2307", "issn-l": "0945-6317", "volume": "481", "issue": "1", "pages": "73-82"}, "abstract": "The presence of perineural invasion (PNI) by carcinoma in prostate biopsies has been shown to be associated with poor prognosis. The assessment and quantification of PNI are, however, labor intensive. To aid pathologists in this task, we developed an artificial intelligence (AI) algorithm based on deep neural networks. We collected, digitized, and pixel-wise annotated the PNI findings in each of the approximately 80,000 biopsy cores from the 7406 men who underwent biopsy in a screening trial between 2012 and 2014. In total, 485 biopsy cores showed PNI. We also digitized more than 10% (n = 8318) of the PNI negative biopsy cores. Digitized biopsies from a random selection of 80% of the men were used to build the AI algorithm, while 20% were used to evaluate its performance. For detecting PNI in prostate biopsy cores, the AI had an estimated area under the receiver operating characteristics curve of 0.98 (95% CI 0.97-0.99) based on 106 PNI positive cores and 1652 PNI negative cores in the independent test set. For a pre-specified operating point, this translates to sensitivity of 0.87 and specificity of 0.97. The corresponding positive and negative predictive values were 0.67 and 0.99, respectively. The concordance of the AI with pathologists, measured by mean pairwise Cohen's kappa (0.74), was comparable to inter-pathologist concordance (0.68 to 0.75). The proposed algorithm detects PNI in prostate biopsies with acceptable performance. This could aid pathologists by reducing the number of biopsies that need to be assessed for PNI and by highlighting regions of diagnostic interest.", "doi": "10.1007/s00428-022-03326-3", "pmid": "35449363", "labels": {"Kimmo Kartasalo": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC9226086"}, {"db": "pii", "key": "10.1007/s00428-022-03326-3"}], "notes": [], "created": "2024-11-05T16:09:36.259Z", "modified": "2024-11-29T09:29:14.824Z"}, {"entity": "publication", "iuid": "47a145341f044ab38d42b8c60fe13b3d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/47a145341f044ab38d42b8c60fe13b3d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/47a145341f044ab38d42b8c60fe13b3d"}}, "title": "Biosynthetic potential of the global ocean microbiome.", "authors": [{"family": "Paoli", "given": "Lucas", "initials": "L", "orcid": "0000-0003-0771-8309", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/116b5518d78f4cdfa7c7d6c7cdc7aeff.json"}}, {"family": "Ruscheweyh", "given": "Hans-Joachim", "initials": "HJ", "orcid": "0000-0001-7473-6086", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b5c268ed49844847a079447ecfe4e88e.json"}}, {"family": "Forneris", "given": "Clarissa C", "initials": "CC"}, {"family": "Hubrich", "given": "Florian", "initials": "F"}, {"family": "Kautsar", "given": "Satria", "initials": "S"}, {"family": "Bhushan", "given": "Agneya", "initials": "A"}, {"family": "Lotti", "given": "Alessandro", "initials": "A"}, {"family": "Clayssen", "given": "Quentin", "initials": "Q"}, {"family": "Salazar", "given": "Guillem", "initials": "G", "orcid": "0000-0002-9786-1493", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e8355f28c644d7ab8085e6b16b2e6d2.json"}}, {"family": "Milanese", "given": "Alessio", "initials": "A", "orcid": "0000-0002-7050-2239", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/45e9fe0111144358960531b419f2e1a7.json"}}, {"family": "Carlstr\u00f6m", "given": "Charlotte I", "initials": "CI"}, {"family": "Papadopoulou", "given": "Chrysa", "initials": "C", "orcid": "0000-0002-3909-7378", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ad57234e149441d1b0b41cc5ad56cc38.json"}}, {"family": "Gehrig", "given": "Daniel", "initials": "D"}, {"family": "Karasikov", "given": "Mikhail", "initials": "M", "orcid": "0000-0001-6200-5972", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/62afc29351cf45229987fc8c46a5058b.json"}}, {"family": "Mustafa", "given": "Harun", "initials": "H"}, {"family": "Larralde", "given": "Martin", "initials": "M", "orcid": "0000-0002-3947-4444", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6e048b839197434d8af8ab34bd50cf5e.json"}}, {"family": "Carroll", "given": "Laura M", "initials": "LM"}, {"family": "S\u00e1nchez", "given": "Pablo", "initials": "P", "orcid": "0000-0003-2787-822X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/485a43fed85b44d59992684545810243.json"}}, {"family": "Zayed", "given": "Ahmed A", "initials": "AA", "orcid": "0000-0003-2793-2679", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a9ce1b7d6c164081bfd089054bbfbbfe.json"}}, {"family": "Cronin", "given": "Dylan R", "initials": "DR"}, {"family": "Acinas", "given": "Silvia G", "initials": "SG", "orcid": "0000-0002-3439-0428", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c3d2775837da4504bc2d078a3ecbd3fe.json"}}, {"family": "Bork", "given": "Peer", "initials": "P", "orcid": "0000-0002-2627-833X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7b2c7fb225454cb592da4b2af6d6b645.json"}}, {"family": "Bowler", "given": "Chris", "initials": "C", "orcid": "0000-0003-3835-6187", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2f9da2e44f754892887a817f5ce71838.json"}}, {"family": "Delmont", "given": "Tom O", "initials": "TO", "orcid": "0000-0001-7053-7848", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/878c9b5ebce5497182da1843d94fc821.json"}}, {"family": "Gasol", "given": "Josep M", "initials": "JM", "orcid": "0000-0001-5238-2387", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cbc878eda2704738b6f85fe4190bbb7f.json"}}, {"family": "Gossert", "given": "Alvar D", "initials": "AD", "orcid": "0000-0001-7732-495X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0a574c3c72f9487b964deb86619874bb.json"}}, {"family": "Kahles", "given": "Andr\u00e9", "initials": "A", "orcid": "0000-0002-3411-0692", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/07956568aa6041ea8e0cc27848f9e039.json"}}, {"family": "Sullivan", "given": "Matthew B", "initials": "MB", "orcid": "0000-0001-8398-8234", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e95585b7d0724fe4b1f95da9953e630e.json"}}, {"family": "Wincker", "given": "Patrick", "initials": "P"}, {"family": "Zeller", "given": "Georg", "initials": "G", "orcid": "0000-0003-1429-7485", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/414382373eb5447186a7e6c925aa067f.json"}}, {"family": "Robinson", "given": "Serina L", "initials": "SL", "orcid": "0000-0001-6947-7913", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/258518282d5f43268420a8bf71ddccd8.json"}}, {"family": "Piel", "given": "J\u00f6rn", "initials": "J", "orcid": "0000-0002-2282-8154", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2ec40bb2c076459885dbe76ca9657099.json"}}, {"family": "Sunagawa", "given": "Shinichi", "initials": "S", "orcid": "0000-0003-3065-0314", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3a02fe8bae87447c914b3fe1cba5a21e.json"}}], "type": "journal article", "published": "2022-07-00", "journal": {"title": "Nature", "issn": "1476-4687", "volume": "607", "issue": "7917", "pages": "111-118", "issn-l": "0028-0836"}, "abstract": "Natural microbial communities are phylogenetically and metabolically diverse. In addition to underexplored organismal groups1, this diversity encompasses a rich discovery potential for ecologically and biotechnologically relevant enzymes and biochemical compounds2,3. However, studying this diversity to identify genomic pathways for the synthesis of such compounds4 and assigning them to their respective hosts remains challenging. The biosynthetic potential of microorganisms in the open ocean remains largely uncharted owing to limitations in the analysis of genome-resolved data at the global scale. Here we investigated the diversity and novelty of biosynthetic gene clusters in the ocean by integrating around 10,000 microbial genomes from cultivated and single cells with more than 25,000 newly reconstructed draft genomes from more than 1,000 seawater samples. These efforts revealed approximately 40,000 putative mostly new biosynthetic gene clusters, several of which were found in previously unsuspected phylogenetic groups. Among these groups, we identified a lineage rich in biosynthetic gene clusters ('Candidatus Eudoremicrobiaceae') that belongs to an uncultivated bacterial phylum and includes some of the most biosynthetically diverse microorganisms in this environment. From these, we characterized the phospeptin and pythonamide pathways, revealing cases of unusual bioactive compound structure and enzymology, respectively. Together, this research demonstrates how microbiomics-driven strategies can enable the investigation of previously undescribed enzymes and natural products in underexplored microbial groups and environments.", "doi": "10.1038/s41586-022-04862-3", "pmid": "35732736", "labels": {"DDLS Fellow": null, "Laura Carroll": null}, "xrefs": [{"db": "pmc", "key": "PMC9259500"}, {"db": "pii", "key": "10.1038/s41586-022-04862-3"}], "notes": [], "created": "2023-05-13T11:52:35.405Z", "modified": "2025-03-18T17:29:17.445Z"}, {"entity": "publication", "iuid": "5abd3e284dc941a7adec38a1ed7d3bad", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5abd3e284dc941a7adec38a1ed7d3bad.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5abd3e284dc941a7adec38a1ed7d3bad"}}, "title": "The healthy female microbiome across body sites: effect of hormonal contraceptives and the menstrual cycle.", "authors": [{"family": "Krog", "given": "Maria Christine", "initials": "MC", "orcid": "0000-0002-2110-0479", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bdd65c5105f4480692383dae8d4ac986.json"}}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW", "orcid": "0000-0001-5432-1764", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/246ed7b405dd4c3f9ec5e7ff9f1d3ade.json"}}, {"family": "Fransson", "given": "Emma", "initials": "E", "orcid": "0000-0001-9010-8522", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8c05290187ec426b8804eefc3d954971.json"}}, {"family": "Bashir", "given": "Zahra", "initials": "Z", "orcid": "0000-0002-2497-282X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2d15fce497fe4cdabd82e994e7cd83ad.json"}}, {"family": "Nyboe Andersen", "given": "Anders", "initials": "A"}, {"family": "Edfeldt", "given": "Gabriella", "initials": "G", "orcid": "0000-0003-0366-5588", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bc30318aa3ca4720ac5aa3a982c9f730.json"}}, {"family": "Engstrand", "given": "Lars", "initials": "L", "orcid": "0000-0002-7713-2373", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02d8684df81e42169e613de803446fbf.json"}}, {"family": "Schuppe-Koistinen", "given": "Ina", "initials": "I", "orcid": "0000-0002-1423-3089", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/659fb04e6a1a430cbd707b8a50d500a3.json"}}, {"family": "Nielsen", "given": "Henriette Svarre", "initials": "HS", "orcid": "0000-0003-2106-8103", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9a99fa7ebb204c618ed70f29be0085b3.json"}}], "type": "journal article", "published": "2022-06-30", "journal": {"title": "Hum. Reprod.", "issn": "1460-2350", "volume": "37", "issue": "7", "pages": "1525-1543", "issn-l": "0268-1161"}, "abstract": "How does hormonal contraceptive use and menstrual cycle phase affect the female microbiome across different body sites?\n\nThe menstrual cycle phase, but not hormonal contraceptive use, is associated with the vaginal and oral but not the gut microbiome composition in healthy young women.\n\nWomen with low vaginal levels of Lactobacillus crispatus are at increased risk of pre-term birth, fertility treatment failure, sexually transmitted infections and gynaecological cancers. Little is known about the effect of hormonal fluctuations on other body site's microbiomes as well as the interplay between them.\n\nThis study includes a cohort of 160 healthy young Danish women using three different contraceptive regimens: non-hormonal methods (n = 54), combined oral contraceptive (COC, n = 52) or levonorgestrel intrauterine system (LNG-IUS, n = 54). Samples were collected from four body sites during the menstrual cycle (menses, follicular and luteal phases) at Copenhagen University Hospital, Rigshospitalet, Denmark.\n\nThe oral, vaginal, rectal and faecal microbiomes were characterized by shotgun sequencing. Microbial diversity and community distance measures were compared between study groups, menstrual phase timepoints and body sites. All participants answered an extensive questionnaire on current health, lifestyle and sex life. Confounding factors such as smoking, BMI and diet were analysed by PERMANOVA. Plasma oestradiol and progesterone levels are correlated with microbiome composition.\n\nThe use of COC and LNG-IUS was not associated with the microbiome composition or diversity. However, increased diversity in the vaginal microbiome was observed during menses, followed by a subsequent expansion of Lactobacillus spp. during the follicular and luteal phases which correlated with measured serum oestradiol levels (r = 0.11, P < 0.001). During menses, 89 women (58%) had a dysbiotic vaginal microbiome with <60% Lactobacillus spp. This declined to 49 (32%) in the follicular phase (P < 0.001) and 44 (29%) in the luteal phase (P < 0.001). During menses, bacterial richness and diversity in saliva reached its lowest point while no differences were observed in the faecal microbiome. The microbiome in different body sites was on average more similar within the same individual than between individuals, despite phase or hormonal treatment. Only the vagina presented a clear cluster structure with dominance of either L. crispatus, Lactobacillus iners, Gardnerella vaginalis or Prevotella spp.\n\nThe microbiome samples analysed in this study were submitted to the European Nucleotide Archive under project number PRJEB37731, samples ERS4421369-ERS4422941.\n\nThe cohort is homogenous which limits extrapolation of the effects of ethnicity and socio-economic status on the microbiome. We only present three defined timepoints across the menstrual phase and miss potential important day to day fluctuations.\n\nThe use of hormonal contraception did not significantly associate with the microbiome composition in the vagina, faeces, rectum or saliva in healthy young women. This is a welcome finding considering the widespread and prolonged use of these highly efficient contraceptive methods. The menstrual cycle is, however, a major confounding factor for the vaginal microbiome. As such, the time point in the menstrual cycle should be considered when analysing the microbiome of women of reproductive age, since stratifying by vaginal dysbiosis status during menstruation could be misleading. This is the first study to confirm by direct measurements of oestradiol, a correlation with the presence of L. crispatus, adding evidence of a possible hormonal mechanism for the maintenance of this desirable microbe.\n\nThis work was partly funded by the Ferring Pharmaceuticals through a research collaboration with The Centre for Translational Microbiome Research (CTMR) at the Karolinska Institutet (L.W.H., E.F., G.E. and I.S.-K.). Ferring Pharmaceuticals also funded the infrastructure to obtain the clinical samples at Copenhagen University Hospital ([#MiHSN01], M.C.K., Z.B., and H.S.N.). This work was also supported by funding from Rigshospitalet's Research Funds ([#E-22614-01 and #E-22614-02] to M.C.K.) and Oda and Hans Svenningsen's Foundation ([#F-22614-08] to H.S.N.). M.C.K., L.W.H., E.F., Z.B., G.E., L.E., I.S.-K. and H.S.N., are partially funded by Ferring Pharmaceuticals, which also provided funds for the collection and processing of the samples analysed in this study. H.S.N.'s research is further supported by Freya Biosciences and the BioInnovation Institute. H.S.N. has received honoraria from Ferring Pharmaceuticals, Merck A/S, Astra-Zeneca, Cook Medical and Ibsa Nordic. A.N.A. reports no competing interests.", "doi": "10.1093/humrep/deac094", "pmid": "35553675", "labels": {"Luisa Hugerth": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC9247429"}, {"db": "pii", "key": "6584540"}], "notes": [], "created": "2022-11-08T07:02:56.315Z", "modified": "2026-09-23T07:27:46.073Z"}, {"entity": "publication", "iuid": "425c4262ef904b00975674fa8927e4e0", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/425c4262ef904b00975674fa8927e4e0.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/425c4262ef904b00975674fa8927e4e0"}}, "title": "Genomic Sequencing of Bacillus cereus Sensu Lato Strains Isolated from Meat and Poultry Products in South Africa Enables Inter- and Intranational Surveillance and Source Tracking.", "authors": [{"family": "Carroll", "given": "Laura M", "initials": "LM"}, {"family": "Pierneef", "given": "Rian", "initials": "R"}, {"family": "Mathole", "given": "Aletta", "initials": "A"}, {"family": "Atanda", "given": "Abimbola", "initials": "A"}, {"family": "Matle", "given": "Itumeleng", "initials": "I", "orcid": "0000-0002-1495-357X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dd13d91d769e49738063ce04919c589f.json"}}], "type": "journal article", "published": "2022-06-29", "journal": {"title": "Microbiol Spectr", "issn": "2165-0497", "volume": "10", "issue": "3", "pages": "e0070022", "issn-l": null}, "abstract": "Members of the Bacillus cereus sensu lato species complex, also known as the B. cereus group, vary in their ability to cause illness but are frequently isolated from foods, including meat products; however, food safety surveillance efforts that use whole-genome sequencing (WGS) often neglect these potential pathogens. Here, we evaluate the surveillance and source tracking potential of WGS as applied to B. cereus sensu lato by (i) using WGS to characterize B. cereus sensu lato strains isolated during routine surveillance of meat products across South Africa (n = 25) and (ii) comparing the genomes sequenced here to all publicly available, high-quality B. cereus sensu lato genomes (n = 2,887 total genomes). Strains sequenced here were collected from meat products obtained from (i) retail outlets, processing plants, and butcheries across six South African provinces (n = 23) and (ii) imports held at port of entry (n = 2). The 25 strains sequenced here were partitioned into 15 lineages via in silico seven-gene multilocus sequence typing (MLST). While none of the South African B. cereus sensu lato strains sequenced here were identical to publicly available genomes, six MLST lineages contained multiple strains sequenced in this study, which were identical or nearly identical at the whole-genome scale (\u22643 core single nucleotide polymorphisms). Five MLST lineages contained (nearly) identical genomes collected from two or three South African provinces; one MLST lineage contained nearly identical genomes from two countries (South Africa and the Netherlands), indicating that B. cereus sensu lato can spread intra- and internationally via foodstuffs. IMPORTANCE Nationwide foodborne pathogen surveillance programs that use high-resolution genomic methods have been shown to provide vast public health and economic benefits. However, Bacillus cereus sensu lato is often overlooked during large-scale routine WGS efforts. Thus, to our knowledge, no studies to date have evaluated the potential utility of WGS for B. cereus sensu lato surveillance and source tracking in foodstuffs. In this preliminary proof-of-concept study, we applied WGS to B. cereus sensu lato strains collected via South Africa's national surveillance program of domestic and imported meat products, and we provide strong evidence that B. cereus sensu lato can be disseminated intra- and internationally via the agro-food supply chain. Our results showcase that WGS has the potential to be used for source tracking of B. cereus sensu lato in foods, although future WGS and metadata collection efforts are needed to ensure that B. cereus sensu lato surveillance initiatives are on par with those of other foodborne pathogens.", "doi": "10.1128/spectrum.00700-22", "pmid": "35475639", "labels": {"DDLS Fellow": null, "Laura Carroll": null}, "xrefs": [{"db": "pmc", "key": "PMC9241823"}], "notes": [], "created": "2023-05-13T11:52:38.515Z", "modified": "2025-03-18T17:29:03.810Z"}, {"entity": "publication", "iuid": "bd4c792e349c48b9b49a4ec09226f70b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/bd4c792e349c48b9b49a4ec09226f70b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/bd4c792e349c48b9b49a4ec09226f70b"}}, "title": "The genomic basis of the plant island syndrome in Darwin's giant daisies.", "authors": [{"family": "Cerca", "given": "Jos\u00e9", "initials": "J", "orcid": "0000-0001-7788-4367", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b9119ffe17f1400ea74e0eaf43c105fc.json"}}, {"family": "Petersen", "given": "Bent", "initials": "B", "orcid": "0000-0002-2472-8317", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d185cf0902d5433cbf2140f684aff51d.json"}}, {"family": "Lazaro-Guevara", "given": "Jos\u00e9 Miguel", "initials": "JM", "orcid": "0000-0003-0741-4225", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/23ba56aadeb84b119183a8be93556afe.json"}}, {"family": "Rivera-Col\u00f3n", "given": "Angel", "initials": "A", "orcid": "0000-0001-9097-3241", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2a758492a5984ec891e34c8e9a2b16aa.json"}}, {"family": "Birkeland", "given": "Siri", "initials": "S"}, {"family": "Vizueta", "given": "Joel", "initials": "J", "orcid": "0000-0003-0139-3013", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/af75fbcee90e4655b5d70c602a482b84.json"}}, {"family": "Li", "given": "Siyu", "initials": "S"}, {"family": "Li", "given": "Qionghou", "initials": "Q"}, {"family": "Loureiro", "given": "Jo\u00e3o", "initials": "J"}, {"family": "Kosawang", "given": "Chatchai", "initials": "C"}, {"family": "D\u00edaz", "given": "Patricia Jaramillo", "initials": "PJ"}, {"family": "Rivas-Torres", "given": "Gonzalo", "initials": "G"}, {"family": "Fern\u00e1ndez-Mazuecos", "given": "Mario", "initials": "M"}, {"family": "Vargas", "given": "Pablo", "initials": "P"}, {"family": "McCauley", "given": "Ross A", "initials": "RA"}, {"family": "Petersen", "given": "Gitte", "initials": "G"}, {"family": "Santos-Bay", "given": "Luisa", "initials": "L", "orcid": "0000-0002-0554-6550", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/12eab341fe62467db8b2d52c0060c3ef.json"}}, {"family": "Wales", "given": "Nathan", "initials": "N"}, {"family": "Catchen", "given": "Julian M", "initials": "JM", "orcid": "0000-0002-4798-660X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1a28fd27e2af4fa5a14eb7ef61dacc7e.json"}}, {"family": "Machado", "given": "Daniel", "initials": "D"}, {"family": "Nowak", "given": "Michael D", "initials": "MD"}, {"family": "Suh", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8979-9992", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e1790a31477c4376957d8c328299db1c.json"}}, {"family": "Sinha", "given": "Neelima R", "initials": "NR", "orcid": "0000-0002-1494-7065", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02d7e54e399a4a4e8013ce240ab28726.json"}}, {"family": "Nielsen", "given": "Lene R", "initials": "LR", "orcid": "0000-0002-7214-8691", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eab1a9189408465a839bd14769132df9.json"}}, {"family": "Seberg", "given": "Ole", "initials": "O", "orcid": "0000-0001-9675-4090", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/04452114afc541189bd0276d64198e71.json"}}, {"family": "Gilbert", "given": "M Thomas P", "initials": "MTP"}, {"family": "Leebens-Mack", "given": "James H", "initials": "JH"}, {"family": "Rieseberg", "given": "Loren H", "initials": "LH"}, {"family": "Martin", "given": "Michael D", "initials": "MD", "orcid": "0000-0002-2010-5139", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/256d16abe41b4056b53ad221ce248c81.json"}}], "type": "journal article", "published": "2022-06-28", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "13", "issue": "1", "pages": "3729", "issn-l": "2041-1723"}, "abstract": "The repeated, rapid and often pronounced patterns of evolutionary divergence observed in insular plants, or the 'plant island syndrome', include changes in leaf phenotypes, growth, as well as the acquisition of a perennial lifestyle. Here, we sequence and describe the genome of the critically endangered, Gal\u00e1pagos-endemic species Scalesia atractyloides Arnot., obtaining a chromosome-resolved, 3.2-Gbp assembly containing 43,093 candidate gene models. Using a combination of fossil transposable elements, k-mer spectra analyses and orthologue assignment, we identify the two ancestral genomes, and date their divergence and the polyploidization event, concluding that the ancestor of all extant Scalesia species was an allotetraploid. There are a comparable number of genes and transposable elements across the two subgenomes, and while their synteny has been mostly conserved, we find multiple inversions that may have facilitated adaptation. We identify clear signatures of selection across genes associated with vascular development, growth, adaptation to salinity and flowering time, thus finding compelling evidence for a genomic basis of the island syndrome in one of Darwin's giant daisies.", "doi": "10.1038/s41467-022-31280-w", "pmid": "35764640", "labels": {"Jos\u00e9 Cerca": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC9240058"}, {"db": "pii", "key": "10.1038/s41467-022-31280-w"}, {"db": "Dryad", "key": "10.5061/dryad.8gtht76rh"}], "notes": [], "created": "2026-08-20T08:51:56.197Z", "modified": "2026-09-23T10:55:56.532Z"}, {"entity": "publication", "iuid": "09e38ac904ad4fb0858f5de82a16deb0", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/09e38ac904ad4fb0858f5de82a16deb0.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/09e38ac904ad4fb0858f5de82a16deb0"}}, "title": "Transcriptome-wide prediction of prostate cancer gene expression from histopathology images using co-expression-based convolutional neural networks.", "authors": [{"family": "Weitz", "given": "Philippe", "initials": "P", "orcid": "0000-0002-1788-0716", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a70939bc05a04f87b9a61e7d98448e09.json"}}, {"family": "Wang", "given": "Yinxi", "initials": "Y"}, {"family": "Kartasalo", "given": "Kimmo", "initials": "K", "orcid": "0000-0002-9470-4783", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7c6fc97c06ed456c8bdd1f03db8a9b72.json"}}, {"family": "Egevad", "given": "Lars", "initials": "L"}, {"family": "Lindberg", "given": "Johan", "initials": "J"}, {"family": "Gr\u00f6nberg", "given": "Henrik", "initials": "H", "orcid": "0000-0002-1073-2753", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/33927307bf964b2fa09e09c0c867b542.json"}}, {"family": "Eklund", "given": "Martin", "initials": "M", "orcid": "0000-0001-5032-5266", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/06721510ebc8462386e0e6fc6c84315b.json"}}, {"family": "Rantalainen", "given": "Mattias", "initials": "M"}], "type": "journal article", "published": "2022-06-27", "journal": {"title": "Bioinformatics", "issn": "1367-4811", "issn-l": "1367-4803", "volume": "38", "issue": "13", "pages": "3462-3469"}, "abstract": "Molecular phenotyping by gene expression profiling is central in contemporary cancer research and in molecular diagnostics but remains resource intense to implement. Changes in gene expression occurring in tumours cause morphological changes in tissue, which can be observed on the microscopic level. The relationship between morphological patterns and some of the molecular phenotypes can be exploited to predict molecular phenotypes from routine haematoxylin and eosin-stained whole slide images (WSIs) using convolutional neural networks (CNNs). In this study, we propose a new, computationally efficient approach to model relationships between morphology and gene expression.\n\nWe conducted the first transcriptome-wide analysis in prostate cancer, using CNNs to predict bulk RNA-sequencing estimates from WSIs for 370 patients from the TCGA PRAD study. Out of 15 586 protein coding transcripts, 6618 had predicted expression significantly associated with RNA-seq estimates (FDR-adjusted P-value <1\u00d710-4) in a cross-validation and 5419 (81.9%) of these associations were subsequently validated in a held-out test set. We furthermore predicted the prognostic cell-cycle progression score directly from WSIs. These findings suggest that contemporary computer vision models offer an inexpensive and scalable solution for prediction of gene expression phenotypes directly from WSIs, providing opportunity for cost-effective large-scale research studies and molecular diagnostics.\n\nA self-contained example is available from http://github.com/phiwei/prostate_coexpression. Model predictions and metrics are available from doi.org/10.5281/zenodo.4739097.\n\nSupplementary data are available at Bioinformatics online.", "doi": "10.1093/bioinformatics/btac343", "pmid": "35595235", "labels": {"Kimmo Kartasalo": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC9237721"}, {"db": "pii", "key": "6589889"}], "notes": [], "created": "2024-11-05T16:09:35.045Z", "modified": "2026-09-23T10:39:48.953Z"}, {"entity": "publication", "iuid": "7e5001475dcb4a998445d222b9eab1c6", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/7e5001475dcb4a998445d222b9eab1c6.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/7e5001475dcb4a998445d222b9eab1c6"}}, "title": "A scalable, open-source implementation of a large-scale mechanistic model for single cell proliferation and death signaling.", "authors": [{"family": "Erdem", "given": "Cemal", "initials": "C", "orcid": "0000-0003-3663-3646", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f71b5af589264614a52eefa8baba3132.json"}}, {"family": "Mutsuddy", "given": "Arnab", "initials": "A"}, {"family": "Bensman", "given": "Ethan M", "initials": "EM"}, {"family": "Dodd", "given": "William B", "initials": "WB", "orcid": "0000-0001-7568-4732", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4ee5a4fc7c8f407c8c1697a1d0b898d1.json"}}, {"family": "Saint-Antoine", "given": "Michael M", "initials": "MM"}, {"family": "Bouhaddou", "given": "Mehdi", "initials": "M"}, {"family": "Blake", "given": "Robert C", "initials": "RC"}, {"family": "Gross", "given": "Sean M", "initials": "SM"}, {"family": "Heiser", "given": "Laura M", "initials": "LM", "orcid": "0000-0003-3330-0950", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ce0d380df324afcbbaa1971aa8472cc.json"}}, {"family": "Feltus", "given": "F Alex", "initials": "FA", "orcid": "0000-0002-2123-6114", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bf88745ea761439c8a75ecc853e881cb.json"}}, {"family": "Birtwistle", "given": "Marc R", "initials": "MR"}], "type": "journal article", "published": "2022-06-21", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "13", "issue": "1", "pages": "3555", "issn-l": "2041-1723"}, "abstract": "Mechanistic models of how single cells respond to different perturbations can help integrate disparate big data sets or predict response to varied drug combinations. However, the construction and simulation of such models have proved challenging. Here, we developed a python-based model creation and simulation pipeline that converts a few structured text files into an SBML standard and is high-performance- and cloud-computing ready. We applied this pipeline to our large-scale, mechanistic pan-cancer signaling model (named SPARCED) and demonstrate it by adding an IFN\u03b3 pathway submodel. We then investigated whether a putative crosstalk mechanism could be consistent with experimental observations from the LINCS MCF10A Data Cube that IFN\u03b3 acts as an anti-proliferative factor. The analyses suggested this observation can be explained by IFN\u03b3-induced SOCS1 sequestering activated EGF receptors. This work forms a foundational recipe for increased mechanistic model-based data integration on a single-cell level, an important building block for clinically-predictive mechanistic models.", "doi": "10.1038/s41467-022-31138-1", "pmid": "35729113", "labels": {"DDLS Fellow": null, "Cemal Erdem": null}, "xrefs": [{"db": "pmc", "key": "PMC9213456"}, {"db": "pii", "key": "10.1038/s41467-022-31138-1"}, {"db": "figshare", "key": "10.6084/m9.figshare.19658802.v1"}], "notes": [], "created": "2023-10-27T08:53:41.726Z", "modified": "2023-10-27T08:53:41.979Z"}, {"entity": "publication", "iuid": "a686795bebef43e7b8bd593444b110db", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a686795bebef43e7b8bd593444b110db.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a686795bebef43e7b8bd593444b110db"}}, "title": "Enhanced metabolism and negative regulation of ER stress support higher erythropoietin production in HEK293 cells.", "authors": [{"family": "Saghaleyni", "given": "Rasool", "initials": "R"}, {"family": "Malm", "given": "Magdalena", "initials": "M"}, {"family": "Moruzzi", "given": "Noah", "initials": "N"}, {"family": "Zrimec", "given": "Jan", "initials": "J"}, {"family": "Razavi", "given": "Ronia", "initials": "R"}, {"family": "Wistbacka", "given": "Num", "initials": "N"}, {"family": "Thorell", "given": "Hannes", "initials": "H"}, {"family": "Pintar", "given": "Anton", "initials": "A"}, {"family": "Hober", "given": "Andreas", "initials": "A"}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Chotteau", "given": "Veronique", "initials": "V"}, {"family": "Berggren", "given": "Per-Olof", "initials": "PO"}, {"family": "Grassi", "given": "Luigi", "initials": "L"}, {"family": "Zelezniak", "given": "Aleksej", "initials": "A"}, {"family": "Svensson", "given": "Thomas", "initials": "T"}, {"family": "Hatton", "given": "Diane", "initials": "D"}, {"family": "Nielsen", "given": "Jens", "initials": "J"}, {"family": "Robinson", "given": "Jonathan L", "initials": "JL"}, {"family": "Rockberg", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2022-06-14", "journal": {"title": "Cell Reports", "issn": "2211-1247", "volume": "39", "issue": "11", "pages": "110936", "issn-l": null}, "abstract": "Recombinant protein production can cause severe stress on cellular metabolism, resulting in limited titer and product quality. To investigate cellular and metabolic characteristics associated with these limitations, we compare HEK293 clones producing either erythropoietin (EPO) (secretory) or GFP (non-secretory) protein at different rates. Transcriptomic and functional analyses indicate significantly higher metabolism and oxidative phosphorylation in EPO producers compared with parental and GFP cells. In addition, ribosomal genes exhibit specific expression patterns depending on the recombinant protein and the production rate. In a clone displaying a dramatically increased EPO secretion, we detect higher gene expression related to negative regulation of endoplasmic reticulum (ER) stress, including upregulation of ATF6B, which aids EPO production in a subset of clones by overexpression or small interfering RNA (siRNA) knockdown. Our results offer potential target pathways and genes for further development of the secretory power in mammalian cell factories.", "doi": "10.1016/j.celrep.2022.110936", "pmid": "35705050", "labels": {"SciLifeLab Fellow": "", "Fredrik Edfors": "", "DDLS Fellow": "", "Aleksej Zelezniak": ""}, "xrefs": [{"db": "pii", "key": "S2211-1247(22)00718-5"}], "notes": [], "created": "2026-09-23T11:17:21.091Z", "modified": "2026-09-23T11:17:21.130Z"}, {"entity": "publication", "iuid": "e675bcd0ba9643d2b38397d12f3dcdf2", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e675bcd0ba9643d2b38397d12f3dcdf2.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e675bcd0ba9643d2b38397d12f3dcdf2"}}, "title": "GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species.", "authors": [{"family": "Kutschera", "given": "Verena E", "initials": "VE", "orcid": "0000-0002-8930-534X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c7185df2f7d44872960d604e9c70c551.json"}}, {"family": "Kierczak", "given": "Marcin", "initials": "M", "orcid": "0000-0003-2629-5655", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/da6834c3cedf4ea1b20b659316b45eb2.json"}}, {"family": "van der Valk", "given": "Tom", "initials": "T"}, {"family": "von Seth", "given": "Johanna", "initials": "J"}, {"family": "Dussex", "given": "Nicolas", "initials": "N"}, {"family": "Lord", "given": "Edana", "initials": "E"}, {"family": "Dehasque", "given": "Marianne", "initials": "M"}, {"family": "Stanton", "given": "David W G", "initials": "DWG"}, {"family": "Khoonsari", "given": "Payam Emami", "initials": "PE"}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L"}, {"family": "D\u00edez-Del-Molino", "given": "David", "initials": "D", "orcid": "0000-0002-9701-5940", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ffd5992faedc45e1bfe19fd498485400.json"}}], "type": "journal article", "published": "2022-06-13", "journal": {"title": "BMC Bioinformatics", "issn": "1471-2105", "volume": "23", "issue": "1", "pages": "228", "issn-l": "1471-2105"}, "abstract": "Many wild species have suffered drastic population size declines over the past centuries, which have led to 'genomic erosion' processes characterized by reduced genetic diversity, increased inbreeding, and accumulation of harmful mutations. Yet, genomic erosion estimates of modern-day populations often lack concordance with dwindling population sizes and conservation status of threatened species. One way to directly quantify the genomic consequences of population declines is to compare genome-wide data from pre-decline museum samples and modern samples. However, doing so requires computational data processing and analysis tools specifically adapted to comparative analyses of degraded, ancient or historical, DNA data with modern DNA data as well as personnel trained to perform such analyses.\n\nHere, we present a highly flexible, scalable, and modular pipeline to compare patterns of genomic erosion using samples from disparate time periods. The GenErode pipeline uses state-of-the-art bioinformatics tools to simultaneously process whole-genome re-sequencing data from ancient/historical and modern samples, and to produce comparable estimates of several genomic erosion indices. No programming knowledge is required to run the pipeline and all bioinformatic steps are well-documented, making the pipeline accessible to users with different backgrounds. GenErode is written in Snakemake and Python3 and uses Conda and Singularity containers to achieve reproducibility on high-performance compute clusters. The source code is freely available on GitHub ( https://github.com/NBISweden/GenErode ).\n\nGenErode is a user-friendly and reproducible pipeline that enables the standardization of genomic erosion indices from temporally sampled whole genome re-sequencing data.", "doi": "10.1186/s12859-022-04757-0", "pmid": "35698034", "labels": {"Tom van der Valk": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC9195343"}, {"db": "pii", "key": "10.1186/s12859-022-04757-0"}], "notes": [], "created": "2022-12-02T13:45:16.525Z", "modified": "2026-09-23T08:49:27.233Z"}, {"entity": "publication", "iuid": "4165644ec87a40248af1140080134d20", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4165644ec87a40248af1140080134d20.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4165644ec87a40248af1140080134d20"}}, "title": "BioImage Model Zoo: A Community-Driven Resource for Accessible Deep Learning in BioImage Analysis", "authors": [{"family": "Ouyang", "given": "Wei", "initials": "W"}, {"family": "Beuttenmueller", "given": "Fynn", "initials": "F"}, {"family": "G\u00f3mez-de-Mariscal", "given": "Estibaliz", "initials": "E"}, {"family": "Pape", "given": "Constantin", "initials": "C"}, {"family": "Burke", "given": "Tom", "initials": "T"}, {"family": "Garcia-L\u00f3pez-de-Haro", "given": "Carlos", "initials": "C"}, {"family": "Russell", "given": "Craig", "initials": "C"}, {"family": "Moya-Sans", "given": "Luc\u00eda", "initials": "L"}, {"family": "de-la-Torre-Guti\u00e9rrez", "given": "Cristina", "initials": "C"}, {"family": "Schmidt", "given": "Deborah", "initials": "D"}, {"family": "Kutra", "given": "Dominik", "initials": "D"}, {"family": "Novikov", "given": "Maksim", "initials": "M"}, {"family": "Weigert", "given": "Martin", "initials": "M"}, {"family": "Schmidt", "given": "Uwe", "initials": "U"}, {"family": "Bankhead", "given": "Peter", "initials": "P", "orcid": "0000-0003-4851-8813", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8e6c4114b6d740958ac32ee6a125c710.json"}}, {"family": "Jacquemet", "given": "Guillaume", "initials": "G", "orcid": "0000-0002-9286-920X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b7a1bac74d1946259e319f067f61e88d.json"}}, {"family": "Sage", "given": "Daniel", "initials": "D"}, {"family": "Henriques", "given": "Ricardo", "initials": "R"}, {"family": "Mu\u00f1oz-Barrutia", "given": "Arrate", "initials": "A", "orcid": "0000-0002-1573-1661", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1f71dcceb0284105a7033f2ed195b9c1.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E"}, {"family": "Jug", "given": "Florian", "initials": "F"}, {"family": "Kreshuk", "given": "Anna", "initials": "A", "orcid": "0000-0003-1334-6388", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1408e8d1447d4b56b3d713994bea8152.json"}}], "type": "posted-content", "published": "2022-06-08", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2022.06.07.495102", "pmid": null, "labels": {"DDLS Fellow": "", "Wei Ouyang": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T10:11:39.144Z", "modified": "2026-09-23T13:41:32.358Z"}, {"entity": "publication", "iuid": "1b5959ae2a0048a2963b6e9fbb0d3a1e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1b5959ae2a0048a2963b6e9fbb0d3a1e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1b5959ae2a0048a2963b6e9fbb0d3a1e"}}, "title": "Sugar-sweetened beverage and sugar consumption and colorectal cancer incidence and mortality according to anatomic subsite.", "authors": [{"family": "Yuan", "given": "Chen", "initials": "C", "orcid": "0000-0002-0708-9648", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cd3904c835394e0d89bba633a0b74c54.json"}}, {"family": "Joh", "given": "Hee-Kyung", "initials": "HK"}, {"family": "Wang", "given": "Qiao-Li", "initials": "QL"}, {"family": "Zhang", "given": "Yin", "initials": "Y"}, {"family": "Smith-Warner", "given": "Stephanie A", "initials": "SA", "orcid": "0000-0003-3462-8608", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/caa1fd8a54d7407aa1f6f9eb33f45383.json"}}, {"family": "Wang", "given": "Molin", "initials": "M"}, {"family": "Song", "given": "Mingyang", "initials": "M", "orcid": "0000-0002-4780-4642", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/92720682df6c466997c4ae4fb4419c56.json"}}, {"family": "Cao", "given": "Yin", "initials": "Y", "orcid": "0000-0001-9835-7662", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a34eb276a5514342adb104aa5df642c9.json"}}, {"family": "Zhang", "given": "Xuehong", "initials": "X"}, {"family": "Zoltick", "given": "Emilie S", "initials": "ES"}, {"family": "Hur", "given": "Jinhee", "initials": "J", "orcid": "0000-0003-0968-208X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/51ce46416a8f4ab0bc5ca87fc9fa11bd.json"}}, {"family": "Chan", "given": "Andrew T", "initials": "AT"}, {"family": "Meyerhardt", "given": "Jeffrey A", "initials": "JA", "orcid": "0000-0002-1120-0898", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1be03d64e6674271953b194ddaac4f29.json"}}, {"family": "Ogino", "given": "Shuji", "initials": "S"}, {"family": "Ng", "given": "Kimmie", "initials": "K", "orcid": "0000-0003-0631-1494", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/00bc0d97cfc44e9398c9bf1db5783402.json"}}, {"family": "Giovannucci", "given": "Edward L", "initials": "EL"}, {"family": "Wu", "given": "Kana", "initials": "K"}], "type": "journal article", "published": "2022-06-07", "journal": {"title": "Am. J. Clin. Nutr.", "issn": "1938-3207", "volume": "115", "issue": "6", "pages": "1481-1489", "issn-l": "0002-9165"}, "abstract": "Recent preclinical research strongly suggests that dietary sugars can enhance colorectal tumorigenesis by direct action, particularly in the proximal colon that unabsorbed fructose reaches.\n\nWe aimed to examine long-term consumption of sugar-sweetened beverages (SSBs) and total fructose in relation to incidence and mortality of colorectal cancer (CRC) by anatomic subsite.\n\nWe followed 121,111 participants from 2 prospective US cohort studies, the Nurses' Health Study (1984-2014) and Health Professionals Follow-Up Study (1986-2014), for incident CRC and related death. Cox proportional hazards regression was used to compute HRs and 95% CIs.\n\nDuring follow-up, we documented 2733 incident cases of CRC with a known anatomic location, of whom 901 died from CRC. Positive associations of SSB and total fructose intakes with cancer incidence and mortality were observed in the proximal colon but not in the distal colon or rectum (Pheterogeneity \u2264 0.03). SSB consumption was associated with a statistically significant increase in the incidence of proximal colon cancer (HR per 1-serving/d increment: 1.18; 95% CI: 1.03, 1.34; Ptrend = 0.02) and a more pronounced elevation in the mortality of proximal colon cancer (HR: 1.39; 95% CI: 1.13, 1.72; Ptrend = 0.002). Similarly, total fructose intake was associated with increased incidence and mortality of proximal colon cancer (HRs per 25-g/d increment: 1.18; 95% CI: 1.03, 1.35; and 1.42; 95% CI: 1.12, 1.79, respectively). Moreover, SSB and total fructose intakes during the most recent 10 y, rather than those from a more distant period, were associated with increased incidence of proximal colon cancer.\n\nSSB and total fructose consumption were associated with increased incidence and mortality of proximal colon cancer, particularly during later stages of tumorigenesis.", "doi": "10.1093/ajcn/nqac040", "pmid": "35470384", "labels": {"DDLS Fellow": null, "Qiaoli Wang": null}, "xrefs": [{"db": "pmc", "key": "PMC9170474"}, {"db": "pii", "key": "S0002-9165(22)00274-X"}], "notes": [], "created": "2025-11-27T18:53:37.269Z", "modified": "2025-11-27T18:53:37.448Z"}, {"entity": "publication", "iuid": "a369585d7b334ff2a61235dee75bca06", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a369585d7b334ff2a61235dee75bca06.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a369585d7b334ff2a61235dee75bca06"}}, "title": "Probing the Link between Pancratistatin and Mitochondrial Apoptosis through Changes in the Membrane Dynamics on the Nanoscale.", "authors": [{"family": "Castillo", "given": "Stuart R", "initials": "SR"}, {"family": "Rickeard", "given": "Brett W", "initials": "BW"}, {"family": "DiPasquale", "given": "Mitchell", "initials": "M"}, {"family": "Nguyen", "given": "Michael H L", "initials": "MHL"}, {"family": "Lewis-Laurent", "given": "Aislyn", "initials": "A"}, {"family": "Doktorova", "given": "Milka", "initials": "M"}, {"family": "Kav", "given": "Batuhan", "initials": "B", "orcid": "0000-0003-4990-373X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f092a8f23a5544aabba740be69a05099.json"}}, {"family": "Miettinen", "given": "Markus S", "initials": "MS", "orcid": "0000-0002-3999-4722", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d2d402ef290145c89c840c1f87a81b17.json"}}, {"family": "Nagao", "given": "Michihiro", "initials": "M", "orcid": "0000-0003-3617-251X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/164a39e5ea05484ca0f7b89d4d6e6b4b.json"}}, {"family": "Kelley", "given": "Elizabeth G", "initials": "EG", "orcid": "0000-0002-6128-8517", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c3bd8f6f01b941a49f4cecc77224ffeb.json"}}, {"family": "Marquardt", "given": "Drew", "initials": "D", "orcid": "0000-0001-6848-2497", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/114cdc1c929d46308422b3b587f8e1d6.json"}}], "type": "journal article", "published": "2022-06-06", "journal": {"title": "Mol. Pharm.", "issn": "1543-8392", "issn-l": "1543-8384", "volume": "19", "issue": "6", "pages": "1839-1852"}, "abstract": "Pancratistatin (PST) is a natural antiviral alkaloid that has demonstrated specificity toward cancerous cells and explicitly targets the mitochondria. PST initiates apoptosis while leaving healthy, noncancerous cells unscathed. However, the manner by which PST induces apoptosis remains elusive and impedes the advancement of PST as a natural anticancer therapeutic agent. Herein, we use neutron spin-echo (NSE) spectroscopy, molecular dynamics (MD) simulations, and supporting small angle scattering techniques to study PST's effect on membrane dynamics using biologically representative model membranes. Our data suggests that PST stiffens the inner mitochondrial membrane (IMM) by being preferentially associated with cardiolipin, which would lead to the relocation and release of cytochrome c. Second, PST has an ordering effect on the lipids and disrupts their distribution within the IMM, which would interfere with the maintenance and functionality of the active forms of proteins in the electron transport chain. These previously unreported findings implicate PST's effect on mitochondrial apoptosis.", "doi": "10.1021/acs.molpharmaceut.1c00926", "pmid": "35559658", "labels": {"Milka Doktorova": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2024-11-27T12:19:21.904Z", "modified": "2024-11-29T12:15:45.480Z"}, {"entity": "publication", "iuid": "d963d1f6aaad43dd91df7a8045deb096", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d963d1f6aaad43dd91df7a8045deb096.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d963d1f6aaad43dd91df7a8045deb096"}}, "title": "Artificial neural networks enable genome-scale simulations of intracellular signaling.", "authors": [{"family": "Nilsson", "given": "Avlant", "initials": "A", "orcid": "0000-0002-9476-4516", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f2e21dbc1c624f6a841c59e959e948e4.json"}}, {"family": "Peters", "given": "Joshua M", "initials": "JM", "orcid": "0000-0001-9163-6706", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7cc62a8588fb4ccc80d4cb52fd584a0f.json"}}, {"family": "Meimetis", "given": "Nikolaos", "initials": "N", "orcid": "0000-0003-2333-0187", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e0e968cb5cc44b52818647cea77762d9.json"}}, {"family": "Bryson", "given": "Bryan", "initials": "B", "orcid": "0000-0003-1716-6712", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/53a00ca82242485d8d0c88ed953bd537.json"}}, {"family": "Lauffenburger", "given": "Douglas A", "initials": "DA", "orcid": "0000-0002-0050-989X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ac0a09cb7c9c49de95b660756a4e5464.json"}}], "type": "journal article", "published": "2022-06-02", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "13", "issue": "1", "pages": "3069"}, "abstract": "Mammalian cells adapt their functional state in response to external signals in form of ligands that bind receptors on the cell-surface. Mechanistically, this involves signal-processing through a complex network of molecular interactions that govern transcription factor activity patterns. Computer simulations of the information flow through this network could help predict cellular responses in health and disease. Here we develop a recurrent neural network framework constrained by prior knowledge of the signaling network with ligand-concentrations as input and transcription factor-activity as output. Applied to synthetic data, it predicts unseen test-data (Pearson correlation r = 0.98) and the effects of gene knockouts (r = 0.8). We stimulate macrophages with 59 different ligands, with and without the addition of lipopolysaccharide, and collect transcriptomics data. The framework predicts this data under cross-validation (r = 0.8) and knockout simulations suggest a role for RIPK1 in modulating the lipopolysaccharide response. This work demonstrates the feasibility of genome-scale simulations of intracellular signaling.", "doi": "10.1038/s41467-022-30684-y", "pmid": "35654811", "labels": {"Avlant Nilsson": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC9163072"}, {"db": "pii", "key": "10.1038/s41467-022-30684-y"}], "notes": [], "created": "2025-03-20T11:09:57.547Z", "modified": "2025-03-21T13:18:02.146Z"}, {"entity": "publication", "iuid": "ac4305ef7b684705b92d872cab31564f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ac4305ef7b684705b92d872cab31564f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ac4305ef7b684705b92d872cab31564f"}}, "title": "The limits of human microRNA annotation have been met.", "authors": [{"family": "Fromm", "given": "Bastian", "initials": "B", "orcid": "0000-0003-0352-3037", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cdc4c42e06604b759dd6225c5f8362b5.json"}}, {"family": "Zhong", "given": "Xiangfu", "initials": "X", "orcid": "0000-0002-1872-1186", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7294e8fb054340e5be637556540ca10e.json"}}, {"family": "Tarbier", "given": "Marcel", "initials": "M", "orcid": "0000-0003-0556-2531", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9678d0797def441e9870afe6ffbb08d0.json"}}, {"family": "Friedl\u00e4nder", "given": "Marc R", "initials": "MR", "orcid": "0000-0001-6577-4363", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ac5a2794be7c4cab89d1e4f1570c9417.json"}}, {"family": "Hackenberg", "given": "Michael", "initials": "M", "orcid": "0000-0003-2248-3114", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b5d460b880634ea5befd132426191afe.json"}}], "type": "journal article", "published": "2022-06-00", "journal": {"title": "RNA", "issn": "1469-9001", "volume": "28", "issue": "6", "pages": "781-785", "issn-l": "1355-8382"}, "abstract": "Over the last few years, the number of microRNAs in the human genome has become a controversially debated issue. Several publications reported thousands of putative novel microRNAs not included in the curated microRNA gene database MirGeneDB and the repository miRBase. Recently, by using sequencing of \u223c300 human tissues and cell lines, the human RNA atlas, an expanded inventory of human RNA annotations, was published, reporting thousands of putative microRNAs. We, the developers of established microRNA prediction tools and hosts of MirGeneDB, raise concerns about the frequently applied prediction and functional validation strategies, briefly discussing the drawbacks of false positive detections. By means of quantifying well-established biogenesis-derived features, we show that the reported novel microRNAs essentially represent false-positives and argue that the human microRNA complement, at about 550 microRNA genes, is already near complete. Output of available tools must be curated as false predictions will misguide scientists looking for biomarkers or therapeutic targets.", "doi": "10.1261/rna.079098.122", "pmid": "35236776", "labels": {"Marc Friedl\u00e4nder": "", "SciLifeLab Fellow": "", "DDLS Fellow": "", "Marcel Tarbier": ""}, "xrefs": [{"db": "pmc", "key": "PMC9074900"}, {"db": "pii", "key": "rna.079098.122"}, {"db": "medline", "key": "9509184"}], "notes": [], "created": "2022-12-06T09:06:33.942Z", "modified": "2026-09-23T08:46:38.377Z"}, {"entity": "publication", "iuid": "10b5b7a1918d4b41946b103a175f76c0", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/10b5b7a1918d4b41946b103a175f76c0.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/10b5b7a1918d4b41946b103a175f76c0"}}, "title": "FISH-quant v2: a scalable and modular tool for smFISH image analysis.", "authors": [{"family": "Imbert", "given": "Arthur", "initials": "A"}, {"family": "Ouyang", "given": "Wei", "initials": "W"}, {"family": "Safieddine", "given": "Adham", "initials": "A", "orcid": "0000-0002-9324-9037", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9631fea704c2481dba933e59b12873d5.json"}}, {"family": "Coleno", "given": "Emeline", "initials": "E"}, {"family": "Zimmer", "given": "Christophe", "initials": "C"}, {"family": "Bertrand", "given": "Edouard", "initials": "E"}, {"family": "Walter", "given": "Thomas", "initials": "T"}, {"family": "Mueller", "given": "Florian", "initials": "F", "orcid": "0000-0002-9622-4396", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8df07352fbd44ef39300b8067904c5c7.json"}}], "type": "journal article", "published": "2022-06-00", "journal": {"title": "RNA", "issn": "1469-9001", "volume": "28", "issue": "6", "pages": "786-795", "issn-l": "1355-8382"}, "abstract": "Regulation of RNA abundance and localization is a key step in gene expression control. Single-molecule RNA fluorescence in situ hybridization (smFISH) is a widely used single-cell-single-molecule imaging technique enabling quantitative studies of gene expression and its regulatory mechanisms. Today, these methods are applicable at a large scale, which in turn come with a need for adequate tools for data analysis and exploration. Here, we present FISH-quant v2, a highly modular tool accessible for both experts and non-experts. Our user-friendly package allows the user to segment nuclei and cells, detect isolated RNAs, decompose dense RNA clusters, quantify RNA localization patterns and visualize these results both at the single-cell level and variations within the cell population. This tool was validated and applied on large-scale smFISH image data sets, revealing diverse subcellular RNA localization patterns and a surprisingly high degree of cell-to-cell heterogeneity.", "doi": "10.1261/rna.079073.121", "pmid": "35347070", "labels": {"DDLS Fellow": "", "Wei Ouyang": ""}, "xrefs": [{"db": "pmc", "key": "PMC9074904"}, {"db": "pii", "key": "rna.079073.121"}, {"db": "medline", "key": "9509184"}], "notes": [], "created": "2026-08-21T12:42:59.122Z", "modified": "2026-10-01T08:23:14.062Z"}, {"entity": "publication", "iuid": "6d37e94b33be464385ae77bce25aa3c9", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/6d37e94b33be464385ae77bce25aa3c9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/6d37e94b33be464385ae77bce25aa3c9"}}, "title": "Machine Learning Analysis Reveals Biomarkers for the Detection of Neurological Diseases.", "authors": [{"family": "Lam", "given": "Simon", "initials": "S"}, {"family": "Arif", "given": "Muhammad", "initials": "M"}, {"family": "Song", "given": "Xiya", "initials": "X"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}], "type": "journal article", "published": "2022-05-31", "journal": {"title": "Front Mol Neurosci", "issn": "1662-5099", "volume": "15", "pages": "889728", "issn-l": "1662-5099"}, "abstract": "It is critical to identify biomarkers for neurological diseases (NLDs) to accelerate drug discovery for effective treatment of patients of diseases that currently lack such treatments. In this work, we retrieved genotyping and clinical data from 1,223 UK Biobank participants to identify genetic and clinical biomarkers for NLDs, including Alzheimer's disease (AD), Parkinson's disease (PD), motor neuron disease (MND), and myasthenia gravis (MG). Using a machine learning modeling approach with Monte Carlo randomization, we identified a panel of informative diagnostic biomarkers for predicting AD, PD, MND, and MG, including classical liver disease markers such as alanine aminotransferase, alkaline phosphatase, and bilirubin. A multinomial model trained on accessible clinical markers could correctly predict an NLD diagnosis with an accuracy of 88.3%. We also explored genetic biomarkers. In a genome-wide association study of AD, PD, MND, and MG patients, we identified single nucleotide polymorphisms (SNPs) implicated in several craniofacial disorders such as apnoea and branchiootic syndrome. We found evidence for shared genetic risk loci among NLDs, including SNPs in cancer-related genes and SNPs known to be associated with non-brain cancers such as Wilms tumor, leukemia, and colon cancer. This indicates overlapping genetic characterizations among NLDs which challenges current clinical definitions of the neurological disorders. Taken together, this work demonstrates the value of data-driven approaches to identify novel biomarkers in the absence of any known or promising biomarkers.", "doi": "10.3389/fnmol.2022.889728", "pmid": "35711735", "labels": {"Adil Mardinoglu": "", "SciLifeLab Fellow": "", "DDLS Fellow": "", "Muhammad Arif": ""}, "xrefs": [{"db": "pmc", "key": "PMC9194858"}], "notes": [], "created": "2023-12-04T15:02:08.222Z", "modified": "2026-09-23T10:58:46.288Z"}, {"entity": "publication", "iuid": "0d21479fbfb947ab9ec181554bcad455", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0d21479fbfb947ab9ec181554bcad455.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0d21479fbfb947ab9ec181554bcad455"}}, "title": "Comprehensive analysis of pathways in Coronavirus 2019 (COVID-19) using an unsupervised machine learning method", "authors": [{"family": "Taheri", "given": "Golnaz", "initials": "G"}, {"family": "Habibi", "given": "Mahnaz", "initials": "M"}], "type": "posted-content", "published": "2022-05-19", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2022.05.18.492441", "pmid": null, "labels": {"Golnaz Taheri": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T10:11:16.480Z", "modified": "2026-09-23T14:33:49.261Z"}, {"entity": "publication", "iuid": "b22f94d7469443e69b2dc22f4f678b5f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b22f94d7469443e69b2dc22f4f678b5f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b22f94d7469443e69b2dc22f4f678b5f"}}, "title": "Using unsupervised learning algorithms to identify essential genes associated with SARS-CoV-2 as potential therapeutic targets for COVID-19", "authors": [{"family": "Taheri", "given": "Golnaz", "initials": "G"}, {"family": "Habibi", "given": "Mahnaz", "initials": "M"}], "type": "posted-content", "published": "2022-05-18", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2022.05.18.492443", "pmid": null, "labels": {"Golnaz Taheri": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T10:11:18.269Z", "modified": "2026-09-23T14:14:11.603Z"}, {"entity": "publication", "iuid": "caa8d2da6ccc4054825f8f3aa303d17b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/caa8d2da6ccc4054825f8f3aa303d17b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/caa8d2da6ccc4054825f8f3aa303d17b"}}, "title": "The vaginal microbiome and the risk of preterm birth: a systematic review and network meta-analysis.", "authors": [{"family": "Gudnadottir", "given": "Unnur", "initials": "U", "orcid": "0000-0002-4663-9921", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8702d95608284348b837ebbe275cc6af.json"}}, {"family": "Debelius", "given": "Justine W", "initials": "JW"}, {"family": "Du", "given": "Juan", "initials": "J"}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW"}, {"family": "Danielsson", "given": "Hanna", "initials": "H"}, {"family": "Schuppe-Koistinen", "given": "Ina", "initials": "I"}, {"family": "Fransson", "given": "Emma", "initials": "E"}, {"family": "Brusselaers", "given": "Nele", "initials": "N"}], "type": "journal article", "published": "2022-05-13", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "12", "issue": "1", "pages": "7926", "issn-l": "2045-2322"}, "abstract": "Preterm birth is a major cause of neonatal morbidity and mortality worldwide. Increasing evidence links the vaginal microbiome to the risk of spontaneous preterm labour that leads to preterm birth. The aim of this systematic review and network meta-analysis was to investigate the association between the vaginal microbiome, defined as community state types (CSTs, i.e. dominance of specific lactobacilli spp, or not (low-lactobacilli)), and the risk of preterm birth. Systematic review using PubMed, Web of Science, Embase and Cochrane library was performed. Longitudinal studies using culture-independent methods categorizing the vaginal microbiome in at least three different CSTs to assess the risk of preterm birth were included. A (network) meta-analysis was conducted, presenting pooled odds ratios (OR) and 95% confidence intervals (CI); and weighted proportions and 95% CI. All 17 studies were published between 2014 and 2021 and included 38-539 pregnancies and 8-107 preterm births. Women presenting with \"low-lactobacilli\" vaginal microbiome were at increased risk (OR 1.69, 95% CI 1.15-2.49) for delivering preterm compared to Lactobacillus crispatus dominant women. Our network meta-analysis supports the microbiome being predictive of preterm birth, where low abundance of lactobacilli is associated with the highest risk, and L. crispatus dominance the lowest.", "doi": "10.1038/s41598-022-12007-9", "pmid": "35562576", "labels": {"DDLS Fellow": "", "Luisa Hugerth": ""}, "xrefs": [{"db": "pmc", "key": "PMC9106729"}, {"db": "pii", "key": "10.1038/s41598-022-12007-9"}], "notes": [], "created": "2023-05-12T13:20:06.440Z", "modified": "2026-09-23T07:25:38.608Z"}, {"entity": "publication", "iuid": "520bd20cb8d0415eb98887ce8e395d07", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/520bd20cb8d0415eb98887ce8e395d07.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/520bd20cb8d0415eb98887ce8e395d07"}}, "title": "Genetics of smoking and risk of clonal hematopoiesis.", "authors": [{"family": "Levin", "given": "Michael G", "initials": "MG", "orcid": "0000-0002-9937-9932", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ed963b203f1b41ac94c167cdc2767468.json"}}, {"family": "Nakao", "given": "Tetsushi", "initials": "T", "orcid": "0000-0001-9979-2682", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7e818cd4544c41c2a7fa91dbce13429e.json"}}, {"family": "Zekavat", "given": "Seyedeh M", "initials": "SM", "orcid": "0000-0003-4026-8944", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6234b31f08e442a9b71a711ec7b1147a.json"}}, {"family": "Koyama", "given": "Satoshi", "initials": "S", "orcid": "0000-0002-9286-0360", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8e79637c05b54d7089b1d23155db2b3a.json"}}, {"family": "Bick", "given": "Alexander G", "initials": "AG", "orcid": "0000-0001-5824-9595", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d2da5a35a4984921b19dfafe64cea2de.json"}}, {"family": "Niroula", "given": "Abhishek", "initials": "A"}, {"family": "Ebert", "given": "Benjamin", "initials": "B"}, {"family": "Damrauer", "given": "Scott M", "initials": "SM", "orcid": "0000-0001-8009-1632", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f35b78d4384d41f2bfae2639b23b1e82.json"}}, {"family": "Natarajan", "given": "Pradeep", "initials": "P", "orcid": "0000-0001-8402-7435", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fe8bd48c61c047cd8e61c35d9e9ac650.json"}}], "type": "journal article", "published": "2022-05-04", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "12", "issue": "1", "pages": "7248", "issn-l": "2045-2322"}, "abstract": "Clonal hematopoiesis of indeterminate potential (CHIP) and mosaic chromosomal alterations (mCAs) represent two forms of clonal hematopoiesis where clones bearing expanded somatic mutations have been linked to both oncologic and non-oncologic clinical outcomes including atherosclerosis and all-cause mortality. Epidemiologic studies have highlighted smoking as an important driver of somatic mutations across multiple tissues. However, establishing the causal role of smoking in clonal hematopoiesis has been limited by observational study designs, which may suffer from confounding and reverse-causality. We performed two complementary analyses to investigate the role of smoking in mCAs and CHIP. First, using an observational study design among UK Biobank participants, we confirmed strong associations between smoking and mCAs. Second, using two-sample Mendelian randomization, smoking was strongly associated with mCA but not with CHIP. Overall, these results support a causal association between smoking and mCAs and suggest smoking may variably shape the fitness of clones bearing somatic mutations.", "doi": "10.1038/s41598-022-09604-z", "pmid": "35508625", "labels": {"Abhishek Niroula": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC9068754"}, {"db": "pii", "key": "10.1038/s41598-022-09604-z"}], "notes": [], "created": "2023-11-20T11:36:19.186Z", "modified": "2023-11-20T11:36:19.393Z"}, {"entity": "publication", "iuid": "f8d37a88f5464cbc8d699d723401d0c7", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f8d37a88f5464cbc8d699d723401d0c7.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f8d37a88f5464cbc8d699d723401d0c7"}}, "title": "Cancer-Associated Fibroblasts and Squamous Epithelial Cells Constitute a Unique Microenvironment in a Mouse Model of Inflammation-Induced Colon Cancer.", "authors": [{"family": "Vega", "given": "Paige N", "initials": "PN"}, {"family": "Nilsson", "given": "Avlant", "initials": "A", "orcid": "0000-0002-9476-4516", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f2e21dbc1c624f6a841c59e959e948e4.json"}}, {"family": "Kumar", "given": "Manu P", "initials": "MP"}, {"family": "Niitsu", "given": "Hiroaki", "initials": "H"}, {"family": "Simmons", "given": "Alan J", "initials": "AJ"}, {"family": "Ro", "given": "James", "initials": "J"}, {"family": "Wang", "given": "Jiawei", "initials": "J"}, {"family": "Chen", "given": "Zhengyi", "initials": "Z"}, {"family": "Joughin", "given": "Brian A", "initials": "BA"}, {"family": "Li", "given": "Wei", "initials": "W", "orcid": "0000-0003-3344-1403", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8a26a8c8ad0c4fb2a03f541eac672081.json"}}, {"family": "McKinley", "given": "Eliot T", "initials": "ET"}, {"family": "Liu", "given": "Qi", "initials": "Q"}, {"family": "Roland", "given": "Joseph T", "initials": "JT"}, {"family": "Washington", "given": "M Kay", "initials": "MK"}, {"family": "Coffey", "given": "Robert J", "initials": "RJ"}, {"family": "Lauffenburger", "given": "Douglas A", "initials": "DA", "orcid": "0000-0002-0050-989X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ac0a09cb7c9c49de95b660756a4e5464.json"}}, {"family": "Lau", "given": "Ken S", "initials": "KS"}], "type": "journal article", "published": "2022-05-04", "journal": {"title": "Front Oncol", "issn": "2234-943X", "issn-l": "2234-943X", "volume": "12", "issue": null, "pages": "878920"}, "abstract": "The tumor microenvironment plays a key role in the pathogenesis of colorectal tumors and contains various cell types including epithelial, immune, and mesenchymal cells. Characterization of the interactions between these cell types is necessary for revealing the complex nature of tumors. In this study, we used single-cell RNA-seq (scRNA-seq) to compare the tumor microenvironments between a mouse model of sporadic colorectal adenoma (Lrig1CreERT2/+;Apc2lox14/+) and a mouse model of inflammation-driven colorectal cancer induced by azoxymethane and dextran sodium sulfate (AOM/DSS). While both models develop tumors in the distal colon, we found that the two tumor types have distinct microenvironments. AOM/DSS tumors have an increased abundance of two populations of cancer-associated fibroblasts (CAFs) compared with APC tumors, and we revealed their divergent spatial association with tumor cells using multiplex immunofluorescence (MxIF) imaging. We also identified a unique squamous cell population in AOM/DSS tumors, whose origins were distinct from anal squamous epithelial cells. These cells were in higher proportions upon administration of a chemotherapy regimen of 5-Fluorouracil/Irinotecan. We used computational inference algorithms to predict cell-cell communication mediated by ligand-receptor interactions and downstream pathway activation, and identified potential mechanistic connections between CAFs and tumor cells, as well as CAFs and squamous epithelial cells. This study provides important preclinical insight into the microenvironment of two distinct models of colorectal tumors and reveals unique roles for CAFs and squamous epithelial cells in the AOM/DSS model of inflammation-driven cancer.", "doi": "10.3389/fonc.2022.878920", "pmid": "35600339", "labels": {"Avlant Nilsson": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC9114773"}], "notes": [], "created": "2025-03-20T11:09:59.914Z", "modified": "2025-03-21T13:18:25.710Z"}, {"entity": "publication", "iuid": "50db625e5d3149828022de90fad377f8", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/50db625e5d3149828022de90fad377f8.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/50db625e5d3149828022de90fad377f8"}}, "title": "The right bug in the right place: opportunities for bacterial vaginosis treatment.", "authors": [{"family": "Wu", "given": "Shengru", "initials": "S", "orcid": "0000-0002-1046-3477", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/aca8b8740fd64cc6bb9daef87587bdc9.json"}}, {"family": "Hugerth", "given": "Luisa Warchavchik", "initials": "LW"}, {"family": "Schuppe-Koistinen", "given": "Ina", "initials": "I", "orcid": "0000-0002-1423-3089", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/659fb04e6a1a430cbd707b8a50d500a3.json"}}, {"family": "Du", "given": "Juan", "initials": "J", "orcid": "0000-0001-7649-9571", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f67834a614ca4cd4aff026e5e9a1a1e4.json"}}], "type": "journal article", "published": "2022-05-02", "journal": {"title": "NPJ Biofilms Microbiomes", "issn": "2055-5008", "volume": "8", "issue": "1", "pages": "34", "issn-l": null}, "abstract": "Bacterial vaginosis (BV) is a condition in which the vaginal microbiome presents an overgrowth of obligate and facultative anaerobes, which disturbs the vaginal microbiome balance. BV is a common and recurring vaginal infection among women of reproductive age and is associated with adverse health outcomes and a decreased quality of life. The current recommended first-line treatment for BV is antibiotics, despite the high recurrence rate. Live biopharmaceutical products/probiotics and vaginal microbiome transplantation (VMT) have also been tested in clinical trials for BV. In this review, we discuss the advantages and challenges of current BV treatments and interventions. Furthermore, we provide our understanding of why current clinical trials with probiotics have had mixed results, which is mainly due to not administering the correct bacteria to the correct body site. Here, we propose a great opportunity for large clinical trials with probiotic strains isolated from the vaginal tract (e.g., Lactobacillus crispatus) and administered directly into the vagina after pretreatment.", "doi": "10.1038/s41522-022-00295-y", "pmid": "35501321", "labels": {"DDLS Fellow": "", "Luisa Hugerth": ""}, "xrefs": [{"db": "pmc", "key": "PMC9061781"}, {"db": "pii", "key": "10.1038/s41522-022-00295-y"}], "notes": [], "created": "2023-05-12T13:20:11.596Z", "modified": "2026-09-23T08:31:00.629Z"}, {"entity": "publication", "iuid": "52882b46aaaf41ff8157d59b5ddce4f5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/52882b46aaaf41ff8157d59b5ddce4f5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/52882b46aaaf41ff8157d59b5ddce4f5"}}, "title": "Subtypes of Alzheimer's disease: questions, controversy, and meaning.", "authors": [{"family": "Vogel", "given": "Jacob W", "initials": "JW"}, {"family": "Hansson", "given": "Oskar", "initials": "O"}], "type": "journal article", "published": "2022-05-00", "journal": {"title": "Trends Neurosci", "issn": "1878-108X", "issn-l": null, "volume": "45", "issue": "5", "pages": "342-345"}, "abstract": "The distribution of Alzheimer's disease (AD) tau pathology varies systematically and causes a diverse array of syndromes. This forum article provides a brief overview of key controversies in untangling the complexity of AD subtypes, explores potential causes of AD variability in the population, and discusses clinical relevance and future directions of research into AD heterogeneity.", "doi": "10.1016/j.tins.2022.02.001", "pmid": "35227519", "labels": {"Jacob W Vogel": null, "DDLS Fellow": null}, "xrefs": [{"db": "pii", "key": "S0166-2236(22)00033-9"}], "notes": [], "created": "2023-05-28T17:58:06.012Z", "modified": "2023-11-29T06:39:19.329Z"}, {"entity": "publication", "iuid": "a011a457c6814c8997806c6024c28807", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a011a457c6814c8997806c6024c28807.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a011a457c6814c8997806c6024c28807"}}, "title": "Clonal Hematopoiesis and CKD Progression.", "authors": [{"family": "Niroula", "given": "Abhishek", "initials": "A"}, {"family": "Belizaire", "given": "Roger", "initials": "R"}], "type": "editorial", "published": "2022-05-00", "journal": {"title": "J. Am. Soc. Nephrol.", "issn": "1533-3450", "volume": "33", "issue": "5", "pages": "878-879", "issn-l": "1046-6673"}, "abstract": null, "doi": "10.1681/ASN.2022030262", "pmid": "35387875", "labels": {"Abhishek Niroula": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC9063899"}, {"db": "pii", "key": "00001751-202205000-00004"}], "notes": [], "created": "2023-11-20T11:27:56.689Z", "modified": "2023-11-20T11:27:56.694Z"}, {"entity": "publication", "iuid": "182595d2a42745e3846816c5f389a79f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/182595d2a42745e3846816c5f389a79f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/182595d2a42745e3846816c5f389a79f"}}, "title": "Global Estimation and Mapping of the Conservation Status of Tree Species Using Artificial Intelligence.", "authors": [{"family": "Silva", "given": "Sandro Valerio", "initials": "SV"}, {"family": "Andermann", "given": "Tobias", "initials": "T"}, {"family": "Zizka", "given": "Alexander", "initials": "A"}, {"family": "Kozlowski", "given": "Gregor", "initials": "G"}, {"family": "Silvestro", "given": "Daniele", "initials": "D"}], "type": "journal article", "published": "2022-04-29", "journal": {"title": "Front Plant Sci", "issn": "1664-462X", "volume": "13", "pages": "839792", "issn-l": null}, "abstract": "Trees are fundamental for Earth's biodiversity as primary producers and ecosystem engineers and are responsible for many of nature's contributions to people. Yet, many tree species at present are threatened with extinction by human activities. Accurate identification of threatened tree species is necessary to quantify the current biodiversity crisis and to prioritize conservation efforts. However, the most comprehensive dataset of tree species extinction risk-the Red List of the International Union for the Conservation of Nature (IUCN RL)-lacks assessments for a substantial number of known tree species. The RL is based on a time-consuming expert-based assessment process, which hampers the inclusion of less-known species and the continued updating of extinction risk assessments. In this study, we used a computational pipeline to approximate RL extinction risk assessments for more than 21,000 tree species (leading to an overall assessment of 89% of all known tree species) using a supervised learning approach trained based on available IUCN RL assessments. We harvested the occurrence data for tree species worldwide from online databases, which we used with other publicly available data to design features characterizing the species' geographic range, biome and climatic affinities, and exposure to human footprint. We trained deep neural network models to predict their conservation status, based on these features. We estimated 43% of the assessed tree species to be threatened with extinction and found taxonomic and geographic heterogeneities in the distribution of threatened species. The results are consistent with the recent estimates by the Global Tree Assessment initiative, indicating that our approach provides robust and time-efficient approximations of species' IUCN RL extinction risk assessments.", "doi": "10.3389/fpls.2022.839792", "pmid": "35574125", "labels": {"Tobias Andermann": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC9100559"}], "notes": [], "created": "2022-11-11T09:10:54.561Z", "modified": "2022-11-11T09:10:54.589Z"}, {"entity": "publication", "iuid": "22d2f24174bc4ce5ba990e38bbbe4bdb", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/22d2f24174bc4ce5ba990e38bbbe4bdb.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/22d2f24174bc4ce5ba990e38bbbe4bdb"}}, "title": "Multiple Cortical to Striatal Accumulation Trajectories of \u03b2-Amyloid: Do All Roads Lead to Rome?", "authors": [{"family": "Vogel", "given": "Jacob W", "initials": "JW", "orcid": "0000-0001-6394-9940", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d2ad5af780c245da9b59a8c80a0b00ff.json"}}, {"family": "Tosun", "given": "Duygu", "initials": "D"}], "type": "editorial", "published": "2022-04-26", "journal": {"title": "Neurology", "issn": "1526-632X", "issn-l": "0028-3878", "volume": "98", "issue": "17", "pages": "695-696"}, "abstract": null, "doi": "10.1212/WNL.0000000000200191", "pmid": "35338076", "labels": {"Jacob W Vogel": null, "DDLS Fellow": null}, "xrefs": [{"db": "pii", "key": "WNL.0000000000200191"}], "notes": [], "created": "2023-05-28T17:54:17.102Z", "modified": "2023-11-29T06:39:09.188Z"}, {"entity": "publication", "iuid": "96af492329ee4d1ea3fff71aebbbdc39", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/96af492329ee4d1ea3fff71aebbbdc39.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/96af492329ee4d1ea3fff71aebbbdc39"}}, "title": "Intrapersonal Stability of Plasma Metabolomic Profiles over 10 Years among Women.", "authors": [{"family": "Zeleznik", "given": "Oana A", "initials": "OA", "orcid": "0000-0002-8705-1163", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f6b162661d75438880a6a3248645c8ee.json"}}, {"family": "Wittenbecher", "given": "Clemens", "initials": "C"}, {"family": "Deik", "given": "Amy", "initials": "A", "orcid": "0000-0002-9687-0953", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1d7a5e5188a24d4685e06993a6f93f01.json"}}, {"family": "Jeanfavre", "given": "Sarah", "initials": "S"}, {"family": "Avila-Pacheco", "given": "Julian", "initials": "J"}, {"family": "Rosner", "given": "Bernard", "initials": "B"}, {"family": "Rexrode", "given": "Kathryn M", "initials": "KM"}, {"family": "Clish", "given": "Clary B", "initials": "CB"}, {"family": "Hu", "given": "Frank B", "initials": "FB"}, {"family": "Eliassen", "given": "A Heather", "initials": "AH", "orcid": "0000-0002-3961-6609", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f288e05e7e6449be856ad8955b546ad2.json"}}], "type": "journal article", "published": "2022-04-20", "journal": {"title": "Metabolites", "issn": "2218-1989", "volume": "12", "issue": "5", "issn-l": null}, "abstract": "In epidemiological studies, samples are often collected long before disease onset or outcome assessment. Understanding the long-term stability of biomarkers measured in these samples is crucial. We estimated within-person stability over 10 years of metabolites and metabolite features (n = 5938) in the Nurses' Health Study (NHS): the primary dataset included 1880 women with 1184 repeated samples donated 10 years apart while the secondary dataset included 1456 women with 488 repeated samples donated 10 years apart. We quantified plasma metabolomics using two liquid chromatography mass spectrometry platforms (lipids and polar metabolites) at the Broad Institute (Cambridge, MA, USA). Intra-class correlations (ICC) were used to estimate long-term (10 years) within-person stability of metabolites and were calculated as the proportion of the total variability (within-person + between-person) attributable to between-person variability. Within-person variability was estimated among participants who donated two blood samples approximately 10 years apart while between-person variability was estimated among all participants. In the primary dataset, the median ICC was 0.43 (1st quartile (Q1): 0.36; 3rd quartile (Q3): 0.50) among known metabolites and 0.41 (Q1: 0.34; Q3: 0.48) among unknown metabolite features. The three most stable metabolites were N6,N6-dimethyllysine (ICC = 0.82), dimethylguanidino valerate (ICC = 0.72), and N-acetylornithine (ICC = 0.72). The three least stable metabolites were palmitoylethanolamide (ICC = 0.05), ectoine (ICC = 0.09), and trimethylamine-N-oxide (ICC = 0.16). Results in the secondary dataset were similar (Spearman correlation = 0.87) to corresponding results in the primary dataset. Within-person stability over 10 years is reasonable for lipid, lipid-related, and polar metabolites, and varies by metabolite class. Additional studies are required to estimate within-person stability over 10 years of other metabolites groups.", "doi": "10.3390/metabo12050372", "pmid": "35629875", "labels": {"Clemens Wittenbecher": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC9147746"}, {"db": "pii", "key": "metabo12050372"}], "notes": [], "created": "2025-12-09T13:39:00.773Z", "modified": "2025-12-09T13:39:00.849Z"}, {"entity": "publication", "iuid": "c690352b04a74cf98e5ca3b43fde1a1e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c690352b04a74cf98e5ca3b43fde1a1e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c690352b04a74cf98e5ca3b43fde1a1e"}}, "title": "Estimating Alpha, Beta, and Gamma Diversity Through Deep Learning.", "authors": [{"family": "Andermann", "given": "Tobias", "initials": "T"}, {"family": "Antonelli", "given": "Alexandre", "initials": "A"}, {"family": "Barrett", "given": "Russell L", "initials": "RL"}, {"family": "Silvestro", "given": "Daniele", "initials": "D"}], "type": "journal article", "published": "2022-04-19", "journal": {"title": "Front Plant Sci", "issn": "1664-462X", "volume": "13", "pages": "839407", "issn-l": null}, "abstract": "The reliable mapping of species richness is a crucial step for the identification of areas of high conservation priority, alongside other value and threat considerations. This is commonly done by overlapping range maps of individual species, which requires dense availability of occurrence data or relies on assumptions about the presence of species in unsampled areas deemed suitable by environmental niche models. Here, we present a deep learning approach that directly estimates species richness, skipping the step of estimating individual species ranges. We train a neural network model based on species lists from inventory plots, which provide ground truth data for supervised machine learning. The model learns to predict species richness based on spatially associated variables, including climatic and geographic predictors, as well as counts of available species records from online databases. We assess the empirical utility of our approach by producing independently verifiable maps of alpha, beta, and gamma plant diversity at high spatial resolutions for Australia, a continent with highly heterogeneous diversity patterns. Our deep learning framework provides a powerful and flexible new approach for estimating biodiversity patterns, constituting a step forward toward automated biodiversity assessments.", "doi": "10.3389/fpls.2022.839407", "pmid": "35519811", "labels": {"Tobias Andermann": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC9062518"}], "notes": [], "created": "2022-11-11T09:08:35.484Z", "modified": "2022-11-11T09:08:35.507Z"}, {"entity": "publication", "iuid": "b5d0fd1e975849cdad30488ae539834b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b5d0fd1e975849cdad30488ae539834b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b5d0fd1e975849cdad30488ae539834b"}}, "title": "Differentiating amyloid beta spread in autosomal dominant and sporadic Alzheimer's disease.", "authors": [{"family": "Levitis", "given": "Elizabeth", "initials": "E", "orcid": "0000-0003-0905-6687", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8502b40316ed44b88fd0fa9196afab5e.json"}}, {"family": "Vogel", "given": "Jacob W", "initials": "JW"}, {"family": "Funck", "given": "Thomas", "initials": "T"}, {"family": "Hachinski", "given": "Vladimir", "initials": "V"}, {"family": "Gauthier", "given": "Serge", "initials": "S"}, {"family": "V\u00f6glein", "given": "Jonathan", "initials": "J", "orcid": "0000-0002-5965-838X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ab1ff43b43404eba8972957fa0327c4d.json"}}, {"family": "Levin", "given": "Johannes", "initials": "J"}, {"family": "Gordon", "given": "Brian A", "initials": "BA", "orcid": "0000-0003-2109-2955", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5d260cb618f240bc839bdb8b607c5418.json"}}, {"family": "Benzinger", "given": "Tammie", "initials": "T"}, {"family": "Iturria-Medina", "given": "Yasser", "initials": "Y"}, {"family": "Evans", "given": "Alan C", "initials": "AC"}, {"family": "Dominantly Inherited Alzheimer Network", "given": "", "initials": ""}, {"family": "Alzheimer\u2019s Disease Neuroimaging Initiative", "given": "", "initials": ""}], "type": "journal article", "published": "2022-04-13", "journal": {"title": "Brain Commun", "issn": "2632-1297", "issn-l": null, "volume": "4", "issue": "3", "pages": "fcac085"}, "abstract": "Amyloid-beta deposition is one of the hallmark pathologies in both sporadic Alzheimer's disease and autosomal-dominant Alzheimer's disease, the latter of which is caused by mutations in genes involved in amyloid-beta processing. Despite amyloid-beta deposition being a centrepiece to both sporadic Alzheimer's disease and autosomal-dominant Alzheimer's disease, some differences between these Alzheimer's disease subtypes have been observed with respect to the spatial pattern of amyloid-beta. Previous work has shown that the spatial pattern of amyloid-beta in individuals spanning the sporadic Alzheimer's disease spectrum can be reproduced with high accuracy using an epidemic spreading model which simulates the diffusion of amyloid-beta across neuronal connections and is constrained by individual rates of amyloid-beta production and clearance. However, it has not been investigated whether amyloid-beta deposition in the rarer autosomal-dominant Alzheimer's disease can be modelled in the same way, and if so, how congruent the spreading patterns of amyloid-beta across sporadic Alzheimer's disease and autosomal-dominant Alzheimer's disease are. We leverage the epidemic spreading model as a data-driven approach to probe individual-level variation in the spreading patterns of amyloid-beta across three different large-scale imaging datasets (2 sporadic Alzheimer's disease, 1 autosomal-dominant Alzheimer's disease). We applied the epidemic spreading model separately to the Alzheimer's Disease Neuroimaging initiative (n = 737), the Open Access Series of Imaging Studies (n = 510) and the Dominantly Inherited Alzheimer's Network (n = 249), the latter two of which were processed using an identical pipeline. We assessed inter- and intra-individual model performance in each dataset separately and further identified the most likely subject-specific epicentre of amyloid-beta spread. Using epicentres defined in previous work in sporadic Alzheimer's disease, the epidemic spreading model provided moderate prediction of the regional pattern of amyloid-beta deposition across all three datasets. We further find that, whilst the most likely epicentre for most amyloid-beta-positive subjects overlaps with the default mode network, 13% of autosomal-dominant Alzheimer's disease individuals were best characterized by a striatal origin of amyloid-beta spread. These subjects were also distinguished by being younger than autosomal-dominant Alzheimer's disease subjects with a default mode network amyloid-beta origin, despite having a similar estimated age of symptom onset. Together, our results suggest that most autosomal-dominant Alzheimer's disease patients express amyloid-beta spreading patterns similar to those of sporadic Alzheimer's disease, but that there may be a subset of autosomal-dominant Alzheimer's disease patients with a separate, striatal phenotype.", "doi": "10.1093/braincomms/fcac085", "pmid": "35602652", "labels": {"Jacob W Vogel": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC9116976"}, {"db": "pii", "key": "fcac085"}], "notes": [], "created": "2023-05-28T17:58:10.997Z", "modified": "2023-11-29T06:38:53.762Z"}, {"entity": "publication", "iuid": "e2ff08b0813449bbaf185a646263aa8e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e2ff08b0813449bbaf185a646263aa8e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e2ff08b0813449bbaf185a646263aa8e"}}, "title": "Experiences From Developing Software for Large X-Ray Crystallography-Driven Protein-Ligand Studies.", "authors": [{"family": "Pearce", "given": "Nicholas M", "initials": "NM"}, {"family": "Skyner", "given": "Rachael", "initials": "R"}, {"family": "Krojer", "given": "Tobias", "initials": "T"}], "type": "journal article", "published": "2022-04-11", "journal": {"title": "Front Mol Biosci", "issn": "2296-889X", "volume": "9", "pages": "861491", "issn-l": null}, "abstract": "The throughput of macromolecular X-ray crystallography experiments has surged over the last decade. This remarkable gain in efficiency has been facilitated by increases in the availability of high-intensity X-ray beams, (ultra)fast detectors and high degrees of automation. These developments have in turn spurred the development of several dedicated centers for crystal-based fragment screening which enable the preparation and collection of hundreds of single-crystal diffraction datasets per day. Crystal structures of target proteins in complex with small-molecule ligands are of immense importance for structure-based drug design (SBDD) and their rapid turnover is a prerequisite for accelerated development cycles. While the experimental part of the process is well defined and has by now been established at several synchrotron sites, it is noticeable that software and algorithmic aspects have received far less attention, as well as the implications of new methodologies on established paradigms for structure determination, analysis, and visualization. We will review three key areas of development of large-scale protein-ligand studies. First, we will look into new software developments for batch data processing, followed by a discussion of the methodological changes in the analysis, modeling, refinement and deposition of structures for SBDD, and the changes in mindset that these new methods require, both on the side of depositors and users of macromolecular models. Finally, we will highlight key new developments for the presentation and analysis of the collections of structures that these experiments produce, and provide an outlook for future developments.", "doi": "10.3389/fmolb.2022.861491", "pmid": "35480897", "labels": {"Nicholas Pearce": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC9035521"}, {"db": "pii", "key": "861491"}], "notes": [], "created": "2022-12-05T19:30:48.355Z", "modified": "2022-12-05T19:30:48.370Z"}, {"entity": "publication", "iuid": "5a4b7afcc7f14c88b78aa139fc346ea0", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5a4b7afcc7f14c88b78aa139fc346ea0.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5a4b7afcc7f14c88b78aa139fc346ea0"}}, "title": "Mendelian randomization supports bidirectional causality between telomere length and clonal hematopoiesis of indeterminate potential.", "authors": [{"family": "Nakao", "given": "Tetsushi", "initials": "T", "orcid": "0000-0001-9979-2682", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7e818cd4544c41c2a7fa91dbce13429e.json"}}, {"family": "Bick", "given": "Alexander G", "initials": "AG", "orcid": "0000-0001-5824-9595", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d2da5a35a4984921b19dfafe64cea2de.json"}}, {"family": "Taub", "given": "Margaret A", "initials": "MA"}, {"family": "Zekavat", "given": "Seyedeh M", "initials": "SM", "orcid": "0000-0003-4026-8944", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6234b31f08e442a9b71a711ec7b1147a.json"}}, {"family": "Uddin", "given": "Md M", "initials": "MM", "orcid": "0000-0003-1846-0411", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/42f1ac7010c34ba997a3fd9e56c6a56a.json"}}, {"family": "Niroula", "given": "Abhishek", "initials": "A", "orcid": "0000-0002-5904-0635", "researcher": {"href": 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"https://publications-affiliated.scilifelab.se/researcher/39fb20acff0442bd92fc7931d3ee6cf9.json"}}, {"family": "Ellinor", "given": "Patrick T", "initials": "PT", "orcid": "0000-0002-2067-0533", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fd1830794e884e6e849fd4f7645c9b61.json"}}, {"family": "Pankratz", "given": "Nathan", "initials": "N", "orcid": "0000-0001-5958-693X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ad5e6b749b264d1e83ea58d5bce6c88e.json"}}, {"family": "Ebert", "given": "Benjamin L", "initials": "BL", "orcid": "0000-0003-0197-5451", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56e4f1c53a4348e2b0ceb44a38850a17.json"}}, {"family": "Reiner", "given": "Alexander P", "initials": "AP"}, {"family": "Mathias", "given": "Rasika A", "initials": "RA", "orcid": "0000-0002-2282-9042", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/71dfe469451f4573bcccc96f981f7915.json"}}, {"family": "Do", "given": "Ron", "initials": "R", "orcid": "0000-0002-3144-3627", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4ab0c452994042219ca6120d45e72604.json"}}, {"family": "NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium", "given": "", "initials": ""}, {"family": "Natarajan", "given": "Pradeep", "initials": "P", "orcid": "0000-0001-8402-7435", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fe8bd48c61c047cd8e61c35d9e9ac650.json"}}], "type": "journal article", "published": "2022-04-08", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "8", "issue": "14", "pages": "eabl6579", "issn-l": "2375-2548"}, "abstract": "Human genetic studies support an inverse causal relationship between leukocyte telomere length (LTL) and coronary artery disease (CAD), but directionally mixed effects for LTL and diverse malignancies. Clonal hematopoiesis of indeterminate potential (CHIP), characterized by expansion of hematopoietic cells bearing leukemogenic mutations, predisposes both hematologic malignancy and CAD. TERT (which encodes telomerase reverse transcriptase) is the most significantly associated germline locus for CHIP in genome-wide association studies. Here, we investigated the relationship between CHIP, LTL, and CAD in the Trans-Omics for Precision Medicine (TOPMed) program (n = 63,302) and UK Biobank (n = 47,080). Bidirectional Mendelian randomization studies were consistent with longer genetically imputed LTL increasing propensity to develop CHIP, but CHIP then, in turn, hastens to shorten measured LTL (mLTL). We also demonstrated evidence of modest mediation between CHIP and CAD by mLTL. Our data promote an understanding of potential causal relationships across CHIP and LTL toward prevention of CAD.", "doi": "10.1126/sciadv.abl6579", "pmid": "35385311", "labels": {"Abhishek Niroula": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC8986098"}], "notes": [], "created": "2023-11-20T11:36:14.966Z", "modified": "2023-11-20T11:36:17.765Z"}, {"entity": "publication", "iuid": "4b1423e593aa4d229030a96e91462964", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4b1423e593aa4d229030a96e91462964.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4b1423e593aa4d229030a96e91462964"}}, "title": "Elastic dosage compensation by X-chromosome upregulation.", "authors": [{"family": "Lentini", "given": "Antonio", "initials": "A", "orcid": "0000-0003-1239-5495", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c5042d3005814ad0a2d1eaeee5d2de3b.json"}}, {"family": "Cheng", "given": "Huaitao", "initials": "H", "orcid": "0000-0001-7948-2417", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/96a1521902334a14ac61643eda24dded.json"}}, {"family": "Noble", "given": "J C", "initials": "JC"}, {"family": "Papanicolaou", "given": "Natali", "initials": "N"}, {"family": "Coucoravas", "given": "Christos", "initials": "C"}, {"family": "Andrews", "given": "Nathanael", "initials": "N", "orcid": "0000-0003-4139-2904", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c19585a4f14c4e8d9e49d5e02a4ef23e.json"}}, {"family": "Deng", "given": "Qiaolin", "initials": "Q", "orcid": "0000-0001-5934-7816", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2b95d2e59ca64184a336cca7050f43cc.json"}}, {"family": "Enge", "given": "Martin", "initials": "M", "orcid": "0000-0001-8748-8931", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d5e1bd50cc0543e88bb737343f98a270.json"}}, {"family": "Reinius", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0002-7021-5248", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a7c1abacc8d446bf8855254246b8d899.json"}}], "type": "journal article", "published": "2022-04-06", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "13", "issue": "1", "pages": "1854", "issn-l": "2041-1723"}, "abstract": "X-chromosome inactivation and X-upregulation are the fundamental modes of chromosome-wide gene regulation that collectively achieve dosage compensation in mammals, but the regulatory link between the two remains elusive and the X-upregulation dynamics are unknown. Here, we use allele-resolved single-cell RNA-seq combined with chromatin accessibility profiling and finely dissect their separate effects on RNA levels during mouse development. Surprisingly, we uncover that X-upregulation elastically tunes expression dosage in a sex- and lineage-specific manner, and moreover along varying degrees of X-inactivation progression. Male blastomeres achieve X-upregulation upon zygotic genome activation while females experience two distinct waves of upregulation, upon imprinted and random X-inactivation; and ablation of Xist impedes female X-upregulation. Female cells carrying two active X chromosomes lack upregulation, yet their collective RNA output exceeds that of a single hyperactive allele. Importantly, this conflicts the conventional dosage compensation model in which na\u00efve female cells are initially subject to biallelic X-upregulation followed by X-inactivation of one allele to correct the X dosage. Together, our study provides key insights to the chain of events of dosage compensation, explaining how transcript copy numbers can remain remarkably stable across developmental windows wherein severe dose imbalance would otherwise be experienced by the cell.", "doi": "10.1038/s41467-022-29414-1", "pmid": "35388014", "labels": {"Antonio Lentini": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC8987076"}, {"db": "pii", "key": "10.1038/s41467-022-29414-1"}], "notes": [], "created": "2025-03-28T07:09:51.738Z", "modified": "2025-03-28T07:09:51.939Z"}, {"entity": "publication", "iuid": "fa93aa1d655e4117bf3ef9f200c9aef5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/fa93aa1d655e4117bf3ef9f200c9aef5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/fa93aa1d655e4117bf3ef9f200c9aef5"}}, "title": "Metabolomics and Type 2 Diabetes Risk: An Updated Systematic Review and Meta-analysis of Prospective Cohort Studies.", "authors": [{"family": "Morze", "given": "Jakub", "initials": "J", "orcid": "0000-0002-7119-0273", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/91e8ec498bc6462986a824de9c42af47.json"}}, {"family": "Wittenbecher", "given": "Clemens", "initials": "C", "orcid": "0000-0001-7792-877X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2f7d2c289b3c47d5a79d23bd48a3225a.json"}}, {"family": "Schwingshackl", "given": "Lukas", "initials": "L"}, {"family": "Danielewicz", "given": "Anna", "initials": "A"}, {"family": "Rynkiewicz", "given": "Andrzej", "initials": "A"}, {"family": "Hu", "given": "Frank B", "initials": "FB"}, {"family": "Guasch-Ferr\u00e9", "given": "Marta", "initials": "M", "orcid": "0000-0001-8525-1404", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2d1a49f5df124e96a9285b43d628cee9.json"}}], "type": "journal article", "published": "2022-04-01", "journal": {"title": "Diabetes Care", "issn": "1935-5548", "volume": "45", "issue": "4", "pages": "1013-1024", "issn-l": null}, "abstract": "Due to the rapidly increasing availability of metabolomics data in prospective studies, an update of the meta evidence on metabolomics and type 2 diabetes risk is warranted.\n\nTo conduct an updated systematic review and meta-analysis of plasma, serum, and urine metabolite markers and incident type 2 diabetes.\n\nWe searched PubMed and Embase until 6 March 2021.\n\nWe selected prospective observational studies where investigators used high-throughput techniques to investigate the relationship between plasma, serum, or urine metabolites and incident type 2 diabetes.\n\nBaseline metabolites per-SD risk estimates and 95% CIs for incident type 2 diabetes were extracted from all eligible studies.\n\nA total of 61 reports with 71,196 participants and 11,771 type 2 diabetes cases/events were included in the updated review. Meta-analysis was performed for 412 metabolites, of which 123 were statistically significantly associated (false discovery rate-corrected P < 0.05) with type 2 diabetes risk. Higher plasma and serum levels of certain amino acids (branched-chain, aromatic, alanine, glutamate, lysine, and methionine), carbohydrates and energy-related metabolites (mannose, trehalose, and pyruvate), acylcarnitines (C4-DC, C4-OH, C5, C5-OH, and C8:1), the majority of glycerolipids (di- and triacylglycerols), (lyso)phosphatidylethanolamines, and ceramides included in meta-analysis were associated with higher risk of type 2 diabetes (hazard ratio 1.07-2.58). Higher levels of glycine, glutamine, betaine, indolepropionate, and (lyso)phosphatidylcholines were associated with lower type 2 diabetes risk (hazard ratio 0.69-0.90).\n\nSubstantial heterogeneity (I2 > 50%, \u03c42 > 0.1) was observed for some of the metabolites.\n\nSeveral plasma and serum metabolites, including amino acids, lipids, and carbohydrates, are associated with type 2 diabetes risk.", "doi": "10.2337/dc21-1705", "pmid": "35349649", "labels": {"Clemens Wittenbecher": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC9016744"}, {"db": "pii", "key": "144892"}, {"db": "figshare", "key": "10.2337/figshare.18857807"}], "notes": [], "created": "2025-12-09T13:39:02.933Z", "modified": "2025-12-09T13:39:02.979Z"}, {"entity": "publication", "iuid": "aad9dc6f82fa4fb6a1c5398b184fc96c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/aad9dc6f82fa4fb6a1c5398b184fc96c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/aad9dc6f82fa4fb6a1c5398b184fc96c"}}, "title": "Target sequence capture of Barnadesioideae (Compositae) demonstrates the utility of low coverage loci in phylogenomic analyses.", "authors": [{"family": "Ferreira", "given": "Paola de Lima", "initials": "PL"}, {"family": "Batista", "given": "Romina", "initials": "R"}, {"family": "Andermann", "given": "Tobias", "initials": "T"}, {"family": "Groppo", "given": "Milton", "initials": "M"}, {"family": "Bacon", "given": "Christine D", "initials": "CD"}, {"family": "Antonelli", "given": "Alexandre", "initials": "A"}], "type": "journal article", "published": "2022-04-00", "journal": {"title": "Mol. Phylogenet. Evol.", "issn": "1095-9513", "volume": "169", "pages": "107432", "issn-l": "1055-7903"}, "abstract": "Target sequence capture has emerged as a powerful method to sequence hundreds or thousands of genomic regions in a cost- and time-efficient approach. In most cases, however, targeted regions lack full sequence information for certain samples, due to taxonomic, laboratory, or stochastic factors. Loci lacking molecular data for a large number of samples are commonly excluded from downstream analyses, even though they may still contain valuable information. On the other hand, including data-poor loci may bias phylogenetic analyses. Here we use a target sequence capture dataset of an ecologically and taxonomically diverse group of spiny sunflowers (Asteraceae, or Compositae: Barnadesioideae) to test how the inclusion or exclusion of such data-poor loci affects phylogenetic inference. We investigate the sensitivity of concatenation and coalescent approaches to missing data with matrices of varying taxonomic completeness by filtering loci with different proportions of missing samples prior to data analysis. We find that missing data affect both the topology and branch support of the resulting phylogenies. The matrix containing all loci yielded the overall highest node support values, independently of the amount of missing nucleotides. These results provide empirical support to earlier suggestions based on single genes and data simulations that taxa with high amounts of missing data should not be readily dismissed as they can provide essential information for phylogenomic reconstruction.", "doi": "10.1016/j.ympev.2022.107432", "pmid": "35131421", "labels": {"Tobias Andermann": null, "DDLS Fellow": null}, "xrefs": [{"db": "pii", "key": "S1055-7903(22)00045-8"}], "notes": [], "created": "2022-11-11T09:10:44.671Z", "modified": "2022-11-11T09:10:44.701Z"}, {"entity": "publication", "iuid": "9aa137daa0064a4c9a929132bdf12b9a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9aa137daa0064a4c9a929132bdf12b9a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9aa137daa0064a4c9a929132bdf12b9a"}}, "title": "Multiomics Analysis Reveals the Impact of Microbiota on Host Metabolism in Hepatic Steatosis.", "authors": [{"family": "Zeybel", "given": "Mujdat", "initials": "M"}, {"family": "Arif", "given": "Muhammad", "initials": "M"}, {"family": "Li", "given": "Xiangyu", "initials": "X"}, {"family": "Altay", "given": "Ozlem", "initials": "O"}, {"family": "Yang", "given": "Hong", "initials": "H"}, {"family": "Shi", "given": "Mengnan", "initials": "M"}, {"family": "Akyildiz", "given": "Murat", "initials": "M"}, {"family": "Saglam", "given": "Burcin", "initials": "B"}, {"family": "Gonenli", "given": "Mehmet Gokhan", "initials": "MG"}, {"family": "Yigit", "given": "Buket", "initials": "B"}, {"family": "Ulukan", "given": "Burge", "initials": "B"}, {"family": "Ural", "given": "Dilek", "initials": "D"}, {"family": "Shoaie", "given": "Saeed", "initials": "S"}, {"family": "Turkez", "given": "Hasan", "initials": "H"}, {"family": "Nielsen", "given": "Jens", "initials": "J"}, {"family": "Zhang", "given": "Cheng", "initials": "C"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Bor\u00e9n", "given": "Jan", "initials": "J"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca58bf2d214047e0ae5e38a42a0f2808.json"}}], "type": "journal article", "published": "2022-04-00", "journal": {"title": "Adv Sci (Weinh)", "issn": "2198-3844", "volume": "9", "issue": "11", "pages": "e2104373", "issn-l": null}, "abstract": "Metabolic dysfunction-associated fatty liver disease (MAFLD) is a complex disease involving alterations in multiple biological processes regulated by the interactions between obesity, genetic background, and environmental factors including the microbiome. To decipher hepatic steatosis (HS) pathogenesis by excluding critical confounding factors including genetic variants and diabetes, 56 heterogenous MAFLD patients are characterized by generating multiomics data including oral and gut metagenomics as well as plasma metabolomics and inflammatory proteomics data. The dysbiosis in the oral and gut microbiome is explored and the host-microbiome interactions based on global metabolic and inflammatory processes are revealed. These multiomics data are integrated using the biological network and HS's key features are identified using multiomics data. HS is finally predicted using these key features and findings are validated in a follow-up cohort, where 22 subjects with varying degree of HS are characterized.", "doi": "10.1002/advs.202104373", "pmid": "35128832", "labels": {"Adil Mardinoglu": "", "SciLifeLab Fellow": "", "Saeed Shoaie": "", "DDLS Fellow": "", "Muhammad Arif": ""}, "xrefs": [{"db": "pmc", "key": "PMC9008426"}], "notes": [], "created": "2023-12-04T15:04:48.857Z", "modified": "2026-09-23T08:34:04.156Z"}, {"entity": "publication", "iuid": "ed945573ae864ba28e23e60d4909aa91", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ed945573ae864ba28e23e60d4909aa91.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ed945573ae864ba28e23e60d4909aa91"}}, "title": "Integrative study of diet-induced mouse models of NAFLD identifies PPAR\u03b1 as a sexually dimorphic drug target.", "authors": [{"family": "Smati", "given": "Sarra", "initials": "S", "orcid": "0000-0002-5749-983X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f9c523f25a1d4ae185656e3ed1156709.json"}}, {"family": "Polizzi", "given": "Arnaud", "initials": "A"}, {"family": "Fougerat", "given": "Anne", "initials": "A"}, {"family": "Ellero-Simatos", "given": "Sandrine", "initials": "S"}, {"family": "Blum", "given": "Yuna", "initials": "Y"}, {"family": "Lippi", "given": "Yannick", "initials": "Y"}, {"family": "R\u00e9gnier", "given": "Marion", "initials": "M"}, {"family": "Laroyenne", "given": "Alexia", "initials": "A"}, {"family": "Huillet", "given": "Marine", "initials": "M"}, {"family": "Arif", "given": "Muhammad", "initials": "M"}, {"family": "Zhang", "given": "Cheng", "initials": "C"}, {"family": "Lasserre", "given": "Frederic", "initials": "F"}, {"family": "Marrot", "given": "Alain", "initials": "A"}, {"family": "Al Saati", "given": "Talal", "initials": "T"}, {"family": "Wan", "given": "JingHong", "initials": "J"}, {"family": "Sommer", "given": "Caroline", "initials": "C"}, {"family": "Naylies", "given": "Claire", "initials": "C"}, {"family": "Batut", "given": "Aurelie", "initials": "A"}, {"family": "Lukowicz", "given": "Celine", "initials": "C"}, {"family": "Fougeray", "given": "Tiffany", "initials": "T"}, {"family": "Tramunt", "given": "Blandine", "initials": "B"}, {"family": "Dubot", "given": "Patricia", "initials": "P"}, {"family": "Smith", "given": "Lorraine", "initials": "L"}, {"family": "Bertrand-Michel", "given": "Justine", "initials": "J"}, {"family": "Hennuyer", "given": "Nathalie", "initials": "N"}, {"family": "Pradere", "given": "Jean-Philippe", "initials": "JP"}, {"family": "Staels", "given": "Bart", "initials": "B", "orcid": "0000-0002-3784-1503", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d4403d33764d45af8a864123ec7ab822.json"}}, {"family": "Burcelin", "given": "Remy", "initials": "R", "orcid": "0000-0002-7942-8346", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cb654f4e5c5c4b86b9ba2e041196d514.json"}}, {"family": "Lenfant", "given": "Fran\u00e7oise", "initials": "F"}, {"family": "Arnal", "given": "Jean-Fran\u00e7ois", "initials": "JF"}, {"family": "Levade", "given": "Thierry", "initials": "T"}, {"family": "Gamet-Payrastre", "given": "Laurence", "initials": "L"}, {"family": "Lagarrigue", "given": "Sandrine", "initials": "S"}, {"family": "Loiseau", "given": "Nicolas", "initials": "N"}, {"family": "Lotersztajn", "given": "Sophie", "initials": "S"}, {"family": "Postic", "given": "Catherine", "initials": "C"}, {"family": "Wahli", "given": "Walter", "initials": "W", "orcid": "0000-0002-5966-9089", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ee554b81a79143599b984946397a41fe.json"}}, {"family": "Bureau", "given": "Christophe", "initials": "C"}, {"family": "Guillaume", "given": "Maeva", "initials": "M"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Montagner", "given": "Alexandra", "initials": "A", "orcid": "0000-0002-4800-5105", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/46373ea8c82c4f6c93b2493f2003b1ff.json"}}, {"family": "Gourdy", "given": "Pierre", "initials": "P", "orcid": "0000-0002-5362-3813", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/184aaac222a843aca96be4b16d97969a.json"}}, {"family": "Guillou", "given": "Herv\u00e9", "initials": "H", "orcid": "0000-0002-5363-9081", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/abef7b3bf4574b87a90ab2c3f67c5d4d.json"}}], "type": "journal article", "published": "2022-04-00", "journal": {"title": "Gut", "issn": "1468-3288", "volume": "71", "issue": "4", "pages": "807-821", "issn-l": "0017-5749"}, "abstract": "We evaluated the influence of sex on the pathophysiology of non-alcoholic fatty liver disease (NAFLD). We investigated diet-induced phenotypic responses to define sex-specific regulation between healthy liver and NAFLD to identify influential pathways in different preclinical murine models and their relevance in humans.\n\nDifferent models of diet-induced NAFLD (high-fat diet, choline-deficient high-fat diet, Western diet or Western diet supplemented with fructose and glucose in drinking water) were compared with a control diet in male and female mice. We performed metabolic phenotyping, including plasma biochemistry and liver histology, untargeted large-scale approaches (liver metabolome, lipidome and transcriptome), gene expression profiling and network analysis to identify sex-specific pathways in the mouse liver.\n\nThe different diets induced sex-specific responses that illustrated an increased susceptibility to NAFLD in male mice. The most severe lipid accumulation and inflammation/fibrosis occurred in males receiving the high-fat diet and Western diet, respectively. Sex-biased hepatic gene signatures were identified for these different dietary challenges. The peroxisome proliferator-activated receptor \u03b1 (PPAR\u03b1) co-expression network was identified as sexually dimorphic, and in vivo experiments in mice demonstrated that hepatocyte PPAR\u03b1 determines a sex-specific response to fasting and treatment with pemafibrate, a selective PPAR\u03b1 agonist. Liver molecular signatures in humans also provided evidence of sexually dimorphic gene expression profiles and the sex-specific co-expression network for PPAR\u03b1.\n\nThese findings underscore the sex specificity of NAFLD pathophysiology in preclinical studies and identify PPAR\u03b1 as a pivotal, sexually dimorphic, pharmacological target.\n\nNCT02390232.", "doi": "10.1136/gutjnl-2020-323323", "pmid": "33903148", "labels": {"Adil Mardinoglu": "", "SciLifeLab Fellow": "", "DDLS Fellow": "", "Muhammad Arif": ""}, "xrefs": [{"db": "pii", "key": "gutjnl-2020-323323"}, {"db": "ClinicalTrials.gov", "key": "NCT02390232"}], "notes": [], "created": "2023-12-04T15:08:04.605Z", "modified": "2026-09-23T07:49:08.195Z"}, {"entity": "publication", "iuid": "8de89096ab744894a78415f61ae247c6", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8de89096ab744894a78415f61ae247c6.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8de89096ab744894a78415f61ae247c6"}}, "title": "Brain charts for the human lifespan.", "authors": [{"family": "Bethlehem", "given": "R A I", "initials": "RAI"}, {"family": "Seidlitz", "given": "J", "initials": "J"}, {"family": "White", "given": "S R", "initials": "SR"}, {"family": "Vogel", "given": "J W", "initials": "JW"}, {"family": "Anderson", "given": "K M", "initials": "KM"}, {"family": "Adamson", "given": "C", "initials": "C"}, {"family": "Adler", "given": "S", "initials": "S"}, {"family": "Alexopoulos", "given": "G S", "initials": "GS"}, {"family": "Anagnostou", "given": "E", "initials": "E"}, {"family": "Areces-Gonzalez", "given": "A", "initials": "A"}, {"family": "Astle", "given": "D E", "initials": "DE"}, {"family": "Auyeung", "given": "B", "initials": "B"}, {"family": "Ayub", "given": "M", "initials": "M"}, {"family": "Bae", "given": "J", "initials": "J"}, {"family": "Ball", "given": "G", "initials": "G"}, {"family": "Baron-Cohen", "given": "S", "initials": "S"}, {"family": "Beare", "given": "R", "initials": "R"}, {"family": "Bedford", "given": "S A", "initials": "SA"}, {"family": "Benegal", "given": "V", "initials": "V"}, {"family": "Beyer", "given": "F", "initials": "F"}, {"family": "Blangero", "given": "J", "initials": "J"}, {"family": "Blesa C\u00e1bez", "given": "M", "initials": "M"}, {"family": "Boardman", "given": "J P", "initials": "JP"}, {"family": "Borzage", "given": "M", "initials": "M"}, {"family": "Bosch-Bayard", "given": "J F", "initials": "JF"}, {"family": "Bourke", "given": "N", "initials": "N"}, {"family": "Calhoun", "given": "V D", "initials": "VD"}, {"family": "Chakravarty", "given": "M M", "initials": "MM"}, {"family": "Chen", "given": "C", "initials": "C"}, {"family": "Chertavian", "given": "C", "initials": "C"}, {"family": "Chetelat", "given": "G", "initials": "G"}, {"family": "Chong", "given": "Y S", "initials": "YS"}, {"family": "Cole", "given": "J H", "initials": "JH"}, {"family": "Corvin", "given": "A", "initials": "A"}, {"family": "Costantino", "given": "M", "initials": "M"}, {"family": "Courchesne", "given": "E", "initials": "E"}, {"family": "Crivello", "given": "F", "initials": "F"}, {"family": "Cropley", "given": "V L", "initials": "VL"}, {"family": "Crosbie", "given": "J", "initials": "J"}, {"family": "Crossley", "given": "N", "initials": "N"}, {"family": "Delarue", "given": "M", "initials": "M"}, {"family": "Delorme", "given": "R", "initials": "R"}, {"family": "Desrivieres", "given": "S", "initials": "S"}, {"family": "Devenyi", "given": "G A", "initials": "GA"}, {"family": "Di Biase", "given": "M A", "initials": "MA"}, {"family": "Dolan", "given": "R", "initials": "R"}, {"family": "Donald", "given": "K A", "initials": "KA"}, {"family": "Donohoe", "given": "G", "initials": "G"}, {"family": "Dunlop", "given": "K", "initials": "K"}, {"family": "Edwards", "given": "A D", "initials": "AD"}, {"family": "Elison", "given": "J T", "initials": "JT"}, {"family": "Ellis", "given": "C T", "initials": "CT"}, {"family": "Elman", "given": "J A", "initials": "JA"}, {"family": "Eyler", "given": "L", "initials": "L"}, {"family": "Fair", "given": "D A", "initials": "DA"}, {"family": "Feczko", "given": "E", "initials": "E"}, {"family": "Fletcher", "given": "P C", "initials": "PC"}, {"family": "Fonagy", "given": "P", "initials": "P"}, {"family": "Franz", "given": "C E", "initials": "CE"}, {"family": "Galan-Garcia", "given": "L", "initials": "L"}, {"family": "Gholipour", "given": "A", "initials": "A"}, {"family": "Giedd", "given": "J", "initials": "J"}, {"family": "Gilmore", "given": "J H", "initials": "JH"}, {"family": "Glahn", "given": "D C", "initials": "DC"}, {"family": "Goodyer", "given": "I M", "initials": "IM"}, {"family": "Grant", "given": "P E", "initials": "PE"}, {"family": "Groenewold", "given": "N A", "initials": "NA"}, {"family": "Gunning", "given": "F M", "initials": "FM"}, {"family": "Gur", "given": "R E", "initials": "RE"}, {"family": "Gur", "given": "R C", "initials": "RC"}, {"family": "Hammill", "given": "C F", "initials": "CF"}, {"family": "Hansson", "given": "O", "initials": "O"}, {"family": "Hedden", "given": "T", "initials": "T"}, {"family": "Heinz", "given": "A", "initials": "A"}, {"family": "Henson", "given": "R N", "initials": "RN"}, {"family": "Heuer", "given": "K", "initials": "K"}, {"family": "Hoare", "given": "J", "initials": "J"}, {"family": "Holla", "given": "B", "initials": "B"}, {"family": "Holmes", "given": "A J", "initials": "AJ"}, {"family": "Holt", "given": "R", "initials": "R"}, {"family": "Huang", "given": "H", "initials": "H"}, {"family": "Im", "given": "K", "initials": "K"}, {"family": "Ipser", "given": "J", "initials": "J"}, {"family": "Jack", "given": "C R", "initials": "CR"}, {"family": "Jackowski", "given": "A P", "initials": "AP"}, {"family": "Jia", "given": "T", "initials": "T"}, {"family": "Johnson", "given": "K A", "initials": "KA"}, {"family": "Jones", "given": "P B", "initials": "PB"}, {"family": "Jones", "given": "D T", "initials": "DT"}, {"family": "Kahn", "given": "R S", "initials": "RS"}, {"family": "Karlsson", "given": "H", "initials": "H"}, {"family": "Karlsson", "given": "L", "initials": "L"}, {"family": "Kawashima", "given": "R", "initials": "R"}, {"family": "Kelley", "given": "E A", "initials": "EA"}, {"family": "Kern", "given": "S", "initials": "S"}, {"family": "Kim", "given": "K W", "initials": "KW"}, {"family": "Kitzbichler", "given": "M G", "initials": "MG"}, {"family": "Kremen", "given": "W S", "initials": "WS"}, {"family": "Lalonde", "given": "F", "initials": "F"}, {"family": "Landeau", "given": "B", "initials": "B"}, {"family": "Lee", "given": "S", "initials": "S"}, {"family": "Lerch", "given": "J", "initials": "J"}, {"family": "Lewis", "given": "J D", "initials": "JD"}, {"family": "Li", "given": "J", "initials": "J"}, {"family": "Liao", "given": "W", "initials": "W"}, {"family": "Liston", "given": "C", "initials": "C"}, {"family": "Lombardo", "given": "M V", "initials": "MV"}, {"family": "Lv", "given": "J", "initials": "J"}, {"family": "Lynch", "given": "C", "initials": "C"}, {"family": "Mallard", "given": "T T", "initials": "TT"}, {"family": "Marcelis", "given": "M", "initials": "M"}, {"family": "Markello", "given": "R D", "initials": "RD"}, {"family": "Mathias", "given": "S R", "initials": "SR"}, {"family": "Mazoyer", "given": "B", "initials": "B"}, {"family": "McGuire", "given": "P", "initials": "P"}, {"family": "Meaney", "given": "M J", "initials": "MJ"}, {"family": "Mechelli", "given": "A", "initials": "A"}, {"family": "Medic", "given": "N", "initials": "N"}, {"family": "Misic", "given": "B", "initials": "B"}, {"family": "Morgan", "given": "S E", "initials": "SE"}, {"family": "Mothersill", "given": "D", "initials": "D"}, {"family": "Nigg", "given": "J", "initials": "J"}, {"family": "Ong", "given": "M Q W", "initials": "MQW"}, {"family": "Ortinau", "given": "C", "initials": "C"}, {"family": "Ossenkoppele", "given": "R", "initials": "R"}, {"family": "Ouyang", "given": "M", "initials": "M"}, {"family": "Palaniyappan", "given": "L", "initials": "L"}, {"family": "Paly", "given": "L", "initials": "L"}, {"family": "Pan", "given": "P M", "initials": "PM"}, {"family": "Pantelis", "given": "C", "initials": "C"}, {"family": "Park", "given": "M M", "initials": "MM"}, {"family": "Paus", "given": "T", "initials": "T"}, {"family": "Pausova", "given": "Z", "initials": "Z"}, {"family": "Paz-Linares", "given": "D", "initials": "D"}, {"family": "Pichet Binette", "given": "A", "initials": "A"}, {"family": "Pierce", "given": "K", "initials": "K"}, {"family": "Qian", "given": "X", "initials": "X"}, {"family": "Qiu", "given": "J", "initials": "J"}, {"family": "Qiu", "given": "A", "initials": "A"}, {"family": "Raznahan", "given": "A", "initials": "A"}, {"family": "Rittman", "given": "T", "initials": "T"}, {"family": "Rodrigue", "given": "A", "initials": "A"}, {"family": "Rollins", "given": "C K", "initials": "CK"}, {"family": "Romero-Garcia", "given": "R", "initials": "R"}, {"family": "Ronan", "given": "L", "initials": "L"}, {"family": "Rosenberg", "given": "M D", "initials": "MD"}, {"family": "Rowitch", "given": "D H", "initials": "DH"}, {"family": "Salum", "given": "G A", "initials": "GA"}, {"family": "Satterthwaite", "given": "T D", "initials": "TD"}, {"family": "Schaare", "given": "H L", "initials": "HL"}, {"family": "Schachar", "given": "R J", "initials": "RJ"}, {"family": "Schultz", "given": "A P", "initials": "AP"}, {"family": "Schumann", "given": "G", "initials": "G"}, {"family": "Sch\u00f6ll", "given": "M", "initials": "M"}, {"family": "Sharp", "given": "D", "initials": "D"}, {"family": "Shinohara", "given": "R T", "initials": "RT"}, {"family": "Skoog", "given": "I", "initials": "I"}, {"family": "Smyser", "given": "C D", "initials": "CD"}, {"family": "Sperling", "given": "R A", "initials": "RA"}, {"family": "Stein", "given": "D J", "initials": "DJ"}, {"family": "Stolicyn", "given": "A", "initials": "A"}, {"family": "Suckling", "given": "J", "initials": "J"}, {"family": "Sullivan", "given": "G", "initials": "G"}, {"family": "Taki", "given": "Y", "initials": "Y"}, {"family": "Thyreau", "given": "B", "initials": "B"}, {"family": "Toro", "given": "R", "initials": "R"}, {"family": "Traut", "given": "N", "initials": "N"}, {"family": "Tsvetanov", "given": "K A", "initials": "KA"}, {"family": "Turk-Browne", "given": "N B", "initials": "NB"}, {"family": "Tuulari", "given": "J J", "initials": "JJ"}, {"family": "Tzourio", "given": "C", "initials": "C"}, {"family": "Vachon-Presseau", "given": "\u00c9", "initials": "\u00c9"}, {"family": "Valdes-Sosa", "given": "M J", "initials": "MJ"}, {"family": "Valdes-Sosa", "given": "P A", "initials": "PA"}, {"family": "Valk", "given": "S L", "initials": "SL"}, {"family": "van Amelsvoort", "given": "T", "initials": "T"}, {"family": "Vandekar", "given": "S N", "initials": "SN"}, {"family": "Vasung", "given": "L", "initials": "L"}, {"family": "Victoria", "given": "L W", "initials": "LW"}, {"family": "Villeneuve", "given": "S", "initials": "S"}, {"family": "Villringer", "given": "A", "initials": "A"}, {"family": "V\u00e9rtes", "given": "P E", "initials": "PE"}, {"family": "Wagstyl", "given": "K", "initials": "K"}, {"family": "Wang", "given": "Y S", "initials": "YS"}, {"family": "Warfield", "given": "S K", "initials": "SK"}, {"family": "Warrier", "given": "V", "initials": "V"}, {"family": "Westman", "given": "E", "initials": "E"}, {"family": "Westwater", "given": "M L", "initials": "ML"}, {"family": "Whalley", "given": "H C", "initials": "HC"}, {"family": "Witte", "given": "A V", "initials": "AV"}, {"family": "Yang", "given": "N", "initials": "N"}, {"family": "Yeo", "given": "B", "initials": "B"}, {"family": "Yun", "given": "H", "initials": "H"}, {"family": "Zalesky", "given": "A", "initials": "A"}, {"family": "Zar", "given": "H J", "initials": "HJ"}, {"family": "Zettergren", "given": "A", "initials": "A"}, {"family": "Zhou", "given": "J H", "initials": "JH"}, {"family": "Ziauddeen", "given": "H", "initials": "H"}, {"family": "Zugman", "given": "A", "initials": "A"}, {"family": "Zuo", "given": "X N", "initials": "XN"}, {"family": "3R-BRAIN", "given": "", "initials": ""}, {"family": "AIBL", "given": "", "initials": ""}, {"family": "Alzheimer\u2019s Disease Neuroimaging Initiative", "given": "", "initials": ""}, {"family": "Alzheimer\u2019s Disease Repository Without Borders Investigators", "given": "", "initials": ""}, {"family": "CALM Team", "given": "", "initials": ""}, {"family": "Cam-CAN", "given": "", "initials": ""}, {"family": "CCNP", "given": "", "initials": ""}, {"family": "COBRE", "given": "", "initials": ""}, {"family": "cVEDA", "given": "", "initials": ""}, {"family": "ENIGMA Developmental Brain Age Working Group", "given": "", "initials": ""}, {"family": "Developing Human Connectome Project", "given": "", "initials": ""}, {"family": "FinnBrain", "given": "", "initials": ""}, {"family": "Harvard Aging Brain Study", "given": "", "initials": ""}, {"family": "IMAGEN", "given": "", "initials": ""}, {"family": "KNE96", "given": "", "initials": ""}, {"family": "Mayo Clinic Study of Aging", "given": "", "initials": ""}, {"family": "NSPN", "given": "", "initials": ""}, {"family": "POND", "given": "", "initials": ""}, {"family": "PREVENT-AD Research Group", "given": "", "initials": ""}, {"family": "VETSA", "given": "", "initials": ""}, {"family": "Bullmore", "given": "E T", "initials": "ET"}, {"family": "Alexander-Bloch", "given": "A F", "initials": "AF"}], "type": "journal article", "published": "2022-04-00", "journal": {"title": "Nature", "issn": "1476-4687", "issn-l": "0028-0836", "volume": "604", "issue": "7906", "pages": "525-533"}, "abstract": "Over the past few decades, neuroimaging has become a ubiquitous tool in basic research and clinical studies of the human brain. However, no reference standards currently exist to quantify individual differences in neuroimaging metrics over time, in contrast to growth charts for anthropometric traits such as height and weight1. Here we assemble an interactive open resource to benchmark brain morphology derived from any current or future sample of MRI data ( http://www.brainchart.io/ ). With the goal of basing these reference charts on the largest and most inclusive dataset available, acknowledging limitations due to known biases of MRI studies relative to the diversity of the global population, we aggregated 123,984 MRI scans, across more than 100 primary studies, from 101,457 human participants between 115 days post-conception to 100 years of age. MRI metrics were quantified by centile scores, relative to non-linear trajectories2 of brain structural changes, and rates of change, over the lifespan. Brain charts identified previously unreported neurodevelopmental milestones3, showed high stability of individuals across longitudinal assessments, and demonstrated robustness to technical and methodological differences between primary studies. Centile scores showed increased heritability compared with non-centiled MRI phenotypes, and provided a standardized measure of atypical brain structure that revealed patterns of neuroanatomical variation across neurological and psychiatric disorders. In summary, brain charts are an essential step towards robust quantification of individual variation benchmarked to normative trajectories in multiple, commonly used neuroimaging phenotypes.", "doi": "10.1038/s41586-022-04554-y", "pmid": "35388223", "labels": {"Jacob W Vogel": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC9021021"}, {"db": "pii", "key": "10.1038/s41586-022-04554-y"}], "notes": [], "created": "2023-05-28T17:54:19.683Z", "modified": "2023-11-29T06:38:22.566Z"}, {"entity": "publication", "iuid": "e69abfcba55147bc9c0e884a88a1b87c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e69abfcba55147bc9c0e884a88a1b87c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e69abfcba55147bc9c0e884a88a1b87c"}}, "title": "B cell-related gene signature and cancer immunotherapy response.", "authors": [{"family": "Lundberg", "given": "Arian", "initials": "A", "orcid": "0000-0002-6630-2787", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/baa2c7c8963840bfb6a22d7c5cfe35f9.json"}}, {"family": "Li", "given": "Bailiang", "initials": "B"}, {"family": "Li", "given": "Ruijiang", "initials": "R", "orcid": "0000-0002-0232-5998", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/adee5b06fdf743139a8bb3ac8bff4d4a.json"}}], "type": "journal article", "published": "2022-04-00", "journal": {"title": "Br. J. Cancer", "issn": "1532-1827", "volume": "126", "issue": "6", "pages": "899-906", "issn-l": "0007-0920"}, "abstract": "B lymphocytes have multifaceted functions in the tumour microenvironment, and their prognostic role in human cancers is controversial. Here we aimed to identify tumour microenvironmental factors that influence the prognostic effects of B cells.\n\nWe conducted a gene expression analysis of 3585 patients for whom the clinical outcome information was available. We further investigated the clinical relevance for predicting immunotherapy response.\n\nWe identified a novel B cell-related gene (BCR) signature consisting of nine cytokine signalling genes whose high expression could diminish the beneficial impact of B cells on patient prognosis. In triple-negative breast cancer, higher B cell abundance was associated with favourable survival only when the BCR signature was low (HR = 0.68, p = 0.0046). By contrast, B cell abundance had no impact on prognosis when the BCR signature was high (HR = 0.93, p = 0.80). This pattern was consistently observed across multiple cancer types including lung, colorectal, and melanoma. Further, the BCR signature predicted response to immune checkpoint blockade in metastatic melanoma and compared favourably with the established markers.\n\nThe prognostic impact of tumour-infiltrating B cells depends on the status of cytokine signalling genes, which together could predict response to cancer immunotherapy.", "doi": "10.1038/s41416-021-01674-6", "pmid": "34921229", "labels": {"DDLS Fellow": null, "Arian Lundberg": null}, "xrefs": [{"db": "pmc", "key": "PMC8927337"}, {"db": "pii", "key": "10.1038/s41416-021-01674-6"}], "notes": [], "created": "2025-11-14T07:51:48.669Z", "modified": "2025-11-14T07:51:48.750Z"}, {"entity": "publication", "iuid": "d14f7981a1474219bbb4402db50fb771", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d14f7981a1474219bbb4402db50fb771.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d14f7981a1474219bbb4402db50fb771"}}, "title": "Associations between Listeria monocytogenes genomic characteristics and adhesion to polystyrene at 8 \u00b0C.", "authors": [{"family": "Mahoney", "given": "David Burke James", "initials": "DBJ"}, {"family": "Falardeau", "given": "Justin", "initials": "J"}, {"family": "Hingston", "given": "Patricia", "initials": "P"}, {"family": "Chmielowska", "given": "Cora", "initials": "C"}, {"family": "Carroll", "given": "Laura M", "initials": "LM"}, {"family": "Wiedmann", "given": "Martin", "initials": "M"}, {"family": "Jang", "given": "Sung Sik", "initials": "SS"}, {"family": "Wang", "given": "Siyun", "initials": "S"}], "type": "journal article", "published": "2022-04-00", "journal": {"title": "Food Microbiol", "issn": "1095-9998", "volume": "102", "pages": "103915", "issn-l": null}, "abstract": "Listeria monocytogenes remains a threat to the food system and has led to numerous foodborne outbreaks worldwide. L. monocytogenes can establish itself in food production facilities by adhering to surfaces, resulting in increased resistance to environmental stressors. The aim of this study was to evaluate the adhesion ability of L. monocytogenes at 8 \u00b0C and to analyse associations between the observed phenotypes and genetic factors such as internalin A (inlA) genotypes, stress survival islet 1 (SSI-1) genotype, and clonal complex (CC). L. monocytogenes isolates (n = 184) were grown at 8 \u00b0C and 100% relative humidity for 15 days. The growth was measured by optical density at 600 nm every 24 h. Adherent cells were stained using crystal violet and quantified spectrophotometrically. Genotyping of inlA and SSI-1, multi-locus sequence typing, and a genome-wide association study (GWAS) were performed to elucidate the phenotype-genotype relationships in L. monocytogenes cold adhesion. Among all inlA genotypes, truncated inlA isolates had the highest mean adhered cells, ABS595nm = 0.30 \u00b1 0.15 (Tukey HSD; P < 0.05), while three-codon deletion inlA isolates had the least mean adhered cells (Tukey HSD; P < 0.05). When SSI-1 was present, more cells adhered; less cells adhered when SSI-1 was absent (Welch's t-test; P < 0.05). Adhesion was associated with clonal complexes which have low clinical frequency, while reduced adhesion was associated with clonal complexes which have high frequency. The results of this study support that premature stop codons in the virulence gene inlA are associated with increased cold adhesion and that an invasion enhancing deletion in inlA is associated with decreased cold adhesion. This study also provides evidence to suggest that there is an evolutionary trade off between virulence and adhesion in L. monocytogenes. These results provide a greater understanding of L. monocytogenes adhesion which will aid in the development of strategies to reduce L. monocytogenes in the food system.", "doi": "10.1016/j.fm.2021.103915", "pmid": "34809941", "labels": {"DDLS Fellow": null, "Laura Carroll": null}, "xrefs": [{"db": "pii", "key": "S0740-0020(21)00181-7"}], "notes": [], "created": "2023-05-13T11:52:41.044Z", "modified": "2025-03-18T17:28:49.610Z"}, {"entity": "publication", "iuid": "6d5151bbccf94e4887c6eb2f698be76a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/6d5151bbccf94e4887c6eb2f698be76a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/6d5151bbccf94e4887c6eb2f698be76a"}}, "title": "An Open-Source Modular Framework for Automated Pipetting and Imaging Applications.", "authors": [{"family": "Ouyang", "given": "Wei", "initials": "W"}, {"family": "Bowman", "given": "Richard W", "initials": "RW"}, {"family": "Wang", "given": "Haoran", "initials": "H"}, {"family": "Bumke", "given": "Kaspar E", "initials": "KE"}, {"family": "Collins", "given": "Joel T", "initials": "JT"}, {"family": "Spjuth", "given": "Ola", "initials": "O"}, {"family": "Carreras-Puigvert", "given": "Jordi", "initials": "J"}, {"family": "Diederich", "given": "Benedict", "initials": "B", "orcid": "0000-0003-0453-6286", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/25fb1523d3854ce59fdfe3841250ac3c.json"}}], "type": "journal article", "published": "2022-04-00", "journal": {"title": "Adv Biol (Weinh)", "issn": "2701-0198", "volume": "6", "issue": "4", "pages": "e2101063", "issn-l": null}, "abstract": "The number of samples in biological experiments is continuously increasing, but complex protocols and human error in many cases lead to suboptimal data quality and hence difficulties in reproducing scientific findings. Laboratory automation can alleviate many of these problems by precisely reproducing machine-readable protocols. These instruments generally require high up-front investments, and due to the lack of open application programming interfaces (APIs), they are notoriously difficult for scientists to customize and control outside of the vendor-supplied software. Here, automated, high-throughput experiments are demonstrated for interdisciplinary research in life science that can be replicated on a modest budget, using open tools to ensure reproducibility by combining the tools OpenFlexure, Opentrons, ImJoy, and UC2. This automated sample preparation and imaging pipeline can easily be replicated and established in many laboratories as well as in educational contexts through easy-to-understand algorithms and easy-to-build microscopes. Additionally, the creation of feedback loops, with later pipetting or imaging steps depending on the analysis of previously acquired images, enables the realization of fully autonomous \"smart\" microscopy experiments. All documents and source files are publicly available to prove the concept of smart lab automation using inexpensive, open tools. It is believed this democratizes access to the power and repeatability of automated experiments.", "doi": "10.1002/adbi.202101063", "pmid": "34693668", "labels": {"DDLS Fellow": "", "Wei Ouyang": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T06:27:21.416Z", "modified": "2026-09-23T10:06:09.703Z"}, {"entity": "publication", "iuid": "abe0fcfa5eca477384d4348b12aa56a3", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/abe0fcfa5eca477384d4348b12aa56a3.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/abe0fcfa5eca477384d4348b12aa56a3"}}, "title": "Author Correction: Improved prediction of protein-protein interactions using AlphaFold2.", "authors": [{"family": "Bryant", "given": "Patrick", "initials": "P", "orcid": "0000-0003-3439-1866", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a683bcf98234ff09b2398976583b66f.json"}}, {"family": "Pozzati", "given": "Gabriele", "initials": "G", "orcid": "0000-0002-4303-9939", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/94129216debe4e22ab3f3b74c33f9ab9.json"}}, {"family": "Elofsson", "given": "Arne", "initials": "A", "orcid": "0000-0002-7115-9751", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/248e70e81bd64f31a5f83e6e329bba95.json"}}], "type": "published erratum", "published": "2022-03-24", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "13", "issue": "1", "pages": "1694", "issn-l": "2041-1723"}, "abstract": null, "doi": "10.1038/s41467-022-29480-5", "pmid": "35332153", "labels": {"Patrick Bryant": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC8948285"}, {"db": "pii", "key": "10.1038/s41467-022-29480-5"}], "notes": [], "created": "2026-08-20T08:51:54.323Z", "modified": "2026-09-23T13:45:21.995Z"}, {"entity": "publication", "iuid": "5da495110d404371b5693f5854cbfca2", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5da495110d404371b5693f5854cbfca2.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5da495110d404371b5693f5854cbfca2"}}, "title": "The microbiome in reproductive health: protocol for a systems biology approach using a prospective, observational study design.", "authors": [{"family": "Krog", "given": "Maria Christine", "initials": "MC", "orcid": "0000-0002-2110-0479", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bdd65c5105f4480692383dae8d4ac986.json"}}, {"family": "Madsen", "given": "Mette Elkj\u00e6r", "initials": "ME", "orcid": "0000-0001-7767-9849", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1c8d263e2f4d4507bc2510f04869a5a5.json"}}, {"family": "Bliddal", "given": "Sofie", "initials": "S", "orcid": "0000-0002-2456-1019", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/58a6059b93a14a6e80514e744893acdd.json"}}, {"family": "Bashir", "given": "Zahra", "initials": "Z", "orcid": "0000-0002-2497-282X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2d15fce497fe4cdabd82e994e7cd83ad.json"}}, {"family": "Vex\u00f8", "given": "Laura Emilie", "initials": "LE"}, {"family": "Hartwell", "given": "Dorthe", "initials": "D"}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW", "orcid": "0000-0001-5432-1764", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/246ed7b405dd4c3f9ec5e7ff9f1d3ade.json"}}, {"family": "Fransson", "given": "Emma", "initials": "E", "orcid": "0000-0001-9010-8522", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8c05290187ec426b8804eefc3d954971.json"}}, {"family": "Hamsten", "given": "Marica", "initials": "M"}, {"family": "Boulund", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-3806-323X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a5c6814a31e644b9bc544d4da759a438.json"}}, {"family": "Wannerberger", "given": "Kristin", "initials": "K"}, {"family": "Engstrand", "given": "Lars", "initials": "L", "orcid": "0000-0002-7713-2373", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02d8684df81e42169e613de803446fbf.json"}}, {"family": "Schuppe-Koistinen", "given": "Ina", "initials": "I", "orcid": "0000-0002-1423-3089", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/659fb04e6a1a430cbd707b8a50d500a3.json"}}, {"family": "Nielsen", "given": "Henriette Svarre", "initials": "HS", "orcid": "0000-0003-2106-8103", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9a99fa7ebb204c618ed70f29be0085b3.json"}}], "type": "journal article", "published": "2022-03-23", "journal": {"title": "Hum Reprod Open", "issn": "2399-3529", "volume": "2022", "issue": "2", "pages": "hoac015", "issn-l": null}, "abstract": "What is the microbiome profile across different body sites in relation to the normal menstrual cycle (with and without hormonal contraception), recurrent pregnancy loss (RPL) (before and during pregnancy, pregnancy loss or birth) and endometriosis (before, during and after surgery)? How do these profiles interact with genetics, environmental exposures, immunological and endocrine biomarkers?\n\nThe microbiome is a key factor influencing human health and disease in areas as diverse as immune functioning, gastrointestinal disease and mental and metabolic disorders. There is mounting evidence to suggest that the reproductive microbiome may be influential in general and reproductive health, fertility and pregnancy outcomes.\n\nThis is a prospective, longitudinal, observational study using a systems biology approach in three cohorts totalling 920 participants. Since microbiome profiles by shot-gun sequencing have never been investigated in healthy controls during varying phases of the menstrual cycle, patients with RPL and patients with endometriosis, no formal sample size calculation can be performed. The study period is from 2017 to 2024 and allows for longitudinal profiling of study participants to enable deeper understanding of the role of the microbiome and of host-microbe interactions in reproductive health.\n\nParticipants in each cohort are as follows: Part 1 MiMens-150 healthy women with or without hormonal contraception; Part 2 MiRPL-200 couples with RPL, 50 healthy couples with prior uncomplicated pregnancy and 150 newborns; Part 3 MiEndo-120 patients with endometriosis requiring surgery with or without hormonal treatment. Microbiome profiles from saliva, faeces, rectal mucosa, vaginal fluid and endometrium will be studied, as well as the Omics profile, endocrine disrupting chemicals and endocrine and immune factors in blood, hair, saliva and urine. Pregnancy loss products, seminal microbiome, HLA types, endometriotic tissue and genetic risk and comprehensive questionnaire data will also be studied, where appropriate. Correlations with mental and physical health will be evaluated.\n\nThis work is supported by funding from Ferring Pharmaceuticals ([#MiHSN01] to H.S.N., M.C.K., M.E.M., L.E.V., L.E., I.S.-K., F.B., L.W.H., E.F. and M.H.), Rigshospitalet's Research Funds ([#E-22614-01 and #E-22614-02] to M.C.K. and [#E-22222-06] to S.B.), Niels and Desiree Yde's Foundation (S.B., endocrine analyses [#2015-2784]), the Musikforl\u00e6ggerne Agnes and Knut M\u00f8rk's Foundation (S.B., endocrine and immune analyses [#35108-001]) and Oda and Hans Svenningsen's Foundation ([#F-22614-08] to H.S.N.). Medical writing assistance with this manuscript was provided by Caroline Loat, PhD, and funded by Ferring Pharmaceuticals. H.S.N. reports personal fees from Ferring Pharmaceuticals, Merck Denmark A/S, Ibsa Nordic, Astra Zeneca and Cook Medical outside the submitted work. K.W. is a full-time employee of Ferring Pharmaceuticals. No other conflicts are reported.\n\nN/A.\n\nN/A.\n\nN/A.", "doi": "10.1093/hropen/hoac015", "pmid": "35441092", "labels": {"DDLS Fellow": null, "Luisa Hugerth": null}, "xrefs": [{"db": "pmc", "key": "PMC9014536"}, {"db": "pii", "key": "hoac015"}], "notes": [], "created": "2023-05-12T13:20:12.988Z", "modified": "2023-10-27T09:28:00.116Z"}, {"entity": "publication", "iuid": "a7ef7b5645ea42cea42f0f56879378a8", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a7ef7b5645ea42cea42f0f56879378a8.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a7ef7b5645ea42cea42f0f56879378a8"}}, "title": "Genome-wide association study on 13 167 individuals identifies regulators of blood CD34+cell levels.", "authors": [{"family": "Lopez de Lapuente Portilla", "given": "Aitzkoa", "initials": "A"}, {"family": "Ekdahl", "given": "Ludvig", "initials": "L", "orcid": "0000-0002-4257-7284", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4a3d35910b344c849efbb73fe4a630a3.json"}}, {"family": "Cafaro", "given": "Caterina", "initials": "C"}, {"family": "Ali", "given": "Zain", "initials": "Z"}, {"family": "Miharada", "given": "Natsumi", "initials": "N"}, {"family": "Thorleifsson", "given": "Gudmar", "initials": "G"}, {"family": "\u017demaitis", "given": "Kristijonas", "initials": "K", "orcid": "0000-0002-4098-0184", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/623fb0a2c32247e4845e84f830dd18fe.json"}}, {"family": "Lamarca Arrizabalaga", "given": "Antton", "initials": "A"}, {"family": "Thodberg", "given": "Malte", "initials": "M", "orcid": "0000-0001-6244-3841", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7f2c232400714922bdbd28e77ede971e.json"}}, {"family": "Pertesi", "given": "Maroulio", "initials": "M"}, {"family": "Dhapola", "given": "Parashar", "initials": "P", "orcid": "0000-0002-8070-7238", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e18a6fdfca924c549d5b20c79111867c.json"}}, {"family": "Bao", "given": "Erik", "initials": "E"}, {"family": "Niroula", "given": "Abhishek", "initials": "A"}, {"family": "Bali", "given": "Divya", "initials": "D", "orcid": "0000-0003-3178-1586", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bbcd91ef892d4eeca466eed9adf596f7.json"}}, {"family": "Norddahl", "given": "Gudmundur", "initials": "G"}, {"family": "Ugidos Damboriena", "given": "Nerea", "initials": "N", "orcid": "0000-0003-4938-3973", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8deff5e6dcb64aa1b6f24292cde28d03.json"}}, {"family": "Sankaran", "given": "Vijay G", "initials": "VG", "orcid": "0000-0003-0044-443X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0a967a5a378f406299b3fefe244361c9.json"}}, {"family": "Karlsson", "given": "G\u00f6ran", "initials": "G"}, {"family": "Thorsteinsdottir", "given": "Unnur", "initials": "U"}, {"family": "Larsson", "given": "Jonas", "initials": "J"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "Nilsson", "given": "Bj\u00f6rn", "initials": "B"}], "type": "journal article", "published": "2022-03-17", "journal": {"title": "Blood", "issn": "1528-0020", "volume": "139", "issue": "11", "pages": "1659-1669", "issn-l": "0006-4971"}, "abstract": "Stem cell transplantation is a cornerstone in the treatment of blood malignancies. The most common method to harvest stem cells for transplantation is by leukapheresis, requiring mobilization of CD34+ hematopoietic stem and progenitor cells (HSPCs) from the bone marrow into the blood. Identifying the genetic factors that control blood CD34+ cell levels could reveal new drug targets for HSPC mobilization. Here we report the first large-scale, genome-wide association study on blood CD34+ cell levels. Across 13 167 individuals, we identify 9 significant and 2 suggestive associations, accounted for by 8 loci (PPM1H, CXCR4, ENO1-RERE, ITGA9, ARHGAP45, CEBPA, TERT, and MYC). Notably, 4 of the identified associations map to CXCR4, showing that bona fide regulators of blood CD34+ cell levels can be identified through genetic variation. Further, the most significant association maps to PPM1H, encoding a serine/threonine phosphatase never previously implicated in HSPC biology. PPM1H is expressed in HSPCs, and the allele that confers higher blood CD34+ cell levels downregulates PPM1H. Through functional fine-mapping, we find that this downregulation is caused by the variant rs772557-A, which abrogates an MYB transcription factor-binding site in PPM1H intron 1 that is active in specific HSPC subpopulations, including hematopoietic stem cells, and interacts with the promoter by chromatin looping. Furthermore, PPM1H knockdown increases the proportion of CD34+ and CD34+90+ cells in cord blood assays. Our results provide the first large-scale analysis of the genetic architecture of blood CD34+ cell levels and warrant further investigation of PPM1H as a potential inhibition target for stem cell mobilization.", "doi": "10.1182/blood.2021013220", "pmid": "35007327", "labels": {"Abhishek Niroula": null, "DDLS Fellow": null}, "xrefs": [{"db": "pii", "key": "S0006-4971(22)00038-6"}], "notes": [], "created": "2023-11-20T11:36:11.310Z", "modified": "2023-11-20T11:36:11.572Z"}, {"entity": "publication", "iuid": "0be796669e584dfa8ea662af78c39431", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0be796669e584dfa8ea662af78c39431.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0be796669e584dfa8ea662af78c39431"}}, "title": "Metabolite interactions in the bacterial Calvin cycle and implications for flux regulation", "authors": [{"family": "Sporre", "given": "Emil", "initials": "E", "orcid": "0000-0003-4105-7567", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2250c46520424ec69e3d736c2bf30099.json"}}, {"family": "Karlsen", "given": "Jan", "initials": "J", "orcid": "0000-0002-2821-9026", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4a1c2fa8404749b0a797e90e9c6cb09e.json"}}, {"family": "Schriever", "given": "Karen", "initials": "K", "orcid": "0000-0002-3677-5508", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/282cce0f6c054fd8a7858977be549b24.json"}}, {"family": "Samuelsson", "given": "Johannes Asplund", "initials": "JA", "orcid": "0000-0001-8077-5305", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e1cf0c49cbb849b194b0b46582441d09.json"}}, {"family": "Janasch", "given": "Markus", "initials": "M", "orcid": "0000-0001-7745-720X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/115ab90674ba4090be1b3ef9a01549e4.json"}}, {"family": "Strandberg", "given": "Linn\u00e9a", "initials": "L", "orcid": "0000-0001-5386-5460", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ea4741b77234afe83e92c3dfff0a799.json"}}, {"family": "Kotol", "given": "David", "initials": "D", "orcid": "0000-0002-5388-3826", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c41f8f491c474e6bba2047b5d04b4af5.json"}}, {"family": "Zeckey", "given": "Luise", "initials": "L"}, {"family": "Piazza", "given": "Ilaria", "initials": "I", "orcid": "0000-0001-5895-6134", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5258dce396444d9a8f5e5bc2fd13b282.json"}}, {"family": "Syr\u00e9n", "given": "Per Olof", "initials": "PO", "orcid": "0000-0002-4066-2776", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b035f26bd71e42f9942f9a4943ed0d1a.json"}}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e213b04f8984c8eb00c68f5bc2f6a36.json"}}, {"family": "Hudson", "given": "Elton P", "initials": "EP", "orcid": "0000-0003-1899-7649", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3b1c894d4c8b48569b9879d0342b91dd.json"}}], "type": "posted-content", "published": "2022-03-15", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2022.03.15.483797", "pmid": null, "labels": {"Paul Hudson": "", "SciLifeLab Fellow": "", "Fredrik Edfors": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T10:10:14.448Z", "modified": "2026-09-23T14:26:07.003Z"}, {"entity": "publication", "iuid": "44e0c5637503434fbb7cb7c997c86105", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/44e0c5637503434fbb7cb7c997c86105.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/44e0c5637503434fbb7cb7c997c86105"}}, "title": "Predicting the structure of large protein complexes using AlphaFold and Monte Carlo tree search", "authors": [{"family": "Bryant", "given": "Patrick", "initials": "P", "orcid": "0000-0003-3439-1866", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a683bcf98234ff09b2398976583b66f.json"}}, {"family": "Pozzati", "given": "Gabriele", "initials": "G", "orcid": "0000-0002-4303-9939", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/94129216debe4e22ab3f3b74c33f9ab9.json"}}, {"family": "Zhu", "given": "Wensi", "initials": "W"}, {"family": "Shenoy", "given": "Aditi", "initials": "A", "orcid": "0000-0001-7748-2501", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/35bef00b985a45d59602675316e3d706.json"}}, {"family": "Kundrotas", "given": "Petras", "initials": "P", "orcid": "0000-0001-5080-1664", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e645003f2000464c9e289ccd3b92ce68.json"}}, {"family": "Elofsson", "given": "Arne", "initials": "A", "orcid": "0000-0002-7115-9751", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/248e70e81bd64f31a5f83e6e329bba95.json"}}], "type": "posted-content", "published": "2022-03-12", "journal": {"title": "bioRxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2022.03.12.484089", "pmid": null, "labels": {"Patrick Bryant": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2026-08-20T10:10:09.009Z", "modified": "2026-10-05T07:31:43.884Z"}, {"entity": "publication", "iuid": "1dfa3174fd1847d4b909d3625bcedb14", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1dfa3174fd1847d4b909d3625bcedb14.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1dfa3174fd1847d4b909d3625bcedb14"}}, "title": "Improved prediction of protein-protein interactions using AlphaFold2.", "authors": [{"family": "Bryant", "given": "Patrick", "initials": "P", "orcid": "0000-0003-3439-1866", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a683bcf98234ff09b2398976583b66f.json"}}, {"family": "Pozzati", "given": "Gabriele", "initials": "G", "orcid": "0000-0002-4303-9939", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/94129216debe4e22ab3f3b74c33f9ab9.json"}}, {"family": "Elofsson", "given": "Arne", "initials": "A", "orcid": "0000-0002-7115-9751", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/248e70e81bd64f31a5f83e6e329bba95.json"}}], "type": "journal article", "published": "2022-03-10", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "13", "issue": "1", "pages": "1265", "issn-l": "2041-1723"}, "abstract": "Predicting the structure of interacting protein chains is a fundamental step towards understanding protein function. Unfortunately, no computational method can produce accurate structures of protein complexes. AlphaFold2, has shown unprecedented levels of accuracy in modelling single chain protein structures. Here, we apply AlphaFold2 for the prediction of heterodimeric protein complexes. We find that the AlphaFold2 protocol together with optimised multiple sequence alignments, generate models with acceptable quality (DockQ \u2265 0.23) for 63% of the dimers. From the predicted interfaces we create a simple function to predict the DockQ score which distinguishes acceptable from incorrect models as well as interacting from non-interacting proteins with state-of-art accuracy. We find that, using the predicted DockQ scores, we can identify 51% of all interacting pairs at 1% FPR.", "doi": "10.1038/s41467-022-28865-w", "pmid": "35273146", "labels": {"Patrick Bryant": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC8913741"}, {"db": "pii", "key": "10.1038/s41467-022-28865-w"}], "notes": [], "created": "2026-08-20T08:51:52.439Z", "modified": "2026-09-22T19:59:14.208Z"}, {"entity": "publication", "iuid": "266c0b648bbe4bd8b3357671878ab856", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/266c0b648bbe4bd8b3357671878ab856.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/266c0b648bbe4bd8b3357671878ab856"}}, "title": "Mechanistic insights into the C55-P targeting lipopeptide antibiotics revealed by structure-activity studies and high-resolution crystal structures.", "authors": [{"family": "Wood", "given": "Thomas M", "initials": "TM", "orcid": "0000-0001-7270-147X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/85c18349e93f4314872bf645c83c4162.json"}}, {"family": "Zeronian", "given": "Matthieu R", "initials": "MR", "orcid": "0000-0001-9790-4097", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2ecfac3d1fdc41c881ed6ad1dc3bd87c.json"}}, {"family": "Buijs", "given": "Ned", "initials": "N"}, {"family": "Bertheussen", "given": "Kristine", "initials": "K"}, {"family": "Abedian", "given": "Hanieh K", "initials": "HK"}, {"family": "Johnson", "given": "Aidan V", "initials": "AV"}, {"family": "Pearce", "given": "Nicholas M", "initials": "NM", "orcid": "0000-0002-6693-8603", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/07d6d5de91cc4120b2bf996ca578a13e.json"}}, {"family": "Lutz", "given": "Martin", "initials": "M"}, {"family": "Kemmink", "given": "Johan", "initials": "J"}, {"family": "Seirsma", "given": "Tjalling", "initials": "T"}, {"family": "Hamoen", "given": "Leendert W", "initials": "LW"}, {"family": "Janssen", "given": "Bert J C", "initials": "BJC", "orcid": "0000-0002-8101-8370", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9d507563acd44967b52a4860621ea365.json"}}, {"family": "Martin", "given": "Nathaniel I", "initials": "NI", "orcid": "0000-0001-8246-3006", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ac5e6d2689244197a3f3c3e38bff0d34.json"}}], "type": "journal article", "published": "2022-03-09", "journal": {"title": "Chem Sci", "issn": "2041-6520", "volume": "13", "issue": "10", "pages": "2985-2991", "issn-l": null}, "abstract": "The continued rise of antibiotic resistance is a global concern that threatens to undermine many aspects of modern medical practice. Key to addressing this threat is the discovery and development of new antibiotics that operate by unexploited modes of action. The so-called calcium-dependent lipopeptide antibiotics (CDAs) are an important emerging class of natural products that provides a source of new antibiotic agents rich in structural and mechanistic diversity. Notable in this regard is the subset of CDAs comprising the laspartomycins and amphomycins/friulimicins that specifically target the bacterial cell wall precursor undecaprenyl phosphate (C55-P). In this study we describe the design and synthesis of new C55-P-targeting CDAs with structural features drawn from both the laspartomycin and amphomycin/friulimicin classes. Assessment of these lipopeptides revealed previously unknown and surprisingly subtle structural features that are required for antibacterial activity. High-resolution crystal structures further indicate that the amphomycin/friulimicin-like lipopeptides adopt a unique crystal packing that governs their interaction with C55-P and provides an explanation for their antibacterial effect. In addition, live-cell microscopy studies provide further insights into the biological activity of the C55-P targeting CDAs highlighting their unique mechanism of action relative to the clinically used CDA daptomycin.", "doi": "10.1039/d1sc07190d", "pmid": "35382464", "labels": {"Nicholas Pearce": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC8905900"}, {"db": "pii", "key": "d1sc07190d"}], "notes": [], "created": "2022-12-05T19:30:43.285Z", "modified": "2022-12-05T19:30:43.418Z"}, {"entity": "publication", "iuid": "b134edad970a4c61b185b6ab6ec7ed52", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b134edad970a4c61b185b6ab6ec7ed52.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b134edad970a4c61b185b6ab6ec7ed52"}}, "title": "GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species", "authors": [{"family": "Kutschera", "given": "Verena E", "initials": "VE", "orcid": "0000-0002-8930-534X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c7185df2f7d44872960d604e9c70c551.json"}}, {"family": "Kierczak", "given": "Marcin", "initials": "M", "orcid": "0000-0003-2629-5655", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/da6834c3cedf4ea1b20b659316b45eb2.json"}}, {"family": "van der Valk", "given": "Tom", "initials": "T", "orcid": "0000-0001-6582-3452", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/aa0dba3cc12143cba213f7f3a052216c.json"}}, {"family": "von Seth", "given": "Johanna", "initials": "J", "orcid": "0000-0002-1324-7489", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dd70195ca85f415caf1e4660681e1bbc.json"}}, {"family": "Dussex", "given": "Nicolas", "initials": "N", "orcid": "0000-0002-9179-8593", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3c93917b1e544c6eae92fd4aa0617fd8.json"}}, {"family": "Lord", "given": "Edana", "initials": "E", "orcid": "0000-0002-4717-1988", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/82cf4b7f99494f27b98ead0e6a0bee4f.json"}}, {"family": "Dehasque", "given": "Marianne", "initials": "M", "orcid": "0000-0002-4640-8306", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/873b625c6ce44ec48f30d92fbc9b3e2f.json"}}, {"family": "Stanton", "given": "David W G", "initials": "DWG"}, {"family": "Khoonsari", "given": "Payam Emami", "initials": "PE", "orcid": "0000-0002-4137-5517", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3f0f1758926845329c02b1ee8164ce60.json"}}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/33ba67b99d2b477d9588d40e8cc0fed2.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L"}, {"family": "D\u00edez-del-Molino", "given": "David", "initials": "D", "orcid": "0000-0002-9701-5940", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ffd5992faedc45e1bfe19fd498485400.json"}}], "type": "posted-content", "published": "2022-03-07", "journal": {"title": "bioRxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2022.03.04.482637", "pmid": null, "labels": {"DDLS Fellow": null, "Tom van der Valk": null}, "xrefs": [], "notes": [], "created": "2026-08-20T10:10:03.420Z", "modified": "2026-10-05T08:39:19.042Z"}, {"entity": "publication", "iuid": "cbb940ee91824068953811d87c83f3a3", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/cbb940ee91824068953811d87c83f3a3.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/cbb940ee91824068953811d87c83f3a3"}}, "title": "The relationship between ageing and changes in the human blood and brain methylomes.", "authors": [{"family": "Bryant", "given": "Patrick", "initials": "P", "orcid": "0000-0003-3439-1866", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a683bcf98234ff09b2398976583b66f.json"}}, {"family": "Elofsson", "given": "Arne", "initials": "A", "orcid": "0000-0002-7115-9751", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/248e70e81bd64f31a5f83e6e329bba95.json"}}], "type": "journal article", "published": "2022-03-00", "journal": {"title": "NAR Genomics and Bioinformatics", "issn": "2631-9268", "volume": "4", "issue": "1", "pages": "lqac001", "issn-l": null}, "abstract": "Changes in DNA methylation have been found to be strongly correlated with age, enabling the creation of 'epigenetic clocks'. Previously, studies on the relationship between ageing and DNA methylation have assumed a linear relationship. Here, we show that several markers show a non-linear behaviour. In particular, we observe a tendency for saturation with age, especially in the cerebellum. Further, we show that the relationships between significant methylation changes and ageing are different in different tissues. We suggest a straightforward method of assessing all methylation-age relationships and cluster them according to their relative fold change. Our fold change selection outperforms the most common epigenetic clocks in predicting age for the cerebellum, but not for Blood or the Frontal Cortex. Further, we find that the saturation of methylation observed at older ages for the cerebellum explains why epigenetic clocks consistently underestimate the age there. The findings imply that assuming linear correlations might cause biologically important markers to be missed.", "doi": "10.1093/nargab/lqac001", "pmid": "35118376", "labels": {"Patrick Bryant": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC8808541"}, {"db": "pii", "key": "lqac001"}], "notes": [], "created": "2026-08-20T09:42:49.076Z", "modified": "2026-09-23T13:29:15.350Z"}, {"entity": "publication", "iuid": "5819853106a34353b16132eb6de3c998", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5819853106a34353b16132eb6de3c998.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5819853106a34353b16132eb6de3c998"}}, "title": "The SWI/SNF subunit BRG1 affects alternative splicing by changing RNA binding factor interactions with nascent RNA.", "authors": [{"family": "Ga\u00f1ez-Zapater", "given": "Antoni", "initials": "A"}, {"family": "Mackowiak", "given": "Sebastian D", "initials": "SD"}, {"family": "Guo", "given": "Yuan", "initials": "Y"}, {"family": "Tarbier", "given": "Marcel", "initials": "M"}, {"family": "Jord\u00e1n-Pla", "given": "Antonio", "initials": "A"}, {"family": "Friedl\u00e4nder", "given": "Marc R", "initials": "MR"}, {"family": "Visa", "given": "Neus", "initials": "N"}, {"family": "\u00d6stlund Farrants", "given": "Ann-Kristin", "initials": "AK", "orcid": "0000-0001-9225-3264", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/51275e6a196d44a09e6d7907efee282b.json"}}], "type": "journal article", "published": "2022-03-00", "journal": {"title": "Mol. Genet. Genomics", "issn": "1617-4623", "volume": "297", "issue": "2", "pages": "463-484", "issn-l": null}, "abstract": "BRG1 and BRM are ATPase core subunits of the human SWI/SNF chromatin remodelling complexes mainly associated with transcriptional initiation. They also have a role in alternative splicing, which has been shown for BRM-containing SWI/SNF complexes at a few genes. Here, we have identified a subset of genes which harbour alternative exons that are affected by SWI/SNF ATPases by expressing the ATPases BRG1 and BRM in C33A cells, a BRG1- and BRM-deficient cell line, and analysed the effect on splicing by RNA sequencing. BRG1- and BRM-affected sub-sets of genes favouring both exon inclusion and exon skipping, with only a minor overlap between the ATPase. Some of the changes in alternative splicing induced by BRG1 and BRM expression did not require the ATPase activity. The BRG1-ATPase independent included exons displayed an exon signature of a high GC content. By investigating three genes with exons affected by the BRG-ATPase-deficient variant, we show that these exons accumulated phosphorylated RNA pol II CTD, both serine 2 and serine 5 phosphorylation, without an enrichment of the RNA polymerase II. The ATPases were recruited to the alternative exons, together with both core and signature subunits of SWI/SNF complexes, and promoted the binding of RNA binding factors to chromatin and RNA at the alternative exons. The interaction with the nascent RNP, however, did not reflect the association to chromatin. The hnRNPL, hnRNPU and SAM68 proteins associated with chromatin in cells expressing BRG1 and BRM wild type, but the binding of hnRNPU to the nascent RNP was excluded. This suggests that SWI/SNF can regulate alternative splicing by interacting with splicing-RNA binding factor and influence their binding to the nascent pre-mRNA particle.", "doi": "10.1007/s00438-022-01863-9", "pmid": "35187582", "labels": {"Marc Friedl\u00e4nder": "", "SciLifeLab Fellow": "", "Marcel Tarbier": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC8960663"}, {"db": "pii", "key": "10.1007/s00438-022-01863-9"}], "notes": [], "created": "2022-12-06T09:11:25.038Z", "modified": "2026-09-23T10:58:20.220Z"}, {"entity": "publication", "iuid": "2e3a5fb7fe1c492bb41cb2a2c46c00b9", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/2e3a5fb7fe1c492bb41cb2a2c46c00b9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/2e3a5fb7fe1c492bb41cb2a2c46c00b9"}}, "title": "Proteomics in thrombosis research.", "authors": [{"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Iglesias", "given": "Maria Jesus", "initials": "MJ"}, {"family": "Butler", "given": "Lynn M", "initials": "LM"}, {"family": "Odeberg", "given": "Jacob", "initials": "J"}], "type": "journal article", "published": "2022-03-00", "journal": {"title": "Res Pract Thromb Haemost", "issn": "2475-0379", "volume": "6", "issue": "3", "pages": "e12706", "issn-l": null}, "abstract": "A State of the Art lecture titled \"Proteomics in Thrombosis Research\" was presented at the ISTH Congress in 2021. In clinical practice, there is a need for improved plasma biomarker-based tools for diagnosis and risk prediction of venous thromboembolism (VTE). Analysis of blood, to identify plasma proteins with potential utility for such tools, could enable an individualized approach to treatment and prevention. Technological advances to study the plasma proteome on a large scale allows broad screening for the identification of novel plasma biomarkers, both by targeted and nontargeted proteomics methods. However, assay limitations need to be considered when interpreting results, with orthogonal validation required before conclusions are drawn. Here, we review and provide perspectives on the application of affinity- and mass spectrometry-based methods for the identification and analysis of plasma protein biomarkers, with potential application in the field of VTE. We also provide a future perspective on discovery strategies and emerging technologies for targeted proteomics in thrombosis research. Finally, we summarize relevant new data on this topic, presented during the 2021 ISTH Congress.", "doi": "10.1002/rth2.12706", "pmid": "35494505", "labels": {"Fredrik Edfors": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC9039028"}, {"db": "pii", "key": "S2475-0379(22)01197-9"}], "notes": [], "created": "2026-08-20T06:35:40.200Z", "modified": "2026-09-23T12:01:25.177Z"}, {"entity": "publication", "iuid": "e3d6a0ff74a844b3a8dcb3dfd59a67ad", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e3d6a0ff74a844b3a8dcb3dfd59a67ad.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e3d6a0ff74a844b3a8dcb3dfd59a67ad"}}, "title": "Longitudinal trajectories of lifetime body shape and prostate cancer angiogenesis.", "authors": [{"family": "Wang", "given": "Qiao-Li", "initials": "QL", "orcid": "0000-0003-4152-7821", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/357edb3116b64ad5aa929dcb7d07a1be.json"}}, {"family": "Song", "given": "Mingyang", "initials": "M"}, {"family": "Clinton", "given": "Steven K", "initials": "SK"}, {"family": "Mucci", "given": "Lorelei A", "initials": "LA"}, {"family": "Lagergren", "given": "Jesper", "initials": "J"}, {"family": "Giovannucci", "given": "Edward L", "initials": "EL"}], "type": "journal article", "published": "2022-03-00", "journal": {"title": "Eur. J. Epidemiol.", "issn": "1573-7284", "volume": "37", "issue": "3", "pages": "261-270", "issn-l": "0393-2990"}, "abstract": "Angiogenesis potentially underlies the pathway between excess adiposity and prostate carcinogenesis. This study examined the association between lifetime body shape trajectories and prostate cancer angiogenesis. 521 prostate cancer patients who underwent prostatectomy or transurethral resection between 1986 and 2000 were enrolled from the Health Professionals Follow-up Study. Cancers were immunostained and quantitated for cancer vessel regularity, diameter, area, and density, and composite angiogenesis (factor analysis). To identify distinct groups of body shape change, we conducted group-based trajectory modeling. We used multivariable linear regression to estimate the percentage difference in angiogenesis score and 95% confidence interval (CI) between body shape change trajectories during lifetime (age 5-60 years), early life (age 5-30 years), or later life (age 30-60 years). Compared to men with lifetime lean or medium body shape, higher angiogenesis scores were observed in men with moderate increase [percentage difference of 35% (95% CI 5-64)], marked increase [24% (95% CI - 2 to 51)], and constantly heavy with mild increase body shape [38% (95% CI 8-69)]. However, a lower angiogenesis score was noted in men with early-life marked increase (- 22%, 95% CI - 44 to 0) and stable medium body shape (- 14%, 95% CI - 40 to 12), compared to moderate increase body shape. Increased angiogenesis was also found for absolute weight gain from age 21-60 years. Lifetime body fatness accumulation, especially after age 21, was associated with increased prostate cancer angiogenesis, while weight gain in early-life adulthood was associated with lower cancer angiogenesis.", "doi": "10.1007/s10654-021-00838-1", "pmid": "35025021", "labels": {"DDLS Fellow": null, "Qiaoli Wang": null}, "xrefs": [{"db": "pii", "key": "10.1007/s10654-021-00838-1"}], "notes": [], "created": "2025-11-27T18:53:36.167Z", "modified": "2025-11-27T18:53:36.225Z"}, {"entity": "publication", "iuid": "b837a84ffda94d9e83cc9cc8229e3422", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b837a84ffda94d9e83cc9cc8229e3422.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b837a84ffda94d9e83cc9cc8229e3422"}}, "title": "Evolution of the G Matrix under Nonlinear Genotype-Phenotype Maps.", "authors": [{"family": "Milocco", "given": "Lisandro", "initials": "L"}, {"family": "Salazar-Ciudad", "given": "Isaac", "initials": "I"}], "type": "journal article", "published": "2022-03-00", "journal": {"title": "Am Nat", "issn": "1537-5323", "volume": "199", "issue": "3", "pages": "420-435", "issn-l": null}, "abstract": "AbstractThe G matrix is a statistical summary of the genetic basis of a set of traits and a central pillar of quantitative genetics. A persistent controversy is whether G changes slowly or quickly over time. The evolution of G is important because it affects the ability to predict, or reconstruct, evolution by selection. Empirical studies have found mixed results on how fast G evolves. Theoretical work has largely been developed under the assumption that the relationship between genetic variation and phenotypic variation-the genotype-phenotype map (GPM)-is linear. Under this assumption, G is expected to remain constant over long periods of time. However, according to developmental biology, the GPM is typically complex and nonlinear. Here, we use a GPM model based on the development of a multicellular organ to study how G evolves. We find that G can change relatively fast and in qualitative different ways, which we describe in detail. Changes can be particularly large when the population crosses between regions of the GPM that have different properties. This can result in the additive genetic variance in the direction of selection fluctuating over time and even increasing despite the eroding effect of selection.", "doi": "10.1086/717814", "pmid": "35175900", "labels": {"DDLS Fellow": null, "Lisandro Milocco": null}, "xrefs": [{"db": "Dryad", "key": "10.5061/dryad.z34tmpgck"}], "notes": [], "created": "2025-11-28T14:28:18.929Z", "modified": "2025-11-28T14:28:57.262Z"}, {"entity": "publication", "iuid": "2ceeb693d6a344a3a3e5349640de619b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/2ceeb693d6a344a3a3e5349640de619b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/2ceeb693d6a344a3a3e5349640de619b"}}, "title": "Clonal Hematopoiesis Is Associated With Higher Risk of Stroke.", "authors": [{"family": "Bhattacharya", "given": "Romit", "initials": "R", "orcid": "0000-0002-0782-4753", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/adea681afe7c431c91b30900a92baf8f.json"}}, {"family": "Zekavat", "given": "Seyedeh M", "initials": "SM", "orcid": "0000-0003-4026-8944", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6234b31f08e442a9b71a711ec7b1147a.json"}}, {"family": "Haessler", "given": "Jeffrey", "initials": "J"}, {"family": "Fornage", "given": "Myriam", "initials": "M", "orcid": "0000-0003-0677-8158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f637ca1a5edd4ece9dd2f88f3620f0b2.json"}}, {"family": "Raffield", "given": "Laura", "initials": "L", "orcid": "0000-0002-7892-193X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/686393c583e94c919f8e39fc8a03d4bc.json"}}, {"family": "Uddin", "given": "Md Mesbah", "initials": "MM", "orcid": "0000-0003-1846-0411", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/42f1ac7010c34ba997a3fd9e56c6a56a.json"}}, {"family": "Bick", "given": "Alexander G", "initials": "AG", "orcid": "0000-0001-5824-9595", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d2da5a35a4984921b19dfafe64cea2de.json"}}, {"family": "Niroula", "given": "Abhishek", "initials": "A", "orcid": "0000-0002-5904-0635", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/05df7afc7a494ba5af8a378e5ffa53f0.json"}}, {"family": "Yu", "given": "Bing", "initials": "B", "orcid": "0000-0003-4818-1077", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e408849bd8f14fd99a2ae255990c1f49.json"}}, {"family": "Gibson", "given": "Christopher", "initials": "C", "orcid": "0000-0002-3700-5310", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/71ce9f64755e483496f8c28a76a2a1ff.json"}}, {"family": "Griffin", "given": "Gabriel", "initials": "G"}, {"family": "Morrison", "given": "Alanna C", "initials": "AC", "orcid": "0000-0001-6381-4296", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fe80874c488943cfb7a5590b7e8d6159.json"}}, {"family": "Psaty", "given": "Bruce M", "initials": "BM", "orcid": "0000-0002-7278-2190", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8b4dfcdad9074df781cd6c8f3c303789.json"}}, {"family": "Longstreth", "given": "William T", "initials": "WT"}, {"family": "Bis", "given": "Joshua C", "initials": "JC", "orcid": "0000-0002-3409-1110", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/de8dd43c6fe64ebbaf718500e4fef3d9.json"}}, {"family": "Rich", "given": "Stephen S", "initials": "SS", "orcid": "0000-0003-3872-7793", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b55061262f4541c1b28d3081e4001833.json"}}, {"family": "Rotter", "given": "Jerome I", "initials": "JI", "orcid": "0000-0001-7191-1723", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/50edc25b80cc48b699db367e372fded5.json"}}, {"family": "Tracy", "given": "Russell P", "initials": "RP"}, {"family": "Correa", "given": "Adolfo", "initials": "A", "orcid": "0000-0002-9501-600X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5148730ad2904845aafb1bf3c4d30211.json"}}, {"family": "Seshadri", "given": "Sudha", "initials": "S"}, {"family": "Johnson", "given": "Andrew", "initials": "A", "orcid": "0000-0001-6369-5178", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8b268f8da3f247ba90dc37ea73d93c2f.json"}}, {"family": "Collins", "given": "Jason M", "initials": "JM", "orcid": "0000-0002-2903-797X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8e55c6f4136342ad8c1874d0c0e13924.json"}}, {"family": "Hayden", "given": "Kathleen M", "initials": "KM", "orcid": "0000-0002-7745-3513", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4200bc918d4a4142a39f93b3985fc067.json"}}, {"family": "Madsen", "given": "Tracy E", "initials": "TE", "orcid": "0000-0001-5101-0776", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/58814b872ec4412c9ff2f0a446410966.json"}}, {"family": "Ballantyne", "given": "Christie M", "initials": "CM", "orcid": "0000-0002-6432-1730", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/27dc5297c262410bad3bbb66a488d4b4.json"}}, {"family": "Jaiswal", "given": "Siddhartha", "initials": "S", "orcid": "0000-0002-9597-0477", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a1901e08f989434fb01dfa17b0a85470.json"}}, {"family": "Ebert", "given": "Benjamin L", "initials": "BL", "orcid": "0000-0003-0197-5451", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56e4f1c53a4348e2b0ceb44a38850a17.json"}}, {"family": "Kooperberg", "given": "Charles", "initials": "C", "orcid": "0000-0002-7986-8560", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f8fbc0fa2df5467ca8c6e65def4485cd.json"}}, {"family": "Manson", "given": "JoAnn E", "initials": "JE", "orcid": "0000-0002-9426-7595", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6e39f122c5fd4f0ea0dcf2353ed4a274.json"}}, {"family": "Whitsel", "given": "Eric A", "initials": "EA", "orcid": "0000-0003-4843-3641", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4a41a19cd08a4908993b3a9a7cd46395.json"}}, {"family": "NHLBI Trans-Omics for Precision Medicine Program", "given": "", "initials": ""}, {"family": "Natarajan", "given": "Pradeep", "initials": "P", "orcid": "0000-0001-8402-7435", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fe8bd48c61c047cd8e61c35d9e9ac650.json"}}, {"family": "Reiner", "given": "Alexander P", "initials": "AP", "orcid": "0000-0002-1427-4470", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/244e81f4f21645e9b66f7b2ba6a8eb07.json"}}], "type": "journal article", "published": "2022-03-00", "journal": {"title": "Stroke", "issn": "1524-4628", "volume": "53", "issue": "3", "pages": "788-797", "issn-l": "0039-2499"}, "abstract": "Clonal hematopoiesis of indeterminate potential (CHIP) is a novel age-related risk factor for cardiovascular disease-related morbidity and mortality. The association of CHIP with risk of incident ischemic stroke was reported previously in an exploratory analysis including a small number of incident stroke cases without replication and lack of stroke subphenotyping. The purpose of this study was to discover whether CHIP is a risk factor for ischemic or hemorrhagic stroke.\n\nWe utilized plasma genome sequence data of blood DNA to identify CHIP in 78 752 individuals from 8 prospective cohorts and biobanks. We then assessed the association of CHIP and commonly mutated individual CHIP driver genes (DNMT3A, TET2, and ASXL1) with any stroke, ischemic stroke, and hemorrhagic stroke.\n\nCHIP was associated with an increased risk of total stroke (hazard ratio, 1.14 [95% CI, 1.03-1.27]; P=0.01) after adjustment for age, sex, and race. We observed associations with CHIP with risk of hemorrhagic stroke (hazard ratio, 1.24 [95% CI, 1.01-1.51]; P=0.04) and with small vessel ischemic stroke subtypes. In gene-specific association results, TET2 showed the strongest association with total stroke and ischemic stroke, whereas DMNT3A and TET2 were each associated with increased risk of hemorrhagic stroke.\n\nCHIP is associated with an increased risk of stroke, particularly with hemorrhagic and small vessel ischemic stroke. Future studies clarifying the relationship between CHIP and subtypes of stroke are needed.", "doi": "10.1161/STROKEAHA.121.037388", "pmid": "34743536", "labels": {"Abhishek Niroula": null, "DDLS Fellow": null}, "xrefs": [{"db": "mid", "key": "NIHMS1751326"}, {"db": "pmc", "key": "PMC8885769"}], "notes": [], "created": "2023-11-20T11:28:04.969Z", "modified": "2023-11-20T11:28:06.112Z"}, {"entity": "publication", "iuid": "fe20a85245624d24a5969df04b3a7ae4", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/fe20a85245624d24a5969df04b3a7ae4.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/fe20a85245624d24a5969df04b3a7ae4"}}, "title": "Abstract 016: Artificially Sweetened Beverage Consumption, Plasma Metabolomics, And Risk Of Type 2 Diabetes Among US Adults", "authors": [{"family": "Haslam", "given": "Danielle E", "initials": "DE"}, {"family": "Wang", "given": "Biqi", "initials": "B"}, {"family": "Li", "given": "Jun", "initials": "J"}, {"family": "Guasch", "given": "Marta", "initials": "M"}, {"family": "Liang", "given": "Liming", "initials": "L"}, {"family": "Clish", "given": "Clary B", "initials": "CB"}, {"family": "Manson", "given": "Joann E", "initials": "JE"}, {"family": "Tobias", "given": "Deirdre K", "initials": "DK"}, {"family": "Wittenbecher", "given": "Clemens", "initials": "C"}, {"family": "Willett", "given": "Walter C", "initials": "WC"}, {"family": "Stampfer", "given": "Meir J", "initials": "MJ"}, {"family": "Herman", "given": "Mark A", "initials": "MA"}, {"family": "Dupuis", "given": "Josee", "initials": "J"}, {"family": "McKeown", "given": "Nicola M", "initials": "NM"}, {"family": "Malik", "given": "Vasanti S", "initials": "VS"}, {"family": "Meigs", "given": "James B", "initials": "JB"}, {"family": "Hu", "given": "Frank B", "initials": "FB"}, {"family": "Bhupathiraju", "given": "Shilpa N", "initials": "SN"}], "type": "journal-article", "published": "2022-03-00", "journal": {"title": "Circulation", "issn": "0009-7322", "volume": "145", "issue": "Suppl_1", "issn-l": null}, "abstract": null, "doi": "10.1161/circ.145.suppl_1.016", "pmid": null, "labels": {"Clemens Wittenbecher": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2025-12-09T13:38:50.249Z", "modified": "2025-12-09T13:38:50.257Z"}, {"entity": "publication", "iuid": "7bb4a3f814ba4143977167cdfeb47159", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/7bb4a3f814ba4143977167cdfeb47159.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/7bb4a3f814ba4143977167cdfeb47159"}}, "title": "A Swedish Genome-Wide Haplotype Association Analysis Identifies a Novel Breast Cancer Susceptibility Locus in 8p21.2 and Characterizes Three Loci on Chromosomes 10, 11 and 16.", "authors": [{"family": "Barnekow", "given": "Elin", "initials": "E", "orcid": "0000-0002-4960-664X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4d1565675a50453db71ed36cf1a90eb1.json"}}, {"family": "Liu", "given": "Wen", "initials": "W"}, {"family": "Helgadottir", "given": "Hafdis T", "initials": "HT", "orcid": "0000-0003-4352-152X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1a706bf443234460b87378cb4a554e6c.json"}}, {"family": "Michailidou", "given": "Kyriaki", "initials": "K", "orcid": "0000-0001-7065-1237", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d02c4c4067b44686a6d229ee5fcba2df.json"}}, {"family": "Dennis", "given": "Joe", "initials": "J", "orcid": "0000-0003-4591-1214", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/032b9f64191b4deb9ed0bfa6e56652ed.json"}}, {"family": "Bryant", "given": "Patrick", "initials": "P"}, {"family": "Thutkawkorapin", "given": "Jessada", "initials": "J"}, {"family": "Wendt", "given": "Camilla", "initials": "C"}, {"family": "Czene", "given": "Kamila", "initials": "K"}, {"family": "Hall", "given": "Per", "initials": "P", "orcid": "0000-0002-5640-9126", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d59cc296ca1649ceb0d0734d20f1510a.json"}}, {"family": "Margolin", "given": "Sara", "initials": "S"}, {"family": "Lindblom", "given": "Annika", "initials": "A", "orcid": "0000-0001-7675-7569", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3e02a7812ec342ab88bf638ba09f47f8.json"}}], "type": "journal article", "published": "2022-02-25", "journal": {"title": "Cancers (Basel)", "issn": "2072-6694", "volume": "14", "issue": "5", "issn-l": "2072-6694"}, "abstract": "(1) Background: The heritability of breast cancer is partly explained but much of the genetic contribution remains to be identified. Haplotypes are often used as markers of ethnicity as they are preserved through generations. We have previously demonstrated that haplotype analysis, in addition to standard SNP association studies, could give novel and more detailed information on genetic cancer susceptibility. (2) Methods: In order to examine the association of a SNP or a haplotype to breast cancer risk, we performed a genome wide haplotype association study, using sliding window analysis of window sizes 1\u221225 and 50 SNPs, in 3200 Swedish breast cancer cases and 5021 controls. (3) Results: We identified a novel breast cancer susceptibility locus in 8p21.1 (OR 2.08; p 3.92 \u00d7 10\u22128), confirmed three known loci in 10q26.13, 11q13.3, 16q12.1-2 and further identified novel subloci within these three loci. Altogether 76 risk SNPs, 3302 risk haplotypes of window size 2\u221225 and 113 risk haplotypes of window size 50 at p < 5 \u00d7 10\u22128 on chromosomes 8, 10, 11 and 16 were identified. In the known loci haplotype analysis reached an OR of 1.48 in overall breast cancer and in familial cases OR 1.68. (4) Conclusions: Analyzing haplotypes, rather than single variants, could detect novel susceptibility loci even in small study populations but the method requires a fairly homogenous study population.", "doi": "10.3390/cancers14051206", "pmid": "35267517", "labels": {"Patrick Bryant": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC8909613"}, {"db": "pii", "key": "cancers14051206"}], "notes": [], "created": "2026-08-20T13:39:41.461Z", "modified": "2026-09-23T12:15:17.170Z"}, {"entity": "publication", "iuid": "26dafc22b288484cbf4acdbecf5fd524", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/26dafc22b288484cbf4acdbecf5fd524.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/26dafc22b288484cbf4acdbecf5fd524"}}, "title": "Importance of Binding Site Hydration and Flexibility Revealed When Optimizing a Macrocyclic Inhibitor of the Keap1-Nrf2 Protein-Protein Interaction.", "authors": [{"family": "Begnini", "given": "Fabio", "initials": "F"}, {"family": "Geschwindner", "given": "Stefan", "initials": "S", "orcid": "0000-0002-2154-8345", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4aebcef57b424d7f95563837936b8e58.json"}}, {"family": "Johansson", "given": "Patrik", "initials": "P"}, {"family": "Wissler", "given": "Lisa", "initials": "L"}, {"family": "Lewis", "given": "Richard J", "initials": "RJ", "orcid": "0000-0001-9404-8520", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bf0bf1fe8db343bf8a3a8c73ae00e625.json"}}, {"family": "Danelius", "given": "Emma", "initials": "E"}, {"family": "Luttens", "given": "Andreas", "initials": "A", "orcid": "0000-0003-2915-7901", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d2944edc47eb4b639f1c61ae7b94b60a.json"}}, {"family": "Matricon", "given": "Pierre", "initials": "P", "orcid": "0000-0001-9350-896X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/19dcd180ddc54eb48269a1638d83ece1.json"}}, {"family": "Carlsson", "given": "Jens", "initials": "J", "orcid": "0000-0003-4623-2977", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/792c1cd4aca248dc94b967115ffa82df.json"}}, {"family": "Lenders", "given": "Stijn", "initials": "S", "orcid": "0000-0002-8833-9353", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a31115b0796d478db7435109ad5954bc.json"}}, {"family": "K\u00f6nig", "given": "Beate", "initials": "B"}, {"family": "Friedel", "given": "Anna", "initials": "A"}, {"family": "Sj\u00f6", "given": "Peter", "initials": "P"}, {"family": "Schiesser", "given": "Stefan", "initials": "S", "orcid": "0000-0002-8668-2844", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56e8ac0b1e544ccf829da7522f07d0c1.json"}}, {"family": "Kihlberg", "given": "Jan", "initials": "J", "orcid": "0000-0002-4205-6040", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7edb4dfa7c4b4d6c8c4cf0282a9c9a1a.json"}}], "type": "journal article", "published": "2022-02-24", "journal": {"title": "J Med Chem", "issn": "1520-4804", "volume": "65", "issue": "4", "pages": "3473-3517", "issn-l": "0022-2623"}, "abstract": "Upregulation of the transcription factor Nrf2 by inhibition of the interaction with its negative regulator Keap1 constitutes an opportunity for the treatment of disease caused by oxidative stress. We report a structurally unique series of nanomolar Keap1 inhibitors obtained from a natural product-derived macrocyclic lead. Initial exploration of the structure-activity relationship of the lead, followed by structure-guided optimization, resulted in a 100-fold improvement in inhibitory potency. The macrocyclic core of the nanomolar inhibitors positions three pharmacophore units for productive interactions with key residues of Keap1, including R415, R483, and Y572. Ligand optimization resulted in the displacement of a coordinated water molecule from the Keap1 binding site and a significantly altered thermodynamic profile. In addition, minor reorganizations of R415 and R483 were accompanied by major differences in affinity between ligands. This study therefore indicates the importance of accounting both for the hydration and flexibility of the Keap1 binding site when designing high-affinity ligands.", "doi": "10.1021/acs.jmedchem.1c01975", "pmid": "35108001", "labels": {"SciLifeLab Fellow": "", "Jens Carlsson": "", "Andreas Luttens": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC8883477"}], "notes": [], "created": "2022-11-07T16:29:55.468Z", "modified": "2026-09-23T10:21:02.183Z"}, {"entity": "publication", "iuid": "f2067c963a9a47c8a7559cba30dd401e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f2067c963a9a47c8a7559cba30dd401e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f2067c963a9a47c8a7559cba30dd401e"}}, "title": "Ultralarge Virtual Screening Identifies SARS-CoV-2 Main Protease Inhibitors with Broad-Spectrum Activity against Coronaviruses.", "authors": [{"family": "Luttens", "given": "Andreas", "initials": "A", "orcid": "0000-0003-2915-7901", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d2944edc47eb4b639f1c61ae7b94b60a.json"}}, {"family": "Gullberg", "given": "Hjalmar", "initials": "H"}, {"family": "Abdurakhmanov", "given": "Eldar", "initials": "E"}, {"family": "Vo", "given": "Duy Duc", "initials": "DD"}, {"family": "Akaberi", "given": "Dario", "initials": "D", "orcid": "0000-0002-9595-9796", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d9782674a8ef4e1faac01dc50b349f14.json"}}, {"family": "Talibov", "given": "Vladimir O", "initials": "VO"}, {"family": "Nekhotiaeva", "given": "Natalia", "initials": "N"}, {"family": "Vangeel", "given": "Laura", "initials": "L"}, {"family": "De Jonghe", "given": "Steven", "initials": "S", "orcid": "0000-0002-3872-6558", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6c498a38425a42f1a3eb2e6c0f6374af.json"}}, {"family": "Jochmans", "given": "Dirk", "initials": "D"}, {"family": "Krambrich", "given": "Janina", "initials": "J"}, {"family": "Tas", "given": "Ali", "initials": "A"}, {"family": "Lundgren", "given": "Bo", "initials": "B"}, {"family": "Gravenfors", "given": "Ylva", "initials": "Y", "orcid": "0000-0001-6025-4908", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/40ea78e284e947cdbd0d176e4cbb880c.json"}}, {"family": "Craig", "given": "Alexander J", "initials": "AJ"}, {"family": "Atilaw", "given": "Yoseph", "initials": "Y"}, {"family": "Sandstr\u00f6m", "given": "Anja", "initials": "A"}, {"family": "Moodie", "given": "Lindon W K", "initials": "LWK", "orcid": "0000-0002-9500-4535", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/97fa4eb1c24a4b24850358e0e6c2a200.json"}}, {"family": "Lundkvist", "given": "\u00c5ke", "initials": "\u00c5"}, {"family": "van Hemert", "given": "Martijn J", "initials": "MJ"}, {"family": "Neyts", "given": "Johan", "initials": "J"}, {"family": "Lennerstrand", "given": "Johan", "initials": "J"}, {"family": "Kihlberg", "given": "Jan", "initials": "J", "orcid": "0000-0002-4205-6040", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7edb4dfa7c4b4d6c8c4cf0282a9c9a1a.json"}}, {"family": "Sandberg", "given": "Kristian", "initials": "K"}, {"family": "Danielson", "given": "U Helena", "initials": "UH", "orcid": "0000-0003-2728-0340", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c1be15d9a1ea49e1b0e7bb712522696e.json"}}, {"family": "Carlsson", "given": "Jens", "initials": "J", "orcid": "0000-0003-4623-2977", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/792c1cd4aca248dc94b967115ffa82df.json"}}], "type": "journal article", "published": "2022-02-23", "journal": {"title": "Journal of the American Chemical Society", "issn": "1520-5126", "volume": "144", "issue": "7", "pages": "2905-2920", "issn-l": "0002-7863"}, "abstract": "Drugs targeting SARS-CoV-2 could have saved millions of lives during the COVID-19 pandemic, and it is now crucial to develop inhibitors of coronavirus replication in preparation for future outbreaks. We explored two virtual screening strategies to find inhibitors of the SARS-CoV-2 main protease in ultralarge chemical libraries. First, structure-based docking was used to screen a diverse library of 235 million virtual compounds against the active site. One hundred top-ranked compounds were tested in binding and enzymatic assays. Second, a fragment discovered by crystallographic screening was optimized guided by docking of millions of elaborated molecules and experimental testing of 93 compounds. Three inhibitors were identified in the first library screen, and five of the selected fragment elaborations showed inhibitory effects. Crystal structures of target-inhibitor complexes confirmed docking predictions and guided hit-to-lead optimization, resulting in a noncovalent main protease inhibitor with nanomolar affinity, a promising in vitro pharmacokinetic profile, and broad-spectrum antiviral effect in infected cells.", "doi": "10.1021/jacs.1c08402", "pmid": "35142215", "labels": {"SciLifeLab Fellow": "", "Jens Carlsson": "", "Andreas Luttens": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC8848513"}], "notes": [], "created": "2022-11-07T16:30:42.909Z", "modified": "2026-09-23T06:41:14.970Z"}, {"entity": "publication", "iuid": "ebb8671ddf934fd48ec54e4d95bfc70f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ebb8671ddf934fd48ec54e4d95bfc70f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ebb8671ddf934fd48ec54e4d95bfc70f"}}, "title": "Reclassifying Cancer: Defining tumour cell cycle activity in terms of its tissue of origin in over 13,000 samples", "authors": [{"family": "Lundberg", "given": "Arian", "initials": "A", "orcid": "0000-0002-6630-2787", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/baa2c7c8963840bfb6a22d7c5cfe35f9.json"}}, {"family": "Yi", "given": "Joan Jong Jing", "initials": "JJJ"}, {"family": "Lindstr\u00f6m", "given": "Linda S", "initials": "LS", "orcid": "0000-0002-7722-7532", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/99821dac16e64ad48325a1314398b927.json"}}, {"family": "Tobin", "given": "Nicholas P", "initials": "NP"}], "type": "posted-content", "published": "2022-02-18", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2022.02.15.480623", "pmid": null, "labels": {"DDLS Fellow": null, "Arian Lundberg": null}, "xrefs": [], "notes": [], "created": "2026-04-27T19:29:56.492Z", "modified": "2026-04-27T19:29:56.529Z"}, {"entity": "publication", "iuid": "2bc12def0509430884f71f5954dfa120", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/2bc12def0509430884f71f5954dfa120.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/2bc12def0509430884f71f5954dfa120"}}, "title": "Discovery of therapeutic agents targeting PKLR for NAFLD using drug repositioning", "authors": [{"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f46e4161be08458994efddb75ed75874.json"}}, {"family": "Shi", "given": "Mengnan", "initials": "M"}, {"family": "Kim", "given": "Woonghee", "initials": "W"}, {"family": "Arif", "given": "Muhammad", "initials": "M"}, {"family": "Klevstig", "given": "Martina", "initials": "M"}, {"family": "Li", "given": "Xiangyu", "initials": "X", "orcid": "0000-0002-8301-9959", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5c452ad4e8bb4302a572693103742047.json"}}, {"family": "Yang", "given": "Hong", "initials": "H"}, {"family": "Bayram", "given": "Cemil", "initials": "C"}, {"family": "Bolat", "given": "Ismail", "initials": "I"}, {"family": "Tozlu", "given": "\u00d6zlem \u00d6zdemir", "initials": "\u00d6\u00d6"}, {"family": "Hac\u0131muftuoglu", "given": "Ahmet", "initials": "A"}, {"family": "Y\u0131ld\u0131r\u0131m", "given": "Serkan", "initials": "S"}, {"family": "Wei", "given": "Yongjun", "initials": "Y"}, {"family": "Shi", "given": "Xiaojing", "initials": "X"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/33f2b49a39ed4e54ba77dfe397ed3087.json"}}, {"family": "Turkez", "given": "Hasan", "initials": "H"}, {"family": "Uhlen", "given": "Mathias", "initials": "M"}, {"family": "Boren", "given": "Jan", "initials": "J"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca58bf2d214047e0ae5e38a42a0f2808.json"}}], "type": "posted-content", "published": "2022-02-17", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2022.02.15.480557", "pmid": null, "labels": {"SciLifeLab Fellow": "", "DDLS Fellow": "", "Adil Mardinoglu": "", "Muhammad Arif": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T10:09:45.032Z", "modified": "2026-09-23T15:12:03.280Z"}, {"entity": "publication", "iuid": "736aff8c5fbd4d4cb890a02393015794", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/736aff8c5fbd4d4cb890a02393015794.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/736aff8c5fbd4d4cb890a02393015794"}}, "title": "Dihydroceramide- and ceramide-profiling provides insights into human cardiometabolic disease etiology.", "authors": [{"family": "Wittenbecher", "given": "C", "initials": "C", "orcid": "0000-0001-7792-877X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2f7d2c289b3c47d5a79d23bd48a3225a.json"}}, {"family": "Cuadrat", "given": "R", "initials": "R", "orcid": "0000-0001-8289-2599", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ceeede64cec04a118cb0a4c461c659d1.json"}}, {"family": "Johnston", "given": "L", "initials": "L", "orcid": "0000-0003-4169-2616", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3a60fe7a30b843bc9bf630cc2e240e35.json"}}, {"family": "Eichelmann", "given": "F", "initials": "F", "orcid": "0000-0002-3975-5596", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4f6083a259c6440ab3201d53f44a0d55.json"}}, {"family": "J\u00e4ger", "given": "S", "initials": "S", "orcid": "0000-0001-6619-0861", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/28dce9f2224f4278bd7cd44639793f8d.json"}}, {"family": "Kuxhaus", "given": "O", "initials": "O"}, {"family": "Prada", "given": "M", "initials": "M"}, {"family": "Del Greco M", "given": "F", "initials": "F"}, {"family": "Hicks", "given": "A A", "initials": "AA", "orcid": "0000-0001-6320-0411", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/08bfcbd859e848698883ad840f02594f.json"}}, {"family": "Hoffman", "given": "P", "initials": "P", "orcid": "0000-0002-6573-983X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f214980c8ffe4f01a4db472618de29c4.json"}}, {"family": "Krumsiek", "given": "J", "initials": "J"}, {"family": "Hu", "given": "F B", "initials": "FB"}, {"family": "Schulze", "given": "M B", "initials": "MB", "orcid": "0000-0002-0830-5277", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/853ded2c43b64f26a8b47da7ea7b79c0.json"}}], "type": "journal article", "published": "2022-02-17", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "13", "issue": "1", "pages": "936", "issn-l": "2041-1723"}, "abstract": "Metabolic alterations precede cardiometabolic disease onset. Here we present ceramide- and dihydroceramide-profiling data from a nested case-cohort (type 2 diabetes [T2D, n = 775]; cardiovascular disease [CVD, n = 551]; random subcohort [n = 1137]) in the prospective EPIC-Potsdam study. We apply the novel NetCoupler-algorithm to link a data-driven (dihydro)ceramide network to T2D and CVD risk. Controlling for confounding by other (dihydro)ceramides, ceramides C18:0 and C22:0 and dihydroceramides C20:0 and C22:2 are associated with higher and ceramide C20:0 and dihydroceramide C26:1 with lower T2D risk. Ceramide C16:0 and dihydroceramide C22:2 are associated with higher CVD risk. Genome-wide association studies and Mendelian randomization analyses support a role of ceramide C22:0 in T2D etiology. Our results also suggest that (dh)ceramides partly mediate the putative adverse effect of high red meat consumption and benefits of coffee consumption on T2D risk. Thus, (dihydro)ceramides may play a critical role in linking genetic predisposition and dietary habits to cardiometabolic disease risk.", "doi": "10.1038/s41467-022-28496-1", "pmid": "35177612", "labels": {"Clemens Wittenbecher": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC8854598"}, {"db": "pii", "key": "10.1038/s41467-022-28496-1"}], "notes": [], "created": "2025-12-09T13:38:56.544Z", "modified": "2025-12-09T13:38:56.697Z"}, {"entity": "publication", "iuid": "2bbb7353d3a7480899d2824cb0e6dd69", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/2bbb7353d3a7480899d2824cb0e6dd69.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/2bbb7353d3a7480899d2824cb0e6dd69"}}, "title": "Machine learning analysis reveals biomarkers for the detection of neurodegenerative diseases", "authors": [{"family": "Lam", "given": "Simon", "initials": "S", "orcid": "0000-0002-4476-0971", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bdf5adecfed749b4a66cdda5cd08ee24.json"}}, {"family": "Arif", "given": "Muhammad", "initials": "M"}, {"family": "Song", "given": "Xiya", "initials": "X"}, {"family": "Uhlen", "given": "Mathias", "initials": "M"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}], "type": "posted-content", "published": "2022-02-15", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2022.02.15.22270625", "pmid": null, "labels": {"SciLifeLab Fellow": "", "DDLS Fellow": "", "Adil Mardinoglu": "", "Muhammad Arif": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T10:09:40.973Z", "modified": "2026-09-23T15:11:59.251Z"}, {"entity": "publication", "iuid": "ff68427f44894be7a46874bae0d4b756", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ff68427f44894be7a46874bae0d4b756.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ff68427f44894be7a46874bae0d4b756"}}, "title": "Biomarker-Based Prediction of Longitudinal Tau Positron Emission Tomography in Alzheimer Disease.", "authors": [{"family": "Leuzy", "given": "Antoine", "initials": "A"}, {"family": "Smith", "given": "Ruben", "initials": "R"}, {"family": "Cullen", "given": "Nicholas C", "initials": "NC"}, {"family": "Strandberg", "given": "Olof", "initials": "O"}, {"family": "Vogel", "given": "Jacob W", "initials": "JW"}, {"family": "Binette", "given": "Alexa Pichet", "initials": "AP"}, {"family": "Borroni", "given": "Edilio", "initials": "E"}, {"family": "Janelidze", "given": "Shorena", "initials": "S"}, {"family": "Ohlsson", "given": "Tomas", "initials": "T"}, {"family": "J\u00f6gi", "given": "Jonas", "initials": "J"}, {"family": "Ossenkoppele", "given": "Rik", "initials": "R"}, {"family": "Palmqvist", "given": "Sebastian", "initials": "S"}, {"family": "Mattsson-Carlgren", "given": "Niklas", "initials": "N"}, {"family": "Klein", "given": "Gregory", "initials": "G"}, {"family": "Stomrud", "given": "Erik", "initials": "E"}, {"family": "Hansson", "given": "Oskar", "initials": "O"}], "type": "journal article", "published": "2022-02-01", "journal": {"title": "JAMA Neurol", "issn": "2168-6157", "issn-l": null, "volume": "79", "issue": "2", "pages": "149-158"}, "abstract": "There is currently no consensus as to which biomarkers best predict longitudinal tau accumulation at different clinical stages of Alzheimer disease (AD).\r\n\r\nTo describe longitudinal [18F]RO948 tau positron emission tomography (PET) findings across the clinical continuum of AD and determine which biomarker combinations showed the strongest associations with longitudinal tau PET and best optimized clinical trial enrichment.\r\n\r\nThis longitudinal cohort study consecutively enrolled amyloid-\u03b2 (A\u03b2)-negative cognitively unimpaired (CU) participants, A\u03b2-positive CU individuals, A\u03b2-positive individuals with mild cognitive impairment (MCI), and individuals with AD dementia between September 2017 and November 2020 from the Swedish BioFINDER-2 (discovery cohort) and BioFINDER-1 (validation cohort) studies.\r\n\r\nBaseline plasma and cerebrospinal fluid A\u03b242/A\u03b240, tau phosphorylated at threonine-217 (p-tau217), p-tau181 and neurofilament light, magnetic resonance imaging, amyloid PET ([18F]flutemetamol), and tau PET ([18F]RO948 in the BioFINDER-2 study; [18F]flortaucipir in the BioFINDER-1 study).\r\n\r\nBaseline tau PET standardized uptake value ratio (SUVR) and annual percent change in tau PET SUVR across regions of interest derived using a data-driven approach combining clustering and event-based modeling. Regression models were used to examine associations between individual biomarkers and longitudinal tau PET and to identify which combinations best predicted longitudinal tau PET. These combinations were then entered in a power analysis to examine how their use as an enrichment strategy would affect sample size in a simulated clinical trial.\r\n\r\nOf 343 participants, the mean (SD) age was 72.56 (7.24) years, and 157 (51.1%) were female. The clustering/event-based modeling-based approach identified 5 regions of interest (stages). In A\u03b2-positive CU individuals, the largest annual increase in tau PET SUVR was seen in stage I (entorhinal cortex, hippocampus, and amygdala; 4.04% [95% CI, 2.67%-5.32%]). In A\u03b2-positive individuals with MCI and with AD dementia, the greatest increases were seen in stages II (temporal cortical regions; 4.45% [95% CI, 3.41%-5.49%]) and IV (certain frontal regions; 5.22% [95% CI, 3.95%-6.49%]), respectively. In A\u03b2-negative CU individuals and those with MCI, modest change was seen in stage I (1.38% [95% CI, 0.78%-1.99%] and 1.80% [95% CI, 0.76%-2.84%], respectively). When looking at individual predictors and longitudinal tau PET in the stages that showed most change, plasma p-tau217 (R2 = 0.27, P < .005), tau PET (stage I baseline SUVR; R2 = 0.13, P < .05) and amyloid PET (R2 = 0.10, P < .05) were significantly associated with longitudinal tau PET in stage I in A\u03b2-positive CU individuals. In A\u03b2-positive individuals with MCI, plasma p-tau217 (R2 = 0.24, P < .005) and tau PET (stage II baseline SUVR; R2 = 0.44, P < .001) were significantly associated with longitudinal tau PET in stage II. Findings were replicated in BioFINDER-1 using longitudinal [18F]flortaucipir. For the power analysis component, plasma p-tau217 with tau PET resulted in sample size reductions of 43% (95% CI, 34%-46%; P < .005) in A\u03b2-positive CU individuals and of 68% (95% CI, 61%-73%; P < .001) in A\u03b2-positive individuals with MCI.\r\n\r\nIn trials using tau PET as the outcome, plasma p-tau217 with tau PET may prove optimal for enrichment in preclinical and prodromal AD. However, plasma p-tau217 was most important in preclinical AD, while tau PET was more important in prodromal AD.", "doi": "10.1001/jamaneurol.2021.4654", "pmid": "34928318", "labels": {"Jacob W Vogel": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC8689441"}, {"db": "pii", "key": "2787209"}], "notes": [], "created": "2023-05-28T17:58:08.557Z", "modified": "2023-11-29T06:37:38.579Z"}, {"entity": "publication", "iuid": "08f36318a05141af8694dd06984f2df9", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/08f36318a05141af8694dd06984f2df9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/08f36318a05141af8694dd06984f2df9"}}, "title": "IUCNN \u2013 Deep learning approaches to approximate species' extinction risk", "authors": [{"family": "Zizka", "given": "Alexander", "initials": "A", "orcid": "0000-0002-1680-9192", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c62a905324e94d869ccd715ebbc98828.json"}}, {"family": "Andermann", "given": "Tobias", "initials": "T", "orcid": "0000-0002-0932-1623", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dfff478dfcfc43ddbd40bb1bafbcb0a7.json"}}, {"family": "Silvestro", "given": "Daniele", "initials": "D", "orcid": "0000-0003-0100-0961", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4870742190514c5b83450c567c11398a.json"}}], "type": "journal-article", "published": "2022-02-00", "journal": {"title": "Diversity and Distributions", "issn": "1366-9516", "volume": "28", "issue": "2", "pages": "227-241", "issn-l": null}, "abstract": null, "doi": "10.1111/ddi.13450", "pmid": null, "labels": {"Tobias Andermann": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2022-11-11T09:11:47.006Z", "modified": "2025-12-04T16:58:05.576Z"}, {"entity": "publication", "iuid": "06666b5ae8b94390ab6c73ad20a7942f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/06666b5ae8b94390ab6c73ad20a7942f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/06666b5ae8b94390ab6c73ad20a7942f"}}, "title": "A global baseline for qPCR-determined antimicrobial resistance gene prevalence across environments", "authors": [{"family": "Abramova", "given": "Anna", "initials": "A", "orcid": "0000-0002-0493-7808", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dd75cbcc659c4ca398eb678fad1dc498.json"}}, {"family": "Berendonk", "given": "Thomas U", "initials": "TU", "orcid": "0000-0002-9301-1803", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c66286f83a8430f954fbc5c52db10c5.json"}}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J", "orcid": "0000-0002-6528-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c666068e9d34939b0252a627007cec7.json"}}], "type": "posted-content", "published": "2022-01-30", "journal": {"title": "bioRxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2022.01.29.478248", "pmid": null, "labels": {"DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2026-08-20T10:09:22.646Z", "modified": "2026-10-05T08:34:33.342Z"}, {"entity": "publication", "iuid": "fcff6c7b82c146f796271b8706d21849", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/fcff6c7b82c146f796271b8706d21849.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/fcff6c7b82c146f796271b8706d21849"}}, "title": "The genomic basis of the plant island syndrome in Darwin\u2019s giant daisies", "authors": [{"family": "Cerca", "given": "Jos\u00e9", "initials": "J", "orcid": "0000-0001-7788-4367", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b9119ffe17f1400ea74e0eaf43c105fc.json"}}, {"family": "Petersen", "given": "Bent", "initials": "B"}, {"family": "Lazaro Guevara", "given": "Jos\u00e9 Miguel", "initials": "JM"}, {"family": "Rivera-Col\u00f3n", "given": "Angel", "initials": "A"}, {"family": "Birkeland", "given": "Siri", "initials": "S"}, {"family": "Vizueta", "given": "Joel", "initials": "J"}, {"family": "Li", "given": "Siyu", "initials": "S"}, {"family": "Loureiro", "given": "Jo\u00e3o", "initials": "J"}, {"family": "Kosawang", "given": "Chatchai", "initials": "C"}, {"family": "D\u00edaz", "given": "Patricia Jaramillo", "initials": "PJ"}, {"family": "Rivas-Torres", "given": "Gonzalo", "initials": "G"}, {"family": "Fern\u00e1ndez-Mazuecos", "given": "Mario", "initials": "M"}, {"family": "Vargas", "given": "Pablo", "initials": "P"}, {"family": "McCauley", "given": "Ross", "initials": "R"}, {"family": "Petersen", "given": "Gitte", "initials": "G"}, {"family": "Santos-Bay", "given": "Luisa", "initials": "L"}, {"family": "Wales", "given": "Nathan", "initials": "N"}, {"family": "Catchen", "given": "Julian", "initials": "J"}, {"family": "Machado", "given": "Daniel", "initials": "D"}, {"family": "Nowak", "given": "Michael D", "initials": "MD"}, {"family": "Suh", "given": "Alexander", "initials": "A"}, {"family": "Sinha", "given": "Neelima", "initials": "N"}, {"family": "Nielsen", "given": "Lene R", "initials": "LR"}, {"family": "Seberg", "given": "Ole", "initials": "O"}, {"family": "Gilbert", "given": "M Thomas P", "initials": "MTP"}, {"family": "Leebens-Mack", "given": "James H", "initials": "JH"}, {"family": "Rieseberg", "given": "Loren", "initials": "L"}, {"family": "Martin", "given": "Michael D", "initials": "MD"}], "type": "posted-content", "published": "2022-01-28", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2022.01.26.477903", "pmid": null, "labels": {"Jos\u00e9 Cerca": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T10:09:18.908Z", "modified": "2026-09-23T15:11:23.534Z"}, {"entity": "publication", "iuid": "6461c7cf3855472d8f035a3389fbd986", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/6461c7cf3855472d8f035a3389fbd986.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/6461c7cf3855472d8f035a3389fbd986"}}, "title": "Genome-wide annotation of protein-coding genes in pig.", "authors": [{"family": "Karlsson", "given": "Max", "initials": "M"}, {"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E"}, {"family": "Oksvold", "given": "Per", "initials": "P"}, {"family": "Sivertsson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Huang", "given": "Jinrong", "initials": "J"}, {"family": "\u00c1lvez", "given": "Mar\u00eda Bueno", "initials": "MB"}, {"family": "Arif", "given": "Muhammad", "initials": "M"}, {"family": "Li", "given": "Xiangyu", "initials": "X"}, {"family": "Lin", "given": "Lin", "initials": "L"}, {"family": "Yu", "given": "Jiaying", "initials": "J"}, {"family": "Ma", "given": "Tao", "initials": "T"}, {"family": "Xu", "given": "Fengping", "initials": "F"}, {"family": "Han", "given": "Peng", "initials": "P"}, {"family": "Jiang", "given": "Hui", "initials": "H"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Zhang", "given": "Cheng", "initials": "C"}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K"}, {"family": "Xu", "given": "Xun", "initials": "X"}, {"family": "Wang", "given": "Jian", "initials": "J"}, {"family": "Yang", "given": "Huanming", "initials": "H"}, {"family": "Bolund", "given": "Lars", "initials": "L"}, {"family": "Zhong", "given": "Wen", "initials": "W"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Lindskog", "given": "Cecilia", "initials": "C"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Mulder", "given": "Jan", "initials": "J"}, {"family": "Luo", "given": "Yonglun", "initials": "Y"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ea446aa574042a295d5f69437402f76.json"}}], "type": "journal article", "published": "2022-01-25", "journal": {"title": "BMC Biol.", "issn": "1741-7007", "volume": "20", "issue": "1", "pages": "25", "issn-l": "1741-7007"}, "abstract": "There is a need for functional genome-wide annotation of the protein-coding genes to get a deeper understanding of mammalian biology. Here, a new annotation strategy is introduced based on dimensionality reduction and density-based clustering of whole-body co-expression patterns. This strategy has been used to explore the gene expression landscape in pig, and we present a whole-body map of all protein-coding genes in all major pig tissues and organs.\n\nAn open-access pig expression map ( www.rnaatlas.org ) is presented based on the expression of 350 samples across 98 well-defined pig tissues divided into 44 tissue groups. A new UMAP-based classification scheme is introduced, in which all protein-coding genes are stratified into tissue expression clusters based on body-wide expression profiles. The distribution and tissue specificity of all 22,342 protein-coding pig genes are presented.\n\nHere, we present a new genome-wide annotation strategy based on dimensionality reduction and density-based clustering. A genome-wide resource of the transcriptome map across all major tissues and organs in pig is presented, and the data is available as an open-access resource ( www.rnaatlas.org ), including a comparison to the expression of human orthologs.", "doi": "10.1186/s12915-022-01229-y", "pmid": "35073880", "labels": {"Adil Mardinoglu": "", "SciLifeLab Fellow": "", "DDLS Fellow": "", "Muhammad Arif": ""}, "xrefs": [{"db": "pmc", "key": "PMC8788080"}, {"db": "pii", "key": "10.1186/s12915-022-01229-y"}], "notes": [], "created": "2023-12-04T15:04:51.646Z", "modified": "2026-09-23T10:19:10.937Z"}, {"entity": "publication", "iuid": "fcfb0e1d38a147a49c665e262fbab1dc", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/fcfb0e1d38a147a49c665e262fbab1dc.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/fcfb0e1d38a147a49c665e262fbab1dc"}}, "title": "Association of clonal hematopoiesis with chronic obstructive pulmonary disease.", "authors": [{"family": "Miller", "given": "Peter G", "initials": "PG"}, {"family": "Qiao", "given": "Dandi", "initials": "D"}, {"family": "Rojas-Quintero", "given": "Joselyn", "initials": "J", "orcid": "0000-0003-4994-075X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8db27250fd19432ca53d51078504b012.json"}}, {"family": "Honigberg", "given": "Michael C", "initials": "MC", "orcid": "0000-0001-8630-5021", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c541cd0864c947a6bafa7ad6e78bfe49.json"}}, {"family": "Sperling", "given": "Adam S", "initials": "AS"}, {"family": "Gibson", "given": "Christopher J", "initials": "CJ"}, {"family": "Bick", "given": "Alexander G", "initials": "AG"}, {"family": "Niroula", "given": "Abhishek", "initials": "A", "orcid": "0000-0002-5904-0635", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/05df7afc7a494ba5af8a378e5ffa53f0.json"}}, {"family": "McConkey", "given": "Marie E", "initials": "ME"}, {"family": "Sandoval", "given": "Brittany", "initials": "B"}, {"family": "Miller", "given": "Brian C", "initials": "BC", "orcid": "0000-0001-5931-4184", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/46db11bb7a464d578da0ade0de710705.json"}}, {"family": "Shi", "given": "Weiwei", "initials": "W"}, {"family": "Viswanathan", "given": "Kaushik", "initials": "K"}, {"family": "Leventhal", "given": "Matthew", "initials": "M"}, {"family": "Werner", "given": "Lillian", "initials": "L"}, {"family": "Moll", "given": "Matthew", "initials": "M"}, {"family": "Cade", "given": "Brian E", "initials": "BE", "orcid": "0000-0003-1424-0673", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/16c3230c37d046aabfd0d50aaed26f3c.json"}}, {"family": "Barr", "given": "R Graham", "initials": "RG"}, {"family": "Correa", "given": "Adolfo", "initials": "A", "orcid": "0000-0002-9501-600X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5148730ad2904845aafb1bf3c4d30211.json"}}, {"family": "Cupples", "given": "L Adrienne", "initials": "LA"}, {"family": "Gharib", "given": "Sina A", "initials": "SA", "orcid": "0000-0002-2480-4367", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4e4f2fc8491f4ebabe7d1e8eee2d3dd2.json"}}, {"family": "Jain", "given": "Deepti", "initials": "D"}, {"family": "Gogarten", "given": "Stephanie M", "initials": "SM", "orcid": "0000-0002-7231-9745", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d1811db824324d309ebc1d017f9eec7e.json"}}, {"family": "Lange", "given": "Leslie A", "initials": "LA"}, {"family": "London", "given": "Stephanie J", "initials": "SJ"}, {"family": "Manichaikul", "given": "Ani", "initials": "A"}, {"family": "O'Connor", "given": "George T", "initials": "GT"}, {"family": "Oelsner", "given": "Elizabeth C", "initials": "EC"}, {"family": "Redline", "given": "Susan", "initials": "S"}, {"family": "Rich", "given": "Stephen S", "initials": "SS", "orcid": "0000-0003-3872-7793", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b55061262f4541c1b28d3081e4001833.json"}}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Ramachandran", "given": "Vasan", "initials": "V"}, {"family": "Yu", "given": "Bing", "initials": "B"}, {"family": "Sholl", "given": "Lynette", "initials": "L", "orcid": "0000-0002-9532-9735", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/aa76d878993c49fb97ec706850240ee2.json"}}, {"family": "Neuberg", "given": "Donna", "initials": "D"}, {"family": "Jaiswal", "given": "Siddhartha", "initials": "S", "orcid": "0000-0002-9597-0477", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a1901e08f989434fb01dfa17b0a85470.json"}}, {"family": "Levy", "given": "Bruce D", "initials": "BD", "orcid": "0000-0001-9515-5731", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8bffe9fd9bf6408ebe20f3c7322302d5.json"}}, {"family": "Owen", "given": "Caroline A", "initials": "CA", "orcid": "0000-0003-4377-3591", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a83b8dbbb589461b9c08dbdc6937b344.json"}}, {"family": "Natarajan", "given": "Pradeep", "initials": "P", "orcid": "0000-0001-8402-7435", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fe8bd48c61c047cd8e61c35d9e9ac650.json"}}, {"family": "Silverman", "given": "Edwin K", "initials": "EK"}, {"family": "van Galen", "given": "Peter", "initials": "P", "orcid": "0000-0002-0735-1570", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7a7c23a8364a4a94a8def3b967de1549.json"}}, {"family": "Tesfaigzi", "given": "Yohannes", "initials": "Y", "orcid": "0000-0002-3997-5839", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7ed032038a2b428286f53b537174a784.json"}}, {"family": "Cho", "given": "Michael H", "initials": "MH", "orcid": "0000-0002-4907-1657", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a80666dedf27482ba21cd3861ca1328d.json"}}, {"family": "Ebert", "given": "Benjamin L", "initials": "BL", "orcid": "0000-0003-0197-5451", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56e4f1c53a4348e2b0ceb44a38850a17.json"}}, {"family": "COPDGene Study Investigators, National Heart, Lung, and Blood Institute Trans-Omics for Precision Medicine Consortium", "given": "", "initials": ""}], "type": "journal article", "published": "2022-01-20", "journal": {"title": "Blood", "issn": "1528-0020", "volume": "139", "issue": "3", "pages": "357-368", "issn-l": "0006-4971"}, "abstract": "Chronic obstructive pulmonary disease (COPD) is associated with age and smoking, but other determinants of the disease are incompletely understood. Clonal hematopoiesis of indeterminate potential (CHIP) is a common, age-related state in which somatic mutations in clonal blood populations induce aberrant inflammatory responses. Patients with CHIP have an elevated risk for cardiovascular disease, but the association of CHIP with COPD remains unclear. We analyzed whole-genome sequencing and whole-exome sequencing data to detect CHIP in 48 835 patients, of whom 8444 had moderate to very severe COPD, from four separate cohorts with COPD phenotyping and smoking history. We measured emphysema in murine models in which Tet2 was deleted in hematopoietic cells. In the COPDGene cohort, individuals with CHIP had risks of moderate-to-severe, severe, or very severe COPD that were 1.6 (adjusted 95% confidence interval [CI], 1.1-2.2) and 2.2 (adjusted 95% CI, 1.5-3.2) times greater than those for noncarriers. These findings were consistently observed in three additional cohorts and meta-analyses of all patients. CHIP was also associated with decreased FEV1% predicted in the COPDGene cohort (mean between-group differences, -5.7%; adjusted 95% CI, -8.8% to -2.6%), a finding replicated in additional cohorts. Smoke exposure was associated with a small but significant increased risk of having CHIP (odds ratio, 1.03 per 10 pack-years; 95% CI, 1.01-1.05 per 10 pack-years) in the meta-analysis of all patients. Inactivation of Tet2 in mouse hematopoietic cells exacerbated the development of emphysema and inflammation in models of cigarette smoke exposure. Somatic mutations in blood cells are associated with the development and severity of COPD, independent of age and cumulative smoke exposure.", "doi": "10.1182/blood.2021013531", "pmid": "34855941", "labels": {"Abhishek Niroula": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC8777202"}, {"db": "pii", "key": "S0006-4971(21)01875-9"}], "notes": [], "created": "2023-11-20T11:36:09.269Z", "modified": "2023-11-20T11:36:09.920Z"}, {"entity": "publication", "iuid": "6c36fbd87814421c9d019b4d974c92fd", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/6c36fbd87814421c9d019b4d974c92fd.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/6c36fbd87814421c9d019b4d974c92fd"}}, "title": "Functional dissection of inherited non-coding variation influencing multiple myeloma risk.", "authors": [{"family": "Ajore", "given": "Ram", "initials": "R"}, {"family": "Niroula", "given": "Abhishek", "initials": "A", "orcid": "0000-0002-5904-0635", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/05df7afc7a494ba5af8a378e5ffa53f0.json"}}, {"family": "Pertesi", "given": "Maroulio", "initials": "M", "orcid": "0000-0002-4869-8925", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1395ddcc49604bc1a05ea52f7b1ad79a.json"}}, {"family": "Cafaro", "given": "Caterina", "initials": "C"}, {"family": "Thodberg", "given": "Malte", "initials": "M", "orcid": "0000-0001-6244-3841", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7f2c232400714922bdbd28e77ede971e.json"}}, {"family": "Went", "given": "Molly", "initials": "M"}, {"family": "Bao", "given": "Erik L", "initials": "EL", "orcid": "0000-0002-6074-6766", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7b5eac9b5ee541258aea4146fcbb7d49.json"}}, {"family": "Duran-Lozano", "given": "Laura", "initials": "L"}, {"family": "Lopez de Lapuente Portilla", "given": "Aitzkoa", "initials": "A"}, {"family": "Olafsdottir", "given": "Thorunn", "initials": "T", "orcid": "0000-0001-5454-938X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/417237ea231141ce83a9f314aacc4714.json"}}, {"family": "Ugidos-Damboriena", "given": "Nerea", "initials": "N"}, {"family": "Magnusson", "given": "Olafur", "initials": "O"}, {"family": "Samur", "given": "Mehmet", "initials": "M", "orcid": "0000-0002-9978-5682", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0b458dd507e6487c86b67a7189842894.json"}}, {"family": "Lareau", "given": "Caleb A", "initials": "CA", "orcid": "0000-0003-4179-4807", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6458fb4cee9e45808ce001ed492d5d1b.json"}}, {"family": "Halldorsson", "given": "Gisli H", "initials": "GH", "orcid": "0000-0001-7067-9862", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/28549aa56c4543178dd7626dbc9e4667.json"}}, {"family": "Thorleifsson", "given": "Gudmar", "initials": "G"}, {"family": "Norddahl", "given": "Gudmundur L", "initials": "GL"}, {"family": "Gunnarsdottir", "given": "Kristbjorg", "initials": "K"}, {"family": "F\u00f6rsti", "given": "Asta", "initials": "A", "orcid": "0000-0002-9857-4728", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a2356cdc19c040348a7924e3dd4b8c32.json"}}, {"family": "Goldschmidt", "given": "Hartmut", "initials": "H", "orcid": "0000-0003-0961-0035", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f634b54dfdbd48bb9f53f574e0cfd023.json"}}, {"family": "Hemminki", "given": "Kari", "initials": "K"}, {"family": "van Rhee", "given": "Frits", "initials": "F"}, {"family": "Kimber", "given": "Scott", "initials": "S"}, {"family": "Sperling", "given": "Adam S", "initials": "AS", "orcid": "0000-0002-9369-4413", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b8fef41b72dd464f9f0e46ddcd0a2434.json"}}, {"family": "Kaiser", "given": "Martin", "initials": "M", "orcid": "0000-0002-3677-4804", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/61695044f08e4490a7feaf7db2aacc07.json"}}, {"family": "Anderson", "given": "Kenneth", "initials": "K", "orcid": "0000-0002-6418-0886", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eaec398be2ff4e25b8522e1a921f3215.json"}}, {"family": "Jonsdottir", "given": "Ingileif", "initials": "I", "orcid": "0000-0001-8339-150X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4f4e82de44504a55b50b0378447318f8.json"}}, {"family": "Munshi", "given": "Nikhil", "initials": "N", "orcid": "0000-0002-7344-9795", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/885baa458ac84ec8b7b3acb26fef7ec4.json"}}, {"family": "Rafnar", "given": "Thorunn", "initials": "T", "orcid": "0000-0003-0491-7046", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/67a01e1ebd79473dbc0059d38f066e55.json"}}, {"family": "Waage", "given": "Anders", "initials": "A"}, {"family": "Weinhold", "given": "Niels", "initials": "N"}, {"family": "Thorsteinsdottir", "given": "Unnur", "initials": "U"}, {"family": "Sankaran", "given": "Vijay G", "initials": "VG", "orcid": "0000-0003-0044-443X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0a967a5a378f406299b3fefe244361c9.json"}}, {"family": "Stefansson", "given": "Kari", "initials": "K", "orcid": "0000-0003-1676-864X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9edf80871ac84e76a4d1316fc7079d7d.json"}}, {"family": "Houlston", "given": "Richard", "initials": "R", "orcid": "0000-0002-5268-0242", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e7605f3f03f94e1b95c011318f5e5d4c.json"}}, {"family": "Nilsson", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-5542-0254", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2e9df5bbe6f948b196a65176963748c8.json"}}], "type": "journal article", "published": "2022-01-10", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "13", "issue": "1", "pages": "151", "issn-l": "2041-1723"}, "abstract": "Thousands of non-coding variants have been associated with increased risk of human diseases, yet the causal variants and their mechanisms-of-action remain obscure. In an integrative study combining massively parallel reporter assays (MPRA), expression analyses (eQTL, meQTL, PCHiC) and chromatin accessibility analyses in primary cells (caQTL), we investigate 1,039 variants associated with multiple myeloma (MM). We demonstrate that MM susceptibility is mediated by gene-regulatory changes in plasma cells and B-cells, and identify putative causal variants at six risk loci (SMARCD3, WAC, ELL2, CDCA7L, CEP120, and PREX1). Notably, three of these variants co-localize with significant plasma cell caQTLs, signaling the presence of causal activity at these precise genomic positions in an endogenous chromosomal context in vivo. Our results provide a systematic functional dissection of risk loci for a hematologic malignancy.", "doi": "10.1038/s41467-021-27666-x", "pmid": "35013207", "labels": {"Abhishek Niroula": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC8748989"}, {"db": "pii", "key": "10.1038/s41467-021-27666-x"}], "notes": [], "created": "2023-11-20T11:36:12.941Z", "modified": "2023-11-20T11:36:13.588Z"}, {"entity": "publication", "iuid": "6a5cbe82f7cc4420ace491fe336507c6", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/6a5cbe82f7cc4420ace491fe336507c6.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/6a5cbe82f7cc4420ace491fe336507c6"}}, "title": "MirGeneDB 2.1: toward a complete sampling of all major animal phyla.", "authors": [{"family": "Fromm", "given": "Bastian", "initials": "B", "orcid": "0000-0003-0352-3037", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cdc4c42e06604b759dd6225c5f8362b5.json"}}, {"family": "H\u00f8ye", "given": "Eirik", "initials": "E", "orcid": "0000-0002-9782-756X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/99cb7a71d3be45f0be2536859f5fb499.json"}}, {"family": "Domanska", "given": "Diana", "initials": "D"}, {"family": "Zhong", "given": "Xiangfu", "initials": "X", "orcid": "0000-0002-1872-1186", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7294e8fb054340e5be637556540ca10e.json"}}, {"family": "Aparicio-Puerta", "given": "Ernesto", "initials": "E"}, {"family": "Ovchinnikov", "given": "Vladimir", "initials": "V"}, {"family": "Umu", "given": "Sinan U", "initials": "SU"}, {"family": "Chabot", "given": "Peter J", "initials": "PJ"}, {"family": "Kang", "given": "Wenjing", "initials": "W"}, {"family": "Aslanzadeh", "given": "Morteza", "initials": "M"}, {"family": "Tarbier", "given": "Marcel", "initials": "M", "orcid": "0000-0003-0556-2531", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9678d0797def441e9870afe6ffbb08d0.json"}}, {"family": "M\u00e1rmol-S\u00e1nchez", "given": "Emilio", "initials": "E"}, {"family": "Urgese", "given": "Gianvito", "initials": "G", "orcid": "0000-0003-2672-7593", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/784cc943dae64b1596dcd33dae7e3dd3.json"}}, {"family": "Johansen", "given": "Morten", "initials": "M"}, {"family": "Hovig", "given": "Eivind", "initials": "E"}, {"family": "Hackenberg", "given": "Michael", "initials": "M", "orcid": "0000-0003-2248-3114", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b5d460b880634ea5befd132426191afe.json"}}, {"family": "Friedl\u00e4nder", "given": "Marc R", "initials": "MR"}, {"family": "Peterson", "given": "Kevin J", "initials": "KJ"}], "type": "journal article", "published": "2022-01-07", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "volume": "50", "issue": "D1", "pages": "D204-D210", "issn-l": "0305-1048"}, "abstract": "We describe an update of MirGeneDB, the manually curated microRNA gene database. Adhering to uniform and consistent criteria for microRNA annotation and nomenclature, we substantially expanded MirGeneDB with 30 additional species representing previously missing metazoan phyla such as sponges, jellyfish, rotifers and flatworms. MirGeneDB 2.1 now consists of 75 species spanning over \u223c800 million years of animal evolution, and contains a total number of 16 670 microRNAs from 1549 families. Over 6000 microRNAs were added in this update using \u223c550 datasets with \u223c7.5 billion sequencing reads. By adding new phylogenetically important species, especially those relevant for the study of whole genome duplication events, and through updating evolutionary nodes of origin for many families and genes, we were able to substantially refine our nomenclature system. All changes are traceable in the specifically developed MirGeneDB version tracker. The performance of read-pages is improved and microRNA expression matrices for all tissues and species are now also downloadable. Altogether, this update represents a significant step toward a complete sampling of all major metazoan phyla, and a widely needed foundation for comparative microRNA genomics and transcriptomics studies. MirGeneDB 2.1 is part of RNAcentral and Elixir Norway, publicly and freely available at http://www.mirgenedb.org/.", "doi": "10.1093/nar/gkab1101", "pmid": "34850127", "labels": {"Marc Friedl\u00e4nder": "", "SciLifeLab Fellow": "", "DDLS Fellow": "", "Marcel Tarbier": ""}, "xrefs": [{"db": "pmc", "key": "PMC8728216"}, {"db": "pii", "key": "6439665"}], "notes": [], "created": "2021-11-30T16:09:03.502Z", "modified": "2026-09-23T07:25:15.043Z"}, {"entity": "publication", "iuid": "40c6985e72684542af5bdcee3e4e1539", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/40c6985e72684542af5bdcee3e4e1539.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/40c6985e72684542af5bdcee3e4e1539"}}, "title": "Spatial analysis of histology in 3D: quantification and visualization of organ and tumor level tissue environment.", "authors": [{"family": "Ruusuvuori", "given": "Pekka", "initials": "P"}, {"family": "Valkonen", "given": "Masi", "initials": "M"}, {"family": "Kartasalo", "given": "Kimmo", "initials": "K"}, {"family": "Valkonen", "given": "Mira", "initials": "M"}, {"family": "Visakorpi", "given": "Tapio", "initials": "T"}, {"family": "Nykter", "given": "Matti", "initials": "M"}, {"family": "Latonen", "given": "Leena", "initials": "L"}], "type": "journal article", "published": "2022-01-00", "journal": {"title": "Heliyon", "issn": "2405-8440", "issn-l": "2405-8440", "volume": "8", "issue": "1", "pages": "e08762"}, "abstract": "Histological changes in tissue are of primary importance in pathological research and diagnosis. Automated histological analysis requires ability to computationally separate pathological alterations from normal tissue. Conventional histopathological assessments are performed from individual tissue sections, leading to the loss of three-dimensional context of the tissue. Yet, the tissue context and spatial determinants are critical in several pathologies, such as in understanding growth patterns of cancer in its local environment. Here, we develop computational methods for visualization and quantitative assessment of histopathological alterations in three dimensions. First, we reconstruct the 3D representation of the whole organ from serial sectioned tissue. Then, we proceed to analyze the histological characteristics and regions of interest in 3D. As our example cases, we use whole slide images representing hematoxylin-eosin stained whole mouse prostates in a Pten+/- mouse prostate tumor model. We show that quantitative assessment of tumor sizes, shapes, and separation between spatial locations within the organ enable characterizing and grouping tumors. Further, we show that 3D visualization of tissue with computationally quantified features provides an intuitive way to observe tissue pathology. Our results underline the heterogeneity in composition and cellular organization within individual tumors. As an example, we show how prostate tumors have nuclear density gradients indicating areas of tumor growth directions and reflecting varying pressure from the surrounding tissue. The methods presented here are applicable to any tissue and different types of pathologies. This work provides a proof-of-principle for gaining a comprehensive view from histology by studying it quantitatively in 3D.", "doi": "10.1016/j.heliyon.2022.e08762", "pmid": "35128089", "labels": {"Kimmo Kartasalo": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC8800033"}, {"db": "pii", "key": "S2405-8440(22)00050-0"}], "notes": [], "created": "2024-11-05T16:09:30.745Z", "modified": "2024-11-29T10:41:38.295Z"}, {"entity": "publication", "iuid": "9ba42e1c7aeb4605b2110b24751ce7d4", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9ba42e1c7aeb4605b2110b24751ce7d4.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9ba42e1c7aeb4605b2110b24751ce7d4"}}, "title": "Publisher Correction: A practical guide to large-scale docking.", "authors": [{"family": "Bender", "given": "Brian J", "initials": "BJ"}, {"family": "Gahbauer", "given": "Stefan", "initials": "S", "orcid": "0000-0002-3115-9757", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e4fe0c3bcf964f63a9244f5a93219fec.json"}}, {"family": "Luttens", "given": "Andreas", "initials": "A", "orcid": "0000-0003-2915-7901", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d2944edc47eb4b639f1c61ae7b94b60a.json"}}, {"family": "Lyu", "given": "Jiankun", "initials": "J"}, {"family": "Webb", "given": "Chase M", "initials": "CM"}, {"family": "Stein", "given": "Reed M", "initials": "RM"}, {"family": "Fink", "given": "Elissa A", "initials": "EA"}, {"family": "Balius", "given": "Trent E", "initials": "TE", "orcid": "0000-0002-6811-4667", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7c4b9d95e87549c487f4a386273264a2.json"}}, {"family": "Carlsson", "given": "Jens", "initials": "J"}, {"family": "Irwin", "given": "John J", "initials": "JJ"}, {"family": "Shoichet", "given": "Brian K", "initials": "BK"}], "type": "published erratum", "published": "2022-01-00", "journal": {"title": "Nat Protoc", "issn": "1750-2799", "volume": "17", "issue": "1", "pages": "177", "issn-l": null}, "abstract": null, "doi": "10.1038/s41596-021-00650-x", "pmid": "34887579", "labels": {"SciLifeLab Fellow": "", "Jens Carlsson": "", "Andreas Luttens": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pii", "key": "10.1038/s41596-021-00650-x"}], "notes": [], "created": "2026-08-20T09:03:57.178Z", "modified": "2026-09-23T14:10:58.478Z"}, {"entity": "publication", "iuid": "f208e5a2109b485a93d298cbcf125500", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f208e5a2109b485a93d298cbcf125500.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f208e5a2109b485a93d298cbcf125500"}}, "title": "Changes in metabolomics profiles over ten years and subsequent risk of developing type 2 diabetes: Results from the Nurses' Health Study.", "authors": [{"family": "Wittenbecher", "given": "Clemens", "initials": "C"}, {"family": "Guasch-Ferr\u00e9", "given": "Marta", "initials": "M"}, {"family": "Haslam", "given": "Danielle E", "initials": "DE"}, {"family": "Dennis", "given": "Courtney", "initials": "C"}, {"family": "Li", "given": "Jun", "initials": "J"}, {"family": "Bhupathiraju", "given": "Shilpa N", "initials": "SN"}, {"family": "Lee", "given": "Chih-Hao", "initials": "CH"}, {"family": "Qi", "given": "Qibin", "initials": "Q"}, {"family": "Liang", "given": "Liming", "initials": "L"}, {"family": "Eliassen", "given": "A Heather", "initials": "AH"}, {"family": "Clish", "given": "Clary", "initials": "C"}, {"family": "Sun", "given": "Qi", "initials": "Q"}, {"family": "Hu", "given": "Frank B", "initials": "FB"}], "type": "journal article", "published": "2022-01-00", "journal": {"title": "EBioMedicine", "issn": "2352-3964", "volume": "75", "pages": "103799", "issn-l": "2352-3964"}, "abstract": "Metabolomics profiles were consistently associated with type 2 diabetes (T2D) risk, but evidence on long-term metabolite changes and T2D incidence is lacking. We examined the associations of 10-year plasma metabolite changes with subsequent T2D risk.\n\nWe conducted a nested T2D case-control study (n=244 cases, n=244 matched controls) within the Nurses' Health Study. Repeated metabolomics profiling (170 targeted metabolites) was conducted in participant blood specimens from 1989/1990 and 2000/2001, and T2D occurred between 2002 and 2008. We related 10-year metabolite changes (\u0394-values) to subsequent T2D risk using conditional logistic models, adjusting for baseline metabolite levels and baseline levels and concurrent changes of BMI, diet quality, physical activity, and smoking status.\n\nThe 10-year changes of thirty-one metabolites were associated with subsequent T2D risk (false discovery rate-adjusted p-values [FDR]<0.05). The top three high T2D risk-associated 10-year changes were (odds ratio [OR] per standard deviation [SD], 95%CI): \u0394isoleucine (2.72, 1.97-3.79), \u0394leucine (2.53, 1.86-3.47), and \u0394valine (1.93, 1.52-2.44); other high-risk-associated metabolite changes included alanine, tri-/diacylglycerol-fragments, short-chain acylcarnitines, phosphatidylethanolamines, some vitamins, and bile acids (ORs per SD between 1.31and 1.82). The top three low T2D risk-associated 10-year metabolite changes were (OR per SD, 95% CI): \u0394N-acetylaspartic acid (0.54, 0.42-0.70), \u0394C20:0 lysophosphatidylethanolamine (0.68, 0.56-0.82), and \u0394C16:1 sphingomyelin (0.68, 0.56-0.83); 10-year changes of other sphingomyelins, plasmalogens, glutamine, and glycine were also associated with lower subsequent T2D risk (ORs per SD between 0.66 and 0.78).\n\nRepeated metabolomics profiles reflecting the long-term deterioration of amino acid and lipid metabolism are associated with subsequent risk of T2D.", "doi": "10.1016/j.ebiom.2021.103799", "pmid": "34979341", "labels": {"Clemens Wittenbecher": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC8733263"}, {"db": "pii", "key": "S2352-3964(21)00593-4"}], "notes": [], "created": "2025-12-09T13:38:52.235Z", "modified": "2025-12-09T13:38:52.239Z"}, {"entity": "publication", "iuid": "90b36d42fc5b4fb98ab07730320e52f5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/90b36d42fc5b4fb98ab07730320e52f5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/90b36d42fc5b4fb98ab07730320e52f5"}}, "title": "Artificial intelligence for diagnosis and Gleason grading of prostate cancer: the PANDA challenge.", "authors": [{"family": "Bulten", "given": "Wouter", "initials": "W", "orcid": "0000-0002-6129-5039", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f592c80c84c34a70971251c380a8578b.json"}}, {"family": "Kartasalo", "given": "Kimmo", "initials": "K", "orcid": "0000-0002-9470-4783", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7c6fc97c06ed456c8bdd1f03db8a9b72.json"}}, {"family": "Chen", "given": "Po-Hsuan Cameron", "initials": "PC", "orcid": "0000-0002-0083-4991", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dd162c57871947aea109e009fc1d2daf.json"}}, {"family": "Str\u00f6m", "given": "Peter", "initials": "P", "orcid": "0000-0002-1631-806X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2798ea6ef2ed4ae88b78dd04d2f14437.json"}}, {"family": "Pinckaers", "given": "Hans", "initials": "H"}, {"family": "Nagpal", "given": "Kunal", "initials": "K"}, {"family": "Cai", "given": "Yuannan", "initials": "Y"}, {"family": "Steiner", "given": "David F", "initials": "DF", "orcid": "0000-0003-1297-0023", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a209b0168a394a09bd0cfe9cd1e1934b.json"}}, {"family": "van Boven", "given": "Hester", "initials": "H"}, {"family": "Vink", "given": "Robert", "initials": "R"}, {"family": "Hulsbergen-van de Kaa", "given": "Christina", "initials": "C"}, {"family": "van der Laak", "given": "Jeroen", "initials": "J", "orcid": "0000-0001-7982-0754", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/188f689ad0304f28b42bc9d3dbf6a56e.json"}}, {"family": "Amin", "given": "Mahul B", "initials": "MB", "orcid": "0000-0001-5943-3634", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d7974058596e4429b0035f1eff340a4c.json"}}, {"family": "Evans", "given": "Andrew J", "initials": "AJ"}, {"family": "van der Kwast", "given": "Theodorus", "initials": "T", "orcid": "0000-0001-8640-5786", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/176f93a02e394a659619ae2ff57398e4.json"}}, {"family": "Allan", "given": "Robert", "initials": "R"}, {"family": "Humphrey", "given": "Peter A", "initials": "PA"}, {"family": "Gr\u00f6nberg", "given": "Henrik", "initials": "H", "orcid": "0000-0002-1073-2753", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/33927307bf964b2fa09e09c0c867b542.json"}}, {"family": "Samaratunga", "given": "Hemamali", "initials": "H"}, {"family": "Delahunt", "given": "Brett", "initials": "B"}, {"family": "Tsuzuki", "given": "Toyonori", "initials": "T", "orcid": "0000-0002-4855-4366", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/42c993c2c0ab4b50afa03134f70118d9.json"}}, {"family": "H\u00e4kkinen", "given": "Tomi", "initials": "T"}, {"family": "Egevad", "given": "Lars", "initials": "L", "orcid": "0000-0001-8531-222X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a7d46f1f5fc047dc8edb910eb4f0645c.json"}}, {"family": "Demkin", "given": "Maggie", "initials": "M"}, {"family": "Dane", "given": "Sohier", "initials": "S"}, {"family": "Tan", "given": "Fraser", "initials": "F"}, {"family": "Valkonen", "given": "Masi", "initials": "M", "orcid": "0000-0003-3091-2484", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ae4841e8a4124dc79c921b3af09096fe.json"}}, {"family": "Corrado", "given": "Greg S", "initials": "GS"}, {"family": "Peng", "given": "Lily", "initials": "L"}, {"family": "Mermel", "given": "Craig H", "initials": "CH", "orcid": "0000-0002-0816-3395", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ff69bed2b4394cd8972c937ebb642c55.json"}}, {"family": "Ruusuvuori", "given": "Pekka", "initials": "P", "orcid": "0000-0001-9086-9591", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb947cd395e84612a53569f4a39abd19.json"}}, {"family": "Litjens", "given": "Geert", "initials": "G", "orcid": "0000-0003-1554-1291", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3792b285bcf04c11b268da1088160a9d.json"}}, {"family": "Eklund", "given": "Martin", "initials": "M", "orcid": "0000-0001-5032-5266", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/06721510ebc8462386e0e6fc6c84315b.json"}}, {"family": "PANDA challenge consortium", "given": "", "initials": ""}], "type": "journal article", "published": "2022-01-00", "journal": {"title": "Nat. Med.", "issn": "1546-170X", "issn-l": "1078-8956", "volume": "28", "issue": "1", "pages": "154-163"}, "abstract": "Artificial intelligence (AI) has shown promise for diagnosing prostate cancer in biopsies. However, results have been limited to individual studies, lacking validation in multinational settings. Competitions have been shown to be accelerators for medical imaging innovations, but their impact is hindered by lack of reproducibility and independent validation. With this in mind, we organized the PANDA challenge-the largest histopathology competition to date, joined by 1,290 developers-to catalyze development of reproducible AI algorithms for Gleason grading using 10,616 digitized prostate biopsies. We validated that a diverse set of submitted algorithms reached pathologist-level performance on independent cross-continental cohorts, fully blinded to the algorithm developers. On United States and European external validation sets, the algorithms achieved agreements of 0.862 (quadratically weighted \u03ba, 95% confidence interval (CI), 0.840-0.884) and 0.868 (95% CI, 0.835-0.900) with expert uropathologists. Successful generalization across different patient populations, laboratories and reference standards, achieved by a variety of algorithmic approaches, warrants evaluating AI-based Gleason grading in prospective clinical trials.", "doi": "10.1038/s41591-021-01620-2", "pmid": "35027755", "labels": {"Kimmo Kartasalo": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC8799467"}, {"db": "pii", "key": "10.1038/s41591-021-01620-2"}], "notes": [], "created": "2024-11-05T16:09:31.876Z", "modified": "2024-11-29T09:30:09.852Z"}, {"entity": "publication", "iuid": "35c165efce87414bb9abfcff0a7849bb", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/35c165efce87414bb9abfcff0a7849bb.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/35c165efce87414bb9abfcff0a7849bb"}}, "title": "Cholesterol stiffening of lipid membranes and drug interactions: Insights from neutron spin echo and deuterium NMR spectroscopy", "authors": [{"family": "Gupta", "given": "Sudipta", "initials": "S"}, {"family": "Doole", "given": "Fathima T", "initials": "FT"}, {"family": "Kumarage", "given": "Teshani", "initials": "T"}, {"family": "Doktorova", "given": "Milka", "initials": "M"}, {"family": "Khelashvili", "given": "George", "initials": "G"}, {"family": "Ashkar", "given": "Rana", "initials": "R"}, {"family": "Brown", "given": "Michael F", "initials": "MF"}], "type": "book-chapter", "published": "2022-00-00", "journal": {"title": null, "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": "771-796"}, "abstract": null, "doi": "10.1016/b978-0-323-85857-1.00037-7", "pmid": null, "labels": {"Milka Doktorova": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2024-11-27T12:26:46.720Z", "modified": "2024-11-29T12:15:56.583Z"}, {"entity": "publication", "iuid": "ce33baa2344a46f2a266278abbc3541e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ce33baa2344a46f2a266278abbc3541e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ce33baa2344a46f2a266278abbc3541e"}}, "title": "Towards a structurally resolved human protein interaction network", "authors": [{"family": "Elofsson", "given": "Arne", "initials": "A", "orcid": "0000-0002-7115-9751", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/248e70e81bd64f31a5f83e6e329bba95.json"}}, {"family": "Burke", "given": "David", "initials": "D", "orcid": "0000-0001-8830-3951", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0ae9a94abf5e47778d59e4f3c9d8e62e.json"}}, {"family": "Bryant", "given": "Patrick", "initials": "P", "orcid": "0000-0003-3439-1866", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a683bcf98234ff09b2398976583b66f.json"}}, {"family": "Barrio-Hernandez", "given": "Inigo", "initials": "I", "orcid": "0000-0002-5686-0451", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/59ccf621e75c48868e9c215b04dcf787.json"}}, {"family": "Memon", "given": "Danish", "initials": "D", "orcid": "0000-0002-1365-0710", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0f9e1ae20abe4f7f94af1f6856d026bc.json"}}, {"family": "Pozzati", "given": "Gabriele", "initials": "G", "orcid": "0000-0002-4303-9939", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/94129216debe4e22ab3f3b74c33f9ab9.json"}}, {"family": "Shenoy", "given": "Aditi", "initials": "A", "orcid": "0000-0001-7748-2501", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/35bef00b985a45d59602675316e3d706.json"}}, {"family": "Zhu", "given": "Wensi", "initials": "W"}, {"family": "Dunham", "given": "Alistair", "initials": "A"}, {"family": "Albanese", "given": "Pascal", "initials": "P"}, {"family": "Keller", "given": "Andrew", "initials": "A"}, {"family": "Scheltema", "given": "Richard", "initials": "R", "orcid": "0000-0002-1668-0253", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/de6c6b9b87574d7eb67d48a73ab5f230.json"}}, {"family": "Bruce", "given": "James", "initials": "J", "orcid": "0000-0001-6441-6089", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/66c3622f73ef4c62a4100d87ab6aeded.json"}}, {"family": "Leitner", "given": "Alexander", "initials": "A", "orcid": "0000-0003-4126-0725", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca32a3af642745ea9d26f0e7f1413b6a.json"}}, {"family": "Kundrotas", "given": "Petras", "initials": "P"}, {"family": "Beltrao", "given": "Pedro", "initials": "P", "orcid": "0000-0002-2724-7703", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/952eba119d2e4d4b89e14b294c5c6885.json"}}], "type": "posted-content", "published": "2021-12-16", "journal": {"issn-l": null}, "abstract": null, "doi": "10.21203/rs.3.rs-1098605/v1", "pmid": null, "labels": {"Patrick Bryant": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T12:57:59.578Z", "modified": "2026-09-23T14:16:49.732Z"}, {"entity": "publication", "iuid": "0709f0961e804395ab578550eca4c11a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0709f0961e804395ab578550eca4c11a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0709f0961e804395ab578550eca4c11a"}}, "title": "What Is the Role of the Environment in the Emergence of Novel Antibiotic Resistance Genes? A Modeling Approach.", "authors": [{"family": "Bengtsson-Palme", "given": "Johan", "initials": "J", "orcid": "0000-0002-6528-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c666068e9d34939b0252a627007cec7.json"}}, {"family": "Jonsson", "given": "Viktor", "initials": "V", "orcid": "0000-0002-1445-5220", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8068fef596794494add13b3a4bc35768.json"}}, {"family": "He\u00df", "given": "Stefanie", "initials": "S", "orcid": "0000-0002-9293-4622", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/054fe98a937b4e8787c84df52b7c7a76.json"}}], "type": "journal article", "published": "2021-12-07", "journal": {"title": "Environ. Sci. Technol.", "issn": "1520-5851", "volume": "55", "issue": "23", "pages": "15734-15743", "issn-l": "0013-936X"}, "abstract": "It is generally accepted that intervention strategies to curb antibiotic resistance cannot solely focus on human and veterinary medicine but must also consider environmental settings. While the environment clearly has a role in transmission of resistant bacteria, its role in the emergence of novel antibiotic resistance genes (ARGs) is less clear. It has been suggested that the environment constitutes an enormous recruitment ground for ARGs to pathogens, but its extent is practically unknown. We have constructed a model framework for resistance emergence and used available quantitative data on relevant processes to identify limiting steps in the appearance of ARGs in human pathogens. We found that in a majority of possible scenarios, the environment would only play a minor role in the emergence of novel ARGs. However, the uncertainty is enormous, highlighting an urgent need for more quantitative data. Specifically, more data is most needed on the fitness costs of ARG carriage, the degree of dispersal of resistant bacteria from the environment to humans, and the rates of mobilization and horizontal transfer of ARGs. This type of data is instrumental to determine which processes should be targeted for interventions to curb development and transmission of ARGs in the environment.", "doi": "10.1021/acs.est.1c02977", "pmid": "34792330", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pmc", "key": "PMC8655980"}], "notes": [], "created": "2022-11-08T09:24:48.879Z", "modified": "2023-06-19T13:59:25.223Z"}, {"entity": "publication", "iuid": "52464b798110423d9a8e29770cfa84a5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/52464b798110423d9a8e29770cfa84a5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/52464b798110423d9a8e29770cfa84a5"}}, "title": "Dnmt3a-mutated clonal hematopoiesis promotes osteoporosis.", "authors": [{"family": "Kim", "given": "Peter Geon", "initials": "PG", "orcid": "0000-0002-8716-8759", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bab07a767447416fa8e4004c6cbe7b7f.json"}}, {"family": "Niroula", "given": "Abhishek", "initials": "A", "orcid": "0000-0002-5904-0635", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/05df7afc7a494ba5af8a378e5ffa53f0.json"}}, {"family": "Shkolnik", "given": "Veronica", "initials": "V", "orcid": "0000-0002-9043-1503", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/509e4c48124649a29675f21de034504f.json"}}, {"family": "McConkey", "given": "Marie", "initials": "M", "orcid": "0000-0002-9500-018X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e5174577207f4e46b75a2f0170e76ff3.json"}}, {"family": "Lin", "given": "Amy E", "initials": "AE", "orcid": "0000-0001-6723-5443", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f6d80e192e27498b9c63898e7136af68.json"}}, {"family": "S\u0142abicki", "given": "Miko\u0142aj", "initials": "M", "orcid": "0000-0001-6317-9296", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/98e216db96f944ffb3f32454b487a4d0.json"}}, {"family": "Kemp", "given": "John P", "initials": "JP", "orcid": "0000-0002-9105-2249", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/97d7ab51837846cca8a4ec1fac0bc462.json"}}, {"family": "Bick", "given": "Alexander", "initials": "A", "orcid": "0000-0001-5824-9595", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d2da5a35a4984921b19dfafe64cea2de.json"}}, {"family": "Gibson", "given": "Christopher J", "initials": "CJ", "orcid": "0000-0002-3700-5310", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/71ce9f64755e483496f8c28a76a2a1ff.json"}}, {"family": "Griffin", "given": "Gabriel", "initials": "G", "orcid": "0000-0002-4042-6757", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f6153204e19d4660b640dc4467605973.json"}}, {"family": "Sekar", "given": "Aswin", "initials": "A", "orcid": "0000-0003-0406-0935", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2cff21c3699340a3a10c13447b59c7ff.json"}}, {"family": "Brooks", "given": "Daniel J", "initials": "DJ", "orcid": "0000-0001-7408-9851", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/89eefb6cb22245a3a0cb94e93efc0eb3.json"}}, {"family": "Wong", "given": "Waihay J", "initials": "WJ", "orcid": "0000-0003-2023-6590", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3a4e1a5be5c54646ab5881bc338bf6cd.json"}}, {"family": "Cohen", "given": "Drew N", "initials": "DN", "orcid": "0000-0001-5263-4409", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0d561a8c372244aa95e1a9b1ed82c4d7.json"}}, {"family": "Uddin", "given": "Md Mesbah", "initials": "MM", "orcid": "0000-0003-1846-0411", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/42f1ac7010c34ba997a3fd9e56c6a56a.json"}}, {"family": "Shin", "given": "Wesley J", "initials": "WJ", "orcid": "0000-0003-0627-0821", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/961f875b160341b6b31afa58a8f47680.json"}}, {"family": "Pirruccello", "given": "James", "initials": "J", "orcid": "0000-0001-6088-4037", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/60d2e9f23cce41f5b1f40ce0f010e9d9.json"}}, {"family": "Tsai", "given": "Jonathan M", "initials": "JM", "orcid": "0000-0001-5868-2305", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1030f0fcd7a749d4862319fd5d7e6a9f.json"}}, {"family": "Agrawal", "given": "Mridul", "initials": "M", "orcid": "0000-0002-5455-2543", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a2e1aab434af4a05a350e2be61ae5e4f.json"}}, {"family": "Kiel", "given": "Douglas P", "initials": "DP", "orcid": "0000-0001-8474-0310", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f10765c4b3a3446bb420c81ffee3f0f7.json"}}, {"family": "Bouxsein", "given": "Mary L", "initials": "ML", "orcid": "0000-0002-7027-7414", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7c547e0d1028464b8cb407e45d9e1596.json"}}, {"family": "Richards", "given": "J Brent", "initials": "JB", "orcid": "0000-0002-3746-9086", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ed87dd6607bd4dcdbc150d5432ebfb05.json"}}, {"family": "Evans", "given": "David M", "initials": "DM", "orcid": "0000-0003-0663-4621", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fd3b234756eb4580804c61705bf72d5c.json"}}, {"family": "Wein", "given": "Marc N", "initials": "MN", "orcid": "0000-0002-6015-8147", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/13ba103bbb2940978d471e36ab3e4787.json"}}, {"family": "Charles", "given": "Julia F", "initials": "JF", "orcid": "0000-0002-5875-314X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/878a909b8f214e20b88bbc4916b957a4.json"}}, {"family": "Jaiswal", "given": "Siddhartha", "initials": "S", "orcid": "0000-0002-9597-0477", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a1901e08f989434fb01dfa17b0a85470.json"}}, {"family": "Natarajan", "given": "Pradeep", "initials": "P", "orcid": "0000-0001-8402-7435", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fe8bd48c61c047cd8e61c35d9e9ac650.json"}}, {"family": "Ebert", "given": "Benjamin L", "initials": "BL", "orcid": "0000-0003-0197-5451", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56e4f1c53a4348e2b0ceb44a38850a17.json"}}], "type": "journal article", "published": "2021-12-06", "journal": {"title": "J. Exp. Med.", "issn": "1540-9538", "volume": "218", "issue": "12", "issn-l": "0022-1007"}, "abstract": "Osteoporosis is caused by an imbalance of osteoclasts and osteoblasts, occurring in close proximity to hematopoietic cells in the bone marrow. Recurrent somatic mutations that lead to an expanded population of mutant blood cells is termed clonal hematopoiesis of indeterminate potential (CHIP). Analyzing exome sequencing data from the UK Biobank, we found CHIP to be associated with increased incident osteoporosis diagnoses and decreased bone mineral density. In murine models, hematopoietic-specific mutations in Dnmt3a, the most commonly mutated gene in CHIP, decreased bone mass via increased osteoclastogenesis. Dnmt3a-/- demethylation opened chromatin and altered activity of inflammatory transcription factors. Bone loss was driven by proinflammatory cytokines, including Irf3-NF-\u03baB-mediated IL-20 expression from Dnmt3a mutant macrophages. Increased osteoclastogenesis due to the Dnmt3a mutations was ameliorated by alendronate or IL-20 neutralization. These results demonstrate a novel source of osteoporosis-inducing inflammation.", "doi": "10.1084/jem.20211872", "pmid": "34698806", "labels": {"Abhishek Niroula": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC8552148"}, {"db": "pii", "key": "212724"}], "notes": [], "created": "2023-11-20T11:28:02.188Z", "modified": "2023-11-20T11:28:03.284Z"}, {"entity": "publication", "iuid": "ca14abf3c10b45c4beb88eec46dbb948", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ca14abf3c10b45c4beb88eec46dbb948.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ca14abf3c10b45c4beb88eec46dbb948"}}, "title": "Smart3-ATAC: a highly sensitive method for joint accessibility and full-length transcriptome analysis in single cells", "authors": [{"family": "Cheng", "given": "Huaitao", "initials": "H"}, {"family": "Pui", "given": "Han pin", "initials": "Hp"}, {"family": "Lentini", "given": "Antonio", "initials": "A"}, {"family": "Kolbeinsd\u00f3ttir", "given": "Solr\u00fan", "initials": "S"}, {"family": "Andrews", "given": "Nathanael", "initials": "N"}, {"family": "Pei", "given": "Yu", "initials": "Y"}, {"family": "Reinius", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Deng", "given": "Qiaolin", "initials": "Q"}, {"family": "Enge", "given": "Martin", "initials": "M"}], "type": "posted-content", "published": "2021-12-03", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2021.12.02.470912", "pmid": null, "labels": {"Antonio Lentini": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2025-03-28T07:09:53.912Z", "modified": "2025-03-28T07:09:53.913Z"}, {"entity": "publication", "iuid": "c1d55c3a4d614fd3ba70009150f65b48", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c1d55c3a4d614fd3ba70009150f65b48.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c1d55c3a4d614fd3ba70009150f65b48"}}, "title": "Next generation plasma proteome profiling of COVID-19 patients with mild to moderate symptoms.", "authors": [{"family": "Zhong", "given": "Wen", "initials": "W"}, {"family": "Altay", "given": "Ozlem", "initials": "O"}, {"family": "Arif", "given": "Muhammad", "initials": "M"}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Doganay", "given": "Levent", "initials": "L"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Uhlen", "given": "Mathias", "initials": "M"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}], "type": "clinical trial, phase ii", "published": "2021-12-00", "journal": {"title": "EBioMedicine", "issn": "2352-3964", "volume": "74", "pages": "103723", "issn-l": "2352-3964"}, "abstract": "COVID-19 has caused millions of deaths globally, yet the cellular mechanisms underlying the various effects of the disease remain poorly understood. Recently, a new analytical platform for comprehensive analysis of plasma protein profiles using proximity extension assays combined with next generation sequencing has been developed, which allows for multiple proteins to be analyzed simultaneously without sacrifice on accuracy or sensitivity.\n\nWe analyzed the plasma protein profiles of COVID-19 patients (n = 50) with mild and moderate symptoms by comparing the protein levels in newly diagnosed patients with the protein levels in the same individuals after 14 days.\n\nThe study has identified more than 200 proteins that are significantly elevated during infection and many of these are related to cytokine response and other immune-related functions. In addition, several other proteins are shown to be elevated, including SCARB2, a host cell receptor protein involved in virus entry. A comparison with the plasma protein response in patients with severe symptoms shows a highly similar pattern, but with some interesting differences.\n\nThe study presented here demonstrates the usefulness of \"next generation plasma protein profiling\" to identify molecular signatures of importance for disease progression and to allow monitoring of disease during recovery from the infection. The results will facilitate further studies to understand the molecular mechanism of the immune-related response of the SARS-CoV-2 virus.\n\nThis work was financially supported by Knut and Alice Wallenberg Foundation.", "doi": "10.1016/j.ebiom.2021.103723", "pmid": "34844191", "labels": {"Adil Mardinoglu": "", "SciLifeLab Fellow": "", "Fredrik Edfors": "", "DDLS Fellow": "", "Muhammad Arif": ""}, "xrefs": [{"db": "pmc", "key": "PMC8626206"}, {"db": "pii", "key": "S2352-3964(21)00517-X"}], "notes": [], "created": "2023-12-04T15:04:55.555Z", "modified": "2026-09-23T08:47:44.788Z"}, {"entity": "publication", "iuid": "212bb1b5db754d05af928064c2f1c66e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/212bb1b5db754d05af928064c2f1c66e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/212bb1b5db754d05af928064c2f1c66e"}}, "title": "A multi-scale map of cell structure fusing protein images and interactions.", "authors": [{"family": "Qin", "given": "Yue", "initials": "Y", "orcid": "0000-0002-0496-7134", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e9f5a7e6677c435082cf618d1af68ee6.json"}}, {"family": "Huttlin", "given": "Edward L", "initials": "EL", "orcid": "0000-0002-1822-1173", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/447db4d2b72445ec87d03bd6f73a2b1e.json"}}, {"family": "Winsnes", "given": "Casper F", "initials": "CF", "orcid": "0000-0002-0028-5865", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/edeb3bc6c95d4185bf2098bf1e4a5e3c.json"}}, {"family": "Gosztyla", "given": "Maya L", "initials": "ML", "orcid": "0000-0003-4758-4800", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/35255274a1864fdd8f6e2800f74042b3.json"}}, {"family": "Wacheul", "given": "Ludivine", "initials": "L", "orcid": "0000-0002-0443-8865", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e2b0157e32c74d44abab10d8fd0a8b3a.json"}}, {"family": "Kelly", "given": "Marcus R", "initials": "MR"}, {"family": "Blue", "given": "Steven M", "initials": "SM", "orcid": "0000-0003-0279-6690", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02c5a67d9bff4811b3ceddac9baec8ae.json"}}, {"family": "Zheng", "given": "Fan", "initials": "F"}, {"family": "Chen", "given": "Michael", "initials": "M"}, {"family": "Schaffer", "given": "Leah V", "initials": "LV"}, {"family": "Licon", "given": "Katherine", "initials": "K"}, {"family": "B\u00e4ckstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Vaites", "given": "Laura Pontano", "initials": "LP"}, {"family": "Lee", "given": "John J", "initials": "JJ", "orcid": "0000-0002-7967-3384", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b58ad4c0b35c46978a58e213f219c9ba.json"}}, {"family": "Ouyang", "given": "Wei", "initials": "W", "orcid": "0000-0002-0291-926X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56f601e1d1c6448aab0c3a1e3cffdbfc.json"}}, {"family": "Liu", "given": "Sophie N", "initials": "SN", "orcid": "0000-0001-7934-8605", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0e690e30ba984511946856e270b4e05e.json"}}, {"family": "Zhang", "given": "Tian", "initials": "T"}, {"family": "Silva", "given": "Erica", "initials": "E"}, {"family": "Park", "given": "Jisoo", "initials": "J"}, {"family": "Pitea", "given": "Adriana", "initials": "A"}, {"family": "Kreisberg", "given": "Jason F", "initials": "JF", "orcid": "0000-0002-3616-079X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cf842fcdd7b44056b75dc1c9059a3714.json"}}, {"family": "Gygi", "given": "Steven P", "initials": "SP", "orcid": "0000-0001-7626-0034", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2d4ecd32810e4a59a334036ded6dabec.json"}}, {"family": "Ma", "given": "Jianzhu", "initials": "J", "orcid": "0000-0002-8236-6609", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1cec6131f74345bcabfd07aa573fe0ab.json"}}, {"family": "Harper", "given": "J Wade", "initials": "JW", "orcid": "0000-0002-6944-7236", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/47dbdfbc595c4d1896fa0baa245210d0.json"}}, {"family": "Yeo", "given": "Gene W", "initials": "GW", "orcid": "0000-0002-0799-6037", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/76c57b25929f487abc4d49301fabd048.json"}}, {"family": "Lafontaine", "given": "Denis L J", "initials": "DLJ", "orcid": "0000-0001-7295-6288", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a9ca9bf9e09e45afa0da65f8ed40d8c7.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb07e6d0122c4528a927c1fe922e3bc8.json"}}, {"family": "Ideker", "given": "Trey", "initials": "T", "orcid": "0000-0002-1708-8454", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8701a4e92863420dbe8b77bb44a7deeb.json"}}], "type": "journal article", "published": "2021-12-00", "journal": {"title": "Nature", "issn": "1476-4687", "volume": "600", "issue": "7889", "pages": "536-542", "issn-l": "0028-0836"}, "abstract": "The cell is a multi-scale structure with modular organization across at least four orders of magnitude1. Two central approaches for mapping this structure-protein fluorescent imaging and protein biophysical association-each generate extensive datasets, but of distinct qualities and resolutions that are typically treated separately2,3. Here we integrate immunofluorescence images in the Human Protein Atlas4 with affinity purifications in BioPlex5 to create a unified hierarchical map of human cell architecture. Integration is achieved by configuring each approach as a general measure of protein distance, then calibrating the two measures using machine learning. The map, known as the multi-scale integrated cell (MuSIC 1.0), resolves 69 subcellular systems, of which approximately half are to our knowledge undocumented. Accordingly, we perform 134 additional affinity purifications and validate subunit associations for the majority of systems. The map reveals a pre-ribosomal RNA processing assembly and accessory factors, which we show govern rRNA maturation, and functional roles for SRRM1 and FAM120C in chromatin and RPS3A in splicing. By integration across scales, MuSIC increases the resolution of imaging while giving protein interactions a spatial dimension, paving the way to incorporate diverse types of data in proteome-wide cell maps.", "doi": "10.1038/s41586-021-04115-9", "pmid": "34819669", "labels": {"DDLS Fellow": "", "Wei Ouyang": ""}, "xrefs": [{"db": "mid", "key": "NIHMS1784657"}, {"db": "pmc", "key": "PMC9053732"}, {"db": "pii", "key": "10.1038/s41586-021-04115-9"}], "notes": [], "created": "2026-09-23T07:49:09.919Z", "modified": "2026-09-23T07:49:10.251Z"}, {"entity": "publication", "iuid": "2dec272352c540b3a552e3bae3c28d08", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/2dec272352c540b3a552e3bae3c28d08.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/2dec272352c540b3a552e3bae3c28d08"}}, "title": "A bioinformatic platform to integrate target capture and whole genome sequences of various read depths for phylogenomics.", "authors": [{"family": "G Ribeiro", "given": "Pedro", "initials": "P", "orcid": "0000-0001-5964-1978", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/80cd041ee9b04f169d157d8a98f43888.json"}}, {"family": "Torres Jim\u00e9nez", "given": "Mar\u00eda Fernanda", "initials": "MF"}, {"family": "Andermann", "given": "Tobias", "initials": "T"}, {"family": "Antonelli", "given": "Alexandre", "initials": "A"}, {"family": "Bacon", "given": "Christine D", "initials": "CD", "orcid": "0000-0003-2341-2705", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/659f1ab881cf4890b80ebbdf23188ebc.json"}}, {"family": "Matos-Marav\u00ed", "given": "P\u00e1vel", "initials": "P", "orcid": "0000-0002-2885-4919", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b15935e4e29343969d17a958df5e2eaa.json"}}], "type": "journal article", "published": "2021-12-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "volume": "30", "issue": "23", "pages": "6021-6035", "issn-l": "0962-1083"}, "abstract": "The increasing availability of short-read whole genome sequencing (WGS) provides unprecedented opportunities to study ecological and evolutionary processes. Although loci of interest can be extracted from WGS data and combined with target sequence data, this requires suitable bioinformatic workflows. Here, we test different assembly and locus extraction strategies and implement them into secapr, a pipeline that processes short-read data into multilocus alignments for phylogenetics and molecular ecology analyses. We integrate the processing of data from low-coverage WGS (<30\u00d7) and target sequence capture into a flexible framework, while optimizing de novo contig assembly and loci extraction. Specifically, we test different assembly strategies by contrasting their ability to recover loci from targeted butterfly protein-coding genes, using four data sets: a WGS data set across different average coverages (10\u00d7, 5\u00d7 and 2\u00d7) and a data set for which these loci were enriched prior to sequencing via target sequence capture. Using the resulting de novo contigs, we account for potential errors within contigs and infer phylogenetic trees to evaluate the ability of each assembly strategy to recover species relationships. We demonstrate that choosing multiple sizes of kmer simultaneously for assembly results in the highest yield of extracted loci from de novo assembled contigs, while data sets derived from sequencing read depths as low as 5\u00d7 recovers the expected species relationships in phylogenetic trees. By making the tested assembly approaches available in the secapr pipeline, we hope to inspire future studies to incorporate complementary data and make an informed choice on the optimal assembly strategy.", "doi": "10.1111/mec.16240", "pmid": "34674330", "labels": {"Tobias Andermann": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC9298010"}], "notes": [], "created": "2022-11-11T09:10:47.008Z", "modified": "2022-11-11T09:10:47.127Z"}, {"entity": "publication", "iuid": "3f01a7c61c26461182ce88813f2e7047", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3f01a7c61c26461182ce88813f2e7047.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3f01a7c61c26461182ce88813f2e7047"}}, "title": "Genomic and niche divergence in an Amazonian palm species complex", "authors": [{"family": "Bacon", "given": "Christine D", "initials": "CD"}, {"family": "Roncal", "given": "Julissa", "initials": "J"}, {"family": "Andermann", "given": "Tobias", "initials": "T"}, {"family": "Barnes", "given": "Christopher J", "initials": "CJ"}, {"family": "Balslev", "given": "Henrik", "initials": "H"}, {"family": "Guti\u00e9rrez-Pinto", "given": "Natalia", "initials": "N"}, {"family": "Morales", "given": "Hern\u00e1n", "initials": "H"}, {"family": "N\u00fa\u00f1ez-Avelleneda", "given": "Luis Alberto", "initials": "LA"}, {"family": "Tunarosa", "given": "Natalia", "initials": "N"}, {"family": "Antonelli", "given": "Alexandre", "initials": "A"}], "type": "journal-article", "published": "2021-11-29", "journal": {"issn": "0024-4074", "volume": "197", "issue": "4", "pages": "498-512", "issn-l": null}, "abstract": null, "doi": "10.1093/botlinnean/boab012", "pmid": null, "labels": {"Tobias Andermann": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2022-11-11T09:10:35.626Z", "modified": "2025-12-04T16:58:34.236Z"}, {"entity": "publication", "iuid": "5a98c42869ca40649beb73baa9385def", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5a98c42869ca40649beb73baa9385def.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5a98c42869ca40649beb73baa9385def"}}, "title": "A network-based approach reveals the dysregulated transcriptional regulation in non-alcoholic fatty liver disease.", "authors": [{"family": "Yang", "given": "Hong", "initials": "H"}, {"family": "Arif", "given": "Muhammad", "initials": "M"}, {"family": "Yuan", "given": "Meng", "initials": "M"}, {"family": "Li", "given": "Xiangyu", "initials": "X"}, {"family": "Shong", "given": "Koeun", "initials": "K"}, {"family": "T\u00fcrkez", "given": "Hasan", "initials": "H"}, {"family": "Nielsen", "given": "Jens", "initials": "J"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Bor\u00e9n", "given": "Jan", "initials": "J"}, {"family": "Zhang", "given": "Cheng", "initials": "C"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}], "type": "journal article", "published": "2021-11-19", "journal": {"title": "iScience", "issn": "2589-0042", "volume": "24", "issue": "11", "pages": "103222", "issn-l": null}, "abstract": "Non-alcoholic fatty liver disease (NAFLD) is a leading cause of chronic liver disease worldwide. We performed network analysis to investigate the dysregulated biological processes in the disease progression and revealed the molecular mechanism underlying NAFLD. Based on network analysis, we identified a highly conserved disease-associated gene module across three different NAFLD cohorts and highlighted the predominant role of key transcriptional regulators associated with lipid and cholesterol metabolism. In addition, we revealed the detailed metabolic differences between heterogeneous NAFLD patients through integrative systems analysis of transcriptomic data and liver-specific genome-scale metabolic model. Furthermore, we identified transcription factors (TFs), including SREBF2, HNF4A, SREBF1, YY1, and KLF13, showing regulation of hepatic expression of genes in the NAFLD-associated modules and validated the TFs using data generated from a mouse NAFLD model. In conclusion, our integrative analysis facilitates the understanding of the regulatory mechanism of these perturbed TFs and their associated biological processes.", "doi": "10.1016/j.isci.2021.103222", "pmid": "34712920", "labels": {"Adil Mardinoglu": "", "SciLifeLab Fellow": "", "DDLS Fellow": "", "Muhammad Arif": ""}, "xrefs": [{"db": "pmc", "key": "PMC8529555"}, {"db": "pii", "key": "S2589-0042(21)01190-1"}], "notes": [], "created": "2023-12-04T15:06:16.728Z", "modified": "2026-09-23T10:26:45.297Z"}, {"entity": "publication", "iuid": "e42414db412d45758a0c40e86bad9d59", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e42414db412d45758a0c40e86bad9d59.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e42414db412d45758a0c40e86bad9d59"}}, "title": "Glucosylceramide synthase deficiency in the heart compromises \u03b21-adrenergic receptor trafficking.", "authors": [{"family": "Andersson", "given": "Linda", "initials": "L"}, {"family": "Cinato", "given": "Mathieu", "initials": "M", "orcid": "0000-0002-8490-4335", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5b2d3790356a446e85061a007b50bb28.json"}}, {"family": "Mardani", "given": "Ismena", "initials": "I"}, {"family": "Miljanovic", "given": "Azra", "initials": "A"}, {"family": "Arif", "given": "Muhammad", "initials": "M", "orcid": "0000-0003-2261-0881", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c8ffc9889ace44e3b992816601b817e2.json"}}, {"family": "Koh", "given": "Ara", "initials": "A", "orcid": "0000-0001-7673-034X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b3dd91ff18d24c8a9d1369bd1c6c28fb.json"}}, {"family": "Lindbom", "given": "Malin", "initials": "M"}, {"family": "Laudette", "given": "Marion", "initials": "M"}, {"family": "Bollano", "given": "Entela", "initials": "E", "orcid": "0000-0003-3341-2434", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/30e6f290d9094fdb9abbc3e053bd3054.json"}}, {"family": "Omerovic", "given": "Elmir", "initials": "E", "orcid": "0000-0002-3875-8621", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/86ecd8364efe43a2911675790963b8e5.json"}}, {"family": "Klevstig", "given": "Martina", "initials": "M"}, {"family": "Henricsson", "given": "Marcus", "initials": "M", "orcid": "0000-0002-4202-0339", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e0fbd663456e4767acbfbe87f79a930b.json"}}, {"family": "Fogelstrand", "given": "Per", "initials": "P"}, {"family": "Sw\u00e4rd", "given": "Karl", "initials": "K"}, {"family": "Ekstrand", "given": "Matias", "initials": "M", "orcid": "0000-0002-0403-9266", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/36c3e3c2978e467097d8e29deb7b2380.json"}}, {"family": "Levin", "given": "Max", "initials": "M", "orcid": "0000-0001-9676-5582", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7743cfcad6784ae9856e88643dd35f5f.json"}}, {"family": "Wikstr\u00f6m", "given": "Johannes", "initials": "J"}, {"family": "Doran", "given": "Stephen", "initials": "S", "orcid": "0000-0002-9236-5407", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/836142c593f64f98a4c5a5ea20663485.json"}}, {"family": "Hy\u00f6tyl\u00e4inen", "given": "Tuulia", "initials": "T", "orcid": "0000-0002-1389-8302", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fc08a199297b42afa85e07adc381a8f4.json"}}, {"family": "Sinisalu", "given": "Lisanna", "initials": "L"}, {"family": "Ore\u0161i\u010d", "given": "Matej", "initials": "M", "orcid": "0000-0002-2856-9165", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d38bde57ca0145cda655fe9967ac8a01.json"}}, {"family": "Tivesten", "given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0002-8318-0486", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3cea6421d33a480581a55f5edd6bc954.json"}}, {"family": "Adiels", "given": "Martin", "initials": "M", "orcid": "0000-0002-3667-589X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b13d83037e4149f09db6f7a47e9a6dd9.json"}}, {"family": "Bergo", "given": "Martin O", "initials": "MO", "orcid": "0000-0002-6915-7140", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bdb71f7c401340bab38ab3606934ef89.json"}}, {"family": "Proia", "given": "Richard", "initials": "R", "orcid": "0000-0003-0456-1270", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2213cec582e84ee1b620bb282c9a216c.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Jeppsson", "given": "Anders", "initials": "A", "orcid": "0000-0003-2356-2295", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b429b50a3e7d4b62b4b48323368f36b0.json"}}, {"family": "Bor\u00e9n", "given": "Jan", "initials": "J"}, {"family": "Levin", "given": "Malin C", "initials": "MC"}], "type": "journal article", "published": "2021-11-14", "journal": {"title": "Eur. Heart J.", "issn": "1522-9645", "volume": "42", "issue": "43", "pages": "4481-4492", "issn-l": "0195-668X"}, "abstract": "Cardiac injury and remodelling are associated with the rearrangement of cardiac lipids. Glycosphingolipids are membrane lipids that are important for cellular structure and function, and cardiac dysfunction is a characteristic of rare monogenic diseases with defects in glycosphingolipid synthesis and turnover. However, it is not known how cardiac glycosphingolipids regulate cellular processes in the heart. The aim of this study is to determine the role of cardiac glycosphingolipids in heart function.\n\nUsing human myocardial biopsies, we showed that the glycosphingolipids glucosylceramide and lactosylceramide are present at very low levels in non-ischaemic human heart with normal function and are elevated during remodelling. Similar results were observed in mouse models of cardiac remodelling. We also generated mice with cardiomyocyte-specific deficiency in Ugcg, the gene encoding glucosylceramide synthase (hUgcg-/- mice). In 9- to 10-week-old hUgcg-/- mice, contractile capacity in response to dobutamine stress was reduced. Older hUgcg-/- mice developed severe heart failure and left ventricular dilatation even under baseline conditions and died prematurely. Using RNA-seq and cell culture models, we showed defective endolysosomal retrograde trafficking and autophagy in Ugcg-deficient cardiomyocytes. We also showed that responsiveness to \u03b2-adrenergic stimulation was reduced in cardiomyocytes from hUgcg-/- mice and that Ugcg knockdown suppressed the internalization and trafficking of \u03b21-adrenergic receptors.\n\nOur findings suggest that cardiac glycosphingolipids are required to maintain \u03b2-adrenergic signalling and contractile capacity in cardiomyocytes and to preserve normal heart function.", "doi": "10.1093/eurheartj/ehab412", "pmid": "34297830", "labels": {"Adil Mardinoglu": "", "SciLifeLab Fellow": "", "DDLS Fellow": "", "Muhammad Arif": ""}, "xrefs": [{"db": "pmc", "key": "PMC8599074"}, {"db": "pii", "key": "6327090"}], "notes": [], "created": "2023-12-04T15:06:27.939Z", "modified": "2026-09-23T10:30:32.557Z"}, {"entity": "publication", "iuid": "fd3b178cf732463ca5ea90e57ca56245", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/fd3b178cf732463ca5ea90e57ca56245.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/fd3b178cf732463ca5ea90e57ca56245"}}, "title": "GutMicroNet: an interactive platform for gut microbiome interaction exploration", "authors": [{"family": "Arif", "given": "Muhammad", "initials": "M", "orcid": "0000-0003-2261-0881", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c8ffc9889ace44e3b992816601b817e2.json"}}, {"family": "Portlock", "given": "Theo", "initials": "T"}, {"family": "G\u00fcng\u00f6r", "given": "Cem", "initials": "C"}, {"family": "Ko\u00e7", "given": "Elif", "initials": "E"}, {"family": "\u00d6zcan", "given": "Berkay", "initials": "B"}, {"family": "Suba\u015f", "given": "O\u011fuzhan", "initials": "O"}, {"family": "\u00c7akmak", "given": "Bu\u011fra", "initials": "B"}, {"family": "Turkez", "given": "Hassan", "initials": "H"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Shoaie", "given": "Saeed", "initials": "S"}], "type": "posted-content", "published": "2021-11-11", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2021.11.10.468051", "pmid": null, "labels": {"SciLifeLab Fellow": "", "Saeed Shoaie": "", "DDLS Fellow": "", "Adil Mardinoglu": "", "Muhammad Arif": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T10:07:29.686Z", "modified": "2026-09-23T14:32:43.903Z"}, {"entity": "publication", "iuid": "1be1bcb2fb5a44e4b1c129f2af52fc32", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1be1bcb2fb5a44e4b1c129f2af52fc32.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1be1bcb2fb5a44e4b1c129f2af52fc32"}}, "title": "Towards a structurally resolved human protein interaction network", "authors": [{"family": "Burke", "given": "David F", "initials": "DF", "orcid": "0000-0001-8830-3951", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0ae9a94abf5e47778d59e4f3c9d8e62e.json"}}, {"family": "Bryant", "given": "Patrick", "initials": "P", "orcid": "0000-0003-3439-1866", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a683bcf98234ff09b2398976583b66f.json"}}, {"family": "Barrio-Hernandez", "given": "Inigo", "initials": "I", "orcid": "0000-0002-5686-0451", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/59ccf621e75c48868e9c215b04dcf787.json"}}, {"family": "Memon", "given": "Danish", "initials": "D", "orcid": "0000-0002-1365-0710", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0f9e1ae20abe4f7f94af1f6856d026bc.json"}}, {"family": "Pozzati", "given": "Gabriele", "initials": "G", "orcid": "0000-0002-4303-9939", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/94129216debe4e22ab3f3b74c33f9ab9.json"}}, {"family": "Shenoy", "given": "Aditi", "initials": "A"}, {"family": "Zhu", "given": "Wensi", "initials": "W"}, {"family": "Dunham", "given": "Alistair S", "initials": "AS", "orcid": "0000-0001-9076-3025", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/41348047cf374b149851ea1b9bca2014.json"}}, {"family": "Albanese", "given": "Pascal", "initials": "P"}, {"family": "Keller", "given": "Andrew", "initials": "A"}, {"family": "Scheltema", "given": "Richard A", "initials": "RA", "orcid": "0000-0002-1668-0253", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/de6c6b9b87574d7eb67d48a73ab5f230.json"}}, {"family": "Bruce", "given": "James E", "initials": "JE"}, {"family": "Leitner", "given": "Alexander", "initials": "A"}, {"family": "Kundrotas", "given": "Petras", "initials": "P", "orcid": "0000-0001-5080-1664", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e645003f2000464c9e289ccd3b92ce68.json"}}, {"family": "Beltrao", "given": "Pedro", "initials": "P", "orcid": "0000-0002-2724-7703", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/952eba119d2e4d4b89e14b294c5c6885.json"}}, {"family": "Elofsson", "given": "Arne", "initials": "A", "orcid": "0000-0002-7115-9751", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/248e70e81bd64f31a5f83e6e329bba95.json"}}], "type": "posted-content", "published": "2021-11-09", "journal": {"title": "bioRxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2021.11.08.467664", "pmid": null, "labels": {"Patrick Bryant": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2026-08-20T10:07:27.911Z", "modified": "2026-10-05T07:25:45.053Z"}, {"entity": "publication", "iuid": "420dba57c6a245ccb45c48fa4865206d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/420dba57c6a245ccb45c48fa4865206d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/420dba57c6a245ccb45c48fa4865206d"}}, "title": "Rapid and sensitive detection of SARS-CoV-2 infection using quantitative peptide enrichment LC-MS analysis.", "authors": [{"family": "Hober", "given": "Andreas", "initials": "A", "orcid": "0000-0001-8947-2562", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/06cbc187628340278395a00ab9dd6c89.json"}}, {"family": "Tran-Minh", "given": "Khue Hua", "initials": "KH"}, {"family": "Foley", "given": "Dominic", "initials": "D"}, {"family": "McDonald", "given": "Thomas", "initials": "T"}, {"family": "Vissers", "given": "Johannes Pc", "initials": "JP"}, {"family": "Pattison", "given": "Rebecca", "initials": "R"}, {"family": "Ferries", "given": "Samantha", "initials": "S"}, {"family": "Hermansson", "given": "Sigurd", "initials": "S"}, {"family": "Betner", "given": "Ingvar", "initials": "I"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Razavi", "given": "Morteza", "initials": "M"}, {"family": "Yip", "given": "Richard", "initials": "R"}, {"family": "Pope", "given": "Matthew E", "initials": "ME"}, {"family": "Pearson", "given": "Terry W", "initials": "TW"}, {"family": "Andersson", "given": "Leigh N", "initials": "LN"}, {"family": "Bartlett", "given": "Amy", "initials": "A"}, {"family": "Calton", "given": "Lisa", "initials": "L"}, {"family": "Alm", "given": "Jessica J", "initials": "JJ"}, {"family": "Engstrand", "given": "Lars", "initials": "L"}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e213b04f8984c8eb00c68f5bc2f6a36.json"}}], "type": "journal article", "published": "2021-11-08", "journal": {"title": "Elife", "issn": "2050-084X", "volume": "10", "issn-l": "2050-084X"}, "abstract": "Reliable, robust, large-scale molecular testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is essential for monitoring the ongoing coronavirus disease 2019 (COVID-19) pandemic. We have developed a scalable analytical approach to detect viral proteins based on peptide immuno-affinity enrichment combined with liquid chromatography-mass spectrometry (LC-MS). This is a multiplexed strategy, based on targeted proteomics analysis and read-out by LC-MS, capable of precisely quantifying and confirming the presence of SARS-CoV-2 in phosphate-buffered saline (PBS) swab media from combined throat/nasopharynx/saliva samples. The results reveal that the levels of SARS-CoV-2 measured by LC-MS correlate well with their correspondingreal-time polymerase chain reaction (RT-PCR) read-out (r = 0.79). The analytical workflow shows similar turnaround times as regular RT-PCR instrumentation with a quantitative read-out of viral proteins corresponding to cycle thresholds (Ct) equivalents ranging from 21 to 34. Using RT-PCR as a reference, we demonstrate that the LC-MS-based method has 100% negative percent agreement (estimated specificity) and 95% positive percent agreement (estimated sensitivity) when analyzing clinical samples collected from asymptomatic individuals with a Ct within the limit of detection of the mass spectrometer (Ct \u2264 30). These results suggest that a scalable analytical method based on LC-MS has a place in future pandemic preparedness centers to complement current virus detection technologies.", "doi": "10.7554/eLife.70843", "pmid": "34747696", "labels": {"Fredrik Edfors": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC8626084"}, {"db": "pii", "key": "70843"}], "notes": [], "created": "2026-08-21T13:07:44.123Z", "modified": "2026-09-23T10:40:08.526Z"}, {"entity": "publication", "iuid": "9900bd886963425bb691338c471bedf9", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9900bd886963425bb691338c471bedf9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9900bd886963425bb691338c471bedf9"}}, "title": "OpenPhi: an interface to access Philips iSyntax whole slide images for computational pathology.", "authors": [{"family": "Mulliqi", "given": "Nita", "initials": "N"}, {"family": "Kartasalo", "given": "Kimmo", "initials": "K", "orcid": "0000-0002-9470-4783", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7c6fc97c06ed456c8bdd1f03db8a9b72.json"}}, {"family": "Olsson", "given": "Henrik", "initials": "H", "orcid": "0000-0002-2270-2017", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/da0547e978264d9c88fc6a222dcbfd5f.json"}}, {"family": "Ji", "given": "Xiaoyi", "initials": "X"}, {"family": "Egevad", "given": "Lars", "initials": "L", "orcid": "0000-0001-8531-222X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a7d46f1f5fc047dc8edb910eb4f0645c.json"}}, {"family": "Eklund", "given": "Martin", "initials": "M", "orcid": "0000-0001-5032-5266", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/06721510ebc8462386e0e6fc6c84315b.json"}}, {"family": "Ruusuvuori", "given": "Pekka", "initials": "P", "orcid": "0000-0001-9086-9591", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb947cd395e84612a53569f4a39abd19.json"}}], "type": "journal article", "published": "2021-11-05", "journal": {"title": "Bioinformatics", "issn": "1367-4811", "issn-l": "1367-4803", "volume": "37", "issue": "21", "pages": "3995-3997"}, "abstract": "Digital pathology enables applying computational methods, such as deep learning, in pathology for improved diagnostics and prognostics, but lack of interoperability between whole slide image formats of different scanner vendors is a challenge for algorithm developers. We present OpenPhi-Open PatHology Interface, an Application Programming Interface for seamless access to the iSyntax format used by the Philips Ultra Fast Scanner, the first digital pathology scanner approved by the United States Food and Drug Administration. OpenPhi is extensible and easily interfaced with existing vendor-neutral applications.\r\n\r\nOpenPhi is implemented in Python and is available as open-source under the MIT license at: https://gitlab.com/BioimageInformaticsGroup/openphi. The Philips Software Development Kit is required and available at: https://www.openpathology.philips.com. OpenPhi version 1.1.1 is additionally provided as Supplementary Data.\r\n\r\nSupplementary data are available at Bioinformatics online.", "doi": "10.1093/bioinformatics/btab578", "pmid": "34358287", "labels": {"Kimmo Kartasalo": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC8570784"}, {"db": "pii", "key": "6343446"}], "notes": [], "created": "2024-11-05T16:08:25.508Z", "modified": "2024-11-29T09:30:27.734Z"}, {"entity": "publication", "iuid": "8eecf0b367a042d3b95a3afcc8abb9aa", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8eecf0b367a042d3b95a3afcc8abb9aa.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8eecf0b367a042d3b95a3afcc8abb9aa"}}, "title": "Vesicle Viewer: Online visualization and analysis of small-angle scattering from lipid vesicles.", "authors": [{"family": "Lewis-Laurent", "given": "Aislyn", "initials": "A"}, {"family": "Doktorova", "given": "Milka", "initials": "M"}, {"family": "Heberle", "given": "Frederick A", "initials": "FA"}, {"family": "Marquardt", "given": "Drew", "initials": "D"}], "type": "journal article", "published": "2021-11-02", "journal": {"title": "Biophys. J.", "issn": "1542-0086", "issn-l": "0006-3495", "volume": "120", "issue": "21", "pages": "4639-4648"}, "abstract": "Small-angle X-ray and neutron scattering are among the most powerful experimental techniques for investigating the structure of biological membranes. Much of the critical information contained in small-angle scattering (SAS) data is not easily accessible to researchers who have limited time to analyze results by hand or to nonexperts who may lack the necessary scientific background to process such data. Easy-to-use data visualization software can allow them to take full advantage of their SAS data and maximize the use of limited resources. To this end, we developed an internet-based application called Vesicle Viewer to visualize and analyze SAS data from unilamellar lipid bilayer vesicles. Vesicle Viewer utilizes a modified scattering density profile (SDP) analysis called EZ-SDP in which key bilayer structural parameters, such as area per lipid and bilayer thickness, are easily and robustly determined. Notably, we introduce a bilayer model that is able to describe an asymmetric bilayer, whether it be chemically or isotopically asymmetric. The application primarily uses Django, a Python package specialized for the development of robust web applications. In addition, several other libraries are used to support the more technical aspects of the project; notable examples are Matplotlib (for graphs) and NumPy (for calculations). By eliminating the barrier of downloading and installing software, this web-based application will allow scientists to analyze their own vesicle scattering data using their preferred operating system. The web-based application can be found at https://vesicleviewer.dmarquardt.ca/.", "doi": "10.1016/j.bpj.2021.09.018", "pmid": "34571013", "labels": {"Milka Doktorova": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC8595566"}, {"db": "pii", "key": "S0006-3495(21)00752-9"}], "notes": [], "created": "2024-11-27T12:19:17.417Z", "modified": "2024-11-29T12:16:05.562Z"}, {"entity": "publication", "iuid": "722ca7e0840a46c3bc167257e2555d3c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/722ca7e0840a46c3bc167257e2555d3c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/722ca7e0840a46c3bc167257e2555d3c"}}, "title": "Improving sampling of crystallographic disorder in ensemble refinement.", "authors": [{"family": "Ploscariu", "given": "Nicoleta", "initials": "N", "orcid": "0000-0002-8317-3630", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/149571dc2cea40a1a6450529046013f6.json"}}, {"family": "Burnley", "given": "Tom", "initials": "T", "orcid": "0000-0001-5307-348X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7e1f3880bab54e8fa989b6f9525d646a.json"}}, {"family": "Gros", "given": "Piet", "initials": "P", "orcid": "0000-0002-7782-2585", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/590881ded1d542b8b61831c00b0fdb87.json"}}, {"family": "Pearce", "given": "Nicholas M", "initials": "NM", "orcid": "0000-0002-6693-8603", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/07d6d5de91cc4120b2bf996ca578a13e.json"}}], "type": "journal article", "published": "2021-11-01", "journal": {"title": "Acta Crystallogr D Struct Biol", "issn": "2059-7983", "volume": "77", "issue": "Pt 11", "pages": "1357-1364", "issn-l": "2059-7983"}, "abstract": "Ensemble refinement, the application of molecular dynamics to crystallographic refinement, explicitly models the disorder inherent in macromolecular structures. These ensemble models have been shown to produce more accurate structures than traditional single-model structures. However, suboptimal sampling of the molecular-dynamics simulation and modelling of crystallographic disorder has limited the utility of the method, and can lead to unphysical and strained models. Here, two improvements to the ensemble refinement method implemented within Phenix are presented: DEN restraints, which guide the local sampling of conformations and allow a more robust exploration of local conformational landscapes, and ECHT disorder models, which allow the selection of more physically meaningful and effective disorder models for parameterizing the continuous disorder components within a crystal. These improvements lead to more consistent and physically interpretable simulations of macromolecules in crystals, and allow structural heterogeneity and disorder to be systematically explored on different scales. The new approach is demonstrated on several case studies and the SARS-CoV-2 main protease, and demonstrates how the choice of disorder model affects the type of disorder that is sampled by the restrained molecular-dynamics simulation.", "doi": "10.1107/S2059798321010044", "pmid": "34726164", "labels": {"Nicholas Pearce": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC8561732"}, {"db": "pii", "key": "S2059798321010044"}], "notes": [], "created": "2022-12-05T19:30:50.961Z", "modified": "2022-12-05T19:30:51.040Z"}, {"entity": "publication", "iuid": "920bb620b87743b99e1024ce1c6dc6f7", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/920bb620b87743b99e1024ce1c6dc6f7.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/920bb620b87743b99e1024ce1c6dc6f7"}}, "title": "Distinction of lymphoid and myeloid clonal hematopoiesis.", "authors": [{"family": "Niroula", "given": "Abhishek", "initials": "A", "orcid": "0000-0002-5904-0635", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/05df7afc7a494ba5af8a378e5ffa53f0.json"}}, {"family": "Sekar", "given": "Aswin", "initials": "A"}, {"family": "Murakami", "given": "Mark A", "initials": "MA"}, {"family": "Trinder", "given": "Mark", "initials": "M"}, {"family": "Agrawal", "given": "Mridul", "initials": "M"}, {"family": "Wong", "given": "Waihay J", "initials": "WJ"}, {"family": "Bick", "given": "Alexander G", "initials": "AG"}, {"family": "Uddin", "given": "Md Mesbah", "initials": "MM", "orcid": "0000-0003-1846-0411", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/42f1ac7010c34ba997a3fd9e56c6a56a.json"}}, {"family": "Gibson", "given": "Christopher J", "initials": "CJ", "orcid": "0000-0002-3700-5310", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/71ce9f64755e483496f8c28a76a2a1ff.json"}}, {"family": "Griffin", "given": "Gabriel K", "initials": "GK"}, {"family": "Honigberg", "given": "Michael C", "initials": "MC", "orcid": "0000-0001-8630-5021", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c541cd0864c947a6bafa7ad6e78bfe49.json"}}, {"family": "Zekavat", "given": "Seyedeh M", "initials": "SM"}, {"family": "Paruchuri", "given": "Kaavya", "initials": "K"}, {"family": "Natarajan", "given": "Pradeep", "initials": "P", "orcid": "0000-0001-8402-7435", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fe8bd48c61c047cd8e61c35d9e9ac650.json"}}, {"family": "Ebert", "given": "Benjamin L", "initials": "BL", "orcid": "0000-0003-0197-5451", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56e4f1c53a4348e2b0ceb44a38850a17.json"}}], "type": "journal article", "published": "2021-11-00", "journal": {"title": "Nat. Med.", "issn": "1546-170X", "volume": "27", "issue": "11", "pages": "1921-1927", "issn-l": "1078-8956"}, "abstract": "Clonal hematopoiesis (CH) results from somatic genomic alterations that drive clonal expansion of blood cells. Somatic gene mutations associated with hematologic malignancies detected in hematopoietic cells of healthy individuals, referred to as CH of indeterminate potential (CHIP), have been associated with myeloid malignancies, while mosaic chromosomal alterations (mCAs) have been associated with lymphoid malignancies. Here, we analyzed CHIP in 55,383 individuals and autosomal mCAs in 420,969 individuals with no history of hematologic malignancies in the UK Biobank and Mass General Brigham Biobank. We distinguished myeloid and lymphoid somatic gene mutations, as well as myeloid and lymphoid mCAs, and found both to be associated with risk of lineage-specific hematologic malignancies. Further, we performed an integrated analysis of somatic alterations with peripheral blood count parameters to stratify the risk of incident myeloid and lymphoid malignancies. These genetic alterations can be readily detected in clinical sequencing panels and used with blood count parameters to identify individuals at high risk of developing hematologic malignancies.", "doi": "10.1038/s41591-021-01521-4", "pmid": "34663986", "labels": {"Abhishek Niroula": null, "DDLS Fellow": null}, "xrefs": [{"db": "mid", "key": "NIHMS1756847"}, {"db": "pmc", "key": "PMC8621497"}, {"db": "pii", "key": "10.1038/s41591-021-01521-4"}], "notes": [], "created": "2023-11-20T11:28:00.594Z", "modified": "2023-11-20T11:28:00.793Z"}, {"entity": "publication", "iuid": "352420bc195b49d3ac07aaeaf338d5f7", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/352420bc195b49d3ac07aaeaf338d5f7.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/352420bc195b49d3ac07aaeaf338d5f7"}}, "title": "Revealing the Molecular Mechanisms of Alzheimer's Disease Based on Network Analysis.", "authors": [{"family": "Bayraktar", "given": "Abdulahad", "initials": "A", "orcid": "0000-0001-5287-5026", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ae17b201286c4b608cfc54649fe5d1c0.json"}}, {"family": "Lam", "given": "Simon", "initials": "S", "orcid": "0000-0002-4476-0971", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bdf5adecfed749b4a66cdda5cd08ee24.json"}}, {"family": "Altay", "given": "Ozlem", "initials": "O"}, {"family": "Li", "given": "Xiangyu", "initials": "X", "orcid": "0000-0002-8301-9959", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5c452ad4e8bb4302a572693103742047.json"}}, {"family": "Yuan", "given": "Meng", "initials": "M"}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f46e4161be08458994efddb75ed75874.json"}}, {"family": "Arif", "given": "Muhammad", "initials": "M", "orcid": "0000-0003-2261-0881", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c8ffc9889ace44e3b992816601b817e2.json"}}, {"family": "Turkez", "given": "Hasan", "initials": "H", "orcid": "0000-0002-7046-8990", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cf2f1748757d45cabfe56fdfaccead6a.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Shoaie", "given": "Saeed", "initials": "S"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca58bf2d214047e0ae5e38a42a0f2808.json"}}], "type": "journal article", "published": "2021-10-26", "journal": {"title": "Int J Mol Sci", "issn": "1422-0067", "issn-l": null, "volume": "22", "issue": "21", "pages": "11556"}, "abstract": "The complex pathology of Alzheimer's disease (AD) emphasises the need for comprehensive modelling of the disease, which may lead to the development of efficient treatment strategies. To address this challenge, we analysed transcriptome data of post-mortem human brain samples of healthy elders and individuals with late-onset AD from the Religious Orders Study and Rush Memory and Aging Project (ROSMAP) and Mayo Clinic (MayoRNAseq) studies in the AMP-AD consortium. In this context, we conducted several bioinformatics and systems medicine analyses including the construction of AD-specific co-expression networks and genome-scale metabolic modelling of the brain in AD patients to identify key genes, metabolites and pathways involved in the progression of AD. We identified AMIGO1 and GRPRASP2 as examples of commonly altered marker genes in AD patients. Moreover, we found alterations in energy metabolism, represented by reduced oxidative phosphorylation and ATPase activity, as well as the depletion of hexanoyl-CoA, pentanoyl-CoA, (2E)-hexenoyl-CoA and numerous other unsaturated fatty acids in the brain. We also observed that neuroprotective metabolites (e.g., vitamins, retinoids and unsaturated fatty acids) tend to be depleted in the AD brain, while neurotoxic metabolites (e.g., \u03b2-alanine, bilirubin) were more abundant. In summary, we systematically revealed the key genes and pathways related to the progression of AD, gained insight into the crucial mechanisms of AD and identified some possible targets that could be used in the treatment of AD.", "doi": "10.3390/ijms222111556", "pmid": "34768988", "labels": {"Saeed Shoaie": "", "SciLifeLab Fellow": "", "Adil Mardinoglu": "", "DDLS Fellow": "", "Muhammad Arif": ""}, "xrefs": [{"db": "pmc", "key": "PMC8584243"}, {"db": "pii", "key": "ijms222111556"}], "notes": [], "created": "2021-12-13T15:30:22.884Z", "modified": "2026-09-23T10:30:45.169Z"}, {"entity": "publication", "iuid": "5302fe686113479cbe34837a615e82bc", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5302fe686113479cbe34837a615e82bc.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5302fe686113479cbe34837a615e82bc"}}, "title": "Virtual reality for 3D histology: multi-scale visualization of organs with interactive feature exploration.", "authors": [{"family": "Liimatainen", "given": "Kaisa", "initials": "K"}, {"family": "Latonen", "given": "Leena", "initials": "L"}, {"family": "Valkonen", "given": "Masi", "initials": "M"}, {"family": "Kartasalo", "given": "Kimmo", "initials": "K"}, {"family": "Ruusuvuori", "given": "Pekka", "initials": "P", "orcid": "0000-0001-9086-9591", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb947cd395e84612a53569f4a39abd19.json"}}], "type": "journal article", "published": "2021-10-22", "journal": {"title": "BMC Cancer", "issn": "1471-2407", "issn-l": "1471-2407", "volume": "21", "issue": "1", "pages": "1133"}, "abstract": "Virtual reality (VR) enables data visualization in an immersive and engaging manner, and it can be used for creating ways to explore scientific data. Here, we use VR for visualization of 3D histology data, creating a novel interface for digital pathology to aid cancer research.\r\n\r\nOur contribution includes 3D modeling of a whole organ and embedded objects of interest, fusing the models with associated quantitative features and full resolution serial section patches, and implementing the virtual reality application. Our VR application is multi-scale in nature, covering two object levels representing different ranges of detail, namely organ level and sub-organ level. In addition, the application includes several data layers, including the measured histology image layer and multiple representations of quantitative features computed from the histology.\r\n\r\nIn our interactive VR application, the user can set visualization properties, select different samples and features, and interact with various objects, which is not possible in the traditional 2D-image view used in digital pathology. In this work, we used whole mouse prostates (organ level) with prostate cancer tumors (sub-organ objects of interest) as example cases, and included quantitative histological features relevant for tumor biology in the VR model.\r\n\r\nOur application enables a novel way for exploration of high-resolution, multidimensional data for biomedical research purposes, and can also be used in teaching and researcher training. Due to automated processing of the histology data, our application can be easily adopted to visualize other organs and pathologies from various origins.", "doi": "10.1186/s12885-021-08542-9", "pmid": "34686173", "labels": {"Kimmo Kartasalo": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC8539837"}, {"db": "pii", "key": "10.1186/s12885-021-08542-9"}], "notes": [], "created": "2024-11-05T16:09:29.649Z", "modified": "2024-11-29T10:44:47.277Z"}, {"entity": "publication", "iuid": "7a0463d90eb0444f906edecfad697ddd", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/7a0463d90eb0444f906edecfad697ddd.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/7a0463d90eb0444f906edecfad697ddd"}}, "title": "Author response: Rapid and sensitive detection of SARS-CoV-2 infection using quantitative peptide enrichment LC-MS analysis", "authors": [{"family": "Hober", "given": "Andreas", "initials": "A", "orcid": "0000-0001-8947-2562", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/06cbc187628340278395a00ab9dd6c89.json"}}, {"family": "Tran-Minh", "given": "Khue Hua", "initials": "KH"}, {"family": "Foley", "given": "Dominic", "initials": "D"}, {"family": "McDonald", "given": "Thomas", "initials": "T"}, {"family": "Vissers", "given": "Johannes PC", "initials": "JP"}, {"family": "Pattison", "given": "Rebecca", "initials": "R"}, {"family": "Ferries", "given": "Samantha", "initials": "S"}, {"family": "Hermansson", "given": "Sigurd", "initials": "S"}, {"family": "Betner", "given": "Ingvar", "initials": "I"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Razavi", "given": "Morteza", "initials": "M"}, {"family": "Yip", "given": "Richard", "initials": "R"}, {"family": "Pope", "given": "Matthew E", "initials": "ME"}, {"family": "Pearson", "given": "Terry W", "initials": "TW"}, {"family": "Andersson", "given": "Leigh N", "initials": "LN"}, {"family": "Bartlett", "given": "Amy", "initials": "A"}, {"family": "Calton", "given": "Lisa", "initials": "L"}, {"family": "Alm", "given": "Jessica J", "initials": "JJ"}, {"family": "Engstrand", "given": "Lars", "initials": "L"}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e213b04f8984c8eb00c68f5bc2f6a36.json"}}], "type": "peer-review", "published": "2021-10-19", "journal": {"issn-l": null}, "abstract": null, "doi": "10.7554/elife.70843.sa2", "pmid": null, "labels": {"Fredrik Edfors": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T13:53:59.135Z", "modified": "2026-09-23T15:10:17.431Z"}, {"entity": "publication", "iuid": "ff8b9bf52fc2404dbe8b5d03df791f30", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ff8b9bf52fc2404dbe8b5d03df791f30.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ff8b9bf52fc2404dbe8b5d03df791f30"}}, "title": "Monitoring the Microevolution of Salmonella enterica in Healthy Dairy Cattle Populations at the Individual Farm Level Using Whole-Genome Sequencing.", "authors": [{"family": "Carroll", "given": "Laura M", "initials": "LM"}, {"family": "Buehler", "given": "Ariel J", "initials": "AJ"}, {"family": "Gaballa", "given": "Ahmed", "initials": "A"}, {"family": "Siler", "given": "Julie D", "initials": "JD"}, {"family": "Cummings", "given": "Kevin J", "initials": "KJ"}, {"family": "Cheng", "given": "Rachel A", "initials": "RA"}, {"family": "Wiedmann", "given": "Martin", "initials": "M"}], "type": "journal article", "published": "2021-10-18", "journal": {"title": "Front Microbiol", "issn": "1664-302X", "volume": "12", "pages": "763669", "issn-l": "1664-302X"}, "abstract": "Livestock represent a possible reservoir for facilitating the transmission of the zoonotic foodborne pathogen Salmonella enterica to humans; there is also concern that strains can acquire resistance to antimicrobials in the farm environment. Here, whole-genome sequencing (WGS) was used to characterize Salmonella strains (n = 128) isolated from healthy dairy cattle and their associated environments on 13 New York State farms to assess the diversity and microevolution of this important pathogen at the level of the individual herd. Additionally, the accuracy and concordance of multiple in silico tools are assessed, including: (i) two in silico serotyping tools, (ii) combinations of five antimicrobial resistance (AMR) determinant detection tools and one to five AMR determinant databases, and (iii) one antimicrobial minimum inhibitory concentration (MIC) prediction tool. For the isolates sequenced here, in silico serotyping methods outperformed traditional serotyping and resolved all un-typable and/or ambiguous serotype assignments. Serotypes assigned in silico showed greater congruency with the Salmonella whole-genome phylogeny than traditional serotype assignments, and in silico methods showed high concordance (99% agreement). In silico AMR determinant detection methods additionally showed a high degree of concordance, regardless of the pipeline or database used (\u226598% agreement among susceptible/resistant assignments for all pipeline/database combinations). For AMR detection methods that relied exclusively on nucleotide BLAST, accuracy could be maximized by using a range of minimum nucleotide identity and coverage thresholds, with thresholds of 75% nucleotide identity and 50-60% coverage adequate for most pipeline/database combinations. In silico characterization of the microevolution and AMR dynamics of each of six serotype groups (S. Anatum, Cerro, Kentucky, Meleagridis, Newport, Typhimurium/Typhimurium variant Copenhagen) revealed that some lineages were strongly associated with individual farms, while others were distributed across multiple farms. Numerous AMR determinant acquisition and loss events were identified, including the recent acquisition of cephalosporin resistance-conferring bla CMY- and bla CTX-M-type beta-lactamases. The results presented here provide high-resolution insight into the temporal dynamics of AMR Salmonella at the scale of the individual farm and highlight both the strengths and limitations of WGS in tracking zoonotic pathogens and their associated AMR determinants at the livestock-human interface.", "doi": "10.3389/fmicb.2021.763669", "pmid": "34733267", "labels": {"DDLS Fellow": null, "Laura Carroll": null}, "xrefs": [{"db": "pmc", "key": "PMC8558520"}], "notes": [], "created": "2023-05-13T11:52:43.527Z", "modified": "2025-03-18T17:28:36.750Z"}, {"entity": "publication", "iuid": "204a710ec66d401d8f64c2559f2bbffd", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/204a710ec66d401d8f64c2559f2bbffd.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/204a710ec66d401d8f64c2559f2bbffd"}}, "title": "Recent Evolution and Genomic Profile of Salmonella enterica Serovar Heidelberg Isolates from Poultry Flocks in Brazil.", "authors": [{"family": "Kipper", "given": "Di\u00e9ssy", "initials": "D"}, {"family": "Orsi", "given": "Renato H", "initials": "RH", "orcid": "0000-0003-4933-9817", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/faa4bd30679547898c7bd57690ba18bf.json"}}, {"family": "Carroll", "given": "Laura M", "initials": "LM"}, {"family": "Mascitti", "given": "Andrea K", "initials": "AK"}, {"family": "Streck", "given": "Andr\u00e9 F", "initials": "AF", "orcid": "0000-0002-4798-0777", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7e3f45fa7b4a4937bdd166ef667549e0.json"}}, {"family": "Fonseca", "given": "Andr\u00e9 S K", "initials": "ASK"}, {"family": "Ikuta", "given": "Nilo", "initials": "N"}, {"family": "Tondo", "given": "Eduardo C", "initials": "EC"}, {"family": "Wiedmann", "given": "Martin", "initials": "M", "orcid": "0000-0002-4168-5662", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ff5ceeea60684abeb83951c53f7b6e31.json"}}, {"family": "Lunge", "given": "Vagner R", "initials": "VR", "orcid": "0000-0003-4012-8650", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/33c4324875e6436d9cb3433bf215a1bb.json"}}], "type": "journal article", "published": "2021-10-14", "journal": {"title": "Applied and environmental microbiology", "issn": "1098-5336", "volume": "87", "issue": "21", "pages": "e0103621", "issn-l": "0099-2240"}, "abstract": "Salmonella enterica serovar Heidelberg is isolated from poultry-producing regions around the world. In Brazil, S. Heidelberg has been frequently detected in poultry flocks, slaughterhouses, and chicken meat. The goal of the present study was to assess the population structure, recent temporal evolution, and some important genetic characteristics of S. Heidelberg isolated from Brazilian poultry farms. Phylogenetic analysis of 68 S. Heidelberg genomes sequenced here and additional whole-genome data from NCBI demonstrated that all isolates from the Brazilian poultry production chain clustered into a monophyletic group, here called S. Heidelberg Brazilian poultry lineage (SH-BPL). Bayesian analysis defined the time of the most recent common ancestor (tMRCA) as 2004, and the overall population size (N) was constant until 2008, when an \u223c10-fold eN increase was observed until circa 2013. SH-BPL presented at least two plasmids with replicons ColpVC (en = 68; 100%), IncX1 (n = 66; 97%), IncA/C2 (n = 65; 95.5%), ColRNAI (n = 43; 63.2%), IncI1 (n = 32; 47%), ColMG828, Col156, IncHI2A, IncHI2, IncQ1, IncX4, IncY, and TrfA (each with n < 4; <4% each). Antibiotic resistance genes were found, with high frequencies of fosA7 (n = 68; 100%), mdf(A) (n = 68; 100%), tet(34) (n = 68; 100%), sul2 (n = 64; 94.1%), and blaCMY-2 (n = 56; 82.3%), along with an overall multidrug resistance (MDR) profile. Ten Salmonella pathogenicity islands (SPI1 to SPI5, SPI9, and SPI11 to SPI14) and 139 virulence genes were also detected. The SH-BPL profile was like those of other previous S. Heidelberg isolates from poultry around the world in the 1990s. In conclusion, the present study demonstrates the recent introduction (2004) and high level of dissemination of an MDR S. Heidelberg lineage in Brazilian poultry operations. IMPORTANCES. Heidelberg is the most frequent serovar in several broiler farms from the main Brazilian poultry-producing regions. Therefore, avian-source foods (mainly chicken carcasses) commercialized in the country and exported to other continents are contaminated with this foodborne pathogen, generating several national and international economic losses. In addition, isolates of this serovar are usually resistant to antibiotics and can cause human invasive and septicemic infection, representing a public health concern. This study demonstrates the use of whole-genome sequencing (WGS) to obtain epidemiological information for one S. Heidelberg lineage highly spread among Brazilian poultry farms. This information will help to define biosecurity measures to control this important Salmonella serovar in Brazilian and worldwide poultry operations.", "doi": "10.1128/AEM.01036-21", "pmid": "34406824", "labels": {"Laura Carroll": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC8516049"}], "notes": [], "created": "2025-03-18T17:27:36.310Z", "modified": "2025-03-18T17:27:36.482Z"}, {"entity": "publication", "iuid": "56f45fa5198d473ba1c5f8678fa0ce6e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/56f45fa5198d473ba1c5f8678fa0ce6e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/56f45fa5198d473ba1c5f8678fa0ce6e"}}, "title": "Population genomics of the critically endangered k\u0101k\u0101p\u014d.", "authors": [{"family": "Dussex", "given": "Nicolas", "initials": "N"}, {"family": "van der Valk", "given": "Tom", "initials": "T"}, {"family": "Morales", "given": "Hern\u00e1n E", "initials": "HE"}, {"family": "Wheat", "given": "Christopher W", "initials": "CW"}, {"family": "D\u00edez-Del-Molino", "given": "David", "initials": "D"}, {"family": "von Seth", "given": "Johanna", "initials": "J"}, {"family": "Foster", "given": "Yasmin", "initials": "Y"}, {"family": "Kutschera", "given": "Verena E", "initials": "VE"}, {"family": "Guschanski", "given": "Katerina", "initials": "K"}, {"family": "Rhie", "given": "Arang", "initials": "A"}, {"family": "Phillippy", "given": "Adam M", "initials": "AM"}, {"family": "Korlach", "given": "Jonas", "initials": "J"}, {"family": "Howe", "given": "Kerstin", "initials": "K"}, {"family": "Chow", "given": "William", "initials": "W"}, {"family": "Pelan", "given": "Sarah", "initials": "S"}, {"family": "Mendes Damas", "given": "Joanna D", "initials": "JD"}, {"family": "Lewin", "given": "Harris A", "initials": "HA"}, {"family": "Hastie", "given": "Alex R", "initials": "AR"}, {"family": "Formenti", "given": "Giulio", "initials": "G"}, {"family": "Fedrigo", "given": "Olivier", "initials": "O"}, {"family": "Guhlin", "given": "Joseph", "initials": "J"}, {"family": "Harrop", "given": "Thomas W R", "initials": "TWR"}, {"family": "Le Lec", "given": "Marissa F", "initials": "MF"}, {"family": "Dearden", "given": "Peter K", "initials": "PK"}, {"family": "Haggerty", "given": "Leanne", "initials": "L"}, {"family": "Martin", "given": "Fergal J", "initials": "FJ"}, {"family": "Kodali", "given": "Vamsi", "initials": "V"}, {"family": "Thibaud-Nissen", "given": "Fran\u00e7oise", "initials": "F"}, {"family": "Iorns", "given": "David", "initials": "D"}, {"family": "Knapp", "given": "Michael", "initials": "M"}, {"family": "Gemmell", "given": "Neil J", "initials": "NJ"}, {"family": "Robertson", "given": "Fiona", "initials": "F"}, {"family": "Moorhouse", "given": "Ron", "initials": "R"}, {"family": "Digby", "given": "Andrew", "initials": "A"}, {"family": "Eason", "given": "Daryl", "initials": "D"}, {"family": "Vercoe", "given": "Deidre", "initials": "D"}, {"family": "Howard", "given": "Jason", "initials": "J"}, {"family": "Jarvis", "given": "Erich D", "initials": "ED"}, {"family": "Robertson", "given": "Bruce C", "initials": "BC"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L"}], "type": "journal article", "published": "2021-10-13", "journal": {"title": "Cell Genom", "issn": "2666-979X", "volume": "1", "issue": "1", "pages": "100002", "issn-l": null}, "abstract": "The k\u0101k\u0101p\u014d is a flightless parrot endemic to New Zealand. Once common in the archipelago, only 201 individuals remain today, most of them descending from an isolated island population. We report the first genome-wide analyses of the species, including a high-quality genome assembly for k\u0101k\u0101p\u014d, one of the first chromosome-level reference genomes sequenced by the Vertebrate Genomes Project (VGP). We also sequenced and analyzed 35 modern genomes from the sole surviving island population and 14 genomes from the extinct mainland population. While theory suggests that such a small population is likely to have accumulated deleterious mutations through genetic drift, our analyses on the impact of the long-term small population size in k\u0101k\u0101p\u014d indicate that present-day island k\u0101k\u0101p\u014d have a reduced number of harmful mutations compared to mainland individuals. We hypothesize that this reduced mutational load is due to the island population having been subjected to a combination of genetic drift and purging of deleterious mutations, through increased inbreeding and purifying selection, since its isolation from the mainland \u223c10,000 years ago. Our results provide evidence that small populations can survive even when isolated for hundreds of generations. This work provides key insights into k\u0101k\u0101p\u014d breeding and recovery and more generally into the application of genetic tools in conservation efforts for endangered species.", "doi": "10.1016/j.xgen.2021.100002", "pmid": "36777713", "labels": {"DDLS Fellow": "", "Tom van der Valk": ""}, "xrefs": [{"db": "pmc", "key": "PMC9903828"}, {"db": "pii", "key": "S2666-979X(21)00002-1"}], "notes": [], "created": "2026-09-23T06:41:41.058Z", "modified": "2026-09-23T06:41:41.072Z"}, {"entity": "publication", "iuid": "fdf379ddc1c042a7826463d0f9c66759", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/fdf379ddc1c042a7826463d0f9c66759.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/fdf379ddc1c042a7826463d0f9c66759"}}, "title": "Characterization of Basal Transcriptomes Identifies Potential Metabolic and Virulence-Associated Adaptations Among Diverse Nontyphoidal Salmonella enterica Serovars.", "authors": [{"family": "Cohn", "given": "Alexa R", "initials": "AR"}, {"family": "Orsi", "given": "Renato H", "initials": "RH"}, {"family": "Carroll", "given": "Laura M", "initials": "LM"}, {"family": "Chen", "given": "Ruixi", "initials": "R"}, {"family": "Wiedmann", "given": "Martin", "initials": "M"}, {"family": "Cheng", "given": "Rachel A", "initials": "RA"}], "type": "journal article", "published": "2021-10-13", "journal": {"title": "Front Microbiol", "issn": "1664-302X", "volume": "12", "pages": "730411", "issn-l": "1664-302X"}, "abstract": "The zoonotic pathogen Salmonella enterica includes >2,600 serovars, which differ in the range of hosts they infect and the severity of disease they cause. To further elucidate the mechanisms behind these differences, we performed transcriptomic comparisons of nontyphoidal Salmonella (NTS) serovars with the model for NTS pathogenesis, S. Typhimurium. Specifically, we used RNA-seq to characterize the understudied NTS serovars S. Javiana and S. Cerro, representing a serovar frequently attributed to human infection via contact with amphibians and reptiles, and a serovar primarily associated with cattle, respectively. Whole-genome sequence (WGS) data were utilized to ensure that strains characterized with RNA-seq were representative of their respective serovars. RNA extracted from representative strains of each serovar grown to late exponential phase in Luria-Bertani (LB) broth showed that transcript abundances of core genes were significantly higher (p<0.001) than those of accessory genes for all three serovars. Inter-serovar comparisons identified that transcript abundances of genes in Salmonella Pathogenicity Island (SPI) 1 were significantly higher in both S. Javiana and S. Typhimurium compared to S. Cerro. Together, our data highlight potential transcriptional mechanisms that may facilitate S. Cerro and S. Javiana survival in and adaptation to their respective hosts and impact their ability to cause disease in others. Furthermore, our analyses demonstrate the utility of omics approaches in advancing our understanding of the diversity of metabolic and virulence mechanisms of different NTS serovars.", "doi": "10.3389/fmicb.2021.730411", "pmid": "34721328", "labels": {"DDLS Fellow": null, "Laura Carroll": null}, "xrefs": [{"db": "pmc", "key": "PMC8552914"}], "notes": [], "created": "2023-05-13T11:52:50.811Z", "modified": "2025-03-18T17:27:50.251Z"}, {"entity": "publication", "iuid": "5c2c2b7323134df9a9c39805b565908a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5c2c2b7323134df9a9c39805b565908a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5c2c2b7323134df9a9c39805b565908a"}}, "title": "Genomic Characterization of Endemic and Ecdemic Non-typhoidal Salmonella enterica Lineages Circulating Among Animals and Animal Products in South Africa.", "authors": [{"family": "Carroll", "given": "Laura M", "initials": "LM"}, {"family": "Pierneef", "given": "Rian", "initials": "R"}, {"family": "Mathole", "given": "Masenyabu", "initials": "M"}, {"family": "Matle", "given": "Itumeleng", "initials": "I"}], "type": "journal article", "published": "2021-10-04", "journal": {"title": "Front Microbiol", "issn": "1664-302X", "volume": "12", "pages": "748611", "issn-l": "1664-302X"}, "abstract": "In Africa, the burden of illness caused by non-typhoidal Salmonella enterica is disproportionally high; however, whole-genome sequencing (WGS) efforts are overwhelmingly concentrated in world regions with lower burdens. While WGS is being increasingly employed in South Africa to characterize Salmonella enterica, the bulk of these efforts have centered on characterizing human clinical strains. Thus, very little is known about lineages circulating among animals in the country on a genomic scale. Here, we used WGS to characterize 63 Salmonella enterica strains isolated from livestock, companion animals, wildlife, and animal products in South Africa over a 60-year period. Genomes were assigned to serotypes Dublin, Hadar, Enteritidis, and Typhimurium (n = 18, 8, 13, and 24 strains, respectively) and sequence types (STs) ST10 (all S. Dublin), ST33 (all S. Hadar), ST11/ST366 (n = 12 and 1 S. Enteritidis, respectively), and ST19/ST34 (n = 23 and 1 S. Typhimurium, respectively; via seven-gene multi-locus sequence typing). Within-ST phylogenies were constructed using genomes sequenced in this study, plus publicly available genomes representative of each ST's (i) global (n = 2,802 and 1,569 S. Dublin and Hadar genomes, respectively) and (ii) African (n = 716 and 343 S. Enteritidis and Typhimurium genomes, respectively) population. For S. Dublin ST10, a largely antimicrobial-susceptible, endemic lineage circulating among humans, animals, and food in South Africa was identified, as well as a lineage that was likely recently introduced from the United States. For S. Hadar ST33, multiple South African lineages harboring streptomycin and tetracycline resistance-conferring genes were identified. African S. Enteritidis ST11 could be primarily partitioned into one largely antimicrobial-susceptible and one largely multidrug-resistant (MDR) clade, with South African isolates confined to the largely antimicrobial-susceptible clade. S. Typhimurium ST19/ST34 strains sequenced here were distributed across the African S. Typhimurium ST19/ST34 phylogeny, representing a diverse range of lineages, including numerous MDR lineages. Overall, this study provides critical insights into endemic and ecdemic non-typhoidal Salmonella enterica lineages circulating among animals, foods, and humans in South Africa and showcases the utility of WGS in characterizing animal-associated strains from a world region with a high salmonellosis burden.", "doi": "10.3389/fmicb.2021.748611", "pmid": "34671335", "labels": {"DDLS Fellow": null, "Laura Carroll": null}, "xrefs": [{"db": "pmc", "key": "PMC8521152"}], "notes": [], "created": "2023-05-13T11:52:45.995Z", "modified": "2025-03-18T17:28:20.004Z"}, {"entity": "publication", "iuid": "15b43437cf7f4c9088cb8c614a832f0a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/15b43437cf7f4c9088cb8c614a832f0a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/15b43437cf7f4c9088cb8c614a832f0a"}}, "title": "Predicting Molecular Phenotypes from Histopathology Images: A Transcriptome-Wide Expression-Morphology Analysis in Breast Cancer.", "authors": [{"family": "Wang", "given": "Yinxi", "initials": "Y", "orcid": "0000-0002-1651-7763", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cb79b8566b0e4eefba67e9c8d8cc3808.json"}}, {"family": "Kartasalo", "given": "Kimmo", "initials": "K", "orcid": "0000-0002-9470-4783", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7c6fc97c06ed456c8bdd1f03db8a9b72.json"}}, {"family": "Weitz", "given": "Philippe", "initials": "P", "orcid": "0000-0002-1788-0716", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a70939bc05a04f87b9a61e7d98448e09.json"}}, {"family": "\u00c1cs", "given": "Bal\u00e1zs", "initials": "B", "orcid": "0000-0002-0972-4633", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9d642b1db48643f497be9a35a71dadde.json"}}, {"family": "Valkonen", "given": "Masi", "initials": "M", "orcid": "0000-0003-3091-2484", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ae4841e8a4124dc79c921b3af09096fe.json"}}, {"family": "Larsson", "given": "Christer", "initials": "C"}, {"family": "Ruusuvuori", "given": "Pekka", "initials": "P", "orcid": "0000-0001-9086-9591", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb947cd395e84612a53569f4a39abd19.json"}}, {"family": "Hartman", "given": "Johan", "initials": "J", "orcid": "0000-0002-6500-8527", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d62d622200d443b7b5be34ff3c0945be.json"}}, {"family": "Rantalainen", "given": "Mattias", "initials": "M"}], "type": "journal article", "published": "2021-10-01", "journal": {"title": "Cancer Res.", "issn": "1538-7445", "issn-l": "0008-5472", "volume": "81", "issue": "19", "pages": "5115-5126"}, "abstract": "Molecular profiling is central in cancer precision medicine but remains costly and is based on tumor average profiles. Morphologic patterns observable in histopathology sections from tumors are determined by the underlying molecular phenotype and therefore have the potential to be exploited for prediction of molecular phenotypes. We report here the first transcriptome-wide expression-morphology (EMO) analysis in breast cancer, where individual deep convolutional neural networks were optimized and validated for prediction of mRNA expression in 17,695 genes from hematoxylin and eosin-stained whole slide images. Predicted expressions in 9,334 (52.75%) genes were significantly associated with RNA sequencing estimates. We also demonstrated successful prediction of an mRNA-based proliferation score with established clinical value. The results were validated in independent internal and external test datasets. Predicted spatial intratumor variabilities in expression were validated through spatial transcriptomics profiling. These results suggest that EMO provides a cost-efficient and scalable approach to predict both tumor average and intratumor spatial expression from histopathology images. SIGNIFICANCE: Transcriptome-wide expression morphology deep learning analysis enables prediction of mRNA expression and proliferation markers from routine histopathology whole slide images in breast cancer.", "doi": "10.1158/0008-5472.CAN-21-0482", "pmid": "34341074", "labels": {"Kimmo Kartasalo": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC9397635"}, {"db": "pii", "key": "0008-5472.CAN-21-0482"}], "notes": [], "created": "2024-11-05T16:08:24.047Z", "modified": "2024-11-29T09:30:42.787Z"}, {"entity": "publication", "iuid": "284bfa4f6ed34e1cb0fff9134bd8f51a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/284bfa4f6ed34e1cb0fff9134bd8f51a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/284bfa4f6ed34e1cb0fff9134bd8f51a"}}, "title": "Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 9: Polymyxins: colistin.", "authors": [{"family": "EFSA Panel on Biological Hazards (BIOHAZ)", "given": "", "initials": ""}, {"family": "Koutsoumanis", "given": "Konstantinos", "initials": "K"}, {"family": "Allende", "given": "Ana", "initials": "A"}, {"family": "Alvarez-Ord\u00f3\u00f1ez", "given": "Avelino", "initials": "A"}, {"family": "Bolton", "given": "Declan", "initials": "D"}, {"family": "Bover-Cid", "given": "Sara", "initials": "S"}, {"family": "Chemaly", "given": "Marianne", "initials": "M"}, {"family": "Davies", "given": "Robert", "initials": "R"}, {"family": "De Cesare", "given": "Alessandra", "initials": "A"}, {"family": "Herman", "given": "Lieve", "initials": "L"}, {"family": "Hilbert", "given": "Friederike", "initials": "F"}, {"family": "Lindqvist", "given": "Roland", "initials": "R"}, {"family": "Nauta", "given": "Maarten", "initials": "M"}, {"family": "Ru", "given": "Giuseppe", "initials": "G"}, {"family": "Simmons", "given": "Marion", "initials": "M"}, {"family": "Skandamis", "given": "Panagiotis", "initials": "P"}, {"family": "Suffredini", "given": "Elisabetta", "initials": "E"}, {"family": "Andersson", "given": "Dan I", "initials": "DI"}, {"family": "Bampidis", "given": "Vasileios", "initials": "V"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Bouchard", "given": "Damien", "initials": "D"}, {"family": "Ferran", "given": "Aude", "initials": "A"}, {"family": "Kouba", "given": "Maryline", "initials": "M"}, {"family": "L\u00f3pez Puente", "given": "Secundino", "initials": "S"}, {"family": "L\u00f3pez-Alonso", "given": "Marta", "initials": "M"}, {"family": "Nielsen", "given": "S\u00f8ren Saxmose", "initials": "SS"}, {"family": "Pechov\u00e1", "given": "Alena", "initials": "A"}, {"family": "Petkova", "given": "Mariana", "initials": "M"}, {"family": "Girault", "given": "Sebastien", "initials": "S"}, {"family": "Broglia", "given": "Alessandro", "initials": "A"}, {"family": "Guerra", "given": "Beatriz", "initials": "B"}, {"family": "Innocenti", "given": "Matteo Lorenzo", "initials": "ML"}, {"family": "Li\u00e9bana", "given": "Ernesto", "initials": "E"}, {"family": "L\u00f3pez-G\u00e1lvez", "given": "Gloria", "initials": "G"}, {"family": "Manini", "given": "Paola", "initials": "P"}, {"family": "Stella", "given": "Pietro", "initials": "P"}, {"family": "Peixe", "given": "Luisa", "initials": "L"}], "type": "journal article", "published": "2021-10-00", "journal": {"title": "EFSA J", "issn": "1831-4732", "volume": "19", "issue": "10", "pages": "e06861", "issn-l": null}, "abstract": "The specific concentrations of colistin in non-target feed for food-producing animals, below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in terms of growth promotion/increased yield were assessed by EFSA in collaboration with EMA. Details of the methodology used for this assessment, associated data gaps and uncertainties, are presented in a separate document. To address antimicrobial resistance, the Feed Antimicrobial Resistance Selection Concentration (FARSC) model developed specifically for the assessment was applied. However, due to the lack of data on the parameters required to calculate the FARSC, it was not possible to conclude the assessment until further experimental data become available. To address growth promotion, data from scientific publications obtained from an extensive literature review were used. Levels of colistin in feed that showed to have an effect on growth promotion/increased yield were reported. It was recommended to carry out studies to generate the data that are required to fill the gaps which prevented the calculation of the FARSC for these antimicrobials.", "doi": "10.2903/j.efsa.2021.6861", "pmid": "34729089", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pii", "key": "EFS26861"}, {"db": "pmc", "key": "PMC8546797"}], "notes": [], "created": "2022-11-08T09:25:46.846Z", "modified": "2022-11-08T09:25:46.849Z"}, {"entity": "publication", "iuid": "974d9e87adc34b6fa14de2ff1d78a2fb", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/974d9e87adc34b6fa14de2ff1d78a2fb.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/974d9e87adc34b6fa14de2ff1d78a2fb"}}, "title": "Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 8: Pleuromutilins: tiamulin and valnemulin.", "authors": [{"family": "EFSA Panel on Biological Hazards (BIOHAZ)", "given": "", "initials": ""}, {"family": "Koutsoumanis", "given": "Konstantinos", "initials": "K"}, {"family": "Allende", "given": "Ana", "initials": "A"}, {"family": "Alvarez-Ord\u00f3\u00f1ez", "given": "Avelino", "initials": "A"}, {"family": "Bolton", "given": "Declan", "initials": "D"}, {"family": "Bover-Cid", "given": "Sara", "initials": "S"}, {"family": "Chemaly", "given": "Marianne", "initials": "M"}, {"family": "Davies", "given": "Robert", "initials": "R"}, {"family": "De Cesare", "given": "Alessandra", "initials": "A"}, {"family": "Herman", "given": "Lieve", "initials": "L"}, {"family": "Hilbert", "given": "Friederike", "initials": "F"}, {"family": "Lindqvist", "given": "Roland", "initials": "R"}, {"family": "Nauta", "given": "Maarten", "initials": "M"}, {"family": "Ru", "given": "Giuseppe", "initials": "G"}, {"family": "Simmons", "given": "Marion", "initials": "M"}, {"family": "Skandamis", "given": "Panagiotis", "initials": "P"}, {"family": "Suffredini", "given": "Elisabetta", "initials": "E"}, {"family": "Andersson", "given": "Dan I", "initials": "DI"}, {"family": "Bampidis", "given": "Vasileios", "initials": "V"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Bouchard", "given": "Damien", "initials": "D"}, {"family": "Ferran", "given": "Aude", "initials": "A"}, {"family": "Kouba", "given": "Maryline", "initials": "M"}, {"family": "L\u00f3pez Puente", "given": "Secundino", "initials": "S"}, {"family": "L\u00f3pez-Alonso", "given": "Marta", "initials": "M"}, {"family": "Nielsen", "given": "S\u00f8ren Saxmose", "initials": "SS"}, {"family": "Pechov\u00e1", "given": "Alena", "initials": "A"}, {"family": "Petkova", "given": "Mariana", "initials": "M"}, {"family": "Girault", "given": "Sebastien", "initials": "S"}, {"family": "Broglia", "given": "Alessandro", "initials": "A"}, {"family": "Guerra", "given": "Beatriz", "initials": "B"}, {"family": "Innocenti", "given": "Matteo Lorenzo", "initials": "ML"}, {"family": "Li\u00e9bana", "given": "Ernesto", "initials": "E"}, {"family": "L\u00f3pez-G\u00e1lvez", "given": "Gloria", "initials": "G"}, {"family": "Manini", "given": "Paola", "initials": "P"}, {"family": "Stella", "given": "Pietro", "initials": "P"}, {"family": "Peixe", "given": "Luisa", "initials": "L"}], "type": "journal article", "published": "2021-10-00", "journal": {"title": "EFSA J", "issn": "1831-4732", "volume": "19", "issue": "10", "pages": "e06860", "issn-l": null}, "abstract": "The specific concentrations of tiamulin and valnemulin in non-target feed for food-producing animals, below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in terms of growth promotion/increased yield were assessed by EFSA in collaboration with EMA. Details of the methodology used for this assessment, associated data gaps and uncertainties, are presented in a separate document. To address antimicrobial resistance, the Feed Antimicrobial Resistance Selection Concentration (FARSC) model developed specifically for the assessment was applied. However, due to the lack of data on the parameters required to calculate the FARSC, it was not possible to conclude the assessment until further experimental data become available. To address growth promotion, data from scientific publications obtained from an extensive literature review were used. Levels in feed that showed to have an effect on growth promotion/increased yield were reported for tiamulin, while for valnemulin no suitable data for the assessment were available. It was recommended to carry out studies to generate the data that are required to fill the gaps which prevented the calculation of the FARSC for these two antimicrobials.", "doi": "10.2903/j.efsa.2021.6860", "pmid": "34729088", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pii", "key": "EFS26860"}, {"db": "pmc", "key": "PMC8546795"}], "notes": [], "created": "2022-11-08T09:25:44.477Z", "modified": "2022-11-08T09:25:44.481Z"}, {"entity": "publication", "iuid": "74ec30b0ebcf49c6b566b5a8c448f298", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/74ec30b0ebcf49c6b566b5a8c448f298.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/74ec30b0ebcf49c6b566b5a8c448f298"}}, "title": "Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 7: Amphenicols: florfenicol and thiamphenicol.", "authors": [{"family": "EFSA Panel on Biological Hazards (BIOHAZ)", "given": "", "initials": ""}, {"family": "Koutsoumanis", "given": "Konstantinos", "initials": "K"}, {"family": "Allende", "given": "Ana", "initials": "A"}, {"family": "Alvarez-Ord\u00f3\u00f1ez", "given": "Avelino", "initials": "A"}, {"family": "Bolton", "given": "Declan", "initials": "D"}, {"family": "Bover-Cid", "given": "Sara", "initials": "S"}, {"family": "Chemaly", "given": "Marianne", "initials": "M"}, {"family": "Davies", "given": "Robert", "initials": "R"}, {"family": "De Cesare", "given": "Alessandra", "initials": "A"}, {"family": "Herman", "given": "Lieve", "initials": "L"}, {"family": "Hilbert", "given": "Friederike", "initials": "F"}, {"family": "Lindqvist", "given": "Roland", "initials": "R"}, {"family": "Nauta", "given": "Maarten", "initials": "M"}, {"family": "Ru", "given": "Giuseppe", "initials": "G"}, {"family": "Simmons", "given": "Marion", "initials": "M"}, {"family": "Skandamis", "given": "Panagiotis", "initials": "P"}, {"family": "Suffredini", "given": "Elisabetta", "initials": "E"}, {"family": "Andersson", "given": "Dan I", "initials": "DI"}, {"family": "Bampidis", "given": "Vasileios", "initials": "V"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Bouchard", "given": "Damien", "initials": "D"}, {"family": "Ferran", "given": "Aude", "initials": "A"}, {"family": "Kouba", "given": "Maryline", "initials": "M"}, {"family": "L\u00f3pez Puente", "given": "Secundino", "initials": "S"}, {"family": "L\u00f3pez-Alonso", "given": "Marta", "initials": "M"}, {"family": "Nielsen", "given": "S\u00f8ren Saxmose", "initials": "SS"}, {"family": "Pechov\u00e1", "given": "Alena", "initials": "A"}, {"family": "Petkova", "given": "Mariana", "initials": "M"}, {"family": "Girault", "given": "Sebastien", "initials": "S"}, {"family": "Broglia", "given": "Alessandro", "initials": "A"}, {"family": "Guerra", "given": "Beatriz", "initials": "B"}, {"family": "Innocenti", "given": "Matteo Lorenzo", "initials": "ML"}, {"family": "Li\u00e9bana", "given": "Ernesto", "initials": "E"}, {"family": "L\u00f3pez-G\u00e1lvez", "given": "Gloria", "initials": "G"}, {"family": "Manini", "given": "Paola", "initials": "P"}, {"family": "Stella", "given": "Pietro", "initials": "P"}, {"family": "Peixe", "given": "Luisa", "initials": "L"}], "type": "journal article", "published": "2021-10-00", "journal": {"title": "EFSA J", "issn": "1831-4732", "volume": "19", "issue": "10", "pages": "e06859", "issn-l": null}, "abstract": "The specific concentrations of florfenicol and thiamphenicol in non-target feed for food-producing animals, below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in terms of growth promotion/increased yield, were assessed by EFSA in collaboration with EMA. Details of the methodology used for this assessment, associated data gaps and uncertainties, are presented in a separate document. To address antimicrobial resistance, the Feed Antimicrobial Resistance Selection Concentration (FARSC) model developed specifically for the assessment was applied. The FARSC for florfenicol was estimated. However, due to the lack of data, the calculation of the FARSC for thiamphenicol was not possible until further experimental data become available. To address growth promotion, data from scientific publications obtained from an extensive literature review were used. Levels in feed that showed to have an effect on growth promotion/increased yield were reported for florfenicol, whilst for thiamphenicol no suitable data for the assessment were available. Uncertainties and data gaps associated to the levels reported were addressed. For florfenicol, it was recommended to perform further studies to supply more diverse and complete data related to the requirements for calculation of the FARSC, whereas for thiamphenicol, the recommendation was to generate the data required to fill the gaps which prevented the FARSC calculation.", "doi": "10.2903/j.efsa.2021.6859", "pmid": "34729087", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pii", "key": "EFS26859"}, {"db": "pmc", "key": "PMC8546524"}], "notes": [], "created": "2022-11-08T09:25:07.517Z", "modified": "2022-11-08T09:27:17.178Z"}, {"entity": "publication", "iuid": "5003f27303004f4e99973d41fbccde20", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5003f27303004f4e99973d41fbccde20.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5003f27303004f4e99973d41fbccde20"}}, "title": "Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 6: Macrolides: tilmicosin, tylosin and tylvalosin.", "authors": [{"family": "EFSA Panel on Biological Hazards (BIOHAZ)", "given": "", "initials": ""}, {"family": "Koutsoumanis", "given": "Konstantinos", "initials": "K"}, {"family": "Allende", "given": "Ana", "initials": "A"}, {"family": "Alvarez-Ord\u00f3\u00f1ez", "given": "Avelino", "initials": "A"}, {"family": "Bolton", "given": "Declan", "initials": "D"}, {"family": "Bover-Cid", "given": "Sara", "initials": "S"}, {"family": "Chemaly", "given": "Marianne", "initials": "M"}, {"family": "Davies", "given": "Robert", "initials": "R"}, {"family": "De Cesare", "given": "Alessandra", "initials": "A"}, {"family": "Herman", "given": "Lieve", "initials": "L"}, {"family": "Hilbert", "given": "Friederike", "initials": "F"}, {"family": "Lindqvist", "given": "Roland", "initials": "R"}, {"family": "Nauta", "given": "Maarten", "initials": "M"}, {"family": "Ru", "given": "Giuseppe", "initials": "G"}, {"family": "Simmons", "given": "Marion", "initials": "M"}, {"family": "Skandamis", "given": "Panagiotis", "initials": "P"}, {"family": "Suffredini", "given": "Elisabetta", "initials": "E"}, {"family": "Andersson", "given": "Dan I", "initials": "DI"}, {"family": "Bampidis", "given": "Vasileios", "initials": "V"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Bouchard", "given": "Damien", "initials": "D"}, {"family": "Ferran", "given": "Aude", "initials": "A"}, {"family": "Kouba", "given": "Maryline", "initials": "M"}, {"family": "L\u00f3pez Puente", "given": "Secundino", "initials": "S"}, {"family": "L\u00f3pez-Alonso", "given": "Marta", "initials": "M"}, {"family": "Nielsen", "given": "S\u00f8ren Saxmose", "initials": "SS"}, {"family": "Pechov\u00e1", "given": "Alena", "initials": "A"}, {"family": "Petkova", "given": "Mariana", "initials": "M"}, {"family": "Girault", "given": "Sebastien", "initials": "S"}, {"family": "Broglia", "given": "Alessandro", "initials": "A"}, {"family": "Guerra", "given": "Beatriz", "initials": "B"}, {"family": "Innocenti", "given": "Matteo Lorenzo", "initials": "ML"}, {"family": "Li\u00e9bana", "given": "Ernesto", "initials": "E"}, {"family": "L\u00f3pez-G\u00e1lvez", "given": "Gloria", "initials": "G"}, {"family": "Manini", "given": "Paola", "initials": "P"}, {"family": "Stella", "given": "Pietro", "initials": "P"}, {"family": "Peixe", "given": "Luisa", "initials": "L"}], "type": "journal article", "published": "2021-10-00", "journal": {"title": "EFSA J", "issn": "1831-4732", "volume": "19", "issue": "10", "pages": "e06858", "issn-l": null}, "abstract": "The specific concentrations of tilmicosin, tylosin and tylvalosin in non-target feed for food-producing animals, below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in terms of growth promotion/increased yield, were assessed by EFSA in collaboration with EMA. Details of the methodology used for this assessment, associated data gaps and uncertainties, are presented in a separate document. To address antimicrobial resistance, the Feed Antimicrobial Resistance Selection Concentration (FARSC) model developed specifically for the assessment was applied. However, due to the lack of data on the parameters required to calculate the FARSC, it was not possible to conclude the assessment until further experimental data become available. To address growth promotion, data from scientific publications obtained from an extensive literature review were used. Levels in feed that showed to have an effect on growth promotion/increased yield were reported for tilmicosin and tylosin, whilst for tylvalosin no suitable data for the assessment were available. It was recommended to carry out studies to generate the data that are required to fill the gaps which prevented the calculation of the FARSC for these three antimicrobials.", "doi": "10.2903/j.efsa.2021.6858", "pmid": "34729086", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pii", "key": "EFS26858"}, {"db": "pmc", "key": "PMC8546505"}], "notes": [], "created": "2022-11-08T09:25:05.174Z", "modified": "2022-11-08T09:27:14.714Z"}, {"entity": "publication", "iuid": "8967090f31a34bcd8d4e3bf4570366b9", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8967090f31a34bcd8d4e3bf4570366b9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8967090f31a34bcd8d4e3bf4570366b9"}}, "title": "Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 5: Lincosamides: lincomycin.", "authors": [{"family": "EFSA Panel on Biological Hazards (BIOHAZ)", "given": "", "initials": ""}, {"family": "Koutsoumanis", "given": "Konstantinos", "initials": "K"}, {"family": "Allende", "given": "Ana", "initials": "A"}, {"family": "Alvarez-Ord\u00f3\u00f1ez", "given": "Avelino", "initials": "A"}, {"family": "Bolton", "given": "Declan", "initials": "D"}, {"family": "Bover-Cid", "given": "Sara", "initials": "S"}, {"family": "Chemaly", "given": "Marianne", "initials": "M"}, {"family": "Davies", "given": "Robert", "initials": "R"}, {"family": "De Cesare", "given": "Alessandra", "initials": "A"}, {"family": "Herman", "given": "Lieve", "initials": "L"}, {"family": "Hilbert", "given": "Friederike", "initials": "F"}, {"family": "Lindqvist", "given": "Roland", "initials": "R"}, {"family": "Nauta", "given": "Maarten", "initials": "M"}, {"family": "Ru", "given": "Giuseppe", "initials": "G"}, {"family": "Simmons", "given": "Marion", "initials": "M"}, {"family": "Skandamis", "given": "Panagiotis", "initials": "P"}, {"family": "Suffredini", "given": "Elisabetta", "initials": "E"}, {"family": "Andersson", "given": "Dan I", "initials": "DI"}, {"family": "Bampidis", "given": "Vasileios", "initials": "V"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Bouchard", "given": "Damien", "initials": "D"}, {"family": "Ferran", "given": "Aude", "initials": "A"}, {"family": "Kouba", "given": "Maryline", "initials": "M"}, {"family": "L\u00f3pez Puente", "given": "Secundino", "initials": "S"}, {"family": "L\u00f3pez-Alonso", "given": "Marta", "initials": "M"}, {"family": "Nielsen", "given": "S\u00f8ren Saxmose", "initials": "SS"}, {"family": "Pechov\u00e1", "given": "Alena", "initials": "A"}, {"family": "Petkova", "given": "Mariana", "initials": "M"}, {"family": "Girault", "given": "Sebastien", "initials": "S"}, {"family": "Broglia", "given": "Alessandro", "initials": "A"}, {"family": "Guerra", "given": "Beatriz", "initials": "B"}, {"family": "Innocenti", "given": "Matteo Lorenzo", "initials": "ML"}, {"family": "Li\u00e9bana", "given": "Ernesto", "initials": "E"}, {"family": "L\u00f3pez-G\u00e1lvez", "given": "Gloria", "initials": "G"}, {"family": "Manini", "given": "Paola", "initials": "P"}, {"family": "Stella", "given": "Pietro", "initials": "P"}, {"family": "Peixe", "given": "Luisa", "initials": "L"}], "type": "journal article", "published": "2021-10-00", "journal": {"title": "EFSA J", "issn": "1831-4732", "volume": "19", "issue": "10", "pages": "e06856", "issn-l": null}, "abstract": "The specific concentrations of lincomycin in non-target feed for food-producing animals, below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in terms of growth promotion/increased yield were assessed by EFSA in collaboration with EMA. Details of the methodology used for this assessment, associated data gaps and uncertainties, are presented in a separate document. To address antimicrobial resistance, the Feed Antimicrobial Resistance Selection Concentration (FARSC) model developed specifically for the assessment was applied. However, due to the lack of data on the parameters required to calculate the FARSC, it was not possible to conclude the assessment until further experimental data become available. To address growth promotion, data from scientific publications obtained from an extensive literature review were used. Levels of lincomycin in feed that showed to have an effect on growth promotion/increased yield were reported. It was recommended to carry out studies to generate the data that are required to fill the gaps which prevented the calculation of the FARSC for lincomycin.", "doi": "10.2903/j.efsa.2021.6856", "pmid": "34729085", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pii", "key": "EFS26856"}, {"db": "pmc", "key": "PMC8546522"}], "notes": [], "created": "2022-11-08T09:25:02.833Z", "modified": "2022-11-08T09:27:12.329Z"}, {"entity": "publication", "iuid": "3da69a58f13e48268d71da728bbfac79", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3da69a58f13e48268d71da728bbfac79.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3da69a58f13e48268d71da728bbfac79"}}, "title": "Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 4: \u03b2-Lactams: amoxicillin and penicillin V.", "authors": [{"family": "EFSA Panel on Biological Hazards (BIOHAZ)", "given": "", "initials": ""}, {"family": "Koutsoumanis", "given": "Konstantinos", "initials": "K"}, {"family": "Allende", "given": "Ana", "initials": "A"}, {"family": "Alvarez-Ord\u00f3\u00f1ez", "given": "Avelino", "initials": "A"}, {"family": "Bolton", "given": "Declan", "initials": "D"}, {"family": "Bover-Cid", "given": "Sara", "initials": "S"}, {"family": "Chemaly", "given": "Marianne", "initials": "M"}, {"family": "Davies", "given": "Robert", "initials": "R"}, {"family": "De Cesare", "given": "Alessandra", "initials": "A"}, {"family": "Herman", "given": "Lieve", "initials": "L"}, {"family": "Hilbert", "given": "Friederike", "initials": "F"}, {"family": "Lindqvist", "given": "Roland", "initials": "R"}, {"family": "Nauta", "given": "Maarten", "initials": "M"}, {"family": "Ru", "given": "Giuseppe", "initials": "G"}, {"family": "Simmons", "given": "Marion", "initials": "M"}, {"family": "Skandamis", "given": "Panagiotis", "initials": "P"}, {"family": "Suffredini", "given": "Elisabetta", "initials": "E"}, {"family": "Andersson", "given": "Dan I", "initials": "DI"}, {"family": "Bampidis", "given": "Vasileios", "initials": "V"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Bouchard", "given": "Damien", "initials": "D"}, {"family": "Ferran", "given": "Aude", "initials": "A"}, {"family": "Kouba", "given": "Maryline", "initials": "M"}, {"family": "L\u00f3pez Puente", "given": "Secundino", "initials": "S"}, {"family": "L\u00f3pez-Alonso", "given": "Marta", "initials": "M"}, {"family": "Nielsen", "given": "S\u00f8ren Saxmose", "initials": "SS"}, {"family": "Pechov\u00e1", "given": "Alena", "initials": "A"}, {"family": "Petkova", "given": "Mariana", "initials": "M"}, {"family": "Girault", "given": "Sebastien", "initials": "S"}, {"family": "Broglia", "given": "Alessandro", "initials": "A"}, {"family": "Guerra", "given": "Beatriz", "initials": "B"}, {"family": "Innocenti", "given": "Matteo Lorenzo", "initials": "ML"}, {"family": "Li\u00e9bana", "given": "Ernesto", "initials": "E"}, {"family": "L\u00f3pez-G\u00e1lvez", "given": "Gloria", "initials": "G"}, {"family": "Manini", "given": "Paola", "initials": "P"}, {"family": "Stella", "given": "Pietro", "initials": "P"}, {"family": "Peixe", "given": "Luisa", "initials": "L"}], "type": "journal article", "published": "2021-10-00", "journal": {"title": "EFSA J", "issn": "1831-4732", "volume": "19", "issue": "10", "pages": "e06855", "issn-l": null}, "abstract": "The specific concentrations of amoxicillin and penicillin V in non-target feed for food-producing animals, below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in terms of growth promotion/increased yield were assessed by EFSA in collaboration with EMA. Details of the methodology used for this assessment, associated data gaps and uncertainties, are presented in a separate document. To address antimicrobial resistance, the Feed Antimicrobial Resistance Selection Concentration (FARSC) model developed specifically for the assessment was applied. However, due to the lack of data on the parameters required to calculate the FARSC, it was not possible to conclude the assessment until further experimental data become available. To address growth promotion, data from scientific publications obtained from an extensive literature review were used. Levels in feed that showed to have an effect on growth promotion/increased yield were reported for amoxicillin, whilst for penicillin V no suitable data for the assessment were available. It was recommended to carry out studies to generate the data that are required to fill the gaps which prevented the calculation of the FARSC for these two antimicrobials.", "doi": "10.2903/j.efsa.2021.6855", "pmid": "34729084", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pii", "key": "EFS26855"}, {"db": "pmc", "key": "PMC8547409"}], "notes": [], "created": "2022-11-08T09:25:00.484Z", "modified": "2022-11-08T09:27:10.010Z"}, {"entity": "publication", "iuid": "b7d8ecc62c474594a820b6b818741c38", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b7d8ecc62c474594a820b6b818741c38.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b7d8ecc62c474594a820b6b818741c38"}}, "title": "Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 3: Amprolium.", "authors": [{"family": "EFSA Panel on Biological Hazards (BIOHAZ)", "given": "", "initials": ""}, {"family": "Koutsoumanis", "given": "Konstantinos", "initials": "K"}, {"family": "Allende", "given": "Ana", "initials": "A"}, {"family": "Alvarez-Ord\u00f3\u00f1ez", "given": "Avelino", "initials": "A"}, {"family": "Bolton", "given": "Declan", "initials": "D"}, {"family": "Bover-Cid", "given": "Sara", "initials": "S"}, {"family": "Chemaly", "given": "Marianne", "initials": "M"}, {"family": "Davies", "given": "Robert", "initials": "R"}, {"family": "De Cesare", "given": "Alessandra", "initials": "A"}, {"family": "Herman", "given": "Lieve", "initials": "L"}, {"family": "Hilbert", "given": "Friederike", "initials": "F"}, {"family": "Lindqvist", "given": "Roland", "initials": "R"}, {"family": "Nauta", "given": "Maarten", "initials": "M"}, {"family": "Ru", "given": "Giuseppe", "initials": "G"}, {"family": "Simmons", "given": "Marion", "initials": "M"}, {"family": "Skandamis", "given": "Panagiotis", "initials": "P"}, {"family": "Suffredini", "given": "Elisabetta", "initials": "E"}, {"family": "Andersson", "given": "Dan I", "initials": "DI"}, {"family": "Bampidis", "given": "Vasileios", "initials": "V"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Bouchard", "given": "Damien", "initials": "D"}, {"family": "Ferran", "given": "Aude", "initials": "A"}, {"family": "Kouba", "given": "Maryline", "initials": "M"}, {"family": "L\u00f3pez Puente", "given": "Secundino", "initials": "S"}, {"family": "L\u00f3pez-Alonso", "given": "Marta", "initials": "M"}, {"family": "Nielsen", "given": "S\u00f8ren Saxmose", "initials": "SS"}, {"family": "Pechov\u00e1", "given": "Alena", "initials": "A"}, {"family": "Petkova", "given": "Mariana", "initials": "M"}, {"family": "Girault", "given": "Sebastien", "initials": "S"}, {"family": "Broglia", "given": "Alessandro", "initials": "A"}, {"family": "Guerra", "given": "Beatriz", "initials": "B"}, {"family": "Innocenti", "given": "Matteo Lorenzo", "initials": "ML"}, {"family": "Li\u00e9bana", "given": "Ernesto", "initials": "E"}, {"family": "L\u00f3pez-G\u00e1lvez", "given": "Gloria", "initials": "G"}, {"family": "Manini", "given": "Paola", "initials": "P"}, {"family": "Stella", "given": "Pietro", "initials": "P"}, {"family": "Peixe", "given": "Luisa", "initials": "L"}], "type": "journal article", "published": "2021-10-00", "journal": {"title": "EFSA J", "issn": "1831-4732", "volume": "19", "issue": "10", "pages": "e06854", "issn-l": null}, "abstract": "The specific concentrations of amprolium in non-target feed for food-producing animals, below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in terms of growth promotion/increased yield were assessed by EFSA in collaboration with EMA. Details of the methodology used for this assessment, associated data gaps and uncertainties, are presented in a separate document. To address antimicrobial resistance, the Feed Antimicrobial Resistance Selection Concentration (FARSC) model developed specifically for the assessment was applied. However, due to the lack of data on the parameters required to calculate the FARSC for amprolium, it was not possible to conclude the assessment. To address growth promotion, data from scientific publications obtained from an extensive literature review were used. Levels of amprolium in feed that showed to have an effect on growth promotion/increased yield were reported. The lack of antibacterial activity at clinically relevant concentrations for amprolium suggests that further studies relating to bacterial resistance are not a priority.", "doi": "10.2903/j.efsa.2021.6854", "pmid": "34729083", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pii", "key": "EFS26854"}, {"db": "pmc", "key": "PMC8546521"}], "notes": [], "created": "2022-11-08T09:24:58.114Z", "modified": "2022-11-08T09:27:07.685Z"}, {"entity": "publication", "iuid": "586dccfcec154d3296d2c9fe9faede6d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/586dccfcec154d3296d2c9fe9faede6d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/586dccfcec154d3296d2c9fe9faede6d"}}, "title": "Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 2: Aminoglycosides/aminocyclitols: apramycin, paromomycin, neomycin and spectinomycin.", "authors": [{"family": "EFSA Panel on Biological Hazards (BIOHAZ)", "given": "", "initials": ""}, {"family": "Allende", "given": "Ana", "initials": "A"}, {"family": "Koutsoumanis", "given": "Konstantinos", "initials": "K"}, {"family": "Alvarez-Ord\u00f3\u00f1ez", "given": "Avelino", "initials": "A"}, {"family": "Bolton", "given": "Declan", "initials": "D"}, {"family": "Bover-Cid", "given": "Sara", "initials": "S"}, {"family": "Chemaly", "given": "Marianne", "initials": "M"}, {"family": "Davies", "given": "Robert", "initials": "R"}, {"family": "De Cesare", "given": "Alessandra", "initials": "A"}, {"family": "Herman", "given": "Lieve", "initials": "L"}, {"family": "Hilbert", "given": "Friederike", "initials": "F"}, {"family": "Lindqvist", "given": "Roland", "initials": "R"}, {"family": "Nauta", "given": "Maarten", "initials": "M"}, {"family": "Ru", "given": "Giuseppe", "initials": "G"}, {"family": "Simmons", "given": "Marion", "initials": "M"}, {"family": "Skandamis", "given": "Panagiotis", "initials": "P"}, {"family": "Suffredini", "given": "Elisabetta", "initials": "E"}, {"family": "Andersson", "given": "Dan I", "initials": "DI"}, {"family": "Bampidis", "given": "Vasileios", "initials": "V"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Bouchard", "given": "Damien", "initials": "D"}, {"family": "Ferran", "given": "Aude", "initials": "A"}, {"family": "Kouba", "given": "Maryline", "initials": "M"}, {"family": "L\u00f3pez Puente", "given": "Secundino", "initials": "S"}, {"family": "L\u00f3pez-Alonso", "given": "Marta", "initials": "M"}, {"family": "Nielsen", "given": "S\u00f8ren Saxmose", "initials": "SS"}, {"family": "Pechov\u00e1", "given": "Alena", "initials": "A"}, {"family": "Petkova", "given": "Mariana", "initials": "M"}, {"family": "Girault", "given": "Sebastien", "initials": "S"}, {"family": "Broglia", "given": "Alessandro", "initials": "A"}, {"family": "Guerra", "given": "Beatriz", "initials": "B"}, {"family": "Innocenti", "given": "Matteo Lorenzo", "initials": "ML"}, {"family": "Li\u00e9bana", "given": "Ernesto", "initials": "E"}, {"family": "L\u00f3pez-G\u00e1lvez", "given": "Gloria", "initials": "G"}, {"family": "Manini", "given": "Paola", "initials": "P"}, {"family": "Stella", "given": "Pietro", "initials": "P"}, {"family": "Peixe", "given": "Luisa", "initials": "L"}], "type": "journal article", "published": "2021-10-00", "journal": {"title": "EFSA J", "issn": "1831-4732", "volume": "19", "issue": "10", "pages": "e06853", "issn-l": null}, "abstract": "The specific concentrations of apramycin, paromomycin, neomycin and spectinomycin in non-target feed for food-producing animals, below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in terms of growth promotion/increased yield, were assessed by EFSA in collaboration with EMA. Details of the methodology used for this assessment, associated data gaps and uncertainties, are presented in a separate document. To address antimicrobial resistance, the Feed Antimicrobial Resistance Selection Concentration (FARSC) model developed specifically for the assessment was applied. However, due to the lack of data on the parameters required to calculate the FARSC for these antimicrobials, it was not possible to conclude the assessment until further experimental data become available. To address growth promotion, data from scientific publications obtained from an extensive literature review were used. Levels in feed that showed to have an effect on growth promotion/increased yield were reported for apramycin and neomycin, whilst for paromomycin and spectinomycin, no suitable data for the assessment were available. It was recommended to carry out studies to generate the data that are required to fill the gaps which prevented the calculation of the FARSC for these four antimicrobials.", "doi": "10.2903/j.efsa.2021.6853", "pmid": "34729082", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pii", "key": "EFS26853"}, {"db": "pmc", "key": "PMC8546520"}], "notes": [], "created": "2022-11-08T09:24:55.875Z", "modified": "2022-11-08T09:27:05.454Z"}, {"entity": "publication", "iuid": "587cacb40f28481288a6319e0202eb16", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/587cacb40f28481288a6319e0202eb16.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/587cacb40f28481288a6319e0202eb16"}}, "title": "Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 1: Methodology, general data gaps and uncertainties.", "authors": [{"family": "EFSA Panel on Biological Hazards (BIOHAZ)", "given": "", "initials": ""}, {"family": "Koutsoumanis", "given": "Konstantinos", "initials": "K"}, {"family": "Allende", "given": "Ana", "initials": "A"}, {"family": "Alvarez-Ord\u00f3\u00f1ez", "given": "Avelino", "initials": "A"}, {"family": "Bolton", "given": "Declan", "initials": "D"}, {"family": "Bover-Cid", "given": "Sara", "initials": "S"}, {"family": "Chemaly", "given": "Marianne", "initials": "M"}, {"family": "Davies", "given": "Robert", "initials": "R"}, {"family": "De Cesare", "given": "Alessandra", "initials": "A"}, {"family": "Herman", "given": "Lieve", "initials": "L"}, {"family": "Hilbert", "given": "Friederike", "initials": "F"}, {"family": "Lindqvist", "given": "Roland", "initials": "R"}, {"family": "Nauta", "given": "Maarten", "initials": "M"}, {"family": "Ru", "given": "Giuseppe", "initials": "G"}, {"family": "Simmons", "given": "Marion", "initials": "M"}, {"family": "Skandamis", "given": "Panagiotis", "initials": "P"}, {"family": "Suffredini", "given": "Elisabetta", "initials": "E"}, {"family": "Andersson", "given": "Dan I", "initials": "DI"}, {"family": "Bampidis", "given": "Vasileios", "initials": "V"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Bouchard", "given": "Damien", "initials": "D"}, {"family": "Ferran", "given": "Aude", "initials": "A"}, {"family": "Kouba", "given": "Maryline", "initials": "M"}, {"family": "L\u00f3pez Puente", "given": "Secundino", "initials": "S"}, {"family": "L\u00f3pez-Alonso", "given": "Marta", "initials": "M"}, {"family": "Nielsen", "given": "S\u00f8ren Saxmose", "initials": "SS"}, {"family": "Pechov\u00e1", "given": "Alena", "initials": "A"}, {"family": "Petkova", "given": "Mariana", "initials": "M"}, {"family": "Girault", "given": "Sebastien", "initials": "S"}, {"family": "Broglia", "given": "Alessandro", "initials": "A"}, {"family": "Guerra", "given": "Beatriz", "initials": "B"}, {"family": "Innocenti", "given": "Matteo Lorenzo", "initials": "ML"}, {"family": "Li\u00e9bana", "given": "Ernesto", "initials": "E"}, {"family": "L\u00f3pez-G\u00e1lvez", "given": "Gloria", "initials": "G"}, {"family": "Manini", "given": "Paola", "initials": "P"}, {"family": "Stella", "given": "Pietro", "initials": "P"}, {"family": "Peixe", "given": "Luisa", "initials": "L"}], "type": "journal article", "published": "2021-10-00", "journal": {"title": "EFSA J", "issn": "1831-4732", "volume": "19", "issue": "10", "pages": "e06852", "issn-l": null}, "abstract": "The European Commission requested EFSA to assess, in collaboration with EMA, the specific concentrations of antimicrobials resulting from cross-contamination in non-target feed for food-producing animals below which there would not be an effect on the emergence of, and/or selection for, resistance in microbial agents relevant for human and animal health, as well as the levels of the antimicrobials which could have a growth promotion/increase yield effect. The assessment was performed for 24 antimicrobial active substances, as specified in the mandate. This scientific opinion describes the methodology used, and the main associated data gaps and uncertainties. To estimate the antimicrobial levels in the non-target feed that would not result in emergence of, and/or selection for, resistance, a model was developed. This 'Feed Antimicrobial Resistance Selection Concentration' (FARSC) model is based on the minimal selective concentration (MSC), or the predicted MSC (PMSC) if MSC for the most susceptible bacterial species is unavailable, the fraction of antimicrobial dose available for exposure to microorganisms in the large intestine or rumen (considering pharmacokinetic parameters), the daily faecal output or rumen volume and the daily feed intake. Currently, lack of data prevents the establishment of PMSC and/or FARSC for several antimicrobials and animal species. To address growth promotion, data from an extensive literature search were used. Specific assessments of the different substances grouped by antimicrobial classes are addressed in separate scientific opinions. General conclusions and recommendations were made.", "doi": "10.2903/j.efsa.2021.6852", "pmid": "34729081", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pii", "key": "EFS26852"}, {"db": "pmc", "key": "PMC8547316"}], "notes": [], "created": "2022-11-08T09:24:51.207Z", "modified": "2022-11-08T09:27:00.047Z"}, {"entity": "publication", "iuid": "4f17dd56a9e042cd8fbd69dc9373bdc2", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4f17dd56a9e042cd8fbd69dc9373bdc2.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4f17dd56a9e042cd8fbd69dc9373bdc2"}}, "title": "Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 13: Diaminopyrimidines: trimethoprim.", "authors": [{"family": "EFSA Panel on Biological Hazards (BIOHAZ)", "given": "", "initials": ""}, {"family": "Koutsoumanis", "given": "Konstantinos", "initials": "K"}, {"family": "Allende", "given": "Ana", "initials": "A"}, {"family": "Alvarez-Ord\u00f3\u00f1ez", "given": "Avelino", "initials": "A"}, {"family": "Bolton", "given": "Declan", "initials": "D"}, {"family": "Bover-Cid", "given": "Sara", "initials": "S"}, {"family": "Chemaly", "given": "Marianne", "initials": "M"}, {"family": "Davies", "given": "Robert", "initials": "R"}, {"family": "De Cesare", "given": "Alessandra", "initials": "A"}, {"family": "Herman", "given": "Lieve", "initials": "L"}, {"family": "Hilbert", "given": "Friederike", "initials": "F"}, {"family": "Lindqvist", "given": "Roland", "initials": "R"}, {"family": "Nauta", "given": "Maarten", "initials": "M"}, {"family": "Ru", "given": "Giuseppe", "initials": "G"}, {"family": "Simmons", "given": "Marion", "initials": "M"}, {"family": "Skandamis", "given": "Panagiotis", "initials": "P"}, {"family": "Suffredini", "given": "Elisabetta", "initials": "E"}, {"family": "Andersson", "given": "Dan I", "initials": "DI"}, {"family": "Bampidis", "given": "Vasileios", "initials": "V"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Bouchard", "given": "Damien", "initials": "D"}, {"family": "Ferran", "given": "Aude", "initials": "A"}, {"family": "Kouba", "given": "Maryline", "initials": "M"}, {"family": "L\u00f3pez Puente", "given": "Secundino", "initials": "S"}, {"family": "L\u00f3pez-Alonso", "given": "Marta", "initials": "M"}, {"family": "Nielsen", "given": "S\u00f8ren Saxmose", "initials": "SS"}, {"family": "Pechov\u00e1", "given": "Alena", "initials": "A"}, {"family": "Petkova", "given": "Mariana", "initials": "M"}, {"family": "Girault", "given": "Sebastien", "initials": "S"}, {"family": "Broglia", "given": "Alessandro", "initials": "A"}, {"family": "Guerra", "given": "Beatriz", "initials": "B"}, {"family": "Innocenti", "given": "Matteo Lorenzo", "initials": "ML"}, {"family": "Li\u00e9bana", "given": "Ernesto", "initials": "E"}, {"family": "L\u00f3pez-G\u00e1lvez", "given": "Gloria", "initials": "G"}, {"family": "Manini", "given": "Paola", "initials": "P"}, {"family": "Stella", "given": "Pietro", "initials": "P"}, {"family": "Peixe", "given": "Luisa", "initials": "L"}], "type": "journal article", "published": "2021-10-00", "journal": {"title": "EFSA J", "issn": "1831-4732", "volume": "19", "issue": "10", "pages": "e06865", "issn-l": null}, "abstract": "The specific concentrations of trimethoprim in non-target feed for food-producing animals below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in terms of growth promotion/increased yield were assessed by EFSA in collaboration with EMA. Details of the methodology used for this assessment, associated data gaps and uncertainties, are presented in a separate document. To address antimicrobial resistance, the Feed Antimicrobial Resistance Selection Concentration (FARSC) model developed specifically for the assessment was applied. The FARSC for trimethoprim was estimated. Uncertainties and data gaps associated to the levels reported were addressed. To address growth promotion, data from scientific publications obtained from an extensive literature review were used. No suitable data for the assessment were available. It was recommended to perform further studies to supply more diverse and complete data related to the requirements for calculation of the FARSC for trimethoprim.", "doi": "10.2903/j.efsa.2021.6865", "pmid": "34729093", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pii", "key": "EFS26865"}, {"db": "pmc", "key": "PMC8546793"}], "notes": [], "created": "2022-11-08T09:25:56.571Z", "modified": "2022-11-08T09:25:56.597Z"}, {"entity": "publication", "iuid": "e6b16bf3b8d64f83aa67a2516217c2e6", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e6b16bf3b8d64f83aa67a2516217c2e6.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e6b16bf3b8d64f83aa67a2516217c2e6"}}, "title": "Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 12: Tetracyclines: tetracycline, chlortetracycline, oxytetracycline, and doxycycline.", "authors": [{"family": "EFSA Panel on Biological Hazards (BIOHAZ)", "given": "", "initials": ""}, {"family": "Koutsoumanis", "given": "Konstantinos", "initials": "K"}, {"family": "Allende", "given": "Ana", "initials": "A"}, {"family": "Alvarez-Ord\u00f3\u00f1ez", "given": "Avelino", "initials": "A"}, {"family": "Bolton", "given": "Declan", "initials": "D"}, {"family": "Bover-Cid", "given": "Sara", "initials": "S"}, {"family": "Chemaly", "given": "Marianne", "initials": "M"}, {"family": "Davies", "given": "Robert", "initials": "R"}, {"family": "De Cesare", "given": "Alessandra", "initials": "A"}, {"family": "Herman", "given": "Lieve", "initials": "L"}, {"family": "Hilbert", "given": "Friederike", "initials": "F"}, {"family": "Lindqvist", "given": "Roland", "initials": "R"}, {"family": "Nauta", "given": "Maarten", "initials": "M"}, {"family": "Ru", "given": "Giuseppe", "initials": "G"}, {"family": "Simmons", "given": "Marion", "initials": "M"}, {"family": "Skandamis", "given": "Panagiotis", "initials": "P"}, {"family": "Suffredini", "given": "Elisabetta", "initials": "E"}, {"family": "Andersson", "given": "Dan I", "initials": "DI"}, {"family": "Bampidis", "given": "Vasileios", "initials": "V"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Bouchard", "given": "Damien", "initials": "D"}, {"family": "Ferran", "given": "Aude", "initials": "A"}, {"family": "Kouba", "given": "Maryline", "initials": "M"}, {"family": "L\u00f3pez Puente", "given": "Secundino", "initials": "S"}, {"family": "L\u00f3pez-Alonso", "given": "Marta", "initials": "M"}, {"family": "Nielsen", "given": "S\u00f8ren Saxmose", "initials": "SS"}, {"family": "Pechov\u00e1", "given": "Alena", "initials": "A"}, {"family": "Petkova", "given": "Mariana", "initials": "M"}, {"family": "Girault", "given": "Sebastien", "initials": "S"}, {"family": "Broglia", "given": "Alessandro", "initials": "A"}, {"family": "Guerra", "given": "Beatriz", "initials": "B"}, {"family": "Innocenti", "given": "Matteo Lorenzo", "initials": "ML"}, {"family": "Li\u00e9bana", "given": "Ernesto", "initials": "E"}, {"family": "L\u00f3pez-G\u00e1lvez", "given": "Gloria", "initials": "G"}, {"family": "Manini", "given": "Paola", "initials": "P"}, {"family": "Stella", "given": "Pietro", "initials": "P"}, {"family": "Peixe", "given": "Luisa", "initials": "L"}], "type": "journal article", "published": "2021-10-00", "journal": {"title": "EFSA J", "issn": "1831-4732", "volume": "19", "issue": "10", "pages": "e06864", "issn-l": null}, "abstract": "The specific concentrations of tetracycline, chlortetracycline, oxytetracycline and doxycycline in non-target feed for food-producing animals, below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in terms of growth promotion/increased yield were assessed by EFSA in collaboration with EMA. Details of the methodology used for this assessment, associated data gaps and uncertainties are presented in a separate document. To address antimicrobial resistance, the Feed Antimicrobial Resistance Selection Concentration (FARSC) model developed specifically for the assessment was applied. The FARSC for these four tetracyclines was estimated. To address growth promotion, data from scientific publications obtained from an extensive literature review were used. Levels in feed that showed to have an effect on growth promotion/increased yield were reported for tetracycline, chlortetracycline, oxytetracycline, whilst for doxycycline no suitable data for the assessment were available. Uncertainties and data gaps associated with the levels reported were addressed. It was recommended to perform further studies to supply more diverse and complete data related to the requirements for calculation of the FARSC for these antimicrobials.", "doi": "10.2903/j.efsa.2021.6864", "pmid": "34729092", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pii", "key": "EFS26864"}, {"db": "pmc", "key": "PMC8546800"}], "notes": [], "created": "2022-11-08T09:25:54.325Z", "modified": "2022-11-08T09:25:54.328Z"}, {"entity": "publication", "iuid": "94c263fb5ff04d2ea6b3ab34c0139d02", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/94c263fb5ff04d2ea6b3ab34c0139d02.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/94c263fb5ff04d2ea6b3ab34c0139d02"}}, "title": "Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 11: Sulfonamides.", "authors": [{"family": "EFSA Panel on Biological Hazards (BIOHAZ)", "given": "", "initials": ""}, {"family": "Koutsoumanis", "given": "Konstantinos", "initials": "K"}, {"family": "Allende", "given": "Ana", "initials": "A"}, {"family": "Alvarez-Ord\u00f3\u00f1ez", "given": "Avelino", "initials": "A"}, {"family": "Bolton", "given": "Declan", "initials": "D"}, {"family": "Bover-Cid", "given": "Sara", "initials": "S"}, {"family": "Chemaly", "given": "Marianne", "initials": "M"}, {"family": "Davies", "given": "Robert", "initials": "R"}, {"family": "De Cesare", "given": "Alessandra", "initials": "A"}, {"family": "Herman", "given": "Lieve", "initials": "L"}, {"family": "Hilbert", "given": "Friederike", "initials": "F"}, {"family": "Lindqvist", "given": "Roland", "initials": "R"}, {"family": "Nauta", "given": "Maarten", "initials": "M"}, {"family": "Ru", "given": "Giuseppe", "initials": "G"}, {"family": "Simmons", "given": "Marion", "initials": "M"}, {"family": "Skandamis", "given": "Panagiotis", "initials": "P"}, {"family": "Suffredini", "given": "Elisabetta", "initials": "E"}, {"family": "Andersson", "given": "Dan I", "initials": "DI"}, {"family": "Bampidis", "given": "Vasileios", "initials": "V"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Bouchard", "given": "Damien", "initials": "D"}, {"family": "Ferran", "given": "Aude", "initials": "A"}, {"family": "Kouba", "given": "Maryline", "initials": "M"}, {"family": "L\u00f3pez Puente", "given": "Secundino", "initials": "S"}, {"family": "L\u00f3pez-Alonso", "given": "Marta", "initials": "M"}, {"family": "Nielsen", "given": "S\u00f8ren Saxmose", "initials": "SS"}, {"family": "Pechov\u00e1", "given": "Alena", "initials": "A"}, {"family": "Petkova", "given": "Mariana", "initials": "M"}, {"family": "Girault", "given": "Sebastien", "initials": "S"}, {"family": "Broglia", "given": "Alessandro", "initials": "A"}, {"family": "Guerra", "given": "Beatriz", "initials": "B"}, {"family": "Innocenti", "given": "Matteo Lorenzo", "initials": "ML"}, {"family": "Li\u00e9bana", "given": "Ernesto", "initials": "E"}, {"family": "L\u00f3pez-G\u00e1lvez", "given": "Gloria", "initials": "G"}, {"family": "Manini", "given": "Paola", "initials": "P"}, {"family": "Stella", "given": "Pietro", "initials": "P"}, {"family": "Peixe", "given": "Luisa", "initials": "L"}], "type": "journal article", "published": "2021-10-00", "journal": {"title": "EFSA J", "issn": "1831-4732", "volume": "19", "issue": "10", "pages": "e06863", "issn-l": null}, "abstract": "The specific concentrations of sulfonamides in non-target feed for food-producing animals, below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in terms of growth promotion/increased yield were assessed by EFSA in collaboration with EMA. Details of the methodology used for this assessment, associated data gaps and uncertainties, are presented in a separate document. To address antimicrobial resistance, the Feed Antimicrobial Resistance Selection Concentration (FARSC) model developed specifically for the assessment was applied. However, due to the lack of data on the parameters required to calculate the FARSC, it was not possible to conclude the assessment until further experimental data are available. To address growth promotion, data from scientific publications obtained from an extensive literature review were used. Levels in feed that showed to have an effect on growth promotion/increased yield were identified for three sulfonamides: sulfamethazine, sulfathiazole and sulfamerazine. It was recommended to carry out studies to generate the data that are required to fill the gaps which prevented the calculation of the FARSC for these antimicrobials.", "doi": "10.2903/j.efsa.2021.6863", "pmid": "34729091", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pii", "key": "EFS26863"}, {"db": "pmc", "key": "PMC8546515"}], "notes": [], "created": "2022-11-08T09:25:51.911Z", "modified": "2022-11-08T09:25:51.936Z"}, {"entity": "publication", "iuid": "f51dddadeb0149fa85e6b2ffa1344b01", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f51dddadeb0149fa85e6b2ffa1344b01.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f51dddadeb0149fa85e6b2ffa1344b01"}}, "title": "Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 10: Quinolones: flumequine and oxolinic acid.", "authors": [{"family": "EFSA Panel on Biological Hazards (BIOHAZ)", "given": "", "initials": ""}, {"family": "Koutsoumanis", "given": "Konstantinos", "initials": "K"}, {"family": "Allende", "given": "Ana", "initials": "A"}, {"family": "Alvarez-Ord\u00f3\u00f1ez", "given": "Avelino", "initials": "A"}, {"family": "Bolton", "given": "Declan", "initials": "D"}, {"family": "Bover-Cid", "given": "Sara", "initials": "S"}, {"family": "Chemaly", "given": "Marianne", "initials": "M"}, {"family": "Davies", "given": "Robert", "initials": "R"}, {"family": "De Cesare", "given": "Alessandra", "initials": "A"}, {"family": "Herman", "given": "Lieve", "initials": "L"}, {"family": "Hilbert", "given": "Friederike", "initials": "F"}, {"family": "Lindqvist", "given": "Roland", "initials": "R"}, {"family": "Nauta", "given": "Maarten", "initials": "M"}, {"family": "Ru", "given": "Giuseppe", "initials": "G"}, {"family": "Simmons", "given": "Marion", "initials": "M"}, {"family": "Skandamis", "given": "Panagiotis", "initials": "P"}, {"family": "Suffredini", "given": "Elisabetta", "initials": "E"}, {"family": "Andersson", "given": "Dan I", "initials": "DI"}, {"family": "Bampidis", "given": "Vasileios", "initials": "V"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Bouchard", "given": "Damien", "initials": "D"}, {"family": "Ferran", "given": "Aude", "initials": "A"}, {"family": "Kouba", "given": "Maryline", "initials": "M"}, {"family": "L\u00f3pez Puente", "given": "Secundino", "initials": "S"}, {"family": "L\u00f3pez-Alonso", "given": "Marta", "initials": "M"}, {"family": "Nielsen", "given": "S\u00f8ren Saxmose", "initials": "SS"}, {"family": "Pechov\u00e1", "given": "Alena", "initials": "A"}, {"family": "Petkova", "given": "Mariana", "initials": "M"}, {"family": "Girault", "given": "Sebastien", "initials": "S"}, {"family": "Broglia", "given": "Alessandro", "initials": "A"}, {"family": "Guerra", "given": "Beatriz", "initials": "B"}, {"family": "Innocenti", "given": "Matteo Lorenzo", "initials": "ML"}, {"family": "Li\u00e9bana", "given": "Ernesto", "initials": "E"}, {"family": "L\u00f3pez-G\u00e1lvez", "given": "Gloria", "initials": "G"}, {"family": "Manini", "given": "Paola", "initials": "P"}, {"family": "Stella", "given": "Pietro", "initials": "P"}, {"family": "Peixe", "given": "Luisa", "initials": "L"}], "type": "journal article", "published": "2021-10-00", "journal": {"title": "EFSA J", "issn": "1831-4732", "volume": "19", "issue": "10", "pages": "e06862", "issn-l": null}, "abstract": "The specific concentrations of flumequine and oxolinic acid in non-target feed for food-producing animals, below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in terms of growth promotion/increased yield were assessed by EFSA in collaboration with EMA. Details of the methodology used for this assessment, associated data gaps and uncertainties, are presented in a separate document. To address antimicrobial resistance, the Feed Antimicrobial Resistance Selection Concentration (FARSC) model developed specifically for the assessment was applied. However, due to the lack of data on the parameters required to calculate the FARSC, it was not possible to conclude the assessment until further experimental data are available. To address growth promotion, data from scientific publications obtained from an extensive literature review were used. No suitable data for the assessment were available. It was recommended to carry out studies to generate the data that are required to fill the gaps which prevented the calculation of the FARSC for these antimicrobials.", "doi": "10.2903/j.efsa.2021.6862", "pmid": "34729090", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pii", "key": "EFS26862"}, {"db": "pmc", "key": "PMC8546796"}], "notes": [], "created": "2022-11-08T09:25:49.213Z", "modified": "2022-11-08T09:25:49.245Z"}, {"entity": "publication", "iuid": "fb8612db660c481d9be4a872507534e2", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/fb8612db660c481d9be4a872507534e2.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/fb8612db660c481d9be4a872507534e2"}}, "title": "DeepImageJ: A user-friendly environment to run deep learning models in ImageJ.", "authors": [{"family": "G\u00f3mez-de-Mariscal", "given": "Estibaliz", "initials": "E", "orcid": "0000-0003-2082-3277", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cdcc04b3b1534abc8457380935970dd5.json"}}, {"family": "Garc\u00eda-L\u00f3pez-de-Haro", "given": "Carlos", "initials": "C"}, {"family": "Ouyang", "given": "Wei", "initials": "W"}, {"family": "Donati", "given": "Laur\u00e8ne", "initials": "L"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb07e6d0122c4528a927c1fe922e3bc8.json"}}, {"family": "Unser", "given": "Michael", "initials": "M"}, {"family": "Mu\u00f1oz-Barrutia", "given": "Arrate", "initials": "A", "orcid": "0000-0002-1573-1661", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1f71dcceb0284105a7033f2ed195b9c1.json"}}, {"family": "Sage", "given": "Daniel", "initials": "D", "orcid": "0000-0002-1150-1623", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/919b0180005444d88757db8e63b80d83.json"}}], "type": "journal article", "published": "2021-10-00", "journal": {"title": "Nat. Methods", "issn": "1548-7105", "volume": "18", "issue": "10", "pages": "1192-1195", "issn-l": "1548-7091"}, "abstract": "DeepImageJ is a user-friendly solution that enables the generic use of pre-trained deep learning models for biomedical image analysis in ImageJ. The deepImageJ environment gives access to the largest bioimage repository of pre-trained deep learning models (BioImage Model Zoo). Hence, nonexperts can easily perform common image processing tasks in life-science research with deep learning-based tools including pixel and object classification, instance segmentation, denoising or virtual staining. DeepImageJ is compatible with existing state of the art solutions and it is equipped with utility tools for developers to include new models. Very recently, several training frameworks have adopted the deepImageJ format to deploy their work in one of the most used softwares in the field (ImageJ). Beyond its direct use, we expect deepImageJ to contribute to the broader dissemination and reuse of deep learning models in life sciences applications and bioimage informatics.", "doi": "10.1038/s41592-021-01262-9", "pmid": "34594030", "labels": {"DDLS Fellow": "", "Wei Ouyang": ""}, "xrefs": [{"db": "pii", "key": "10.1038/s41592-021-01262-9"}], "notes": [], "created": "2026-08-20T09:02:47.487Z", "modified": "2026-09-23T06:42:20.513Z"}, {"entity": "publication", "iuid": "57540c0030c844ecb2c1b3bbe718c865", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/57540c0030c844ecb2c1b3bbe718c865.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/57540c0030c844ecb2c1b3bbe718c865"}}, "title": "Combined metabolic activators therapy ameliorates liver fat in nonalcoholic fatty liver disease patients.", "authors": [{"family": "Zeybel", "given": "Mujdat", "initials": "M"}, {"family": "Altay", "given": "Ozlem", "initials": "O"}, {"family": "Arif", "given": "Muhammad", "initials": "M", "orcid": "0000-0003-2261-0881", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c8ffc9889ace44e3b992816601b817e2.json"}}, {"family": "Li", "given": "Xiangyu", "initials": "X"}, {"family": "Yang", "given": "Hong", "initials": "H"}, {"family": "Fredolini", "given": "Claudia", "initials": "C"}, {"family": "Akyildiz", "given": "Murat", "initials": "M"}, {"family": "Saglam", "given": "Burcin", "initials": "B"}, {"family": "Gonenli", "given": "Mehmet Gokhan", "initials": "MG", "orcid": "0000-0003-2925-7048", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2dd670c20c0d4a138211a430b2313be6.json"}}, {"family": "Ural", "given": "Dilek", "initials": "D", "orcid": "0000-0003-0224-1433", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/adb6b767f9504957a4ff3a7b3daee987.json"}}, {"family": "Kim", "given": "Woonghee", "initials": "W"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/022e140799b6466ea123319c3d70c76e.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f46e4161be08458994efddb75ed75874.json"}}, {"family": "Shoaie", "given": "Saeed", "initials": "S"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/33f2b49a39ed4e54ba77dfe397ed3087.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Bor\u00e9n", "given": "Jan", "initials": "J", "orcid": "0000-0003-0786-8091", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/73a770eb9e614448a046b8e9199052e9.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca58bf2d214047e0ae5e38a42a0f2808.json"}}], "type": "journal article", "published": "2021-10-00", "journal": {"title": "Mol Syst Biol", "issn": "1744-4292", "issn-l": "1744-4292", "volume": "17", "issue": "10", "pages": "e10459"}, "abstract": "Nonalcoholic fatty liver disease (NAFLD) refers to excess fat accumulation in the liver. In animal experiments and human kinetic study, we found that administration of combined metabolic activators (CMAs) promotes the oxidation of fat, attenuates the resulting oxidative stress, activates mitochondria, and eventually removes excess fat from the liver. Here, we tested the safety and efficacy of CMA in NAFLD patients in a placebo-controlled 10-week study. We found that CMA significantly decreased hepatic steatosis and levels of aspartate aminotransferase, alanine aminotransferase, uric acid, and creatinine, whereas found no differences on these variables in the placebo group after adjustment for weight loss. By integrating clinical data with plasma metabolomics and inflammatory proteomics as well as oral and gut metagenomic data, we revealed the underlying molecular mechanisms associated with the reduced hepatic fat and inflammation in NAFLD patients and identified the key players involved in the host-microbiome interactions. In conclusion, we showed that CMA can be used to develop a pharmacological treatment strategy in NAFLD patients.", "doi": "10.15252/msb.202110459", "pmid": "34694070", "labels": {"Saeed Shoaie": "", "SciLifeLab Fellow": "", "Adil Mardinoglu": "", "DDLS Fellow": "", "Muhammad Arif": ""}, "xrefs": [{"db": "pmc", "key": "PMC8724764"}, {"db": "ClinicalTrials.gov", "key": "NCT04330326"}], "notes": [], "created": "2021-12-13T15:23:23.220Z", "modified": "2026-09-23T10:25:02.022Z"}, {"entity": "publication", "iuid": "9579d91056f847f588d28f0d90762921", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9579d91056f847f588d28f0d90762921.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9579d91056f847f588d28f0d90762921"}}, "title": "A practical guide to large-scale docking.", "authors": [{"family": "Bender", "given": "Brian J", "initials": "BJ"}, {"family": "Gahbauer", "given": "Stefan", "initials": "S", "orcid": "0000-0002-3115-9757", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e4fe0c3bcf964f63a9244f5a93219fec.json"}}, {"family": "Luttens", "given": "Andreas", "initials": "A", "orcid": "0000-0003-2915-7901", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d2944edc47eb4b639f1c61ae7b94b60a.json"}}, {"family": "Lyu", "given": "Jiankun", "initials": "J"}, {"family": "Webb", "given": "Chase M", "initials": "CM"}, {"family": "Stein", "given": "Reed M", "initials": "RM"}, {"family": "Fink", "given": "Elissa A", "initials": "EA"}, {"family": "Balius", "given": "Trent E", "initials": "TE", "orcid": "0000-0002-6811-4667", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7c4b9d95e87549c487f4a386273264a2.json"}}, {"family": "Carlsson", "given": "Jens", "initials": "J"}, {"family": "Irwin", "given": "John J", "initials": "JJ"}, {"family": "Shoichet", "given": "Brian K", "initials": "BK"}], "type": "journal article", "published": "2021-10-00", "journal": {"title": "Nat Protoc", "issn": "1750-2799", "volume": "16", "issue": "10", "pages": "4799-4832", "issn-l": null}, "abstract": "Structure-based docking screens of large compound libraries have become common in early drug and probe discovery. As computer efficiency has improved and compound libraries have grown, the ability to screen hundreds of millions, and even billions, of compounds has become feasible for modest-sized computer clusters. This allows the rapid and cost-effective exploration and categorization of vast chemical space into a subset enriched with potential hits for a given target. To accomplish this goal at speed, approximations are used that result in undersampling of possible configurations and inaccurate predictions of absolute binding energies. Accordingly, it is important to establish controls, as are common in other fields, to enhance the likelihood of success in spite of these challenges. Here we outline best practices and control docking calculations that help evaluate docking parameters for a given target prior to undertaking a large-scale prospective screen, with exemplification in one particular target, the melatonin receptor, where following this procedure led to direct docking hits with activities in the subnanomolar range. Additional controls are suggested to ensure specific activity for experimentally validated hit compounds. These guidelines should be useful regardless of the docking software used. Docking software described in the outlined protocol (DOCK3.7) is made freely available for academic research to explore new hits for a range of targets.", "doi": "10.1038/s41596-021-00597-z", "pmid": "34561691", "labels": {"Jens Carlsson": "", "SciLifeLab Fellow": "", "Andreas Luttens": "", "DDLS Fellow": ""}, "xrefs": [{"db": "mid", "key": "NIHMS1744552"}, {"db": "pmc", "key": "PMC8522653"}, {"db": "pii", "key": "10.1038/s41596-021-00597-z"}], "notes": [], "created": "2021-12-05T12:23:55.418Z", "modified": "2026-09-23T06:32:09.433Z"}, {"entity": "publication", "iuid": "b65e6e54c6054588b6912118bfd56f84", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b65e6e54c6054588b6912118bfd56f84.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b65e6e54c6054588b6912118bfd56f84"}}, "title": "Morphological Features Extracted by AI Associated with Spatial Transcriptomics in Prostate Cancer.", "authors": [{"family": "Chelebian", "given": "Eduard", "initials": "E", "orcid": "0000-0001-6852-6605", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a91f8ed142fa424c9a81328bf2595fbe.json"}}, {"family": "Avenel", "given": "Christophe", "initials": "C", "orcid": "0000-0002-1835-921X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b65fab9c103c4551b457a801988ce728.json"}}, {"family": "Kartasalo", "given": "Kimmo", "initials": "K", "orcid": "0000-0002-9470-4783", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7c6fc97c06ed456c8bdd1f03db8a9b72.json"}}, {"family": "Marklund", "given": "Maja", "initials": "M", "orcid": "0000-0003-2627-2437", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/037e17f3f330479fa3bd48fcd0c55684.json"}}, {"family": "Tanoglidi", "given": "Anna", "initials": "A", "orcid": "0000-0002-1217-2219", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/71297f7922214a47bad7d21f2dfb1d51.json"}}, {"family": "Mirtti", "given": "Tuomas", "initials": "T", "orcid": "0000-0003-0455-9891", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c1963bc5086f4b45b9a48cb60115d578.json"}}, {"family": "Colling", "given": "Richard", "initials": "R", "orcid": "0000-0001-6344-9081", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/368d85f93e2346e5be917031d742ec51.json"}}, {"family": "Erickson", "given": "Andrew", "initials": "A", "orcid": "0000-0002-4850-4086", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e1725ce48b1945af8a7df8d084403a37.json"}}, {"family": "Lamb", "given": "Alastair D", "initials": "AD", "orcid": "0000-0002-2968-7155", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f447a100ea1f440f820859d85d66770d.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d9fa47767cd14ef2b9528c8b998cf095.json"}}, {"family": "W\u00e4hlby", "given": "Carolina", "initials": "C", "orcid": "0000-0002-4139-7003", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/833afe3444d84c24be12ea1468563bea.json"}}], "type": "journal article", "published": "2021-09-28", "journal": {"title": "Cancers (Basel)", "issn": "2072-6694", "issn-l": "2072-6694", "volume": "13", "issue": "19", "pages": null}, "abstract": "Prostate cancer is a common cancer type in men, yet some of its traits are still under-explored. One reason for this is high molecular and morphological heterogeneity. The purpose of this study was to develop a method to gain new insights into the connection between morphological changes and underlying molecular patterns. We used artificial intelligence (AI) to analyze the morphology of seven hematoxylin and eosin (H&E)-stained prostatectomy slides from a patient with multi-focal prostate cancer. We also paired the slides with spatially resolved expression for thousands of genes obtained by a novel spatial transcriptomics (ST) technique. As both spaces are highly dimensional, we focused on dimensionality reduction before seeking associations between them. Consequently, we extracted morphological features from H&E images using an ensemble of pre-trained convolutional neural networks and proposed a workflow for dimensionality reduction. To summarize the ST data into genetic profiles, we used a previously proposed factor analysis. We found that the regions were automatically defined, outlined by unsupervised clustering, associated with independent manual annotations, in some cases, finding further relevant subdivisions. The morphological patterns were also correlated with molecular profiles and could predict the spatial variation of individual genes. This novel approach enables flexible unsupervised studies relating morphological and genetic heterogeneity using AI to be carried out.", "doi": "10.3390/cancers13194837", "pmid": "34638322", "labels": {"Kimmo Kartasalo": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC8507756"}, {"db": "pii", "key": "cancers13194837"}], "notes": [], "created": "2024-11-05T16:08:22.249Z", "modified": "2026-09-23T10:40:01.595Z"}, {"entity": "publication", "iuid": "c6102e8d1468457bbe1d45499dd63de3", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c6102e8d1468457bbe1d45499dd63de3.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c6102e8d1468457bbe1d45499dd63de3"}}, "title": "Inferring Genome-Wide Correlations of Mutation Fitness Effects between Populations.", "authors": [{"family": "Huang", "given": "Xin", "initials": "X", "orcid": "0000-0002-9918-9602", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/27a6d482c13b437a8ba45a652135aef7.json"}}, {"family": "Fortier", "given": "Alyssa Lyn", "initials": "AL", "orcid": "0000-0001-5964-2540", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/11d3d037ce724d80b7d2ea2164df1c5d.json"}}, {"family": "Coffman", "given": "Alec J", "initials": "AJ"}, {"family": "Struck", "given": "Travis J", "initials": "TJ", "orcid": "0000-0001-7161-5107", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7b3ae2b67f30416cad05239492693184.json"}}, {"family": "Irby", "given": "Megan N", "initials": "MN"}, {"family": "James", "given": "Jennifer E", "initials": "JE", "orcid": "0000-0003-0518-6783", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4b807f7ab8f46f8a5e927e1b090d662.json"}}, {"family": "Le\u00f3n-Burguete", "given": "Jos\u00e9 E", "initials": "JE"}, {"family": "Ragsdale", "given": "Aaron P", "initials": "AP", "orcid": "0000-0003-0715-3432", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6cfa150360d54232b73bed31a8f6fa44.json"}}, {"family": "Gutenkunst", "given": "Ryan N", "initials": "RN", "orcid": "0000-0002-8659-0579", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9a32f8c1377947e0bc6185bd9c645a7e.json"}}], "type": "journal article", "published": "2021-09-27", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "issn-l": "0737-4038", "volume": "38", "issue": "10", "pages": "4588-4602"}, "abstract": "The effect of a mutation on fitness may differ between populations depending on environmental and genetic context, but little is known about the factors that underlie such differences. To quantify genome-wide correlations in mutation fitness effects, we developed a novel concept called a joint distribution of fitness effects (DFE) between populations. We then proposed a new statistic w to measure the DFE correlation between populations. Using simulation, we showed that inferring the DFE correlation from the joint allele frequency spectrum is statistically precise and robust. Using population genomic data, we inferred DFE correlations of populations in humans, Drosophila melanogaster, and wild tomatoes. In these species, we found that the overall correlation of the joint DFE was inversely related to genetic differentiation. In humans and D. melanogaster, deleterious mutations had a lower DFE correlation than tolerated mutations, indicating a complex joint DFE. Altogether, the DFE correlation can be reliably inferred, and it offers extensive insight into the genetics of population divergence.", "doi": "10.1093/molbev/msab162", "pmid": "34043790", "labels": {"Jennifer James": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC8476148"}, {"db": "pii", "key": "6287068"}], "notes": [], "created": "2024-11-27T09:25:37.774Z", "modified": "2024-11-29T09:36:38.141Z"}, {"entity": "publication", "iuid": "ac4436481a8e4c5fa3c6f8589d010029", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ac4436481a8e4c5fa3c6f8589d010029.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ac4436481a8e4c5fa3c6f8589d010029"}}, "title": "A structural biology community assessment of AlphaFold 2 applications", "authors": [{"family": "Akdel", "given": "Mehmet", "initials": "M", "orcid": "0000-0002-6092-3494", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/adcc39b269804e179cbea223cc8dc83d.json"}}, {"family": "Pires", "given": "Douglas E V", "initials": "DEV", "orcid": "0000-0002-3004-2119", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/536bf1b7030d40a49643ccaa4e6a6c8e.json"}}, {"family": "Porta Pardo", "given": "Eduard", "initials": "E", "orcid": "0000-0001-7900-4239", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3705290c0dc44526afe59c6837df09c2.json"}}, {"family": "J\u00e4nes", "given": "J\u00fcrgen", "initials": "J", "orcid": "0000-0002-2540-1236", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/59c4858a6ab9448695b233e09ff58698.json"}}, {"family": "Zalevsky", "given": "Arthur O", "initials": "AO", "orcid": "0000-0001-6987-8119", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7fdb6c4d5c9b4feb83952a3674708a12.json"}}, {"family": "M\u00e9sz\u00e1ros", "given": "B\u00e1lint", "initials": "B", "orcid": "0000-0003-0919-4449", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f5847cba0f8f43e6b6827a40ddf47f2c.json"}}, {"family": "Bryant", "given": "Patrick", "initials": "P", "orcid": "0000-0003-3439-1866", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a683bcf98234ff09b2398976583b66f.json"}}, {"family": "Good", "given": "Lydia L", "initials": "LL", "orcid": "0000-0001-5308-8542", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6b413593ce63451b9e3a3e79cbd20a53.json"}}, {"family": "Laskowski", "given": "Roman A", "initials": "RA", "orcid": "0000-0001-5528-0087", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1b0e4268b73b406d823b6b66059f2a53.json"}}, {"family": "Pozzati", "given": "Gabriele", "initials": "G", "orcid": "0000-0002-4303-9939", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/94129216debe4e22ab3f3b74c33f9ab9.json"}}, {"family": "Shenoy", "given": "Aditi", "initials": "A", "orcid": "0000-0001-7748-2501", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/35bef00b985a45d59602675316e3d706.json"}}, {"family": "Zhu", "given": "Wensi", "initials": "W"}, {"family": "Kundrotas", "given": "Petras", "initials": "P", "orcid": "0000-0001-5080-1664", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e645003f2000464c9e289ccd3b92ce68.json"}}, {"family": "Ruiz Serra", "given": "Victoria", "initials": "V", "orcid": "0000-0003-3991-0514", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0e03258443954d6d978ce8efb02a37b6.json"}}, {"family": "Rodrigues", "given": "Carlos H M", "initials": "CHM"}, {"family": "Dunham", "given": "Alistair S", "initials": "AS", "orcid": "0000-0001-9076-3025", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/41348047cf374b149851ea1b9bca2014.json"}}, {"family": "Burke", "given": "David", "initials": "D", "orcid": "0000-0001-8830-3951", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0ae9a94abf5e47778d59e4f3c9d8e62e.json"}}, {"family": "Borkakoti", "given": "Neera", "initials": "N", "orcid": "0000-0002-5878-1490", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/13aef1cd03bd4ed0803d58e78851fad4.json"}}, {"family": "Velankar", "given": "Sameer", "initials": "S"}, {"family": "Frost", "given": "Adam", "initials": "A", "orcid": "0000-0003-2231-2577", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2b31e4961e0c457c85f8b0729a492a57.json"}}, {"family": "Lindorff-Larsen", "given": "Kresten", "initials": "K", "orcid": "0000-0002-4750-6039", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2cd1f0559c6d4d58a1459dd38f851c93.json"}}, {"family": "Valencia", "given": "Alfonso", "initials": "A"}, {"family": "Ovchinnikov", "given": "Sergey", "initials": "S", "orcid": "0000-0003-2774-2744", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9c1c152b72314d178a2f01630d3ebbb7.json"}}, {"family": "Durairaj", "given": "Janani", "initials": "J", "orcid": "0000-0002-1698-4556", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bbc37e3024a34e18b93c50bd7ce6c3a7.json"}}, {"family": "Ascher", "given": "David B", "initials": "DB", "orcid": "0000-0003-2948-2413", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d141d7d1cbad4e87aef2a8878a845872.json"}}, {"family": "Thornton", "given": "Janet M", "initials": "JM", "orcid": "0000-0003-0824-4096", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/af0a3c9c4f12412d9709e6065c8d0813.json"}}, {"family": "Davey", "given": "Norman E", "initials": "NE", "orcid": "0000-0001-6988-4850", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dbb4780925604932b0853a1f8ad75145.json"}}, {"family": "Stein", "given": "Amelie", "initials": "A", "orcid": "0000-0002-5862-1681", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b99e2fc33a714b929e442e312f7513f1.json"}}, {"family": "Elofsson", "given": "Arne", "initials": "A", "orcid": "0000-0002-7115-9751", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/248e70e81bd64f31a5f83e6e329bba95.json"}}, {"family": "Croll", "given": "Tristan I", "initials": "TI", "orcid": "0000-0002-3514-8377", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/71c79d83429041ee8f4f47e6e4fa55f9.json"}}, {"family": "Beltrao", "given": "Pedro", "initials": "P", "orcid": "0000-0002-2724-7703", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/952eba119d2e4d4b89e14b294c5c6885.json"}}], "type": "posted-content", "published": "2021-09-26", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2021.09.26.461876", "pmid": null, "labels": {"Patrick Bryant": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T10:06:50.640Z", "modified": "2026-09-23T13:40:56.430Z"}, {"entity": "publication", "iuid": "9c34f14cd06c4798b7ab4770dcae41b6", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9c34f14cd06c4798b7ab4770dcae41b6.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9c34f14cd06c4798b7ab4770dcae41b6"}}, "title": "Systems Analysis Reveals Ageing-Related Perturbations in Retinoids and Sex Hormones in Alzheimer's and Parkinson's Diseases.", "authors": [{"family": "Lam", "given": "Simon", "initials": "S", "orcid": "0000-0002-4476-0971", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bdf5adecfed749b4a66cdda5cd08ee24.json"}}, {"family": "Hartmann", "given": "Nils", "initials": "N"}, {"family": "Benfeitas", "given": "Rui", "initials": "R", "orcid": "0000-0001-7972-0083", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e2ec344c501496796be3250fd563699.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f46e4161be08458994efddb75ed75874.json"}}, {"family": "Arif", "given": "Muhammad", "initials": "M", "orcid": "0000-0003-2261-0881", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c8ffc9889ace44e3b992816601b817e2.json"}}, {"family": "Turkez", "given": "Hasan", "initials": "H"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Englert", "given": "Christoph", "initials": "C", "orcid": "0000-0002-5931-3189", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/edbf24bf4c4c463e8215619ca54b2630.json"}}, {"family": "Knight", "given": "Robert", "initials": "R"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca58bf2d214047e0ae5e38a42a0f2808.json"}}], "type": "journal article", "published": "2021-09-24", "journal": {"title": "Biomedicines", "issn": "2227-9059", "volume": "9", "issue": "10", "issn-l": null}, "abstract": "Neurodegenerative diseases, including Alzheimer's (AD) and Parkinson's diseases (PD), are complex heterogeneous diseases with highly variable patient responses to treatment. Due to the growing evidence for ageing-related clinical and pathological commonalities between AD and PD, these diseases have recently been studied in tandem. In this study, we analysed transcriptomic data from AD and PD patients, and stratified these patients into three subclasses with distinct gene expression and metabolic profiles. Through integrating transcriptomic data with a genome-scale metabolic model and validating our findings by network exploration and co-analysis using a zebrafish ageing model, we identified retinoids as a key ageing-related feature in all subclasses of AD and PD. We also demonstrated that the dysregulation of androgen metabolism by three different independent mechanisms is a source of heterogeneity in AD and PD. Taken together, our work highlights the need for stratification of AD/PD patients and development of personalised and precision medicine approaches based on the detailed characterisation of these subclasses.", "doi": "10.3390/biomedicines9101310", "pmid": "34680427", "labels": {"Adil Mardinoglu": "", "SciLifeLab Fellow": "", "DDLS Fellow": "", "Muhammad Arif": ""}, "xrefs": [{"db": "pmc", "key": "PMC8533098"}, {"db": "pii", "key": "biomedicines9101310"}], "notes": [], "created": "2023-12-04T15:06:22.249Z", "modified": "2026-09-23T11:45:55.742Z"}, {"entity": "publication", "iuid": "1291a8b321634882844a3e6520ab3515", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1291a8b321634882844a3e6520ab3515.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1291a8b321634882844a3e6520ab3515"}}, "title": "Using informative features in machine learning based method for COVID-19 drug repurposing.", "authors": [{"family": "Aghdam", "given": "Rosa", "initials": "R", "orcid": "0000-0001-9045-9592", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0179bdcc8b8e4bd68549403ed5b66b79.json"}}, {"family": "Habibi", "given": "Mahnaz", "initials": "M", "orcid": "0000-0002-8969-2706", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f04af4e059814b78bfb107c3a5782f70.json"}}, {"family": "Taheri", "given": "Golnaz", "initials": "G", "orcid": "0000-0002-2741-0355", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/014c217121d346b2b371bbc1c2fede57.json"}}], "type": "journal article", "published": "2021-09-20", "journal": {"title": "J Cheminform", "issn": "1758-2946", "issn-l": "1758-2946", "volume": "13", "issue": "1", "pages": "70"}, "abstract": "Coronavirus disease 2019 (COVID-19) is caused by a novel virus named Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). This virus induced a large number of deaths and millions of confirmed cases worldwide, creating a serious danger to public health. However, there are no specific therapies or drugs available for COVID-19 treatment. While new drug discovery is a long process, repurposing available drugs for COVID-19 can help recognize treatments with known clinical profiles. Computational drug repurposing methods can reduce the cost, time, and risk of drug toxicity. In this work, we build a graph as a COVID-19 related biological network. This network is related to virus targets or their associated biological processes. We select essential proteins in the constructed biological network that lead to a major disruption in the network. Our method from these essential proteins chooses 93 proteins related to COVID-19 pathology. Then, we propose multiple informative features based on drug-target and protein-protein interaction information. Through these informative features, we find five appropriate clusters of drugs that contain some candidates as potential COVID-19 treatments. To evaluate our results, we provide statistical and clinical evidence for our candidate drugs. From our proposed candidate drugs, 80% of them were studied in other studies and clinical trials.", "doi": "10.1186/s13321-021-00553-9", "pmid": "34544500", "labels": {"Golnaz Taheri": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC8451172"}, {"db": "pii", "key": "10.1186/s13321-021-00553-9"}], "notes": [], "created": "2025-03-21T09:08:40.624Z", "modified": "2026-09-23T10:28:39.502Z"}, {"entity": "publication", "iuid": "966ba2ab1a9f462abbffa87893acb845", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/966ba2ab1a9f462abbffa87893acb845.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/966ba2ab1a9f462abbffa87893acb845"}}, "title": "A method for intuitively extracting macromolecular dynamics from structural disorder", "authors": [{"family": "Pearce", "given": "Nicholas M", "initials": "NM", "orcid": "0000-0002-6693-8603", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/07d6d5de91cc4120b2bf996ca578a13e.json"}}, {"family": "Gros", "given": "Piet", "initials": "P", "orcid": "0000-0002-7782-2585", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/590881ded1d542b8b61831c00b0fdb87.json"}}], "type": "journal-article", "published": "2021-09-17", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "12", "issue": "1", "pages": "5493"}, "abstract": "Macromolecular dynamics manifest as disorder in structure determination, which is subsequently accounted for by displacement parameters (also called temperature factors, or B-factors) or alternate conformations. Though B-factors contain detailed information about structural dynamics, they are the total of multiple sources of disorder, making them difficult to interpret and thus little-used in structural analysis. We report here an analytical approach for decomposing molecular disorder into a parsimonious hierarchical series of contributions, providing an intuitive basis for quantitative structural-dynamics analysis. We demonstrate the decomposition of disorder on example SARS-CoV-2 and STEAP4 structures, from both crystallographic and cryo-electron microscopy data, and reveal how understanding of the macromolecular disorder leads to deeper understanding of molecular motions and flexibility, and suggests hypotheses for molecular mechanisms.", "doi": "10.1038/s41467-021-25814-x", "pmid": "34535675", "labels": {"Nicholas Pearce": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC8448762"}, {"db": "pii", "key": "10.1038/s41467-021-25814-x"}], "notes": [], "created": "2022-12-05T18:57:28.772Z", "modified": "2025-12-04T16:56:51.562Z"}, {"entity": "publication", "iuid": "e598104896bd469db9c0e49977fbeae2", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e598104896bd469db9c0e49977fbeae2.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e598104896bd469db9c0e49977fbeae2"}}, "title": "Ancient and modern genomes unravel the evolutionary history of the rhinoceros family.", "authors": [{"family": "Liu", "given": "Shanlin", "initials": "S"}, {"family": "Westbury", "given": "Michael V", "initials": "MV"}, {"family": "Dussex", "given": "Nicolas", "initials": "N"}, {"family": "Mitchell", "given": "Kieren J", "initials": "KJ"}, {"family": "Sinding", "given": "Mikkel-Holger S", "initials": "MS"}, {"family": "Heintzman", "given": "Peter D", "initials": "PD"}, {"family": "Duch\u00eane", "given": "David A", "initials": "DA"}, {"family": "Kapp", "given": "Joshua D", "initials": "JD"}, {"family": "von Seth", "given": "Johanna", "initials": "J"}, {"family": "Heiniger", "given": "Holly", "initials": "H"}, {"family": "S\u00e1nchez-Barreiro", "given": "F\u00e1tima", "initials": "F"}, {"family": "Margaryan", "given": "Ashot", "initials": "A"}, {"family": "Andr\u00e9-Olsen", "given": "Remi", "initials": "R"}, {"family": "De Cahsan", "given": "Binia", "initials": "B"}, {"family": "Meng", "given": "Guanliang", "initials": "G"}, {"family": "Yang", "given": "Chentao", "initials": "C"}, {"family": "Chen", "given": "Lei", "initials": "L"}, {"family": "van der Valk", "given": "Tom", "initials": "T"}, {"family": "Moodley", "given": "Yoshan", "initials": "Y"}, {"family": "Rookmaaker", "given": "Kees", "initials": "K"}, {"family": "Bruford", "given": "Michael W", "initials": "MW"}, {"family": "Ryder", "given": "Oliver", "initials": "O"}, {"family": "Steiner", "given": "Cynthia", "initials": "C"}, {"family": "Bruins-van Sonsbeek", "given": "Linda G R", "initials": "LGR"}, {"family": "Vartanyan", "given": "Sergey", "initials": "S"}, {"family": "Guo", "given": "Chunxue", "initials": "C"}, {"family": "Cooper", "given": "Alan", "initials": "A"}, {"family": "Kosintsev", "given": "Pavel", "initials": "P"}, {"family": "Kirillova", "given": "Irina", "initials": "I"}, {"family": "Lister", "given": "Adrian M", "initials": "AM"}, {"family": "Marques-Bonet", "given": "Tomas", "initials": "T"}, {"family": "Gopalakrishnan", "given": "Shyam", "initials": "S"}, {"family": "Dunn", "given": "Robert R", "initials": "RR"}, {"family": "Lorenzen", "given": "Eline D", "initials": "ED"}, {"family": "Shapiro", "given": "Beth", "initials": "B"}, {"family": "Zhang", "given": "Guojie", "initials": "G"}, {"family": "Antoine", "given": "Pierre-Olivier", "initials": "PO"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L"}, {"family": "Gilbert", "given": "M Thomas P", "initials": "MTP"}], "type": "journal article", "published": "2021-09-16", "journal": {"title": "Cell", "issn": "1097-4172", "volume": "184", "issue": "19", "pages": "4874-4885.e16", "issn-l": "0092-8674"}, "abstract": "Only five species of the once-diverse Rhinocerotidae remain, making the reconstruction of their evolutionary history a challenge to biologists since Darwin. We sequenced genomes from five rhinoceros species (three extinct and two living), which we compared to existing data from the remaining three living species and a range of outgroups. We identify an early divergence between extant African and Eurasian lineages, resolving a key debate regarding the phylogeny of extant rhinoceroses. This early Miocene (\u223c16 million years ago [mya]) split post-dates the land bridge formation between the Afro-Arabian and Eurasian landmasses. Our analyses also show that while rhinoceros genomes in general exhibit low levels of genome-wide diversity, heterozygosity is lowest and inbreeding is highest in the modern species. These results suggest that while low genetic diversity is a long-term feature of the family, it has been particularly exacerbated recently, likely reflecting recent anthropogenic-driven population declines.", "doi": "10.1016/j.cell.2021.07.032", "pmid": "34433011", "labels": {"DDLS Fellow": "", "Tom van der Valk": ""}, "xrefs": [{"db": "pii", "key": "S0092-8674(21)00891-6"}], "notes": [], "created": "2026-09-23T07:39:28.719Z", "modified": "2026-09-23T07:39:28.739Z"}, {"entity": "publication", "iuid": "04185d7a1c7b4735b6468035b587a9e2", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/04185d7a1c7b4735b6468035b587a9e2.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/04185d7a1c7b4735b6468035b587a9e2"}}, "title": "Improved prediction of protein-protein interactions using AlphaFold2", "authors": [{"family": "Bryant", "given": "P", "initials": "P", "orcid": "0000-0003-3439-1866", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a683bcf98234ff09b2398976583b66f.json"}}, {"family": "Pozzati", "given": "G", "initials": "G", "orcid": "0000-0002-4303-9939", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/94129216debe4e22ab3f3b74c33f9ab9.json"}}, {"family": "Elofsson", "given": "A", "initials": "A", "orcid": "0000-0002-7115-9751", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/248e70e81bd64f31a5f83e6e329bba95.json"}}], "type": "posted-content", "published": "2021-09-15", "journal": {"title": "bioRxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2021.09.15.460468", "pmid": null, "labels": {"Patrick Bryant": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2026-08-20T10:06:48.845Z", "modified": "2026-10-05T07:14:11.083Z"}, {"entity": "publication", "iuid": "47ed89c5564e49e39e4ca77e20223fcf", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/47ed89c5564e49e39e4ca77e20223fcf.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/47ed89c5564e49e39e4ca77e20223fcf"}}, "title": "ShareLoc \u2013 an open platform for sharing localization microscopy data", "authors": [{"family": "Bai", "given": "Jiachuan", "initials": "J"}, {"family": "Ouyang", "given": "Wei", "initials": "W"}, {"family": "Singh", "given": "Manish Kumar", "initials": "MK"}, {"family": "Leterrier", "given": "Christophe", "initials": "C"}, {"family": "Barthelemy", "given": "Paul", "initials": "P"}, {"family": "Barnett", "given": "Samuel F H", "initials": "SFH"}, {"family": "Klein", "given": "Teresa", "initials": "T"}, {"family": "Sauer", "given": "Markus", "initials": "M"}, {"family": "Kanchanawong", "given": "Pakorn", "initials": "P"}, {"family": "Bourg", "given": "Nicolas", "initials": "N"}, {"family": "Cohen", "given": "Mickael M", "initials": "MM"}, {"family": "Lelandais", "given": "Beno\u00eet", "initials": "B"}, {"family": "Zimmer", "given": "Christophe", "initials": "C"}], "type": "posted-content", "published": "2021-09-09", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2021.09.08.459385", "pmid": null, "labels": {"DDLS Fellow": "", "Wei Ouyang": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T10:06:44.548Z", "modified": "2026-09-23T14:43:45.853Z"}, {"entity": "publication", "iuid": "d959760812644e3384dd9a59dcad7c95", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d959760812644e3384dd9a59dcad7c95.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d959760812644e3384dd9a59dcad7c95"}}, "title": "Multi-omics approaches for revealing the complexity of cardiovascular disease.", "authors": [{"family": "Doran", "given": "Stephen", "initials": "S"}, {"family": "Arif", "given": "Muhammad", "initials": "M"}, {"family": "Lam", "given": "Simon", "initials": "S"}, {"family": "Bayraktar", "given": "Abdulahad", "initials": "A"}, {"family": "Turkez", "given": "Hasan", "initials": "H"}, {"family": "Uhlen", "given": "Mathias", "initials": "M"}, {"family": "Boren", "given": "Jan", "initials": "J"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}], "type": "journal article", "published": "2021-09-02", "journal": {"title": "Brief. Bioinformatics", "issn": "1477-4054", "volume": "22", "issue": "5", "issn-l": "1467-5463"}, "abstract": "The development and progression of cardiovascular disease (CVD) can mainly be attributed to the narrowing of blood vessels caused by atherosclerosis and thrombosis, which induces organ damage that will result in end-organ dysfunction characterized by events such as myocardial infarction or stroke. It is also essential to consider other contributory factors to CVD, including cardiac remodelling caused by cardiomyopathies and co-morbidities with other diseases such as chronic kidney disease. Besides, there is a growing amount of evidence linking the gut microbiota to CVD through several metabolic pathways. Hence, it is of utmost importance to decipher the underlying molecular mechanisms associated with these disease states to elucidate the development and progression of CVD. A wide array of systems biology approaches incorporating multi-omics data have emerged as an invaluable tool in establishing alterations in specific cell types and identifying modifications in signalling events that promote disease development. Here, we review recent studies that apply multi-omics approaches to further understand the underlying causes of CVD and provide possible treatment strategies by identifying novel drug targets and biomarkers. We also discuss very recent advances in gut microbiota research with an emphasis on how diet and microbial composition can impact the development of CVD. Finally, we present various biological network analyses and other independent studies that have been employed for providing mechanistic explanation and developing treatment strategies for end-stage CVD, namely myocardial infarction and stroke.", "doi": "10.1093/bib/bbab061", "pmid": "33725119", "labels": {"SciLifeLab Fellow": "", "DDLS Fellow": "", "Adil Mardinoglu": "", "Muhammad Arif": ""}, "xrefs": [{"db": "pmc", "key": "PMC8425417"}, {"db": "pii", "key": "6174236"}], "notes": [], "created": "2026-08-20T09:38:58.375Z", "modified": "2026-09-23T07:39:10.902Z"}, {"entity": "publication", "iuid": "6e534e4c274348dd95cc16c98e36c2d8", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/6e534e4c274348dd95cc16c98e36c2d8.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/6e534e4c274348dd95cc16c98e36c2d8"}}, "title": "Association of Diet Quality With Prevalence of Clonal Hematopoiesis and Adverse Cardiovascular Events.", "authors": [{"family": "Bhattacharya", "given": "Romit", "initials": "R"}, {"family": "Zekavat", "given": "Seyedeh Maryam", "initials": "SM"}, {"family": "Uddin", "given": "Md Mesbah", "initials": "MM"}, {"family": "Pirruccello", "given": "James", "initials": "J"}, {"family": "Niroula", "given": "Abhishek", "initials": "A"}, {"family": "Gibson", "given": "Christopher", "initials": "C"}, {"family": "Griffin", "given": "Gabriel K", "initials": "GK"}, {"family": "Libby", "given": "Peter", "initials": "P"}, {"family": "Ebert", "given": "Benjamin L", "initials": "BL"}, {"family": "Bick", "given": "Alexander", "initials": "A"}, {"family": "Natarajan", "given": "Pradeep", "initials": "P"}], "type": "journal article", "published": "2021-09-01", "journal": {"title": "JAMA Cardiol", "issn": "2380-6591", "volume": "6", "issue": "9", "pages": "1069-1077", "issn-l": "2380-6583"}, "abstract": "Clonal hematopoiesis of indeterminate potential (CHIP), the expansion of somatic leukemogenic variations in hematopoietic stem cells, has been associated with atherosclerotic cardiovascular disease. Because the inherited risk of developing CHIP is low, lifestyle elements such as dietary factors may be associated with the development and outcomes of CHIP.\n\nTo examine whether there is an association between diet quality and the prevalence of CHIP.\n\nThis retrospective cohort study used data from participants in the UK Biobank, an ongoing population-based study in the United Kingdom that examines whole-exome sequencing data and survey-based information on health-associated behaviors. Individuals from the UK Biobank were recruited between 2006 and 2010 and followed up prospectively with linkage to health data records through May 2020. The present study included 44 111 participants in the UK Biobank who were age 40 to 70 years, had data available from whole-exome sequencing of blood DNA, and were free of coronary artery disease (CAD) or hematologic cancer at baseline.\n\nDiet quality was categorized as unhealthy if the intake of healthy elements (fruits and vegetables) was lower than the median of all survey responses, and the intake of unhealthy elements (red meat, processed food, and added salt) was higher than the median. Diets were classified as healthy if the intake of healthy elements was higher than the median, and the intake of unhealthy elements was lower than the median. The presence of CHIP was detected by data from whole-exome sequencing of blood DNA.\n\nThe primary outcome was CHIP prevalence. Multivariable logistic regression analysis was used to examine the association between diet quality and the presence of CHIP. Multivariable Cox proportional hazards models were used to assess the association of incident events (acute coronary syndromes, coronary revascularization, or death) in each diet quality category stratified by the presence of CHIP.\n\nAmong 44 111 participants (mean [SD] age at time of blood sample collection, 56.3 [8.0] years; 24 507 women [55.6%]), 2271 individuals (5.1%) had an unhealthy diet, 38 552 individuals (87.4%) had an intermediate diet, and 3288 individuals (7.5%) had a healthy diet. A total of 2507 individuals (5.7%) had CHIP, and the prevalence of CHIP decreased as diet quality improved from unhealthy (162 of 2271 participants [7.1%]) to intermediate (2177 of 38 552 participants [5.7%]) to healthy (168 of 3288 participants [5.1%]; P = .003 for trend). Compared with individuals without CHIP who had an intermediate diet, the rates of incident cardiovascular events progressively decreased among those with CHIP who had an unhealthy diet (hazard ratio [HR], 1.52; 95% CI, 1.04-2.22) and those with CHIP who had a healthy diet (HR, 0.99; 95% CI, 0.62-1.58) over a median of 10.0 years (interquartile range, 9.6-10.4 years) of follow-up.\n\nThis cohort study suggests that an unhealthy diet quality may be associated with a higher prevalence of CHIP and higher rates of adverse cardiovascular events and death independent of CHIP status.", "doi": "10.1001/jamacardio.2021.1678", "pmid": "34106216", "labels": {"Abhishek Niroula": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC8190703"}, {"db": "pii", "key": "2780386"}], "notes": [], "created": "2023-11-20T11:27:52.476Z", "modified": "2023-11-20T11:27:52.501Z"}, {"entity": "publication", "iuid": "bb90da726f464519afc00e7c5c27b60a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/bb90da726f464519afc00e7c5c27b60a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/bb90da726f464519afc00e7c5c27b60a"}}, "title": "ZBTB33 is mutated in clonal hematopoiesis and myelodysplastic syndromes and impacts RNA splicing.", "authors": [{"family": "Beauchamp", "given": "Ellen M", "initials": "EM"}, {"family": "Leventhal", "given": "Matthew", "initials": "M"}, {"family": "Bernard", "given": "Elsa", "initials": "E", "orcid": "0000-0002-2057-7187", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cb3c2a92df6647f6ab8d6376d341cb35.json"}}, {"family": "Hoppe", "given": "Emma R", "initials": "ER", "orcid": "0000-0002-8544-9055", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b620bf8fe7954a388b70e646b7947178.json"}}, {"family": "Todisco", "given": "Gabriele", "initials": "G", "orcid": "0000-0001-6583-3829", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/769f70d382bc46cfbfffa0b5cd16710f.json"}}, {"family": "Creignou", "given": "Maria", "initials": "M", "orcid": "0000-0002-7629-0871", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7a6d401562a24e75922151cf45dba249.json"}}, {"family": "Gall\u00ec", "given": "Anna", "initials": "A", "orcid": "0000-0002-4039-3756", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/33104939e0fe439b892c5c0a28ef0032.json"}}, {"family": "Castellano", "given": "Cecilia A", "initials": "CA"}, {"family": "McConkey", "given": "Marie", "initials": "M"}, {"family": "Tarun", "given": "Akansha", "initials": "A"}, {"family": "Wong", "given": "Waihay", "initials": "W", "orcid": "0000-0003-2023-6590", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3a4e1a5be5c54646ab5881bc338bf6cd.json"}}, {"family": "Schenone", "given": "Monica", "initials": "M", "orcid": "0000-0002-6456-8768", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1941520ade1c43769f20eab7ee79970e.json"}}, {"family": "Stanclift", "given": "Caroline", "initials": "C", "orcid": "0000-0002-9208-8550", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e3e8016f9dce456197333416421b3e5e.json"}}, {"family": "Tanenbaum", "given": "Benjamin", "initials": "B"}, {"family": "Malolepsza", "given": "Edyta", "initials": "E"}, {"family": "Nilsson", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Bick", "given": "Alexander G", "initials": "AG", "orcid": "0000-0001-5824-9595", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d2da5a35a4984921b19dfafe64cea2de.json"}}, {"family": "Weinstock", "given": "Joshua S", "initials": "JS"}, {"family": "Miller", "given": "Mendy", "initials": "M"}, {"family": "Niroula", "given": "Abhishek", "initials": "A"}, {"family": "Dunford", "given": "Andrew", "initials": "A"}, {"family": "Taylor-Weiner", "given": "Amaro", "initials": "A"}, {"family": "Wood", "given": "Timothy", "initials": "T"}, {"family": "Barbera", "given": "Alex", "initials": "A"}, {"family": "Anand", "given": "Shankara", "initials": "S", "orcid": "0000-0003-4514-0835", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e68ba33c9c694f5d95d98bd910f0bf83.json"}}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Desai", "given": "Pinkal", "initials": "P"}, {"family": "Cho", "given": "Michael H", "initials": "MH"}, {"family": "Johnson", "given": "Andrew D", "initials": "AD"}, {"family": "Loos", "given": "Ruth", "initials": "R"}, {"family": "NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium", "given": "", "initials": ""}, {"family": "MacArthur", "given": "Daniel G", "initials": "DG"}, {"family": "Lek", "given": "Monkol", "initials": "M"}, {"family": "Exome Aggregation Consortium", "given": "", "initials": ""}, {"family": "Neuberg", "given": "Donna S", "initials": "DS", "orcid": "0000-0003-2566-3145", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/70b2f9e23251469987cbe7b42d38dc58.json"}}, {"family": "Lage", "given": "Kasper", "initials": "K"}, {"family": "Carr", "given": "Steven A", "initials": "SA", "orcid": "0000-0002-7203-4299", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4a841c201019435fbfc3e6441aaa4119.json"}}, {"family": "Hellstrom-Lindberg", "given": "Eva", "initials": "E"}, {"family": "Malcovati", "given": "Luca", "initials": "L"}, {"family": "Papaemmanuil", "given": "Elli", "initials": "E"}, {"family": "Stewart", "given": "Chip", "initials": "C", "orcid": "0000-0003-2245-9552", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f684d3543cc04aacb06738349fcf0ae5.json"}}, {"family": "Getz", "given": "Gad", "initials": "G", "orcid": "0000-0002-0936-0753", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fc65099492394065bb61f94c89425aa3.json"}}, {"family": "Bradley", "given": "Robert K", "initials": "RK", "orcid": "0000-0002-8046-1063", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9b511b3a09d246d2a8cf0092a6733d84.json"}}, {"family": "Jaiswal", "given": "Siddhartha", "initials": "S"}, {"family": "Ebert", "given": "Benjamin L", "initials": "BL"}], "type": "journal article", "published": "2021-09-00", "journal": {"title": "Blood Cancer Discov", "issn": "2643-3249", "volume": "2", "issue": "5", "pages": "500-517", "issn-l": null}, "abstract": "Clonal hematopoiesis results from somatic mutations in cancer driver genes in hematopoietic stem cells. We sought to identify novel drivers of clonal expansion using an unbiased analysis of sequencing data from 84,683 persons and identified common mutations in the 5-methylcytosine reader, ZBTB33, as well as in YLPM1, SRCAP, and ZNF318. We also identified these mutations at low frequency in myelodysplastic syndrome patients. Zbtb33 edited mouse hematopoietic stem and progenitor cells exhibited a competitive advantage in vivo and increased genome-wide intron retention. ZBTB33 mutations potentially link DNA methylation and RNA splicing, the two most commonly mutated pathways in clonal hematopoiesis and MDS.", "doi": "10.1158/2643-3230.BCD-20-0224", "pmid": "34568833", "labels": {"Abhishek Niroula": null, "DDLS Fellow": null}, "xrefs": [{"db": "mid", "key": "NIHMS1722951"}, {"db": "pmc", "key": "PMC8462124"}, {"db": "pii", "key": "2643-3230.BCD-20-0224"}], "notes": [], "created": "2023-11-20T11:27:58.144Z", "modified": "2023-11-20T11:27:59.030Z"}, {"entity": "publication", "iuid": "80a9264ab4f849f99036d794e504e051", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/80a9264ab4f849f99036d794e504e051.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/80a9264ab4f849f99036d794e504e051"}}, "title": "Targeted proteomics analysis of plasma proteins using recombinant protein standards for addition only workflows.", "authors": [{"family": "Kotol", "given": "David", "initials": "D", "orcid": "0000-0002-5388-3826", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c41f8f491c474e6bba2047b5d04b4af5.json"}}, {"family": "Hober", "given": "Andreas", "initials": "A", "orcid": "0000-0001-8947-2562", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/06cbc187628340278395a00ab9dd6c89.json"}}, {"family": "Strandberg", "given": "Linn\u00e9a", "initials": "L"}, {"family": "Svensson", "given": "Anne-Sophie", "initials": "AS"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ea446aa574042a295d5f69437402f76.json"}}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e213b04f8984c8eb00c68f5bc2f6a36.json"}}], "type": "journal article", "published": "2021-09-00", "journal": {"title": "BioTechniques", "issn": "1940-9818", "volume": "71", "issue": "3", "pages": "473-483", "issn-l": "0736-6205"}, "abstract": "Targeted proteomics is an attractive approach for the analysis of blood proteins. Here, we describe a novel analytical platform based on isotope-labeled recombinant protein standards stored in a chaotropic agent and subsequently dried down to allow storage at ambient temperature. This enables a straightforward protocol suitable for robotic workstations. Plasma samples to be analyzed are simply added to the dried pellet followed by enzymatic treatment and mass spectrometry analysis. Here, we show that this approach can be used to precisely (coefficient of variation <10%) determine the absolute concentrations in human plasma of hundred clinically relevant protein targets, spanning four orders of magnitude, using simultaneous analysis of 292 peptides. The use of this next-generation analytical platform for high-throughput clinical proteome profiling is discussed.", "doi": "10.2144/btn-2021-0047", "pmid": "34431357", "labels": {"Fredrik Edfors": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T13:02:05.154Z", "modified": "2026-09-23T11:55:00.022Z"}, {"entity": "publication", "iuid": "1a0b0a437a9b429bbe0c4a8733cf2064", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1a0b0a437a9b429bbe0c4a8733cf2064.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1a0b0a437a9b429bbe0c4a8733cf2064"}}, "title": "Combined Metabolic Activators Accelerates Recovery in Mild-to-Moderate COVID-19.", "authors": [{"family": "Altay", "given": "Ozlem", "initials": "O"}, {"family": "Arif", "given": "Muhammad", "initials": "M"}, {"family": "Li", "given": "Xiangyu", "initials": "X"}, {"family": "Yang", "given": "Hong", "initials": "H"}, {"family": "Ayd\u0131n", "given": "Mehtap", "initials": "M"}, {"family": "Alkurt", "given": "Gizem", "initials": "G"}, {"family": "Kim", "given": "Woonghee", "initials": "W"}, {"family": "Akyol", "given": "Dogukan", "initials": "D"}, {"family": "Zhang", "given": "Cheng", "initials": "C"}, {"family": "Dinler-Doganay", "given": "Gizem", "initials": "G"}, {"family": "Turkez", "given": "Hasan", "initials": "H"}, {"family": "Shoaie", "given": "Saeed", "initials": "S"}, {"family": "Nielsen", "given": "Jens", "initials": "J"}, {"family": "Bor\u00e9n", "given": "Jan", "initials": "J"}, {"family": "Olmuscelik", "given": "Oktay", "initials": "O"}, {"family": "Doganay", "given": "Levent", "initials": "L"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca58bf2d214047e0ae5e38a42a0f2808.json"}}], "type": "clinical trial, phase ii", "published": "2021-09-00", "journal": {"title": "Adv Sci (Weinh)", "issn": "2198-3844", "volume": "8", "issue": "17", "pages": "e2101222", "issn-l": null}, "abstract": "COVID-19 is associated with mitochondrial dysfunction and metabolic abnormalities, including the deficiencies in nicotinamide adenine dinucleotide (NAD+ ) and glutathione metabolism. Here it is investigated if administration of a mixture of combined metabolic activators (CMAs) consisting of glutathione and NAD+ precursors can restore metabolic function and thus aid the recovery of COVID-19 patients. CMAs include l-serine, N-acetyl-l-cysteine, nicotinamide riboside, and l-carnitine tartrate, salt form of l-carnitine. Placebo-controlled, open-label phase 2 study and double-blinded phase 3 clinical trials are conducted to investigate the time of symptom-free recovery on ambulatory patients using CMAs. The results of both studies show that the time to complete recovery is significantly shorter in the CMA group (6.6 vs 9.3 d) in phase 2 and (5.7 vs 9.2 d) in phase 3 trials compared to placebo group. A comprehensive analysis of the plasma metabolome and proteome reveals major metabolic changes. Plasma levels of proteins and metabolites associated with inflammation and antioxidant metabolism are significantly improved in patients treated with CMAs as compared to placebo. The results show that treating patients infected with COVID-19 with CMAs lead to a more rapid symptom-free recovery, suggesting a role for such a therapeutic regime in the treatment of infections leading to respiratory problems.", "doi": "10.1002/advs.202101222", "pmid": "34180141", "labels": {"Adil Mardinoglu": "", "SciLifeLab Fellow": "", "Saeed Shoaie": "", "DDLS Fellow": "", "Muhammad Arif": ""}, "xrefs": [{"db": "pmc", "key": "PMC8420376"}], "notes": [], "created": "2023-12-04T15:07:53.113Z", "modified": "2026-09-23T07:50:03.421Z"}, {"entity": "publication", "iuid": "d658666a62534e2fb497f2f4974200a6", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d658666a62534e2fb497f2f4974200a6.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d658666a62534e2fb497f2f4974200a6"}}, "title": "TET2 as a tumor suppressor and therapeutic target in T-cell acute lymphoblastic leukemia.", "authors": [{"family": "Bensberg", "given": "Maike", "initials": "M", "orcid": "0000-0003-2395-6083", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3fe8907522864854b5d2c87cd8144e73.json"}}, {"family": "Rundquist", "given": "Olof", "initials": "O", "orcid": "0000-0002-1424-3658", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5cc1e656de624b48b89fe8917923c672.json"}}, {"family": "Selimovi\u0107", "given": "Aida", "initials": "A", "orcid": "0000-0001-9580-4455", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1b2bf25a24ec417ea5b8c1db74bce5d4.json"}}, {"family": "Lagerwall", "given": "Cathrine", "initials": "C", "orcid": "0000-0002-3605-1470", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/027e9b72f5b946d185e88d42759a07be.json"}}, {"family": "Benson", "given": "Mikael", "initials": "M"}, {"family": "Gustafsson", "given": "Mika", "initials": "M"}, {"family": "Vogt", "given": "Hartmut", "initials": "H"}, {"family": "Lentini", "given": "Antonio", "initials": "A", "orcid": "0000-0003-1239-5495", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c5042d3005814ad0a2d1eaeee5d2de3b.json"}}, {"family": "Nestor", "given": "Colm E", "initials": "CE", "orcid": "0000-0001-5853-1769", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/53da1d2e5d714a368bcb61c4001abd0f.json"}}], "type": "journal article", "published": "2021-08-24", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "118", "issue": "34", "issn-l": "0027-8424"}, "abstract": "Pediatric T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive malignancy resulting from overproduction of immature T-cells in the thymus and is typified by widespread alterations in DNA methylation. As survival rates for relapsed T-ALL remain dismal (10 to 25%), development of targeted therapies to prevent relapse is key to improving prognosis. Whereas mutations in the DNA demethylating enzyme TET2 are frequent in adult T-cell malignancies, TET2 mutations in T-ALL are rare. Here, we analyzed RNA-sequencing data of 321 primary T-ALLs, 20 T-ALL cell lines, and 25 normal human tissues, revealing that TET2 is transcriptionally repressed or silenced in 71% and 17% of T-ALL, respectively. Furthermore, we show that TET2 silencing is often associated with hypermethylation of the TET2 promoter in primary T-ALL. Importantly, treatment with the DNA demethylating agent, 5-azacytidine (5-aza), was significantly more toxic to TET2-silenced T-ALL cells and resulted in stable re-expression of the TET2 gene. Additionally, 5-aza led to up-regulation of methylated genes and human endogenous retroviruses (HERVs), which was further enhanced by the addition of physiological levels of vitamin C, a potent enhancer of TET activity. Together, our results clearly identify 5-aza as a potential targeted therapy for TET2-silenced T-ALL.", "doi": "10.1073/pnas.2110758118", "pmid": "34413196", "labels": {"Antonio Lentini": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC8403940"}, {"db": "pii", "key": "2110758118"}], "notes": [], "created": "2025-03-28T07:09:56.059Z", "modified": "2025-03-28T07:09:56.210Z"}, {"entity": "publication", "iuid": "433844c8662d4f7fb4a08946ed38441c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/433844c8662d4f7fb4a08946ed38441c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/433844c8662d4f7fb4a08946ed38441c"}}, "title": "Harnessing secretory pathway differences between HEK293 and CHO to rescue production of difficult to express proteins", "authors": [{"family": "Malm", "given": "Magdalena", "initials": "M", "orcid": "0000-0003-1763-9073", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a69f7651977a4b4a92bdf5f9d6408d04.json"}}, {"family": "Kuo", "given": "Chih Chung", "initials": "CC"}, {"family": "Barzadd", "given": "Mona Moradi", "initials": "MM"}, {"family": "Mebrahtu", "given": "Aman", "initials": "A"}, {"family": "Wistbacka", "given": "Num", "initials": "N"}, {"family": "Razavi", "given": "Ronia", "initials": "R"}, {"family": "Volk", "given": "Anna Luisa", "initials": "AL"}, {"family": "Lundqvist", "given": "Magnus", "initials": "M"}, {"family": "Kotol", "given": "David", "initials": "D"}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Gr\u00e4slund", "given": "Torbj\u00f6rn", "initials": "T"}, {"family": "Chotteau", "given": "Veronique", "initials": "V"}, {"family": "Field", "given": "Ray", "initials": "R"}, {"family": "Varley", "given": "Paul G", "initials": "PG"}, {"family": "Roth", "given": "Robert G", "initials": "RG"}, {"family": "Lewis", "given": "Nathan E", "initials": "NE"}, {"family": "Hatton", "given": "Diane", "initials": "D"}, {"family": "Rockberg", "given": "Johan", "initials": "J"}], "type": "posted-content", "published": "2021-08-17", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2021.08.16.455786", "pmid": null, "labels": {"Fredrik Edfors": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T10:06:19.995Z", "modified": "2026-09-23T14:25:24.347Z"}, {"entity": "publication", "iuid": "e232b87320bd43c48799ac19a57c9776", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e232b87320bd43c48799ac19a57c9776.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e232b87320bd43c48799ac19a57c9776"}}, "title": "Combined Metabolic Activators Improve Cognitive Functions without Altering Motor Scores in Parkinson\u2019s Disease", "authors": [{"family": "Yulug", "given": "Burak", "initials": "B"}, {"family": "Altay", "given": "Ozlem", "initials": "O"}, {"family": "Li", "given": "Xiangyu", "initials": "X"}, {"family": "Hanoglu", "given": "Lutfu", "initials": "L"}, {"family": "Cankaya", "given": "Seyda", "initials": "S"}, {"family": "Lam", "given": "Simon", "initials": "S"}, {"family": "Yang", "given": "Hong", "initials": "H"}, {"family": "Coskun", "given": "Ebru", "initials": "E"}, {"family": "\u0130dil", "given": "Ezgi", "initials": "E"}, {"family": "Nogaylar", "given": "Rahim", "initials": "R"}, {"family": "Hac\u0131muftuoglu", "given": "Ahmet", "initials": "A"}, {"family": "Arif", "given": "Muhammad", "initials": "M"}, {"family": "Shoaie", "given": "Saeed", "initials": "S"}, {"family": "Zhang", "given": "Cheng", "initials": "C"}, {"family": "Nielsen", "given": "Jens", "initials": "J"}, {"family": "Turkez", "given": "Hasan", "initials": "H"}, {"family": "Bor\u00e9n", "given": "Jan", "initials": "J"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}], "type": "posted-content", "published": "2021-08-04", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2021.07.28.21261293", "pmid": null, "labels": {"SciLifeLab Fellow": "", "Saeed Shoaie": "", "DDLS Fellow": "", "Adil Mardinoglu": "", "Muhammad Arif": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T10:06:00.737Z", "modified": "2026-09-23T14:10:53.048Z"}, {"entity": "publication", "iuid": "2ad116c7698b48e78c2977f38586eec7", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/2ad116c7698b48e78c2977f38586eec7.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/2ad116c7698b48e78c2977f38586eec7"}}, "title": "Microbial retention and resistances in stormwater quality improvement devices treating road runoff", "authors": [{"family": "Liguori", "given": "Renato", "initials": "R", "orcid": "0000-0002-5704-9409", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9b63f9e4c4734826b1eb3563f3b0a7b5.json"}}, {"family": "Rommel", "given": "Steffen H", "initials": "SH", "orcid": "0000-0002-8415-6744", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8d8b1dd6ca3b4d31bcd483f7f7c559b9.json"}}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J", "orcid": "0000-0002-6528-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c666068e9d34939b0252a627007cec7.json"}}, {"family": "Helmreich", "given": "Brigitte", "initials": "B", "orcid": "0000-0003-4224-3329", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/16f092cacd39435fb7a9cc62549c6720.json"}}, {"family": "Wurzbacher", "given": "Christian", "initials": "C", "orcid": "0000-0001-7418-0831", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a8303415592c4c46b9fcf27904aec4fa.json"}}], "type": "journal-article", "published": "2021-08-03", "journal": {"title": "FEMS Microbes", "issn": "2633-6685", "issn-l": null, "volume": "2", "issue": null, "pages": null}, "abstract": null, "doi": "10.1093/femsmc/xtab008", "pmid": null, "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [], "notes": [], "created": "2022-11-08T09:35:13.701Z", "modified": "2023-06-16T13:04:42.780Z"}, {"entity": "publication", "iuid": "420a84041b274384a9013b51da6bafd9", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/420a84041b274384a9013b51da6bafd9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/420a84041b274384a9013b51da6bafd9"}}, "title": "Response to Lai.", "authors": [{"family": "Wang", "given": "Qiao-Li", "initials": "QL"}, {"family": "Lagergren", "given": "Jesper", "initials": "J"}], "type": "letter", "published": "2021-08-01", "journal": {"title": "Am J Gastroenterol", "issn": "1572-0241", "volume": "116", "issue": "8", "pages": "1758", "issn-l": null}, "abstract": null, "doi": "10.14309/ajg.0000000000001312", "pmid": "34028365", "labels": {"DDLS Fellow": null, "Qiaoli Wang": null}, "xrefs": [{"db": "pii", "key": "00000434-202108000-00040"}], "notes": [], "created": "2025-11-27T18:53:35.078Z", "modified": "2025-11-27T18:53:35.081Z"}, {"entity": "publication", "iuid": "04f79eeab24c442cbced6875778e2da9", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/04f79eeab24c442cbced6875778e2da9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/04f79eeab24c442cbced6875778e2da9"}}, "title": "The emerging role of artificial intelligence in the reporting of prostate pathology.", "authors": [{"family": "Egevad", "given": "Lars", "initials": "L"}, {"family": "Delahunt", "given": "Brett", "initials": "B"}, {"family": "Samaratunga", "given": "Hemamali", "initials": "H"}, {"family": "Tsuzuki", "given": "Toyonori", "initials": "T"}, {"family": "Yamamoto", "given": "Yoichiro", "initials": "Y"}, {"family": "Yaxley", "given": "John", "initials": "J"}, {"family": "Ruusuvuori", "given": "Pekka", "initials": "P"}, {"family": "Kartasalo", "given": "Kimmo", "initials": "K"}, {"family": "Eklund", "given": "Martin", "initials": "M"}], "type": "editorial", "published": "2021-08-00", "journal": {"title": "Pathology", "issn": "1465-3931", "issn-l": null, "volume": "53", "issue": "5", "pages": "565-567"}, "abstract": null, "doi": "10.1016/j.pathol.2021.04.002", "pmid": "34108086", "labels": {"Kimmo Kartasalo": null, "DDLS Fellow": null}, "xrefs": [{"db": "pii", "key": "S0031-3025(21)00230-0"}], "notes": [], "created": "2024-11-05T16:10:27.595Z", "modified": "2024-11-29T10:44:55.063Z"}, {"entity": "publication", "iuid": "7306c56a458846f5a3bc9d66336fb7e8", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/7306c56a458846f5a3bc9d66336fb7e8.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/7306c56a458846f5a3bc9d66336fb7e8"}}, "title": "Structure and Interdigitation of Chain-Asymmetric Phosphatidylcholines and Milk Sphingomyelin in the Fluid Phase.", "authors": [{"family": "Frewein", "given": "Moritz P K", "initials": "MPK", "orcid": "0000-0002-0329-5305", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8b85796085844d93ad922842aeb0ed63.json"}}, {"family": "Doktorova", "given": "Milka", "initials": "M", "orcid": "0000-0003-4366-2242", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/791384c319f04584bac8ffb21df7271f.json"}}, {"family": "Heberle", "given": "Frederick A", "initials": "FA", "orcid": "0000-0002-0424-3240", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2557f5621a0b4c87b5f4702fbc7b6bdb.json"}}, {"family": "Scott", "given": "Haden L", "initials": "HL", "orcid": "0000-0002-5778-4905", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a1e768fa75c34598807728aaf9d3a0be.json"}}, {"family": "Semeraro", "given": "Enrico F", "initials": "EF", "orcid": "0000-0002-6096-1108", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c09f2727844b49f0a93375b80e8760f3.json"}}, {"family": "Porcar", "given": "Lionel", "initials": "L", "orcid": "0000-0003-4674-7591", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0f3d4d1f353d4326b609f53b899fe12b.json"}}, {"family": "Pabst", "given": "Georg", "initials": "G", "orcid": "0000-0003-1967-1536", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ec4ae71525c9411ea39715388b46afee.json"}}], "type": "journal article", "published": "2021-08-00", "journal": {"title": "Symmetry (Basel)", "issn": "2073-8994", "issn-l": null, "volume": "13", "issue": "8", "pages": null}, "abstract": "We addressed the frequent occurrence of mixed-chain lipids in biological membranes and their impact on membrane structure by studying several chain-asymmetric phosphatidylcholines and the highly asymmetric milk sphingomyelin. Specifically, we report trans-membrane structures of the corresponding fluid lamellar phases using small-angle X-ray and neutron scattering, which were jointly analyzed in terms of a membrane composition-specific model, including a headgroup hydration shell. Focusing on terminal methyl groups at the bilayer center, we found a linear relation between hydrocarbon chain length mismatch and the methyl-overlap for phosphatidylcholines, and a non-negligible impact of the glycerol backbone-tilting, letting the sn1-chain penetrate deeper into the opposing leaflet by half a CH2 group. That is, penetration-depth differences due to the ester-linked hydrocarbons at the glycerol backbone, previously reported for gel phase structures, also extend to the more relevant physiological fluid phase, but are significantly reduced. Moreover, milk sphingomyelin was found to follow the same linear relationship suggesting a similar tilt of the sphingosine backbone. Complementarily performed molecular dynamics simulations revealed that there is always a part of the lipid tails bending back, even if there is a high interdigitation with the opposing chains. The extent of this back-bending was similar to that in chain symmetric bilayers. For both cases of adaptation to chain length mismatch, chain-asymmetry has a large impact on hydrocarbon chain ordering, inducing disorder in the longer of the two hydrocarbons.", "doi": "10.3390/sym13081441", "pmid": "35530371", "labels": {"Milka Doktorova": null, "DDLS Fellow": null}, "xrefs": [{"db": "mid", "key": "NIHMS1749599"}, {"db": "pmc", "key": "PMC9075682"}, {"db": "pii", "key": "1441"}], "notes": [], "created": "2024-11-27T12:18:11.915Z", "modified": "2024-11-29T10:52:35.151Z"}, {"entity": "publication", "iuid": "4f894b3f6bd2416da96aa8f460b2148b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4f894b3f6bd2416da96aa8f460b2148b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4f894b3f6bd2416da96aa8f460b2148b"}}, "title": "Model Membrane Systems Used to Study Plasma Membrane Lipid Asymmetry.", "authors": [{"family": "Scott", "given": "Haden L", "initials": "HL", "orcid": "0000-0002-5778-4905", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a1e768fa75c34598807728aaf9d3a0be.json"}}, {"family": "Kennison", "given": "Kristen B", "initials": "KB"}, {"family": "Enoki", "given": "Thais A", "initials": "TA", "orcid": "0000-0003-4639-9160", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5f7fe2d712f04451addf84b9cab37ca5.json"}}, {"family": "Doktorova", "given": "Milka", "initials": "M", "orcid": "0000-0003-4366-2242", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/791384c319f04584bac8ffb21df7271f.json"}}, {"family": "Kinnun", "given": "Jacob J", "initials": "JJ"}, {"family": "Heberle", "given": "Frederick A", "initials": "FA", "orcid": "0000-0002-0424-3240", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2557f5621a0b4c87b5f4702fbc7b6bdb.json"}}, {"family": "Katsaras", "given": "John", "initials": "J", "orcid": "0000-0002-8937-4177", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/732f1e95fed546efb3427a9b223a23c0.json"}}], "type": "journal article", "published": "2021-08-00", "journal": {"title": "Symmetry (Basel)", "issn": "2073-8994", "issn-l": null, "volume": "13", "issue": "8", "pages": null}, "abstract": "It is well known that the lipid distribution in the bilayer leaflets of mammalian plasma membranes (PMs) is not symmetric. Despite this, model membrane studies have largely relied on chemically symmetric model membranes for the study of lipid-lipid and lipid-protein interactions. This is primarily due to the difficulty in preparing stable, asymmetric model membranes that are amenable to biophysical studies. However, in the last 20 years, efforts have been made in producing more biologically faithful model membranes. Here, we review several recently developed experimental and computational techniques for the robust generation of asymmetric model membranes and highlight a new and particularly promising technique to study membrane asymmetry.", "doi": "10.3390/sym13081356", "pmid": "35498375", "labels": {"Milka Doktorova": null, "DDLS Fellow": null}, "xrefs": [{"db": "mid", "key": "NIHMS1749596"}, {"db": "pmc", "key": "PMC9053528"}, {"db": "pii", "key": "1356"}], "notes": [], "created": "2024-11-27T12:19:23.220Z", "modified": "2024-11-29T10:52:25.822Z"}, {"entity": "publication", "iuid": "db0e70c3c5f549da9c966a8cf1960cce", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/db0e70c3c5f549da9c966a8cf1960cce.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/db0e70c3c5f549da9c966a8cf1960cce"}}, "title": "Dynamic closed states of a ligand-gated ion channel captured by cryo-EM and simulations.", "authors": [{"family": "Rov\u0161nik", "given": "Ur\u0161ka", "initials": "U"}, {"family": "Zhuang", "given": "Yuxuan", "initials": "Y"}, {"family": "Forsberg", "given": "Bj\u00f6rn O", "initials": "BO"}, {"family": "Carroni", "given": "Marta", "initials": "M"}, {"family": "Yvonnesdotter", "given": "Linnea", "initials": "L"}, {"family": "Howard", "given": "Rebecca J", "initials": "RJ", "orcid": "0000-0003-2049-3378", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ce04593b5b24aaa8978fda1447dd0bf.json"}}, {"family": "Lindahl", "given": "Erik", "initials": "E", "orcid": "0000-0002-2734-2794", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9eb30fa60f9b4b95842ac9d9f3a0eaa9.json"}}], "type": "journal article", "published": "2021-08-00", "journal": {"title": "Life Sci. Alliance", "issn": "2575-1077", "volume": "4", "issue": "8", "issn-l": null}, "abstract": "Ligand-gated ion channels are critical mediators of electrochemical signal transduction across evolution. Biophysical and pharmacological characterization of these receptor proteins relies on high-quality structures in multiple, subtly distinct functional states. However, structural data in this family remain limited, particularly for resting and intermediate states on the activation pathway. Here, we report cryo-electron microscopy (cryo-EM) structures of the proton-activated Gloeobacter violaceus ligand-gated ion channel (GLIC) under three pH conditions. Decreased pH was associated with improved resolution and side chain rearrangements at the subunit/domain interface, particularly involving functionally important residues in the \u03b21-\u03b22 and M2-M3 loops. Molecular dynamics simulations substantiated flexibility in the closed-channel extracellular domains relative to the transmembrane ones and supported electrostatic remodeling around E35 and E243 in proton-induced gating. Exploration of secondary cryo-EM classes further indicated a low-pH population with an expanded pore. These results allow us to define distinct protonation and activation steps in pH-stimulated conformational cycling in GLIC, including interfacial rearrangements largely conserved in the pentameric channel family.", "doi": "10.26508/lsa.202101011", "pmid": "34210687", "labels": {"DDLS Fellow": "", "Bj\u00f6rn Forsberg": ""}, "xrefs": [{"db": "pmc", "key": "PMC8326787"}, {"db": "pii", "key": "4/8/e202101011"}, {"db": "PDB", "key": "4NPQ"}, {"db": "PDB", "key": "4HFI"}, {"db": "PDB", "key": "6ZGD"}, {"db": "PDB", "key": "6ZGJ"}, {"db": "PDB", "key": "6ZGK"}], "notes": [], "created": "2026-08-20T13:03:57.561Z", "modified": "2026-09-23T10:53:00.851Z"}, {"entity": "publication", "iuid": "d07397c1852d4069b2fb791eba9d0352", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d07397c1852d4069b2fb791eba9d0352.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d07397c1852d4069b2fb791eba9d0352"}}, "title": "Topological network based drug repurposing for coronavirus 2019.", "authors": [{"family": "Habibi", "given": "Mahnaz", "initials": "M", "orcid": "0000-0002-8969-2706", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f04af4e059814b78bfb107c3a5782f70.json"}}, {"family": "Taheri", "given": "Golnaz", "initials": "G", "orcid": "0000-0002-2741-0355", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/014c217121d346b2b371bbc1c2fede57.json"}}], "type": "journal article", "published": "2021-07-29", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "issn-l": "1932-6203", "volume": "16", "issue": "7", "pages": "e0255270"}, "abstract": "The COVID-19 pandemic caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has become the current health concern and threat to the entire world. Thus, the world needs the fast recognition of appropriate drugs to restrict the spread of this disease. The global effort started to identify the best drug compounds to treat COVID-19, but going through a series of clinical trials and our lack of information about the details of the virus's performance has slowed down the time to reach this goal. In this work, we try to select the subset of human proteins as candidate sets that can bind to approved drugs. Our method is based on the information on human-virus protein interaction and their effect on the biological processes of the host cells. We also define some informative topological and statistical features for proteins in the protein-protein interaction network. We evaluate our selected sets with two groups of drugs. The first group contains the experimental unapproved treatments for COVID-19, and we show that from 17 drugs in this group, 15 drugs are approved by our selected sets. The second group contains the external clinical trials for COVID-19, and we show that 85% of drugs in this group, target at least one protein of our selected sets. We also study COVID-19 associated protein sets and identify proteins that are essential to disease pathology. For this analysis, we use DAVID tools to show and compare disease-associated genes that are contributed between the COVID-19 comorbidities. Our results for shared genes show significant enrichment for cardiovascular-related, hypertension, diabetes type 2, kidney-related and lung-related diseases. In the last part of this work, we recommend 56 potential effective drugs for further research and investigation for COVID-19 treatment. Materials and implementations are available at: https://github.com/MahnazHabibi/Drug-repurposing.", "doi": "10.1371/journal.pone.0255270", "pmid": "34324563", "labels": {"Golnaz Taheri": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC8320924"}, {"db": "pii", "key": "PONE-D-21-13445"}], "notes": [], "created": "2025-03-21T09:11:19.825Z", "modified": "2026-09-23T11:54:57.661Z"}, {"entity": "publication", "iuid": "25d34fc5acf44711a7415e7edb45d3eb", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/25d34fc5acf44711a7415e7edb45d3eb.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/25d34fc5acf44711a7415e7edb45d3eb"}}, "title": "Publisher Correction: A SARS-CoV-2 (COVID-19) biological network to find targets for drug repurposing.", "authors": [{"family": "Habibi", "given": "Mahnaz", "initials": "M"}, {"family": "Taheri", "given": "Golnaz", "initials": "G"}, {"family": "Aghdam", "given": "Rosa", "initials": "R"}], "type": "published erratum", "published": "2021-07-26", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "11", "issue": "1", "pages": "15550", "issn-l": "2045-2322"}, "abstract": null, "doi": "10.1038/s41598-021-94440-w", "pmid": "34312434", "labels": {"Golnaz Taheri": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC8312203"}, {"db": "pii", "key": "10.1038/s41598-021-94440-w"}], "notes": [], "created": "2026-08-20T09:05:33.675Z", "modified": "2026-09-23T15:08:11.301Z"}, {"entity": "publication", "iuid": "893afa778f1b4dd9a315a58f25dad6af", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/893afa778f1b4dd9a315a58f25dad6af.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/893afa778f1b4dd9a315a58f25dad6af"}}, "title": "A network-based approach reveals the dysregulated transcriptional regulation in non-alcohol fatty liver disease", "authors": [{"family": "Yang", "given": "Hong", "initials": "H"}, {"family": "Arif", "given": "Muhammad", "initials": "M"}, {"family": "Yuan", "given": "Meng", "initials": "M"}, {"family": "Li", "given": "Xiangyu", "initials": "X"}, {"family": "Shong", "given": "Ko Eun", "initials": "KE"}, {"family": "Turkez", "given": "Hasan", "initials": "H"}, {"family": "Nielsen", "given": "Jens", "initials": "J"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Bor\u00e9n", "given": "Jan", "initials": "J"}, {"family": "Cheng", "given": "Zhang", "initials": "Z"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}], "type": "posted-content", "published": "2021-07-26", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2021.07.24.453650", "pmid": null, "labels": {"SciLifeLab Fellow": "", "DDLS Fellow": "", "Adil Mardinoglu": "", "Muhammad Arif": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T10:05:57.059Z", "modified": "2026-09-23T15:08:09.606Z"}, {"entity": "publication", "iuid": "d3e1fb658525438c96d702a4535cd6d3", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d3e1fb658525438c96d702a4535cd6d3.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d3e1fb658525438c96d702a4535cd6d3"}}, "title": "Stratification of patients with clear cell renal cell carcinoma to facilitate drug repositioning.", "authors": [{"family": "Li", "given": "Xiangyu", "initials": "X"}, {"family": "Kim", "given": "Woonghee", "initials": "W"}, {"family": "Juszczak", "given": "Kajetan", "initials": "K"}, {"family": "Arif", "given": "Muhammad", "initials": "M"}, {"family": "Sato", "given": "Yusuke", "initials": "Y"}, {"family": "Kume", "given": "Haruki", "initials": "H"}, {"family": "Ogawa", "given": "Seishi", "initials": "S"}, {"family": "Turkez", "given": "Hasan", "initials": "H"}, {"family": "Boren", "given": "Jan", "initials": "J"}, {"family": "Nielsen", "given": "Jens", "initials": "J"}, {"family": "Uhlen", "given": "Mathias", "initials": "M"}, {"family": "Zhang", "given": "Cheng", "initials": "C"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}], "type": "journal article", "published": "2021-07-23", "journal": {"title": "iScience", "issn": "2589-0042", "volume": "24", "issue": "7", "pages": "102722", "issn-l": null}, "abstract": "Clear cell renal cell carcinoma (ccRCC) is the most common histological type of kidney cancer and has high heterogeneity. Stratification of ccRCC is important since distinct subtypes differ in prognosis and treatment. Here, we applied a systems biology approach to stratify ccRCC into three molecular subtypes with different mRNA expression patterns and prognosis of patients. Further, we developed a set of biomarkers that could robustly classify the patients into each of the three subtypes and predict the prognosis of patients. Then, we reconstructed subtype-specific metabolic models and performed essential gene analysis to identify the potential drug targets. We identified four drug targets, including SOAT1, CRLS1, and ACACB, essential in all the three subtypes and GPD2, exclusively essential to subtype 1. Finally, we repositioned mitotane, an FDA-approved SOAT1 inhibitor, to treat ccRCC and showed that it decreased tumor cell viability and inhibited tumor cell growth based on in vitro experiments.", "doi": "10.1016/j.isci.2021.102722", "pmid": "34258555", "labels": {"Adil Mardinoglu": "", "SciLifeLab Fellow": "", "DDLS Fellow": "", "Muhammad Arif": ""}, "xrefs": [{"db": "pmc", "key": "PMC8253978"}, {"db": "pii", "key": "S2589-0042(21)00690-8"}], "notes": [], "created": "2023-12-04T15:07:51.800Z", "modified": "2026-09-23T12:02:54.118Z"}, {"entity": "publication", "iuid": "366f17f13a4649e884a859b4ea08b5bf", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/366f17f13a4649e884a859b4ea08b5bf.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/366f17f13a4649e884a859b4ea08b5bf"}}, "title": "FISH-quant v2: a scalable and modular analysis tool for smFISH image analysis", "authors": [{"family": "Imbert", "given": "Arthur", "initials": "A"}, {"family": "Ouyang", "given": "Wei", "initials": "W", "orcid": "0000-0002-0291-926X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56f601e1d1c6448aab0c3a1e3cffdbfc.json"}}, {"family": "Safieddine", "given": "Adham", "initials": "A", "orcid": "0000-0002-9324-9037", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9631fea704c2481dba933e59b12873d5.json"}}, {"family": "Coleno", "given": "Emeline", "initials": "E"}, {"family": "Zimmer", "given": "Christophe", "initials": "C", "orcid": "0000-0001-9910-1589", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ab6793e6696c4f8eb149afa2be603687.json"}}, {"family": "Bertrand", "given": "Edouard", "initials": "E", "orcid": "0000-0002-9642-7994", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/099950f08714489abf18bf541fc6583b.json"}}, {"family": "Walter", "given": "Thomas", "initials": "T", "orcid": "0000-0001-7419-7879", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3dde613aba024c74a2e71cc1b80bc1da.json"}}, {"family": "Mueller", "given": "Florian", "initials": "F", "orcid": "0000-0002-9622-4396", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8df07352fbd44ef39300b8067904c5c7.json"}}], "type": "posted-content", "published": "2021-07-20", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2021.07.20.453024", "pmid": null, "labels": {"DDLS Fellow": "", "Wei Ouyang": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T10:05:47.392Z", "modified": "2026-09-23T13:45:01.793Z"}, {"entity": "publication", "iuid": "2444eb11a28b4243a6ba0dc01fbdd517", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/2444eb11a28b4243a6ba0dc01fbdd517.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/2444eb11a28b4243a6ba0dc01fbdd517"}}, "title": "Combined Metabolic Activators Improves Cognitive Functions in Alzheimer\u2019s Disease", "authors": [{"family": "Yulug", "given": "Burak", "initials": "B"}, {"family": "Altay", "given": "Ozlem", "initials": "O"}, {"family": "Li", "given": "Xiangyu", "initials": "X"}, {"family": "Hanoglu", "given": "Lutfu", "initials": "L"}, {"family": "Cankaya", "given": "Seyda", "initials": "S"}, {"family": "Lam", "given": "Simon", "initials": "S"}, {"family": "Yang", "given": "Hong", "initials": "H"}, {"family": "Coskun", "given": "Ebru", "initials": "E"}, {"family": "\u0130dil", "given": "Ezgi", "initials": "E"}, {"family": "Nogaylar", "given": "Rahim", "initials": "R"}, {"family": "Bayram", "given": "Cemil", "initials": "C"}, {"family": "Bolat", "given": "Ismail", "initials": "I"}, {"family": "\u00d6ner", "given": "Sena", "initials": "S"}, {"family": "Tozlu", "given": "\u00d6zlem \u00d6zdemir", "initials": "\u00d6\u00d6"}, {"family": "Arslan", "given": "Mehmet Enes", "initials": "ME"}, {"family": "Hac\u0131muftuoglu", "given": "Ahmet", "initials": "A"}, {"family": "Y\u0131ld\u0131r\u0131m", "given": "Serkan", "initials": "S"}, {"family": "Arif", "given": "Muhammad", "initials": "M"}, {"family": "Shoaie", "given": "Saeed", "initials": "S"}, {"family": "Zhang", "given": "Cheng", "initials": "C"}, {"family": "Nielsen", "given": "Jens", "initials": "J"}, {"family": "Turkez", "given": "Hasan", "initials": "H"}, {"family": "Bor\u00e9n", "given": "Jan", "initials": "J"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}], "type": "posted-content", "published": "2021-07-20", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2021.07.14.21260511", "pmid": null, "labels": {"SciLifeLab Fellow": "", "Saeed Shoaie": "", "DDLS Fellow": "", "Adil Mardinoglu": "", "Muhammad Arif": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T10:05:43.500Z", "modified": "2026-09-23T14:10:44.641Z"}, {"entity": "publication", "iuid": "4ee816e94eb9498598cc8b9c8a3dd5ce", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4ee816e94eb9498598cc8b9c8a3dd5ce.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4ee816e94eb9498598cc8b9c8a3dd5ce"}}, "title": "The Healthy Female Microbiome Across Body Sites: Effect of Hormonal Contraceptives and the Menstrual Cycle", "authors": [{"family": "Krog", "given": "Maria Christine", "initials": "MC", "orcid": "0000-0002-2110-0479", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bdd65c5105f4480692383dae8d4ac986.json"}}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW", "orcid": "0000-0001-5432-1764", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/246ed7b405dd4c3f9ec5e7ff9f1d3ade.json"}}, {"family": "Fransson", "given": "Emma", "initials": "E", "orcid": "0000-0001-9010-8522", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8c05290187ec426b8804eefc3d954971.json"}}, {"family": "Bashir", "given": "Zahra", "initials": "Z", "orcid": "0000-0002-2497-282X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2d15fce497fe4cdabd82e994e7cd83ad.json"}}, {"family": "Andersen", "given": "Anders Nyboe", "initials": "AN"}, {"family": "Edfeldt", "given": "Gabriella", "initials": "G", "orcid": "0000-0003-0366-5588", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bc30318aa3ca4720ac5aa3a982c9f730.json"}}, {"family": "Engstrand", "given": "Lars", "initials": "L", "orcid": "0000-0002-7713-2373", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02d8684df81e42169e613de803446fbf.json"}}, {"family": "Nielsen", "given": "Henriette Svarre", "initials": "HS", "orcid": "0000-0003-2106-8103", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9a99fa7ebb204c618ed70f29be0085b3.json"}}, {"family": "Schuppe-Koistinen", "given": "Ina", "initials": "I"}], "type": "posted-content", "published": "2021-07-14", "journal": {"title": "res sq", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.21203/rs.3.rs-696563/v1", "pmid": null, "labels": {"DDLS Fellow": null, "Luisa Hugerth": null}, "xrefs": [], "notes": [], "created": "2026-08-20T12:59:54.676Z", "modified": "2026-10-05T08:47:56.108Z"}, {"entity": "publication", "iuid": "ce38c07640434cc6b3b95dfe659f82a8", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ce38c07640434cc6b3b95dfe659f82a8.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ce38c07640434cc6b3b95dfe659f82a8"}}, "title": "Supplemental Association of Clonal Hematopoiesis With Incident Heart Failure.", "authors": [{"family": "Yu", "given": "Bing", "initials": "B"}, {"family": "Roberts", "given": "Mary B", "initials": "MB"}, {"family": "Raffield", "given": "Laura M", "initials": "LM"}, {"family": "Zekavat", "given": "Seyedeh Maryam", "initials": "SM"}, {"family": "Nguyen", "given": "Ngoc Quynh H", "initials": "NQH"}, {"family": "Biggs", "given": "Mary L", "initials": "ML"}, {"family": "Brown", "given": "Michael R", "initials": "MR"}, {"family": "Griffin", "given": "Gabriel", "initials": "G"}, {"family": "Desai", "given": "Pinkal", "initials": "P"}, {"family": "Correa", "given": "Adolfo", "initials": "A"}, {"family": "Morrison", "given": "Alanna C", "initials": "AC"}, {"family": "Shah", "given": "Amil M", "initials": "AM"}, {"family": "Niroula", "given": "Abhishek", "initials": "A"}, {"family": "Uddin", "given": "Md Mesbah", "initials": "MM"}, {"family": "Honigberg", "given": "Michael C", "initials": "MC"}, {"family": "Ebert", "given": "Benjamin L", "initials": "BL"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Whitsel", "given": "Eric A", "initials": "EA"}, {"family": "Manson", "given": "JoAnn E", "initials": "JE"}, {"family": "Kooperberg", "given": "Charles", "initials": "C"}, {"family": "Bick", "given": "Alexander G", "initials": "AG"}, {"family": "Ballantyne", "given": "Christie M", "initials": "CM"}, {"family": "Reiner", "given": "Alex P", "initials": "AP"}, {"family": "Natarajan", "given": "Pradeep", "initials": "P"}, {"family": "Eaton", "given": "Charles B", "initials": "CB"}, {"family": "National Heart, Lung, and Blood Institute TOPMed Consortium", "given": "", "initials": ""}], "type": "journal article", "published": "2021-07-06", "journal": {"title": "J. Am. Coll. Cardiol.", "issn": "1558-3597", "volume": "78", "issue": "1", "pages": "42-52", "issn-l": "0735-1097"}, "abstract": "Age-related clonal hematopoiesis of indeterminate potential (CHIP), defined as clonally expanded leukemogenic sequence variations (particularly in DNMT3A, TET2, ASXL1, and JAK2) in asymptomatic individuals, is associated with cardiovascular events, including recurrent heart failure (HF).\n\nThis study sought to evaluate whether CHIP is associated with incident HF.\n\nCHIP status was obtained from whole exome or genome sequencing of blood DNA in participants without prevalent HF or hematological malignancy from 5 cohorts. Cox proportional hazards models were performed within each cohort, adjusting for demographic and clinical risk factors, followed by fixed-effect meta-analyses. Large CHIP clones (defined as variant allele frequency >10%), HF with or without baseline coronary heart disease, and left ventricular ejection fraction were evaluated in secondary analyses.\n\nOf 56,597 individuals (59% women, mean age 58 years at baseline), 3,406 (6%) had CHIP, and 4,694 developed HF (8.3%) over up to 20 years of follow-up. CHIP was prospectively associated with a 25% increased risk of HF in meta-analysis (hazard ratio: 1.25; 95% confidence interval: 1.13-1.38) with consistent associations across cohorts. ASXL1, TET2, and JAK2 sequence variations were each associated with an increased risk of HF, whereas DNMT3A sequence variations were not associated with HF. Secondary analyses suggested large CHIP was associated with a greater risk of HF (hazard ratio: 1.29; 95% confidence interval: 1.15-1.44), and the associations for CHIP on HF with and without prior coronary heart disease were homogenous. ASXL1 sequence variations were associated with reduced left ventricular ejection fraction.\n\nCHIP, particularly sequence variations in ASXL1, TET2, and JAK2, represents a new risk factor for HF.", "doi": "10.1016/j.jacc.2021.04.085", "pmid": "34210413", "labels": {"Abhishek Niroula": null, "DDLS Fellow": null}, "xrefs": [{"db": "mid", "key": "NIHMS1702439"}, {"db": "pmc", "key": "PMC8313294"}, {"db": "pii", "key": "S0735-1097(21)04975-5"}], "notes": [], "created": "2023-11-20T11:27:55.366Z", "modified": "2023-11-20T11:27:55.386Z"}, {"entity": "publication", "iuid": "4e3872a8d7614695b065d71634352d84", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4e3872a8d7614695b065d71634352d84.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4e3872a8d7614695b065d71634352d84"}}, "title": "iNetModels 2.0: an interactive visualization and database of multi-omics data.", "authors": [{"family": "Arif", "given": "Muhammad", "initials": "M"}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f46e4161be08458994efddb75ed75874.json"}}, {"family": "Li", "given": "Xiangyu", "initials": "X"}, {"family": "G\u00fcng\u00f6r", "given": "Cem", "initials": "C"}, {"family": "\u00c7akmak", "given": "Bu\u011fra", "initials": "B"}, {"family": "Arslant\u00fcrk", "given": "Metin", "initials": "M"}, {"family": "Tebani", "given": "Abdellah", "initials": "A"}, {"family": "\u00d6zcan", "given": "Berkay", "initials": "B"}, {"family": "Suba\u015f", "given": "O\u011fuzhan", "initials": "O"}, {"family": "Zhou", "given": "Wenyu", "initials": "W"}, {"family": "Piening", "given": "Brian", "initials": "B"}, {"family": "Turkez", "given": "Hasan", "initials": "H"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Price", "given": "Nathan", "initials": "N"}, {"family": "Hood", "given": "Leroy", "initials": "L"}, {"family": "Snyder", "given": "Michael", "initials": "M"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/33f2b49a39ed4e54ba77dfe397ed3087.json"}}, {"family": "Uhlen", "given": "Mathias", "initials": "M"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca58bf2d214047e0ae5e38a42a0f2808.json"}}], "type": "journal article", "published": "2021-07-02", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "issn-l": "0305-1048", "volume": "49", "issue": "W1", "pages": "W271-W276"}, "abstract": "It is essential to reveal the associations between various omics data for a comprehensive understanding of the altered biological process in human wellness and disease. To date, very few studies have focused on collecting and exhibiting multi-omics associations in a single database. Here, we present iNetModels, an interactive database and visualization platform of Multi-Omics Biological Networks (MOBNs). This platform describes the associations between the clinical chemistry, anthropometric parameters, plasma proteomics, plasma metabolomics, as well as metagenomics for oral and gut microbiome obtained from the same individuals. Moreover, iNetModels includes tissue- and cancer-specific Gene Co-expression Networks (GCNs) for exploring the connections between the specific genes. This platform allows the user to interactively explore a single feature's association with other omics data and customize its particular context (e.g. male/female specific). The users can also register their data for sharing and visualization of the MOBNs and GCNs. Moreover, iNetModels allows users who do not have a bioinformatics background to facilitate human wellness and disease research. iNetModels can be accessed freely at https://inetmodels.com without any limitation.", "doi": "10.1093/nar/gkab254", "pmid": "33849075", "labels": {"Adil Mardinoglu": "", "SciLifeLab Fellow": "", "DDLS Fellow": "", "Muhammad Arif": ""}, "xrefs": [{"db": "pmc", "key": "PMC8262747"}, {"db": "pii", "key": "6225230"}], "notes": [], "created": "2021-10-08T14:09:52.944Z", "modified": "2026-09-23T09:26:21.692Z"}, {"entity": "publication", "iuid": "81e4859dba7a48f0a00aa594a1b51604", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/81e4859dba7a48f0a00aa594a1b51604.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/81e4859dba7a48f0a00aa594a1b51604"}}, "title": "Mammuthus sp. (Early and Middle Pleistocene Mammoths).", "authors": [{"family": "Pe\u010dnerov\u00e1", "given": "Patr\u00edcia", "initials": "P"}, {"family": "D\u00edez-Del-Molino", "given": "David", "initials": "D"}, {"family": "van der Valk", "given": "Tom", "initials": "T"}, {"family": "Dehasque", "given": "Marianne", "initials": "M"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L"}], "type": "journal article", "published": "2021-07-00", "journal": {"title": "Trends in Genetics", "issn": "0168-9525", "volume": "37", "issue": "7", "pages": "682-683", "issn-l": null}, "abstract": null, "doi": "10.1016/j.tig.2021.04.006", "pmid": "33985817", "labels": {"DDLS Fellow": "", "Tom van der Valk": ""}, "xrefs": [{"db": "pii", "key": "S0168-9525(21)00102-5"}], "notes": [], "created": "2026-09-23T13:34:31.074Z", "modified": "2026-09-23T13:34:31.101Z"}, {"entity": "publication", "iuid": "83e293bce57247798beffc5444e5223e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/83e293bce57247798beffc5444e5223e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/83e293bce57247798beffc5444e5223e"}}, "title": "Artificial Intelligence for Diagnosis and Gleason Grading of Prostate Cancer in Biopsies-Current Status and Next Steps.", "authors": [{"family": "Kartasalo", "given": "Kimmo", "initials": "K"}, {"family": "Bulten", "given": "Wouter", "initials": "W"}, {"family": "Delahunt", "given": "Brett", "initials": "B"}, {"family": "Chen", "given": "Po-Hsuan Cameron", "initials": "PC"}, {"family": "Pinckaers", "given": "Hans", "initials": "H"}, {"family": "Olsson", "given": "Henrik", "initials": "H"}, {"family": "Ji", "given": "Xiaoyi", "initials": "X"}, {"family": "Mulliqi", "given": "Nita", "initials": "N"}, {"family": "Samaratunga", "given": "Hemamali", "initials": "H"}, {"family": "Tsuzuki", "given": "Toyonori", "initials": "T"}, {"family": "Lindberg", "given": "Johan", "initials": "J"}, {"family": "Rantalainen", "given": "Mattias", "initials": "M"}, {"family": "W\u00e4hlby", "given": "Carolina", "initials": "C"}, {"family": "Litjens", "given": "Geert", "initials": "G"}, {"family": "Ruusuvuori", "given": "Pekka", "initials": "P"}, {"family": "Egevad", "given": "Lars", "initials": "L"}, {"family": "Eklund", "given": "Martin", "initials": "M"}], "type": "journal article", "published": "2021-07-00", "journal": {"title": "Eur Urol Focus", "issn": "2405-4569", "issn-l": null, "volume": "7", "issue": "4", "pages": "687-691"}, "abstract": "Diagnosis and Gleason grading of prostate cancer in biopsies are critical for the clinical management of men with prostate cancer. Despite this, the high grading variability among pathologists leads to the potential for under- and overtreatment. Artificial intelligence (AI) systems have shown promise in assisting pathologists to perform Gleason grading, which could help address this problem. In this mini-review, we highlight studies reporting on the development of AI systems for cancer detection and Gleason grading, and discuss the progress needed for widespread clinical implementation, as well as anticipated future developments. PATIENT SUMMARY: This mini-review summarizes the evidence relating to the validation of artificial intelligence (AI)-assisted cancer detection and Gleason grading of prostate cancer in biopsies, and highlights the remaining steps required prior to its widespread clinical implementation. We found that, although there is strong evidence to show that AI is able to perform Gleason grading on par with experienced uropathologists, more work is needed to ensure the accuracy of results from AI systems in diverse settings across different patient populations, digitization platforms, and pathology laboratories.", "doi": "10.1016/j.euf.2021.07.002", "pmid": "34393083", "labels": {"Kimmo Kartasalo": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pii", "key": "S2405-4569(21)00181-4"}], "notes": [], "created": "2024-11-05T16:08:19.943Z", "modified": "2026-09-23T08:48:09.757Z"}, {"entity": "publication", "iuid": "4f6689f3561b4019a8c559f790e808f1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4f6689f3561b4019a8c559f790e808f1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4f6689f3561b4019a8c559f790e808f1"}}, "title": "A single-cell type transcriptomics map of human tissues.", "authors": [{"family": "Karlsson", "given": "Max", "initials": "M", "orcid": "0000-0002-7000-4416", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b93284f942e44f1086616357d77267c3.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f46e4161be08458994efddb75ed75874.json"}}, {"family": "M\u00e9ar", "given": "Loren", "initials": "L", "orcid": "0000-0001-9333-0110", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0dcfbca8ff5446ef9d6d219f23480e0c.json"}}, {"family": "Zhong", "given": "Wen", "initials": "W", "orcid": "0000-0002-7422-6104", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d6ffb1140aaa42c5ac63fe76653fc63b.json"}}, {"family": "Digre", "given": "Andreas", "initials": "A", "orcid": "0000-0003-1145-6700", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3deb03dd3c21410282f4a414d6c394be.json"}}, {"family": "Katona", "given": "Borbala", "initials": "B"}, {"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E", "orcid": "0000-0002-0327-7377", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ec6fb5a1c88b44798144fd2de255fb00.json"}}, {"family": "Butler", "given": "Lynn", "initials": "L"}, {"family": "Odeberg", "given": "Jacob", "initials": "J", "orcid": "0000-0003-0996-1644", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d6abb3fc822a4cacbf1d45224f2442f5.json"}}, {"family": "Dusart", "given": "Philip", "initials": "P"}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e213b04f8984c8eb00c68f5bc2f6a36.json"}}, {"family": "Oksvold", "given": "Per", "initials": "P", "orcid": "0000-0003-3014-5502", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/16beca5822c747128300910b5c74dbfc.json"}}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K", "orcid": "0000-0002-0257-7554", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f4c4545bd2324b7d9b6696dab5bcb7dd.json"}}, {"family": "Zwahlen", "given": "Martin", "initials": "M", "orcid": "0000-0002-0064-4776", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/456805fa3f4f47328f3923b78bf66996.json"}}, {"family": "Arif", "given": "Muhammad", "initials": "M", "orcid": "0000-0003-2261-0881", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c8ffc9889ace44e3b992816601b817e2.json"}}, {"family": "Altay", "given": "Ozlem", "initials": "O"}, {"family": "Li", "given": "Xiangyu", "initials": "X", "orcid": "0000-0002-8301-9959", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5c452ad4e8bb4302a572693103742047.json"}}, {"family": "Ozcan", "given": "Mehmet", "initials": "M", "orcid": "0000-0002-1222-2802", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e690dbebe4144d72b97aad264290fd72.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca58bf2d214047e0ae5e38a42a0f2808.json"}}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/abbbf8193d5a4376a5c726768d039439.json"}}, {"family": "Mulder", "given": "Jan", "initials": "J", "orcid": "0000-0003-3717-5018", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/40ed8170792444b491519e499d51c434.json"}}, {"family": "Luo", "given": "Yonglun", "initials": "Y", "orcid": "0000-0002-0007-7759", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f0283cb6c284428f906b0d03fda62a1e.json"}}, {"family": "Ponten", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9f5294424542413c9ba4432c839c2b63.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ea446aa574042a295d5f69437402f76.json"}}, {"family": "Lindskog", "given": "Cecilia", "initials": "C", "orcid": "0000-0001-5611-1015", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/21610a810a87459c962d6da3f2ad38ad.json"}}], "type": "journal article", "published": "2021-07-00", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "7", "issue": "31", "issn-l": "2375-2548"}, "abstract": "Advances in molecular profiling have opened up the possibility to map the expression of genes in cells, tissues, and organs in the human body. Here, we combined single-cell transcriptomics analysis with spatial antibody-based protein profiling to create a high-resolution single-cell type map of human tissues. An open access atlas has been launched to allow researchers to explore the expression of human protein-coding genes in 192 individual cell type clusters. An expression specificity classification was performed to determine the number of genes elevated in each cell type, allowing comparisons with bulk transcriptomics data. The analysis highlights distinct expression clusters corresponding to cell types sharing similar functions, both within the same organs and between organs.", "doi": "10.1126/sciadv.abh2169", "pmid": "34321199", "labels": {"Adil Mardinoglu": "", "SciLifeLab Fellow": "", "Fredrik Edfors": "", "DDLS Fellow": "", "Muhammad Arif": ""}, "xrefs": [{"db": "pmc", "key": "PMC8318366"}, {"db": "pii", "key": "7/31/eabh2169"}], "notes": [], "created": "2023-12-04T15:06:26.354Z", "modified": "2026-09-22T19:58:16.587Z"}, {"entity": "publication", "iuid": "849012b13e6d40bebf1e5edd27cc7d24", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/849012b13e6d40bebf1e5edd27cc7d24.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/849012b13e6d40bebf1e5edd27cc7d24"}}, "title": "An Open-Source Modular Framework for Automated Pipetting and Imaging Applications", "authors": [{"family": "Ouyang", "given": "Wei", "initials": "W", "orcid": "0000-0002-0291-926X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56f601e1d1c6448aab0c3a1e3cffdbfc.json"}}, {"family": "Bowman", "given": "Richard", "initials": "R", "orcid": "0000-0002-1531-8199", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dd8285f431ce4ff59d9b6b288cec6b9d.json"}}, {"family": "Wang", "given": "Haoran", "initials": "H"}, {"family": "Bumke", "given": "Kaspar E", "initials": "KE"}, {"family": "Collins", "given": "Joel T", "initials": "JT"}, {"family": "Spjuth", "given": "Ola", "initials": "O", "orcid": "0000-0002-8083-2864", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2c192389f99d4801b91f3350e07dfb9e.json"}}, {"family": "Carreras-Puigvert", "given": "Jordi", "initials": "J", "orcid": "0000-0002-7671-3707", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a9c300823ae241eea419a01e4397fcc2.json"}}, {"family": "Diederich", "given": "Benedict", "initials": "B", "orcid": "0000-0003-0453-6286", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/25fb1523d3854ce59fdfe3841250ac3c.json"}}], "type": "posted-content", "published": "2021-06-24", "journal": {"title": "bioRxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2021.06.24.449732", "pmid": null, "labels": {"DDLS Fellow": null, "Wei Ouyang": null}, "xrefs": [], "notes": [], "created": "2026-08-20T10:05:13.473Z", "modified": "2026-10-05T08:28:47.921Z"}, {"entity": "publication", "iuid": "6391f724e5854d8e878be745c27c180d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/6391f724e5854d8e878be745c27c180d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/6391f724e5854d8e878be745c27c180d"}}, "title": "Next generation plasma proteome profiling of COVID-19 patients with mild to moderate symptoms", "authors": [{"family": "Zhong", "given": "Wen", "initials": "W", "orcid": "0000-0002-7422-6104", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d6ffb1140aaa42c5ac63fe76653fc63b.json"}}, {"family": "Altay", "given": "Ozlem", "initials": "O"}, {"family": "Arif", "given": "Muhammad", "initials": "M"}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}], "type": "posted-content", "published": "2021-06-21", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2021.06.15.21258940", "pmid": null, "labels": {"SciLifeLab Fellow": "", "Fredrik Edfors": "", "DDLS Fellow": "", "Adil Mardinoglu": "", "Muhammad Arif": ""}, "xrefs": [], "notes": [], "created": "2026-09-23T14:25:12.473Z", "modified": "2026-09-23T14:25:12.490Z"}, {"entity": "publication", "iuid": "98711a2f404142c198b105f924a21136", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/98711a2f404142c198b105f924a21136.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/98711a2f404142c198b105f924a21136"}}, "title": "Prognostic implications of troponin T variations in inherited cardiomyopathies using systems biology.", "authors": [{"family": "Shakur", "given": "Rameen", "initials": "R", "orcid": "0000-0001-5515-2296", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e3278bfecb994f6dbb3a92d4c6e30ec4.json"}}, {"family": "Ochoa", "given": "Juan Pablo", "initials": "JP"}, {"family": "Robinson", "given": "Alan J", "initials": "AJ"}, {"family": "Niroula", "given": "Abhishek", "initials": "A"}, {"family": "Chandran", "given": "Aneesh", "initials": "A"}, {"family": "Rahman", "given": "Taufiq", "initials": "T"}, {"family": "Vihinen", "given": "Mauno", "initials": "M"}, {"family": "Monserrat", "given": "Lorenzo", "initials": "L", "orcid": "0000-0001-5776-0623", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/11495e5a665a46e884876da28d594385.json"}}], "type": "journal article", "published": "2021-06-14", "journal": {"title": "NPJ Genom Med", "issn": "2056-7944", "volume": "6", "issue": "1", "pages": "47", "issn-l": null}, "abstract": "The cardiac troponin T variations have often been used as an example of the application of clinical genotyping for prognostication and risk stratification measures for the management of patients with a family history of sudden cardiac death or familial cardiomyopathy. Given the disparity in patient outcomes and therapy options, we investigated the impact of variations on the intermolecular interactions across the thin filament complex as an example of an unbiased systems biology method to better define clinical prognosis to aid future management options. We present a novel unbiased dynamic model to define and analyse the functional, structural and physico-chemical consequences of genetic variations among the troponins. This was subsequently integrated with clinical data from accessible global multi-centre systematic reviews of familial cardiomyopathy cases from 106 articles of the literature: 136 disease-causing variations pertaining to 981 global clinical cases. Troponin T variations showed distinct pathogenic hotspots for dilated and hypertrophic cardiomyopathies; considering the causes of cardiovascular death separately, there was a worse survival in terms of sudden cardiac death for patients with a variation at regions 90-129 and 130-179 when compared to amino acids 1-89 and 200-288. Our data support variations among 90-130 as being a hotspot for sudden cardiac death and the region 131-179 for heart failure death/transplantation outcomes wherein the most common phenotype was dilated cardiomyopathy. Survival analysis into regions of high risk (regions 90-129 and 130-180) and low risk (regions 1-89 and 200-288) was significant for sudden cardiac death (p = 0.011) and for heart failure death/transplant (p = 0.028). Our integrative genomic, structural, model from genotype to clinical data integration has implications for enhancing clinical genomics methodologies to improve risk stratification.", "doi": "10.1038/s41525-021-00204-w", "pmid": "34127679", "labels": {"Abhishek Niroula": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC8203786"}, {"db": "pii", "key": "10.1038/s41525-021-00204-w"}], "notes": [], "created": "2023-11-20T11:27:53.798Z", "modified": "2023-11-20T11:27:53.947Z"}, {"entity": "publication", "iuid": "db2dc24351b64a8fa84c99bf0b65956a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/db2dc24351b64a8fa84c99bf0b65956a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/db2dc24351b64a8fa84c99bf0b65956a"}}, "title": "Bicyclic \u03b2-Sheet Mimetics that Target the Transcriptional Coactivator \u03b2-Catenin and Inhibit Wnt Signaling.", "authors": [{"family": "Wendt", "given": "Mathias", "initials": "M", "orcid": "0000-0002-9851-5437", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/788d92f356a54d78bc745c3e770fc55b.json"}}, {"family": "Bellavita", "given": "Rosa", "initials": "R"}, {"family": "Gerber", "given": "Alan", "initials": "A", "orcid": "0000-0003-3909-3606", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4a35e709e1f941e4930291998ac61962.json"}}, {"family": "Efr\u00e9m", "given": "Nina-Louisa", "initials": "NL"}, {"family": "van Ramshorst", "given": "Thirza", "initials": "T"}, {"family": "Pearce", "given": "Nicholas M", "initials": "NM", "orcid": "0000-0002-6693-8603", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/07d6d5de91cc4120b2bf996ca578a13e.json"}}, {"family": "Davey", "given": "Paul R J", "initials": "PRJ"}, {"family": "Everard", "given": "Isabel", "initials": "I"}, {"family": "Vazquez-Chantada", "given": "Mercedes", "initials": "M"}, {"family": "Chiarparin", "given": "Elisabetta", "initials": "E"}, {"family": "Grieco", "given": "Paolo", "initials": "P"}, {"family": "Hennig", "given": "Sven", "initials": "S", "orcid": "0000-0002-8297-6845", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/971105c9d0874625b8904648c321ede9.json"}}, {"family": "Grossmann", "given": "Tom N", "initials": "TN", "orcid": "0000-0003-0179-4116", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a7f56817dde44e4395f0271c2a155b5a.json"}}], "type": "journal article", "published": "2021-06-14", "journal": {"title": "Angew. Chem. Int. Ed. Engl.", "issn": "1521-3773", "volume": "60", "issue": "25", "pages": "13937-13944", "issn-l": "1433-7851"}, "abstract": "Protein complexes are defined by the three-dimensional structure of participating binding partners. Knowledge about these structures can facilitate the design of peptidomimetics which have been applied for example, as inhibitors of protein-protein interactions (PPIs). Even though \u03b2-sheets participate widely in PPIs, they have only rarely served as the basis for peptidomimetic PPI inhibitors, in particular when addressing intracellular targets. Here, we present the structure-based design of \u03b2-sheet mimetics targeting the intracellular protein \u03b2-catenin, a central component of the Wnt signaling pathway. Based on a protein binding partner of \u03b2-catenin, a macrocyclic peptide was designed and its crystal structure in complex with \u03b2-catenin obtained. Using this structure, we designed a library of bicyclic \u03b2-sheet mimetics employing a late-stage diversification strategy. Several mimetics were identified that compete with transcription factor binding to \u03b2-catenin and inhibit Wnt signaling in cells. The presented design strategy can support the development of inhibitors for other \u03b2-sheet-mediated PPIs.", "doi": "10.1002/anie.202102082", "pmid": "33783110", "labels": {"Nicholas Pearce": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC8252567"}], "notes": [], "created": "2022-12-05T19:35:20.330Z", "modified": "2022-12-05T19:35:20.468Z"}, {"entity": "publication", "iuid": "875f27e6c9b5419899dea9adb6ce85a9", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/875f27e6c9b5419899dea9adb6ce85a9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/875f27e6c9b5419899dea9adb6ce85a9"}}, "title": "Systems analysis reveals ageing-related perturbations in retinoids and sex hormones in Alzheimer\u2019s and Parkinson\u2019s diseases", "authors": [{"family": "Lam", "given": "Simon", "initials": "S", "orcid": "0000-0002-4476-0971", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bdf5adecfed749b4a66cdda5cd08ee24.json"}}, {"family": "Hartmann", "given": "Nils", "initials": "N"}, {"family": "Benfeitas", "given": "Rui", "initials": "R", "orcid": "0000-0001-7972-0083", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e2ec344c501496796be3250fd563699.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f46e4161be08458994efddb75ed75874.json"}}, {"family": "Arif", "given": "Muhammad", "initials": "M", "orcid": "0000-0003-2261-0881", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c8ffc9889ace44e3b992816601b817e2.json"}}, {"family": "Turkez", "given": "Hasan", "initials": "H", "orcid": "0000-0002-7046-8990", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cf2f1748757d45cabfe56fdfaccead6a.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ea446aa574042a295d5f69437402f76.json"}}, {"family": "Englert", "given": "Christoph", "initials": "C", "orcid": "0000-0002-5931-3189", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/edbf24bf4c4c463e8215619ca54b2630.json"}}, {"family": "Knight", "given": "Robert", "initials": "R", "orcid": "0000-0001-9920-836X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3e7cb50733bd4de4ba51614e9b5e272a.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca58bf2d214047e0ae5e38a42a0f2808.json"}}], "type": "posted-content", "published": "2021-06-10", "journal": {"title": "bioRxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2021.06.10.447367", "pmid": null, "labels": {"SciLifeLab Fellow": null, "DDLS Fellow": null, "Adil Mardinoglu": null, "Muhammad Arif": null}, "xrefs": [], "notes": [], "created": "2026-08-20T10:04:48.621Z", "modified": "2026-10-05T08:22:44.048Z"}, {"entity": "publication", "iuid": "c5b46bfee1bf4d9399c411d029fe7f86", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c5b46bfee1bf4d9399c411d029fe7f86.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c5b46bfee1bf4d9399c411d029fe7f86"}}, "title": "Rapid and Sensitive Detection of SARS-CoV-2 Infection Using Quantitative Peptide Enrichment LC-MS Analysis", "authors": [{"family": "Hober", "given": "Andreas", "initials": "A", "orcid": "0000-0001-8947-2562", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/06cbc187628340278395a00ab9dd6c89.json"}}, {"family": "Hua", "given": "Tran Minh Khue", "initials": "TMK"}, {"family": "Foley", "given": "Dominic", "initials": "D"}, {"family": "McDonald", "given": "Thomas", "initials": "T"}, {"family": "Vissers", "given": "Johannes P C", "initials": "JPC"}, {"family": "Pattison", "given": "Rebecca", "initials": "R"}, {"family": "Ferries", "given": "Samantha", "initials": "S"}, {"family": "Hermansson", "given": "Sigurd", "initials": "S"}, {"family": "Betner", "given": "Ingvar", "initials": "I"}, {"family": "Uhlen", "given": "Mathias", "initials": "M"}, {"family": "Razavi", "given": "Morteza", "initials": "M"}, {"family": "Yip", "given": "Richard", "initials": "R"}, {"family": "Pope", "given": "Matthew E", "initials": "ME"}, {"family": "Pearson", "given": "Terry W", "initials": "TW"}, {"family": "Anderson", "given": "N Leigh", "initials": "NL"}, {"family": "Bartlett", "given": "Amy", "initials": "A"}, {"family": "Calton", "given": "Lisa", "initials": "L"}, {"family": "Alm", "given": "Jessica J", "initials": "JJ"}, {"family": "Engstrand", "given": "Lars", "initials": "L"}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e213b04f8984c8eb00c68f5bc2f6a36.json"}}], "type": "posted-content", "published": "2021-06-04", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2021.06.02.21258097", "pmid": null, "labels": {"Fredrik Edfors": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T10:04:28.835Z", "modified": "2026-09-23T14:16:29.341Z"}, {"entity": "publication", "iuid": "09a071792cf64b67ab7ab31033715e90", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/09a071792cf64b67ab7ab31033715e90.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/09a071792cf64b67ab7ab31033715e90"}}, "title": "Interobserver reproducibility of perineural invasion of prostatic adenocarcinoma in needle biopsies.", "authors": [{"family": "Egevad", "given": "Lars", "initials": "L", "orcid": "0000-0001-8531-222X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a7d46f1f5fc047dc8edb910eb4f0645c.json"}}, {"family": "Delahunt", "given": "Brett", "initials": "B", "orcid": "0000-0002-5398-0300", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/433a3f884f95451383cc746925d9a08c.json"}}, {"family": "Samaratunga", "given": "Hemamali", "initials": "H"}, {"family": "Tsuzuki", "given": "Toyonori", "initials": "T"}, {"family": "Olsson", "given": "Henrik", "initials": "H"}, {"family": "Str\u00f6m", "given": "Peter", "initials": "P", "orcid": "0000-0002-1631-806X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2798ea6ef2ed4ae88b78dd04d2f14437.json"}}, {"family": "Lindskog", "given": "Cecilia", "initials": "C"}, {"family": "H\u00e4kkinen", "given": "Tomi", "initials": "T"}, {"family": "Kartasalo", "given": "Kimmo", "initials": "K"}, {"family": "Eklund", "given": "Martin", "initials": "M"}, {"family": "Ruusuvuori", "given": "Pekka", "initials": "P"}], "type": "journal article", "published": "2021-06-00", "journal": {"title": "Virchows Arch.", "issn": "1432-2307", "issn-l": "0945-6317", "volume": "478", "issue": "6", "pages": "1109-1116"}, "abstract": "Numerous studies have shown a correlation between perineural invasion (PNI) in prostate biopsies and outcome. The reporting of PNI varies widely in the literature. While the interobserver variability of prostate cancer grading has been studied extensively, less is known regarding the reproducibility of PNI. A total of 212 biopsy cores from a population-based screening trial were included in this study (106 with and 106 without PNI according to the original pathology reports). The glass slides were scanned and circulated among four pathologists with a special interest in urological pathology for assessment of PNI. Discordant cases were stained by immunohistochemistry for S-100 protein. PNI was diagnosed by all four observers in 34.0% of cases, while 41.5% were considered to be negative for PNI. In 24.5% of cases, there was a disagreement between the observers. The kappa for interobserver variability was 0.67-0.75 (mean 0.73). The observations from one participant were compared with data from the original reports, and a kappa for intraobserver variability of 0.87 was achieved. Based on immunohistochemical findings among discordant cases, 88.6% had PNI while 11.4% did not. The most common diagnostic pitfall was the presence of bundles of stroma or smooth muscle. It was noted in a few cases that collagenous micronodules could be mistaken for a nerve. The distance between cancer and nerve was another cause of disagreement. Although the results suggest that the reproducibility of PNI may be greater than that of prostate cancer grading, there is still a need for improvement and standardization.", "doi": "10.1007/s00428-021-03039-z", "pmid": "33534005", "labels": {"Kimmo Kartasalo": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC8203540"}, {"db": "pii", "key": "10.1007/s00428-021-03039-z"}], "notes": [], "created": "2024-11-05T16:08:21.035Z", "modified": "2024-11-29T10:45:08.430Z"}, {"entity": "publication", "iuid": "d3b6e672579746f7a9b5d1e3ccaab16d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d3b6e672579746f7a9b5d1e3ccaab16d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d3b6e672579746f7a9b5d1e3ccaab16d"}}, "title": "Inhibition of RPS6K reveals context-dependent Akt activity in luminal breast cancer cells.", "authors": [{"family": "Erdem", "given": "Cemal", "initials": "C", "orcid": "0000-0003-3663-3646", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f71b5af589264614a52eefa8baba3132.json"}}, {"family": "Lee", "given": "Adrian V", "initials": "AV", "orcid": "0000-0001-9917-514X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1cd097a0d7e6445b90061cc59a9c3c91.json"}}, {"family": "Taylor", "given": "D Lansing", "initials": "DL", "orcid": "0000-0001-6947-1343", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b2e9be3a7fbf4f5a96b31c815ff020c3.json"}}, {"family": "Lezon", "given": "Timothy R", "initials": "TR", "orcid": "0000-0001-9802-3961", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ee4fe45a273f47b092630737197e16cb.json"}}], "type": "journal article", "published": "2021-06-00", "journal": {"title": "PLoS Comput Biol", "issn": "1553-7358", "volume": "17", "issue": "6", "pages": "e1009125", "issn-l": "1553-734X"}, "abstract": "Aberrant signaling through insulin (Ins) and insulin-like growth factor I (IGF1) receptors contribute to the risk and advancement of many cancer types by activating cell survival cascades. Similarities between these pathways have thus far prevented the development of pharmacological interventions that specifically target either Ins or IGF1 signaling. To identify differences in early Ins and IGF1 signaling mechanisms, we developed a dual receptor (IGF1R & InsR) computational response model. The model suggested that ribosomal protein S6 kinase (RPS6K) plays a critical role in regulating MAPK and Akt activation levels in response to Ins and IGF1 stimulation. As predicted, perturbing RPS6K kinase activity led to an increased Akt activation with Ins stimulation compared to IGF1 stimulation. Being able to discern differential downstream signaling, we can explore improved anti-IGF1R cancer therapies by eliminating the emergence of compensation mechanisms without disrupting InsR signaling.", "doi": "10.1371/journal.pcbi.1009125", "pmid": "34191793", "labels": {"DDLS Fellow": null, "Cemal Erdem": null}, "xrefs": [{"db": "pmc", "key": "PMC8277016"}, {"db": "pii", "key": "PCOMPBIOL-D-21-00080"}], "notes": [], "created": "2023-10-27T08:53:47.831Z", "modified": "2023-10-27T08:53:48.022Z"}, {"entity": "publication", "iuid": "8a500af1a5624a77bcde65b0c64e3efd", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8a500af1a5624a77bcde65b0c64e3efd.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8a500af1a5624a77bcde65b0c64e3efd"}}, "title": "Achieving Efficient Fragment Screening at XChem Facility at Diamond Light Source.", "authors": [{"family": "Douangamath", "given": "Alice", "initials": "A"}, {"family": "Powell", "given": "Ailsa", "initials": "A"}, {"family": "Fearon", "given": "Daren", "initials": "D"}, {"family": "Collins", "given": "Patrick M", "initials": "PM"}, {"family": "Talon", "given": "Romain", "initials": "R"}, {"family": "Krojer", "given": "Tobias", "initials": "T"}, {"family": "Skyner", "given": "Rachael", "initials": "R"}, {"family": "Brandao-Neto", "given": "Jose", "initials": "J"}, {"family": "Dunnett", "given": "Louise", "initials": "L"}, {"family": "Dias", "given": "Alexandre", "initials": "A"}, {"family": "Aimon", "given": "Anthony", "initials": "A"}, {"family": "Pearce", "given": "Nicholas M", "initials": "NM"}, {"family": "Wild", "given": "Conor", "initials": "C"}, {"family": "Gorrie-Stone", "given": "Tyler", "initials": "T"}, {"family": "von Delft", "given": "Frank", "initials": "F"}], "type": "journal article", "published": "2021-05-29", "journal": {"title": "J Vis Exp", "issn": "1940-087X", "issue": "171", "issn-l": "1940-087X"}, "abstract": "In fragment-based drug discovery, hundreds or often thousands of compounds smaller than ~300 Da are tested against the protein of interest to identify chemical entities that can be developed into potent drug candidates. Since the compounds are small, interactions are weak, and the screening method must therefore be highly sensitive; moreover, structural information tends to be crucial for elaborating these hits into lead-like compounds. Therefore, protein crystallography has always been a gold-standard technique, yet historically too challenging to find widespread use as a primary screen. Initial XChem experiments were demonstrated in 2014 and then trialed with academic and industrial collaborators to validate the process. Since then, a large research effort and significant beamtime have streamlined sample preparation, developed a fragment library with rapid follow-up possibilities, automated and improved the capability of I04-1 beamline for unattended data collection, and implemented new tools for data management, analysis and hit identification. XChem is now a facility for large-scale crystallographic fragment screening, supporting the entire crystals-to-deposition process, and accessible to academic and industrial users worldwide. The peer-reviewed academic user program has been actively developed since 2016, to accommodate projects from as broad a scientific scope as possible, including well-validated as well as exploratory projects. Academic access is allocated through biannual calls for peer-reviewed proposals, and proprietary work is arranged by Diamond's Industrial Liaison group. This workflow has already been routinely applied to over a hundred targets from diverse therapeutic areas, and effectively identifies weak binders (1%-30% hit rate), which both serve as high-quality starting points for compound design and provide extensive structural information on binding sites. The resilience of the process was demonstrated by continued screening of SARS-CoV-2 targets during the COVID-19 pandemic, including a 3-week turn-around for the main protease.", "doi": "10.3791/62414", "pmid": "34125095", "labels": {"Nicholas Pearce": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2022-12-05T19:35:22.875Z", "modified": "2022-12-05T19:35:22.889Z"}, {"entity": "publication", "iuid": "83f9dbab0f6643ecbed86429f6048c8f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/83f9dbab0f6643ecbed86429f6048c8f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/83f9dbab0f6643ecbed86429f6048c8f"}}, "title": "A combined approach for single-cell mRNA and intracellular protein expression analysis.", "authors": [{"family": "Reimeg\u00e5rd", "given": "Johan", "initials": "J"}, {"family": "Tarbier", "given": "Marcel", "initials": "M", "orcid": "0000-0003-0556-2531", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9678d0797def441e9870afe6ffbb08d0.json"}}, {"family": "Danielsson", "given": "Marcus", "initials": "M", "orcid": "0000-0003-4418-0165", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d41181bacaa34f13ad8e4455e36566d4.json"}}, {"family": "Schuster", "given": "Jens", "initials": "J", "orcid": "0000-0002-4383-9880", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b027b5cce9cc488e88cbf8673f5761b2.json"}}, {"family": "Baskaran", "given": "Sathishkumar", "initials": "S"}, {"family": "Panagiotou", "given": "Styliani", "initials": "S"}, {"family": "Dahl", "given": "Niklas", "initials": "N", "orcid": "0000-0002-8122-0800", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/16529ca196d94a699959c276d3c84960.json"}}, {"family": "Friedl\u00e4nder", "given": "Marc R", "initials": "MR", "orcid": "0000-0001-6577-4363", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ac5a2794be7c4cab89d1e4f1570c9417.json"}}, {"family": "Gallant", "given": "Caroline J", "initials": "CJ", "orcid": "0000-0002-1499-8444", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3278c6f58a45424fb2c2cc43e8cf489c.json"}}], "type": "journal article", "published": "2021-05-25", "journal": {"title": "Commun Biol", "issn": "2399-3642", "issn-l": "2399-3642", "volume": "4", "issue": "1", "pages": "624"}, "abstract": "Combined measurements of mRNA and protein expression in single cells enable in-depth analysis of cellular states. We present SPARC, an approach that combines single-cell RNA-sequencing with proximity extension essays to simultaneously measure global mRNA and 89 intracellular proteins in individual cells. We show that mRNA expression fails to accurately reflect protein abundance at the time of measurement, although the direction of changes is in agreement during neuronal differentiation. Moreover, protein levels of transcription factors better predict their downstream effects than do their corresponding transcripts. Finally, we highlight that protein expression variation is overall lower than mRNA variation, but relative protein variation does not reflect the mRNA level. Our results demonstrate that mRNA and protein measurements in single cells provide different and complementary information regarding cell states. SPARC presents a state-of-the-art co-profiling method that overcomes current limitations in throughput and protein localization, including removing the need for cell fixation.", "doi": "10.1038/s42003-021-02142-w", "pmid": "34035432", "labels": {"Marcel Tarbier": "", "DDLS Fellow": "", "SciLifeLab Fellow": "", "Marc Friedl\u00e4nder": ""}, "xrefs": [{"db": "pmc", "key": "PMC8149646"}, {"db": "pii", "key": "10.1038/s42003-021-02142-w"}], "notes": [], "created": "2025-12-03T10:29:51.571Z", "modified": "2026-09-23T07:30:37.163Z"}, {"entity": "publication", "iuid": "4203cf2e4b4045b4b6f4e6b60144adf7", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4203cf2e4b4045b4b6f4e6b60144adf7.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4203cf2e4b4045b4b6f4e6b60144adf7"}}, "title": "Multi-omics analysis reveals the impact of microbiota on host metabolism in hepatic steatosis", "authors": [{"family": "Zeybel", "given": "Mujdat", "initials": "M", "orcid": "0000-0001-5440-4623", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a7bfd631ded14746be0b94b8f1cac968.json"}}, {"family": "Arif", "given": "Muhammad", "initials": "M", "orcid": "0000-0003-2261-0881", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c8ffc9889ace44e3b992816601b817e2.json"}}, {"family": "Li", "given": "Xiangyu", "initials": "X"}, {"family": "Altay", "given": "Ozlem", "initials": "O", "orcid": "0000-0002-2851-9651", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c74345104c784d28a39ad4bd60ded203.json"}}, {"family": "Shi", "given": "Mengnan", "initials": "M", "orcid": "0000-0001-8643-5846", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/642e9296ea7645848f1a28f619447231.json"}}, {"family": "Akyildiz", "given": "Murat", "initials": "M", "orcid": "0000-0002-2080-7528", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1f08e1f43b3641d6b7ef666a99dcad27.json"}}, {"family": "Saglam", "given": "Burcin", "initials": "B"}, {"family": "Gonenli", "given": "Mehmet Gokhan", "initials": "MG", "orcid": "0000-0003-2925-7048", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2dd670c20c0d4a138211a430b2313be6.json"}}, {"family": "Yigit", "given": "Buket", "initials": "B"}, {"family": "Ulukan", "given": "Burge", "initials": "B"}, {"family": "Ural", "given": "Dilek", "initials": "D", "orcid": "0000-0003-0224-1433", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/adb6b767f9504957a4ff3a7b3daee987.json"}}, {"family": "Shoaie", "given": "Saeed", "initials": "S"}, {"family": "Turkez", "given": "Hasan", "initials": "H", "orcid": "0000-0002-7046-8990", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cf2f1748757d45cabfe56fdfaccead6a.json"}}, {"family": "Nielsen", "given": "Jens", "initials": "J"}, {"family": "Zhang", "given": "Cheng", "initials": "C"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ea446aa574042a295d5f69437402f76.json"}}, {"family": "Bor\u00e9n", "given": "Jan", "initials": "J", "orcid": "0000-0003-0786-8091", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/73a770eb9e614448a046b8e9199052e9.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca58bf2d214047e0ae5e38a42a0f2808.json"}}], "type": "posted-content", "published": "2021-05-23", "journal": {"title": "bioRxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2021.05.22.21257482", "pmid": null, "labels": {"SciLifeLab Fellow": null, "Saeed Shoaie": null, "DDLS Fellow": null, "Adil Mardinoglu": null, "Muhammad Arif": null}, "xrefs": [], "notes": [], "created": "2026-08-20T10:04:15.960Z", "modified": "2026-10-05T08:34:22.130Z"}, {"entity": "publication", "iuid": "9057fdcda8db42b792b5a58a61124f7d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9057fdcda8db42b792b5a58a61124f7d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9057fdcda8db42b792b5a58a61124f7d"}}, "title": "Combined Metabolic Activators Reduces Liver Fat in Nonalcoholic Fatty Liver Disease Patients", "authors": [{"family": "Zeybel", "given": "Mujdat", "initials": "M"}, {"family": "Altay", "given": "Ozlem", "initials": "O"}, {"family": "Arif", "given": "Muhammad", "initials": "M"}, {"family": "Li", "given": "Xiangyu", "initials": "X"}, {"family": "Yang", "given": "Hong", "initials": "H"}, {"family": "Fredolini", "given": "Claudia", "initials": "C"}, {"family": "Akyildiz", "given": "Murat", "initials": "M"}, {"family": "Saglam", "given": "Burcin", "initials": "B"}, {"family": "Gonenli", "given": "Mehmet Gokhan", "initials": "MG"}, {"family": "Ural", "given": "Dilek", "initials": "D"}, {"family": "Kim", "given": "Woonghee", "initials": "W"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/022e140799b6466ea123319c3d70c76e.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C"}, {"family": "Shoaie", "given": "Saeed", "initials": "S"}, {"family": "Nielsen", "given": "Jens", "initials": "J"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Bor\u00e9n", "given": "Jan", "initials": "J"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}], "type": "posted-content", "published": "2021-05-23", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2021.05.20.21257480", "pmid": null, "labels": {"SciLifeLab Fellow": "", "Saeed Shoaie": "", "DDLS Fellow": "", "Adil Mardinoglu": "", "Muhammad Arif": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T10:04:11.999Z", "modified": "2026-09-23T14:13:28.930Z"}, {"entity": "publication", "iuid": "f642e8b93c4840d2814bbba888514f64", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f642e8b93c4840d2814bbba888514f64.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f642e8b93c4840d2814bbba888514f64"}}, "title": "Microbial Community Interactions Are Sensitive to Small Changes in Temperature.", "authors": [{"family": "Burman", "given": "Emil", "initials": "E"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2021-05-21", "journal": {"title": "Front Microbiol", "issn": "1664-302X", "volume": "12", "pages": "672910", "issn-l": "1664-302X"}, "abstract": "Microbial communities are essential for human and environmental health, often forming complex interaction networks responsible for driving ecosystem processes affecting their local environment and their hosts. Disturbances of these communities can lead to loss of interactions and thereby important ecosystem functionality. The research on what drives interactions in microbial communities is still in its infancy, and much information has been gained from the study of model communities. One purpose of using these model microbial communities is that they can be cultured under controlled conditions. Yet, it is not well known how fluctuations of abiotic factors such as temperature affect their interaction networks. In this work, we have studied the effect of temperature on interactions between the members of the model community THOR, which consists of three bacterial species: Pseudomonas koreensis, Flavobacterium johnsoniae, and Bacillus cereus. Our results show that the community-intrinsic properties resulting from their interspecies interactions are highly dependent on incubation temperature. We also found that THOR biofilms had remarkably different abundances of their members when grown at 11, 18, and 25\u00b0C. The results suggest that the sensitivity of community interactions to changes in temperature is influenced, but not completely dictated, by different growth rates of the individual members at different temperatures. Our findings likely extend to other microbial communities and environmental parameters. Thus, temperature could affect community stability and may influence diverse processes including soil productivity, bioprocessing, and disease suppression. Moreover, to establish reproducibility between laboratories working with microbial model communities, it is crucial to ensure experimental stability, including carefully managed temperature conditions.", "doi": "10.3389/fmicb.2021.672910", "pmid": "34093493", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pmc", "key": "PMC8175644"}], "notes": [], "created": "2022-11-08T09:26:10.584Z", "modified": "2022-11-08T09:26:10.610Z"}, {"entity": "publication", "iuid": "483ab25fd7a44c2180b493eebc8b2a9b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/483ab25fd7a44c2180b493eebc8b2a9b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/483ab25fd7a44c2180b493eebc8b2a9b"}}, "title": "Reply to Nagle et al.: The universal stiffening effects of cholesterol on lipid membranes.", "authors": [{"family": "Ashkar", "given": "Rana", "initials": "R", "orcid": "0000-0003-4075-2330", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b0cebcd6caec4fae986f23a3669ea406.json"}}, {"family": "Doktorova", "given": "Milka", "initials": "M", "orcid": "0000-0003-4366-2242", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/791384c319f04584bac8ffb21df7271f.json"}}, {"family": "Heberle", "given": "Frederick A", "initials": "FA", "orcid": "0000-0002-0424-3240", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2557f5621a0b4c87b5f4702fbc7b6bdb.json"}}, {"family": "Scott", "given": "Haden L", "initials": "HL", "orcid": "0000-0002-5778-4905", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a1e768fa75c34598807728aaf9d3a0be.json"}}, {"family": "Barrera", "given": "Francisco N", "initials": "FN", "orcid": "0000-0002-5200-7891", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/087fafd10b3d4c7d911a489b656396e5.json"}}, {"family": "Katsaras", "given": "John", "initials": "J", "orcid": "0000-0002-8937-4177", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/732f1e95fed546efb3427a9b223a23c0.json"}}, {"family": "Khelashvili", "given": "George", "initials": "G", "orcid": "0000-0001-7235-8579", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/49b73bce7f8541fd8c959b5117bbe668.json"}}, {"family": "Brown", "given": "Michael F", "initials": "MF", "orcid": "0000-0003-4154-0241", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b57572fcc90e4033b1c705a9c030e7eb.json"}}], "type": "letter", "published": "2021-05-18", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "issn-l": "0027-8424", "volume": "118", "issue": "20", "pages": null}, "abstract": null, "doi": "10.1073/pnas.2102845118", "pmid": "33952694", "labels": {"Milka Doktorova": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC8157964"}, {"db": "pii", "key": "2102845118"}], "notes": [], "created": "2024-11-27T12:19:18.521Z", "modified": "2024-11-29T10:51:56.121Z"}, {"entity": "publication", "iuid": "39ab63206d1b45be81111a4b8983bc8a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/39ab63206d1b45be81111a4b8983bc8a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/39ab63206d1b45be81111a4b8983bc8a"}}, "title": "Integrative transcriptomic analysis of tissue-specific metabolic crosstalk after myocardial infarction.", "authors": [{"family": "Arif", "given": "Muhammad", "initials": "M", "orcid": "0000-0003-2261-0881", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c8ffc9889ace44e3b992816601b817e2.json"}}, {"family": "Klevstig", "given": "Martina", "initials": "M"}, {"family": "Benfeitas", "given": "Rui", "initials": "R", "orcid": "0000-0001-7972-0083", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e2ec344c501496796be3250fd563699.json"}}, {"family": "Doran", "given": "Stephen", "initials": "S"}, {"family": "Turkez", "given": "Hasan", "initials": "H"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Clausen", "given": "Maryam", "initials": "M"}, {"family": "Wikstr\u00f6m", "given": "Johannes", "initials": "J"}, {"family": "Etal", "given": "Damla", "initials": "D"}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f46e4161be08458994efddb75ed75874.json"}}, {"family": "Levin", "given": "Malin", "initials": "M"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca58bf2d214047e0ae5e38a42a0f2808.json"}}, {"family": "Boren", "given": "Jan", "initials": "J"}], "type": "journal article", "published": "2021-05-11", "journal": {"title": "Elife", "issn": "2050-084X", "volume": "10", "issn-l": "2050-084X"}, "abstract": "Myocardial infarction (MI) promotes a range of systemic effects, many of which are unknown. Here, we investigated the alterations associated with MI progression in heart and other metabolically active tissues (liver, skeletal muscle, and adipose) in a mouse model of MI (induced by ligating the left ascending coronary artery) and sham-operated mice. We performed a genome-wide transcriptomic analysis on tissue samples obtained 6- and 24 hr post MI or sham operation. By generating tissue-specific biological networks, we observed: (1) dysregulation in multiple biological processes (including immune system, mitochondrial dysfunction, fatty-acid beta-oxidation, and RNA and protein processing) across multiple tissues post MI and (2) tissue-specific dysregulation in biological processes in liver and heart post MI. Finally, we validated our findings in two independent MI cohorts. Overall, our integrative analysis highlighted both common and specific biological responses to MI across a range of metabolically active tissues.", "doi": "10.7554/eLife.66921", "pmid": "33972017", "labels": {"SciLifeLab Fellow": "", "DDLS Fellow": "", "Adil Mardinoglu": "", "Muhammad Arif": ""}, "xrefs": [{"db": "pmc", "key": "PMC8186902"}, {"db": "pii", "key": "66921"}, {"db": "GEO", "key": "GSE153485"}, {"db": "GEO", "key": "GSE104187"}, {"db": "GEO", "key": "GSE52313"}], "notes": [], "created": "2023-12-04T15:08:00.531Z", "modified": "2026-09-23T09:30:50.959Z"}, {"entity": "publication", "iuid": "6169589ec8104ddc81aee2a52edc00b7", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/6169589ec8104ddc81aee2a52edc00b7.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/6169589ec8104ddc81aee2a52edc00b7"}}, "title": "Accuratede novoidentification of biosynthetic gene clusters with GECCO", "authors": [{"family": "Carroll", "given": "Laura M", "initials": "LM"}, {"family": "Larralde", "given": "Martin", "initials": "M"}, {"family": "Fleck", "given": "Jonas Simon", "initials": "JS"}, {"family": "Ponnudurai", "given": "Ruby", "initials": "R"}, {"family": "Milanese", "given": "Alessio", "initials": "A"}, {"family": "Cappio", "given": "Elisa", "initials": "E"}, {"family": "Zeller", "given": "Georg", "initials": "G"}], "type": "posted-content", "published": "2021-05-04", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2021.05.03.442509", "pmid": null, "labels": {"Laura Carroll": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2025-03-18T17:32:46.932Z", "modified": "2025-03-18T17:32:46.932Z"}, {"entity": "publication", "iuid": "3d2f95463d824ab8bcb4fe089684d3d0", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3d2f95463d824ab8bcb4fe089684d3d0.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3d2f95463d824ab8bcb4fe089684d3d0"}}, "title": "Next generation plasma proteome profiling to monitor health and disease.", "authors": [{"family": "Zhong", "given": "Wen", "initials": "W", "orcid": "0000-0002-7422-6104", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d6ffb1140aaa42c5ac63fe76653fc63b.json"}}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e213b04f8984c8eb00c68f5bc2f6a36.json"}}, {"family": "Gummesson", "given": "Anders", "initials": "A", "orcid": "0000-0003-0024-960X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1703619132e242aaad263d4ecd80a8ae.json"}}, {"family": "Bergstr\u00f6m", "given": "G\u00f6ran", "initials": "G"}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/abbbf8193d5a4376a5c726768d039439.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ea446aa574042a295d5f69437402f76.json"}}], "type": "journal article", "published": "2021-05-03", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "2493", "issn-l": "2041-1723"}, "abstract": "The need for precision medicine approaches to monitor health and disease makes it important to develop sensitive and accurate assays for proteome profiles in blood. Here, we describe an approach for plasma profiling based on proximity extension assay combined with next generation sequencing. First, we analyze the variability of plasma profiles between and within healthy individuals in a longitudinal wellness study, including the influence of genetic variations on plasma levels. Second, we follow patients newly diagnosed with type 2 diabetes before and during therapeutic intervention using plasma proteome profiling. The studies show that healthy individuals have a unique and stable proteome profile and indicate that a panel of proteins could potentially be used for early diagnosis of diabetes, including stratification of patients with regards to response to metformin treatment. Although validation in larger cohorts is needed, the analysis demonstrates the usefulness of comprehensive plasma profiling for precision medicine efforts.", "doi": "10.1038/s41467-021-22767-z", "pmid": "33941778", "labels": {"Fredrik Edfors": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC8093230"}, {"db": "pii", "key": "10.1038/s41467-021-22767-z"}], "notes": [], "created": "2026-08-20T08:51:28.712Z", "modified": "2026-09-23T07:29:24.542Z"}, {"entity": "publication", "iuid": "d7cc9c53657944438b9a85ebf0a87eff", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d7cc9c53657944438b9a85ebf0a87eff.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d7cc9c53657944438b9a85ebf0a87eff"}}, "title": "Keeping up with the Bacillus cereus group: taxonomy through the genomics era and beyond.", "authors": [{"family": "Carroll", "given": "Laura M", "initials": "LM"}, {"family": "Cheng", "given": "Rachel A", "initials": "RA"}, {"family": "Wiedmann", "given": "Martin", "initials": "M"}, {"family": "Kovac", "given": "Jasna", "initials": "J"}], "type": "journal article", "published": "2021-05-03", "journal": {"title": "Crit Rev Food Sci Nutr", "issn": "1549-7852", "volume": "62", "issue": "28", "pages": "7677-7702", "issn-l": null}, "abstract": "The Bacillus cereus group, also known as B. cereus sensu lato (s.l.), is a species complex that contains numerous closely related lineages, which vary in their ability to cause illness in humans and animals. The classification of B. cereus s.l. isolates into species-level taxonomic units is thus essential for informing public health and food safety efforts. However, taxonomic classification of these organisms is challenging. Numerous-often conflicting-taxonomic changes to the group have been proposed over the past two decades, making it difficult to remain up to date. In this review, we discuss the major nomenclatural changes that have accumulated in the B. cereus s.l. taxonomic space prior to 2020, particularly in the genomic sequencing era, and outline the resulting problems. We discuss several contemporary taxonomic frameworks as applied to B. cereus s.l., including (i) phenotypic, (ii) genomic, and (iii) hybrid nomenclatural frameworks, and we discuss the advantages and disadvantages of each. We offer suggestions as to how readers can avoid B. cereus s.l. taxonomic ambiguities, regardless of the nomenclatural framework(s) they choose to employ. Finally, we discuss future directions and open problems in the B. cereus s.l. taxonomic realm, including those that cannot be solved by genomic approaches alone.", "doi": "10.1080/10408398.2021.1916735", "pmid": "33939559", "labels": {"DDLS Fellow": null, "Laura Carroll": null}, "xrefs": [], "notes": [], "created": "2023-05-13T11:52:48.328Z", "modified": "2025-03-18T17:28:05.219Z"}, {"entity": "publication", "iuid": "180db5f8ac7f49d291562d3050a7ba97", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/180db5f8ac7f49d291562d3050a7ba97.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/180db5f8ac7f49d291562d3050a7ba97"}}, "title": "Inflammation and Apolipoproteins Are Potential Biomarkers for Stratification of Cutaneous Melanoma Patients for Immunotherapy and Targeted Therapy.", "authors": [{"family": "Karlsson", "given": "Max J", "initials": "MJ", "orcid": "0000-0002-7000-4416", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b93284f942e44f1086616357d77267c3.json"}}, {"family": "Costa Svedman", "given": "Fernanda", "initials": "F", "orcid": "0000-0001-8065-3375", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fdbe5b9759eb4ee0a13e66bd79cece06.json"}}, {"family": "Tebani", "given": "Abdellah", "initials": "A", "orcid": "0000-0002-8901-2678", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/794215a6625b4fe4b652ec08bcab98ec.json"}}, {"family": "Kotol", "given": "David", "initials": "D", "orcid": "0000-0002-5388-3826", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c41f8f491c474e6bba2047b5d04b4af5.json"}}, {"family": "H\u00f6iom", "given": "Veronica", "initials": "V"}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/abbbf8193d5a4376a5c726768d039439.json"}}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Egyhazi Brage", "given": "Suzanne", "initials": "S", "orcid": "0000-0002-0524-2346", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7b1b43df8e774c498fd4e1e16b00a5fc.json"}}, {"family": "Maddalo", "given": "Gianluca", "initials": "G", "orcid": "0000-0003-2297-6488", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3fbe53488c7848c582122063ecad8e2b.json"}}], "type": "journal article", "published": "2021-05-01", "journal": {"title": "Cancer Res.", "issn": "1538-7445", "volume": "81", "issue": "9", "pages": "2545-2555", "issn-l": "0008-5472"}, "abstract": "Malignant cutaneous melanoma is one of the most common cancers in young adults. During the last decade, targeted and immunotherapies have significantly increased the overall survival of patients with malignant cutaneous melanoma. Nevertheless, disease progression is common, and a lack of predictive biomarkers of patient response to therapy hinders individualized treatment strategies. To address this issue, we performed a longitudinal study using an unbiased proteomics approach to identify and quantify proteins in plasma both before and during treatment from 109 patients treated with either targeted or immunotherapy. Linear modeling and machine learning approaches identified 43 potential prognostic and predictive biomarkers. A reverse correlation between apolipoproteins and proteins related to inflammation was observed. In the immunotherapy group, patients with low pretreatment expression of apolipoproteins and high expression of inflammation markers had shorter progression-free survival. Similarly, increased expression of LDHB during treatment elicited a significant impact on response to immunotherapy. Overall, we identified potential common and treatment-specific biomarkers in malignant cutaneous melanoma, paving the way for clinical use of these biomarkers following validation on a larger cohort. SIGNIFICANCE: This study identifies a potential biomarker panel that could improve the selection of therapy for patients with cutaneous melanoma.", "doi": "10.1158/0008-5472.CAN-20-2000", "pmid": "33574091", "labels": {"DDLS Fellow": "", "Fredrik Edfors": ""}, "xrefs": [{"db": "pii", "key": "0008-5472.CAN-20-2000"}], "notes": [], "created": "2026-08-21T12:28:54.568Z", "modified": "2026-10-01T08:25:19.301Z"}, {"entity": "publication", "iuid": "1339105abbee4ad4b5cdb2de9e4735a3", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1339105abbee4ad4b5cdb2de9e4735a3.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1339105abbee4ad4b5cdb2de9e4735a3"}}, "title": "A SARS-CoV-2 (COVID-19) biological network to find targets for drug repurposing.", "authors": [{"family": "Habibi", "given": "Mahnaz", "initials": "M", "orcid": "0000-0002-8969-2706", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f04af4e059814b78bfb107c3a5782f70.json"}}, {"family": "Taheri", "given": "Golnaz", "initials": "G", "orcid": "0000-0002-2741-0355", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/014c217121d346b2b371bbc1c2fede57.json"}}, {"family": "Aghdam", "given": "Rosa", "initials": "R", "orcid": "0000-0001-9045-9592", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0179bdcc8b8e4bd68549403ed5b66b79.json"}}], "type": "journal article", "published": "2021-04-30", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "11", "issue": "1", "pages": "9378"}, "abstract": "The Coronavirus disease 2019 (COVID-19) caused by the SARS-CoV-2 virus needs a fast recognition of effective drugs to save lives. In the COVID-19 situation, finding targets for drug repurposing can be an effective way to present new fast treatments. We have designed a two-step solution to address this approach. In the first step, we identify essential proteins from virus targets or their associated modules in human cells as possible drug target candidates. For this purpose, we apply two different algorithms to detect some candidate sets of proteins with a minimum size that drive a significant disruption in the COVID-19 related biological networks. We evaluate the resulted candidate proteins sets with three groups of drugs namely Covid-Drug, Clinical-Drug, and All-Drug. The obtained candidate proteins sets approve 16 drugs out of 18 in the Covid-Drug, 273 drugs out of 328 in the Clinical-Drug, and a large number of drugs in the All-Drug. In the second step, we study COVID-19 associated proteins sets and recognize proteins that are essential to disease pathology. This analysis is performed using DAVID to show and compare essential proteins that are contributed between the COVID-19 comorbidities. Our results for shared proteins show significant enrichment for cardiovascular-related, hypertension, diabetes type 2, kidney-related and lung-related diseases.", "doi": "10.1038/s41598-021-88427-w", "pmid": "33931664", "labels": {"Golnaz Taheri": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC8087682"}, {"db": "pii", "key": "10.1038/s41598-021-88427-w"}], "notes": [], "created": "2025-03-21T09:11:21.991Z", "modified": "2026-09-23T11:15:05.007Z"}, {"entity": "publication", "iuid": "7140910f76834ee1962447e406cbb2b5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/7140910f76834ee1962447e406cbb2b5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/7140910f76834ee1962447e406cbb2b5"}}, "title": "Long-read-sequenced reference genomes of the seven major lineages of enterotoxigenic Escherichia coli (ETEC) circulating in modern time.", "authors": [{"family": "von Mentzer", "given": "Astrid", "initials": "A"}, {"family": "Blackwell", "given": "Grace A", "initials": "GA"}, {"family": "Pickard", "given": "Derek", "initials": "D"}, {"family": "Boinett", "given": "Christine J", "initials": "CJ"}, {"family": "Joffr\u00e9", "given": "Enrique", "initials": "E"}, {"family": "Page", "given": "Andrew J", "initials": "AJ"}, {"family": "Svennerholm", "given": "Ann-Mari", "initials": "AM"}, {"family": "Dougan", "given": "Gordon", "initials": "G"}, {"family": "Sj\u00f6ling", "given": "\u00c5sa", "initials": "\u00c5"}], "type": "journal article", "published": "2021-04-29", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "11", "issue": "1", "pages": "9256", "issn-l": "2045-2322"}, "abstract": "Enterotoxigenic Escherichia coli (ETEC) is an enteric pathogen responsible for the majority of diarrheal cases worldwide. ETEC infections are estimated to cause 80,000 deaths annually, with the highest rates of burden, ca 75 million cases per year, amongst children under 5 years of age in resource-poor countries. It is also the leading cause of diarrhoea in travellers. Previous large-scale sequencing studies have found seven major ETEC lineages currently in circulation worldwide. We used PacBio long-read sequencing combined with Illumina sequencing to create high-quality complete reference genomes for each of the major lineages with manually curated chromosomes and plasmids. We confirm that the major ETEC lineages all harbour conserved plasmids that have been associated with their respective background genomes for decades, suggesting that the plasmids and chromosomes of ETEC are both crucial for ETEC virulence and success as pathogens. The in-depth analysis of gene content, synteny and correct annotations of plasmids will elucidate other plasmids with and without virulence factors in related bacterial species. These reference genomes allow for fast and accurate comparison between different ETEC strains, and these data will form the foundation of ETEC genomics research for years to come.", "doi": "10.1038/s41598-021-88316-2", "pmid": "33927221", "labels": {"Astrid von Mentzer": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC8085198"}, {"db": "pii", "key": "10.1038/s41598-021-88316-2"}], "notes": [], "created": "2025-12-02T15:48:46.873Z", "modified": "2025-12-02T15:48:46.888Z"}, {"entity": "publication", "iuid": "8a1ca3a7300f487581f5b89098c107d0", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8a1ca3a7300f487581f5b89098c107d0.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8a1ca3a7300f487581f5b89098c107d0"}}, "title": "Genomic insights into the conservation status of the world's last remaining Sumatran rhinoceros populations.", "authors": [{"family": "von Seth", "given": "Johanna", "initials": "J", "orcid": "0000-0002-1324-7489", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dd70195ca85f415caf1e4660681e1bbc.json"}}, {"family": "Dussex", "given": "Nicolas", "initials": "N", "orcid": "0000-0002-9179-8593", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3c93917b1e544c6eae92fd4aa0617fd8.json"}}, {"family": "D\u00edez-Del-Molino", "given": "David", "initials": "D", "orcid": "0000-0002-9701-5940", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ffd5992faedc45e1bfe19fd498485400.json"}}, {"family": "van der Valk", "given": "Tom", "initials": "T", "orcid": "0000-0001-6582-3452", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/aa0dba3cc12143cba213f7f3a052216c.json"}}, {"family": "Kutschera", "given": "Verena E", "initials": "VE", "orcid": "0000-0002-8930-534X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c7185df2f7d44872960d604e9c70c551.json"}}, {"family": "Kierczak", "given": "Marcin", "initials": "M", "orcid": "0000-0003-2629-5655", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/da6834c3cedf4ea1b20b659316b45eb2.json"}}, {"family": "Steiner", "given": "Cynthia C", "initials": "CC", "orcid": "0000-0002-2131-8072", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9386c16bd7e14ddca60e03e06f6808fe.json"}}, {"family": "Liu", "given": "Shanlin", "initials": "S"}, {"family": "Gilbert", "given": "M Thomas P", "initials": "MTP", "orcid": "0000-0002-5805-7195", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/93cbe282154844588f63bc7cc6983b30.json"}}, {"family": "Sinding", "given": "Mikkel-Holger S", "initials": "MS", "orcid": "0000-0003-1371-219X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cebd0f43f1204602843d51ff84f94061.json"}}, {"family": "Prost", "given": "Stefan", "initials": "S", "orcid": "0000-0002-6229-3596", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/290b46b14a0348c595bc2b9786f56a0b.json"}}, {"family": "Guschanski", "given": "Katerina", "initials": "K", "orcid": "0000-0002-8493-5457", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4e062373c6bc46b98e56215d3ec89eeb.json"}}, {"family": "Nathan", "given": "Senthilvel K S S", "initials": "SKSS"}, {"family": "Brace", "given": "Selina", "initials": "S", "orcid": "0000-0003-2126-6732", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6269e70522db48a38f585df0d10eea89.json"}}, {"family": "Chan", "given": "Yvonne L", "initials": "YL"}, {"family": "Wheat", "given": "Christopher W", "initials": "CW"}, {"family": "Skoglund", "given": "Pontus", "initials": "P"}, {"family": "Ryder", "given": "Oliver A", "initials": "OA"}, {"family": "Goossens", "given": "Benoit", "initials": "B"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/070030648e52418abda45f9f79688168.json"}}], "type": "historical article", "published": "2021-04-26", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "2393", "issn-l": "2041-1723"}, "abstract": "Small populations are often exposed to high inbreeding and mutational load that can increase the risk of extinction. The Sumatran rhinoceros was widespread in Southeast Asia, but is now restricted to small and isolated populations on Sumatra and Borneo, and most likely extinct on the Malay Peninsula. Here, we analyse 5 historical and 16 modern genomes from these populations to investigate the genomic consequences of the recent decline, such as increased inbreeding and mutational load. We find that the Malay Peninsula population experienced increased inbreeding shortly before extirpation, which possibly was accompanied by purging. The populations on Sumatra and Borneo instead show low inbreeding, but high mutational load. The currently small population sizes may thus in the near future lead to inbreeding depression. Moreover, we find little evidence for differences in local adaptation among populations, suggesting that future inbreeding depression could potentially be mitigated by assisted gene flow among populations.", "doi": "10.1038/s41467-021-22386-8", "pmid": "33896938", "labels": {"DDLS Fellow": "", "Tom van der Valk": ""}, "xrefs": [{"db": "pmc", "key": "PMC8071806"}, {"db": "pii", "key": "10.1038/s41467-021-22386-8"}], "notes": [], "created": "2026-09-23T07:30:00.981Z", "modified": "2026-09-23T07:30:01.277Z"}, {"entity": "publication", "iuid": "4b9887a8d3d34fb2b4999db48a4aa6b0", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4b9887a8d3d34fb2b4999db48a4aa6b0.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4b9887a8d3d34fb2b4999db48a4aa6b0"}}, "title": "Author response: Integrative transcriptomic analysis of tissue-specific metabolic crosstalk after myocardial infarction", "authors": [{"family": "Arif", "given": "Muhammad", "initials": "M", "orcid": "0000-0003-2261-0881", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c8ffc9889ace44e3b992816601b817e2.json"}}, {"family": "Klevstig", "given": "Martina", "initials": "M"}, {"family": "Benfeitas", "given": "Rui", "initials": "R", "orcid": "0000-0001-7972-0083", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e2ec344c501496796be3250fd563699.json"}}, {"family": "Doran", "given": "Stephen", "initials": "S"}, {"family": "Turkez", "given": "Hasan", "initials": "H"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Clausen", "given": "Maryam", "initials": "M"}, {"family": "Wikstr\u00f6m", "given": "Johannes", "initials": "J"}, {"family": "Etal", "given": "Damla", "initials": "D"}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f46e4161be08458994efddb75ed75874.json"}}, {"family": "Levin", "given": "Malin", "initials": "M"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca58bf2d214047e0ae5e38a42a0f2808.json"}}, {"family": "Boren", "given": "Jan", "initials": "J"}], "type": "peer-review", "published": "2021-04-21", "journal": {"issn-l": null}, "abstract": null, "doi": "10.7554/elife.66921.sa2", "pmid": null, "labels": {"SciLifeLab Fellow": "", "DDLS Fellow": "", "Adil Mardinoglu": "", "Muhammad Arif": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T13:53:37.411Z", "modified": "2026-09-23T15:07:05.257Z"}, {"entity": "publication", "iuid": "54bd5d052bfe44c8909dfed30dcd1858", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/54bd5d052bfe44c8909dfed30dcd1858.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/54bd5d052bfe44c8909dfed30dcd1858"}}, "title": "Molecular pathways behind acquired obesity: Adipose tissue and skeletal muscle multiomics in monozygotic twin pairs discordant for BMI.", "authors": [{"family": "van der Kolk", "given": "Birgitta W", "initials": "BW"}, {"family": "Saari", "given": "Sina", "initials": "S"}, {"family": "Lovric", "given": "Alen", "initials": "A"}, {"family": "Arif", "given": "Muhammad", "initials": "M"}, {"family": "Alvarez", "given": "Marcus", "initials": "M"}, {"family": "Ko", "given": "Arthur", "initials": "A"}, {"family": "Miao", "given": "Zong", "initials": "Z"}, {"family": "Sahebekhtiari", "given": "Navid", "initials": "N"}, {"family": "Muniandy", "given": "Maheswary", "initials": "M"}, {"family": "Heinonen", "given": "Sini", "initials": "S"}, {"family": "Oghabian", "given": "Ali", "initials": "A"}, {"family": "Jokinen", "given": "Riikka", "initials": "R"}, {"family": "Jukarainen", "given": "Sakari", "initials": "S"}, {"family": "Hakkarainen", "given": "Antti", "initials": "A"}, {"family": "Lundbom", "given": "Jesper", "initials": "J"}, {"family": "Kuula", "given": "Juho", "initials": "J"}, {"family": "Groop", "given": "Per-Henrik", "initials": "PH"}, {"family": "Tukiainen", "given": "Taru", "initials": "T"}, {"family": "Lundbom", "given": "Nina", "initials": "N"}, {"family": "Rissanen", "given": "Aila", "initials": "A"}, {"family": "Kaprio", "given": "Jaakko", "initials": "J"}, {"family": "Williams", "given": "Evan G", "initials": "EG"}, {"family": "Zamboni", "given": "Nicola", "initials": "N"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Pajukanta", "given": "P\u00e4ivi", "initials": "P"}, {"family": "Pietil\u00e4inen", "given": "Kirsi H", "initials": "KH"}], "type": "journal article", "published": "2021-04-20", "journal": {"title": "Cell Rep Med", "issn": "2666-3791", "volume": "2", "issue": "4", "pages": "100226", "issn-l": null}, "abstract": "Tissue-specific mechanisms prompting obesity-related development complications in humans remain unclear. We apply multiomics analyses of subcutaneous adipose tissue and skeletal muscle to examine the effects of acquired obesity among 49 BMI-discordant monozygotic twin pairs. Overall, adipose tissue appears to be more affected by excess body weight than skeletal muscle. In heavier co-twins, we observe a transcriptional pattern of downregulated mitochondrial pathways in both tissues and upregulated inflammatory pathways in adipose tissue. In adipose tissue, heavier co-twins exhibit lower creatine levels; in skeletal muscle, glycolysis- and redox stress-related protein and metabolite levels remain higher. Furthermore, metabolomics analyses in both tissues reveal that several proinflammatory lipids are higher and six of the same lipid derivatives are lower in acquired obesity. Finally, in adipose tissue, but not in skeletal muscle, mitochondrial downregulation and upregulated inflammation are associated with a fatty liver, insulin resistance, and dyslipidemia, suggesting that adipose tissue dominates in acquired obesity.", "doi": "10.1016/j.xcrm.2021.100226", "pmid": "33948567", "labels": {"Adil Mardinoglu": "", "SciLifeLab Fellow": "", "DDLS Fellow": "", "Muhammad Arif": ""}, "xrefs": [{"db": "pmc", "key": "PMC8080113"}, {"db": "pii", "key": "S2666-3791(21)00042-2"}], "notes": [], "created": "2023-12-04T15:08:01.880Z", "modified": "2026-09-23T08:33:37.502Z"}, {"entity": "publication", "iuid": "a23f439e8d27436ea664d32986586d76", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a23f439e8d27436ea664d32986586d76.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a23f439e8d27436ea664d32986586d76"}}, "title": "Germline variants at SOHLH2 influence multiple myeloma risk.", "authors": [{"family": "Duran-Lozano", "given": "Laura", "initials": "L", "orcid": "0000-0003-3557-5018", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/de2e3fde2a084b76bb3951025f53fe43.json"}}, {"family": "Thorleifsson", "given": "Gudmar", "initials": "G"}, {"family": "Lopez de Lapuente Portilla", "given": "Aitzkoa", "initials": "A"}, {"family": "Niroula", "given": "Abhishek", "initials": "A"}, {"family": "Went", "given": "Molly", "initials": "M"}, {"family": "Thodberg", "given": "Malte", "initials": "M"}, {"family": "Pertesi", "given": "Maroulio", "initials": "M"}, {"family": "Ajore", "given": "Ram", "initials": "R"}, {"family": "Cafaro", "given": "Caterina", "initials": "C"}, {"family": "Olason", "given": "Pall I", "initials": "PI"}, {"family": "Stefansdottir", "given": "Lilja", "initials": "L"}, {"family": "Bragi Walters", "given": "G", "initials": "G", "orcid": "0000-0002-5415-6487", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/82463c5a2ff44538a81559d5b83fb76b.json"}}, {"family": "Halldorsson", "given": "Gisli H", "initials": "GH", "orcid": "0000-0001-7067-9862", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/28549aa56c4543178dd7626dbc9e4667.json"}}, {"family": "Turesson", "given": "Ingemar", "initials": "I"}, {"family": "Kaiser", "given": "Martin F", "initials": "MF", "orcid": "0000-0002-3677-4804", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/61695044f08e4490a7feaf7db2aacc07.json"}}, {"family": "Weinhold", "given": "Niels", "initials": "N"}, {"family": "Abildgaard", "given": "Niels", "initials": "N"}, {"family": "Andersen", "given": "Niels Frost", "initials": "NF"}, {"family": "Mellqvist", "given": "Ulf-Henrik", "initials": "UH"}, {"family": "Waage", "given": "Anders", "initials": "A"}, {"family": "Juul-Vangsted", "given": "Annette", "initials": "A", "orcid": "0000-0002-2131-731X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7eadc85ce9564aeb838718479df147ff.json"}}, {"family": "Thorsteinsdottir", "given": "Unnur", "initials": "U"}, {"family": "Hansson", "given": "Markus", "initials": "M", "orcid": "0000-0002-7715-4548", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9aabef8e26ba40d9abd8e229d954795d.json"}}, {"family": "Houlston", "given": "Richard", "initials": "R", "orcid": "0000-0002-5268-0242", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e7605f3f03f94e1b95c011318f5e5d4c.json"}}, {"family": "Rafnar", "given": "Thorunn", "initials": "T", "orcid": "0000-0003-0491-7046", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/67a01e1ebd79473dbc0059d38f066e55.json"}}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "Nilsson", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-5542-0254", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2e9df5bbe6f948b196a65176963748c8.json"}}], "type": "journal article", "published": "2021-04-19", "journal": {"title": "Blood Cancer J", "issn": "2044-5385", "volume": "11", "issue": "4", "pages": "76", "issn-l": null}, "abstract": "Multiple myeloma (MM) is caused by the uncontrolled, clonal expansion of plasma cells. While there is epidemiological evidence for inherited susceptibility, the molecular basis remains incompletely understood. We report a genome-wide association study totalling 5,320 cases and 422,289 controls from four Nordic populations, and find a novel MM risk variant at SOHLH2 at 13q13.3 (risk allele frequency = 3.5%; odds ratio = 1.38; P = 2.2 \u00d7 10-14). This gene encodes a transcription factor involved in gametogenesis that is normally only weakly expressed in plasma cells. The association is represented by 14 variants in linkage disequilibrium. Among these, rs75712673 maps to a genomic region with open chromatin in plasma cells, and upregulates SOHLH2 in this cell type. Moreover, rs75712673 influences transcriptional activity in luciferase assays, and shows a chromatin looping interaction with the SOHLH2 promoter. Our work provides novel insight into MM susceptibility.", "doi": "10.1038/s41408-021-00468-6", "pmid": "33875642", "labels": {"Abhishek Niroula": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC8055668"}, {"db": "pii", "key": "10.1038/s41408-021-00468-6"}], "notes": [], "created": "2023-11-20T11:27:50.066Z", "modified": "2023-11-20T11:27:50.552Z"}, {"entity": "publication", "iuid": "17f17c04e8644878816062cea6b7acbd", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/17f17c04e8644878816062cea6b7acbd.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/17f17c04e8644878816062cea6b7acbd"}}, "title": "Development and Validation of a Risk Prediction Model for Esophageal Squamous Cell Carcinoma Using Cohort Studies.", "authors": [{"family": "Wang", "given": "Qiao-Li", "initials": "QL"}, {"family": "Ness-Jensen", "given": "Eivind", "initials": "E"}, {"family": "Santoni", "given": "Giola", "initials": "G"}, {"family": "Xie", "given": "Shao-Hua", "initials": "SH"}, {"family": "Lagergren", "given": "Jesper", "initials": "J"}], "type": "journal article", "published": "2021-04-00", "journal": {"title": "Am J Gastroenterol", "issn": "1572-0241", "volume": "116", "issue": "4", "pages": "683-691", "issn-l": null}, "abstract": "Esophageal squamous cell carcinoma (ESCC) carries a poor prognosis, but earlier tumor detection would improve survival. We aimed to develop and externally validate a risk prediction model based on exposure to readily available risk factors to identify high-risk individuals of ESCC.\n\nCompeting risk regression modeling was used to develop a risk prediction model. Individuals' absolute risk of ESCC during follow-up was computed with the cumulative incidence function. We used prospectively collected data from the Nord-Tr\u00f8ndelag Health Study (HUNT) for model derivation and the UK Biobank cohort for validation. Candidate predictors were age, sex, tobacco smoking, alcohol consumption, body mass index (BMI), education, cohabitation, physical exercise, and employment. Model performance was validated internally and externally by evaluating model discrimination using the area under the receiver-operating characteristic curve (AUC) and model calibration.\n\nThe developed risk prediction model included age, sex, smoking, alcohol, and BMI. The AUC for 5-year risk of ESCC was 0.76 (95% confidence interval [CI], 0.58-0.93) in the derivation cohort and 0.70 (95% CI, 0.64-0.75) in the validation cohort. The calibration showed close agreement between the predicted cumulative risk and observed probabilities of developing ESCC. Higher net benefit was observed when applying the risk prediction model than considering all participants as being at high risk, indicating good clinical usefulness. A web tool for risk calculation was developed: https://sites.google.com/view/escc-ugis-ki.\n\nThis ESCC risk prediction model showed good discrimination and calibration and validated well in an independent cohort. This readily available model can help select high-risk individuals for preventive interventions.", "doi": "10.14309/ajg.0000000000001094", "pmid": "33982937", "labels": {"DDLS Fellow": null, "Qiaoli Wang": null}, "xrefs": [{"db": "pii", "key": "00000434-202104000-00020"}], "notes": [], "created": "2025-11-27T18:53:33.701Z", "modified": "2025-11-27T18:53:33.725Z"}, {"entity": "publication", "iuid": "a4e81bc2a89a42c589784803bddfcbbb", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a4e81bc2a89a42c589784803bddfcbbb.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a4e81bc2a89a42c589784803bddfcbbb"}}, "title": "A comparison of approaches to scaffolding multiple regions along the 16S rRNA gene for improved resolution", "authors": [{"family": "Debelius", "given": "Justine W", "initials": "JW", "orcid": "0000-0002-8605-3546", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0ab59645351d44e9bc0b7fdf5989f55c.json"}}, {"family": "Robeson", "given": "Michael", "initials": "M", "orcid": "0000-0001-7119-6301", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7f52dcf1867d47cbab3f069ed35f1cc6.json"}}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW", "orcid": "0000-0001-5432-1764", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/246ed7b405dd4c3f9ec5e7ff9f1d3ade.json"}}, {"family": "Boulund", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-3806-323X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a5c6814a31e644b9bc544d4da759a438.json"}}, {"family": "Ye", "given": "Weimin", "initials": "W", "orcid": "0000-0002-6859-4648", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9069984313a74a33a4e5b067b6f37f4e.json"}}, {"family": "Engstrand", "given": "Lars", "initials": "L", "orcid": "0000-0002-7713-2373", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02d8684df81e42169e613de803446fbf.json"}}], "type": "posted-content", "published": "2021-03-23", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2021.03.23.436606", "pmid": null, "labels": {"DDLS Fellow": "", "Luisa Hugerth": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T10:03:25.011Z", "modified": "2026-09-23T13:48:28.462Z"}, {"entity": "publication", "iuid": "afbfd5032fd5404eb14335b4399b1822", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/afbfd5032fd5404eb14335b4399b1822.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/afbfd5032fd5404eb14335b4399b1822"}}, "title": "Dysbiosis of the Human Oral Microbiome During the Menstrual Cycle and Vulnerability to the External Exposures of Smoking and Dietary Sugar.", "authors": [{"family": "Bostanci", "given": "Nagihan", "initials": "N"}, {"family": "Krog", "given": "Maria Christine", "initials": "MC"}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW"}, {"family": "Bashir", "given": "Zahra", "initials": "Z"}, {"family": "Fransson", "given": "Emma", "initials": "E"}, {"family": "Boulund", "given": "Fredrik", "initials": "F"}, {"family": "Belibasakis", "given": "Georgios N", "initials": "GN"}, {"family": "Wannerberger", "given": "Kristin", "initials": "K"}, {"family": "Engstrand", "given": "Lars", "initials": "L"}, {"family": "Nielsen", "given": "Henriette Svarre", "initials": "HS"}, {"family": "Schuppe-Koistinen", "given": "Ina", "initials": "I"}], "type": "journal article", "published": "2021-03-19", "journal": {"title": "Front. Cell. Infect. Microbiol.", "issn": "2235-2988", "volume": "11", "pages": "625229", "issn-l": "2235-2988"}, "abstract": "Physiological hormonal fluctuations exert endogenous pressures on the structure and function of the human microbiome. As such, the menstrual cycle may selectively disrupt the homeostasis of the resident oral microbiome, thus compromising oral health. Hence, the aim of the present study was to structurally and functionally profile the salivary microbiome of 103 women in reproductive age with regular menstrual cycle, while evaluating the modifying influences of hormonal contraceptives, sex hormones, diet, and smoking. Whole saliva was sampled during the menstrual, follicular, and luteal phases (n = 309) of the cycle, and the participants reported questionnaire-based data concerning their life habits and oral or systemic health. No significant differences in alpha-diversity or phase-specific clustering of the overall microbiome were observed. Nevertheless, the salivary abundances of genera Campylobacter, Haemophilus, Prevotella, and Oribacterium varied throughout the cycle, and a higher species-richness was observed during the luteal phase. While the overall community structure maintained relatively intact, its functional properties were drastically affected. In particular, 11 functional modules were differentially abundant throughout the menstrual cycle, including pentose phosphate metabolism, and biosynthesis of cobalamin and neurotransmitter gamma-aminobutyric acid. The menstrual cycle phase, but not oral contraceptive usage, was accountable for greater variations in the metabolic pathways of the salivary microbiome. Further co-risk factor analysis demonstrated that Prevotella and Veillonella were increased in current smokers, whereas high dietary sugar consumption modified the richness and diversity of the microbiome during the cycle. This is the first large study to systematically address dysbiotic variations of the oral microbiome during the course of menstrual cycle, and document the additive effect of smoking and sugar consumption as environmental risk factors. It reveals the structural resilience and functional adaptability of the oral microbiome to the endogenous hormonal pressures of the menstrual cycle, while revealing its vulnerability to the exogenous exposures of diet and smoking.", "doi": "10.3389/fcimb.2021.625229", "pmid": "33816334", "labels": {"Luisa Hugerth": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC8018275"}], "notes": [], "created": "2022-11-08T06:58:59.863Z", "modified": "2026-09-23T09:24:20.703Z"}, {"entity": "publication", "iuid": "ee33a340efc5421db39389b0aff4e163", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ee33a340efc5421db39389b0aff4e163.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ee33a340efc5421db39389b0aff4e163"}}, "title": "Ca2+-dependent mechanism of membrane insertion and destabilization by the SARS-CoV-2 fusion peptide.", "authors": [{"family": "Khelashvili", "given": "George", "initials": "G"}, {"family": "Plante", "given": "Ambrose", "initials": "A"}, {"family": "Doktorova", "given": "Milka", "initials": "M"}, {"family": "Weinstein", "given": "Harel", "initials": "H"}], "type": "journal article", "published": "2021-03-16", "journal": {"title": "Biophys. J.", "issn": "1542-0086", "issn-l": "0006-3495", "volume": "120", "issue": "6", "pages": "1105-1119"}, "abstract": "Cell penetration after recognition of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus by the ACE2 receptor and the fusion of its viral envelope membrane with cellular membranes are the early steps of infectivity. A region of the Spike protein of the virus, identified as the \"fusion peptide\" (FP), is liberated at its N-terminal site by a specific cleavage occurring in concert with the interaction of the receptor-binding domain of the Spike. Studies have shown that penetration is enhanced by the required binding of Ca2+ ions to the FPs of coronaviruses, but the mechanisms of membrane insertion and destabilization remain unclear. We have predicted the preferred positions of Ca2+ binding to the SARS-CoV-2-FP, the role of Ca2+ ions in mediating peptide-membrane interactions, the preferred mode of insertion of the Ca2+-bound SARS-CoV-2-FP, and consequent effects on the lipid bilayer from extensive atomistic molecular dynamics simulations and trajectory analyses. In a systematic sampling of the interactions of the Ca2+-bound peptide models with lipid membranes, SARS-CoV-2-FP penetrated the bilayer and disrupted its organization only in two modes involving different structural domains. In one, the hydrophobic residues F833/I834 from the middle region of the peptide are inserted. In the other, more prevalent mode, the penetration involves residues L822/F823 from the LLF motif, which is conserved in CoV-2-like viruses, and is achieved by the binding of Ca2+ ions to the D830/D839 and E819/D820 residue pairs. FP penetration is shown to modify the molecular organization in specific areas of the bilayer, and the extent of membrane binding of the SARS-CoV-2 FP is significantly reduced in the absence of Ca2+ ions. These findings provide novel mechanistic insights regarding the role of Ca2+ in mediating SARS-CoV-2 fusion and provide a detailed structural platform to aid the ongoing efforts in rational design of compounds to inhibit SARS-CoV-2 cell entry.", "doi": "10.1016/j.bpj.2021.02.023", "pmid": "33631204", "labels": {"Milka Doktorova": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC7899928"}, {"db": "pii", "key": "S0006-3495(21)00162-4"}], "notes": [], "created": "2024-11-27T12:18:14.730Z", "modified": "2024-11-29T12:16:13.023Z"}, {"entity": "publication", "iuid": "7dc3609b9b0949b690a4d7f885777859", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/7dc3609b9b0949b690a4d7f885777859.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/7dc3609b9b0949b690a4d7f885777859"}}, "title": "Pycro-Manager: open-source software for customized and reproducible microscope control.", "authors": [{"family": "Pinkard", "given": "Henry", "initials": "H", "orcid": "0000-0002-4748-5207", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d7cad062e2754a2492c6febdaa3cebac.json"}}, {"family": "Stuurman", "given": "Nico", "initials": "N", "orcid": "0000-0002-6179-8613", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c4da009985664b98997919bb23491ebb.json"}}, {"family": "Ivanov", "given": "Ivan E", "initials": "IE"}, {"family": "Anthony", "given": "Nicholas M", "initials": "NM", "orcid": "0000-0003-2882-2471", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eb8c9c2baa834643b71a60339a3ace4a.json"}}, {"family": "Ouyang", "given": "Wei", "initials": "W"}, {"family": "Li", "given": "Bin", "initials": "B", "orcid": "0000-0003-0695-393X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/422c2243579b47058da45a45d5a194e8.json"}}, {"family": "Yang", "given": "Bin", "initials": "B"}, {"family": "Tsuchida", "given": "Mark A", "initials": "MA"}, {"family": "Chhun", "given": "Bryant", "initials": "B"}, {"family": "Zhang", "given": "Grace", "initials": "G"}, {"family": "Mei", "given": "Ryan", "initials": "R"}, {"family": "Anderson", "given": "Michael", "initials": "M"}, {"family": "Shepherd", "given": "Douglas P", "initials": "DP"}, {"family": "Hunt-Isaak", "given": "Ian", "initials": "I"}, {"family": "Dunn", "given": "Raymond L", "initials": "RL"}, {"family": "Jahr", "given": "Wiebke", "initials": "W", "orcid": "0000-0003-0201-2315", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/48a25c1246864049aed96aea37423357.json"}}, {"family": "Kato", "given": "Saul", "initials": "S"}, {"family": "Royer", "given": "Lo\u00efc A", "initials": "LA", "orcid": "0000-0002-9991-9724", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/38277bc865f047df8c4523ebf0f1261c.json"}}, {"family": "Thiagarajah", "given": "Jay R", "initials": "JR", "orcid": "0000-0002-1437-325X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a143e611ae9945cfb523d3ec401f0d9e.json"}}, {"family": "Eliceiri", "given": "Kevin W", "initials": "KW", "orcid": "0000-0001-8678-670X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d0c430e00d45438c9b0fc3b68e0fbec9.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb07e6d0122c4528a927c1fe922e3bc8.json"}}, {"family": "Mehta", "given": "Shalin B", "initials": "SB"}, {"family": "Waller", "given": "Laura", "initials": "L", "orcid": "0000-0003-1243-2356", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1d4218bfdf8f47489f92f16022b115ca.json"}}], "type": "letter", "published": "2021-03-00", "journal": {"title": "Nat. Methods", "issn": "1548-7105", "volume": "18", "issue": "3", "pages": "226-228", "issn-l": "1548-7091"}, "abstract": null, "doi": "10.1038/s41592-021-01087-6", "pmid": "33674797", "labels": {"DDLS Fellow": "", "Wei Ouyang": ""}, "xrefs": [{"db": "mid", "key": "NIHMS1745499"}, {"db": "pmc", "key": "PMC8532176"}, {"db": "pii", "key": "10.1038/s41592-021-01087-6"}], "notes": [], "created": "2026-08-20T09:02:36.544Z", "modified": "2026-09-23T07:33:36.435Z"}, {"entity": "publication", "iuid": "1dcd1fa0c3e1457a8f1040ae23ba0fe0", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1dcd1fa0c3e1457a8f1040ae23ba0fe0.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1dcd1fa0c3e1457a8f1040ae23ba0fe0"}}, "title": "No evidence for a placental microbiome in human pregnancies at term.", "authors": [{"family": "Sterpu", "given": "Irene", "initials": "I"}, {"family": "Fransson", "given": "Emma", "initials": "E"}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW"}, {"family": "Du", "given": "Juan", "initials": "J"}, {"family": "Pereira", "given": "Marcela", "initials": "M"}, {"family": "Cheng", "given": "Liqin", "initials": "L"}, {"family": "Radu", "given": "Sebastian Alexandru", "initials": "SA"}, {"family": "Calder\u00f3n-P\u00e9rez", "given": "Lorena", "initials": "L"}, {"family": "Zha", "given": "Yinghua", "initials": "Y"}, {"family": "Angelidou", "given": "Pia", "initials": "P"}, {"family": "Pennhag", "given": "Alexandra", "initials": "A"}, {"family": "Boulund", "given": "Fredrik", "initials": "F"}, {"family": "Scheynius", "given": "Annika", "initials": "A"}, {"family": "Engstrand", "given": "Lars", "initials": "L"}, {"family": "Wiberg-Itzel", "given": "Eva", "initials": "E"}, {"family": "Schuppe-Koistinen", "given": "Ina", "initials": "I"}], "type": "journal article", "published": "2021-03-00", "journal": {"title": "Am J Obstet Gynecol", "issn": "1097-6868", "volume": "224", "issue": "3", "pages": "296.e1-296.e23", "issn-l": null}, "abstract": "The placenta plays an important role in the modulation of pregnancy immunity; however, there is no consensus regarding the existence of a placental microbiome in healthy full-term pregnancies.\n\nThis study aimed to investigate the existence and origin of a placental microbiome.\n\nA cross-sectional study comparing samples (3 layers of placental tissue, amniotic fluid, vernix caseosa, and saliva, vaginal, and rectal samples) from 2 groups of full-term births: 50 women not in labor with elective cesarean deliveries and 26 with vaginal deliveries. The comparisons were performed using polymerase chain reaction amplification and DNA sequencing techniques and bacterial culture experiments.\n\nThere were no significant differences regarding background characteristics between women who delivered by elective cesarean and those who delivered vaginally. Quantitative measurements of bacterial content in all 3 placental layers (quantitative polymerase chain reaction of the 16S ribosomal RNA gene) did not show any significant difference among any of the sample types and the negative controls. Here, 16S ribosomal RNA gene sequencing of the maternal side of the placenta could not differentiate between bacteria in the placental tissue and contamination of the laboratory reagents with bacterial DNA. Probe-specific quantitative polymerase chain reaction for bacterial taxa suspected to be present in the placenta could not detect any statistically significant difference between the 2 groups. In bacterial cultures, substantially more bacteria were observed in the placenta layers from vaginal deliveries than those from cesarean deliveries. In addition, 16S ribosomal RNA gene sequencing of bacterial colonies revealed that most of the bacteria that grew on the plates were genera typically found in human skin; moreover, it revealed that placentas delivered vaginally contained a high prevalence of common vaginal bacteria. Bacterial growth inhibition experiments indicated that placental tissue may facilitate the inhibition of bacterial growth.\n\nWe found no evidence to support the existence of a placental microbiome in our study of 76 term pregnancies, which used polymerase chain reaction amplification and sequencing techniques and bacterial culture experiments. Incidental findings of bacterial species could be due to contamination or to low-grade bacterial presence in some locations; such bacteria do not represent a placental microbiome per se.", "doi": "10.1016/j.ajog.2020.08.103", "pmid": "32871131", "labels": {"Luisa Hugerth": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pii", "key": "S0002-9378(20)30984-4"}], "notes": [], "created": "2022-11-08T06:59:02.210Z", "modified": "2026-09-23T07:44:09.426Z"}, {"entity": "publication", "iuid": "9ffea6c397584834b8682a746564a43c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9ffea6c397584834b8682a746564a43c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9ffea6c397584834b8682a746564a43c"}}, "title": "Million-year-old DNA sheds light on the genomic history of mammoths.", "authors": [{"family": "van der Valk", "given": "Tom", "initials": "T", "orcid": "0000-0001-6582-3452", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/aa0dba3cc12143cba213f7f3a052216c.json"}}, {"family": "Pe\u010dnerov\u00e1", "given": "Patr\u00edcia", "initials": "P", "orcid": "0000-0001-9350-1987", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bdf6095a4c8343afbe9d8cd298b273b5.json"}}, {"family": "D\u00edez-Del-Molino", "given": "David", "initials": "D", "orcid": "0000-0002-9701-5940", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ffd5992faedc45e1bfe19fd498485400.json"}}, {"family": "Bergstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Oppenheimer", "given": "Jonas", "initials": "J"}, {"family": "Hartmann", "given": "Stefanie", "initials": "S", "orcid": "0000-0002-3476-0169", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7f0dcf83700b4f63a10503a45af0ef2f.json"}}, {"family": "Xenikoudakis", "given": "Georgios", "initials": "G"}, {"family": "Thomas", "given": "Jessica A", "initials": "JA"}, {"family": "Dehasque", "given": "Marianne", "initials": "M", "orcid": "0000-0002-4640-8306", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/873b625c6ce44ec48f30d92fbc9b3e2f.json"}}, {"family": "Sa\u011fl\u0131can", "given": "Ekin", "initials": "E", "orcid": "0000-0001-8646-1163", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9848f2477f374763bcd4c4d4ab17a903.json"}}, {"family": "Fidan", "given": "Fatma Rabia", "initials": "FR", "orcid": "0000-0001-5877-7945", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b8d12ba6fa434e7cb44e00d34da07484.json"}}, {"family": "Barnes", "given": "Ian", "initials": "I", "orcid": "0000-0001-8322-6918", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e706d69898324d919e97ec1899a2f0c8.json"}}, {"family": "Liu", "given": "Shanlin", "initials": "S"}, {"family": "Somel", "given": "Mehmet", "initials": "M", "orcid": "0000-0002-3138-1307", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/141c364779504facae706bd757e72580.json"}}, {"family": "Heintzman", "given": "Peter D", "initials": "PD", "orcid": "0000-0002-6449-0219", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/54774bc7db094262b111c5245207579f.json"}}, {"family": "Nikolskiy", "given": "Pavel", "initials": "P"}, {"family": "Shapiro", "given": "Beth", "initials": "B"}, {"family": "Skoglund", "given": "Pontus", "initials": "P"}, {"family": "Hofreiter", "given": "Michael", "initials": "M"}, {"family": "Lister", "given": "Adrian M", "initials": "AM", "orcid": "0000-0002-7985-138X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/37a508b04ea84e8881b966b10ed589e2.json"}}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/070030648e52418abda45f9f79688168.json"}}], "type": "journal article", "published": "2021-03-00", "journal": {"title": "Nature", "issn": "1476-4687", "volume": "591", "issue": "7849", "pages": "265-269", "issn-l": "0028-0836"}, "abstract": "Temporal genomic data hold great potential for studying evolutionary processes such as speciation. However, sampling across speciation events would, in many cases, require genomic time series that stretch well back into the Early Pleistocene subepoch. Although theoretical models suggest that DNA should survive on this timescale1, the oldest genomic data recovered so far are from a horse specimen dated to 780-560 thousand years ago2. Here we report the recovery of genome-wide data from three mammoth specimens dating to the Early and Middle Pleistocene subepochs, two of which are more than one million years old. We find that two distinct mammoth lineages were present in eastern Siberia during the Early Pleistocene. One of these lineages gave rise to the woolly mammoth and the other represents a previously unrecognized lineage that was ancestral to the first mammoths to colonize North America. Our analyses reveal that the Columbian mammoth of North America traces its ancestry to a Middle Pleistocene hybridization between these two lineages, with roughly equal admixture proportions. Finally, we show that the majority of protein-coding changes associated with cold adaptation in woolly mammoths were already present one million years ago. These findings highlight the potential of deep-time palaeogenomics to expand our understanding of speciation and long-term adaptive evolution.", "doi": "10.1038/s41586-021-03224-9", "pmid": "33597750", "labels": {"DDLS Fellow": "", "Tom van der Valk": ""}, "xrefs": [{"db": "mid", "key": "EMS114570"}, {"db": "pmc", "key": "PMC7116897"}, {"db": "pii", "key": "10.1038/s41586-021-03224-9"}], "notes": [], "created": "2026-09-23T06:35:53.279Z", "modified": "2026-09-23T06:35:53.542Z"}, {"entity": "publication", "iuid": "13022802a88f46d2ab340d4ad21ad8c8", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/13022802a88f46d2ab340d4ad21ad8c8.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/13022802a88f46d2ab340d4ad21ad8c8"}}, "title": "Author Correction: Inherited causes of clonal haematopoiesis in 97,691 whole genomes.", "authors": [{"family": "Bick", "given": "Alexander G", "initials": "AG"}, {"family": "Weinstock", "given": "Joshua S", "initials": "JS", "orcid": "0000-0001-7013-1899", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2501ed5d8a4e43d488e7267e58ad68cd.json"}}, {"family": "Nandakumar", "given": "Satish K", "initials": "SK"}, {"family": "Fulco", "given": "Charles P", "initials": "CP", "orcid": "0000-0002-6592-1279", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a88d6f1a1767499e94942a47930ba21e.json"}}, {"family": "Bao", "given": "Erik L", "initials": "EL", "orcid": "0000-0002-6074-6766", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7b5eac9b5ee541258aea4146fcbb7d49.json"}}, {"family": "Zekavat", "given": "Seyedeh M", "initials": "SM"}, {"family": "Szeto", "given": "Mindy D", "initials": "MD", "orcid": "0000-0003-3642-3753", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c00a24090c674f2899267e4c3188b5da.json"}}, {"family": "Liao", "given": "Xiaotian", "initials": "X", "orcid": "0000-0002-9715-270X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2ed6215e49504d74b252dc5b93d707b3.json"}}, {"family": "Leventhal", "given": "Matthew J", "initials": "MJ"}, {"family": "Nasser", "given": "Joseph", "initials": "J"}, {"family": "Chang", "given": "Kyle", "initials": "K"}, {"family": "Laurie", "given": "Cecelia", "initials": "C"}, {"family": "Burugula", "given": "Bala Bharathi", "initials": "BB"}, {"family": "Gibson", "given": "Christopher J", "initials": "CJ"}, {"family": "Niroula", "given": "Abhishek", "initials": "A"}, {"family": "Lin", "given": "Amy E", "initials": "AE"}, {"family": "Taub", "given": "Margaret A", "initials": "MA"}, {"family": "Aguet", "given": "Francois", "initials": "F"}, {"family": "Ardlie", "given": "Kristin", "initials": "K"}, {"family": "Mitchell", "given": "Braxton D", "initials": "BD"}, {"family": "Barnes", "given": "Kathleen C", "initials": "KC"}, {"family": "Moscati", "given": "Arden", "initials": "A"}, {"family": "Fornage", "given": "Myriam", "initials": "M"}, {"family": "Redline", "given": "Susan", "initials": "S"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Silverman", "given": "Edwin K", "initials": "EK"}, {"family": "Weiss", "given": "Scott T", "initials": "ST"}, {"family": "Palmer", "given": "Nicholette D", "initials": "ND"}, {"family": "Vasan", "given": "Ramachandran S", "initials": "RS"}, {"family": "Burchard", "given": "Esteban G", "initials": "EG"}, {"family": "Kardia", "given": "Sharon L R", "initials": "SLR"}, {"family": "He", "given": "Jiang", "initials": "J"}, {"family": "Kaplan", "given": "Robert C", "initials": "RC"}, {"family": "Smith", "given": "Nicholas L", "initials": "NL"}, {"family": "Arnett", "given": "Donna K", "initials": "DK"}, {"family": "Schwartz", "given": "David A", "initials": "DA"}, {"family": "Correa", "given": "Adolfo", "initials": "A"}, {"family": "de Andrade", "given": "Mariza", "initials": "M"}, {"family": "Guo", "given": "Xiuqing", "initials": "X"}, {"family": "Konkle", "given": "Barbara A", "initials": "BA"}, {"family": "Custer", "given": "Brian", "initials": "B"}, {"family": "Peralta", "given": "Juan M", "initials": "JM"}, {"family": "Gui", "given": "Hongsheng", "initials": "H"}, {"family": "Meyers", "given": "Deborah A", "initials": "DA"}, {"family": "McGarvey", "given": "Stephen T", "initials": "ST"}, {"family": "Chen", "given": "Ida Yii-Der", "initials": "IY"}, {"family": "Shoemaker", "given": "M Benjamin", "initials": "MB"}, {"family": "Peyser", "given": "Patricia A", "initials": "PA"}, {"family": "Broome", "given": "Jai G", "initials": "JG"}, {"family": "Gogarten", "given": "Stephanie M", "initials": "SM"}, {"family": "Wang", "given": "Fei Fei", "initials": "FF"}, {"family": "Wong", "given": "Quenna", "initials": "Q"}, {"family": "Montasser", "given": "May E", "initials": "ME"}, {"family": "Daya", "given": "Michelle", "initials": "M"}, {"family": "Kenny", "given": "Eimear E", "initials": "EE"}, {"family": "North", "given": "Kari E", "initials": "KE"}, {"family": "Launer", "given": "Lenore J", "initials": "LJ"}, {"family": "Cade", "given": "Brian E", "initials": "BE"}, {"family": "Bis", "given": "Joshua C", "initials": "JC"}, {"family": "Cho", "given": "Michael H", "initials": "MH"}, {"family": "Lasky-Su", "given": "Jessica", "initials": "J"}, {"family": "Bowden", "given": "Donald W", "initials": "DW"}, {"family": "Cupples", "given": "L Adrienne", "initials": "LA"}, {"family": "Mak", "given": "Angel C Y", "initials": "ACY"}, {"family": "Becker", "given": "Lewis C", "initials": "LC"}, {"family": "Smith", "given": "Jennifer A", "initials": "JA"}, {"family": "Kelly", "given": "Tanika N", "initials": "TN"}, {"family": "Aslibekyan", "given": "Stella", "initials": "S"}, {"family": "Heckbert", "given": "Susan R", "initials": "SR"}, {"family": "Tiwari", "given": "Hemant K", "initials": "HK"}, {"family": "Yang", "given": "Ivana V", "initials": "IV"}, {"family": "Heit", "given": "John A", "initials": "JA"}, {"family": "Lubitz", "given": "Steven A", "initials": "SA"}, {"family": "Johnsen", "given": "Jill M", "initials": "JM"}, {"family": "Curran", "given": "Joanne E", "initials": "JE"}, {"family": "Wenzel", "given": "Sally E", "initials": "SE"}, {"family": "Weeks", "given": "Daniel E", "initials": "DE"}, {"family": "Rao", "given": "Dabeeru C", "initials": "DC"}, {"family": "Darbar", "given": "Dawood", "initials": "D"}, {"family": "Moon", "given": "Jee-Young", "initials": "JY"}, {"family": "Tracy", "given": "Russell P", "initials": "RP"}, {"family": "Buth", "given": "Erin J", "initials": "EJ"}, {"family": "Rafaels", "given": "Nicholas", "initials": "N"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJF"}, {"family": "Durda", "given": "Peter", "initials": "P"}, {"family": "Liu", "given": "Yongmei", "initials": "Y"}, {"family": "Hou", "given": "Lifang", "initials": "L"}, {"family": "Lee", "given": "Jiwon", "initials": "J"}, {"family": "Kachroo", "given": "Priyadarshini", "initials": "P"}, {"family": "Freedman", "given": "Barry I", "initials": "BI"}, {"family": "Levy", "given": "Daniel", "initials": "D"}, {"family": "Bielak", "given": "Lawrence F", "initials": "LF"}, {"family": "Hixson", "given": "James E", "initials": "JE"}, {"family": "Floyd", "given": "James S", "initials": "JS"}, {"family": "Whitsel", "given": "Eric A", "initials": "EA"}, {"family": "Ellinor", "given": "Patrick T", "initials": "PT"}, {"family": "Irvin", "given": "Marguerite R", "initials": "MR"}, {"family": "Fingerlin", "given": "Tasha E", "initials": "TE"}, {"family": "Raffield", "given": "Laura M", "initials": "LM"}, {"family": "Armasu", "given": "Sebastian M", "initials": "SM"}, {"family": "Wheeler", "given": "Marsha M", "initials": "MM"}, {"family": "Sabino", "given": "Ester C", "initials": "EC"}, {"family": "Blangero", "given": "John", "initials": "J"}, {"family": "Williams", "given": "L Keoki", "initials": "LK"}, {"family": "Levy", "given": "Bruce D", "initials": "BD"}, {"family": "Sheu", "given": "Wayne Huey-Herng", "initials": "WH"}, {"family": "Roden", "given": "Dan M", "initials": "DM"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Manson", "given": "JoAnn E", "initials": "JE"}, {"family": "Mathias", "given": "Rasika A", "initials": "RA"}, {"family": "Desai", "given": "Pinkal", "initials": "P"}, {"family": "Taylor", "given": "Kent D", "initials": "KD"}, {"family": "Johnson", "given": "Andrew D", "initials": "AD"}, {"family": "NHLBI Trans-Omics for Precision Medicine Consortium", "given": "", "initials": ""}, {"family": "Auer", "given": "Paul L", "initials": "PL"}, {"family": "Kooperberg", "given": "Charles", "initials": "C"}, {"family": "Laurie", "given": "Cathy C", "initials": "CC"}, {"family": "Blackwell", "given": "Thomas W", "initials": "TW"}, {"family": "Smith", "given": "Albert V", "initials": "AV"}, {"family": "Zhao", "given": "Hongyu", "initials": "H", "orcid": "0000-0003-1195-9607", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/300d7037e3ce45df91af53495d9268e5.json"}}, {"family": "Lange", "given": "Ethan", "initials": "E"}, {"family": "Lange", "given": "Leslie", "initials": "L"}, {"family": "Rich", "given": "Stephen S", "initials": "SS"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Wilson", "given": "James G", "initials": "JG"}, {"family": "Scheet", "given": "Paul", "initials": "P"}, {"family": "Kitzman", "given": "Jacob O", "initials": "JO", "orcid": "0000-0002-6145-882X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/91813f215c204b6282450ed930ea63f3.json"}}, {"family": "Lander", "given": "Eric S", "initials": "ES"}, {"family": "Engreitz", "given": "Jesse M", "initials": "JM", "orcid": "0000-0002-5754-1719", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ea813b64b4b04883babcd956c993f462.json"}}, {"family": "Ebert", "given": "Benjamin L", "initials": "BL", "orcid": "0000-0003-0197-5451", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56e4f1c53a4348e2b0ceb44a38850a17.json"}}, {"family": "Reiner", "given": "Alexander P", "initials": "AP"}, {"family": "Jaiswal", "given": "Siddhartha", "initials": "S"}, {"family": "Abecasis", "given": "Gon\u00e7alo", "initials": "G", "orcid": "0000-0003-1509-1825", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca5bd18be2914b6d9b22cfd55dc4838b.json"}}, {"family": "Sankaran", "given": "Vijay G", "initials": "VG", "orcid": "0000-0003-0044-443X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0a967a5a378f406299b3fefe244361c9.json"}}, {"family": "Kathiresan", "given": "Sekar", "initials": "S", "orcid": "0000-0002-6724-032X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fc6443809e2048b189070618dbf870ba.json"}}, {"family": "Natarajan", "given": "Pradeep", "initials": "P", "orcid": "0000-0001-8402-7435", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fe8bd48c61c047cd8e61c35d9e9ac650.json"}}], "type": "published erratum", "published": "2021-03-00", "journal": {"title": "Nature", "issn": "1476-4687", "volume": "591", "issue": "7851", "pages": "E27", "issn-l": "0028-0836"}, "abstract": null, "doi": "10.1038/s41586-021-03280-1", "pmid": "33707633", "labels": {"Abhishek Niroula": null, "DDLS Fellow": null}, "xrefs": [{"db": "pii", "key": "10.1038/s41586-021-03280-1"}], "notes": [], "created": "2023-11-20T11:21:53.328Z", "modified": "2023-11-20T11:21:54.211Z"}, {"entity": "publication", "iuid": "6f7ff2881beb441b90bc5d566f8ca9dd", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/6f7ff2881beb441b90bc5d566f8ca9dd.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/6f7ff2881beb441b90bc5d566f8ca9dd"}}, "title": "Antibiotic Resistance in Shiga Toxigenic Escherichia coli Isolates from Surface Waters and Sediments in a Mixed Use Urban Agricultural Landscape.", "authors": [{"family": "Ma", "given": "Yvonne", "initials": "Y", "orcid": "0000-0001-8075-6104", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e51b4aa6347943a2b5dd10b8ce1c33fc.json"}}, {"family": "Chen", "given": "Jessica", "initials": "J"}, {"family": "Fong", "given": "Karen", "initials": "K"}, {"family": "Nadya", "given": "Stephanie", "initials": "S"}, {"family": "Allen", "given": "Kevin", "initials": "K"}, {"family": "Laing", "given": "Chad", "initials": "C"}, {"family": "Ziebell", "given": "Kim", "initials": "K"}, {"family": "Topp", "given": "Ed", "initials": "E"}, {"family": "Carroll", "given": "Laura M", "initials": "LM"}, {"family": "Wiedmann", "given": "Martin", "initials": "M", "orcid": "0000-0002-4168-5662", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ff5ceeea60684abeb83951c53f7b6e31.json"}}, {"family": "Delaquis", "given": "Pascal", "initials": "P"}, {"family": "Wang", "given": "Siyun", "initials": "S", "orcid": "0000-0003-2468-2483", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/61c4601985d04e8ca7c1abf2737ba405.json"}}], "type": "journal article", "published": "2021-02-26", "journal": {"title": "Antibiotics (Basel)", "issn": "2079-6382", "volume": "10", "issue": "3", "issn-l": null}, "abstract": "Antibiotic resistance (AR) phenotypes and acquired resistance determinants (ARDs) detected by in silico analysis of genome sequences were examined in 55 Shiga toxin-producing Escherichia coli (STEC) isolates representing diverse serotypes recovered from surfaces waters and sediments in a mixed use urban/agricultural landscape in British Columbia, Canada. The isolates displayed decreased susceptibility to florfenicol (65.5%), chloramphenicol (7.3%), tetracycline (52.7%), ampicillin (49.1%), streptomycin (34.5%), kanamycin (20.0%), gentamycin (10.9%), amikacin (1.8%), amoxicillin/clavulanic acid (21.8%), ceftiofur (18.2%), ceftriaxone (3.6%), trimethoprim-sulfamethoxazole (12.7%), and cefoxitin (3.6%). All surface water and sediment isolates were susceptible to ciprofloxacin, nalidixic acid, ertapenem, imipenem and meropenem. Eight isolates (14.6%) were multidrug resistant. ARDs conferring resistance to phenicols (floR), trimethoprim (dfrA), sulfonamides (sul1/2), tetracyclines (tetA/B), and aminoglycosides (aadA and aph) were detected. Additionally, narrow-spectrum \u03b2-lactamase blaTEM-1b and extended-spectrum AmpC \u03b2-lactamase (cephalosporinase) blaCMY-2 were detected in the genomes, as were replicons from plasmid incompatibility groups IncFII, IncB/O/K/Z, IncQ1, IncX1, IncY and Col156. A comparison with surveillance data revealed that AR phenotypes and ARDs were comparable to those reported in generic E. coli from food animals. Aquatic environments in the region are potential reservoirs for the maintenance and transmission of antibiotic resistant STEC, associated ARDs and their plasmids.", "doi": "10.3390/antibiotics10030237", "pmid": "33652953", "labels": {"Laura Carroll": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC7996769"}, {"db": "pii", "key": "antibiotics10030237"}], "notes": [], "created": "2025-03-18T17:27:22.840Z", "modified": "2025-03-18T17:27:22.968Z"}, {"entity": "publication", "iuid": "19a572c3335a4de7914b3a810d3254e3", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/19a572c3335a4de7914b3a810d3254e3.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/19a572c3335a4de7914b3a810d3254e3"}}, "title": "The Organelle in the Ointment: cryptic mitochondria account for many unknown sequences in cross-species microbiome comparisons", "authors": [{"family": "Sonett", "given": "Dylan", "initials": "D", "orcid": "0000-0001-6821-4695", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8b5856f98b0d4ff4b60fbaa463bf1169.json"}}, {"family": "Brown", "given": "Tanya", "initials": "T", "orcid": "0000-0003-0103-7510", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/52bb2f5a91994e0286961713fb099a5d.json"}}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J", "orcid": "0000-0002-6528-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c666068e9d34939b0252a627007cec7.json"}}, {"family": "Padilla-Gami\u00f1o", "given": "Jacqueline L", "initials": "JL", "orcid": "0000-0003-0478-9953", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8c4d81e0f7044728ab945b296b0e3cc9.json"}}, {"family": "Zaneveld", "given": "Jesse R", "initials": "JR", "orcid": "0000-0002-9823-810X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ebe78647d72540e5b42a82874eb6d5c7.json"}}], "type": "posted-content", "published": "2021-02-24", "journal": {"title": "bioRxiv preprint", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2021.02.23.431501", "pmid": null, "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [], "notes": [], "created": "2022-11-08T09:31:17.529Z", "modified": "2025-12-04T16:53:32.234Z"}, {"entity": "publication", "iuid": "6832ce31ea38430286140aa827b1cfb1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/6832ce31ea38430286140aa827b1cfb1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/6832ce31ea38430286140aa827b1cfb1"}}, "title": "Interactive biomedical segmentation tool powered by deep learning and ImJoy", "authors": [{"family": "Ouyang", "given": "Wei", "initials": "W", "orcid": "0000-0002-0291-926X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56f601e1d1c6448aab0c3a1e3cffdbfc.json"}}, {"family": "Le", "given": "Trang", "initials": "T"}, {"family": "Xu", "given": "Hao", "initials": "H", "orcid": "0000-0002-6021-4663", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8940732a47844fc5ae2931de777d5775.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E"}], "type": "journal-article", "published": "2021-02-24", "journal": {"title": "F1000Res", "issn": "2046-1402", "volume": "10", "pages": "142", "issn-l": "2046-1402"}, "abstract": null, "doi": "10.12688/f1000research.50798.1", "pmid": null, "labels": {"DDLS Fellow": "", "Wei Ouyang": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T12:41:42.062Z", "modified": "2026-09-23T12:52:06.896Z"}, {"entity": "publication", "iuid": "0a248820b5834f50a253492bb0ede663", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0a248820b5834f50a253492bb0ede663.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0a248820b5834f50a253492bb0ede663"}}, "title": "Accelerating target deconvolution for therapeutic antibody candidates using highly parallelized genome editing.", "authors": [{"family": "Mattsson", "given": "Jenny", "initials": "J"}, {"family": "Ekdahl", "given": "Ludvig", "initials": "L"}, {"family": "Junghus", "given": "Fredrik", "initials": "F"}, {"family": "Ajore", "given": "Ram", "initials": "R"}, {"family": "Erlandsson", "given": "Eva", "initials": "E"}, {"family": "Niroula", "given": "Abhishek", "initials": "A", "orcid": "0000-0002-5904-0635", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/05df7afc7a494ba5af8a378e5ffa53f0.json"}}, {"family": "Pertesi", "given": "Maroulio", "initials": "M", "orcid": "0000-0002-4869-8925", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1395ddcc49604bc1a05ea52f7b1ad79a.json"}}, {"family": "Frend\u00e9us", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Teige", "given": "Ingrid", "initials": "I"}, {"family": "Nilsson", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-5542-0254", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2e9df5bbe6f948b196a65176963748c8.json"}}], "type": "journal article", "published": "2021-02-24", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "1277", "issn-l": "2041-1723"}, "abstract": "Therapeutic antibodies are transforming the treatment of cancer and autoimmune diseases. Today, a key challenge is finding antibodies against new targets. Phenotypic discovery promises to achieve this by enabling discovery of antibodies with therapeutic potential without specifying the molecular target a priori. Yet, deconvoluting the targets of phenotypically discovered antibodies remains a bottleneck; efficient deconvolution methods are needed for phenotypic discovery to reach its full potential. Here, we report a comprehensive investigation of a target deconvolution approach based on pooled CRISPR/Cas9. Applying this approach within three real-world phenotypic discovery programs, we rapidly deconvolute the targets of 38 of 39 test antibodies (97%), a success rate far higher than with existing approaches. Moreover, the approach scales well, requires much less work, and robustly identifies antibodies against the major histocompatibility complex. Our data establish CRISPR/Cas9 as a highly efficient target deconvolution approach, with immediate implications for the development of antibody-based drugs.", "doi": "10.1038/s41467-021-21518-4", "pmid": "33627649", "labels": {"Abhishek Niroula": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC7904777"}, {"db": "pii", "key": "10.1038/s41467-021-21518-4"}], "notes": [], "created": "2023-11-20T11:27:48.448Z", "modified": "2023-11-20T11:27:48.610Z"}, {"entity": "publication", "iuid": "f62f3ce276da445499b9a70915a65645", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f62f3ce276da445499b9a70915a65645.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f62f3ce276da445499b9a70915a65645"}}, "title": "Continuous human uterine NK cell differentiation in response to endometrial regeneration and pregnancy.", "authors": [{"family": "Strunz", "given": "Benedikt", "initials": "B", "orcid": "0000-0001-9974-6133", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e3f821b6fa714c138059349f9a6a7f35.json"}}, {"family": "Bister", "given": "Jonna", "initials": "J"}, {"family": "J\u00f6nsson", "given": "Hanna", "initials": "H", "orcid": "0000-0001-8389-975X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/85386cb824ad4d8bab7ba442bedf578f.json"}}, {"family": "Filipovic", "given": "Iva", "initials": "I", "orcid": "0000-0002-8166-5500", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b10709e4011e4fdd835e08d778fc9a5f.json"}}, {"family": "Crona-Guterstam", "given": "Ylva", "initials": "Y", "orcid": "0000-0003-4998-4904", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/57df4943fee3481a955167b19c1b6394.json"}}, {"family": "Kvedaraite", "given": "Egle", "initials": "E", "orcid": "0000-0001-5308-092X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/12e2bb98f9ea4186a3fc75703b205484.json"}}, {"family": "Sleiers", "given": "Natalie", "initials": "N", "orcid": "0000-0002-9378-8145", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cf67bebe7391402fb3bbfe06efd4cc68.json"}}, {"family": "Dumitrescu", "given": "Bogdan", "initials": "B", "orcid": "0000-0002-9986-3396", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0def5f9296f445f5a67944a28ea51f83.json"}}, {"family": "Br\u00e4nnstr\u00f6m", "given": "Mats", "initials": "M", "orcid": "0000-0002-6081-9101", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ec95e17b51604eceb6fb74df8bbadce8.json"}}, {"family": "Lentini", "given": "Antonio", "initials": "A", "orcid": "0000-0003-1239-5495", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c5042d3005814ad0a2d1eaeee5d2de3b.json"}}, {"family": "Reinius", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0002-7021-5248", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a7c1abacc8d446bf8855254246b8d899.json"}}, {"family": "Cornillet", "given": "Martin", "initials": "M", "orcid": "0000-0001-7981-0927", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8f2b2dde303f445e8c47f726a9dbf6ae.json"}}, {"family": "Willinger", "given": "Tim", "initials": "T"}, {"family": "Gidl\u00f6f", "given": "Sebastian", "initials": "S"}, {"family": "Hamilton", "given": "Russell S", "initials": "RS", "orcid": "0000-0002-0598-3793", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/879040c102094f91aff5e1fc1b7c1a72.json"}}, {"family": "Ivarsson", "given": "Martin A", "initials": "MA"}, {"family": "Bj\u00f6rkstr\u00f6m", "given": "Niklas K", "initials": "NK", "orcid": "0000-0002-0967-076X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ded8cd7038b4c42ac16f62f89b9229c.json"}}], "type": "journal article", "published": "2021-02-19", "journal": {"title": "Sci Immunol", "issn": "2470-9468", "volume": "6", "issue": "56", "issn-l": "2470-9468"}, "abstract": "Immune cell differentiation is critical for adequate tissue-specific immune responses to occur. Here, we studied differentiation of human uterine natural killer cells (uNK cells). These cells reside in a tissue undergoing constant regeneration and represent the major leukocyte population at the maternal-fetal interface. However, their physiological response during the menstrual cycle and in pregnancy remains elusive. By surface proteome and transcriptome analysis as well as using humanized mice, we identify a differentiation pathway of uNK cells in vitro and in vivo with sequential acquisition of killer cell immunoglobulin-like receptors and CD39. uNK cell differentiation occurred continuously in response to the endometrial regeneration and was driven by interleukin-15. Differentiated uNK cells displayed reduced proliferative capacity and immunomodulatory function including enhanced angiogenic capacity. By studying human uterus transplantation and monozygotic twins, we found that the uNK cell niche could be replenished from circulation and that it was under genetic control. Together, our study uncovers a continuous differentiation pathway of human NK cells in the uterus that is coupled to profound functional changes in response to local tissue regeneration and pregnancy.", "doi": "10.1126/sciimmunol.abb7800", "pmid": "33617461", "labels": {"Antonio Lentini": null, "DDLS Fellow": null}, "xrefs": [{"db": "pii", "key": "6/56/eabb7800"}], "notes": [], "created": "2025-03-28T07:09:58.244Z", "modified": "2025-03-28T07:09:58.645Z"}, {"entity": "publication", "iuid": "62fc60e776784e35bd5c86ae88877a4f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/62fc60e776784e35bd5c86ae88877a4f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/62fc60e776784e35bd5c86ae88877a4f"}}, "title": "Ancient microRNA profiles of 14,300-yr-old canid samples confirm taxonomic origin and provide glimpses into tissue-specific gene regulation from the Pleistocene.", "authors": [{"family": "Fromm", "given": "Bastian", "initials": "B", "orcid": "0000-0003-0352-3037", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cdc4c42e06604b759dd6225c5f8362b5.json"}}, {"family": "Tarbier", "given": "Marcel", "initials": "M", "orcid": "0000-0003-0556-2531", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9678d0797def441e9870afe6ffbb08d0.json"}}, {"family": "Smith", "given": "Oliver", "initials": "O", "orcid": "0000-0002-0146-9244", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4b114f019dad43c580e985932e10a586.json"}}, {"family": "M\u00e1rmol-S\u00e1nchez", "given": "Emilio", "initials": "E", "orcid": "0000-0002-4393-1740", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4afc80fe64684cd2b75c9c0a13630e19.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6ff87fd5aabe4a38954dd96d8e6c261d.json"}}, {"family": "Gilbert", "given": "M Tom P", "initials": "MTP", "orcid": "0000-0002-5805-7195", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/93cbe282154844588f63bc7cc6983b30.json"}}, {"family": "Friedl\u00e4nder", "given": "Marc R", "initials": "MR", "orcid": "0000-0001-6577-4363", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ac5a2794be7c4cab89d1e4f1570c9417.json"}}], "type": "journal article", "published": "2021-02-16", "journal": {"title": "RNA", "issn": "1469-9001", "volume": "27", "issue": "3", "pages": "324-334", "issn-l": "1355-8382"}, "abstract": "DNA sequencing is the current key technology for historic or ancient biological samples and has led to many exciting discoveries in the field of paleogenomics However, functional insights into tissue identity, cellular composition, or gene regulation cannot be gained from DNA. Recent analyses have shown that, under favorable conditions, RNA can also be sequenced from ancient samples, enabling studies at the transcriptomic and regulatory level. Analyzing ancient RNA data from a Pleistocene canid, we find hundreds of intact microRNAs that are taxonomically informative, show tissue specificity and have functionally predictive characteristics. With an extraordinary age of 14,300 yr, these microRNA sequences are by far the oldest ever reported. The authenticity of the sequences is further supported by (i) the presence of canid/Caniformia-specific sequences that never evolved outside of this clade, (ii) tissue-specific expression patterns (cartilage, liver, and muscle) that resemble those of modern dogs, and (iii) RNA damage patterns that are clearly distinct from those of fresh samples. By performing computational microRNA-target enrichment analyses on the ancient sequences, we predict microRNA functions consistent with their tissue pattern of expression. For instance, we find a liver-specific microRNA that regulates carbohydrate metabolism and starvation responses in canids. In summary, we show that straightforward paleotranscriptomic microRNA analyses can give functional glimpses into tissue identity, cellular composition, and gene regulatory activity of ancient samples and biological processes that took place in the Pleistocene, thus holding great promise for deeper insights into gene regulation in extinct animals based on ancient RNA sequencing.", "doi": "10.1261/rna.078410.120", "pmid": "33323528", "labels": {"Marc Friedl\u00e4nder": "", "SciLifeLab Fellow": "", "DDLS Fellow": "", "Marcel Tarbier": ""}, "xrefs": [{"db": "pmc", "key": "PMC7901840"}, {"db": "pii", "key": "rna.078410.120"}, {"db": "medline", "key": "9509184"}], "notes": [], "created": "2021-11-30T16:02:53.166Z", "modified": "2026-09-23T12:06:52.341Z"}, {"entity": "publication", "iuid": "4cc8e73c3cc74c208b1d8b5d1cc805bd", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4cc8e73c3cc74c208b1d8b5d1cc805bd.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4cc8e73c3cc74c208b1d8b5d1cc805bd"}}, "title": "Premature Menopause, Clonal Hematopoiesis, and Coronary Artery Disease in Postmenopausal Women.", "authors": [{"family": "Honigberg", "given": "Michael C", "initials": "MC"}, {"family": "Zekavat", "given": "Seyedeh M", "initials": "SM"}, {"family": "Niroula", "given": "Abhishek", "initials": "A"}, {"family": "Griffin", "given": "Gabriel K", "initials": "GK"}, {"family": "Bick", "given": "Alexander G", "initials": "AG"}, {"family": "Pirruccello", "given": "James P", "initials": "JP"}, {"family": "Nakao", "given": "Tetsushi", "initials": "T"}, {"family": "Whitsel", "given": "Eric A", "initials": "EA"}, {"family": "Farland", "given": "Leslie V", "initials": "LV"}, {"family": "Laurie", "given": "Cecelia", "initials": "C"}, {"family": "Kooperberg", "given": "Charles", "initials": "C"}, {"family": "Manson", "given": "JoAnn E", "initials": "JE"}, {"family": "Gabriel", "given": "Stacey", "initials": "S"}, {"family": "Libby", "given": "Peter", "initials": "P"}, {"family": "Reiner", "given": "Alexander P", "initials": "AP"}, {"family": "Ebert", "given": "Benjamin L", "initials": "BL"}, {"family": "NHLBI Trans-Omics for Precision Medicine Program", "given": "", "initials": ""}, {"family": "Natarajan", "given": "Pradeep", "initials": "P"}], "type": "journal article", "published": "2021-02-02", "journal": {"title": "Circulation", "issn": "1524-4539", "volume": "143", "issue": "5", "pages": "410-423", "issn-l": "0009-7322"}, "abstract": "Premature menopause is an independent risk factor for cardiovascular disease in women, but mechanisms underlying this association remain unclear. Clonal hematopoiesis of indeterminate potential (CHIP), the age-related expansion of hematopoietic cells with leukemogenic mutations without detectable malignancy, is associated with accelerated atherosclerosis. Whether premature menopause is associated with CHIP is unknown.\n\nWe included postmenopausal women from the UK Biobank (n=11 495) aged 40 to 70 years with whole exome sequences and from the Women's Health Initiative (n=8111) aged 50 to 79 years with whole genome sequences. Premature menopause was defined as natural or surgical menopause occurring before age 40 years. Co-primary outcomes were the presence of any CHIP and CHIP with variant allele frequency >0.1. Logistic regression tested the association of premature menopause with CHIP, adjusted for age, race, the first 10 principal components of ancestry, smoking, diabetes, and hormone therapy use. Secondary analyses considered natural versus surgical premature menopause and gene-specific CHIP subtypes. Multivariable-adjusted Cox models tested the association between CHIP and incident coronary artery disease.\n\nThe sample included 19 606 women, including 418 (2.1%) with natural premature menopause and 887 (4.5%) with surgical premature menopause. Across cohorts, CHIP prevalence in postmenopausal women with versus without a history of premature menopause was 8.8% versus 5.5% (P<0.001), respectively. After multivariable adjustment, premature menopause was independently associated with CHIP (all CHIP: odds ratio, 1.36 [95% 1.10-1.68]; P=0.004; CHIP with variant allele frequency >0.1: odds ratio, 1.40 [95% CI, 1.10-1.79]; P=0.007). Associations were larger for natural premature menopause (all CHIP: odds ratio, 1.73 [95% CI, 1.23-2.44]; P=0.001; CHIP with variant allele frequency >0.1: odds ratio, 1.91 [95% CI, 1.30-2.80]; P<0.001) but smaller and nonsignificant for surgical premature menopause. In gene-specific analyses, only DNMT3A CHIP was significantly associated with premature menopause. Among postmenopausal middle-aged women, CHIP was independently associated with incident coronary artery disease (hazard ratio associated with all CHIP: 1.36 [95% CI, 1.07-1.73]; P=0.012; hazard ratio associated with CHIP with variant allele frequency >0.1: 1.48 [95% CI, 1.13-1.94]; P=0.005).\n\nPremature menopause, especially natural premature menopause, is independently associated with CHIP among postmenopausal women. Natural premature menopause may serve as a risk signal for predilection to develop CHIP and CHIP-associated cardiovascular disease.", "doi": "10.1161/CIRCULATIONAHA.120.051775", "pmid": "33161765", "labels": {"Abhishek Niroula": null, "DDLS Fellow": null}, "xrefs": [{"db": "mid", "key": "NIHMS1656471"}, {"db": "pmc", "key": "PMC7911856"}], "notes": [], "created": "2023-11-20T11:21:55.796Z", "modified": "2023-11-20T11:21:55.823Z"}, {"entity": "publication", "iuid": "a56bfb5717d746eea1722911e715cfe6", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a56bfb5717d746eea1722911e715cfe6.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a56bfb5717d746eea1722911e715cfe6"}}, "title": "Spatiotemporal dissection of the cell cycle with single-cell proteogenomics.", "authors": [{"family": "Mahdessian", "given": "Diana", "initials": "D"}, {"family": "Cesnik", "given": "Anthony J", "initials": "AJ", "orcid": "0000-0002-5326-7134", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0fda549f3795457fb60ec3372b98e2d5.json"}}, {"family": "Gnann", "given": "Christian", "initials": "C"}, {"family": "Danielsson", "given": "Frida", "initials": "F"}, {"family": "Stenstr\u00f6m", "given": "Lovisa", "initials": "L"}, {"family": "Arif", "given": "Muhammad", "initials": "M", "orcid": "0000-0003-2261-0881", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c8ffc9889ace44e3b992816601b817e2.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f46e4161be08458994efddb75ed75874.json"}}, {"family": "Le", "given": "Trang", "initials": "T"}, {"family": "Johansson", "given": "Fredric", "initials": "F", "orcid": "0000-0001-5160-9543", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/88e81d055b6f4c23852dfa7768e62c99.json"}}, {"family": "Schutten", "given": "Rutger", "initials": "R"}, {"family": "B\u00e4ckstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Axelsson", "given": "Ulrika", "initials": "U"}, {"family": "Thul", "given": "Peter", "initials": "P", "orcid": "0000-0002-6107-1465", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/af9dad977d4649bbbb883a9836dade94.json"}}, {"family": "Cho", "given": "Nathan H", "initials": "NH"}, {"family": "Carja", "given": "Oana", "initials": "O"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ea446aa574042a295d5f69437402f76.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Stadler", "given": "Charlotte", "initials": "C"}, {"family": "Lindskog", "given": "Cecilia", "initials": "C", "orcid": "0000-0001-5611-1015", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/21610a810a87459c962d6da3f2ad38ad.json"}}, {"family": "Ayoglu", "given": "Burcu", "initials": "B", "orcid": "0000-0001-7843-2960", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4d75c3ce33814d2b961aef643f0d7f0c.json"}}, {"family": "Leonetti", "given": "Manuel D", "initials": "MD"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9f5294424542413c9ba4432c839c2b63.json"}}, {"family": "Sullivan", "given": "Devin P", "initials": "DP"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb07e6d0122c4528a927c1fe922e3bc8.json"}}], "type": "journal article", "published": "2021-02-00", "journal": {"title": "Nature", "issn": "1476-4687", "volume": "590", "issue": "7847", "pages": "649-654", "issn-l": "0028-0836"}, "abstract": "The cell cycle, over which cells grow and divide, is a fundamental process of life. Its dysregulation has devastating consequences, including cancer1-3. The cell cycle is driven by precise regulation of proteins in time and space, which creates variability between individual proliferating cells. To our knowledge, no systematic investigations of such cell-to-cell proteomic variability exist. Here we present a comprehensive, spatiotemporal map of human proteomic heterogeneity by integrating proteomics at subcellular resolution with single-cell transcriptomics and precise temporal measurements of individual cells in the cell cycle. We show that around one-fifth of the human proteome displays cell-to-cell variability, identify hundreds of proteins with previously unknown associations with mitosis and the cell cycle, and provide evidence that several of these proteins have oncogenic functions. Our results show that cell cycle progression explains less than half of all cell-to-cell variability, and that most cycling proteins are regulated post-translationally, rather than by transcriptomic cycling. These proteins are disproportionately phosphorylated by kinases that regulate cell fate, whereas non-cycling proteins that vary between cells are more likely to be modified by kinases that regulate metabolism. This spatially resolved proteomic map of the cell cycle is integrated into the Human Protein Atlas and will serve as a resource for accelerating molecular studies of the human cell cycle and cell proliferation.", "doi": "10.1038/s41586-021-03232-9", "pmid": "33627808", "labels": {"Adil Mardinoglu": "", "SciLifeLab Fellow": "", "DDLS Fellow": "", "Muhammad Arif": ""}, "xrefs": [{"db": "pii", "key": "10.1038/s41586-021-03232-9"}], "notes": [], "created": "2021-10-08T14:12:30.416Z", "modified": "2026-09-23T06:42:49.695Z"}, {"entity": "publication", "iuid": "ef8f26d12fdc47218ca45fe84c5851ff", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ef8f26d12fdc47218ca45fe84c5851ff.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ef8f26d12fdc47218ca45fe84c5851ff"}}, "title": "Phylogenomics of the tropical plant family Ochnaceae using targeted enrichment of nuclear genes and 250+ taxa", "authors": [{"family": "Schneider", "given": "Julio V", "initials": "JV", "orcid": "0000-0002-9823-6569", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e2c9e3969ac94da7a7ce481ff9c40c30.json"}}, {"family": "Jungcurt", "given": "Tanja", "initials": "T"}, {"family": "Cardoso", "given": "Domingos", "initials": "D", "orcid": "0000-0001-7072-2656", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d77373c8cce1413797bd4874c9b6fee2.json"}}, {"family": "Amorim", "given": "Andr\u00e9 M\u00e1rcio", "initials": "AM", "orcid": "0000-0003-0712-3321", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4bdf956585b4a38b202019cb0154511.json"}}, {"family": "T\u00f6pel", "given": "Mats", "initials": "M", "orcid": "0000-0001-7989-696X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0fb21c79c7394ae1af5e1663d722591c.json"}}, {"family": "Andermann", "given": "Tobias", "initials": "T", "orcid": "0000-0002-0932-1623", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dfff478dfcfc43ddbd40bb1bafbcb0a7.json"}}, {"family": "Poncy", "given": "Odile", "initials": "O"}, {"family": "Berberich", "given": "Thomas", "initials": "T", "orcid": "0000-0001-9442-4450", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5195686cb35742fab5c99b1287297405.json"}}, {"family": "Zizka", "given": "Georg", "initials": "G", "orcid": "0000-0002-5030-7049", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/59a282b6878d48b8800f8fae32e00ac1.json"}}], "type": "journal-article", "published": "2021-02-00", "journal": {"title": "TAXON", "issn": "0040-0262", "volume": "70", "issue": "1", "pages": "48-71", "issn-l": null}, "abstract": null, "doi": "10.1002/tax.12421", "pmid": null, "labels": {"Tobias Andermann": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2022-11-11T09:10:51.580Z", "modified": "2025-12-04T16:58:15.384Z"}, {"entity": "publication", "iuid": "93659217fcbe42ae80f8cbca99458e5c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/93659217fcbe42ae80f8cbca99458e5c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/93659217fcbe42ae80f8cbca99458e5c"}}, "title": "iucn_sim<\/i> : a new program to simulate future extinctions based on IUCN threat status", "authors": [{"family": "Andermann", "given": "Tobias", "initials": "T", "orcid": "0000-0002-0932-1623", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dfff478dfcfc43ddbd40bb1bafbcb0a7.json"}}, {"family": "Faurby", "given": "S\u00f8ren", "initials": "S", "orcid": "0000-0002-2974-2628", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e9be75db97d64624a90e272c14ac7f5b.json"}}, {"family": "Cooke", "given": "Robert", "initials": "R", "orcid": "0000-0003-0601-8888", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2a2e0e2acd86409f9ab6ef39b71fd471.json"}}, {"family": "Silvestro", "given": "Daniele", "initials": "D"}, {"family": "Antonelli", "given": "Alexandre", "initials": "A"}], "type": "journal-article", "published": "2021-02-00", "journal": {"title": "Ecography", "issn": "0906-7590", "volume": "44", "issue": "2", "pages": "162-176", "issn-l": null}, "abstract": null, "doi": "10.1111/ecog.05110", "pmid": null, "labels": {"Tobias Andermann": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2022-11-11T09:08:39.821Z", "modified": "2025-12-04T16:58:37.450Z"}, {"entity": "publication", "iuid": "dcd03a2296fd40c3bc3d3cb24f8ecd7b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/dcd03a2296fd40c3bc3d3cb24f8ecd7b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/dcd03a2296fd40c3bc3d3cb24f8ecd7b"}}, "title": "The relationship between ageing and changes in the human blood and brain methylomes", "authors": [{"family": "Bryant", "given": "Patrick", "initials": "P", "orcid": "0000-0003-3439-1866", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a683bcf98234ff09b2398976583b66f.json"}}, {"family": "Elofsson", "given": "Arne", "initials": "A", "orcid": "0000-0002-7115-9751", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/248e70e81bd64f31a5f83e6e329bba95.json"}}], "type": "posted-content", "published": "2021-01-27", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2021.01.26.428239", "pmid": null, "labels": {"Patrick Bryant": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T10:01:17.447Z", "modified": "2026-09-23T15:05:31.005Z"}, {"entity": "publication", "iuid": "8090404eb61f41b0a61db3ae2848e45a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8090404eb61f41b0a61db3ae2848e45a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8090404eb61f41b0a61db3ae2848e45a"}}, "title": "Discovery of Functional Alternatively Spliced PKM Transcripts in Human Cancers.", "authors": [{"family": "Li", "given": "Xiangyu", "initials": "X", "orcid": "0000-0002-8301-9959", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5c452ad4e8bb4302a572693103742047.json"}}, {"family": "Kim", "given": "Woonghee", "initials": "W"}, {"family": "Arif", "given": "Muhammad", "initials": "M", "orcid": "0000-0003-2261-0881", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c8ffc9889ace44e3b992816601b817e2.json"}}, {"family": "Gao", "given": "Chunxia", "initials": "C"}, {"family": "Hober", "given": "Andreas", "initials": "A", "orcid": "0000-0001-8947-2562", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/06cbc187628340278395a00ab9dd6c89.json"}}, {"family": "Kotol", "given": "David", "initials": "D", "orcid": "0000-0002-5388-3826", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c41f8f491c474e6bba2047b5d04b4af5.json"}}, {"family": "Strandberg", "given": "Linn\u00e9a", "initials": "L", "orcid": "0000-0001-5386-5460", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ea4741b77234afe83e92c3dfff0a799.json"}}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Sivertsson", "given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0001-8800-8469", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9397c6e626b1457e8dcd47f037c4cf9d.json"}}, {"family": "Oksvold", "given": "Per", "initials": "P", "orcid": "0000-0003-3014-5502", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/16beca5822c747128300910b5c74dbfc.json"}}, {"family": "Turkez", "given": "Hasan", "initials": "H"}, {"family": "Gr\u00f8tli", "given": "Morten", "initials": "M"}, {"family": "Sato", "given": "Yusuke", "initials": "Y"}, {"family": "Kume", "given": "Haruki", "initials": "H"}, {"family": "Ogawa", "given": "Seishi", "initials": "S"}, {"family": "Boren", "given": "Jan", "initials": "J", "orcid": "0000-0003-0786-8091", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/73a770eb9e614448a046b8e9199052e9.json"}}, {"family": "Nielsen", "given": "Jens", "initials": "J"}, {"family": "Uhlen", "given": "Mathias", "initials": "M"}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f46e4161be08458994efddb75ed75874.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca58bf2d214047e0ae5e38a42a0f2808.json"}}], "type": "journal article", "published": "2021-01-19", "journal": {"title": "Cancers (Basel)", "issn": "2072-6694", "volume": "13", "issue": "2", "issn-l": "2072-6694"}, "abstract": "Pyruvate kinase muscle type (PKM) is a key enzyme in glycolysis and plays an important oncological role in cancer. However, the association of PKM expression and the survival outcome of patients with different cancers is controversial. We employed systems biology methods to reveal prognostic value and potential biological functions of PKM transcripts in different human cancers. Protein products of transcripts were shown and detected by western blot and mass spectrometry analysis. We focused on different transcripts of PKM and investigated the associations between their mRNA expression and the clinical survival of the patients in 25 different cancers. We find that the transcripts encoding PKM2 and three previously unstudied transcripts, namely ENST00000389093, ENST00000568883, and ENST00000561609, exhibited opposite prognostic indications in different cancers. Moreover, we validated the prognostic effect of these transcripts in an independent kidney cancer cohort. Finally, we revealed that ENST00000389093 and ENST00000568883 possess pyruvate kinase enzymatic activity and may have functional roles in metabolism, cell invasion, and hypoxia response in cancer cells. Our study provided a potential explanation to the controversial prognostic indication of PKM, and could invoke future studies focusing on revealing the biological and oncological roles of these alternative spliced variants of PKM.", "doi": "10.3390/cancers13020348", "pmid": "33478099", "labels": {"Adil Mardinoglu": "", "SciLifeLab Fellow": "", "DDLS Fellow": "", "Muhammad Arif": ""}, "xrefs": [{"db": "pmc", "key": "PMC7835739"}, {"db": "pii", "key": "cancers13020348"}], "notes": [], "created": "2021-10-08T14:11:01.959Z", "modified": "2026-09-23T11:52:50.573Z"}, {"entity": "publication", "iuid": "95fff65f500243b9810ad4c680a34ddf", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/95fff65f500243b9810ad4c680a34ddf.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/95fff65f500243b9810ad4c680a34ddf"}}, "title": "Universal and taxon-specific trends in protein sequences as a function of age.", "authors": [{"family": "James", "given": "Jennifer E", "initials": "JE", "orcid": "0000-0003-0518-6783", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4b807f7ab8f46f8a5e927e1b090d662.json"}}, {"family": "Willis", "given": "Sara M", "initials": "SM", "orcid": "0000-0002-1605-6426", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6316b06885844b32a451c3b8ab502060.json"}}, {"family": "Nelson", "given": "Paul G", "initials": "PG", "orcid": "0000-0003-4453-9895", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/90045bdb5a234df4b5448db1ed4a5ff3.json"}}, {"family": "Weibel", "given": "Catherine", "initials": "C", "orcid": "0000-0003-1837-5209", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/54d6dc2af7084fc58d9ab18aa72423e7.json"}}, {"family": "Kosinski", "given": "Luke J", "initials": "LJ", "orcid": "0000-0002-8146-5955", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2347dd3dc6ca4693ba3684c0dfc2cb8c.json"}}, {"family": "Masel", "given": "Joanna", "initials": "J", "orcid": "0000-0002-7398-2127", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eed69f257e574f4aa53f59349c3ff384.json"}}], "type": "journal article", "published": "2021-01-08", "journal": {"title": "Elife", "issn": "2050-084X", "issn-l": "2050-084X", "volume": "10", "issue": null, "pages": null}, "abstract": "Extant protein-coding sequences span a huge range of ages, from those that emerged only recently to those present in the last universal common ancestor. Because evolution has had less time to act on young sequences, there might be 'phylostratigraphy' trends in any properties that evolve slowly with age. A long-term reduction in hydrophobicity and hydrophobic clustering was found in previous, taxonomically restricted studies. Here we perform integrated phylostratigraphy across 435 fully sequenced species, using sensitive HMM methods to detect protein domain homology. We find that the reduction in hydrophobic clustering is universal across lineages. However, only young animal domains have a tendency to have higher structural disorder. Among ancient domains, trends in amino acid composition reflect the order of recruitment into the genetic code, suggesting that the composition of the contemporary descendants of ancient sequences reflects amino acid availability during the earliest stages of life, when these sequences first emerged.", "doi": "10.7554/eLife.57347", "pmid": "33416492", "labels": {"Jennifer James": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC7819706"}, {"db": "pii", "key": "57347"}, {"db": "figshare", "key": "10.6084/m9.figshare.12037281"}], "notes": [], "created": "2024-11-27T09:25:40.076Z", "modified": "2024-11-29T09:36:55.752Z"}, {"entity": "publication", "iuid": "d645a5d770e54019865fca510c30fee4", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d645a5d770e54019865fca510c30fee4.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d645a5d770e54019865fca510c30fee4"}}, "title": "Dynamic closed states of a ligand-gated ion channel captured by cryo-EM and simulations", "authors": [{"family": "Rov\u0161nik", "given": "Ur\u0161ka", "initials": "U", "orcid": "0000-0001-5889-6899", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f0ab87a8712f4ad886da61c1edcf679f.json"}}, {"family": "Zhuang", "given": "Yuxuan", "initials": "Y", "orcid": "0000-0003-4390-8556", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/61b8327a0f32416686748c52c38ecbf1.json"}}, {"family": "Forsberg", "given": "Bj\u00f6rn O", "initials": "BO", "orcid": "0000-0002-6247-4063", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/36ea51bfa66d48b7a43559c3d0eaa59f.json"}}, {"family": "Carroni", "given": "Marta", "initials": "M", "orcid": "0000-0002-7697-6427", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/55fa4ba347a34d7ca80d214e8d718e44.json"}}, {"family": "Yvonnesdotter", "given": "Linnea", "initials": "L"}, {"family": "Howard", "given": "Rebecca J", "initials": "RJ", "orcid": "0000-0003-2049-3378", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ce04593b5b24aaa8978fda1447dd0bf.json"}}, {"family": "Lindahl", "given": "Erik", "initials": "E", "orcid": "0000-0002-2734-2794", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9eb30fa60f9b4b95842ac9d9f3a0eaa9.json"}}], "type": "posted-content", "published": "2021-01-05", "journal": {"title": "bioRxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2021.01.04.425171", "pmid": null, "labels": {"DDLS Fellow": null, "Bj\u00f6rn Forsberg": null}, "xrefs": [], "notes": [], "created": "2026-08-20T10:00:57.976Z", "modified": "2026-10-05T08:33:41.945Z"}, {"entity": "publication", "iuid": "f99bf3fcf86e4742a8778a905011e665", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f99bf3fcf86e4742a8778a905011e665.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f99bf3fcf86e4742a8778a905011e665"}}, "title": "CAFE: a software suite for analysis of paired-sample transposon insertion sequencing data.", "authors": [{"family": "Abramova", "given": "Anna", "initials": "A"}, {"family": "Osi\u0144ska", "given": "Adriana", "initials": "A"}, {"family": "Kunche", "given": "Haveela", "initials": "H"}, {"family": "Burman", "given": "Emil", "initials": "E"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2021-01-04", "journal": {"title": "Bioinformatics", "issn": "1367-4811", "issn-l": "1367-4803"}, "abstract": "Sequencing of transposon insertion libraries is used to determine the relative fitness of individual mutants at a large scale. However, there is a lack of tools for specifically analyzing data from such experiments with paired sample designs. Here, we introduce CAFE-Coefficient-based Analysis of Fitness by read Enrichment-a software package that can analyze data from paired transposon mutant sequencing experiments, generate fitness coefficients for each gene and condition, and perform appropriate statistical testing on these fitness coefficients.\n\nCAFE is implemented in Perl and R. The source code is freely available for download under the MIT License from https://github.com/bengtssonpalme/cafe and http://microbiology.se/software/cafe/.\n\nSupplementary data are available at Bioinformatics online. The evaluation data can be obtained from https://microbiology.se/sw/cafe/example_data.tgz.", "doi": "10.1093/bioinformatics/btaa1086", "pmid": "33393985", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pii", "key": "6062395"}, {"db": "pmc", "key": "PMC8034522"}], "notes": [], "created": "2022-11-08T09:26:12.823Z", "modified": "2022-11-08T09:26:12.847Z"}, {"entity": "publication", "iuid": "4904852a1a23462dab3498170bbe9129", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4904852a1a23462dab3498170bbe9129.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4904852a1a23462dab3498170bbe9129"}}, "title": "Longitudinal plasma protein profiling of newly diagnosed type 2 diabetes.", "authors": [{"family": "Gummesson", "given": "Anders", "initials": "A"}, {"family": "Bj\u00f6rnson", "given": "Elias", "initials": "E"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Zhong", "given": "Wen", "initials": "W"}, {"family": "Tebani", "given": "Abdellah", "initials": "A"}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Schmidt", "given": "Caroline", "initials": "C"}, {"family": "Lundqvist", "given": "Annika", "initials": "A"}, {"family": "Adiels", "given": "Martin", "initials": "M"}, {"family": "B\u00e4ckhed", "given": "Fredrik", "initials": "F"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM"}, {"family": "Jansson", "given": "Per-Anders", "initials": "PA"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Bergstr\u00f6m", "given": "G\u00f6ran", "initials": "G"}], "type": "journal article", "published": "2021-01-00", "journal": {"title": "EBioMedicine", "issn": "2352-3964", "volume": "63", "pages": "103147", "issn-l": "2352-3964"}, "abstract": "Comprehensive proteomics profiling may offer new insights into the dysregulated metabolic milieu of type 2 diabetes, and in the future, serve as a useful tool for personalized medicine. This calls for a better understanding of circulating protein patterns at the early stage of type 2 diabetes as well as the dynamics of protein patterns during changes in metabolic status.\n\nTo elucidate the systemic alterations in early-stage diabetes and to investigate the effects on the proteome during metabolic improvement, we measured 974 circulating proteins in 52 newly diagnosed, treatment-na\u00efve type 2 diabetes subjects at baseline and after 1 and 3 months of guideline-based diabetes treatment, while comparing their protein profiles to that of 94 subjects without diabetes.\n\nEarly stage type 2 diabetes was associated with distinct protein patterns, reflecting key metabolic syndrome features including insulin resistance, adiposity, hyperglycemia and liver steatosis. The protein profiles at baseline were attenuated during guideline-based diabetes treatment and several plasma proteins associated with metformin medication independently of metabolic variables, such as circulating EPCAM.\n\nThe results advance our knowledge about the biochemical manifestations of type 2 diabetes and suggest that comprehensive protein profiling may serve as a useful tool for metabolic phenotyping and for elucidating the biological effects of diabetes treatments.\n\nThis work was supported by the Swedish Heart and Lung Foundation, the Swedish Research Council, the Erling Persson Foundation, the Knut and Alice Wallenberg Foundation, and the Swedish state under the agreement between the Swedish government and the county councils (ALF-agreement).", "doi": "10.1016/j.ebiom.2020.103147", "pmid": "33279861", "labels": {"Fredrik Edfors": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC7718461"}, {"db": "pii", "key": "S2352-3964(20)30523-5"}], "notes": [], "created": "2026-09-23T09:54:12.401Z", "modified": "2026-09-23T10:28:20.937Z"}, {"entity": "publication", "iuid": "9a784fb547df4c2d9dedd7c3e516de53", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9a784fb547df4c2d9dedd7c3e516de53.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9a784fb547df4c2d9dedd7c3e516de53"}}, "title": "Network Analyses Links Epicardial Fat Metabolism to Human Coronary Heart Disease", "authors": [{"family": "Doran", "given": "Stephen", "initials": "S"}, {"family": "Arif", "given": "Muhammad", "initials": "M", "orcid": "0000-0003-2261-0881", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c8ffc9889ace44e3b992816601b817e2.json"}}, {"family": "Clausen", "given": "Maryam", "initials": "M"}, {"family": "Wikstr\u00f6m", "given": "Johannes", "initials": "J"}, {"family": "Bohlooly-Y", "given": "Mohammad", "initials": "M"}, {"family": "Jeppsson", "given": "Anders", "initials": "A", "orcid": "0000-0003-2356-2295", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b429b50a3e7d4b62b4b48323368f36b0.json"}}, {"family": "Levin", "given": "Malin", "initials": "M", "orcid": "0000-0003-1069-5275", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9304477424f04521852ae5aef5f672d6.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca58bf2d214047e0ae5e38a42a0f2808.json"}}, {"family": "Boren", "given": "Jan", "initials": "J", "orcid": "0000-0003-0786-8091", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/73a770eb9e614448a046b8e9199052e9.json"}}], "type": "posted-content", "published": "2021-00-00", "journal": {"issn-l": null}, "abstract": null, "doi": "10.2139/ssrn.3828226", "pmid": null, "labels": {"SciLifeLab Fellow": "", "DDLS Fellow": "", "Adil Mardinoglu": "", "Muhammad Arif": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T13:00:58.105Z", "modified": "2026-09-23T15:07:22.432Z"}, {"entity": "publication", "iuid": "14467caaaca94f8d9bab78fdc520350e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/14467caaaca94f8d9bab78fdc520350e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/14467caaaca94f8d9bab78fdc520350e"}}, "title": "Multiomics Personalized Network Analyses Highlight Progressive Immune Disruption of Central Metabolism Associated with COVID-19 Severity", "authors": [{"family": "Ambikan", "given": "Anoop T", "initials": "AT"}, {"family": "Yang", "given": "Hong", "initials": "H"}, {"family": "Krishnan", "given": "Shuba", "initials": "S"}, {"family": "Svensson-Akusj\u00e4rvi", "given": "Sara", "initials": "S", "orcid": "0000-0002-1086-5409", "researcher": {"href": 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"2026-08-20T13:01:15.332Z", "modified": "2026-09-23T14:25:54.437Z"}, {"entity": "publication", "iuid": "c548fa293ffe41578ffc7fa6a04e7a44", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c548fa293ffe41578ffc7fa6a04e7a44.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c548fa293ffe41578ffc7fa6a04e7a44"}}, "title": "Drug Repositioning for Clear Cell Renal Cell Carcinoma Based on Stratification of Patients", "authors": [{"family": "Li", "given": "Xiangyu", "initials": "X", "orcid": "0000-0002-8301-9959", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5c452ad4e8bb4302a572693103742047.json"}}, {"family": "Kim", "given": "Woonghee", "initials": "W"}, {"family": "Juszczak", "given": "Kajetan", "initials": "K"}, {"family": "Arif", "given": "Muhammad", "initials": "M", "orcid": "0000-0003-2261-0881", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c8ffc9889ace44e3b992816601b817e2.json"}}, {"family": "Sato", "given": "Yusuke", "initials": "Y"}, {"family": "Kume", "given": "Haruki", "initials": "H"}, {"family": "Ogawa", "given": "Seishi", "initials": "S"}, {"family": "Turkez", "given": "Hasan", "initials": "H", "orcid": "0000-0002-7046-8990", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cf2f1748757d45cabfe56fdfaccead6a.json"}}, {"family": "Boren", "given": "Jan", "initials": "J", "orcid": "0000-0003-0786-8091", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/73a770eb9e614448a046b8e9199052e9.json"}}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/33f2b49a39ed4e54ba77dfe397ed3087.json"}}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ea446aa574042a295d5f69437402f76.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f46e4161be08458994efddb75ed75874.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca58bf2d214047e0ae5e38a42a0f2808.json"}}], "type": "posted-content", "published": "2021-00-00", "journal": {"issn-l": null}, "abstract": null, "doi": "10.2139/ssrn.3816950", "pmid": null, "labels": {"SciLifeLab Fellow": "", "DDLS Fellow": "", "Adil Mardinoglu": "", "Muhammad Arif": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T13:00:56.375Z", "modified": "2026-09-23T14:42:41.443Z"}, {"entity": "publication", "iuid": "d812d0000360456a81ce0bffd8d7673b", "links": {"self": {"href": 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"given": "Jochen M", "initials": "JM"}, {"family": "Zhang", "given": "Cheng", "initials": "C"}, {"family": "Shoaie", "given": "Saeed", "initials": "S"}, {"family": "Nielsen", "given": "Jens", "initials": "J"}, {"family": "Uhlen", "given": "Mathias", "initials": "M"}, {"family": "Boren", "given": "Jan", "initials": "J"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}], "type": "journal-article", "published": "2021-00-00", "journal": {"title": "SSRN Journal", "issn": "1556-5068", "issn-l": null}, "abstract": null, "doi": "10.2139/ssrn.3778301", "pmid": null, "labels": {"SciLifeLab Fellow": "", "Saeed Shoaie": "", "DDLS Fellow": "", "Adil Mardinoglu": "", "Muhammad Arif": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T13:00:50.844Z", "modified": "2026-09-23T14:24:47.683Z"}, {"entity": "publication", "iuid": "010799da6cfb45de8f7eaa204768558f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/010799da6cfb45de8f7eaa204768558f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/010799da6cfb45de8f7eaa204768558f"}}, "title": "Combined Metabolic Activators Improves Cognitive Functions in Alzheimer's Disease", "authors": [{"family": "Yulug", "given": "Burak", "initials": "B"}, {"family": "Altay", "given": "Ozlem", "initials": "O"}, {"family": "Li", "given": "Xiangyu", "initials": "X"}, {"family": "Hanoglu", "given": "Lutfu", "initials": "L"}, {"family": "Cankaya", "given": "Seyda", "initials": "S"}, {"family": "Lam", "given": "Simon", "initials": "S"}, {"family": "Yang", "given": "Hong", "initials": "H"}, {"family": "Coskun", "given": "Ebru", "initials": "E"}, {"family": "Idil", "given": "Ezgi", "initials": "E"}, {"family": "Nogaylar", "given": "Rahim", "initials": "R"}, {"family": "Bayram", "given": "Cemil", "initials": "C"}, {"family": "Bolat", "given": "Ismail", "initials": "I"}, {"family": "oner", "given": "sena", "initials": "s"}, {"family": "Tozlu", "given": "Ozlem Ozdemir", "initials": "OO"}, {"family": "Arslan", "given": "Mehmet Enes", "initials": "ME"}, {"family": "Hacimuftuoglu", "given": "Ahmet", "initials": "A"}, {"family": "Yildirim", "given": "Serkan", "initials": "S"}, {"family": "Arif", "given": "Muhammad", "initials": "M"}, {"family": "Shoaie", "given": "Saeed", "initials": "S"}, {"family": "Zhang", "given": "Cheng", "initials": "C"}, {"family": "Nielsen", "given": "Jens", "initials": "J"}, {"family": "Turkez", "given": "Hasan", "initials": "H"}, {"family": "Boren", "given": "Jan", "initials": "J"}, {"family": "Uhlen", "given": "Mathias", "initials": "M"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}], "type": "journal-article", "published": "2021-00-00", "journal": {"title": "SSRN Journal", "issn": "1556-5068", "issn-l": null}, "abstract": null, "doi": "10.2139/ssrn.3924201", "pmid": null, "labels": {"SciLifeLab Fellow": "", "Saeed Shoaie": "", "DDLS Fellow": "", "Adil Mardinoglu": "", "Muhammad Arif": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T13:01:09.518Z", "modified": "2026-09-23T14:44:16.090Z"}, {"entity": "publication", "iuid": "45a32208f0d04fa58fc7c646723d5299", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/45a32208f0d04fa58fc7c646723d5299.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/45a32208f0d04fa58fc7c646723d5299"}}, "title": "A Network-Based Approach Reveals the Dysregulated Transcriptional Regulation in Non- Alcohol Fatty Liver Disease", "authors": [{"family": "Yang", "given": "Hong", "initials": "H"}, {"family": "Arif", "given": "Muhammad", "initials": "M", "orcid": "0000-0003-2261-0881", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c8ffc9889ace44e3b992816601b817e2.json"}}, {"family": "Yuan", "given": "Meng", "initials": "M"}, {"family": "Li", "given": "Xiangyu", "initials": "X", "orcid": "0000-0002-8301-9959", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5c452ad4e8bb4302a572693103742047.json"}}, {"family": "Shong", "given": "Ko Eun", "initials": "KE", "orcid": "0000-0002-2677-8537", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/795e7cc225024c3ca09e79cae62f612e.json"}}, {"family": "Turkez", "given": "Hasan", "initials": "H", "orcid": "0000-0002-7046-8990", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cf2f1748757d45cabfe56fdfaccead6a.json"}}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/33f2b49a39ed4e54ba77dfe397ed3087.json"}}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ea446aa574042a295d5f69437402f76.json"}}, {"family": "Boren", "given": "Jan", "initials": "J", "orcid": "0000-0003-0786-8091", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/73a770eb9e614448a046b8e9199052e9.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f46e4161be08458994efddb75ed75874.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca58bf2d214047e0ae5e38a42a0f2808.json"}}], "type": "posted-content", "published": "2021-00-00", "journal": {"issn-l": null}, "abstract": null, "doi": "10.2139/ssrn.3893909", "pmid": null, "labels": {"SciLifeLab Fellow": "", "DDLS Fellow": "", "Adil Mardinoglu": "", "Muhammad Arif": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T13:01:07.353Z", "modified": "2026-09-23T15:08:17.754Z"}, {"entity": "publication", "iuid": "7241667270314efb8bbd52155bf7d198", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/7241667270314efb8bbd52155bf7d198.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/7241667270314efb8bbd52155bf7d198"}}, "title": "Development and external validation of a COVID-19 mortality risk prediction algorithm: a multicentre retrospective cohort study.", "authors": [{"family": "Mei", "given": "Jin", "initials": "J"}, {"family": "Hu", "given": "Weihua", "initials": "W"}, {"family": "Chen", "given": "Qijian", "initials": "Q"}, {"family": "Li", "given": "Chang", "initials": "C"}, {"family": "Chen", "given": "Zaishu", "initials": "Z"}, {"family": "Fan", "given": "Yanjie", "initials": "Y"}, {"family": "Tian", "given": "Shuwei", "initials": "S"}, {"family": "Zhang", "given": "Zhuheng", "initials": "Z"}, {"family": "Li", "given": "Bin", "initials": "B"}, {"family": "Ye", "given": "Qifa", "initials": "Q"}, {"family": "Yue", "given": "Jiang", "initials": "J", "orcid": "0000-0001-8906-1253", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bc4601749b5d4768ac7e20145f23099c.json"}}, {"family": "Wang", "given": "Qiao-Li", "initials": "QL"}], "type": "journal article", "published": "2020-12-24", "journal": {"title": "BMJ Open", "issn": "2044-6055", "volume": "10", "issue": "12", "pages": "e044028", "issn-l": "2044-6055"}, "abstract": "This study aimed to develop and externally validate a COVID-19 mortality risk prediction algorithm.\n\nRetrospective cohort study.\n\nFive designated tertiary hospitals for COVID-19 in Hubei province, China.\n\nWe routinely collected medical data of 1364 confirmed adult patients with COVID-19 between 8 January and 19 March 2020. Among them, 1088 patients from two designated hospitals in Wuhan were used to develop the prognostic model, and 276 patients from three hospitals outside Wuhan were used for external validation. All patients were followed up for a maximal of 60 days after the diagnosis of COVID-19.\n\nThe model discrimination was assessed by the area under the receiver operating characteristic curve (AUC) and Somers' D test, and calibration was examined by the calibration plot. Decision curve analysis was conducted.\n\nThe primary outcome was all-cause mortality within 60 days after the diagnosis of COVID-19.\n\nThe full model included seven predictors of age, respiratory failure, white cell count, lymphocytes, platelets, D-dimer and lactate dehydrogenase. The simple model contained five indicators of age, respiratory failure, coronary heart disease, renal failure and heart failure. After cross-validation, the AUC statistics based on derivation cohort were 0.96 (95% CI, 0.96 to 0.97) for the full model and 0.92 (95% CI, 0.89 to 0.95) for the simple model. The AUC statistics based on the external validation cohort were 0.97 (95% CI, 0.96 to 0.98) for the full model and 0.88 (95% CI, 0.80 to 0.96) for the simple model. Good calibration accuracy of these two models was found in the derivation and validation cohort.\n\nThe prediction models showed good model performance in identifying patients with COVID-19 with a high risk of death in 60 days. It may be useful for acute risk classification.\n\nWe provided a freely accessible web calculator (https://www.whuyijia.com/).", "doi": "10.1136/bmjopen-2020-044028", "pmid": "33361083", "labels": {"DDLS Fellow": null, "Qiaoli Wang": null}, "xrefs": [{"db": "pmc", "key": "PMC7768618"}, {"db": "pii", "key": "bmjopen-2020-044028"}], "notes": [], "created": "2025-11-27T18:53:32.648Z", "modified": "2025-11-27T18:53:32.677Z"}, {"entity": "publication", "iuid": "56a1916b8bbe47a288eb60b144832134", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/56a1916b8bbe47a288eb60b144832134.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/56a1916b8bbe47a288eb60b144832134"}}, "title": "Erratum for Hugerth et al., \"Assessment of In Vitro and In Silico Protocols for Sequence-Based Characterization of the Human Vaginal Microbiome\".", "authors": [{"family": "Hugerth", "given": "Luisa W", "initials": "LW"}, {"family": "Pereira", "given": "Marcela", "initials": "M"}, {"family": "Zha", "given": "Yinghua", "initials": "Y"}, {"family": "Seifert", "given": "Maike", "initials": "M"}, {"family": "Kaldhusdal", "given": "Vilde", "initials": "V"}, {"family": "Boulund", "given": "Fredrik", "initials": "F"}, {"family": "Krog", "given": "Maria C", "initials": "MC"}, {"family": "Bashir", "given": "Zahra", "initials": "Z"}, {"family": "Hamsten", "given": "Marica", "initials": "M"}, {"family": "Fransson", "given": "Emma", "initials": "E"}, {"family": "Nielsen", "given": "Henriette Svarre", "initials": "HS"}, {"family": "Schuppe-Koistinen", "given": "Ina", "initials": "I"}, {"family": "Engstrand", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2020-12-23", "journal": {"title": "mSphere", "issn": "2379-5042", "volume": "5", "issue": "6", "issn-l": "2379-5042"}, "abstract": null, "doi": "10.1128/mSphere.01253-20", "pmid": "33361132", "labels": {"DDLS Fellow": "", "Luisa Hugerth": ""}, "xrefs": [{"db": "pmc", "key": "PMC7763557"}, {"db": "pii", "key": "5/6/e01253-20"}], "notes": [], "created": "2026-08-20T12:00:52.917Z", "modified": "2026-09-23T13:44:00.477Z"}, {"entity": "publication", "iuid": "0ec863168b49436381959f9aab1093c4", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0ec863168b49436381959f9aab1093c4.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0ec863168b49436381959f9aab1093c4"}}, "title": "Ileocolonic Histopathological and Microbial Alterations in the Irritable Bowel Syndrome: A Nested Community Case-Control Study.", "authors": [{"family": "Talley", "given": "Nicholas J", "initials": "NJ"}, {"family": "Alexander", "given": "James L", "initials": "JL"}, {"family": "Walker", "given": "Marjorie M", "initials": "MM"}, {"family": "Jones", "given": "Michael P", "initials": "MP"}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW"}, {"family": "Engstrand", "given": "Lars", "initials": "L"}, {"family": "Agr\u00e9us", "given": "Lars", "initials": "L"}, {"family": "Powell", "given": "Nicholas", "initials": "N"}, {"family": "Andreasson", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2020-12-22", "journal": {"title": "Clin Transl Gastroenterol", "issn": "2155-384X", "volume": "12", "issue": "1", "pages": "e00296", "issn-l": null}, "abstract": "Histopathological alterations in the ileum and colon in irritable bowel syndrome (IBS) are controversial, and normal values are poorly established. We hypothesized that changes in mucosal immune cells characterize IBS and key changes in immune composition are associated with the mucosa-associated microbiota (MaM).\n\nA nested case-control study (48 IBS and 106 controls included) from 745 colonoscopy participants in a random population sample. Intraepithelial lymphocytes (IELs)/100 enterocytes and eosinophils/5 nonoverlapping high-power fields counted; mast cells identified by immunocytochemistry (CD117)/5 high-power fields. Paneth cells quantified per 5 crypts. 16S rRNA gene amplicon sequencing performed on available sigmoid MaM, n = 55 and fecal microbiota, n = 20. Microbiota profiles compared between samples with high and low IEL counts.\n\nIBS had increased IELs in the terminal ileum (relative risk ratio = 1.70, 95% confidence interval 1.08-2.76, P = 0.022 adjusted for age, sex, and smoking). Cecal IELs were increased in IBS-diarrhea (relative risk ratio = 2.03, 95% confidence interval 1.13-3.63, P = 0.017). No difference was observed in alpha diversity of MaM or fecal microbiota based on IEL count. There was no difference in beta diversity of the MaM according to IEL count in the terminal ileal (TI) (P = 0.079). High TI IEL counts associated with a significant expansion of the genus Blautia (P = 0.024) and unclassified Clostridiales (P = 0.036) in colon MaM.\n\nA modest but significant increase in IELs was observed in IBS vs. controls in a population-based setting. Subtle TI and cecal inflammation may play a pathogenic role in IBS but needs confirmation. Modest but discernible differences in the colonic MaM were seen according to TI IEL count but not IBS status.", "doi": "10.14309/ctg.0000000000000296", "pmid": "33464728", "labels": {"Luisa Hugerth": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC8345925"}, {"db": "pii", "key": "01720094-202101000-00010"}], "notes": [], "created": "2022-11-08T06:59:11.940Z", "modified": "2026-09-23T12:39:51.535Z"}, {"entity": "publication", "iuid": "fadaef0a539e475f9813f623d8ab7b22", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/fadaef0a539e475f9813f623d8ab7b22.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/fadaef0a539e475f9813f623d8ab7b22"}}, "title": "Circulating miRNA Spaceflight Signature Reveals Targets for Countermeasure Development.", "authors": [{"family": "Malkani", "given": "Sherina", "initials": "S"}, {"family": "Chin", "given": "Christopher R", "initials": "CR"}, {"family": "Cekanaviciute", "given": "Egle", "initials": "E"}, {"family": "Mortreux", "given": "Marie", "initials": "M"}, {"family": "Okinula", "given": "Hazeem", "initials": "H"}, {"family": "Tarbier", "given": "Marcel", "initials": "M"}, {"family": "Schreurs", "given": "Ann-Sofie", "initials": "AS"}, {"family": "Shirazi-Fard", "given": "Yasaman", "initials": "Y"}, {"family": "Tahimic", "given": "Candice G T", "initials": "CGT"}, {"family": "Rodriguez", "given": "Deyra N", "initials": "DN"}, {"family": "Sexton", "given": "Brittany S", "initials": "BS"}, {"family": "Butler", "given": "Daniel", "initials": "D"}, {"family": "Verma", "given": "Akanksha", "initials": "A"}, {"family": "Bezdan", "given": "Daniela", "initials": "D"}, {"family": "Durmaz", "given": "Ceyda", "initials": "C"}, {"family": "MacKay", "given": "Matthew", "initials": "M"}, {"family": "Melnick", "given": "Ari", "initials": "A"}, {"family": "Meydan", "given": "Cem", "initials": "C"}, {"family": "Li", "given": "Sheng", "initials": "S"}, {"family": "Garrett-Bakelman", "given": "Francine", "initials": "F"}, {"family": "Fromm", "given": "Bastian", "initials": "B"}, {"family": "Afshinnekoo", "given": "Ebrahim", "initials": "E"}, {"family": "Langhorst", "given": "Brad W", "initials": "BW"}, {"family": "Dimalanta", "given": "Eileen T", "initials": "ET"}, {"family": "Cheng-Campbell", "given": "Margareth", "initials": "M"}, {"family": "Blaber", "given": "Elizabeth", "initials": "E"}, {"family": "Schisler", "given": "Jonathan C", "initials": "JC"}, {"family": "Vanderburg", "given": "Charles", "initials": "C"}, {"family": "Friedl\u00e4nder", "given": "Marc R", "initials": "MR"}, {"family": "McDonald", "given": "J Tyson", "initials": "JT"}, {"family": "Costes", "given": "Sylvain V", "initials": "SV"}, {"family": "Rutkove", "given": "Seward", "initials": "S"}, {"family": "Grabham", "given": "Peter", "initials": "P"}, {"family": "Mason", "given": "Christopher E", "initials": "CE"}, {"family": "Beheshti", "given": "Afshin", "initials": "A"}], "type": "journal article", "published": "2020-12-08", "journal": {"title": "Cell Reports", "issn": "2211-1247", "volume": "33", "issue": "10", "pages": "108448", "issn-l": null}, "abstract": "We have identified and validated a spaceflight-associated microRNA (miRNA) signature that is shared by rodents and humans in response to simulated, short-duration and long-duration spaceflight. Previous studies have identified miRNAs that regulate rodent responses to spaceflight in low-Earth orbit, and we have confirmed the expression of these proposed spaceflight-associated miRNAs in rodents reacting to simulated spaceflight conditions. Moreover, astronaut samples from the NASA Twins Study confirmed these expression signatures in miRNA sequencing, single-cell RNA sequencing (scRNA-seq), and single-cell assay for transposase accessible chromatin (scATAC-seq) data. Additionally, a subset of these miRNAs (miR-125, miR-16, and let-7a) was found to regulate vascular damage caused by simulated deep space radiation. To demonstrate the physiological relevance of key spaceflight-associated miRNAs, we utilized antagomirs to inhibit their expression and successfully rescue simulated deep-space-radiation-mediated damage in human 3D vascular constructs.", "doi": "10.1016/j.celrep.2020.108448", "pmid": "33242410", "labels": {"Marc Friedl\u00e4nder": "", "SciLifeLab Fellow": "", "Marcel Tarbier": "", "DDLS Fellow": ""}, "xrefs": [{"db": "mid", "key": "NIHMS1653539"}, {"db": "pmc", "key": "PMC8441986"}, {"db": "pii", "key": "S2211-1247(20)31437-6"}], "notes": [], "created": "2021-11-30T16:10:27.665Z", "modified": "2026-09-23T08:29:12.220Z"}, {"entity": "publication", "iuid": "2b906f9f91ae44ab8fcea3e1edd36dca", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/2b906f9f91ae44ab8fcea3e1edd36dca.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/2b906f9f91ae44ab8fcea3e1edd36dca"}}, "title": "Mitochondrial DNA Sequence Diversity in Mammals: A Correlation between the Effective and Census Population Sizes.", "authors": [{"family": "James", "given": "Jennifer", "initials": "J"}, {"family": "Eyre-Walker", "given": "Adam", "initials": "A"}], "type": "comparative study", "published": "2020-12-06", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "issn-l": "1759-6653", "volume": "12", "issue": "12", "pages": "2441-2449"}, "abstract": "What determines the level of genetic diversity of a species remains one of the enduring problems of population genetics. Because neutral diversity depends upon the product of the effective population size and mutation rate, there is an expectation that diversity should be correlated to measures of census population size. This correlation is often observed for nuclear but not for mitochondrial DNA. Here, we revisit the question of whether mitochondrial DNA sequence diversity is correlated to census population size by compiling the largest data set to date, using 639 mammalian species. In a multiple regression, we find that nucleotide diversity is significantly correlated to both range size and mass-specific metabolic rate, but not a variety of other factors. We also find that a measure of the effective population size, the ratio of nonsynonymous to synonymous diversity, is also significantly negatively correlated to both range size and mass-specific metabolic rate. These results together suggest that species with larger ranges have larger effective population sizes. The slope of the relationship between diversity and range is such that doubling the range increases diversity by 12-20%, providing one of the first quantifications of the relationship between diversity and the census population size.", "doi": "10.1093/gbe/evaa222", "pmid": "33095231", "labels": {"Jennifer James": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC7719226"}, {"db": "pii", "key": "5936529"}], "notes": [], "created": "2024-11-27T09:25:42.547Z", "modified": "2024-11-29T10:56:50.802Z"}, {"entity": "publication", "iuid": "c06fd397613044e7a9520bbdb2fc8fbd", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c06fd397613044e7a9520bbdb2fc8fbd.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c06fd397613044e7a9520bbdb2fc8fbd"}}, "title": "Longitudinal Plasma Protein Profiling Using Targeted Proteomics and Recombinant Protein Standards.", "authors": [{"family": "Kotol", "given": "David", "initials": "D", "orcid": "0000-0002-5388-3826", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c41f8f491c474e6bba2047b5d04b4af5.json"}}, {"family": "Hunt", "given": "Helian", "initials": "H"}, {"family": "Hober", "given": "Andreas", "initials": "A"}, {"family": "Karlsson", "given": "Max J", "initials": "MJ"}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Gummesson", "given": "Anders", "initials": "A"}, {"family": "Bergstr\u00f6m", "given": "G\u00f6ran", "initials": "G"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e213b04f8984c8eb00c68f5bc2f6a36.json"}}], "type": "journal article", "published": "2020-12-04", "journal": {"title": "J. Proteome Res.", "issn": "1535-3907", "volume": "19", "issue": "12", "pages": "4815-4825", "issn-l": "1535-3893"}, "abstract": "Spike-in of standards of known concentrations used in proteomics-based workflows is an attractive approach for both accurate and precise multiplexed protein quantification. Here, a quantitative method based on targeted proteomics analysis of plasma proteins using isotope-labeled recombinant standards originating from the Human Protein Atlas project has been established. The standards were individually quantified prior to being employed in the final multiplex assay. The assays are mainly directed toward actively secreted proteins produced in the liver, but may also originate from other parts of the human body. This study included 21 proteins classified by the FDA as either drug targets or approved clinical protein biomarkers. We describe the use of this multiplex assay for profiling a well-defined human cohort with sample collection spanning over a one-year period. Samples were collected at four different time points, which allowed for a longitudinal analysis to assess the variable plasma proteome within individuals. Two assays toward APOA1 and APOB had available clinical data, and the two assays were benchmarked against each other. The clinical assay is based on antibodies and shows high correlation between the two orthogonal methods, suggesting that targeted proteomics with highly parallel, multiplex analysis is an attractive alternative to antibody-based protein assays.", "doi": "10.1021/acs.jproteome.0c00194", "pmid": "32820635", "labels": {"Fredrik Edfors": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T08:11:14.164Z", "modified": "2026-09-23T12:06:42.945Z"}, {"entity": "publication", "iuid": "5b0d4ed03e0f40ee8653db21973fbcbb", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5b0d4ed03e0f40ee8653db21973fbcbb.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5b0d4ed03e0f40ee8653db21973fbcbb"}}, "title": "Moose genomes reveal past glacial demography and the origin of modern lineages.", "authors": [{"family": "Dussex", "given": "Nicolas", "initials": "N", "orcid": "0000-0002-9179-8593", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3c93917b1e544c6eae92fd4aa0617fd8.json"}}, {"family": "Alberti", "given": "Federica", "initials": "F"}, {"family": "Heino", "given": "Matti T", "initials": "MT"}, {"family": "Olsen", "given": "Remi-Andre", "initials": "RA"}, {"family": "van der Valk", "given": "Tom", "initials": "T"}, {"family": "Ryman", "given": "Nils", "initials": "N"}, {"family": "Laikre", "given": "Linda", "initials": "L"}, {"family": "Ahlgren", "given": "Hans", "initials": "H"}, {"family": "Askeyev", "given": "Igor V", "initials": "IV"}, {"family": "Askeyev", "given": "Oleg V", "initials": "OV"}, {"family": "Shaymuratova", "given": "Dilyara N", "initials": "DN"}, {"family": "Askeyev", "given": "Arthur O", "initials": "AO"}, {"family": "D\u00f6ppes", "given": "Doris", "initials": "D"}, {"family": "Friedrich", "given": "Ronny", "initials": "R"}, {"family": "Lindauer", "given": "Susanne", "initials": "S"}, {"family": "Rosendahl", "given": "Wilfried", "initials": "W"}, {"family": "Aspi", "given": "Jouni", "initials": "J"}, {"family": "Hofreiter", "given": "Michael", "initials": "M"}, {"family": "Lid\u00e9n", "given": "Kerstin", "initials": "K"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L"}, {"family": "D\u00edez-Del-Molino", "given": "David", "initials": "D"}], "type": "journal article", "published": "2020-12-02", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "21", "issue": "1", "pages": "854", "issn-l": "1471-2164"}, "abstract": "Numerous megafauna species from northern latitudes went extinct during the Pleistocene/Holocene transition as a result of climate-induced habitat changes. However, several ungulate species managed to successfully track their habitats during this period to eventually flourish and recolonise the holarctic regions. So far, the genomic impacts of these climate fluctuations on ungulates from high latitudes have been little explored. Here, we assemble a de-novo genome for the European moose (Alces alces) and analyse it together with re-sequenced nuclear genomes and ancient and modern mitogenomes from across the moose range in Eurasia and North America.\n\nWe found that moose demographic history was greatly influenced by glacial cycles, with demographic responses to the Pleistocene/Holocene transition similar to other temperate ungulates. Our results further support that modern moose lineages trace their origin back to populations that inhabited distinct glacial refugia during the Last Glacial Maximum (LGM). Finally, we found that present day moose in Europe and North America show low to moderate inbreeding levels resulting from post-glacial bottlenecks and founder effects, but no evidence for recent inbreeding resulting from human-induced population declines.\n\nTaken together, our results highlight the dynamic recent evolutionary history of the moose and provide an important resource for further genomic studies.", "doi": "10.1186/s12864-020-07208-3", "pmid": "33267779", "labels": {"DDLS Fellow": "", "Tom van der Valk": ""}, "xrefs": [{"db": "pmc", "key": "PMC7709250"}, {"db": "pii", "key": "10.1186/s12864-020-07208-3"}], "notes": [], "created": "2026-09-23T09:57:58.795Z", "modified": "2026-09-23T10:34:23.925Z"}, {"entity": "publication", "iuid": "1add9ac454fb483eb69e679c8424dc6a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1add9ac454fb483eb69e679c8424dc6a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1add9ac454fb483eb69e679c8424dc6a"}}, "title": "Microbial model communities: To understand complexity, harness the power of simplicity.", "authors": [{"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2020-12-02", "journal": {"title": "Comput Struct Biotechnol J", "issn": "2001-0370", "volume": "18", "pages": "3987-4001", "issn-l": null}, "abstract": "Natural microbial communities are complex ecosystems with myriads of interactions. To deal with this complexity, we can apply lessons learned from the study of model organisms and try to find simpler systems that can shed light on the same questions. Here, microbial model communities are essential, as they can allow us to learn about the metabolic interactions, genetic mechanisms and ecological principles governing and structuring communities. A variety of microbial model communities of varying complexity have already been developed, representing different purposes, environments and phenomena. However, choosing a suitable model community for one's research question is no easy task. This review aims to be a guide in the selection process, which can help the researcher to select a sufficiently well-studied model community that also fulfills other relevant criteria. For example, a good model community should consist of species that are easy to grow, have been evaluated for community behaviors, provide simple readouts and - in some cases - be of relevance for natural ecosystems. Finally, there is a need to standardize growth conditions for microbial model communities and agree on definitions of community-specific phenomena and frameworks for community interactions. Such developments would be the key to harnessing the power of simplicity to start disentangling complex community interactions.", "doi": "10.1016/j.csbj.2020.11.043", "pmid": "33363696", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pii", "key": "S2001-0370(20)30510-9"}, {"db": "pmc", "key": "PMC7744646"}], "notes": [], "created": "2022-11-08T09:26:15.096Z", "modified": "2022-11-08T09:26:15.136Z"}, {"entity": "publication", "iuid": "9732bf6e49f844959c6ba42ea3ca0afc", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9732bf6e49f844959c6ba42ea3ca0afc.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9732bf6e49f844959c6ba42ea3ca0afc"}}, "title": "Structural and functional consequences of reversible lipid asymmetry in living membranes.", "authors": [{"family": "Doktorova", "given": "Milka", "initials": "M", "orcid": "0000-0003-4366-2242", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/791384c319f04584bac8ffb21df7271f.json"}}, {"family": "Symons", "given": "Jessica L", "initials": "JL"}, {"family": "Levental", "given": "Ilya", "initials": "I", "orcid": "0000-0002-1206-9545", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7fe40c2b810348cab78616402d4d1f1f.json"}}], "type": "journal article", "published": "2020-12-00", "journal": {"title": "Nat. Chem. Biol.", "issn": "1552-4469", "issn-l": "1552-4450", "volume": "16", "issue": "12", "pages": "1321-1330"}, "abstract": "Maintenance of lipid asymmetry across the two leaflets of the plasma membrane (PM) bilayer is a ubiquitous feature of eukaryotic cells. Loss of this asymmetry has been widely associated with cell death. However, increasing evidence points to the physiological importance of non-apoptotic, transient changes in PM asymmetry. Such transient scrambling events are associated with a range of biological functions, including intercellular communication and intracellular signaling. Thus, regulation of interleaflet lipid distribution in the PM is a broadly important but underappreciated cellular process with key physiological and structural consequences. Here, we compile the mounting evidence revealing multifaceted, functional roles of PM asymmetry and transient loss thereof. We discuss the consequences of reversible asymmetry on PM structure, biophysical properties and interleaflet coupling. We argue that despite widespread recognition of broad aspects of membrane asymmetry, its importance in cell biology demands more in-depth investigation of its features, regulation, and physiological and pathological implications.", "doi": "10.1038/s41589-020-00688-0", "pmid": "33199908", "labels": {"Milka Doktorova": null, "DDLS Fellow": null}, "xrefs": [{"db": "mid", "key": "NIHMS1653288"}, {"db": "pmc", "key": "PMC7747298"}, {"db": "pii", "key": "10.1038/s41589-020-00688-0"}], "notes": [], "created": "2024-11-27T12:20:13.657Z", "modified": "2024-11-29T10:51:22.029Z"}, {"entity": "publication", "iuid": "19de0071778b44b8939401dbd420fb1a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/19de0071778b44b8939401dbd420fb1a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/19de0071778b44b8939401dbd420fb1a"}}, "title": "S100A6 is a critical regulator of hematopoietic stem cells.", "authors": [{"family": "Grahn", "given": "Tan Hooi Min", "initials": "THM", "orcid": "0000-0002-4737-4320", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2dd4d05a5728436bb7347e2d94df7469.json"}}, {"family": "Niroula", "given": "Abhishek", "initials": "A", "orcid": "0000-0002-5904-0635", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/05df7afc7a494ba5af8a378e5ffa53f0.json"}}, {"family": "V\u00e9gv\u00e1ri", "given": "\u00c1kos", "initials": "\u00c1", "orcid": "0000-0002-1287-0906", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/724d65ef088147c4988093b2b6b5f318.json"}}, {"family": "Oburoglu", "given": "Leal", "initials": "L", "orcid": "0000-0003-0130-6602", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/106d7b2aee2049668bf8fd2f44e98980.json"}}, {"family": "Pertesi", "given": "Maroulio", "initials": "M", "orcid": "0000-0002-4869-8925", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1395ddcc49604bc1a05ea52f7b1ad79a.json"}}, {"family": "Warsi", "given": "Sarah", "initials": "S", "orcid": "0000-0001-8834-3996", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5482fcd0ca464ca890d0f2fc5e042d4e.json"}}, {"family": "Safi", "given": "Fatemeh", "initials": "F", "orcid": "0000-0002-0964-3403", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/53b1ac04a256491aac044b88c009066d.json"}}, {"family": "Miharada", "given": "Natsumi", "initials": "N", "orcid": "0000-0001-6989-5314", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c5a3eef93e34438b58654d3d91e7704.json"}}, {"family": "Garcia", "given": "Sandra C", "initials": "SC", "orcid": "0000-0002-5680-242X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/14786b4c9675431d946b62f3354afab9.json"}}, {"family": "Siva", "given": "Kavitha", "initials": "K"}, {"family": "Liu", "given": "Yang", "initials": "Y"}, {"family": "R\u00f6rby", "given": "Emma", "initials": "E"}, {"family": "Nilsson", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Zubarev", "given": "Roman A", "initials": "RA"}, {"family": "Karlsson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-2353-2531", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/78905b5834b44e8982484b2a910f476d.json"}}], "type": "journal article", "published": "2020-12-00", "journal": {"title": "Leukemia", "issn": "1476-5551", "volume": "34", "issue": "12", "pages": "3323-3337", "issn-l": "0887-6924"}, "abstract": "The fate options of hematopoietic stem cells (HSCs) include self-renewal, differentiation, migration, and apoptosis. HSCs self-renewal divisions in stem cells are required for rapid regeneration during tissue damage and stress, but how precisely intracellular calcium signals are regulated to maintain fate options in normal hematopoiesis is unclear. S100A6 knockout (KO) HSCs have reduced total cell numbers in the HSC compartment, decreased myeloid output, and increased apoptotic HSC numbers in steady state. S100A6KO HSCs had impaired self-renewal and regenerative capacity, not responding to 5-Fluorouracil. Our transcriptomic and proteomic profiling suggested that S100A6 is a critical HSC regulator. Intriguingly, S100A6KO HSCs showed decreased levels of phosphorylated Akt (p-Akt) and Hsp90, with an impairment of mitochondrial respiratory capacity and a reduction of mitochondrial calcium levels. We showed that S100A6 regulates intracellular and mitochondria calcium buffering of HSC upon cytokine stimulation and have demonstrated that Akt activator SC79 reverts the levels of intracellular and mitochondrial calcium in HSC. Hematopoietic colony-forming activity and the Hsp90 activity of S100A6KO are restored through activation of the Akt pathway. We show that p-Akt is the prime downstream mechanism of S100A6 in the regulation of HSC self-renewal by specifically governing mitochondrial metabolic function and Hsp90 protein quality.", "doi": "10.1038/s41375-020-0901-2", "pmid": "32555370", "labels": {"Abhishek Niroula": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC7685984"}, {"db": "pii", "key": "10.1038/s41375-020-0901-2"}], "notes": [], "created": "2023-11-20T11:21:50.994Z", "modified": "2023-11-20T11:21:51.835Z"}, {"entity": "publication", "iuid": "29745e524468452d8313b0884f8360b8", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/29745e524468452d8313b0884f8360b8.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/29745e524468452d8313b0884f8360b8"}}, "title": "Identification of areas of grading difficulties in prostate cancer and comparison with artificial intelligence assisted grading.", "authors": [{"family": "Egevad", "given": "Lars", "initials": "L", "orcid": "0000-0001-8531-222X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a7d46f1f5fc047dc8edb910eb4f0645c.json"}}, {"family": "Swanberg", "given": "Daniela", "initials": "D"}, {"family": "Delahunt", "given": "Brett", "initials": "B"}, {"family": "Str\u00f6m", "given": "Peter", "initials": "P"}, {"family": "Kartasalo", "given": "Kimmo", "initials": "K"}, {"family": "Olsson", "given": "Henrik", "initials": "H"}, {"family": "Berney", "given": "Dan M", "initials": "DM"}, {"family": "Bostwick", "given": "David G", "initials": "DG"}, {"family": "Evans", "given": "Andrew J", "initials": "AJ"}, {"family": "Humphrey", "given": "Peter A", "initials": "PA"}, {"family": "Iczkowski", "given": "Kenneth A", "initials": "KA"}, {"family": "Kench", "given": "James G", "initials": "JG"}, {"family": "Kristiansen", "given": "Glen", "initials": "G"}, {"family": "Leite", "given": "Katia R M", "initials": "KRM"}, {"family": "McKenney", "given": "Jesse K", "initials": "JK"}, {"family": "Oxley", "given": "Jon", "initials": "J"}, {"family": "Pan", "given": "Chin-Chen", "initials": "C"}, {"family": "Samaratunga", "given": "Hemamali", "initials": "H"}, {"family": "Srigley", "given": "John R", "initials": "JR"}, {"family": "Takahashi", "given": "Hiroyuki", "initials": "H"}, {"family": "Tsuzuki", "given": "Toyonori", "initials": "T"}, {"family": "van der Kwast", "given": "Theo", "initials": "T"}, {"family": "Varma", "given": "Murali", "initials": "M"}, {"family": "Zhou", "given": "Ming", "initials": "M"}, {"family": "Clements", "given": "Mark", "initials": "M"}, {"family": "Eklund", "given": "Martin", "initials": "M"}], "type": "comparative study", "published": "2020-12-00", "journal": {"title": "Virchows Arch.", "issn": "1432-2307", "issn-l": "0945-6317", "volume": "477", "issue": "6", "pages": "777-786"}, "abstract": "The International Society of Urological Pathology (ISUP) hosts a reference image database supervised by experts with the purpose of establishing an international standard in prostate cancer grading. Here, we aimed to identify areas of grading difficulties and compare the results with those obtained from an artificial intelligence system trained in grading. In a series of 87 needle biopsies of cancers selected to include problematic cases, experts failed to reach a 2/3 consensus in 41.4% (36/87). Among consensus and non-consensus cases, the weighted kappa was 0.77 (range 0.68-0.84) and 0.50 (range 0.40-0.57), respectively. Among the non-consensus cases, four main causes of disagreement were identified: the distinction between Gleason score 3 + 3 with tangential cutting artifacts vs. Gleason score 3 + 4 with poorly formed or fused glands (13 cases), Gleason score 3 + 4 vs. 4 + 3 (7 cases), Gleason score 4 + 3 vs. 4 + 4 (8 cases) and the identification of a small component of Gleason pattern 5 (6 cases). The AI system obtained a weighted kappa value of 0.53 among the non-consensus cases, placing it as the observer with the sixth best reproducibility out of a total of 24. AI may serve as a decision support and decrease inter-observer variability by its ability to make consistent decisions. The grading of these cancer patterns that best predicts outcome and guides treatment warrants further clinical and genetic studies. Results of such investigations should be used to improve calibration of AI systems.", "doi": "10.1007/s00428-020-02858-w", "pmid": "32542445", "labels": {"Kimmo Kartasalo": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC7683442"}, {"db": "pii", "key": "10.1007/s00428-020-02858-w"}], "notes": [], "created": "2024-11-05T16:08:18.753Z", "modified": "2024-11-29T10:45:14.878Z"}, {"entity": "publication", "iuid": "648d101a01c64132b784096a0d1e8356", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/648d101a01c64132b784096a0d1e8356.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/648d101a01c64132b784096a0d1e8356"}}, "title": "Colonization factor CS30 from enterotoxigenic Escherichia coli binds to sulfatide in human and porcine small intestine.", "authors": [{"family": "Von Mentzer", "given": "Astrid", "initials": "A"}, {"family": "Zalem", "given": "Dani", "initials": "D"}, {"family": "Chrienova", "given": "Zofia", "initials": "Z", "orcid": "0000-0003-2693-9991", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0ee2c270be184f38b4149733caf44cdd.json"}}, {"family": "Teneberg", "given": "Susann", "initials": "S"}], "type": "journal article", "published": "2020-12-00", "journal": {"title": "Virulence", "issn": "2150-5608", "volume": "11", "issue": "1", "pages": "381-390", "issn-l": null}, "abstract": "The ability to adhere via colonization factors to specific receptors located on the intestinal mucosa is a key virulence factor in enterotoxigenic Escherichia coli (ETEC) pathogenesis. Here, the potential glycosphingolipid receptors of the novel human ETEC colonization factor CS30 were examined by binding of CS30-expressing bacteria to glycosphingolipids on thin-layer chromatograms. We thereby found a highly specific binding of CS30-expressing bacteria to a fast-migrating acid glycosphingolipid of human and porcine small intestine, while no binding was obtained with a mutant ETEC strain unable to express CS30 fimbriae. The CS30 binding glycosphingolipid from human small intestine was isolated and characterized by mass spectrometry as sulfatide (SO3-3Gal\u03b21Cer). Comparative binding studies using sulfatides with different ceramide compositions gave a preferential binding of CS30 to sulfatide with d18:1-h24:0 ceramide. This ceramide species of sulfatide was also isolated from human small intestine and characterized by mass spectrometry and antibody binding. These studies implicate sulfatide as candidate receptor for mediating attachment of CS30-fimbriated ETEC to human and porcine small intestinal cells. Our findings may be a basis for designing receptor saccharide analogues for inhibition of the intestinal adhesion of CS30-expressing E. coli.", "doi": "10.1080/21505594.2020.1749497", "pmid": "32245341", "labels": {"Astrid von Mentzer": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC7161690"}], "notes": [], "created": "2025-12-02T15:48:48.849Z", "modified": "2025-12-02T15:48:48.919Z"}, {"entity": "publication", "iuid": "397f64b1e292432395bfc779c01f202d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/397f64b1e292432395bfc779c01f202d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/397f64b1e292432395bfc779c01f202d"}}, "title": "Assessment of In Vitro and In Silico Protocols for Sequence-Based Characterization of the Human Vaginal Microbiome.", "authors": [{"family": "Hugerth", "given": "Luisa W", "initials": "LW", "orcid": "0000-0001-5432-1764", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/246ed7b405dd4c3f9ec5e7ff9f1d3ade.json"}}, {"family": "Pereira", "given": "Marcela", "initials": "M"}, {"family": "Zha", "given": "Yinghua", "initials": "Y"}, {"family": "Seifert", "given": "Maike", "initials": "M"}, {"family": "Kaldhusdal", "given": "Vilde", "initials": "V"}, {"family": "Boulund", "given": "Fredrik", "initials": "F"}, {"family": "Krog", "given": "Maria C", "initials": "MC"}, {"family": "Bashir", "given": "Zahra", "initials": "Z"}, {"family": "Hamsten", "given": "Marica", "initials": "M"}, {"family": "Fransson", "given": "Emma", "initials": "E"}, {"family": "Svarre-Nielsen", "given": "Henriette", "initials": "H"}, {"family": "Schuppe-Koistinen", "given": "Ina", "initials": "I"}, {"family": "Engstrand", "given": "Lars", "initials": "L", "orcid": "0000-0002-7713-2373", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02d8684df81e42169e613de803446fbf.json"}}], "type": "journal article", "published": "2020-11-18", "journal": {"title": "mSphere", "issn": "2379-5042", "volume": "5", "issue": "6", "issn-l": "2379-5042"}, "abstract": "The vaginal microbiome has been connected to a wide range of health outcomes. This has led to a thriving research environment but also to the use of conflicting methodologies to study its microbial composition. Here, we systematically assessed best practices for the sequencing-based characterization of the human vaginal microbiome. As far as 16S rRNA gene sequencing is concerned, the V1-V3 region performed best in silico, but limitations of current sequencing technologies meant that the V3-V4 region performed equally well. Both approaches presented very good agreement with qPCR quantification of key taxa, provided that an appropriate bioinformatic pipeline was used. Shotgun metagenomic sequencing presents an interesting alternative to 16S rRNA gene amplification and sequencing but requires deeper sequencing and more bioinformatic expertise and infrastructure. We assessed different tools for the removal of host reads and the taxonomic annotation of metagenomic reads, including a new, easy-to-build and -use reference database of vaginal taxa. This curated database performed as well as the best-performing previously published strategies. Despite the many advantages of shotgun sequencing, none of the shotgun approaches assessed here agreed with the qPCR data as well as the 16S rRNA gene sequencing.IMPORTANCE The vaginal microbiome has been connected to various aspects of host health, including susceptibility to sexually transmitted infections as well as gynecological cancers and pregnancy outcomes. This has led to a thriving research environment but also to conflicting available methodologies, including many studies that do not report their molecular biological and bioinformatic methods in sufficient detail to be considered reproducible. This can lead to conflicting messages and delay progress from descriptive to intervention studies. By systematically assessing best practices for the characterization of the human vaginal microbiome, this study will enable past studies to be assessed more critically and assist future studies in the selection of appropriate methods for their specific research questions.", "doi": "10.1128/mSphere.00448-20", "pmid": "33208514", "labels": {"DDLS Fellow": "", "Luisa Hugerth": ""}, "xrefs": [{"db": "pmc", "key": "PMC7677004"}, {"db": "pii", "key": "5/6/e00448-20"}], "notes": [], "created": "2022-11-08T06:59:04.474Z", "modified": "2026-09-23T10:47:40.954Z"}, {"entity": "publication", "iuid": "aa4ac3404a084509a55942b0b5de5db4", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/aa4ac3404a084509a55942b0b5de5db4.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/aa4ac3404a084509a55942b0b5de5db4"}}, "title": "The Immunology of Multisystem Inflammatory Syndrome in Children with COVID-19.", "authors": [{"family": "Consiglio", "given": "Camila Rosat", "initials": "CR"}, {"family": "Cotugno", "given": "Nicola", "initials": "N"}, {"family": "Sardh", "given": "Fabian", "initials": "F"}, {"family": "Pou", "given": "Christian", "initials": "C"}, {"family": "Amodio", "given": "Donato", "initials": "D"}, {"family": "Rodriguez", "given": "Lucie", "initials": "L"}, {"family": "Tan", "given": "Ziyang", "initials": "Z"}, {"family": "Zicari", "given": "Sonia", "initials": "S"}, {"family": "Ruggiero", "given": "Alessandra", "initials": "A"}, {"family": "Pascucci", "given": "Giuseppe Rubens", "initials": "GR"}, {"family": "Santilli", "given": "Veronica", "initials": "V"}, {"family": "Campbell", "given": "Tessa", "initials": "T"}, {"family": "Bryceson", "given": "Yenan", "initials": "Y"}, {"family": "Eriksson", "given": "Daniel", "initials": "D"}, {"family": "Wang", "given": "Jun", "initials": "J"}, {"family": "Marchesi", "given": "Alessandra", "initials": "A"}, {"family": "Lakshmikanth", "given": "Tadepally", "initials": "T"}, {"family": "Campana", "given": "Andrea", "initials": "A"}, {"family": "Villani", "given": "Alberto", "initials": "A"}, {"family": "Rossi", "given": "Paolo", "initials": "P"}, {"family": "CACTUS Study Team", "given": "", "initials": ""}, {"family": "Landegren", "given": "Nils", "initials": "N"}, {"family": "Palma", "given": "Paolo", "initials": "P"}, {"family": "Brodin", "given": "Petter", "initials": "P"}], "type": "journal article", "published": "2020-11-12", "journal": {"title": "Cell", "issn": "1097-4172", "volume": "183", "issue": "4", "pages": "968-981.e7", "issn-l": "0092-8674"}, "abstract": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is typically very mild and often asymptomatic in children. A complication is the rare multisystem inflammatory syndrome in children (MIS-C) associated with COVID-19, presenting 4-6 weeks after infection as high fever, organ dysfunction, and strongly elevated markers of inflammation. The pathogenesis is unclear but has overlapping features with Kawasaki disease suggestive of vasculitis and a likely autoimmune etiology. We apply systems-level analyses of blood immune cells, cytokines, and autoantibodies in healthy children, children with Kawasaki disease enrolled prior to COVID-19, children infected with SARS-CoV-2, and children presenting with MIS-C. We find that the inflammatory response in MIS-C differs from the cytokine storm of severe acute COVID-19, shares several features with Kawasaki disease, but also differs from this condition with respect to T cell subsets, interleukin (IL)-17A, and biomarkers associated with arterial damage. Finally, autoantibody profiling suggests multiple autoantibodies that could be involved in the pathogenesis of MIS-C.", "doi": "10.1016/j.cell.2020.09.016", "pmid": "32966765", "labels": {"Camila Consiglio": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC7474869"}, {"db": "pii", "key": "S0092-8674(20)31157-0"}], "notes": [], "created": "2023-11-22T09:16:14.546Z", "modified": "2026-09-23T06:29:40.541Z"}, {"entity": "publication", "iuid": "83ee91e395424d7c933703b7efb26637", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/83ee91e395424d7c933703b7efb26637.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/83ee91e395424d7c933703b7efb26637"}}, "title": "DNA methylation in infants with low and high body fatness.", "authors": [{"family": "Henriksson", "given": "Pontus", "initials": "P", "orcid": "0000-0003-2482-7048", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/14408f93880f4f2ba56c935489f450da.json"}}, {"family": "Lentini", "given": "Antonio", "initials": "A"}, {"family": "Altm\u00e4e", "given": "Signe", "initials": "S"}, {"family": "Brodin", "given": "David", "initials": "D"}, {"family": "M\u00fcller", "given": "Patrick", "initials": "P"}, {"family": "Forsum", "given": "Elisabet", "initials": "E"}, {"family": "Nestor", "given": "Colm E", "initials": "CE"}, {"family": "L\u00f6f", "given": "Marie", "initials": "M"}], "type": "journal article", "published": "2020-11-09", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "21", "issue": "1", "pages": "769", "issn-l": "1471-2164"}, "abstract": "Birth weight is determined by the interplay between infant genetics and the intrauterine environment and is associated with several health outcomes in later life. Many studies have reported an association between birth weight and DNA methylation in infants and suggest that altered epigenetics may underlie birthweight-associated health outcomes. However, birth weight is a relatively nonspecific measure of fetal growth and consists of fat mass and fat-free mass which may have different effects on health outcomes which motivates studies of infant body composition and DNA methylation. Here, we combined genome-wide DNA methylation profiling of buccal cells from 47 full-term one-week old infants with accurate measurements of infant fat mass and fat-free mass using air-displacement plethysmography.\n\nNo significant association was found between DNA methylation in infant buccal cells and infant body composition. Moreover, no association between infant DNA methylation and parental body composition or indicators of maternal glucose metabolism were found.\n\nDespite accurate measures of body composition, we did not identify any associations between infant body fatness and DNA methylation. These results are consistent with recent studies that generally have identified only weak associations between DNA methylation and birthweight. Although our results should be confirmed by additional larger studies, our findings may suggest that differences in DNA methylation between individuals with low and high body fatness may be established later in childhood.", "doi": "10.1186/s12864-020-07169-7", "pmid": "33167873", "labels": {"Antonio Lentini": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC7654595"}, {"db": "pii", "key": "10.1186/s12864-020-07169-7"}], "notes": [], "created": "2025-03-28T07:11:54.965Z", "modified": "2025-03-28T07:11:54.996Z"}, {"entity": "publication", "iuid": "ba547bbe66d747baa3442cbce7431c19", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ba547bbe66d747baa3442cbce7431c19.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ba547bbe66d747baa3442cbce7431c19"}}, "title": "Genomic Characterization of Salmonella Minnesota Clonal Lineages Associated with Poultry Production in Brazil.", "authors": [{"family": "Kipper", "given": "Di\u00e9ssy", "initials": "D"}, {"family": "Carroll", "given": "Laura M", "initials": "LM"}, {"family": "Mascitti", "given": "Andrea K", "initials": "AK"}, {"family": "Streck", "given": "Andr\u00e9 F", "initials": "AF"}, {"family": "Fonseca", "given": "Andr\u00e9 S K", "initials": "ASK"}, {"family": "Ikuta", "given": "Nilo", "initials": "N"}, {"family": "Lunge", "given": "Vagner R", "initials": "VR"}], "type": "journal article", "published": "2020-11-05", "journal": {"title": "Animals (Basel)", "issn": "2076-2615", "volume": "10", "issue": "11", "issn-l": null}, "abstract": "Salmonella serotype Minnesota has been increasingly detected in Brazilian poultry farms and food products (chicken meat, eggs) in recent years. In addition, S. Minnesota isolates from poultry are generally resistant to several antibiotics and persistent in farm environments. The present study aimed to assess phylogenomic diversity of S. Minnesota isolates from the poultry production chain in Brazil. In total, 107 worldwide S. Minnesota whole genomes (including 12 from Brazil) were analyzed using a comparative approach. Phylogenetic analysis demonstrated two clades more related to poultry production in Brazil: S. Minnesota poultry lineages I and II (SM-PLI and SM-PLII). Phylodynamic analysis demonstrated that SM-PLI had a common ancestor in 1915, while SM-PLII originated circa 1971. SM-PLII encompassed a higher number of isolates and presented a recent increase in effective population size (mainly from 2009 to 2012). Plasmids IncA/C2 and ColRNA, antimicrobial resistance genes (aph(3')-Ia, blaCMY-2, qnrB19, sul2, and tet(A)) and mainly a virulence genetic cluster (including the yersiniabactin operon) were detected in isolates from SM-PLI and/or SM-PLII. This study demonstrates the dissemination of two distinct S. Minnesota lineages with high resistance to antibiotics and important virulence genetic clusters in Brazilian poultry farms.", "doi": "10.3390/ani10112043", "pmid": "33167341", "labels": {"Laura Carroll": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC7694379"}, {"db": "pii", "key": "ani10112043"}], "notes": [], "created": "2025-03-18T17:26:44.287Z", "modified": "2025-03-18T17:26:44.309Z"}, {"entity": "publication", "iuid": "4fdeb7f5e7a648eaa943af2cac3f0be1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4fdeb7f5e7a648eaa943af2cac3f0be1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4fdeb7f5e7a648eaa943af2cac3f0be1"}}, "title": "Novel Effective Bacillus cereus Group Species \"Bacillus clarus\" Is Represented by Antibiotic-Producing Strain ATCC 21929 Isolated from Soil.", "authors": [{"family": "M\u00e9ndez Acevedo", "given": "Marysabel", "initials": "M"}, {"family": "Carroll", "given": "Laura M", "initials": "LM"}, {"family": "Mukherjee", "given": "Manjari", "initials": "M"}, {"family": "Mills", "given": "Emma", "initials": "E"}, {"family": "Xiaoli", "given": "Lingzi", "initials": "L"}, {"family": "Dudley", "given": "Edward G", "initials": "EG", "orcid": "0000-0003-1298-1603", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ef1dcea91e7e4688a6810deea00b7341.json"}}, {"family": "Kovac", "given": "Jasna", "initials": "J", "orcid": "0000-0002-9465-4552", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d18e6f5bd24644e18030b59391d1a755.json"}}], "type": "journal article", "published": "2020-11-04", "journal": {"title": "mSphere", "issn": "2379-5042", "volume": "5", "issue": "6", "issn-l": "2379-5042"}, "abstract": "Gram-positive, spore-forming members of the Bacillus cereus group species complex are widespread in natural environments and display various degrees of pathogenicity. Recently, B. cereus group strain Bacillus mycoides Flugge ATCC 21929 was found to represent a novel lineage within the species complex, sharing a relatively low degree of genomic similarity with all B. cereus group genomes (average nucleotide identity [ANI] < 88). ATCC 21929 has been previously associated with the production of a patented antibiotic, antibiotic 60-6 (i.e., cerexin A); however, the virulence potential and growth characteristics of this lineage have never been assessed. Here, we provide an extensive genomic and phenotypic characterization of ATCC 21929, and we assess its pathogenic potential in vitro. ATCC 21929 most closely resembles Bacillus paramycoides NH24A2T (ANI and in silico DNA-DNA hybridization values of 86.70 and 34.10%, respectively). Phenotypically, ATCC 21929 does not possess cytochrome c oxidase activity and is able to grow at a range of temperatures between 15 and 43\u00b0C and a range of pH between 6 and 9. At 32\u00b0C, ATCC 21929 shows weak production of diarrheal enterotoxin hemolysin BL (Hbl) but no production of nonhemolytic enterotoxin (Nhe); at 37\u00b0C, neither Hbl nor Nhe is produced. Additionally, at 37\u00b0C, ATCC 21929 does not exhibit cytotoxic effects toward HeLa cells. With regard to fatty acid composition, ATCC 21929 has iso-C17:0 present in highest abundance. Based on the characterization provided here, ATCC 21929T (= PS00077AT = PS00077BT = PSU-0922T = BHPT) represents a novel effective B. cereus group species, which we propose as effective species \"Bacillus clarus\"IMPORTANCE The B. cereus group comprises numerous closely related lineages with various degrees of pathogenic potential and industrial relevance. Species-level taxonomic classification of B. cereus group strains is important for risk evaluation and communication but remains challenging. Biochemical and phenotypic assays are often used to assign B. cereus group strains to species but are insufficient for accurate taxonomic classification on a genomic scale. Here, we show that antibiotic-producing ATCC 21929 represents a novel lineage within the B. cereus group that, by all metrics used to delineate prokaryotic species, exemplifies a novel effective species. Furthermore, we show that ATCC 21929 is incapable of producing enterotoxins Hbl and Nhe or exhibiting cytotoxic effects on HeLa cells at human body temperature in vitro These results provide greater insight into the genomic and phenotypic diversity of the B. cereus group and may be leveraged to inform future public health and food safety efforts.", "doi": "10.1128/mSphere.00882-20", "pmid": "33148822", "labels": {"Laura Carroll": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC7643830"}, {"db": "pii", "key": "5/6/e00882-20"}], "notes": [], "created": "2025-03-18T17:26:57.955Z", "modified": "2025-03-18T17:26:58.021Z"}, {"entity": "publication", "iuid": "2dc267ccad65401d9f8452fe3deb169a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/2dc267ccad65401d9f8452fe3deb169a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/2dc267ccad65401d9f8452fe3deb169a"}}, "title": "Implications for tetraspanin-enriched microdomain assembly based on structures of CD9 with EWI-F", "authors": [{"family": "Oosterheert", "given": "Wout", "initials": "W", "orcid": "0000-0003-1189-6044", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/df1d46d6083041de97cc808c6c4d8202.json"}}, {"family": "Xenaki", "given": "Katerina T", "initials": "KT", "orcid": "0000-0002-0153-6320", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/caa99e8b5bea4e77a425e06daf14ddf4.json"}}, {"family": "Neviani", "given": "Viviana", "initials": "V", "orcid": "0000-0002-5729-3639", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/67b015ac73c4401a8204611669e977a6.json"}}, {"family": "Pos", "given": "Wouter", "initials": "W"}, {"family": "Doulkeridou", "given": "Sofia", "initials": "S"}, {"family": "Manshande", "given": "Jip", "initials": "J"}, {"family": "Pearce", "given": "Nicholas M", "initials": "NM", "orcid": "0000-0002-6693-8603", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/07d6d5de91cc4120b2bf996ca578a13e.json"}}, {"family": "Kroon-Batenburg", "given": "Loes MJ", "initials": "LM", "orcid": "0000-0002-5321-1392", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8a0a9bf02f884fe09b19e976f2fcbda8.json"}}, {"family": "Lutz", "given": "Martin", "initials": "M"}, {"family": "van Bergen en Henegouwen", "given": "Paul MP", "initials": "PM", "orcid": "0000-0001-6050-9042", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a178ea11c3ce4031877b12c845a886e3.json"}}, {"family": "Gros", "given": "Piet", "initials": "P", "orcid": "0000-0002-7782-2585", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/590881ded1d542b8b61831c00b0fdb87.json"}}], "type": "journal-article", "published": "2020-11-00", "journal": {"title": "Life Sci. Alliance", "issn": "2575-1077", "issn-l": null, "volume": "3", "issue": "11", "pages": "e202000883"}, "abstract": null, "doi": "10.26508/lsa.202000883", "pmid": null, "labels": {"Nicholas Pearce": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2022-12-05T18:57:30.973Z", "modified": "2022-12-05T19:34:10.270Z"}, {"entity": "publication", "iuid": "0ea7b327da6443cdb8fec6e28cd82ad6", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0ea7b327da6443cdb8fec6e28cd82ad6.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0ea7b327da6443cdb8fec6e28cd82ad6"}}, "title": "Docking finds GPCR ligands in dark chemical matter", "authors": [{"family": "Rudling", "given": "Axel", "initials": "A"}, {"family": "Luttens", "given": "Andreas", "initials": "A"}, {"family": "Kihlberg", "given": "Jan", "initials": "J"}, {"family": "Ballante", "given": "Flavio", "initials": "F"}, {"family": "Irwin", "given": "John", "initials": "J"}, {"family": "Vo", "given": "Duy", "initials": "D"}, {"family": "Loza", "given": "Maria", "initials": "M"}, {"family": "Carlsson", "given": "Jens", "initials": "J"}, {"family": "Brea", "given": "Jose", "initials": "J"}, {"family": "Zeifman", "given": "Alexey", "initials": "A"}], "type": "posted-content", "published": "2020-10-31", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1021/scimeetings.0c07066", "pmid": null, "labels": {"SciLifeLab Fellow": "", "Jens Carlsson": "", "Andreas Luttens": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T08:44:01.450Z", "modified": "2026-09-23T15:11:04.428Z"}, {"entity": "publication", "iuid": "f6804ccb788441c6a32b54f384ed938a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f6804ccb788441c6a32b54f384ed938a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f6804ccb788441c6a32b54f384ed938a"}}, "title": "Nuclear gene proximity and protein interactions shape transcript covariations in mammalian single cells.", "authors": [{"family": "Tarbier", "given": "Marcel", "initials": "M", "orcid": "0000-0003-0556-2531", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9678d0797def441e9870afe6ffbb08d0.json"}}, {"family": "Mackowiak", "given": "Sebastian D", "initials": "SD"}, {"family": "Frade", "given": "Jo\u00e3o", "initials": "J", "orcid": "0000-0003-3961-7641", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/631c1c8f3a5941bdb3af84315d39a801.json"}}, {"family": "Catuara-Solarz", "given": "Silvina", "initials": "S"}, {"family": "Biryukova", "given": "Inna", "initials": "I", "orcid": "0000-0003-0701-2808", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d61f8576ba87431d90b18fe5110c993d.json"}}, {"family": "Gelali", "given": "Eleni", "initials": "E", "orcid": "0000-0003-0067-5473", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/742370a413a6480686159d8933f08002.json"}}, {"family": "Men\u00e9ndez", "given": "Diego B\u00e1rcena", "initials": "DB"}, {"family": "Zapata", "given": "Luis", "initials": "L", "orcid": "0000-0002-1386-2019", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3f1cf4d39e25433faff15a7f35184a5c.json"}}, {"family": "Ossowski", "given": "Stephan", "initials": "S"}, {"family": "Bienko", "given": "Magda", "initials": "M", "orcid": "0000-0002-6499-9082", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4b8da7a1f8524d0e812c83b1f5e20ef6.json"}}, {"family": "Gallant", "given": "Caroline J", "initials": "CJ"}, {"family": "Friedl\u00e4nder", "given": "Marc R", "initials": "MR", "orcid": "0000-0001-6577-4363", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ac5a2794be7c4cab89d1e4f1570c9417.json"}}], "type": "journal article", "published": "2020-10-28", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "11", "issue": "1", "pages": "5445"}, "abstract": "Single-cell RNA sequencing studies on gene co-expression patterns could yield important regulatory and functional insights, but have so far been limited by the confounding effects of differentiation and cell cycle. We apply a tailored experimental design that eliminates these confounders, and report thousands of intrinsically covarying gene pairs in mouse embryonic stem cells. These covariations form a network with biological properties, outlining known and novel gene interactions. We provide the first evidence that miRNAs naturally induce transcriptome-wide covariations and compare the relative importance of nuclear organization, transcriptional and post-transcriptional regulation in defining covariations. We find that nuclear organization has the greatest impact, and that genes encoding for physically interacting proteins specifically tend to covary, suggesting importance for protein complex formation. Our results lend support to the concept of post-transcriptional RNA operons, but we further present evidence that nuclear proximity of genes may provide substantial functional regulation in mammalian single cells.", "doi": "10.1038/s41467-020-19011-5", "pmid": "33116115", "labels": {"Marc Friedl\u00e4nder": "", "Magda Bienko": "", "SciLifeLab Fellow": "", "DDLS Fellow": "", "Marcel Tarbier": ""}, "xrefs": [{"db": "pmc", "key": "PMC7595044"}, {"db": "pii", "key": "10.1038/s41467-020-19011-5"}], "notes": [], "created": "2020-11-09T10:06:11.027Z", "modified": "2026-09-23T10:30:22.386Z"}, {"entity": "publication", "iuid": "4be742ce980749e9aa06162234470aab", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4be742ce980749e9aa06162234470aab.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4be742ce980749e9aa06162234470aab"}}, "title": "Modelling the dispersion of SARS-CoV-2 on a dynamic network graph", "authors": [{"family": "Bryant", "given": "Patrick", "initials": "P", "orcid": "0000-0003-3439-1866", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a683bcf98234ff09b2398976583b66f.json"}}, {"family": "Elofsson", "given": "Arne", "initials": "A", "orcid": "0000-0002-7115-9751", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/248e70e81bd64f31a5f83e6e329bba95.json"}}], "type": "posted-content", "published": "2020-10-21", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2020.10.19.20215046", "pmid": null, "labels": {"Patrick Bryant": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T09:59:29.293Z", "modified": "2026-09-23T13:52:44.631Z"}, {"entity": "publication", "iuid": "8820c00d6d9a49caa4eb32fddcee3e8d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8820c00d6d9a49caa4eb32fddcee3e8d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8820c00d6d9a49caa4eb32fddcee3e8d"}}, "title": "Androgen Receptor Signaling Positively Regulates Monocytic Development.", "authors": [{"family": "Consiglio", "given": "Camila Rosat", "initials": "CR"}, {"family": "Gollnick", "given": "Sandra O", "initials": "SO"}], "type": "journal article", "published": "2020-10-15", "journal": {"title": "Front Immunol", "issn": "1664-3224", "volume": "11", "pages": "519383", "issn-l": "1664-3224"}, "abstract": "Myeloid cells are critical cells involved in the orchestration of innate and adaptive immune responses. Most myeloid cells derive from the adult bone marrow in a process called myelopoiesis, a tightly controlled process that ensures constant production of myeloid cells. Sex differences in myeloid cell development have been observed; males exhibit greater monocytic differentiation in the bone marrow, and men have increased blood monocyte numbers when compared to women. Here we use a genetic mouse model of myeloid androgen receptor (AR) knockout (MARKO) and pharmacological inhibition of AR to investigate the role of androgen signaling in monocytic differentiation. We observe that although myeloid AR signaling does not influence total bone marrow cell numbers, it does affect the composition of the bone marrow myeloid population in both homeostatic and emergency settings. Genetic deletion of AR in myeloid cells led to reduced monocytic development in vivo. Similarly, pharmacologic inhibition of AR signaling in vitro reduced monocytic development. However, alteration in monocytic differentiation in the absence of AR signaling did not lead to reduced numbers of circulating myeloid cells, although MARKO male mice display reduced ratio of classical to non-classical monocytes in the blood, implying that blood monocyte subsets are skewed upon myeloid AR deletion. Our results suggest that the sex differences observed in monocytic differentiation are partly attributed to the positive role of the androgen-AR axis in regulating monocytic development directly at the myeloid cell level. Furthermore, we have identified a novel role for AR in regulating blood mature monocyte subset turnover. Investigating how androgen signaling affects monocytic development and monocyte subset heterogeneity will advance our understanding of sex differences in monocytic function at homeostasis and disease and can ultimately impact future therapeutic design targeting monocytes in the clinic.", "doi": "10.3389/fimmu.2020.519383", "pmid": "33193298", "labels": {"Camila Consiglio": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC7604537"}], "notes": [], "created": "2023-11-22T09:16:59.067Z", "modified": "2023-11-22T09:16:59.072Z"}, {"entity": "publication", "iuid": "93662e98a00949349b8506a19647b2ae", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/93662e98a00949349b8506a19647b2ae.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/93662e98a00949349b8506a19647b2ae"}}, "title": "Combined Metabolic Activators accelerates recovery in mild-to-moderate COVID-19", "authors": [{"family": "Altay", "given": "Ozlem", "initials": "O"}, {"family": "Arif", "given": "Muhammad", "initials": "M"}, {"family": "Li", "given": "Xiangyu", "initials": "X"}, {"family": "Yang", "given": "Hong", "initials": "H"}, {"family": "Ayd\u0131n", "given": "Mehtap", "initials": "M"}, {"family": "Alkurt", "given": "Gizem", "initials": "G"}, {"family": "Kim", "given": "Woonghee", "initials": "W"}, {"family": "Akyol", "given": "Dogukan", "initials": "D"}, {"family": "Zhang", "given": "Cheng", "initials": "C"}, {"family": "Dinler-Doganay", "given": "Gizem", "initials": "G"}, {"family": "Turkez", "given": "Hasan", "initials": "H"}, {"family": "Shoaie", "given": "Saeed", "initials": "S"}, {"family": "Nielsen", "given": "Jens", "initials": "J"}, {"family": "Bor\u00e9n", "given": "Jan", "initials": "J"}, {"family": "Olmuscelik", "given": "Oktay", "initials": "O"}, {"family": "Doganay", "given": "Levent", "initials": "L"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}], "type": "posted-content", "published": "2020-10-05", "journal": {"title": "medRxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2020.10.02.20202614", "pmid": null, "labels": {"SciLifeLab Fellow": null, "Saeed Shoaie": null, "DDLS Fellow": null, "Adil Mardinoglu": null, "Muhammad Arif": null}, "xrefs": [], "notes": [], "created": "2026-08-20T09:59:23.434Z", "modified": "2026-10-05T08:17:20.115Z"}, {"entity": "publication", "iuid": "afa290236d2541d5b6bbe0017897c5a6", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/afa290236d2541d5b6bbe0017897c5a6.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/afa290236d2541d5b6bbe0017897c5a6"}}, "title": "Profiles of histidine-rich glycoprotein associate with age and risk of all-cause mortality.", "authors": [{"family": "Hong", "given": "Mun-Gwan", "initials": "MG", "orcid": "0000-0001-8603-8293", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d12504acae5c4f31b83f75c3d7786cd4.json"}}, {"family": "Dodig-Crnkovi\u0107", "given": "Tea", "initials": "T", "orcid": "0000-0002-2875-896X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5365873ed6a7463485fb44550a4826ec.json"}}, {"family": "Chen", "given": "Xu", "initials": "X"}, {"family": "Drobin", "given": "Kimi", "initials": "K"}, {"family": "Lee", "given": "Woojoo", "initials": "W"}, {"family": "Wang", "given": "Yunzhang", "initials": "Y"}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Kotol", "given": "David", "initials": "D", "orcid": "0000-0002-5388-3826", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c41f8f491c474e6bba2047b5d04b4af5.json"}}, {"family": "Thomas", "given": "Cecilia Engel", "initials": "CE", "orcid": "0000-0001-6201-6380", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c2e25790f4c14deabd43b76ff5a5bef4.json"}}, {"family": "Sj\u00f6berg", "given": "Ronald", "initials": "R"}, {"family": "Odeberg", "given": "Jacob", "initials": "J", "orcid": "0000-0003-0996-1644", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d6abb3fc822a4cacbf1d45224f2442f5.json"}}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Silveira", "given": "Angela", "initials": "A", "orcid": "0000-0003-2063-4935", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2d8cbafcc7f04ac3adda984af7d85a16.json"}}, {"family": "Hall", "given": "Per", "initials": "P", "orcid": "0000-0002-5640-9126", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d59cc296ca1649ceb0d0734d20f1510a.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3db33fa3edb94febb8be7927a16838d0.json"}}, {"family": "Pawitan", "given": "Yudi", "initials": "Y"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ea446aa574042a295d5f69437402f76.json"}}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "H\u00e4gg", "given": "Sara", "initials": "S"}, {"family": "Magnusson", "given": "Patrik Ke", "initials": "PK"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/022e140799b6466ea123319c3d70c76e.json"}}], "type": "journal article", "published": "2020-10-00", "journal": {"title": "Life Sci. Alliance", "issn": "2575-1077", "volume": "3", "issue": "10", "issn-l": null}, "abstract": "Despite recognizing aging as a common risk factor of many human diseases, little is known about its molecular traits. To identify age-associated proteins circulating in human blood, we screened 156 individuals aged 50-92 using exploratory and multiplexed affinity proteomics assays. Profiling eight additional study sets (N = 3,987), performing antibody validation, and conducting a meta-analysis revealed a consistent age association (P = 6.61 \u00d7 10-6) for circulating histidine-rich glycoprotein (HRG). Sequence variants of HRG influenced how the protein was recognized in the immunoassays. Indeed, only the HRG profiles affected by rs9898 were associated with age and predicted the risk of mortality (HR = 1.25 per SD; 95% CI = 1.12-1.39; P = 6.45 \u00d7 10-5) during a follow-up period of 8.5 yr after blood sampling (IQR = 7.7-9.3 yr). Our affinity proteomics analysis found associations between the particular molecular traits of circulating HRG with age and all-cause mortality. The distinct profiles of this multipurpose protein could serve as an accessible and informative indicator of the physiological processes related to biological aging.", "doi": "10.26508/lsa.202000817", "pmid": "32737166", "labels": {"Fredrik Edfors": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC7409555"}, {"db": "pii", "key": "3/10/e202000817"}], "notes": [], "created": "2026-09-23T11:58:21.569Z", "modified": "2026-09-23T11:58:21.670Z"}, {"entity": "publication", "iuid": "4383c48bcc0e4140ad22b63d3f5d4af3", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4383c48bcc0e4140ad22b63d3f5d4af3.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4383c48bcc0e4140ad22b63d3f5d4af3"}}, "title": "ANHIR: Automatic Non-Rigid Histological Image Registration Challenge.", "authors": [{"family": "Borovec", "given": "Jiri", "initials": "J"}, {"family": "Kybic", "given": "Jan", "initials": "J"}, {"family": "Arganda-Carreras", "given": "Ignacio", "initials": "I"}, {"family": "Sorokin", "given": "Dmitry V", "initials": "DV"}, {"family": "Bueno", "given": "Gloria", "initials": "G"}, {"family": "Khvostikov", "given": "Alexander V", "initials": "AV"}, {"family": "Bakas", "given": "Spyridon", "initials": "S"}, {"family": "Chang", "given": "Eric I-Chao", "initials": "EI"}, {"family": "Heldmann", "given": "Stefan", "initials": "S"}, {"family": "Kartasalo", "given": "Kimmo", "initials": "K"}, {"family": "Latonen", "given": "Leena", "initials": "L"}, {"family": "Lotz", "given": "Johannes", "initials": "J"}, {"family": "Noga", "given": "Michelle", "initials": "M"}, {"family": "Pati", "given": "Sarthak", "initials": "S"}, {"family": "Punithakumar", "given": "Kumaradevan", "initials": "K"}, {"family": "Ruusuvuori", "given": "Pekka", "initials": "P"}, {"family": "Skalski", "given": "Andrzej", "initials": "A"}, {"family": "Tahmasebi", "given": "Nazanin", "initials": "N"}, {"family": "Valkonen", "given": "Masi", "initials": "M"}, {"family": "Venet", "given": "Ludovic", "initials": "L"}, {"family": "Wang", "given": "Yizhe", "initials": "Y"}, {"family": "Weiss", "given": "Nick", "initials": "N"}, {"family": "Wodzinski", "given": "Marek", "initials": "M"}, {"family": "Xiang", "given": "Yu", "initials": "Y"}, {"family": "Xu", "given": "Yan", "initials": "Y"}, {"family": "Yan", "given": "Yan", "initials": "Y"}, {"family": "Yushkevich", "given": "Paul", "initials": "P"}, {"family": "Zhao", "given": "Shengyu", "initials": "S"}, {"family": "Munoz-Barrutia", "given": "Arrate", "initials": "A"}], "type": "journal article", "published": "2020-10-00", "journal": {"title": "IEEE Trans Med Imaging", "issn": "1558-254X", "issn-l": null, "volume": "39", "issue": "10", "pages": "3042-3052"}, "abstract": "Automatic Non-rigid Histological Image Registration (ANHIR) challenge was organized to compare the performance of image registration algorithms on several kinds of microscopy histology images in a fair and independent manner. We have assembled 8 datasets, containing 355 images with 18 different stains, resulting in 481 image pairs to be registered. Registration accuracy was evaluated using manually placed landmarks. In total, 256 teams registered for the challenge, 10 submitted the results, and 6 participated in the workshop. Here, we present the results of 7 well-performing methods from the challenge together with 6 well-known existing methods. The best methods used coarse but robust initial alignment, followed by non-rigid registration, used multiresolution, and were carefully tuned for the data at hand. They outperformed off-the-shelf methods, mostly by being more robust. The best methods could successfully register over 98% of all landmarks and their mean landmark registration accuracy (TRE) was 0.44% of the image diagonal. The challenge remains open to submissions and all images are available for download.", "doi": "10.1109/TMI.2020.2986331", "pmid": "32275587", "labels": {"Kimmo Kartasalo": null, "DDLS Fellow": null}, "xrefs": [{"db": "mid", "key": "NIHMS1633882"}, {"db": "pmc", "key": "PMC7584382"}], "notes": [], "created": "2024-11-05T16:08:17.591Z", "modified": "2024-11-29T10:45:21.858Z"}, {"entity": "publication", "iuid": "b7f1835bd5bc481886159daff1ef460b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b7f1835bd5bc481886159daff1ef460b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b7f1835bd5bc481886159daff1ef460b"}}, "title": "High throughput generation of a resource of the human secretome in mammalian cells.", "authors": [{"family": "Tegel", "given": "Hanna", "initials": "H"}, {"family": "Dannemeyer", "given": "Melanie", "initials": "M"}, {"family": "Kanje", "given": "Sara", "initials": "S"}, {"family": "Sivertsson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Berling", "given": "Anna", "initials": "A"}, {"family": "Svensson", "given": "Anne-Sophie", "initials": "AS"}, {"family": "Hober", "given": "Andreas", "initials": "A"}, {"family": "Enstedt", "given": "Henric", "initials": "H"}, {"family": "Volk", "given": "Anna-Luisa", "initials": "AL"}, {"family": "Lundqvist", "given": "Magnus", "initials": "M"}, {"family": "Moradi", "given": "Mona", "initials": "M"}, {"family": "Afshari", "given": "Delaram", "initials": "D"}, {"family": "Ekblad", "given": "Siri", "initials": "S"}, {"family": "Xu", "given": "LanLan", "initials": "L"}, {"family": "Westin", "given": "Malin", "initials": "M"}, {"family": "Bidad", "given": "Faranak", "initials": "F"}, {"family": "Schiavone", "given": "Lovisa Holmberg", "initials": "LH"}, {"family": "Davies", "given": "Rick", "initials": "R"}, {"family": "Mayr", "given": "Lorenz M", "initials": "LM"}, {"family": "Knight", "given": "Sinead", "initials": "S"}, {"family": "G\u00f6pel", "given": "Sven O", "initials": "SO"}, {"family": "Voldborg", "given": "Bj\u00f6rn G", "initials": "BG"}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K"}, {"family": "Zwahlen", "given": "Martin", "initials": "M"}, {"family": "Rockberg", "given": "Johan", "initials": "J"}, {"family": "Takanen", "given": "Jenny Ottosson", "initials": "JO"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Hober", "given": "Sophia", "initials": "S"}], "type": "journal article", "published": "2020-09-25", "journal": {"title": "N Biotechnol", "issn": "1876-4347", "volume": "58", "pages": "45-54", "issn-l": "1871-6784"}, "abstract": "The proteins secreted by human tissues and blood cells, the secretome, are important both for the basic understanding of human biology and for identification of potential targets for future diagnosis and therapy. Here, a high-throughput mammalian cell factory is presented that was established to create a resource of recombinant full-length proteins covering the majority of those annotated as 'secreted' in humans. The full-length DNA sequences of each of the predicted secreted proteins were generated by gene synthesis, the constructs were transfected into Chinese hamster ovary (CHO) cells and the recombinant proteins were produced, purified and analyzed. Almost 1,300 proteins were successfully generated and proteins predicted to be secreted into the blood were produced with a success rate of 65%, while the success rates for the other categories of secreted proteins were somewhat lower giving an overall one-pass success rate of ca. 58%. The proteins were used to generate targeted proteomics assays and several of the proteins were shown to be active in a phenotypic assay involving pancreatic \u03b2-cell dedifferentiation. Many of the proteins that failed during production in CHO cells could be rescued in human embryonic kidney (HEK 293) cells suggesting that a cell factory of human origin can be an attractive alternative for production in mammalian cells. In conclusion, a high-throughput protein production and purification system has been successfully established to create a unique resource of the human secretome.", "doi": "10.1016/j.nbt.2020.05.002", "pmid": "32502629", "labels": {"Fredrik Edfors": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pii", "key": "S1871-6784(20)30132-1"}], "notes": [], "created": "2026-08-20T08:01:53.646Z", "modified": "2026-09-23T11:43:36.819Z"}, {"entity": "publication", "iuid": "a0722e98545c488eb638acf18a710033", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a0722e98545c488eb638acf18a710033.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a0722e98545c488eb638acf18a710033"}}, "title": "Effect of molecular phenotype based on Warburg effect pathway on the prognosis and the efficacy of postoperative radiation in cervical cancer", "authors": [{"family": "Li", "given": "N", "initials": "N"}, {"family": "Xu", "given": "H", "initials": "H"}, {"family": "Sun", "given": "X", "initials": "X"}, {"family": "Wang", "given": "QL", "initials": "Q"}, {"family": "Qiu", "given": "H", "initials": "H"}, {"family": "Zhou", "given": "Y", "initials": "Y"}, {"family": "Zhou", "given": "F", "initials": "F"}], "type": null, "published": "2020-09-25", "journal": {"title": "Chinese Journal of Radiological Medicine and Protection", "issn": "02545098", "issn-l": null, "volume": "40", "issue": "9", "pages": "666-673"}, "abstract": "Objective: To investigate the expression of Pyruvate dehydrogenase kinase 1(PDK1), phosphorylated Pyruvate dehydrogenase (p-PDH) and Pyruvate kinase isozyme type M2 (PKM2) based on Warburg effect pathway in cervical cancer tissues, and explore the roles of these molecules on prognosis and recurrence after postoperative radiation. Methods: The expressions of PDK1, p-PDH and PKM2 in primary tissues of 102 patients with cervical cancer were detected by immunohistochemistry, including 63 patients receiving postoperative radiation. The expression of the three molecules on prognosis and the efficacy of postoperative radiation on cervical cancer were analyzed separately and corporately.The level of mRNA were verified by using the 300 patients from GEO database. Kaplan-Meier method and COX proportional hazards regression model were used for univariate and multivariate analysis. Results: High expression of PDK1 and all the three indicators (PDK1high/p-PDHhigh/PKM2high) were positively correlated with pelvic lymphnode metastasis (\u03c72=10.890, 7.407, P<0.05). PDK1high/p-PDHhigh/PKM2high, Federation International of Gynecology and Obstetrics (FIGO) staging, pelvic lymph node metastasis and postoperative radiation could affect the overall survival (OS) and disease-free survival (DFS) (P<0.05). Multivariate analysis showed that PDK1high /PDHhigh/PKM2high, FIGO staging and postoperative radiation were the independent prognosis factors for OS and DFS(P<0.05). The verification result of the GEO dataset showed that PDK1high/PDHhigh/PKM2high was the risk factor for DFS(P<0.05). Pathological type, pelvic lymph node metastasis and PDK1high/p-PDHhigh/PKM2high could affect the DFS of those patients with postoperative radiation (P<0.05). In addition, the multivariate analysis showed that pathological type and PDK1high /p-PDHhigh/PKM2high were the independent prognosis factors for DFS(P<0.05). Conclusions: The patients of PDK1high /p-PDHhigh/PKM2high phenotype have poor prognosis and DFS with postoperative radiation, which may be a high-risk group with poor prognosis and high recurrence rate after postoperative radiotherapy of stage\u2160-\u2161B cervical cancer.This study provides a novel strategy for stratified treatment of cervical cancer.", "doi": "10.3760/cma.j.issn.0254-5098.2020.09.003", "pmid": null, "labels": {"DDLS Fellow": null, "Qiaoli Wang": null}, "xrefs": [], "notes": [], "created": "2025-11-28T12:20:26.106Z", "modified": "2025-12-05T10:19:03.338Z"}, {"entity": "publication", "iuid": "f61f862ae78c4d09a7589be5b13e9e09", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f61f862ae78c4d09a7589be5b13e9e09.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f61f862ae78c4d09a7589be5b13e9e09"}}, "title": "Massive and rapid COVID-19 testing is feasible by extraction-free SARS-CoV-2 RT-PCR.", "authors": [{"family": "Smyrlaki", "given": "Ioanna", "initials": "I"}, {"family": "Ekman", "given": "Martin", "initials": "M"}, {"family": "Lentini", "given": "Antonio", "initials": "A", "orcid": "0000-0003-1239-5495", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c5042d3005814ad0a2d1eaeee5d2de3b.json"}}, {"family": "Rufino de Sousa", "given": "Nuno", "initials": "N", "orcid": "0000-0002-0670-9788", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/366a797e8288463ea7f0c15847fb377b.json"}}, {"family": "Papanicolaou", "given": "Natali", "initials": "N"}, {"family": "Vondracek", "given": "Martin", "initials": "M"}, {"family": "Aarum", "given": "Johan", "initials": "J"}, {"family": "Safari", "given": "Hamzah", "initials": "H"}, {"family": "Muradrasoli", "given": "Shaman", "initials": "S"}, {"family": "Rothfuchs", "given": "Antonio Gigliotti", "initials": "AG", "orcid": "0000-0001-6001-7240", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9d455e35b8fa4c40baade7ec4c9ece3a.json"}}, {"family": "Albert", "given": "Jan", "initials": "J", "orcid": "0000-0001-9020-0521", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5945a41c8836474a8decf9c8b8db52ab.json"}}, {"family": "H\u00f6gberg", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0003-2715-7887", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bc6147217ff7477db7d6c14847da3d58.json"}}, {"family": "Reinius", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0002-7021-5248", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a7c1abacc8d446bf8855254246b8d899.json"}}], "type": "comparative study", "published": "2020-09-23", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "11", "issue": "1", "pages": "4812", "issn-l": "2041-1723"}, "abstract": "Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is commonly diagnosed by reverse transcription polymerase chain reaction (RT-PCR) to detect viral RNA in patient samples, but RNA extraction constitutes a major bottleneck in current testing. Methodological simplification could increase diagnostic availability and efficiency, benefitting patient care and infection control. Here, we describe methods circumventing RNA extraction in COVID-19 testing by performing RT-PCR directly on heat-inactivated or lysed samples. Our data, including benchmarking using 597 clinical patient samples and a standardised diagnostic system, demonstrate that direct RT-PCR is viable option to extraction-based tests. Using controlled amounts of active SARS-CoV-2, we confirm effectiveness of heat inactivation by plaque assay and evaluate various generic buffers as transport medium for direct RT-PCR. Significant savings in time and cost are achieved through RNA-extraction-free protocols that are directly compatible with established PCR-based testing pipelines. This could aid expansion of COVID-19 testing.", "doi": "10.1038/s41467-020-18611-5", "pmid": "32968075", "labels": {"Antonio Lentini": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC7511968"}, {"db": "pii", "key": "10.1038/s41467-020-18611-5"}], "notes": [], "created": "2025-03-28T07:11:57.060Z", "modified": "2025-03-28T07:11:57.197Z"}, {"entity": "publication", "iuid": "fd9058bfdd6d4008b9449de664b7729a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/fd9058bfdd6d4008b9449de664b7729a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/fd9058bfdd6d4008b9449de664b7729a"}}, "title": "No Assembly Required: Using BTyper3 to Assess the Congruency of a Proposed Taxonomic Framework for the Bacillus cereus Group With Historical Typing Methods.", "authors": [{"family": "Carroll", "given": "Laura M", "initials": "LM"}, {"family": "Cheng", "given": "Rachel A", "initials": "RA"}, {"family": "Kovac", "given": "Jasna", "initials": "J"}], "type": "journal article", "published": "2020-09-22", "journal": {"title": "Front Microbiol", "issn": "1664-302X", "volume": "11", "pages": "580691", "issn-l": "1664-302X"}, "abstract": "The Bacillus cereus group, also known as B. cereus sensu lato (s.l.), is a species complex comprising numerous closely related lineages, which vary in their ability to cause illness in humans and animals. The classification of B. cereus s.l. isolates into species-level taxonomic units is essential for facilitating communication between and among microbiologists, clinicians, public health officials, and industry professionals, but is not always straightforward. A recently proposed genomospecies-subspecies-biovar taxonomic framework aims to provide a standardized nomenclature for this species complex but relies heavily on whole-genome sequencing (WGS). It thus is unclear whether popular, low-cost typing methods (e.g., single- and multi-locus sequence typing) remain congruent with the proposed taxonomy. Here, we characterize 2,231 B. cereus s.l. genomes using a combination of in silico (i) average-nucleotide identity (ANI)-based genomospecies assignment, (ii) ANI-based subspecies assignment, (iii) seven-gene multi-locus sequence typing (MLST), (iv) single-locus panC group assignment, (v) rpoB allelic typing, and (vi) virulence factor detection. We show that sequence types (STs) assigned using MLST can be used for genomospecies assignment, and we provide a comprehensive list of ST/genomospecies associations. For panC group assignment, we show that an adjusted, eight-group framework is largely, albeit not perfectly, congruent with the proposed eight-genomospecies taxonomy, as panC alone may not distinguish (i) B. luti from Group II B. mosaicus and (ii) B. paramycoides from Group VI B. mycoides. We additionally provide a list of loci that capture the topology of the whole-genome B. cereus s.l. phylogeny that may be used in future sequence typing efforts. For researchers with access to WGS, MLST, and/or panC data, we showcase how our recently released software, BTyper3 (https://github.com/lmc297/BTyper3), can be used to assign B. cereus s.l. isolates to taxonomic units within this proposed framework with little-to-no user intervention or domain-specific knowledge of B. cereus s.l. taxonomy. We additionally outline a novel method for assigning B. cereus s.l. genomes to pseudo-gene flow units within proposed genomospecies. The results presented here highlight the backward-compatibility and accessibility of the recently proposed genomospecies-subspecies-biovar taxonomic framework and illustrate that WGS is not a necessity for microbiologists who want to use the proposed nomenclature effectively.", "doi": "10.3389/fmicb.2020.580691", "pmid": "33072050", "labels": {"Laura Carroll": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC7536271"}], "notes": [], "created": "2025-03-18T17:26:26.580Z", "modified": "2025-03-18T17:26:26.583Z"}, {"entity": "publication", "iuid": "42ebdd3e87e946709b4bfe2022f86208", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/42ebdd3e87e946709b4bfe2022f86208.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/42ebdd3e87e946709b4bfe2022f86208"}}, "title": "Arrangement and symmetry of the fungal E3BP-containing core of the pyruvate dehydrogenase complex.", "authors": [{"family": "Forsberg", "given": "B O", "initials": "BO", "orcid": "0000-0002-6247-4063", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/36ea51bfa66d48b7a43559c3d0eaa59f.json"}}, {"family": "Aibara", "given": "S", "initials": "S"}, {"family": "Howard", "given": "R J", "initials": "RJ", "orcid": "0000-0003-2049-3378", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ce04593b5b24aaa8978fda1447dd0bf.json"}}, {"family": "Mortezaei", "given": "N", "initials": "N"}, {"family": "Lindahl", "given": "E", "initials": "E"}], "type": "journal article", "published": "2020-09-16", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "11", "issue": "1", "pages": "4667", "issn-l": "2041-1723"}, "abstract": "The pyruvate dehydrogenase complex (PDC) is a multienzyme complex central to aerobic respiration, connecting glycolysis to mitochondrial oxidation of pyruvate. Similar to the E3-binding protein (E3BP) of mammalian PDC, PX selectively recruits E3 to the fungal PDC, but its divergent sequence suggests a distinct structural mechanism. Here, we report reconstructions of PDC from the filamentous fungus Neurospora crassa by cryo-electron microscopy, where we find protein X (PX) interior to the PDC core as opposed to substituting E2 core subunits as in mammals. Steric occlusion limits PX binding, resulting in predominantly tetrahedral symmetry, explaining previous observations in Saccharomyces cerevisiae. The PX-binding site is conserved in (and specific to) fungi, and complements possible C-terminal binding motifs in PX that are absent in mammalian E3BP. Consideration of multiple symmetries thus reveals a differential structural basis for E3BP-like function in fungal PDC.", "doi": "10.1038/s41467-020-18401-z", "pmid": "32938938", "labels": {"DDLS Fellow": "", "Bj\u00f6rn Forsberg": ""}, "xrefs": [{"db": "pmc", "key": "PMC7494870"}, {"db": "pii", "key": "10.1038/s41467-020-18401-z"}], "notes": [], "created": "2026-08-20T08:51:09.710Z", "modified": "2026-09-23T10:26:30.781Z"}, {"entity": "publication", "iuid": "ad2222a551cf4940bacbe386e1760139", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ad2222a551cf4940bacbe386e1760139.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ad2222a551cf4940bacbe386e1760139"}}, "title": "Estimating the impact of mobility patterns on COVID-19 infection rates in 11 European countries.", "authors": [{"family": "Bryant", "given": "Patrick", "initials": "P", "orcid": "0000-0003-3439-1866", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a683bcf98234ff09b2398976583b66f.json"}}, {"family": "Elofsson", "given": "Arne", "initials": "A"}], "type": "journal article", "published": "2020-09-15", "journal": {"title": "PeerJ", "issn": "2167-8359", "volume": "8", "pages": "e9879", "issn-l": "2167-8359"}, "abstract": "As governments across Europe have issued non-pharmaceutical interventions (NPIs) such as social distancing and school closing, the mobility patterns in these countries have changed. Most states have implemented similar NPIs at similar time points. However, it is likely different countries and populations respond differently to the NPIs and that these differences cause mobility patterns and thereby the epidemic development to change.\n\nWe build a Bayesian model that estimates the number of deaths on a given day dependent on changes in the basic reproductive number, R 0, due to differences in mobility patterns. We utilise mobility data from Google mobility reports using five different categories: retail and recreation, grocery and pharmacy, transit stations, workplace and residential. The importance of each mobility category for predicting changes in R 0 is estimated through the model.\n\nThe changes in mobility have a considerable overlap with the introduction of governmental NPIs, highlighting the importance of government action for population behavioural change. The shift in mobility in all categories shows high correlations with the death rates 1 month later. Reduction of movement within the grocery and pharmacy sector is estimated to account for most of the decrease in R 0.\n\nOur model predicts 3-week epidemic forecasts, using real-time observations of changes in mobility patterns, which can provide governments with direct feedback on the effects of their NPIs. The model predicts the changes in a majority of the countries accurately but overestimates the impact of NPIs in Sweden and Denmark and underestimates them in France and Belgium. We also note that the exponential nature of all epidemiological models based on the basic reproductive number, R 0 cause small errors to have extensive effects on the predicted outcome.", "doi": "10.7717/peerj.9879", "pmid": "32983643", "labels": {"Patrick Bryant": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC7500353"}, {"db": "pii", "key": "9879"}], "notes": [], "created": "2026-08-20T13:56:58.526Z", "modified": "2026-09-23T08:41:03.824Z"}, {"entity": "publication", "iuid": "9b1547c45d214302a83bd0d1211df077", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9b1547c45d214302a83bd0d1211df077.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9b1547c45d214302a83bd0d1211df077"}}, "title": "Integration of molecular profiles in a longitudinal wellness profiling cohort.", "authors": [{"family": "Tebani", "given": "Abdellah", "initials": "A", "orcid": "0000-0002-8901-2678", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/794215a6625b4fe4b652ec08bcab98ec.json"}}, {"family": "Gummesson", "given": "Anders", "initials": "A", "orcid": "0000-0003-0024-960X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1703619132e242aaad263d4ecd80a8ae.json"}}, {"family": "Zhong", "given": "Wen", "initials": "W", "orcid": "0000-0002-7422-6104", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d6ffb1140aaa42c5ac63fe76653fc63b.json"}}, {"family": "Koistinen", "given": "Ina Schuppe", "initials": "IS"}, {"family": "Lakshmikanth", "given": "Tadepally", "initials": "T", "orcid": "0000-0001-7256-5770", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/28e45f00f5f247389409f0411d412da1.json"}}, {"family": "Olsson", "given": "Lisa M", "initials": "LM", "orcid": "0000-0001-9730-1915", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ebc33ee3a5840c8b3c71ce912057c39.json"}}, {"family": "Boulund", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-3806-323X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a5c6814a31e644b9bc544d4da759a438.json"}}, {"family": "Neiman", "given": "Maja", "initials": "M"}, {"family": "Stenlund", "given": "Hans", "initials": "H"}, {"family": "Hellstr\u00f6m", "given": "Cecilia", "initials": "C", "orcid": "0000-0003-0880-5375", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2a4f6cc50f094d36a281821ca78821a0.json"}}, {"family": "Karlsson", "given": "Max J", "initials": "MJ", "orcid": "0000-0002-7000-4416", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b93284f942e44f1086616357d77267c3.json"}}, {"family": "Arif", "given": "Muhammad", "initials": "M", "orcid": "0000-0003-2261-0881", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c8ffc9889ace44e3b992816601b817e2.json"}}, {"family": "Dodig-Crnkovi\u0107", "given": "Tea", "initials": "T", "orcid": "0000-0002-2875-896X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5365873ed6a7463485fb44550a4826ec.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca58bf2d214047e0ae5e38a42a0f2808.json"}}, {"family": "Lee", "given": "Sunjae", "initials": "S"}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f46e4161be08458994efddb75ed75874.json"}}, {"family": "Chen", "given": "Yang", "initials": "Y"}, {"family": "Olin", "given": "Axel", "initials": "A", "orcid": "0000-0002-1161-4476", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b1789de408e54413b99ae1f851876a90.json"}}, {"family": "Mikes", "given": "Jaromir", "initials": "J", "orcid": "0000-0002-9941-7855", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b486baedd784487dbf3e5b7b33f950da.json"}}, {"family": "Danielsson", "given": "Hanna", "initials": "H", "orcid": "0000-0001-6959-7704", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1d92443884bf4e25ae040761708edb70.json"}}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K", "orcid": "0000-0002-0257-7554", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f4c4545bd2324b7d9b6696dab5bcb7dd.json"}}, {"family": "Jansson", "given": "Per-Anders", "initials": "PA"}, {"family": "Anger\u00e5s", "given": "Oskar", "initials": "O"}, {"family": "Huss", "given": "Mikael", "initials": "M"}, {"family": "Kjellqvist", "given": "Sanela", "initials": "S"}, {"family": "Odeberg", "given": "Jacob", "initials": "J", "orcid": "0000-0003-0996-1644", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d6abb3fc822a4cacbf1d45224f2442f5.json"}}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e213b04f8984c8eb00c68f5bc2f6a36.json"}}, {"family": "Tremaroli", "given": "Valentina", "initials": "V"}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0002-5248-8568", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a6982072448e4e8889c71fc14d214fed.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/022e140799b6466ea123319c3d70c76e.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3db33fa3edb94febb8be7927a16838d0.json"}}, {"family": "Moritz", "given": "Thomas", "initials": "T"}, {"family": "B\u00e4ckhed", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-4871-8818", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6340409dae344947868b4d6c79413cb5.json"}}, {"family": "Engstrand", "given": "Lars", "initials": "L", "orcid": "0000-0002-7713-2373", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02d8684df81e42169e613de803446fbf.json"}}, {"family": "Brodin", "given": "Petter", "initials": "P"}, {"family": "Bergstr\u00f6m", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0003-4289-5722", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d414b3352a4540a68227ca7eec73cfa6.json"}}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ea446aa574042a295d5f69437402f76.json"}}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/abbbf8193d5a4376a5c726768d039439.json"}}], "type": "journal article", "published": "2020-09-08", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "11", "issue": "1", "pages": "4487"}, "abstract": "An important aspect of precision medicine is to probe the stability in molecular profiles among healthy individuals over time. Here, we sample a longitudinal wellness cohort with 100 healthy individuals and analyze blood molecular profiles including proteomics, transcriptomics, lipidomics, metabolomics, autoantibodies and immune cell profiling, complemented with gut microbiota composition and routine clinical chemistry. Overall, our results show high variation between individuals across different molecular readouts, while the intra-individual baseline variation is low. The analyses show that each individual has a unique and stable plasma protein profile throughout the study period and that many individuals also show distinct profiles with regards to the other omics datasets, with strong underlying connections between the blood proteome and the clinical chemistry parameters. In conclusion, the results support an individual-based definition of health and show that comprehensive omics profiling in a longitudinal manner is a path forward for precision medicine.", "doi": "10.1038/s41467-020-18148-7", "pmid": "32900998", "labels": {"Adil Mardinoglu": "", "SciLifeLab Fellow": "", "Fredrik Edfors": "", "DDLS Fellow": "", "Muhammad Arif": ""}, "xrefs": [{"db": "pmc", "key": "PMC7479148"}, {"db": "pii", "key": "10.1038/s41467-020-18148-7"}], "notes": [], "created": "2020-11-30T03:11:47.205Z", "modified": "2026-09-23T07:27:43.756Z"}, {"entity": "publication", "iuid": "f0b67e6ba51042629666bf4cea37d4ff", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f0b67e6ba51042629666bf4cea37d4ff.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f0b67e6ba51042629666bf4cea37d4ff"}}, "title": "How cholesterol stiffens unsaturated lipid membranes.", "authors": [{"family": "Chakraborty", "given": "Saptarshi", "initials": "S"}, {"family": "Doktorova", "given": "Milka", "initials": "M", "orcid": "0000-0003-4366-2242", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/791384c319f04584bac8ffb21df7271f.json"}}, {"family": "Molugu", "given": "Trivikram R", "initials": "TR", "orcid": "0000-0002-3254-0445", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1003c27b1d7944f7b6e3a90888e180d3.json"}}, {"family": "Heberle", "given": "Frederick A", "initials": "FA", "orcid": "0000-0002-0424-3240", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2557f5621a0b4c87b5f4702fbc7b6bdb.json"}}, {"family": "Scott", "given": "Haden L", "initials": "HL", "orcid": "0000-0002-5778-4905", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a1e768fa75c34598807728aaf9d3a0be.json"}}, {"family": "Dzikovski", "given": "Boris", "initials": "B"}, {"family": "Nagao", "given": "Michihiro", "initials": "M", "orcid": "0000-0003-3617-251X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/164a39e5ea05484ca0f7b89d4d6e6b4b.json"}}, {"family": "Stingaciu", "given": "Laura-Roxana", "initials": "L"}, {"family": "Standaert", "given": "Robert F", "initials": "RF"}, {"family": "Barrera", "given": "Francisco N", "initials": "FN", "orcid": "0000-0002-5200-7891", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/087fafd10b3d4c7d911a489b656396e5.json"}}, {"family": "Katsaras", "given": "John", "initials": "J", "orcid": "0000-0002-8937-4177", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/732f1e95fed546efb3427a9b223a23c0.json"}}, {"family": "Khelashvili", "given": "George", "initials": "G", "orcid": "0000-0001-7235-8579", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/49b73bce7f8541fd8c959b5117bbe668.json"}}, {"family": "Brown", "given": "Michael F", "initials": "MF", "orcid": "0000-0003-4154-0241", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b57572fcc90e4033b1c705a9c030e7eb.json"}}, {"family": "Ashkar", "given": "Rana", "initials": "R", "orcid": "0000-0003-4075-2330", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b0cebcd6caec4fae986f23a3669ea406.json"}}], "type": "journal article", "published": "2020-09-08", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "issn-l": "0027-8424", "volume": "117", "issue": "36", "pages": "21896-21905"}, "abstract": "Cholesterol is an integral component of eukaryotic cell membranes and a key molecule in controlling membrane fluidity, organization, and other physicochemical parameters. It also plays a regulatory function in antibiotic drug resistance and the immune response of cells against viruses, by stabilizing the membrane against structural damage. While it is well understood that, structurally, cholesterol exhibits a densification effect on fluid lipid membranes, its effects on membrane bending rigidity are assumed to be nonuniversal; i.e., cholesterol stiffens saturated lipid membranes, but has no stiffening effect on membranes populated by unsaturated lipids, such as 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC). This observation presents a clear challenge to structure-property relationships and to our understanding of cholesterol-mediated biological functions. Here, using a comprehensive approach-combining neutron spin-echo (NSE) spectroscopy, solid-state deuterium NMR (2H NMR) spectroscopy, and molecular dynamics (MD) simulations-we report that cholesterol locally increases the bending rigidity of DOPC membranes, similar to saturated membranes, by increasing the bilayer's packing density. All three techniques, inherently sensitive to mesoscale bending fluctuations, show up to a threefold increase in effective bending rigidity with increasing cholesterol content approaching a mole fraction of 50%. Our observations are in good agreement with the known effects of cholesterol on the area-compressibility modulus and membrane structure, reaffirming membrane structure-property relationships. The current findings point to a scale-dependent manifestation of membrane properties, highlighting the need to reassess cholesterol's role in controlling membrane bending rigidity over mesoscopic length and time scales of important biological functions, such as viral budding and lipid-protein interactions.", "doi": "10.1073/pnas.2004807117", "pmid": "32843347", "labels": {"Milka Doktorova": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC7486787"}, {"db": "pii", "key": "2004807117"}], "notes": [], "created": "2024-11-27T12:20:14.878Z", "modified": "2024-11-29T10:51:40.929Z"}, {"entity": "publication", "iuid": "32cbf2082eef4e7ca0da7c4676b7d67f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/32cbf2082eef4e7ca0da7c4676b7d67f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/32cbf2082eef4e7ca0da7c4676b7d67f"}}, "title": "Genome sequence of segmented filamentous bacteria present in the human intestine.", "authors": [{"family": "Jonsson", "given": "Hans", "initials": "H"}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW", "orcid": "0000-0001-5432-1764", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/246ed7b405dd4c3f9ec5e7ff9f1d3ade.json"}}, {"family": "Sundh", "given": "John", "initials": "J"}, {"family": "Lundin", "given": "Eva", "initials": "E"}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cc9be99ec6ca47ed8a805ebb4db7c168.json"}}], "type": "journal article", "published": "2020-09-04", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "3", "issue": "1", "pages": "485", "issn-l": "2399-3642"}, "abstract": "Segmented filamentous bacteria (SFB) are unique immune modulatory bacteria colonizing the small intestine of a variety of animals in a host-specific manner. SFB exhibit filamentous growth and attach to the host's intestinal epithelium, offering a physical route of interaction. SFB affect functions of the host immune system, among them IgA production and T-cell maturation. Until now, no human-specific SFB genome has been reported. Here, we report the metagenomic reconstruction of an SFB genome from a human ileostomy sample. Phylogenomic analysis clusters the genome with SFB genomes from mouse, rat and turkey, but the genome is genetically distinct, displaying 65-71% average amino acid identity to the others. By screening human faecal metagenomic datasets, we identified individuals carrying sequences identical to the new SFB genome. We thus conclude that a unique SFB variant exists in humans and foresee a renewed interest in the elucidation of SFB functionality in this environment.", "doi": "10.1038/s42003-020-01214-7", "pmid": "32887924", "labels": {"Luisa Hugerth": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC7474095"}, {"db": "pii", "key": "10.1038/s42003-020-01214-7"}], "notes": [], "created": "2022-11-08T06:59:09.556Z", "modified": "2026-09-23T08:43:51.422Z"}, {"entity": "publication", "iuid": "b1f782005f604a23933c0795c24aa432", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b1f782005f604a23933c0795c24aa432.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b1f782005f604a23933c0795c24aa432"}}, "title": "Twentieth-century emergence of antimicrobial resistant human- and bovine-associated Salmonella enterica serotype Typhimurium lineages in New York State.", "authors": [{"family": "Carroll", "given": "Laura M", "initials": "LM", "orcid": "0000-0002-3677-0192", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02112eccb0664819af916a3c3dc79daa.json"}}, {"family": "Huisman", "given": "Jana S", "initials": "JS", "orcid": "0000-0002-1782-8109", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0b855a6c7cb54933a4db0316b6bc6e18.json"}}, {"family": "Wiedmann", "given": "Martin", "initials": "M"}], "type": "journal article", "published": "2020-09-02", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "14428", "issn-l": "2045-2322"}, "abstract": "Salmonella enterica serotype Typhimurium (S. Typhimurium) boasts a broad host range and can be transmitted between livestock and humans. While members of this serotype can acquire resistance to antimicrobials, the temporal dynamics of this acquisition is not well understood. Using New York State (NYS) and its dairy cattle farms as a model system, 87 S. Typhimurium strains isolated from 1999 to 2016 from either human clinical or bovine-associated sources in NYS were characterized using whole-genome sequencing. More than 91% of isolates were classified into one of four major lineages, two of which were largely susceptible to antimicrobials but showed sporadic antimicrobial resistance (AMR) gene acquisition, and two that were largely multidrug-resistant (MDR). All four lineages clustered by presence and absence of elements in the pan-genome. The two MDR lineages, one of which resembled S. Typhimurium DT104, were predicted to have emerged circa 1960 and 1972. The two largely susceptible lineages emerged earlier, but showcased sporadic AMR determinant acquisition largely after 1960, including acquisition of cephalosporin resistance-conferring genes after 1985. These results confine the majority of AMR acquisition events in NYS S. Typhimurium to the twentieth century, largely within the era of antibiotic usage.", "doi": "10.1038/s41598-020-71344-9", "pmid": "32879348", "labels": {"Laura Carroll": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC7467927"}, {"db": "pii", "key": "10.1038/s41598-020-71344-9"}], "notes": [], "created": "2025-03-18T17:26:09.723Z", "modified": "2025-03-18T17:26:09.783Z"}, {"entity": "publication", "iuid": "f63cf53d1fa14179a632937ee7f514ad", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f63cf53d1fa14179a632937ee7f514ad.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f63cf53d1fa14179a632937ee7f514ad"}}, "title": "The past and future human impact on mammalian diversity.", "authors": [{"family": "Andermann", "given": "Tobias", "initials": "T", "orcid": "0000-0002-0932-1623", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dfff478dfcfc43ddbd40bb1bafbcb0a7.json"}}, {"family": "Faurby", "given": "S\u00f8ren", "initials": "S"}, {"family": "Turvey", "given": "Samuel T", "initials": "ST", "orcid": "0000-0002-3717-4800", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/39f5e762bc454c1c93be257042c05def.json"}}, {"family": "Antonelli", "given": "Alexandre", "initials": "A", "orcid": "0000-0003-1842-9297", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1de98df1bb2140fc9666507cb2fb5614.json"}}, {"family": "Silvestro", "given": "Daniele", "initials": "D"}], "type": "journal article", "published": "2020-09-00", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "6", "issue": "36", "issn-l": "2375-2548"}, "abstract": "To understand the current biodiversity crisis, it is crucial to determine how humans have affected biodiversity in the past. However, the extent of human involvement in species extinctions from the Late Pleistocene onward remains contentious. Here, we apply Bayesian models to the fossil record to estimate how mammalian extinction rates have changed over the past 126,000 years, inferring specific times of rate increases. We specifically test the hypothesis of human-caused extinctions by using posterior predictive methods. We find that human population size is able to predict past extinctions with 96% accuracy. Predictors based on past climate, in contrast, perform no better than expected by chance, suggesting that climate had a negligible impact on global mammal extinctions. Based on current trends, we predict for the near future a rate escalation of unprecedented magnitude. Our results provide a comprehensive assessment of the human impact on past and predicted future extinctions of mammals.", "doi": "10.1126/sciadv.abb2313", "pmid": "32917612", "labels": {"Tobias Andermann": null, "DDLS Fellow": null}, "xrefs": [{"db": "pii", "key": "6/36/eabb2313"}, {"db": "pmc", "key": "PMC7473673"}], "notes": [], "created": "2022-11-11T09:08:42.192Z", "modified": "2022-11-11T09:08:42.302Z"}, {"entity": "publication", "iuid": "48085d36a8e64ee3885505ea6ba80e8b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/48085d36a8e64ee3885505ea6ba80e8b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/48085d36a8e64ee3885505ea6ba80e8b"}}, "title": "SAMHD1 phosphorylation and cytoplasmic relocalization after human cytomegalovirus infection limits its antiviral activity.", "authors": [{"family": "De Meo", "given": "Simone", "initials": "S", "orcid": "0000-0001-7542-8077", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/45816f4396764f2fbf97673e37834fcd.json"}}, {"family": "Dell'Oste", "given": "Valentina", "initials": "V"}, {"family": "Molfetta", "given": "Rosa", "initials": "R", "orcid": "0000-0003-2904-6371", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6203296a7de648838c9ccec8b91be518.json"}}, {"family": "Tassinari", "given": "Valentina", "initials": "V"}, {"family": "Lotti", "given": "Lavinia Vittoria", "initials": "LV", "orcid": "0000-0002-5114-6953", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6cca542320a24996ad80047cd28a689c.json"}}, {"family": "Vespa", "given": "Simone", "initials": "S", "orcid": "0000-0001-6146-9302", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/76b512d912dd4e268df765161735daa4.json"}}, {"family": "Pignoloni", "given": "Benedetta", "initials": "B"}, {"family": "Covino", "given": "Daniela Angela", "initials": "DA"}, {"family": "Fantuzzi", "given": "Laura", "initials": "L", "orcid": "0000-0002-0869-2596", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/04696ef921a34f8486dd738dbe6c1c5e.json"}}, {"family": "Bona", "given": "Roberta", "initials": "R", "orcid": "0000-0002-9226-3734", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/61fb350bc6ee4dc4bdbb8c9b4e6f2fe7.json"}}, {"family": "Zingoni", "given": "Alessandra", "initials": "A", "orcid": "0000-0003-0906-1566", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/76c0f8c614e74dbdb41bce0e656fd6f3.json"}}, {"family": "Nardone", "given": "Ilaria", "initials": "I", "orcid": "0000-0002-3868-3666", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8416dfb4905b4e98a654f2f5542a3e80.json"}}, {"family": "Biolatti", "given": "Matteo", "initials": "M", "orcid": "0000-0001-7675-0762", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0094a40b253241209e6f0790165d37f2.json"}}, {"family": "Coscia", "given": "Alessandra", "initials": "A"}, {"family": "Paolini", "given": "Rossella", "initials": "R", "orcid": "0000-0001-7605-1531", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4ffbaf0e5ed14356b1cb42470824be69.json"}}, {"family": "Benkirane", "given": "Monsef", "initials": "M"}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Sandalova", "given": "Tatyana", "initials": "T"}, {"family": "Achour", "given": "Adnane", "initials": "A", "orcid": "0000-0003-0432-710X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/65fba324156a4fcbafbe636e642587a9.json"}}, {"family": "Hiscott", "given": "John", "initials": "J"}, {"family": "Landolfo", "given": "Santo", "initials": "S"}, {"family": "Santoni", "given": "Angela", "initials": "A"}, {"family": "Cerboni", "given": "Cristina", "initials": "C", "orcid": "0000-0002-0371-9534", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/539ba8ca7737405db5e61f3e608a235a.json"}}], "type": "journal article", "published": "2020-09-00", "journal": {"title": "PLoS Pathog", "issn": "1553-7374", "volume": "16", "issue": "9", "pages": "e1008855", "issn-l": "1553-7366"}, "abstract": "SAMHD1 is a host restriction factor that functions to restrict both retroviruses and DNA viruses, based on its nuclear deoxynucleotide triphosphate (dNTP) hydrolase activity that limits availability of intracellular dNTP pools. In the present study, we demonstrate that SAMHD1 expression was increased following human cytomegalovirus (HCMV) infection, with only a modest effect on infectious virus production. SAMHD1 was rapidly phosphorylated at residue T592 after infection by cellular cyclin-dependent kinases, especially Cdk2, and by the viral kinase pUL97, resulting in a significant fraction of phosho-SAMHD1 being relocalized to the cytoplasm of infected fibroblasts, in association with viral particles and dense bodies. Thus, our findings indicate that HCMV-dependent SAMHD1 cytoplasmic delocalization and inactivation may represent a potential novel mechanism of HCMV evasion from host antiviral restriction activities.", "doi": "10.1371/journal.ppat.1008855", "pmid": "32986788", "labels": {"Fredrik Edfors": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC7544099"}, {"db": "pii", "key": "PPATHOGENS-D-19-02166"}], "notes": [], "created": "2026-08-20T12:44:51.406Z", "modified": "2026-09-23T10:57:50.188Z"}, {"entity": "publication", "iuid": "dbd8cd404e224b3eb87e8a59bde4354d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/dbd8cd404e224b3eb87e8a59bde4354d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/dbd8cd404e224b3eb87e8a59bde4354d"}}, "title": "Index hopping on the Illumina HiseqX platform and its consequences for ancient DNA studies.", "authors": [{"family": "van der Valk", "given": "Tom", "initials": "T", "orcid": "0000-0001-6582-3452", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/aa0dba3cc12143cba213f7f3a052216c.json"}}, {"family": "Vezzi", "given": "Francesco", "initials": "F"}, {"family": "Ormestad", "given": "Mattias", "initials": "M"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L"}, {"family": "Guschanski", "given": "Katerina", "initials": "K", "orcid": "0000-0002-8493-5457", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4e062373c6bc46b98e56215d3ec89eeb.json"}}], "type": "journal article", "published": "2020-09-00", "journal": {"title": "Mol Ecol Resour", "issn": "1755-0998", "volume": "20", "issue": "5", "pages": "1171-1181", "issn-l": "1755-098X"}, "abstract": "The high-throughput capacities of the Illumina sequencing platforms and the possibility to label samples individually have encouraged wide use of sample multiplexing. However, this practice results in read misassignment (usually <1%) across samples sequenced on the same lane. Alarmingly high rates of read misassignment of up to 10% were reported for lllumina sequencing machines with exclusion amplification chemistry. This may make use of these platforms prohibitive, particularly in studies that rely on low-quantity and low-quality samples, such as historical and archaeological specimens. Here, we use barcodes, short sequences that are ligated to both ends of the DNA insert, to directly quantify the rate of index hopping in 100-year old museum-preserved gorilla (Gorilla beringei) samples. Correcting for multiple sources of noise, we identify on average 0.470% of reads containing a hopped index. We show that sample-specific quantity of misassigned reads depends on the number of reads that any given sample contributes to the total sequencing pool, so that samples with few sequenced reads receive the greatest proportion of misassigned reads. This particularly affects ancient DNA samples, as these frequently differ in their DNA quantity and endogenous content. Through simulations we show that even low rates of index hopping, as reported here, can lead to biases in ancient DNA studies when multiplexing samples with vastly different quantities of endogenous material.", "doi": "10.1111/1755-0998.13009", "pmid": "30848092", "labels": {"DDLS Fellow": "", "Tom van der Valk": ""}, "xrefs": [], "notes": [], "created": "2026-09-23T13:48:10.945Z", "modified": "2026-09-23T13:48:10.980Z"}, {"entity": "publication", "iuid": "45beee041496408c8f8f037bf9047c0a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/45beee041496408c8f8f037bf9047c0a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/45beee041496408c8f8f037bf9047c0a"}}, "title": "Enzalutamide, an Androgen Receptor Antagonist, Enhances Myeloid Cell-Mediated Immune Suppression and Tumor Progression.", "authors": [{"family": "Consiglio", "given": "Camila R", "initials": "CR", "orcid": "0000-0002-8901-2328", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a786e29de11b41dd9da2b680ad5b351f.json"}}, {"family": "Udartseva", "given": "Olga", "initials": "O", "orcid": "0000-0003-2896-2300", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6cd3829d41734d99a87fb56e8434a377.json"}}, {"family": "Ramsey", "given": "Kimberly D", "initials": "KD"}, {"family": "Bush", "given": "Chioma", "initials": "C"}, {"family": "Gollnick", "given": "Sandra O", "initials": "SO"}], "type": "journal article", "published": "2020-09-00", "journal": {"title": "Cancer Immunol Res", "issn": "2326-6074", "volume": "8", "issue": "9", "pages": "1215-1227", "issn-l": "2326-6066"}, "abstract": "Androgen receptor (AR) antagonism increases overall survival in prostate cancer; however, treatment failure leads to tumor progression and patient mortality. The effect of AR modulation on AR+ nontumor cells that participate in the resistance to AR antagonism is poorly understood. Tumor-infiltrating myeloid cells, including macrophages and myeloid-derived suppressor cells (MDSC), express AR and promote prostate cancer progression. We investigated how AR antagonism affects myeloid cell function and metabolism in an AR-independent murine colon tumor model. Systemic blockade of AR with enzalutamide resulted in increased MC-38 tumor growth in vivo even when AR was knocked out of MC-38 tumor cells. MC-38 tumor growth was also increased when immunocompetent, but not immunodeficient, mice were coinjected with tumor cells and MDSCs treated with enzalutamide or lacking AR, suggesting that AR regulated the ability of MDSCs to suppress adaptive immunity. Myeloid AR-knockout male mice also displayed increased growth of TRAMP C2 prostate tumors when compared with wild type. Inhibition of AR signaling suppressed mitochondrial respiration in myeloid cells via MPC/AMPK signaling pathways; suppression of mitochondrial respiration increased MDSC tumor-promoting functions. Our work showed that AR regulates a tumor-promoting myeloid cell phenotype and influences myeloid cell metabolism. These findings suggest that tumor resistance to AR antagonism is due, in part, to changes in myeloid cell function and metabolism.", "doi": "10.1158/2326-6066.CIR-19-0371", "pmid": "32661092", "labels": {"Camila Consiglio": null, "DDLS Fellow": null}, "xrefs": [{"db": "mid", "key": "NIHMS1610095"}, {"db": "pmc", "key": "PMC7484281"}, {"db": "pii", "key": "2326-6066.CIR-19-0371"}], "notes": [], "created": "2023-11-22T09:17:11.207Z", "modified": "2023-11-22T09:17:11.302Z"}, {"entity": "publication", "iuid": "13c5968f1eb942638e9eba5e3a07608a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/13c5968f1eb942638e9eba5e3a07608a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/13c5968f1eb942638e9eba5e3a07608a"}}, "title": "Author Correction: Analysis of the Human Protein Atlas Image Classification competition.", "authors": [{"family": "Ouyang", "given": "Wei", "initials": "W", "orcid": "0000-0002-0291-926X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56f601e1d1c6448aab0c3a1e3cffdbfc.json"}}, {"family": "Winsnes", "given": "Casper F", "initials": "CF", "orcid": "0000-0002-0028-5865", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/edeb3bc6c95d4185bf2098bf1e4a5e3c.json"}}, {"family": "Hjelmare", "given": "Martin", "initials": "M", "orcid": "0000-0001-7375-9681", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b13d6d89bd3a43eab43eee98539ed4ad.json"}}, {"family": "Cesnik", "given": "Anthony J", "initials": "AJ"}, {"family": "\u00c5kesson", "given": "Lovisa", "initials": "L"}, {"family": "Xu", "given": "Hao", "initials": "H"}, {"family": "Sullivan", "given": "Devin P", "initials": "DP"}, {"family": "Dai", "given": "Shubin", "initials": "S"}, {"family": "Lan", "given": "Jun", "initials": "J"}, {"family": "Jinmo", "given": "Park", "initials": "P"}, {"family": "Galib", "given": "Shaikat M", "initials": "SM"}, {"family": "Henkel", "given": "Christof", "initials": "C"}, {"family": "Hwang", "given": "Kevin", "initials": "K"}, {"family": "Poplavskiy", "given": "Dmytro", "initials": "D"}, {"family": "Tunguz", "given": "Bojan", "initials": "B"}, {"family": "Wolfinger", "given": "Russel D", "initials": "RD"}, {"family": "Gu", "given": "Yinzheng", "initials": "Y"}, {"family": "Li", "given": "Chuanpeng", "initials": "C"}, {"family": "Xie", "given": "Jinbin", "initials": "J"}, {"family": "Buslov", "given": "Dmitry", "initials": "D"}, {"family": "Fironov", "given": "Sergei", "initials": "S"}, {"family": "Kiselev", "given": "Alexander", "initials": "A"}, {"family": "Panchenko", "given": "Dmytro", "initials": "D"}, {"family": "Cao", "given": "Xuan", "initials": "X"}, {"family": "Wei", "given": "Runmin", "initials": "R"}, {"family": "Wu", "given": "Yuanhao", "initials": "Y"}, {"family": "Zhu", "given": "Xun", "initials": "X"}, {"family": "Tseng", "given": "Kuan-Lun", "initials": "KL"}, {"family": "Gao", "given": "Zhifeng", "initials": "Z"}, {"family": "Ju", "given": "Cheng", "initials": "C"}, {"family": "Yi", "given": "Xiaohan", "initials": "X"}, {"family": "Zheng", "given": "Hongdong", "initials": "H"}, {"family": "Kappel", "given": "Constantin", "initials": "C"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb07e6d0122c4528a927c1fe922e3bc8.json"}}], "type": "published erratum", "published": "2020-09-00", "journal": {"title": "Nat. Methods", "issn": "1548-7105", "volume": "17", "issue": "9", "pages": "948", "issn-l": "1548-7091"}, "abstract": "An amendment to this paper has been published and can be accessed via a link at the top of the paper.", "doi": "10.1038/s41592-020-0937-2", "pmid": "32760039", "labels": {"DDLS Fellow": "", "Wei Ouyang": ""}, "xrefs": [{"db": "pmc", "key": "PMC7462740"}, {"db": "pii", "key": "10.1038/s41592-020-0937-2"}], "notes": [], "created": "2026-08-20T09:02:34.856Z", "modified": "2026-09-23T14:33:22.680Z"}, {"entity": "publication", "iuid": "ae8a1b1bfac54dbf833b3166914ccc86", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ae8a1b1bfac54dbf833b3166914ccc86.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ae8a1b1bfac54dbf833b3166914ccc86"}}, "title": "Systems-Level Immunomonitoring from Acute to Recovery Phase of Severe COVID-19.", "authors": [{"family": "Rodriguez", "given": "Lucie", "initials": "L"}, {"family": "Pekkarinen", "given": "Pirkka T", "initials": "PT"}, {"family": "Lakshmikanth", "given": "Tadepally", "initials": "T"}, {"family": "Tan", "given": "Ziyang", "initials": "Z"}, {"family": "Consiglio", "given": "Camila Rosat", "initials": "CR"}, {"family": "Pou", "given": "Christian", "initials": "C"}, {"family": "Chen", "given": "Yang", "initials": "Y"}, {"family": "Mugabo", "given": "Constantin Habimana", "initials": "CH"}, {"family": "Nguyen", "given": "Ngoc Anh", "initials": "NA"}, {"family": "Nowlan", "given": "Kirsten", "initials": "K"}, {"family": "Strandin", "given": "Tomas", "initials": "T"}, {"family": "Levanov", "given": "Lev", "initials": "L"}, {"family": "Mikes", "given": "Jaromir", "initials": "J"}, {"family": "Wang", "given": "Jun", "initials": "J"}, {"family": "Kantele", "given": "Anu", "initials": "A"}, {"family": "Hepojoki", "given": "Jussi", "initials": "J"}, {"family": "Vapalahti", "given": "Olli", "initials": "O"}, {"family": "Heinonen", "given": "Santtu", "initials": "S"}, {"family": "Kek\u00e4l\u00e4inen", "given": "Eliisa", "initials": "E"}, {"family": "Brodin", "given": "Petter", "initials": "P"}], "type": "journal article", "published": "2020-08-25", "journal": {"title": "Cell Rep Med", "issn": "2666-3791", "volume": "1", "issue": "5", "pages": "100078", "issn-l": null}, "abstract": "Severe disease of SARS-CoV-2 is characterized by vigorous inflammatory responses in the lung, often with a sudden onset after 5-7 days of stable disease. Efforts to modulate this hyperinflammation and the associated acute respiratory distress syndrome rely on the unraveling of the immune cell interactions and cytokines that drive such responses. Given that every patient is captured at different stages of infection, longitudinal monitoring of the immune response is critical and systems-level analyses are required to capture cellular interactions. Here, we report on a systems-level blood immunomonitoring study of 37 adult patients diagnosed with COVID-19 and followed with up to 14 blood samples from acute to recovery phases of the disease. We describe an IFN\u03b3-eosinophil axis activated before lung hyperinflammation and changes in cell-cell co-regulation during different stages of the disease. We also map an immune trajectory during recovery that is shared among patients with severe COVID-19.", "doi": "10.1016/j.xcrm.2020.100078", "pmid": "32838342", "labels": {"Camila Consiglio": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC7405891"}, {"db": "pii", "key": "S2666-3791(20)30099-9"}], "notes": [], "created": "2023-11-22T09:17:05.273Z", "modified": "2026-09-23T06:44:45.495Z"}, {"entity": "publication", "iuid": "9cefd69d86cd41c8a9462265518dc60d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9cefd69d86cd41c8a9462265518dc60d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9cefd69d86cd41c8a9462265518dc60d"}}, "title": "Cereulide Synthetase Acquisition and Loss Events within the Evolutionary History of Group III Bacillus cereus Sensu Lato Facilitate the Transition between Emetic and Diarrheal Foodborne Pathogens.", "authors": [{"family": "Carroll", "given": "Laura M", "initials": "LM"}, {"family": "Wiedmann", "given": "Martin", "initials": "M", "orcid": "0000-0002-4168-5662", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ff5ceeea60684abeb83951c53f7b6e31.json"}}], "type": "journal article", "published": "2020-08-25", "journal": {"title": "MBio", "issn": "2150-7511", "volume": "11", "issue": "4", "issn-l": null}, "abstract": "Cereulide-producing members of Bacillus cereussensu lato group III (also known as emetic B. cereus) possess cereulide synthetase, a plasmid-encoded, nonribosomal peptide synthetase encoded by the ces gene cluster. Despite the documented risks that cereulide-producing strains pose to public health, the level of genomic diversity encompassed by emetic B. cereus has never been evaluated at a whole-genome scale. Here, we employ a phylogenomic approach to characterize group III B. cereussensu lato genomes which possess ces (ces positive) alongside their closely related, ces-negative counterparts (i) to assess the genomic diversity encompassed by emetic B. cereus and (ii) to identify potential ces loss and/or gain events within the evolutionary history of the high-risk and medically relevant sequence type (ST) 26 lineage often associated with emetic foodborne illness. Using all publicly available ces-positive group III B. cereussensu lato genomes and the ces-negative genomes interspersed among them (n = 159), we show that emetic B. cereus is not clonal; rather, multiple lineages within group III harbor cereulide-producing strains, all of which share an ancestor incapable of producing cereulide (posterior probability = 0.86 to 0.89). Members of ST 26 share an ancestor that existed circa 1748 (95% highest posterior density [HPD] interval = 1246.89 to 1915.64) and first acquired the ability to produce cereulide before 1876 (95% HPD = 1641.43 to 1946.70). Within ST 26 alone, two subsequent ces gain events were observed, as well as three ces loss events, including among isolates responsible for B. cereussensu lato toxicoinfection (i.e., \"diarrheal\" illness).IMPORTANCEB. cereus is responsible for thousands of cases of foodborne disease each year worldwide, causing two distinct forms of illness: (i) intoxication via cereulide (i.e., emetic syndrome) or (ii) toxicoinfection via multiple enterotoxins (i.e., diarrheal syndrome). Here, we show that emetic B. cereus is not a clonal, homogenous unit that resulted from a single cereulide synthetase gain event followed by subsequent proliferation; rather, cereulide synthetase acquisition and loss is a dynamic, ongoing process that occurs across lineages, allowing some group III B. cereussensu lato populations to oscillate between diarrheal and emetic foodborne pathogens over the course of their evolutionary histories. We also highlight the care that must be taken when selecting a reference genome for whole-genome sequencing-based investigation of emetic B. cereussensu lato outbreaks, since some reference genome selections can lead to a confounding loss of resolution and potentially hinder epidemiological investigations.", "doi": "10.1128/mBio.01263-20", "pmid": "32843545", "labels": {"Laura Carroll": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC7448271"}, {"db": "pii", "key": "mBio.01263-20"}, {"db": "figshare", "key": "10.6084/m9.figshare.c.5057276.v1"}], "notes": [], "created": "2025-03-18T17:25:56.128Z", "modified": "2025-03-18T17:25:56.177Z"}, {"entity": "publication", "iuid": "eea5778841b54559b6d05d20ef58b67b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/eea5778841b54559b6d05d20ef58b67b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/eea5778841b54559b6d05d20ef58b67b"}}, "title": "Mapping DNA Methylation in Mammals: The State of the Art.", "authors": [{"family": "Lentini", "given": "Antonio", "initials": "A"}, {"family": "Nestor", "given": "Colm E", "initials": "CE"}], "type": "journal article", "published": "2020-08-22", "journal": {"title": "Methods in molecular biology (Clifton, N.J.)", "issn": "1940-6029", "volume": "2198", "pages": "37-50", "issn-l": "1064-3745"}, "abstract": "A complete understanding of the dynamics and function of cytosine modifications in mammalian biology is lacking. Central to achieving this understanding is the availability of techniques that permit sensitive and specific genome-wide mapping of DNA modifications in mammalian DNA. The last decade has seen the development of a vast arsenal of novel profiling approaches enabling epigeneticists to tackle research questions that were previously out of reach. Here, we review the techniques currently available for profiling DNA modifications in mammals, discuss their strengths and weaknesses, and speculate on the future direction of DNA modification profiling technologies.", "doi": "10.1007/978-1-0716-0876-0_4", "pmid": "32822021", "labels": {"Antonio Lentini": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2025-03-28T07:10:02.647Z", "modified": "2025-03-28T07:10:02.661Z"}, {"entity": "publication", "iuid": "2dbd1673c7bf4f8cb656ca65fe73429a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/2dbd1673c7bf4f8cb656ca65fe73429a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/2dbd1673c7bf4f8cb656ca65fe73429a"}}, "title": "Analyzing DNA-Immunoprecipitation Sequencing Data.", "authors": [{"family": "Lentini", "given": "Antonio", "initials": "A"}, {"family": "Nestor", "given": "Colm E", "initials": "CE"}], "type": "journal article", "published": "2020-08-22", "journal": {"title": "Methods in molecular biology (Clifton, N.J.)", "issn": "1940-6029", "volume": "2198", "pages": "431-439", "issn-l": "1064-3745"}, "abstract": "Genome-wide profiling of DNA modifications has advanced our understanding of epigenetics in mammalian biology. Whereas several different methods for profiling DNA modifications have been developed over the last decade, DNA-immunoprecipitation coupled with high-throughput sequencing (DIP-seq) has proven a particularly adaptable and cost-effective approach. DIP-seq was especially valuable in initial studies of the more recently discovered DNA modifications, 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine. As an enrichment-based profiling method, analysis of DIP-seq data poses several unique, and often unappreciated bioinformatics challenges, which if unmet, can profoundly affect the results and conclusions drawn from the data. Here, we outline key considerations in both the design of DIP-seq assays and analysis of DIP-seq data to ensure the accuracy and reproducibility of DIP-seq based studies.", "doi": "10.1007/978-1-0716-0876-0_31", "pmid": "32822048", "labels": {"Antonio Lentini": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2025-03-28T07:10:00.642Z", "modified": "2025-03-28T07:10:00.664Z"}, {"entity": "publication", "iuid": "b5101c6e4a424c21887e02cf667687d0", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b5101c6e4a424c21887e02cf667687d0.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b5101c6e4a424c21887e02cf667687d0"}}, "title": "Natural killer cell immunotypes related to COVID-19 disease severity.", "authors": [{"family": "Maucourant", "given": "Christopher", "initials": "C", "orcid": "0000-0003-1033-2992", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e903a1fde900467ea0fd0c86d26f6d50.json"}}, {"family": "Filipovic", "given": "Iva", "initials": "I", "orcid": "0000-0002-8166-5500", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b10709e4011e4fdd835e08d778fc9a5f.json"}}, {"family": "Ponzetta", "given": "Andrea", "initials": "A", "orcid": "0000-0003-3224-802X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b0d0e3d55efb499bb95adb86f1604082.json"}}, {"family": "Aleman", "given": "Soo", "initials": "S"}, {"family": "Cornillet", "given": "Martin", "initials": "M", "orcid": "0000-0001-7981-0927", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8f2b2dde303f445e8c47f726a9dbf6ae.json"}}, {"family": "Hertwig", "given": "Laura", "initials": "L", "orcid": "0000-0002-1170-0948", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9f7b21346a514d11ae1dbcb86cb02d44.json"}}, {"family": "Strunz", "given": "Benedikt", "initials": "B"}, {"family": "Lentini", "given": "Antonio", "initials": "A", "orcid": "0000-0003-1239-5495", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c5042d3005814ad0a2d1eaeee5d2de3b.json"}}, {"family": "Reinius", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Brownlie", "given": "Demi", "initials": "D", "orcid": "0000-0001-5932-6425", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e619dde6ba3945f9b9c4a543aa3d11eb.json"}}, {"family": "Cuapio", "given": "Angelica", "initials": "A"}, {"family": "Ask", "given": "Eivind Heggernes", "initials": "EH", "orcid": "0000-0001-8655-1433", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/61039bb3de864706b99d4f7ba9f99e3b.json"}}, {"family": "Hull", "given": "Ryan M", "initials": "RM", "orcid": "0000-0001-7153-4198", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4adfcc02af0b422aa81206bf3c56471d.json"}}, {"family": "Haroun-Izquierdo", "given": "Alvaro", "initials": "A", "orcid": "0000-0003-4557-3606", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3ce9327b5d1b4c3f9fc91fd289cea6a8.json"}}, {"family": "Schaffer", "given": "Marie", "initials": "M"}, {"family": "Klingstr\u00f6m", "given": "Jonas", "initials": "J", "orcid": "0000-0001-9076-1441", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6265be732af0469d9d58bf5a46e8cf7d.json"}}, {"family": "Folkesson", "given": "Elin", "initials": "E"}, {"family": "Buggert", "given": "Marcus", "initials": "M", "orcid": "0000-0003-0633-1719", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cf1bb88eef764f8bb81bdd6d8a231113.json"}}, {"family": "Sandberg", "given": "Johan K", "initials": "JK", "orcid": "0000-0002-6275-0750", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d33bfbd945e647ac82e2d2699df02cb9.json"}}, {"family": "Eriksson", "given": "Lars I", "initials": "LI"}, {"family": "Rooyackers", "given": "Olav", "initials": "O", "orcid": "0000-0002-3391-5448", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7e57f563d96a4023a4b2fccc266ca542.json"}}, {"family": "Ljunggren", "given": "Hans-Gustaf", "initials": "HG"}, {"family": "Malmberg", "given": "Karl-Johan", "initials": "KJ"}, {"family": "Micha\u00eblsson", "given": "Jakob", "initials": "J"}, {"family": "Marquardt", "given": "Nicole", "initials": "N", "orcid": "0000-0003-3186-4752", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/11381386e9534479912c2875dbd16376.json"}}, {"family": "Hammer", "given": "Quirin", "initials": "Q", "orcid": "0000-0003-2968-6061", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bd1d59f056c149db98064ff1b0b99ed6.json"}}, {"family": "Str\u00e5lin", "given": "Kristoffer", "initials": "K", "orcid": "0000-0002-8801-3169", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3dcfabbce4304392a6ff67409434745b.json"}}, {"family": "Bj\u00f6rkstr\u00f6m", "given": "Niklas K", "initials": "NK", "orcid": "0000-0002-0967-076X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ded8cd7038b4c42ac16f62f89b9229c.json"}}, {"family": "Karolinska COVID-19 Study Group", "given": "", "initials": ""}], "type": "journal article", "published": "2020-08-21", "journal": {"title": "Sci Immunol", "issn": "2470-9468", "volume": "5", "issue": "50", "issn-l": "2470-9468"}, "abstract": "Understanding innate immune responses in COVID-19 is important to decipher mechanisms of host responses and interpret disease pathogenesis. Natural killer (NK) cells are innate effector lymphocytes that respond to acute viral infections but might also contribute to immunopathology. Using 28-color flow cytometry, we here reveal strong NK cell activation across distinct subsets in peripheral blood of COVID-19 patients. This pattern was mirrored in scRNA-seq signatures of NK cells in bronchoalveolar lavage from COVID-19 patients. Unsupervised high-dimensional analysis of peripheral blood NK cells furthermore identified distinct NK cell immunotypes that were linked to disease severity. Hallmarks of these immunotypes were high expression of perforin, NKG2C, and Ksp37, reflecting increased presence of adaptive NK cells in circulation of patients with severe disease. Finally, arming of CD56bright NK cells was observed across COVID-19 disease states, driven by a defined protein-protein interaction network of inflammatory soluble factors. This study provides a detailed map of the NK cell activation landscape in COVID-19 disease.", "doi": "10.1126/sciimmunol.abd6832", "pmid": "32826343", "labels": {"Antonio Lentini": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC7665314"}, {"db": "pii", "key": "5/50/eabd6832"}], "notes": [], "created": "2025-03-28T07:11:59.324Z", "modified": "2026-09-23T06:33:00.738Z"}, {"entity": "publication", "iuid": "c3ead3663944482e940f569a80c26c8e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c3ead3663944482e940f569a80c26c8e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c3ead3663944482e940f569a80c26c8e"}}, "title": "Direct label-free imaging of nanodomains in biomimetic and biological membranes by cryogenic electron microscopy.", "authors": [{"family": "Heberle", "given": "Frederick A", "initials": "FA", "orcid": "0000-0002-0424-3240", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2557f5621a0b4c87b5f4702fbc7b6bdb.json"}}, {"family": "Doktorova", "given": "Milka", "initials": "M", "orcid": "0000-0003-4366-2242", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/791384c319f04584bac8ffb21df7271f.json"}}, {"family": "Scott", "given": "Haden L", "initials": "HL", "orcid": "0000-0002-5778-4905", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a1e768fa75c34598807728aaf9d3a0be.json"}}, {"family": "Skinkle", "given": "Allison D", "initials": "AD"}, {"family": "Waxham", "given": "M Neal", "initials": "MN", "orcid": "0000-0003-4801-1190", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ba2f5e1eeb4144ecbf0ef9a7bb01cdae.json"}}, {"family": "Levental", "given": "Ilya", "initials": "I", "orcid": "0000-0002-1206-9545", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7fe40c2b810348cab78616402d4d1f1f.json"}}], "type": "journal article", "published": "2020-08-18", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "issn-l": "0027-8424", "volume": "117", "issue": "33", "pages": "19943-19952"}, "abstract": "The nanoscale organization of biological membranes into structurally and compositionally distinct lateral domains is believed to be central to membrane function. The nature of this organization has remained elusive due to a lack of methods to directly probe nanoscopic membrane features. We show here that cryogenic electron microscopy (cryo-EM) can be used to directly image coexisting nanoscopic domains in synthetic and bioderived membranes without extrinsic probes. Analyzing a series of single-component liposomes composed of synthetic lipids of varying chain lengths, we demonstrate that cryo-EM can distinguish bilayer thickness differences as small as 0.5 \u00c5, comparable to the resolution of small-angle scattering methods. Simulated images from computational models reveal that features in cryo-EM images result from a complex interplay between the atomic distribution normal to the plane of the bilayer and imaging parameters. Simulations of phase-separated bilayers were used to predict two sources of contrast between coexisting ordered and disordered phases within a single liposome, namely differences in membrane thickness and molecular density. We observe both sources of contrast in biomimetic membranes composed of saturated lipids, unsaturated lipids, and cholesterol. When extended to isolated mammalian plasma membranes, cryo-EM reveals similar nanoscale lateral heterogeneities. The methods reported here for direct, probe-free imaging of nanodomains in unperturbed membranes open new avenues for investigation of nanoscopic membrane organization.", "doi": "10.1073/pnas.2002200117", "pmid": "32759206", "labels": {"Milka Doktorova": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC7443941"}, {"db": "pii", "key": "2002200117"}], "notes": [], "created": "2024-11-27T12:17:09.301Z", "modified": "2024-11-29T10:49:51.210Z"}, {"entity": "publication", "iuid": "fcd3a634ef874f869e1cdf187d4ab67c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/fcd3a634ef874f869e1cdf187d4ab67c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/fcd3a634ef874f869e1cdf187d4ab67c"}}, "title": "The limits of estimating COVID-19 intervention effects using Bayesian models", "authors": [{"family": "Bryant", "given": "Patrick", "initials": "P"}, {"family": "Elofsson", "given": "Arne", "initials": "A", "orcid": "0000-0002-7115-9751", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/248e70e81bd64f31a5f83e6e329bba95.json"}}], "type": "posted-content", "published": "2020-08-16", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2020.08.14.20175240", "pmid": null, "labels": {"Patrick Bryant": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T09:58:35.033Z", "modified": "2026-09-23T13:54:05.954Z"}, {"entity": "publication", "iuid": "2e98fd7442294d8d90a533f67130f85d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/2e98fd7442294d8d90a533f67130f85d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/2e98fd7442294d8d90a533f67130f85d"}}, "title": "Assembly and symmetry of the fungal E3BP-containing core of the Pyruvate Dehydrogenase Complex", "authors": [{"family": "Forsberg", "given": "B O", "initials": "BO", "orcid": "0000-0002-6247-4063", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/36ea51bfa66d48b7a43559c3d0eaa59f.json"}}, {"family": "Aibara", "given": "S", "initials": "S", "orcid": "0000-0003-2221-482X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b56490b2c675425dbe8008c0d50e38bb.json"}}, {"family": "Howard", "given": "R J", "initials": "RJ", "orcid": "0000-0003-2049-3378", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ce04593b5b24aaa8978fda1447dd0bf.json"}}, {"family": "Mortezaei", "given": "N", "initials": "N", "orcid": "0000-0002-8473-118X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4b6bfdffee74ad796372aed28de961f.json"}}, {"family": "Lindahl", "given": "E", "initials": "E", "orcid": "0000-0002-2734-2794", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9eb30fa60f9b4b95842ac9d9f3a0eaa9.json"}}], "type": "posted-content", "published": "2020-08-14", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2020.08.13.232140", "pmid": null, "labels": {"DDLS Fellow": "", "Bj\u00f6rn Forsberg": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T09:58:33.186Z", "modified": "2026-09-23T15:02:43.711Z"}, {"entity": "publication", "iuid": "11ed15c446ad434ba0f6e7dd2eafaa1c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/11ed15c446ad434ba0f6e7dd2eafaa1c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/11ed15c446ad434ba0f6e7dd2eafaa1c"}}, "title": "Mapping the nucleolar proteome reveals a spatiotemporal organization related to intrinsic protein disorder.", "authors": [{"family": "Stenstr\u00f6m", "given": "Lovisa", "initials": "L", "orcid": "0000-0002-2387-3491", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/08e64ec3c551482db30e11948c9f6fbc.json"}}, {"family": "Mahdessian", "given": "Diana", "initials": "D"}, {"family": "Gnann", "given": "Christian", "initials": "C"}, {"family": "Cesnik", "given": "Anthony J", "initials": "AJ"}, {"family": "Ouyang", "given": "Wei", "initials": "W"}, {"family": "Leonetti", "given": "Manuel D", "initials": "MD"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ea446aa574042a295d5f69437402f76.json"}}, {"family": "Cuylen-Haering", "given": "Sara", "initials": "S"}, {"family": "Thul", "given": "Peter J", "initials": "PJ"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb07e6d0122c4528a927c1fe922e3bc8.json"}}], "type": "journal article", "published": "2020-08-00", "journal": {"title": "Mol Syst Biol", "issn": "1744-4292", "volume": "16", "issue": "8", "pages": "e9469", "issn-l": "1744-4292"}, "abstract": "The nucleolus is essential for ribosome biogenesis and is involved in many other cellular functions. We performed a systematic spatiotemporal dissection of the human nucleolar proteome using confocal microscopy. In total, 1,318 nucleolar proteins were identified; 287 were localized to fibrillar components, and 157 were enriched along the nucleoplasmic border, indicating a potential fourth nucleolar subcompartment: the nucleoli rim. We found 65 nucleolar proteins (36 uncharacterized) to relocate to the chromosomal periphery during mitosis. Interestingly, we observed temporal partitioning into two recruitment phenotypes: early (prometaphase) and late (after metaphase), suggesting phase-specific functions. We further show that the expression of MKI67 is critical for this temporal partitioning. We provide the first proteome-wide analysis of intrinsic protein disorder for the human nucleolus and show that nucleolar proteins in general, and mitotic chromosome proteins in particular, have significantly higher intrinsic disorder level compared to cytosolic proteins. In summary, this study provides a comprehensive and essential resource of spatiotemporal expression data for the nucleolar proteome as part of the Human Protein Atlas.", "doi": "10.15252/msb.20209469", "pmid": "32744794", "labels": {"DDLS Fellow": "", "Wei Ouyang": ""}, "xrefs": [{"db": "pmc", "key": "PMC7397901"}], "notes": [], "created": "2026-08-20T12:51:53.151Z", "modified": "2026-09-23T06:47:29.650Z"}, {"entity": "publication", "iuid": "c15d49242f7b4a60a9d76b23e514d949", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c15d49242f7b4a60a9d76b23e514d949.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c15d49242f7b4a60a9d76b23e514d949"}}, "title": "A pan-cancer analysis of the frequency of DNA alterations across cell cycle activity levels.", "authors": [{"family": "Lundberg", "given": "Arian", "initials": "A", "orcid": "0000-0002-6630-2787", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/baa2c7c8963840bfb6a22d7c5cfe35f9.json"}}, {"family": "Lindstr\u00f6m", "given": "Linda S", "initials": "LS", "orcid": "0000-0002-7722-7532", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/99821dac16e64ad48325a1314398b927.json"}}, {"family": "Parker", "given": "Joel S", "initials": "JS", "orcid": "0000-0003-2080-6901", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/586d6382c81c407983976de4de3c9835.json"}}, {"family": "L\u00f6verli", "given": "Elinor", "initials": "E"}, {"family": "Perou", "given": "Charles M", "initials": "CM", "orcid": "0000-0001-9827-2247", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3f7179d8a91d4703ae5bdfa3e003f941.json"}}, {"family": "Bergh", "given": "Jonas", "initials": "J"}, {"family": "Tobin", "given": "Nicholas P", "initials": "NP", "orcid": "0000-0003-2343-9772", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b9aa223903694c8399b89adc231facce.json"}}], "type": "journal article", "published": "2020-08-00", "journal": {"title": "Oncogene", "issn": "1476-5594", "volume": "39", "issue": "32", "pages": "5430-5440", "issn-l": "0950-9232"}, "abstract": "Pan-cancer genomic analyses based on the magnitude of pathway activity are currently lacking. Focusing on the cell cycle, we examined the DNA mutations and chromosome arm-level aneuploidy within tumours with low, intermediate and high cell-cycle activity in 9515 pan-cancer patients with 32 different tumour types. Boxplots showed that cell-cycle activity varied broadly across and within all cancers. TP53 and PIK3CA mutations were common in all cell cycle score (CCS) tertiles but with increasing frequency as cell-cycle activity levels increased (P < 0.001). Mutations in BRAF and gains in 16p were less frequent in CCS High tumours (P < 0.001). In Kaplan-Meier analysis, patients whose tumours were CCS Low had a longer Progression Free Interval (PFI) relative to Intermediate or High (P < 0.001) and this significance remained in multivariable analysis (CCS Intermediate: HR = 1.37; 95% CI 1.17-1.60, CCS High: 1.54; 1.29-1.84, CCS Low = Ref). These results demonstrate that whilst similar DNA alterations can be found at all cell-cycle activity levels, some notable exceptions exist. Moreover, independent prognostic information can be derived on a pan-cancer level from a simple measure of cell-cycle activity.", "doi": "10.1038/s41388-020-1367-4", "pmid": "32581248", "labels": {"DDLS Fellow": null, "Arian Lundberg": null}, "xrefs": [{"db": "mid", "key": "NIHMS1702965"}, {"db": "pmc", "key": "PMC8159764"}, {"db": "pii", "key": "10.1038/s41388-020-1367-4"}], "notes": [], "created": "2025-11-14T07:51:50.036Z", "modified": "2026-08-09T18:52:23.385Z"}, {"entity": "publication", "iuid": "53936eb1325f4f3b9e8a3766fe24004b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/53936eb1325f4f3b9e8a3766fe24004b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/53936eb1325f4f3b9e8a3766fe24004b"}}, "title": "Decomposing Structural Response Due to Sequence Changes in Protein Domains with Machine Learning.", "authors": [{"family": "Bryant", "given": "Patrick", "initials": "P"}, {"family": "Elofsson", "given": "Arne", "initials": "A"}], "type": "journal article", "published": "2020-07-24", "journal": {"title": "J. Mol. Biol.", "issn": "1089-8638", "volume": "432", "issue": "16", "pages": "4435-4446", "issn-l": "0022-2836"}, "abstract": "How protein domain structure changes in response to mutations is not well understood. Some mutations change the structure drastically, while most only result in small changes. To gain an understanding of this, we decompose the relationship between changes in domain sequence and structure using machine learning. We select pairs of evolutionarily related domains with a broad range of evolutionary distances. In contrast to earlier studies, we do not find a strictly linear relationship between sequence and structural changes. We train a random forest regressor that predicts the structural similarity between pairs with an average accuracy of 0.029 lDDT ( local Distance Difference Test) score, and a correlation coefficient of 0.92. Decomposing the feature importance shows that the domain length, or analogously, size is the most important feature. Our model enables assessing deviations in relative structural response, and thus prediction of evolutionary trajectories, in protein domains across evolution.", "doi": "10.1016/j.jmb.2020.05.021", "pmid": "32485208", "labels": {"Patrick Bryant": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pii", "key": "S0022-2836(20)30370-3"}], "notes": [], "created": "2026-08-20T07:59:37.367Z", "modified": "2026-09-23T13:30:50.072Z"}, {"entity": "publication", "iuid": "e5e1cbdc9a584001bcef589121cc82ba", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e5e1cbdc9a584001bcef589121cc82ba.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e5e1cbdc9a584001bcef589121cc82ba"}}, "title": "The Immunology of Multisystem Inflammatory Syndrome in Children with COVID-19", "authors": [{"family": "Consiglio", "given": "Camila Rosat", "initials": "CR", "orcid": "0000-0002-8901-2328", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a786e29de11b41dd9da2b680ad5b351f.json"}}, {"family": "Cotugno", "given": "Nicola", "initials": "N"}, {"family": "Sardh", "given": "Fabian", "initials": "F"}, {"family": "Pou", "given": "Christian", "initials": "C", "orcid": "0000-0003-3932-788X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7230f1ee7eb34f9aa82e6e5fb62f9dfa.json"}}, {"family": "Amodio", "given": "Donato", "initials": "D"}, {"family": "Rodriguez", "given": "Lucie", "initials": "L", "orcid": "0000-0002-3692-9060", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4bc5e1ca94da426495051d3db0dd7a88.json"}}, {"family": "Tan", "given": "Ziyang", "initials": "Z", "orcid": "0000-0002-7205-4978", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cc33fb49228943c48451f0ac41c5c0be.json"}}, {"family": "Zicari", "given": "Sonia", "initials": "S"}, {"family": "Ruggiero", "given": "Alessandra", "initials": "A"}, {"family": "Pascucci", "given": "Giuseppe Rubens", "initials": "GR"}, {"family": "Santilli", "given": "Veronica", "initials": "V"}, {"family": "Campbell", "given": "Tessa", "initials": "T"}, {"family": "Bryceson", "given": "Yenan", "initials": "Y"}, {"family": "Eriksson", "given": "Daniel", "initials": "D", "orcid": "0000-0001-5473-3312", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b8847907a59147cf95d312afa115a3d3.json"}}, {"family": "Wang", "given": "Jun", "initials": "J"}, {"family": "Marchesi", "given": "Alessandra", "initials": "A"}, {"family": "Lakshmikanth", "given": "Tadepally", "initials": "T", "orcid": "0000-0001-7256-5770", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/28e45f00f5f247389409f0411d412da1.json"}}, {"family": "Campana", "given": "Andrea", "initials": "A"}, {"family": "Villani", "given": "Alberto", "initials": "A"}, {"family": "Rossi", "given": "Paolo", "initials": "P"}, {"family": "Landegren", "given": "Nils", "initials": "N", "orcid": "0000-0002-6163-9540", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6765f1617f51434baf93e4683965f03a.json"}}, {"family": "Palma", "given": "Paolo", "initials": "P"}, {"family": "Brodin", "given": "Petter", "initials": "P"}], "type": "posted-content", "published": "2020-07-10", "journal": {"title": "medRxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2020.07.08.20148353", "pmid": null, "labels": {"Camila Consiglio": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2026-08-20T09:58:08.241Z", "modified": "2026-10-05T07:13:51.498Z"}, {"entity": "publication", "iuid": "7ee854337df54440963206a8614bf3fe", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/7ee854337df54440963206a8614bf3fe.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/7ee854337df54440963206a8614bf3fe"}}, "title": "Natural killer cell activation related to clinical outcome of COVID-19", "authors": [{"family": "Maucourant", "given": "Christopher", "initials": "C"}, {"family": "Filipovic", "given": "Iva", "initials": "I"}, {"family": "Ponzetta", "given": "Andrea", "initials": "A"}, {"family": "Aleman", "given": "Soo", "initials": "S"}, {"family": "Cornillet", "given": "Martin", "initials": "M"}, {"family": "Hertwig", "given": "Laura", "initials": "L"}, {"family": "Strunz", "given": "Benedikt", "initials": "B"}, {"family": "Lentini", "given": "Antonio", "initials": "A"}, {"family": "Reinius", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Brownlie", "given": "Demi", "initials": "D"}, {"family": "Gomez", "given": "Angelica Cuapio", "initials": "AC"}, {"family": "Ask", "given": "Eivind Heggernes", "initials": "EH"}, {"family": "Hull", "given": "Ryan M", "initials": "RM"}, {"family": "Haroun-Izquierdo", "given": "Alvaro", "initials": "A"}, {"family": "Schaffer", "given": "Marie", "initials": "M"}, {"family": "Klingstr\u00f6m", "given": "Jonas", "initials": "J"}, {"family": "Folkesson", "given": "Elin", "initials": "E"}, {"family": "Buggert", "given": "Marcus", "initials": "M"}, {"family": "Sandberg", "given": "Johan K", "initials": "JK"}, {"family": "Eriksson", "given": "Lars I", "initials": "LI"}, {"family": "Rooyackers", "given": "Olav", "initials": "O"}, {"family": "Ljunggren", "given": "Hans Gustaf", "initials": "HG"}, {"family": "Malmberg", "given": "Karl Johan", "initials": "KJ"}, {"family": "Micha\u00eblsson", "given": "Jakob", "initials": "J"}, {"family": "Marquardt", "given": "Nicole", "initials": "N"}, {"family": "Hammer", "given": "Quirin", "initials": "Q"}, {"family": "Str\u00e5lin", "given": "Kristoffer", "initials": "K"}, {"family": "Bj\u00f6rkstr\u00f6m", "given": "Niklas K", "initials": "NK"}], "type": "posted-content", "published": "2020-07-10", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2020.07.07.20148478", "pmid": null, "labels": {"DDLS Fellow": "", "Antonio Lentini": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T09:58:06.287Z", "modified": "2026-09-23T13:45:13.772Z"}, {"entity": "publication", "iuid": "19c7412d58fb44b29df2d0b13c8ace6d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/19c7412d58fb44b29df2d0b13c8ace6d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/19c7412d58fb44b29df2d0b13c8ace6d"}}, "title": "The effect of opening up the US on COVID-19 spread", "authors": [{"family": "Bryant", "given": "Patrick", "initials": "P", "orcid": "0000-0003-3439-1866", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a683bcf98234ff09b2398976583b66f.json"}}, {"family": "Elofsson", "given": "Arne", "initials": "A", "orcid": "0000-0002-7115-9751", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/248e70e81bd64f31a5f83e6e329bba95.json"}}], "type": "posted-content", "published": "2020-07-04", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2020.07.03.20145649", "pmid": null, "labels": {"Patrick Bryant": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T09:57:50.920Z", "modified": "2026-09-23T15:03:32.639Z"}, {"entity": "publication", "iuid": "0500a012350d45e38004213674302acb", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0500a012350d45e38004213674302acb.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0500a012350d45e38004213674302acb"}}, "title": "Facets of individual-specific health signatures determined from longitudinal plasma proteome profiling.", "authors": [{"family": "Dodig-Crnkovi\u0107", "given": "Tea", "initials": "T"}, {"family": "Hong", "given": "Mun-Gwan", "initials": "MG"}, {"family": "Thomas", "given": "Cecilia Engel", "initials": "CE"}, {"family": "H\u00e4ussler", "given": "Ragna S", "initials": "RS"}, {"family": "Bendes", "given": "Annika", "initials": "A"}, {"family": "Dale", "given": "Matilda", "initials": "M"}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}, {"family": "Schuppe-Koistinen", "given": "Ina", "initials": "I"}, {"family": "Odeberg", "given": "Jacob", "initials": "J"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Gummesson", "given": "Anders", "initials": "A"}, {"family": "Bergstr\u00f6m", "given": "G\u00f6ran", "initials": "G"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM"}], "type": "journal article", "published": "2020-07-00", "journal": {"title": "EBioMedicine", "issn": "2352-3964", "volume": "57", "pages": "102854", "issn-l": "2352-3964"}, "abstract": "Precision medicine approaches aim to tackle diseases on an individual level through molecular profiling. Despite the growing knowledge about diseases and the reported diversity of molecular phenotypes, the descriptions of human health on an individual level have been far less elaborate.\n\nTo provide insights into the longitudinal protein signatures of well-being, we profiled blood plasma collected over one year from 101 clinically healthy individuals using multiplexed antibody assays. After applying an antibody validation scheme, we utilized > 700 protein profiles for in-depth analyses of the individuals' short-term health trajectories.\n\nWe found signatures of circulating proteomes to be highly individual-specific. Considering technical and longitudinal variability, we observed that 49% of the protein profiles were stable over one year. We also identified eight networks of proteins in which 11-242 proteins covaried over time. For each participant, there were unique protein profiles of which some could be explained by associations to genetic variants.\n\nThis observational and non-interventional study identifyed noticeable diversity among clinically healthy subjects, and facets of individual-specific signatures emerged by monitoring the variability of the circulating proteomes over time. To enable more personal hence precise assessments of health states, longitudinal profiling of circulating proteomes can provide a valuable component for precision medicine approaches.\n\nThis work was supported by the Erling Persson Foundation, the Swedish Heart and Lung Foundation, the Knut and Alice Wallenberg Foundation, Science for Life Laboratory, and the Swedish Research Council.", "doi": "10.1016/j.ebiom.2020.102854", "pmid": "32629387", "labels": {"Fredrik Edfors": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC7334812"}, {"db": "pii", "key": "S2352-3964(20)30229-2"}], "notes": [], "created": "2026-09-23T08:28:33.453Z", "modified": "2026-09-23T08:28:33.500Z"}, {"entity": "publication", "iuid": "0975152f3c0e48d89ba780a04681382b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0975152f3c0e48d89ba780a04681382b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0975152f3c0e48d89ba780a04681382b"}}, "title": "Comparative genomics reveals different population structures associated with host and geographic origin in antimicrobial-resistant Salmonella enterica.", "authors": [{"family": "Liao", "given": "Jingqiu", "initials": "J", "orcid": "0000-0002-2579-8157", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ac812840b9814e919ed1dca12a484c87.json"}}, {"family": "Orsi", "given": "Renato Hohl", "initials": "RH", "orcid": "0000-0003-4933-9817", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/faa4bd30679547898c7bd57690ba18bf.json"}}, {"family": "Carroll", "given": "Laura M", "initials": "LM"}, {"family": "Wiedmann", "given": "Martin", "initials": "M"}], "type": "journal article", "published": "2020-07-00", "journal": {"title": "Environ. Microbiol.", "issn": "1462-2920", "volume": "22", "issue": "7", "pages": "2811-2828", "issn-l": "1462-2912"}, "abstract": "Genetic variation in a pathogen, including the causative agent of salmonellosis, Salmonella enterica, can occur as a result of eco-evolutionary forces triggered by dissimilarities of ecological niches. Here, we applied comparative genomics to study 90 antimicrobial resistant (AMR) S. enterica isolates from bovine and human hosts in New York and Washington states to understand host- and geographic-associated population structure. Results revealed distinct presence/absence profiles of functional genes and pseudogenes (e.g., virulence genes) associated with bovine and human isolates. Notably, bovine isolates contained significantly more transposase genes but fewer transposase pseudogenes than human isolates, suggesting the occurrence of large-scale transposition in genomes of bovine and human isolates at different times. The high correlation between transposase genes and AMR genes, as well as plasmid replicons, highlights the potential role of horizontally transferred transposons in promoting adaptation to antibiotics. By contrast, a number of potentially geographic-associated single-nucleotide polymorphisms (SNPs), rather than geographic-associated genes, were identified. Interestingly, 38% of these SNPs were in genes annotated as cell surface protein-encoding genes, including some essential for antibiotic resistance and host colonization. Overall, different evolutionary forces and limited recent inter-population transmission appear to shape AMR S. enterica population structure in different hosts and geographic origins.", "doi": "10.1111/1462-2920.15014", "pmid": "32337816", "labels": {"Laura Carroll": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2025-03-18T17:25:39.817Z", "modified": "2025-03-18T17:25:39.889Z"}, {"entity": "publication", "iuid": "670dca7a2dcb4b41b15488745596e258", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/670dca7a2dcb4b41b15488745596e258.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/670dca7a2dcb4b41b15488745596e258"}}, "title": "Molecular Structure of Sphingomyelin in Fluid Phase Bilayers Determined by the Joint Analysis of Small-Angle Neutron and X-ray Scattering Data.", "authors": [{"family": "Doktorova", "given": "Milka", "initials": "M"}, {"family": "Ku\u010derka", "given": "Norbert", "initials": "N"}, {"family": "Kinnun", "given": "Jacob J", "initials": "JJ"}, {"family": "Pan", "given": "Jianjun", "initials": "J", "orcid": "0000-0002-7042-0022", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/628f9fc2c91e4fcfac681556cc374bce.json"}}, {"family": "Marquardt", "given": "Drew", "initials": "D", "orcid": "0000-0001-6848-2497", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/114cdc1c929d46308422b3b587f8e1d6.json"}}, {"family": "Scott", "given": "Haden L", "initials": "HL"}, {"family": "Venable", "given": "Richard M", "initials": "RM"}, {"family": "Pastor", "given": "Richard W", "initials": "RW", "orcid": "0000-0002-2454-5131", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f560f99fbea446f5a41521ef83ff9ddd.json"}}, {"family": "Wassall", "given": "Stephen R", "initials": "SR"}, {"family": "Katsaras", "given": "John", "initials": "J"}, {"family": "Heberle", "given": "Frederick A", "initials": "FA", "orcid": "0000-0002-0424-3240", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2557f5621a0b4c87b5f4702fbc7b6bdb.json"}}], "type": "journal article", "published": "2020-06-25", "journal": {"title": "J Phys Chem B", "issn": "1520-5207", "issn-l": "1520-5207", "volume": "124", "issue": "25", "pages": "5186-5200"}, "abstract": "We have determined the fluid bilayer structure of palmitoyl sphingomyelin (PSM) and stearoyl sphingomyelin (SSM) by simultaneously analyzing small-angle neutron and X-ray scattering data. Using a newly developed scattering density profile (SDP) model for sphingomyelin lipids, we report structural parameters including the area per lipid, total bilayer thickness, and hydrocarbon thickness, in addition to lipid volumes determined by densitometry. Unconstrained all-atom simulations of PSM bilayers at 55 \u00b0C using the C36 CHARMM force field produced a lipid area of 56 \u00c52, a value that is 10% lower than the one determined experimentally by SDP analysis (61.9 \u00c52). Furthermore, scattering form factors calculated from the unconstrained simulations were in poor agreement with experimental form factors, even though segmental order parameter (SCD) profiles calculated from the simulations were in relatively good agreement with SCD profiles obtained from NMR experiments. Conversely, constrained area simulations at 61.9 \u00c52 resulted in good agreement between the simulation and experimental scattering form factors, but not with SCD profiles from NMR. We discuss possible reasons for the discrepancies between these two types of data that are frequently used as validation metrics for molecular dynamics force fields.", "doi": "10.1021/acs.jpcb.0c03389", "pmid": "32468822", "labels": {"Milka Doktorova": null, "DDLS Fellow": null}, "xrefs": [{"db": "mid", "key": "NIHMS1621132"}, {"db": "pmc", "key": "PMC7458099"}], "notes": [], "created": "2024-11-27T12:16:11.940Z", "modified": "2024-11-29T12:16:19.122Z"}, {"entity": "publication", "iuid": "0d4b87d2e1ca4b3091ba443339445cc0", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0d4b87d2e1ca4b3091ba443339445cc0.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0d4b87d2e1ca4b3091ba443339445cc0"}}, "title": "Whole-genome sequence association analysis of blood proteins in a longitudinal wellness cohort.", "authors": [{"family": "Zhong", "given": "Wen", "initials": "W"}, {"family": "Gummesson", "given": "Anders", "initials": "A"}, {"family": "Tebani", "given": "Abdellah", "initials": "A"}, {"family": "Karlsson", "given": "Max J", "initials": "MJ"}, {"family": "Hong", "given": "Mun-Gwan", "initials": "MG"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM"}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Bergstr\u00f6m", "given": "G\u00f6ran", "initials": "G"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ea446aa574042a295d5f69437402f76.json"}}], "type": "journal article", "published": "2020-06-23", "journal": {"title": "Genome Med", "issn": "1756-994X", "volume": "12", "issue": "1", "pages": "53", "issn-l": "1756-994X"}, "abstract": "The human plasma proteome is important for many biological processes and targets for diagnostics and therapy. It is therefore of great interest to understand the interplay of genetic and environmental factors to determine the specific protein levels in individuals and to gain a deeper insight of the importance of genetic architecture related to the individual variability of plasma levels of proteins during adult life.\n\nWe have combined whole-genome sequencing, multiplex plasma protein profiling, and extensive clinical phenotyping in a longitudinal 2-year wellness study of 101 healthy individuals with repeated sampling. Analyses of genetic and non-genetic associations related to the variability of blood levels of proteins in these individuals were performed.\n\nThe analyses showed that each individual has a unique protein profile, and we report on the intra-individual as well as inter-individual variation for 794 plasma proteins. A genome-wide association study (GWAS) using 7.3 million genetic variants identified by whole-genome sequencing revealed 144 independent variants across 107 proteins that showed strong association (P < 6 \u00d7 10-11) between genetics and the inter-individual variability on protein levels. Many proteins not reported before were identified (67 out of 107) with individual plasma level affected by genetics. Our longitudinal analysis further demonstrates that these levels are stable during the 2-year study period. The variability of protein profiles as a consequence of environmental factors was also analyzed with focus on the effects of weight loss and infections.\n\nWe show that the adult blood levels of many proteins are determined at birth by genetics, which is important for efforts aimed to understand the relationship between plasma proteome profiles and human biology and disease.", "doi": "10.1186/s13073-020-00755-0", "pmid": "32576278", "labels": {"Fredrik Edfors": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC7310558"}, {"db": "pii", "key": "10.1186/s13073-020-00755-0"}], "notes": [], "created": "2026-09-23T08:47:35.282Z", "modified": "2026-09-23T08:47:35.368Z"}, {"entity": "publication", "iuid": "3e91d041ebb54d8fb6d90e939c13b4a1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3e91d041ebb54d8fb6d90e939c13b4a1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3e91d041ebb54d8fb6d90e939c13b4a1"}}, "title": "Skeletal Muscle Transcriptomic Comparison between Long-Term Trained and Untrained Men and Women.", "authors": [{"family": "Chapman", "given": "Mark A", "initials": "MA", "orcid": "0000-0001-9905-4022", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/71c4b747b8794745a547d635953c9960.json"}}, {"family": "Arif", "given": "Muhammad", "initials": "M"}, {"family": "Emanuelsson", "given": "Eric B", "initials": "EB"}, {"family": "Reitzner", "given": "Stefan M", "initials": "SM"}, {"family": "Lindholm", "given": "Mal\u00e9ne E", "initials": "ME"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Sundberg", "given": "Carl Johan", "initials": "CJ"}], "type": "comparative study", "published": "2020-06-23", "journal": {"title": "Cell Reports", "issn": "2211-1247", "issn-l": null, "volume": "31", "issue": "12", "pages": "107808"}, "abstract": "To better understand the health benefits of lifelong exercise in humans, we conduct global skeletal muscle transcriptomic analyses of long-term endurance- (9 men, 9 women) and strength-trained (7 men) humans compared with age-matched untrained controls (7 men, 8 women). Transcriptomic analysis, Gene Ontology, and genome-scale metabolic modeling demonstrate changes in pathways related to the prevention of metabolic diseases, particularly with endurance training. Our data also show prominent sex differences between controls and that these differences are reduced with endurance training. Additionally, we compare our data with studies examining muscle gene expression before and after a months-long training period in individuals with metabolic diseases. This analysis reveals that training shifts gene expression in individuals with impaired metabolism to become more similar to our endurance-trained group. Overall, our data provide an extensive examination of the accumulated transcriptional changes that occur with decades-long training and identify important \"exercise-responsive\" genes that could attenuate metabolic disease.", "doi": "10.1016/j.celrep.2020.107808", "pmid": "32579934", "labels": {"Adil Mardinoglu": "", "SciLifeLab Fellow": "", "DDLS Fellow": "", "Muhammad Arif": ""}, "xrefs": [{"db": "pii", "key": "S2211-1247(20)30789-0"}], "notes": [], "created": "2020-11-30T03:12:19.547Z", "modified": "2026-09-23T08:34:30.064Z"}, {"entity": "publication", "iuid": "aaa50b99700a4043946b86586e37a9b9", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/aaa50b99700a4043946b86586e37a9b9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/aaa50b99700a4043946b86586e37a9b9"}}, "title": "Mapping cell structure across scales by fusing protein images and interactions", "authors": [{"family": "Qin", "given": "Yue", "initials": "Y", "orcid": "0000-0002-0496-7134", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e9f5a7e6677c435082cf618d1af68ee6.json"}}, {"family": "Winsnes", "given": "Casper F", "initials": "CF", "orcid": "0000-0002-0028-5865", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/edeb3bc6c95d4185bf2098bf1e4a5e3c.json"}}, {"family": "Huttlin", "given": "Edward L", "initials": "EL", "orcid": "0000-0002-1822-1173", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/447db4d2b72445ec87d03bd6f73a2b1e.json"}}, {"family": "Zheng", "given": "Fan", "initials": "F", "orcid": "0000-0002-4403-112X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fae1ef6b5428431f9539290ae1c7c08a.json"}}, {"family": "Ouyang", "given": "Wei", "initials": "W", "orcid": "0000-0002-0291-926X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56f601e1d1c6448aab0c3a1e3cffdbfc.json"}}, {"family": "Park", "given": "Jisoo", "initials": "J"}, {"family": "Pitea", "given": "Adriana", "initials": "A"}, {"family": "Kreisberg", "given": "Jason F", "initials": "JF", "orcid": "0000-0002-3616-079X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cf842fcdd7b44056b75dc1c9059a3714.json"}}, {"family": "Gygi", "given": "Steven P", "initials": "SP"}, {"family": "Harper", "given": "J Wade", "initials": "JW", "orcid": "0000-0002-6944-7236", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/47dbdfbc595c4d1896fa0baa245210d0.json"}}, {"family": "Ma", "given": "Jianzhu", "initials": "J"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb07e6d0122c4528a927c1fe922e3bc8.json"}}, {"family": "Ideker", "given": "Trey", "initials": "T", "orcid": "0000-0002-1708-8454", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8701a4e92863420dbe8b77bb44a7deeb.json"}}], "type": "posted-content", "published": "2020-06-22", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2020.06.21.163709", "pmid": null, "labels": {"DDLS Fellow": "", "Wei Ouyang": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T09:57:32.707Z", "modified": "2026-09-23T14:10:13.427Z"}, {"entity": "publication", "iuid": "1d00fdf47824456f9caa7ece842dd553", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1d00fdf47824456f9caa7ece842dd553.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1d00fdf47824456f9caa7ece842dd553"}}, "title": "Characterization of the dynamic resting state of a pentameric ligand-gated ion channel by cryo-electron microscopy and simulations", "authors": [{"family": "Rov\u0161nik", "given": "U", "initials": "U", "orcid": "0000-0001-5889-6899", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f0ab87a8712f4ad886da61c1edcf679f.json"}}, {"family": "Zhuang", "given": "Y", "initials": "Y", "orcid": "0000-0003-4390-8556", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/61b8327a0f32416686748c52c38ecbf1.json"}}, {"family": "Axelsson", "given": "L", "initials": "L", "orcid": "0000-0001-7163-7488", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/546941b1ef034cbeb4a16fa9cd9948aa.json"}}, {"family": "Forsberg", "given": "BO", "initials": "B", "orcid": "0000-0002-6247-4063", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/36ea51bfa66d48b7a43559c3d0eaa59f.json"}}, {"family": "Lim", "given": "V", "initials": "V", "orcid": "0000-0003-4030-9312", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d5d54626902c46a7b4b62ebefaa74845.json"}}, {"family": "Carroni", "given": "M", "initials": "M", "orcid": "0000-0002-7697-6427", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/55fa4ba347a34d7ca80d214e8d718e44.json"}}, {"family": "Blau", "given": "C", "initials": "C", "orcid": "0000-0003-2558-0497", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/75324408cf1c44538571789269dff9cb.json"}}, {"family": "Howard", "given": "RJ", "initials": "R", "orcid": "0000-0003-2049-3378", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ce04593b5b24aaa8978fda1447dd0bf.json"}}, {"family": "Lindahl", "given": "E", "initials": "E", "orcid": "0000-0002-2734-2794", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9eb30fa60f9b4b95842ac9d9f3a0eaa9.json"}}], "type": "posted-content", "published": "2020-06-20", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2020.06.19.161356", "pmid": null, "labels": {"DDLS Fellow": "", "Bj\u00f6rn Forsberg": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T09:57:30.784Z", "modified": "2026-09-23T14:30:44.787Z"}, {"entity": "publication", "iuid": "c368ce81e3f54e82a99931b419c5aed0", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c368ce81e3f54e82a99931b419c5aed0.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c368ce81e3f54e82a99931b419c5aed0"}}, "title": "Systems-level immunomonitoring from acute to recovery phase of severe COVID-19", "authors": [{"family": "Rodriguez", "given": "Lucie", "initials": "L", "orcid": "0000-0002-3692-9060", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4bc5e1ca94da426495051d3db0dd7a88.json"}}, {"family": "Pekkarinen", "given": "Pirkka", "initials": "P"}, {"family": "Lakshmikanth", "given": "Tadepally", "initials": "T", "orcid": "0000-0001-7256-5770", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/28e45f00f5f247389409f0411d412da1.json"}}, {"family": "Tan", "given": "Ziyang", "initials": "Z", "orcid": "0000-0002-7205-4978", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cc33fb49228943c48451f0ac41c5c0be.json"}}, {"family": "Consiglio", "given": "Camila Rosat", "initials": "CR", "orcid": "0000-0002-8901-2328", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a786e29de11b41dd9da2b680ad5b351f.json"}}, {"family": "Pou", "given": "Christian", "initials": "C", "orcid": "0000-0003-3932-788X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7230f1ee7eb34f9aa82e6e5fb62f9dfa.json"}}, {"family": "Chen", "given": "Yang", "initials": "Y"}, {"family": "Mugabo", "given": "Constantin Habimana", "initials": "CH"}, {"family": "Quoc", "given": "Anh Nguyen", "initials": "AN"}, {"family": "Nowlan", "given": "Kirsten", "initials": "K"}, {"family": "Strandin", "given": "Tomas", "initials": "T", "orcid": "0000-0002-2454-7479", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/955f45a3a7ee4342b8f1047ad6ebb6e2.json"}}, {"family": "Levanov", "given": "Lev", "initials": "L"}, {"family": "Mikes", "given": "Jaromir", "initials": "J", "orcid": "0000-0002-9941-7855", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b486baedd784487dbf3e5b7b33f950da.json"}}, {"family": "Wang", "given": "Jun", "initials": "J"}, {"family": "Kantele", "given": "Anu", "initials": "A", "orcid": "0000-0002-0004-1000", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/232b375319534904bc586ae646d1f0b5.json"}}, {"family": "Hepojoki", "given": "Jussi", "initials": "J", "orcid": "0000-0001-5699-214X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ac9397d670bf4b5b8c46657c99219e8c.json"}}, {"family": "Vapalahti", "given": "Olli", "initials": "O", "orcid": "0000-0003-2270-6824", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/adcc581bfe28463585c3fc5ecdb717ee.json"}}, {"family": "Heinonen", "given": "Santtu", "initials": "S", "orcid": "0000-0002-6342-0577", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/49c5bc320adf468aa02a7fe4d50541ba.json"}}, {"family": "Kek\u00e4l\u00e4inen", "given": "Eliisa", "initials": "E"}, {"family": "Brodin", "given": "Petter", "initials": "P"}], "type": "posted-content", "published": "2020-06-05", "journal": {"title": "medRxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2020.06.03.20121582", "pmid": null, "labels": {"Camila Consiglio": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2026-08-20T09:57:16.599Z", "modified": "2026-10-05T07:24:29.515Z"}, {"entity": "publication", "iuid": "b58c708415174d08b6e926668122e9d5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b58c708415174d08b6e926668122e9d5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b58c708415174d08b6e926668122e9d5"}}, "title": "Plasma membranes are asymmetric in lipid unsaturation, packing and protein shape.", "authors": [{"family": "Lorent", "given": "J H", "initials": "JH", "orcid": "0000-0002-7537-8521", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6c6a5fdf28de42ff8a14a7ae259939cb.json"}}, {"family": "Levental", "given": "K R", "initials": "KR", "orcid": "0000-0002-2234-3683", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dcde4d3042b349b199c48509444ac8f9.json"}}, {"family": "Ganesan", "given": "L", "initials": "L"}, {"family": "Rivera-Longsworth", "given": "G", "initials": "G"}, {"family": "Sezgin", "given": "E", "initials": "E", "orcid": "0000-0002-4915-388X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f7bd3619c7fd48318bc4c1e7a9910df8.json"}}, {"family": "Doktorova", "given": "M", "initials": "M"}, {"family": "Lyman", "given": "E", "initials": "E"}, {"family": "Levental", "given": "I", "initials": "I", "orcid": "0000-0002-1206-9545", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7fe40c2b810348cab78616402d4d1f1f.json"}}], "type": "journal article", "published": "2020-06-00", "journal": {"title": "Nat. Chem. Biol.", "issn": "1552-4469", "issn-l": "1552-4450", "volume": "16", "issue": "6", "pages": "644-652"}, "abstract": "A fundamental feature of cellular plasma membranes (PMs) is an asymmetric lipid distribution between the bilayer leaflets. However, neither the detailed, comprehensive compositions of individual PM leaflets nor how these contribute to structural membrane asymmetries have been defined. We report the distinct lipidomes and biophysical properties of both monolayers in living mammalian PMs. Phospholipid unsaturation is dramatically asymmetric, with the cytoplasmic leaflet being approximately twofold more unsaturated than the exoplasmic leaflet. Atomistic simulations and spectroscopy of leaflet-selective fluorescent probes reveal that the outer PM leaflet is more packed and less diffusive than the inner leaflet, with this biophysical asymmetry maintained in the endocytic system. The structural asymmetry of the PM is reflected in the asymmetric structures of protein transmembrane domains. These structural asymmetries are conserved throughout Eukaryota, suggesting fundamental cellular design principles.", "doi": "10.1038/s41589-020-0529-6", "pmid": "32367017", "labels": {"Erdinc Sezgin": "", "SciLifeLab Fellow": "", "Milka Doktorova": "", "DDLS Fellow": ""}, "xrefs": [{"db": "mid", "key": "NIHMS1580184"}, {"db": "pmc", "key": "PMC7246138"}, {"db": "pii", "key": "10.1038/s41589-020-0529-6"}], "notes": [], "created": "2020-11-05T16:09:26.127Z", "modified": "2026-09-23T06:30:02.825Z"}, {"entity": "publication", "iuid": "c88c0bad902a4361ae98e9187f3092d5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c88c0bad902a4361ae98e9187f3092d5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c88c0bad902a4361ae98e9187f3092d5"}}, "title": "No distinct microbiome signature of irritable bowel syndrome found in a Swedish random population.", "authors": [{"family": "Hugerth", "given": "Luisa W", "initials": "LW", "orcid": "0000-0001-5432-1764", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/246ed7b405dd4c3f9ec5e7ff9f1d3ade.json"}}, {"family": "Andreasson", "given": "Anna", "initials": "A"}, {"family": "Talley", "given": "Nicholas J", "initials": "NJ", "orcid": "0000-0003-2537-3092", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b9dd6bee0a1b4cf4831de933a8d28ecf.json"}}, {"family": "Forsberg", "given": "Anna M", "initials": "AM"}, {"family": "Kjellstr\u00f6m", "given": "Lars", "initials": "L"}, {"family": "Schmidt", "given": "Peter Thelin", "initials": "PT"}, {"family": "Agreus", "given": "Lars", "initials": "L"}, {"family": "Engstrand", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2020-06-00", "journal": {"title": "Gut", "issn": "1468-3288", "volume": "69", "issue": "6", "pages": "1076-1084", "issn-l": "0017-5749"}, "abstract": "The ethiopathogenesis of irritable bowel syndrome (IBS) is unknown. While a link to the gut microbiome is postulated, the heterogeneity of the healthy gut makes it difficult to draw definitive conclusions. We aimed to describe the faecal and mucosa-associated microbiome (MAM) and health correlates on a community cohort of healthy and IBS individuals with no colonoscopic findings.\n\nThe PopCol study recruited a random sample of 3556 adults; 745 underwent colonoscopy. IBS was defined by Rome IV criteria and organic disease excluded. 16S rRNA gene sequencing was conducted on sigmoid biopsy samples from 376 representative individuals (63 IBS cases) and faecal samples from 185 individuals (32 IBS cases).\n\nWhile sigmoid MAM was dominated by Lachnospiraceae, faeces presented a higher relative abundance of Ruminococcaceae. Microbial richness in MAM was linearly correlated to that in faeces from the same individual (R\u00b2=0.255, p<3E-11) as was diversity (R\u00b2=0.06, p=0.0022). MAM diversity decreased with increasing body mass index (BMI; Pearson's r=-0.1, p=0.08) and poorer self-rated health (r=-0.15, p=0.007), but no other health correlates. Faecal microbiome diversity was correlated to stool consistency (r=-0.16, p=0.043). Several taxonomic groups were correlated to age, BMI, depression and self-reported health, including Coprococcus catus associated with lower levels of depression (r=-0.003, p=0.00017). The degree of heterogeneity observed between IBS patients is higher than that observed between healthy individuals.\n\nNo distinct microbial signature was observed in IBS. Individuals presenting with low self-rated health or high BMI have lower gut microbiome richness.", "doi": "10.1136/gutjnl-2019-318717", "pmid": "31601615", "labels": {"Luisa Hugerth": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC7282555"}, {"db": "pii", "key": "gutjnl-2019-318717"}], "notes": [], "created": "2022-11-08T06:59:14.279Z", "modified": "2026-09-23T07:39:04.490Z"}, {"entity": "publication", "iuid": "ef0cc25fd2704d53b02f40b5f28c9e85", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ef0cc25fd2704d53b02f40b5f28c9e85.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ef0cc25fd2704d53b02f40b5f28c9e85"}}, "title": "Author Correction: Plasma membranes are asymmetric in lipid unsaturation, packing and protein shape.", "authors": [{"family": "Lorent", "given": "J H", "initials": "JH", "orcid": "0000-0002-7537-8521", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6c6a5fdf28de42ff8a14a7ae259939cb.json"}}, {"family": "Levental", "given": "K R", "initials": "KR", "orcid": "0000-0002-2234-3683", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dcde4d3042b349b199c48509444ac8f9.json"}}, {"family": "Ganesan", "given": "L", "initials": "L"}, {"family": "Rivera-Longsworth", "given": "G", "initials": "G"}, {"family": "Sezgin", "given": "E", "initials": "E", "orcid": "0000-0002-4915-388X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f7bd3619c7fd48318bc4c1e7a9910df8.json"}}, {"family": "Doktorova", "given": "M", "initials": "M"}, {"family": "Lyman", "given": "E", "initials": "E"}, {"family": "Levental", "given": "I", "initials": "I", "orcid": "0000-0002-1206-9545", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7fe40c2b810348cab78616402d4d1f1f.json"}}], "type": "journal article", "published": "2020-06-00", "journal": {"title": "Nat. Chem. Biol.", "issn": "1552-4469", "volume": "16", "issue": "6", "pages": "710", "issn-l": "1552-4450"}, "abstract": "An amendment to this paper has been published and can be accessed via a link at the top of the paper.", "doi": "10.1038/s41589-020-0564-3", "pmid": "32415286", "labels": {"SciLifeLab Fellow": "", "Milka Doktorova": "", "DDLS Fellow": "", "Erdinc Sezgin": ""}, "xrefs": [{"db": "pii", "key": "10.1038/s41589-020-0564-3"}], "notes": [], "created": "2026-08-20T09:00:24.575Z", "modified": "2026-09-23T13:47:08.554Z"}, {"entity": "publication", "iuid": "349fd0a5fd4c4f6bae88342e15a74169", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/349fd0a5fd4c4f6bae88342e15a74169.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/349fd0a5fd4c4f6bae88342e15a74169"}}, "title": "Quantitative analysis of amino acid metabolism in liver cancer links glutamate excretion to nucleotide synthesis.", "authors": [{"family": "Nilsson", "given": "Avlant", "initials": "A", "orcid": "0000-0002-9476-4516", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f2e21dbc1c624f6a841c59e959e948e4.json"}}, {"family": "Haanstra", "given": "Jurgen R", "initials": "JR", "orcid": "0000-0001-9652-0219", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3bf355cfa5a040d180c267a9a917552f.json"}}, {"family": "Engqvist", "given": "Martin", "initials": "M", "orcid": "0000-0003-2174-2225", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9d236bff3a8a49e7aabadd8a9f0249bc.json"}}, {"family": "Gerding", "given": "Albert", "initials": "A", "orcid": "0000-0002-6004-2398", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8548150aa9464442947930dc2e097c1d.json"}}, {"family": "Bakker", "given": "Barbara M", "initials": "BM", "orcid": "0000-0001-6274-3633", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/65f0b7d9f6bb4296a28c9f33edf1aa2b.json"}}, {"family": "Klingm\u00fcller", "given": "Ursula", "initials": "U", "orcid": "0000-0001-9845-3099", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a0ac66a4112543a4adf7209bf6cd9647.json"}}, {"family": "Teusink", "given": "Bas", "initials": "B", "orcid": "0000-0003-3929-0423", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/68e4ce6dd53d40428d44d8490060b6a6.json"}}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/33f2b49a39ed4e54ba77dfe397ed3087.json"}}], "type": "journal article", "published": "2020-05-12", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "issn-l": "0027-8424", "volume": "117", "issue": "19", "pages": "10294-10304"}, "abstract": "Many cancer cells consume glutamine at high rates; counterintuitively, they simultaneously excrete glutamate, the first intermediate in glutamine metabolism. Glutamine consumption has been linked to replenishment of tricarboxylic acid cycle (TCA) intermediates and synthesis of adenosine triphosphate (ATP), but the reason for glutamate excretion is unclear. Here, we dynamically profile the uptake and excretion fluxes of a liver cancer cell line (HepG2) and use genome-scale metabolic modeling for in-depth analysis. We find that up to 30% of the glutamine is metabolized in the cytosol, primarily for nucleotide synthesis, producing cytosolic glutamate. We hypothesize that excreting glutamate helps the cell to increase the nucleotide synthesis rate to sustain growth. Indeed, we show experimentally that partial inhibition of glutamate excretion reduces cell growth. Our integrative approach thus links glutamine addiction to glutamate excretion in cancer and points toward potential drug targets.", "doi": "10.1073/pnas.1919250117", "pmid": "32341162", "labels": {"Avlant Nilsson": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC7229649"}, {"db": "pii", "key": "1919250117"}], "notes": [], "created": "2025-03-20T11:09:40.628Z", "modified": "2025-03-21T13:16:51.788Z"}, {"entity": "publication", "iuid": "3800f63ce9a94765bba849b1e611a4ba", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3800f63ce9a94765bba849b1e611a4ba.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3800f63ce9a94765bba849b1e611a4ba"}}, "title": "Optimal protocols for sequence-based characterization of the human vaginal microbiome", "authors": [{"family": "Hugerth", "given": "Luisa W", "initials": "LW", "orcid": "0000-0001-5432-1764", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/246ed7b405dd4c3f9ec5e7ff9f1d3ade.json"}}, {"family": "Pereira", "given": "Marcela", "initials": "M"}, {"family": "Zha", "given": "Yinghua", "initials": "Y"}, {"family": "Seifert", "given": "Maike", "initials": "M"}, {"family": "Kaldhusdal", "given": "Vilde", "initials": "V"}, {"family": "Boulund", "given": "Fredrik", "initials": "F"}, {"family": "Krog", "given": "Maria C", "initials": "MC"}, {"family": "Bashir", "given": "Zahra", "initials": "Z"}, {"family": "Hamsten", "given": "Marica", "initials": "M"}, {"family": "Fransson", "given": "Emma", "initials": "E"}, {"family": "Svarre-Nielsen", "given": "Henriette", "initials": "H"}, {"family": "Schuppe-Koistinen", "given": "Ina", "initials": "I"}, {"family": "Engstrand", "given": "Lars", "initials": "L"}], "type": "posted-content", "published": "2020-05-07", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2020.05.05.079996", "pmid": null, "labels": {"DDLS Fellow": "", "Luisa Hugerth": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T09:57:01.719Z", "modified": "2026-09-23T14:30:42.947Z"}, {"entity": "publication", "iuid": "dff59e54af7840869940bde067e21612", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/dff59e54af7840869940bde067e21612.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/dff59e54af7840869940bde067e21612"}}, "title": "National Cancer Institute Think-Tank Meeting Report on Proteomic Cartography and Biomarkers at the Single-Cell Level: Interrogation of Premalignant Lesions.", "authors": [{"family": "Kagan", "given": "Jacob", "initials": "J", "orcid": "0000-0002-1294-9606", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6b1296ec61ad4cd08f510fb2a94ebc75.json"}}, {"family": "Moritz", "given": "Robert L", "initials": "RL"}, {"family": "Mazurchuk", "given": "Richard", "initials": "R"}, {"family": "Lee", "given": "Je Hyuk", "initials": "JH"}, {"family": "Kharchenko", "given": "Peter Vasili", "initials": "PV"}, {"family": "Rozenblatt-Rosen", "given": "Orit", "initials": "O"}, {"family": "Ruppin", "given": "Eytan", "initials": "E"}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e213b04f8984c8eb00c68f5bc2f6a36.json"}}, {"family": "Ginty", "given": "Fiona", "initials": "F"}, {"family": "Goltsev", "given": "Yury", "initials": "Y"}, {"family": "Wells", "given": "James A", "initials": "JA", "orcid": "0000-0001-8267-5519", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f0c1fc2f2b584824bd489884424e333c.json"}}, {"family": "LaCava", "given": "John", "initials": "J"}, {"family": "Riesterer", "given": "Jessica L", "initials": "JL"}, {"family": "Germain", "given": "Ronald N", "initials": "RN"}, {"family": "Shi", "given": "Tujin", "initials": "T", "orcid": "0000-0002-5592-3588", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6743cfa5c22b469aa8c3e041c74800f9.json"}}, {"family": "Chee", "given": "Mark S", "initials": "MS"}, {"family": "Budnik", "given": "Bogdan A", "initials": "BA"}, {"family": "Yates", "given": "John R", "initials": "JR", "orcid": "0000-0001-5267-1672", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7cc4e6ccc4cd445e8f4e13ef2eb6b907.json"}}, {"family": "Chait", "given": "Brian T", "initials": "BT"}, {"family": "Moffitt", "given": "Jeffery R", "initials": "JR"}, {"family": "Smith", "given": "Richard D", "initials": "RD"}, {"family": "Srivastava", "given": "Sudhir", "initials": "S"}], "type": "journal article", "published": "2020-05-01", "journal": {"title": "J. Proteome Res.", "issn": "1535-3907", "volume": "19", "issue": "5", "pages": "1900-1912", "issn-l": "1535-3893"}, "abstract": "A Think-Tank Meeting was convened by the National Cancer Institute (NCI) to solicit experts' opinion on the development and application of multiomic single-cell analyses, and especially single-cell proteomics, to improve the development of a new generation of biomarkers for cancer risk, early detection, diagnosis, and prognosis as well as to discuss the discovery of new targets for prevention and therapy. It is anticipated that such markers and targets will be based on cellular, subcellular, molecular, and functional aberrations within the lesion and within individual cells. Single-cell proteomic data will be essential for the establishment of new tools with searchable and scalable features that include spatial and temporal cartographies of premalignant and malignant lesions. Challenges and potential solutions that were discussed included (i) The best way/s to analyze single-cells from fresh and preserved tissue; (ii) Detection and analysis of secreted molecules and from single cells, especially from a tissue slice; (iii) Detection of new, previously undocumented cell type/s in the premalignant and early stage cancer tissue microenvironment; (iv) Multiomic integration of data to support and inform proteomic measurements; (v) Subcellular organelles-identifying abnormal structure, function, distribution, and location within individual premalignant and malignant cells; (vi) How to improve the dynamic range of single-cell proteomic measurements for discovery of differentially expressed proteins and their post-translational modifications (PTM); (vii) The depth of coverage measured concurrently using single-cell techniques; (viii) Quantitation - absolute or semiquantitative? (ix) Single methodology or multiplexed combinations? (x) Application of analytical methods for identification of biologically significant subsets; (xi) Data visualization of N-dimensional data sets; (xii) How to construct intercellular signaling networks in individual cells within premalignant tumor microenvironments (TME); (xiii) Associations between intrinsic cellular processes and extrinsic stimuli; (xiv) How to predict cellular responses to stress-inducing stimuli; (xv) Identification of new markers for prediction of progression from precursor, benign, and localized lesions to invasive cancer, based on spatial and temporal changes within individual cells; (xvi) Identification of new targets for immunoprevention or immunotherapy-identification of neoantigens and surfactome of individual cells within a lesion.", "doi": "10.1021/acs.jproteome.0c00021", "pmid": "32163288", "labels": {"Fredrik Edfors": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T08:11:12.386Z", "modified": "2026-09-23T12:51:45.922Z"}, {"entity": "publication", "iuid": "09ab7a2cbe9041f19abb08c0d6434642", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/09ab7a2cbe9041f19abb08c0d6434642.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/09ab7a2cbe9041f19abb08c0d6434642"}}, "title": "The utility of artificial intelligence in the assessment of prostate pathology.", "authors": [{"family": "Egevad", "given": "Lars", "initials": "L", "orcid": "0000-0001-8531-222X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a7d46f1f5fc047dc8edb910eb4f0645c.json"}}, {"family": "Str\u00f6m", "given": "Peter", "initials": "P", "orcid": "0000-0002-1631-806X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2798ea6ef2ed4ae88b78dd04d2f14437.json"}}, {"family": "Kartasalo", "given": "Kimmo", "initials": "K"}, {"family": "Olsson", "given": "Henrik", "initials": "H"}, {"family": "Samaratunga", "given": "Hemamali", "initials": "H"}, {"family": "Delahunt", "given": "Brett", "initials": "B", "orcid": "0000-0002-5398-0300", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/433a3f884f95451383cc746925d9a08c.json"}}, {"family": "Eklund", "given": "Martin", "initials": "M"}], "type": "editorial", "published": "2020-05-00", "journal": {"title": "Histopathology", "issn": "1365-2559", "issn-l": "0309-0167", "volume": "76", "issue": "6", "pages": "790-792"}, "abstract": null, "doi": "10.1111/his.14060", "pmid": "32402150", "labels": {"Kimmo Kartasalo": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2024-11-05T16:10:26.497Z", "modified": "2024-11-29T10:45:28.264Z"}, {"entity": "publication", "iuid": "da98bcc100634df685732bae1935fc3f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/da98bcc100634df685732bae1935fc3f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/da98bcc100634df685732bae1935fc3f"}}, "title": "Estimating the impact of mobility patterns on COVID-19 infection rates in 11 European countries", "authors": [{"family": "Bryant", "given": "Patrick", "initials": "P", "orcid": "0000-0003-3439-1866", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a683bcf98234ff09b2398976583b66f.json"}}, {"family": "Elofsson", "given": "Arne", "initials": "A", "orcid": "0000-0002-7115-9751", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/248e70e81bd64f31a5f83e6e329bba95.json"}}], "type": "posted-content", "published": "2020-04-17", "journal": {"title": "medRxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2020.04.13.20063644", "pmid": null, "labels": {"Patrick Bryant": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2026-08-20T09:56:51.844Z", "modified": "2026-10-05T08:15:21.721Z"}, {"entity": "publication", "iuid": "27a24712c2d94c4aab8153ffb0e14f24", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/27a24712c2d94c4aab8153ffb0e14f24.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/27a24712c2d94c4aab8153ffb0e14f24"}}, "title": "The acute effect of metabolic cofactor supplementation: a potential therapeutic strategy against non-alcoholic fatty liver disease.", "authors": [{"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f46e4161be08458994efddb75ed75874.json"}}, {"family": "Bjornson", "given": "Elias", "initials": "E"}, {"family": "Arif", "given": "Muhammad", "initials": "M"}, {"family": "Tebani", "given": "Abdellah", "initials": "A", "orcid": "0000-0002-8901-2678", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/794215a6625b4fe4b652ec08bcab98ec.json"}}, {"family": "Lovric", "given": "Alen", "initials": "A"}, {"family": "Benfeitas", "given": "Rui", "initials": "R", "orcid": "0000-0001-7972-0083", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e2ec344c501496796be3250fd563699.json"}}, {"family": "Ozcan", "given": "Mehmet", "initials": "M", "orcid": "0000-0002-1222-2802", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e690dbebe4144d72b97aad264290fd72.json"}}, {"family": "Juszczak", "given": "Kajetan", "initials": "K"}, {"family": "Kim", "given": "Woonghee", "initials": "W"}, {"family": "Kim", "given": "Jung Tae", "initials": "JT"}, {"family": "Bidkhori", "given": "Gholamreza", "initials": "G"}, {"family": "St\u00e5hlman", "given": "Marcus", "initials": "M"}, {"family": "Bergh", "given": "Per-Olof", "initials": "PO", "orcid": "0000-0001-9993-6965", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0340d8f630034124a106f49ebd3101f3.json"}}, {"family": "Adiels", "given": "Martin", "initials": "M"}, {"family": "Turkez", "given": "Hasan", "initials": "H"}, {"family": "Taskinen", "given": "Marja-Riitta", "initials": "MR"}, {"family": "Bosley", "given": "Jim", "initials": "J"}, {"family": "Marschall", "given": "Hanns-Ulrich", "initials": "HU"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/33f2b49a39ed4e54ba77dfe397ed3087.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ea446aa574042a295d5f69437402f76.json"}}, {"family": "Bor\u00e9n", "given": "Jan", "initials": "J", "orcid": "0000-0003-0786-8091", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/73a770eb9e614448a046b8e9199052e9.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca58bf2d214047e0ae5e38a42a0f2808.json"}}], "type": "journal article", "published": "2020-04-00", "journal": {"title": "Mol Syst Biol", "issn": "1744-4292", "issn-l": "1744-4292", "volume": "16", "issue": "4", "pages": "e9495"}, "abstract": "The prevalence of non-alcoholic fatty liver disease (NAFLD) continues to increase dramatically, and there is no approved medication for its treatment. Recently, we predicted the underlying molecular mechanisms involved in the progression of NAFLD using network analysis and identified metabolic cofactors that might be beneficial as supplements to decrease human liver fat. Here, we first assessed the tolerability of the combined metabolic cofactors including l-serine, N-acetyl-l-cysteine (NAC), nicotinamide riboside (NR), and l-carnitine by performing a 7-day rat toxicology study. Second, we performed a human calibration study by supplementing combined metabolic cofactors and a control study to study the kinetics of these metabolites in the plasma of healthy subjects with and without supplementation. We measured clinical parameters and observed no immediate side effects. Next, we generated plasma metabolomics and inflammatory protein markers data to reveal the acute changes associated with the supplementation of the metabolic cofactors. We also integrated metabolomics data using personalized genome-scale metabolic modeling and observed that such supplementation significantly affects the global human lipid, amino acid, and antioxidant metabolism. Finally, we predicted blood concentrations of these compounds during daily long-term supplementation by generating an ordinary differential equation model and liver concentrations of serine by generating a pharmacokinetic model and finally adjusted the doses of individual metabolic cofactors for future human clinical trials.", "doi": "10.15252/msb.209495", "pmid": "32337855", "labels": {"Adil Mardinoglu": "", "SciLifeLab Fellow": "", "DDLS Fellow": "", "Muhammad Arif": ""}, "xrefs": [{"db": "pmc", "key": "PMC7184219"}], "notes": [], "created": "2020-11-30T03:12:49.297Z", "modified": "2026-09-23T08:47:00.954Z"}, {"entity": "publication", "iuid": "29ee70e5750c4da7bccbbe44c1a968fb", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/29ee70e5750c4da7bccbbe44c1a968fb.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/29ee70e5750c4da7bccbbe44c1a968fb"}}, "title": "An atlas of human metabolism.", "authors": [{"family": "Robinson", "given": "Jonathan L", "initials": "JL", "orcid": "0000-0001-8567-5960", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/528edd3ba8374bdd8e3187556978c5ef.json"}}, {"family": "Kocaba\u015f", "given": "P\u0131nar", "initials": "P", "orcid": "0000-0001-9788-2019", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/87f4b6d6a9b24100b74913dbe2441a64.json"}}, {"family": "Wang", "given": "Hao", "initials": "H", "orcid": "0000-0001-7475-0136", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/77429d26b3884b328ef827033ff1e7b6.json"}}, {"family": "Cholley", "given": "Pierre-Etienne", "initials": "PE"}, {"family": "Cook", "given": "Daniel", "initials": "D", "orcid": "0000-0001-5534-8600", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ea66e464f79c40ddb214951d977e8812.json"}}, {"family": "Nilsson", "given": "Avlant", "initials": "A", "orcid": "0000-0002-9476-4516", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f2e21dbc1c624f6a841c59e959e948e4.json"}}, {"family": "Anton", "given": "Mihail", "initials": "M", "orcid": "0000-0002-7753-9042", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/733c89e6b386409392abf45608738222.json"}}, {"family": "Ferreira", "given": "Raphael", "initials": "R", "orcid": "0000-0001-9881-6232", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e49665e6eabf40bd83ef8f573ff030ef.json"}}, {"family": "Domenzain", "given": "Iv\u00e1n", "initials": "I", "orcid": "0000-0002-5322-2040", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/588d2eed593448689fd63a7e656b5615.json"}}, {"family": "Billa", "given": "Virinchi", "initials": "V"}, {"family": "Limeta", "given": "Angelo", "initials": "A"}, {"family": "Hedin", "given": "Alex", "initials": "A", "orcid": "0000-0002-0829-2496", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7913daea4e3640fa9c2c00c631e23685.json"}}, {"family": "Gustafsson", "given": "Johan", "initials": "J", "orcid": "0000-0001-5072-2659", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/39eef1abb23c4ecab986fe0646830f07.json"}}, {"family": "Kerkhoven", "given": "Eduard J", "initials": "EJ", "orcid": "0000-0002-3593-5792", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/182c8731b6744479864cc75ced13d229.json"}}, {"family": "Svensson", "given": "L Thomas", "initials": "LT", "orcid": "0000-0002-9190-2979", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/540426d33d3b44d28cb823e6557dda36.json"}}, {"family": "Palsson", "given": "Bernhard O", "initials": "BO", "orcid": "0000-0003-2357-6785", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fd602b497a2f48f39452f55f1fc28ac9.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca58bf2d214047e0ae5e38a42a0f2808.json"}}, {"family": "Hansson", "given": "Lena", "initials": "L"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ea446aa574042a295d5f69437402f76.json"}}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/33f2b49a39ed4e54ba77dfe397ed3087.json"}}], "type": "journal article", "published": "2020-03-24", "journal": {"title": "Sci Signal", "issn": "1937-9145", "issn-l": "1945-0877", "volume": "13", "issue": "624", "pages": "eaaz1482"}, "abstract": "Genome-scale metabolic models (GEMs) are valuable tools to study metabolism and provide a scaffold for the integrative analysis of omics data. Researchers have developed increasingly comprehensive human GEMs, but the disconnect among different model sources and versions impedes further progress. We therefore integrated and extensively curated the most recent human metabolic models to construct a consensus GEM, Human1. We demonstrated the versatility of Human1 through the generation and analysis of cell- and tissue-specific models using transcriptomic, proteomic, and kinetic data. We also present an accompanying web portal, Metabolic Atlas (https://www.metabolicatlas.org/), which facilitates further exploration and visualization of Human1 content. Human1 was created using a version-controlled, open-source model development framework to enable community-driven curation and refinement. This framework allows Human1 to be an evolving shared resource for future studies of human health and disease.", "doi": "10.1126/scisignal.aaz1482", "pmid": "32209698", "labels": {"Adil Mardinoglu": "", "SciLifeLab Fellow": "", "Avlant Nilsson": "", "DDLS Fellow": ""}, "xrefs": [{"db": "mid", "key": "NIHMS1590510"}, {"db": "pmc", "key": "PMC7331181"}, {"db": "pii", "key": "13/624/eaaz1482"}], "notes": [], "created": "2020-11-30T03:10:14.353Z", "modified": "2026-09-23T06:33:15.510Z"}, {"entity": "publication", "iuid": "9037578f3ed640738238509f5b0c2994", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9037578f3ed640738238509f5b0c2994.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9037578f3ed640738238509f5b0c2994"}}, "title": "Facets of individual-specific health signatures determined from longitudinal plasma proteome profiling", "authors": [{"family": "Dodig-Crnkovi\u0107", "given": "Tea", "initials": "T", "orcid": "0000-0002-2875-896X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5365873ed6a7463485fb44550a4826ec.json"}}, {"family": "Hong", "given": "Mun Gwan", "initials": "MG", "orcid": "0000-0001-8603-8293", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d12504acae5c4f31b83f75c3d7786cd4.json"}}, {"family": "Thomas", "given": "Cecilia Engel", "initials": "CE", "orcid": "0000-0001-6201-6380", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c2e25790f4c14deabd43b76ff5a5bef4.json"}}, {"family": "H\u00e4ussler", "given": "Ragna S", "initials": "RS", "orcid": "0000-0003-1664-8875", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7cc0ab2ae97c4f968d6218ca2915389f.json"}}, {"family": "Bendes", "given": "Annika", "initials": "A", "orcid": "0000-0001-9329-2353", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b84a8aa3e3b4439bb0b3a9fabdebcb70.json"}}, {"family": "Dale", "given": "Matilda", "initials": "M", "orcid": "0000-0002-5788-7744", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ceec63ec0dea45eaa5ad3c4d34b10959.json"}}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE", "orcid": "0000-0002-7315-7899", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d6fa8b01df9f4bf68607603c51c5a106.json"}}, {"family": "Schuppe-Koistinen", "given": "Ina", "initials": "I"}, {"family": "Odeberg", "given": "Jacob", "initials": "J", "orcid": "0000-0003-0996-1644", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d6abb3fc822a4cacbf1d45224f2442f5.json"}}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/abbbf8193d5a4376a5c726768d039439.json"}}, {"family": "Gummesson", "given": "Anders", "initials": "A", "orcid": "0000-0003-0024-960X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1703619132e242aaad263d4ecd80a8ae.json"}}, {"family": "Bergstr\u00f6m", "given": "G\u00f6ran", "initials": "G"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ea446aa574042a295d5f69437402f76.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/022e140799b6466ea123319c3d70c76e.json"}}], "type": "posted-content", "published": "2020-03-15", "journal": {"title": "bioRxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2020.03.13.988683", "pmid": null, "labels": {"Fredrik Edfors": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2026-08-20T09:56:21.219Z", "modified": "2026-10-05T08:42:30.854Z"}, {"entity": "publication", "iuid": "182e6aed60fd4f9d98929d3a67a46248", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/182e6aed60fd4f9d98929d3a67a46248.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/182e6aed60fd4f9d98929d3a67a46248"}}, "title": "Identification of germline variants in adults with hemophagocytic lymphohistiocytosis.", "authors": [{"family": "Miller", "given": "Peter G", "initials": "PG"}, {"family": "Niroula", "given": "Abhishek", "initials": "A"}, {"family": "Ceremsak", "given": "John J", "initials": "JJ"}, {"family": "Gibson", "given": "Christopher J", "initials": "CJ"}, {"family": "Taylor", "given": "Martin S", "initials": "MS"}, {"family": "Birndt", "given": "Sebastian", "initials": "S"}, {"family": "Perner", "given": "Florian", "initials": "F"}, {"family": "Arnason", "given": "Jon", "initials": "J"}, {"family": "Sperling", "given": "Adam S", "initials": "AS"}, {"family": "Agrawal", "given": "Mridul", "initials": "M"}, {"family": "Schram", "given": "Alison M", "initials": "AM"}, {"family": "Nikiforow", "given": "Sarah", "initials": "S"}, {"family": "Pihan", "given": "German", "initials": "G"}, {"family": "Hasserjian", "given": "Robert P", "initials": "RP"}, {"family": "Aster", "given": "Jon C", "initials": "JC"}, {"family": "La Ros\u00e9e", "given": "Paul", "initials": "P"}, {"family": "Morgan", "given": "Elizabeth A", "initials": "EA"}, {"family": "Berliner", "given": "Nancy", "initials": "N"}, {"family": "Ebert", "given": "Benjamin L", "initials": "BL"}], "type": "journal article", "published": "2020-03-10", "journal": {"title": "Blood Adv", "issn": "2473-9529", "volume": "4", "issue": "5", "pages": "925-929", "issn-l": null}, "abstract": "Some germline variants are predicted to disrupt protein function in HLH-associated genes. Such variants are neither enriched in adult-onset HLH nor associated with specific clinical or laboratory features of HLH.", "doi": "10.1182/bloodadvances.2019001272", "pmid": "32150605", "labels": {"Abhishek Niroula": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC7065469"}, {"db": "pii", "key": "S2473-9529(20)31457-9"}], "notes": [], "created": "2023-11-20T11:21:49.546Z", "modified": "2023-11-20T11:21:49.555Z"}, {"entity": "publication", "iuid": "8a42f5400d8d48eaa6671775fcf9a1f4", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8a42f5400d8d48eaa6671775fcf9a1f4.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8a42f5400d8d48eaa6671775fcf9a1f4"}}, "title": "An atlas of the protein-coding genes in the human, pig, and mouse brain.", "authors": [{"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E", "orcid": "0000-0002-0327-7377", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ec6fb5a1c88b44798144fd2de255fb00.json"}}, {"family": "Zhong", "given": "Wen", "initials": "W", "orcid": "0000-0002-7422-6104", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d6ffb1140aaa42c5ac63fe76653fc63b.json"}}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/abbbf8193d5a4376a5c726768d039439.json"}}, {"family": "Karlsson", "given": "Max", "initials": "M", "orcid": "0000-0002-7000-4416", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b93284f942e44f1086616357d77267c3.json"}}, {"family": "Mitsios", "given": "Nicholas", "initials": "N", "orcid": "0000-0001-6243-4953", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9443771d4c464bf6b18fc130b329444b.json"}}, {"family": "Adori", "given": "Csaba", "initials": "C"}, {"family": "Oksvold", "given": "Per", "initials": "P", "orcid": "0000-0003-3014-5502", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/16beca5822c747128300910b5c74dbfc.json"}}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e213b04f8984c8eb00c68f5bc2f6a36.json"}}, {"family": "Limiszewska", "given": "Agnieszka", "initials": "A", "orcid": "0000-0003-1601-8195", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4a01140f24e6413989da73df262d4bd5.json"}}, {"family": "Hikmet", "given": "Feria", "initials": "F", "orcid": "0000-0002-3750-9308", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0193c8f793be4446827f92db9871e2a7.json"}}, {"family": "Huang", "given": "Jinrong", "initials": "J", "orcid": "0000-0001-8085-9939", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/457018fbd5e44986bf72a18e60e681c7.json"}}, {"family": "Du", "given": "Yutao", "initials": "Y"}, {"family": "Lin", "given": "Lin", "initials": "L", "orcid": "0000-0002-7546-4948", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bcc1572910494eb191e316307d213606.json"}}, {"family": "Dong", "given": "Zhanying", "initials": "Z"}, {"family": "Yang", "given": "Ling", "initials": "L", "orcid": "0000-0002-5425-8256", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fab12296b935480d85e05798a2cab0a1.json"}}, {"family": "Liu", "given": "Xin", "initials": "X", "orcid": "0000-0003-3256-2940", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2e3b0dc19f9440358b76e52e48ef1e45.json"}}, {"family": "Jiang", "given": "Hui", "initials": "H"}, {"family": "Xu", "given": "Xun", "initials": "X", "orcid": "0000-0002-5338-5173", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4a6e2e5d236148c7ba386c89941f2d41.json"}}, {"family": "Wang", "given": "Jian", "initials": "J"}, {"family": "Yang", "given": "Huanming", "initials": "H", "orcid": "0000-0003-1703-3012", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c8728405c7d7499287d1a85e050a3188.json"}}, {"family": "Bolund", "given": "Lars", "initials": "L"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca58bf2d214047e0ae5e38a42a0f2808.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f46e4161be08458994efddb75ed75874.json"}}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K", "orcid": "0000-0002-0257-7554", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f4c4545bd2324b7d9b6696dab5bcb7dd.json"}}, {"family": "Lindskog", "given": "Cecilia", "initials": "C", "orcid": "0000-0001-5611-1015", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/21610a810a87459c962d6da3f2ad38ad.json"}}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9f5294424542413c9ba4432c839c2b63.json"}}, {"family": "Luo", "given": "Yonglun", "initials": "Y", "orcid": "0000-0002-0007-7759", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f0283cb6c284428f906b0d03fda62a1e.json"}}, {"family": "H\u00f6kfelt", "given": "Tomas", "initials": "T"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ea446aa574042a295d5f69437402f76.json"}}, {"family": "Mulder", "given": "Jan", "initials": "J", "orcid": "0000-0003-3717-5018", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/40ed8170792444b491519e499d51c434.json"}}], "type": "comparative study", "published": "2020-03-06", "journal": {"title": "Science (New York, N.Y.)", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "367", "issue": "6482", "pages": "eaay5947"}, "abstract": "The brain, with its diverse physiology and intricate cellular organization, is the most complex organ of the mammalian body. To expand our basic understanding of the neurobiology of the brain and its diseases, we performed a comprehensive molecular dissection of 10 major brain regions and multiple subregions using a variety of transcriptomics methods and antibody-based mapping. This analysis was carried out in the human, pig, and mouse brain to allow the identification of regional expression profiles, as well as to study similarities and differences in expression levels between the three species. The resulting data have been made available in an open-access Brain Atlas resource, part of the Human Protein Atlas, to allow exploration and comparison of the expression of individual protein-coding genes in various parts of the mammalian brain.", "doi": "10.1126/science.aay5947", "pmid": "32139519", "labels": {"Adil Mardinoglu": "", "SciLifeLab Fellow": "", "Fredrik Edfors": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pii", "key": "367/6482/eaay5947"}], "notes": [], "created": "2020-11-30T03:09:29.619Z", "modified": "2026-09-22T19:58:48.334Z"}, {"entity": "publication", "iuid": "621d2a0798224349bae5862bbb56e574", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/621d2a0798224349bae5862bbb56e574.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/621d2a0798224349bae5862bbb56e574"}}, "title": "Stressful Beginnings with Long-Term Consequences.", "authors": [{"family": "Consiglio", "given": "Camila Rosat", "initials": "CR"}, {"family": "Brodin", "given": "Petter", "initials": "P"}], "type": "journal article", "published": "2020-03-05", "journal": {"title": "Cell", "issn": "1097-4172", "volume": "180", "issue": "5", "pages": "820-821", "issn-l": "0092-8674"}, "abstract": "Early-life stress can have long-term health consequences, but the mechanisms of this are unknown. In this issue of Cell, Hong et al. demonstrate one such mechanism linking perinatal corticosteroid exposure to reduced CD8+ T cell function later in life and impaired anti-cancer and anti-bacterial immune responses.", "doi": "10.1016/j.cell.2020.02.021", "pmid": "32142672", "labels": {"Camila Consiglio": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pii", "key": "S0092-8674(20)30165-3"}], "notes": [], "created": "2023-11-22T09:16:33.084Z", "modified": "2026-09-23T13:05:46.696Z"}, {"entity": "publication", "iuid": "2743435362f74bbeae10c2a031886125", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/2743435362f74bbeae10c2a031886125.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/2743435362f74bbeae10c2a031886125"}}, "title": "Membrane lipids are both the substrates and a mechanistically responsive environment of TMEM16 scramblase proteins.", "authors": [{"family": "Khelashvili", "given": "George", "initials": "G"}, {"family": "Cheng", "given": "Xiaolu", "initials": "X"}, {"family": "Falzone", "given": "Maria E", "initials": "ME"}, {"family": "Doktorova", "given": "Milka", "initials": "M"}, {"family": "Accardi", "given": "Alessio", "initials": "A"}, {"family": "Weinstein", "given": "Harel", "initials": "H", "orcid": "0000-0003-3473-9818", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d92af3f7c4bb4ca1abe3d658a824c446.json"}}], "type": "journal article", "published": "2020-03-05", "journal": {"title": "J Comput Chem", "issn": "1096-987X", "issn-l": "0192-8651", "volume": "41", "issue": "6", "pages": "538-551"}, "abstract": "Recent discoveries about functional mechanisms of proteins in the TMEM16 family of phospholipid scramblases have illuminated the dual role of the membrane as both the substrate and a mechanistically responsive environment in the wide range of physiological processes and genetic disorders in which they are implicated. This is highlighted in the review of recent findings from our collaborative investigations of molecular mechanisms of TMEM16 scramblases that emerged from iterative functional, structural, and computational experimentation. In the context of this review, we present new MD simulations and trajectory analyses motivated by the fact that new structural information about the TMEM16 scramblases is emerging from cryo-EM determinations in lipid nanodiscs. Because the functional environment of these proteins in in vivo and in in vitro is closer to flat membranes, we studied comparatively the responses of the membrane to the TMEM16 proteins in flat membranes and nanodiscs. We find that bilayer shapes in the nanodiscs are very different from those observed in the flat membrane systems, but the function-related slanting of the membrane observed at the nhTMEM16 boundary with the protein is similar in the nanodiscs and in the flat bilayers. This changes, however, in the bilayer composed of longer-tail lipids, which is thicker near the phospholipid translocation pathway, which may reflect an enhanced tendency of the long tails to penetrate the pathway and create, as shown previously, a nonconductive environment. These findings support the correspondence between the mechanistic involvement of the lipid environment in the flat membranes, and the nanodiscs. \u00a9 2019 Wiley Periodicals, Inc.", "doi": "10.1002/jcc.26105", "pmid": "31750558", "labels": {"Milka Doktorova": null, "DDLS Fellow": null}, "xrefs": [{"db": "mid", "key": "NIHMS1591693"}, {"db": "pmc", "key": "PMC7261202"}], "notes": [], "created": "2024-11-27T12:17:10.491Z", "modified": "2024-11-29T12:16:25.788Z"}, {"entity": "publication", "iuid": "5b3c486c52504b35985f784b52f174a0", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5b3c486c52504b35985f784b52f174a0.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5b3c486c52504b35985f784b52f174a0"}}, "title": "No evidence for DNA N 6-methyladenine in mammals.", "authors": [{"family": "Douvlataniotis", "given": "Karolos", "initials": "K", "orcid": "0000-0002-5511-2232", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b82c735ba61d4862b373683f1210ce19.json"}}, {"family": "Bensberg", "given": "Maike", "initials": "M", "orcid": "0000-0003-2395-6083", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3fe8907522864854b5d2c87cd8144e73.json"}}, {"family": "Lentini", "given": "Antonio", "initials": "A", "orcid": "0000-0003-1239-5495", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c5042d3005814ad0a2d1eaeee5d2de3b.json"}}, {"family": "Gylemo", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-5253-6737", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/87b7679215e543d285e315e5dc841b9e.json"}}, {"family": "Nestor", "given": "Colm E", "initials": "CE", "orcid": "0000-0001-5853-1769", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/53da1d2e5d714a368bcb61c4001abd0f.json"}}], "type": "journal article", "published": "2020-03-00", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "6", "issue": "12", "pages": "eaay3335", "issn-l": "2375-2548"}, "abstract": "N 6-methyladenine (6mdA) is a widespread DNA modification in bacteria. More recently, 6mdA has also been characterized in mammalian DNA. However, measurements of 6mdA abundance and profiles are often very dissimilar between studies, even when performed on DNA from identical mammalian cell types. Using comprehensive bioinformatics analyses of published data and novel experimental approaches, we reveal that efforts to assay 6mdA in mammals have been severely compromised by bacterial contamination, RNA contamination, technological limitations, and antibody nonspecificity. These complications render 6mdA an exceptionally problematic DNA modification to study and have resulted in erroneous detection of 6mdA in several mammalian systems. Together, our results strongly imply that the evidence published to date is not sufficient to support the presence of 6mdA in mammals.", "doi": "10.1126/sciadv.aay3335", "pmid": "32206710", "labels": {"Antonio Lentini": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC7080441"}, {"db": "pii", "key": "aay3335"}], "notes": [], "created": "2025-03-28T07:14:44.512Z", "modified": "2025-03-28T07:14:44.539Z"}, {"entity": "publication", "iuid": "8d531f116272411fbef85aad255682ef", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8d531f116272411fbef85aad255682ef.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8d531f116272411fbef85aad255682ef"}}, "title": "Proposal of a Taxonomic Nomenclature for the Bacillus cereus Group Which Reconciles Genomic Definitions of Bacterial Species with Clinical and Industrial Phenotypes.", "authors": [{"family": "Carroll", "given": "Laura M", "initials": "LM"}, {"family": "Wiedmann", "given": "Martin", "initials": "M"}, {"family": "Kovac", "given": "Jasna", "initials": "J", "orcid": "0000-0002-9465-4552", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d18e6f5bd24644e18030b59391d1a755.json"}}], "type": "journal article", "published": "2020-02-25", "journal": {"title": "MBio", "issn": "2150-7511", "volume": "11", "issue": "1", "issn-l": null}, "abstract": "The Bacillus cereus group comprises numerous closely related species, including bioterrorism agent B. anthracis, foodborne pathogen B. cereus, and biopesticide B. thuringiensis Differentiating organisms capable of causing illness or death from those used in industry is essential for risk assessment and outbreak preparedness. However, current species definitions facilitate species-phenotype incongruences, particularly when horizontally acquired genes are responsible for a phenotype. Using all publicly available B. cereus group genomes (n = 2,231), we show that current species definitions lead to overlapping genomospecies clusters, in which 66.2% of genomes belong to multiple genomospecies at a conventional 95 average nucleotide identity (ANI) genomospecies threshold. A genomospecies threshold of \u224892.5 ANI is shown to reflect a natural gap in genome similarity for the B. cereus group, and medoid genomes identified at this threshold are shown to yield resolvable genomospecies clusters with minimal overlap (six of 2,231 genomes assigned to multiple genomospecies; 0.269%). We thus propose a nomenclatural framework for the B. cereus group which accounts for (i) genomospecies using resolvable genomospecies clusters obtained at \u224892.5 ANI, (ii) established lineages of medical importance using a formal collection of subspecies names, and (iii) heterogeneity of clinically and industrially important phenotypes using a formalized and extended collection of biovar terms. We anticipate that the proposed nomenclature will remain interpretable to clinicians, without sacrificing genomic species definitions, which can in turn aid in pathogen surveillance; early detection of emerging, high-risk genotypes; and outbreak preparedness.IMPORTANCE Historical species definitions for many prokaryotes, including pathogens, have relied on phenotypic characteristics that are inconsistent with genome evolution. This scenario forces microbiologists and clinicians to face a tradeoff between taxonomic rigor and clinical interpretability. Using the Bacillus cereus group as a model, a conceptual framework for the taxonomic delineation of prokaryotes which reconciles genomic definitions of species with clinically and industrially relevant phenotypes is presented. The nomenclatural framework outlined here serves as a model for genomics-based bacterial taxonomy that moves beyond arbitrarily set genomospecies thresholds while maintaining congruence with phenotypes and historically important species names.", "doi": "10.1128/mBio.00034-20", "pmid": "32098810", "labels": {"Laura Carroll": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC7042689"}, {"db": "pii", "key": "mBio.00034-20"}], "notes": [], "created": "2025-03-18T17:25:27.627Z", "modified": "2025-03-18T17:25:27.643Z"}, {"entity": "publication", "iuid": "fa5d84f5499043a6b66d777ace1eb518", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/fa5d84f5499043a6b66d777ace1eb518.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/fa5d84f5499043a6b66d777ace1eb518"}}, "title": "A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project.", "authors": [{"family": "Andermann", "given": "Tobias", "initials": "T"}, {"family": "Torres Jim\u00e9nez", "given": "Maria Fernanda", "initials": "MF"}, {"family": "Matos-Marav\u00ed", "given": "P\u00e1vel", "initials": "P"}, {"family": "Batista", "given": "Romina", "initials": "R"}, {"family": "Blanco-Pastor", "given": "Jos\u00e9 L", "initials": "JL"}, {"family": "Gustafsson", "given": "A Lovisa S", "initials": "ALS"}, {"family": "Kistler", "given": "Logan", "initials": "L"}, {"family": "Liberal", "given": "Isabel M", "initials": "IM"}, {"family": "Oxelman", "given": "Bengt", "initials": "B"}, {"family": "Bacon", "given": "Christine D", "initials": "CD"}, {"family": "Antonelli", "given": "Alexandre", "initials": "A"}], "type": "journal article", "published": "2020-02-21", "journal": {"title": "Front Genet", "issn": "1664-8021", "volume": "10", "pages": "1407", "issn-l": "1664-8021"}, "abstract": "High-throughput DNA sequencing techniques enable time- and cost-effective sequencing of large portions of the genome. Instead of sequencing and annotating whole genomes, many phylogenetic studies focus sequencing effort on large sets of pre-selected loci, which further reduces costs and bioinformatic challenges while increasing coverage. One common approach that enriches loci before sequencing is often referred to as target sequence capture. This technique has been shown to be applicable to phylogenetic studies of greatly varying evolutionary depth. Moreover, it has proven to produce powerful, large multi-locus DNA sequence datasets suitable for phylogenetic analyses. However, target capture requires careful considerations, which may greatly affect the success of experiments. Here we provide a simple flowchart for designing phylogenomic target capture experiments. We discuss necessary decisions from the identification of target loci to the final bioinformatic processing of sequence data. We outline challenges and solutions related to the taxonomic scope, sample quality, and available genomic resources of target capture projects. We hope this review will serve as a useful roadmap for designing and carrying out successful phylogenetic target capture studies.", "doi": "10.3389/fgene.2019.01407", "pmid": "32153629", "labels": {"Tobias Andermann": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC7047930"}], "notes": [], "created": "2022-11-11T09:08:49.161Z", "modified": "2022-11-11T09:08:49.186Z"}, {"entity": "publication", "iuid": "bf5556b972fd431194aa533795947741", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/bf5556b972fd431194aa533795947741.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/bf5556b972fd431194aa533795947741"}}, "title": "Regulation of lipid saturation without sensing membrane fluidity.", "authors": [{"family": "Ballweg", "given": "Stephanie", "initials": "S"}, {"family": "Sezgin", "given": "Erdinc", "initials": "E", "orcid": "0000-0002-4915-388X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f7bd3619c7fd48318bc4c1e7a9910df8.json"}}, {"family": "Doktorova", "given": "Milka", "initials": "M"}, {"family": "Covino", "given": "Roberto", "initials": "R", "orcid": "0000-0003-0884-0402", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c7da64cbd2264200a010eb56a9ff58f7.json"}}, {"family": "Reinhard", "given": "John", "initials": "J"}, {"family": "Wunnicke", "given": "Dorith", "initials": "D"}, {"family": "H\u00e4nelt", "given": "Inga", "initials": "I", "orcid": "0000-0003-1495-3163", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/75660c0be0e14b1f8cd63e65af90146b.json"}}, {"family": "Levental", "given": "Ilya", "initials": "I", "orcid": "0000-0002-1206-9545", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7fe40c2b810348cab78616402d4d1f1f.json"}}, {"family": "Hummer", "given": "Gerhard", "initials": "G", "orcid": "0000-0001-7768-746X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1c5c18c18252491ab252dd6c6af46bb1.json"}}, {"family": "Ernst", "given": "Robert", "initials": "R", "orcid": "0000-0002-0283-3490", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d2cdc47d392249968823a56f0d3854f4.json"}}], "type": "journal article", "published": "2020-02-06", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "11", "issue": "1", "pages": "756"}, "abstract": "Cells maintain membrane fluidity by regulating lipid saturation, but the molecular mechanisms of this homeoviscous adaptation remain poorly understood. We have reconstituted the core machinery for regulating lipid saturation in baker's yeast to study its molecular mechanism. By combining molecular dynamics simulations with experiments, we uncover a remarkable sensitivity of the transcriptional regulator Mga2 to the abundance, position, and configuration of double bonds in lipid acyl chains, and provide insights into the molecular rules of membrane adaptation. Our data challenge the prevailing hypothesis that membrane fluidity serves as the measured variable for regulating lipid saturation. Rather, we show that Mga2 senses the molecular lipid-packing density in a defined region of the membrane. Our findings suggest that membrane property sensors have evolved remarkable sensitivities to highly specific aspects of membrane structure and dynamics, thus paving the way toward the development of genetically encoded reporters for such properties in the future.", "doi": "10.1038/s41467-020-14528-1", "pmid": "32029718", "labels": {"Erdinc Sezgin": null, "SciLifeLab Fellow": null, "Milka Doktorova": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC7005026"}, {"db": "pii", "key": "10.1038/s41467-020-14528-1"}], "notes": [], "created": "2020-11-05T16:08:00.361Z", "modified": "2024-11-29T12:16:33.378Z"}, {"entity": "publication", "iuid": "bc2e0d95b2974e3893ee33215d183251", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/bc2e0d95b2974e3893ee33215d183251.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/bc2e0d95b2974e3893ee33215d183251"}}, "title": "Selective sweeps on novel and introgressed variation shape mimicry loci in a butterfly adaptive radiation.", "authors": [{"family": "Moest", "given": "Markus", "initials": "M", "orcid": "0000-0003-2370-2788", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/68ebb42ec8a04e78ac67b2002b361d83.json"}}, {"family": "Van Belleghem", "given": "Steven M", "initials": "SM", "orcid": "0000-0001-9399-1007", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ce786f23c8334751b73d3fd6b79aa8e8.json"}}, {"family": "James", "given": "Jennifer E", "initials": "JE", "orcid": "0000-0003-0518-6783", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4b807f7ab8f46f8a5e927e1b090d662.json"}}, {"family": "Salazar", "given": "Camilo", "initials": "C", "orcid": "0000-0001-9217-6588", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b1047fb6ca864cd08eb7876b190ebd8d.json"}}, {"family": "Martin", "given": "Simon H", "initials": "SH", "orcid": "0000-0002-0747-7456", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/68ae66fad62c4ebdb028816ec56a4283.json"}}, {"family": "Barker", "given": "Sarah L", "initials": "SL"}, {"family": "Moreira", "given": "Gilson R P", "initials": "GRP"}, {"family": "M\u00e9rot", "given": "Claire", "initials": "C", "orcid": "0000-0003-2607-7818", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4730b49cb0db4560baa7454d8044ae79.json"}}, {"family": "Joron", "given": "Mathieu", "initials": "M", "orcid": "0000-0003-1043-4147", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ee1b5386def34ee9aee4327a4991e69b.json"}}, {"family": "Nadeau", "given": "Nicola J", "initials": "NJ", "orcid": "0000-0002-9319-921X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a57ba1ad6be044079645609d75cd41d7.json"}}, {"family": "Steiner", "given": "Florian M", "initials": "FM"}, {"family": "Jiggins", "given": "Chris D", "initials": "CD", "orcid": "0000-0002-7809-062X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9bd55f1db6ab4e7daaa61e052886060b.json"}}], "type": "journal article", "published": "2020-02-00", "journal": {"title": "PLoS Biol.", "issn": "1545-7885", "issn-l": "1544-9173", "volume": "18", "issue": "2", "pages": "e3000597"}, "abstract": "Natural selection leaves distinct signatures in the genome that can reveal the targets and history of adaptive evolution. By analysing high-coverage genome sequence data from 4 major colour pattern loci sampled from nearly 600 individuals in 53 populations, we show pervasive selection on wing patterns in the Heliconius adaptive radiation. The strongest signatures correspond to loci with the greatest phenotypic effects, consistent with visual selection by predators, and are found in colour patterns with geographically restricted distributions. These recent sweeps are similar between co-mimics and indicate colour pattern turn-over events despite strong stabilising selection. Using simulations, we compare sweep signatures expected under classic hard sweeps with those resulting from adaptive introgression, an important aspect of mimicry evolution in Heliconius butterflies. Simulated recipient populations show a distinct 'volcano' pattern with peaks of increased genetic diversity around the selected target, characteristic of sweeps of introgressed variation and consistent with diversity patterns found in some populations. Our genomic data reveal a surprisingly dynamic history of colour pattern selection and co-evolution in this adaptive radiation.", "doi": "10.1371/journal.pbio.3000597", "pmid": "32027643", "labels": {"Jennifer James": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC7029882"}, {"db": "pii", "key": "PBIOLOGY-D-19-01905"}], "notes": [], "created": "2024-11-27T09:29:03.471Z", "modified": "2024-11-29T09:37:04.682Z"}, {"entity": "publication", "iuid": "dcc1555e1af64f9dbcbfe7efdec6f186", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/dcc1555e1af64f9dbcbfe7efdec6f186.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/dcc1555e1af64f9dbcbfe7efdec6f186"}}, "title": "Publisher Correction: Analysis of the Human Protein Atlas Image Classification competition.", "authors": [{"family": "Ouyang", "given": "Wei", "initials": "W", "orcid": "0000-0002-0291-926X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56f601e1d1c6448aab0c3a1e3cffdbfc.json"}}, {"family": "Winsnes", "given": "Casper F", "initials": "CF", "orcid": "0000-0002-0028-5865", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/edeb3bc6c95d4185bf2098bf1e4a5e3c.json"}}, {"family": "Hjelmare", "given": "Martin", "initials": "M", "orcid": "0000-0001-7375-9681", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b13d6d89bd3a43eab43eee98539ed4ad.json"}}, {"family": "Cesnik", "given": "Anthony J", "initials": "AJ"}, {"family": "\u00c5kesson", "given": "Lovisa", "initials": "L"}, {"family": "Xu", "given": "Hao", "initials": "H"}, {"family": "Sullivan", "given": "Devin P", "initials": "DP"}, {"family": "Dai", "given": "Shubin", "initials": "S"}, {"family": "Lan", "given": "Jun", "initials": "J"}, {"family": "Jinmo", "given": "Park", "initials": "P"}, {"family": "Galib", "given": "Shaikat M", "initials": "SM", "orcid": "0000-0002-8192-578X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d73568f63e9c4f4f8687af3846410d38.json"}}, {"family": "Henkel", "given": "Christof", "initials": "C"}, {"family": "Hwang", "given": "Kevin", "initials": "K"}, {"family": "Poplavskiy", "given": "Dmytro", "initials": "D"}, {"family": "Tunguz", "given": "Bojan", "initials": "B"}, {"family": "Wolfinger", "given": "Russel D", "initials": "RD"}, {"family": "Gu", "given": "Yinzheng", "initials": "Y"}, {"family": "Li", "given": "Chuanpeng", "initials": "C"}, {"family": "Xie", "given": "Jinbin", "initials": "J"}, {"family": "Buslov", "given": "Dmitry", "initials": "D"}, {"family": "Fironov", "given": "Sergei", "initials": "S"}, {"family": "Kiselev", "given": "Alexander", "initials": "A"}, {"family": "Panchenko", "given": "Dmytro", "initials": "D"}, {"family": "Cao", "given": "Xuan", "initials": "X"}, {"family": "Wei", "given": "Runmin", "initials": "R"}, {"family": "Wu", "given": "Yuanhao", "initials": "Y"}, {"family": "Zhu", "given": "Xun", "initials": "X"}, {"family": "Tseng", "given": "Kuan-Lun", "initials": "KL"}, {"family": "Gao", "given": "Zhifeng", "initials": "Z"}, {"family": "Ju", "given": "Cheng", "initials": "C"}, {"family": "Yi", "given": "Xiaohan", "initials": "X"}, {"family": "Zheng", "given": "Hongdong", "initials": "H"}, {"family": "Kappel", "given": "Constantin", "initials": "C"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb07e6d0122c4528a927c1fe922e3bc8.json"}}], "type": "published erratum", "published": "2020-02-00", "journal": {"title": "Nat. Methods", "issn": "1548-7105", "volume": "17", "issue": "2", "pages": "241", "issn-l": "1548-7091"}, "abstract": "An amendment to this paper has been published and can be accessed via a link at the top of the paper.", "doi": "10.1038/s41592-020-0734-y", "pmid": "31969731", "labels": {"DDLS Fellow": "", "Wei Ouyang": ""}, "xrefs": [{"db": "pmc", "key": "PMC7000326"}, {"db": "pii", "key": "10.1038/s41592-020-0734-y"}], "notes": [], "created": "2026-08-20T09:02:30.977Z", "modified": "2026-09-23T14:40:54.568Z"}, {"entity": "publication", "iuid": "fd8b51db3fff4e129a4cf2a2f67a92d5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/fd8b51db3fff4e129a4cf2a2f67a92d5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/fd8b51db3fff4e129a4cf2a2f67a92d5"}}, "title": "Is evolution predictable? Quantitative genetics under complex genotype-phenotype maps.", "authors": [{"family": "Milocco", "given": "Lisandro", "initials": "L", "orcid": "0000-0003-3953-0407", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/74f9e4dfff0e4b008c46b75e3d319673.json"}}, {"family": "Salazar-Ciudad", "given": "Isaac", "initials": "I", "orcid": "0000-0003-1607-0962", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5d1949fc8c294af6b5231b0c308460ee.json"}}], "type": "journal article", "published": "2020-02-00", "journal": {"title": "Evolution", "issn": "1558-5646", "volume": "74", "issue": "2", "pages": "230-244", "issn-l": "0014-3820"}, "abstract": "A fundamental aim of post-genomic 21st century biology is to understand the genotype-phenotype map (GPM) or how specific genetic variation relates to specific phenotypic variation. Quantitative genetics approximates such maps using linear models, and has developed methods to predict the response to selection in a population. The other major field of research concerned with the GPM, developmental evolutionary biology, or evo-devo, has found the GPM to be highly nonlinear and complex. Here, we quantify how the predictions of quantitative genetics are affected by a complex, nonlinear map based on the development of a multicellular organ. We compared the predicted change in mean phenotype for a single generation using the multivariate breeder's equation, with the change observed from the model of development. We found that there are frequent disagreements between predicted and observed responses to selection due to the nonlinear nature of the genotype-phenotype map. Our results are a step toward integrating the fields studying the GPM.", "doi": "10.1111/evo.13907", "pmid": "31883344", "labels": {"DDLS Fellow": null, "Lisandro Milocco": null}, "xrefs": [{"db": "Dryad", "key": "10.5061/dryad.9cnp5hqdr"}], "notes": [], "created": "2025-11-28T14:28:15.053Z", "modified": "2025-11-28T14:28:55.122Z"}, {"entity": "publication", "iuid": "e33d0ab288fe48179ee5450e7247d7c6", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e33d0ab288fe48179ee5450e7247d7c6.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e33d0ab288fe48179ee5450e7247d7c6"}}, "title": "Classification of clear cell renal cell carcinoma based on PKM alternative splicing.", "authors": [{"family": "Li", "given": "Xiangyu", "initials": "X", "orcid": "0000-0002-8301-9959", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5c452ad4e8bb4302a572693103742047.json"}}, {"family": "Turanli", "given": "Beste", "initials": "B"}, {"family": "Juszczak", "given": "Kajetan", "initials": "K"}, {"family": "Kim", "given": "Woonghee", "initials": "W"}, {"family": "Arif", "given": "Muhammad", "initials": "M", "orcid": "0000-0003-2261-0881", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c8ffc9889ace44e3b992816601b817e2.json"}}, {"family": "Sato", "given": "Yusuke", "initials": "Y"}, {"family": "Ogawa", "given": "Seishi", "initials": "S"}, {"family": "Turkez", "given": "Hasan", "initials": "H"}, {"family": "Nielsen", "given": "Jens", "initials": "J"}, {"family": "Boren", "given": "Jan", "initials": "J"}, {"family": "Uhlen", "given": "Mathias", "initials": "M"}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f46e4161be08458994efddb75ed75874.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}], "type": "journal article", "published": "2020-02-00", "journal": {"title": "Heliyon", "issn": "2405-8440", "issn-l": "2405-8440", "volume": "6", "issue": "2", "pages": "e03440"}, "abstract": "Clear cell renal cell carcinoma (ccRCC) accounts for 70-80% of kidney cancer diagnoses and displays high molecular and histologic heterogeneity. Hence, it is necessary to reveal the underlying molecular mechanisms involved in progression of ccRCC to better stratify the patients and design effective treatment strategies. Here, we analyzed the survival outcome of ccRCC patients as a consequence of the differential expression of four transcript isoforms of the pyruvate kinase muscle type (PKM). We first extracted a classification biomarker consisting of eight gene pairs whose within-sample relative expression orderings (REOs) could be used to robustly classify the patients into two groups with distinct molecular characteristics and survival outcomes. Next, we validated our findings in a validation cohort and an independent Japanese ccRCC cohort. We finally performed drug repositioning analysis based on transcriptomic expression profiles of drug-perturbed cancer cell lines and proposed that paracetamol, nizatidine, dimethadione and conessine can be repurposed to treat the patients in one of the subtype of ccRCC whereas chenodeoxycholic acid, fenoterol and hexylcaine can be repurposed to treat the patients in the other subtype.", "doi": "10.1016/j.heliyon.2020.e03440", "pmid": "32095654", "labels": {"Adil Mardinoglu": "", "SciLifeLab Fellow": "", "DDLS Fellow": "", "Muhammad Arif": ""}, "xrefs": [{"db": "pmc", "key": "PMC7033363"}, {"db": "pii", "key": "S2405-8440(20)30285-1"}], "notes": [], "created": "2020-09-25T13:07:40.592Z", "modified": "2026-09-23T12:46:54.881Z"}, {"entity": "publication", "iuid": "8d04406e2b8441d2bef75dd39dc068b5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8d04406e2b8441d2bef75dd39dc068b5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8d04406e2b8441d2bef75dd39dc068b5"}}, "title": "Artificial intelligence for diagnosis and grading of prostate cancer in biopsies: a population-based, diagnostic study.", "authors": [{"family": "Str\u00f6m", "given": "Peter", "initials": "P"}, {"family": "Kartasalo", "given": "Kimmo", "initials": "K"}, {"family": "Olsson", "given": "Henrik", "initials": "H"}, {"family": "Solorzano", "given": "Leslie", "initials": "L"}, {"family": "Delahunt", "given": "Brett", "initials": "B"}, {"family": "Berney", "given": "Daniel M", "initials": "DM"}, {"family": "Bostwick", "given": "David G", "initials": "DG"}, {"family": "Evans", "given": "Andrew J", "initials": "AJ"}, {"family": "Grignon", "given": "David J", "initials": "DJ"}, {"family": "Humphrey", "given": "Peter A", "initials": "PA"}, {"family": "Iczkowski", "given": "Kenneth A", "initials": "KA"}, {"family": "Kench", "given": "James G", "initials": "JG"}, {"family": "Kristiansen", "given": "Glen", "initials": "G"}, {"family": "van der Kwast", "given": "Theodorus H", "initials": "TH"}, {"family": "Leite", "given": "Katia R M", "initials": "KRM"}, {"family": "McKenney", "given": "Jesse K", "initials": "JK"}, {"family": "Oxley", "given": "Jon", "initials": "J"}, {"family": "Pan", "given": "Chin-Chen", "initials": "CC"}, {"family": "Samaratunga", "given": "Hemamali", "initials": "H"}, {"family": "Srigley", "given": "John R", "initials": "JR"}, {"family": "Takahashi", "given": "Hiroyuki", "initials": "H"}, {"family": "Tsuzuki", "given": "Toyonori", "initials": "T"}, {"family": "Varma", "given": "Murali", "initials": "M"}, {"family": "Zhou", "given": "Ming", "initials": "M"}, {"family": "Lindberg", "given": "Johan", "initials": "J"}, {"family": "Lindskog", "given": "Cecilia", "initials": "C"}, {"family": "Ruusuvuori", "given": "Pekka", "initials": "P"}, {"family": "W\u00e4hlby", "given": "Carolina", "initials": "C"}, {"family": "Gr\u00f6nberg", "given": "Henrik", "initials": "H"}, {"family": "Rantalainen", "given": "Mattias", "initials": "M"}, {"family": "Egevad", "given": "Lars", "initials": "L"}, {"family": "Eklund", "given": "Martin", "initials": "M"}], "type": "journal article", "published": "2020-02-00", "journal": {"title": "Lancet Oncol", "issn": "1474-5488", "issn-l": null, "volume": "21", "issue": "2", "pages": "222-232"}, "abstract": "An increasing volume of prostate biopsies and a worldwide shortage of urological pathologists puts a strain on pathology departments. Additionally, the high intra-observer and inter-observer variability in grading can result in overtreatment and undertreatment of prostate cancer. To alleviate these problems, we aimed to develop an artificial intelligence (AI) system with clinically acceptable accuracy for prostate cancer detection, localisation, and Gleason grading.\n\nWe digitised 6682 slides from needle core biopsies from 976 randomly selected participants aged 50-69 in the Swedish prospective and population-based STHLM3 diagnostic study done between May 28, 2012, and Dec 30, 2014 (ISRCTN84445406), and another 271 from 93 men from outside the study. The resulting images were used to train deep neural networks for assessment of prostate biopsies. The networks were evaluated by predicting the presence, extent, and Gleason grade of malignant tissue for an independent test dataset comprising 1631 biopsies from 246 men from STHLM3 and an external validation dataset of 330 biopsies from 73 men. We also evaluated grading performance on 87 biopsies individually graded by 23 experienced urological pathologists from the International Society of Urological Pathology. We assessed discriminatory performance by receiver operating characteristics and tumour extent predictions by correlating predicted cancer length against measurements by the reporting pathologist. We quantified the concordance between grades assigned by the AI system and the expert urological pathologists using Cohen's kappa.\n\nThe AI achieved an area under the receiver operating characteristics curve of 0\u00b7997 (95% CI 0\u00b7994-0\u00b7999) for distinguishing between benign (n=910) and malignant (n=721) biopsy cores on the independent test dataset and 0\u00b7986 (0\u00b7972-0\u00b7996) on the external validation dataset (benign n=108, malignant n=222). The correlation between cancer length predicted by the AI and assigned by the reporting pathologist was 0\u00b796 (95% CI 0\u00b795-0\u00b797) for the independent test dataset and 0\u00b787 (0\u00b784-0\u00b790) for the external validation dataset. For assigning Gleason grades, the AI achieved a mean pairwise kappa of 0\u00b762, which was within the range of the corresponding values for the expert pathologists (0\u00b760-0\u00b773).\n\nAn AI system can be trained to detect and grade cancer in prostate needle biopsy samples at a ranking comparable to that of international experts in prostate pathology. Clinical application could reduce pathology workload by reducing the assessment of benign biopsies and by automating the task of measuring cancer length in positive biopsy cores. An AI system with expert-level grading performance might contribute a second opinion, aid in standardising grading, and provide pathology expertise in parts of the world where it does not exist.\n\nSwedish Research Council, Swedish Cancer Society, Swedish eScience Research Center, EIT Health.", "doi": "10.1016/S1470-2045(19)30738-7", "pmid": "31926806", "labels": {"Kimmo Kartasalo": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pii", "key": "S1470-2045(19)30738-7"}], "notes": [], "created": "2024-11-05T16:08:16.435Z", "modified": "2026-09-23T06:31:34.143Z"}, {"entity": "publication", "iuid": "bb5535c446cd46238c883eafb646aee5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/bb5535c446cd46238c883eafb646aee5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/bb5535c446cd46238c883eafb646aee5"}}, "title": "Mapping the nucleolar proteome reveals a spatiotemporal organization related to intrinsic protein disorder", "authors": [{"family": "Stenstr\u00f6m", "given": "Lovisa", "initials": "L", "orcid": "0000-0002-2387-3491", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/08e64ec3c551482db30e11948c9f6fbc.json"}}, {"family": "Mahdessian", "given": "Diana", "initials": "D"}, {"family": "Gnann", "given": "Christian", "initials": "C", "orcid": "0000-0001-6566-3559", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ac838ae59a574620bc8c9fb84271ee9c.json"}}, {"family": "Cesnik", "given": "Anthony J", "initials": "AJ", "orcid": "0000-0002-5326-7134", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0fda549f3795457fb60ec3372b98e2d5.json"}}, {"family": "Ouyang", "given": "Wei", "initials": "W", "orcid": "0000-0002-0291-926X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56f601e1d1c6448aab0c3a1e3cffdbfc.json"}}, {"family": "Leonetti", "given": "Manuel D", "initials": "MD", "orcid": "0000-0002-4881-405X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a7a2148955042f3985f39e11c7558f4.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ea446aa574042a295d5f69437402f76.json"}}, {"family": "Cuylen-H\u00e4ring", "given": "Sara", "initials": "S"}, {"family": "Thul", "given": "Peter J", "initials": "PJ"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb07e6d0122c4528a927c1fe922e3bc8.json"}}], "type": "posted-content", "published": "2020-01-30", "journal": {"title": "bioRxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2020.01.30.923003", "pmid": null, "labels": {"DDLS Fellow": null, "Wei Ouyang": null}, "xrefs": [], "notes": [], "created": "2026-08-20T09:55:45.188Z", "modified": "2026-10-05T08:17:02.421Z"}, {"entity": "publication", "iuid": "0262f92add9841849d45c5e48d15d683", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0262f92add9841849d45c5e48d15d683.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0262f92add9841849d45c5e48d15d683"}}, "title": "Phylogenomics and biogeography of the world's thrushes (Aves, Turdus): new evidence for a more parsimonious evolutionary history.", "authors": [{"family": "Batista", "given": "Romina", "initials": "R"}, {"family": "Olsson", "given": "Urban", "initials": "U"}, {"family": "Andermann", "given": "Tobias", "initials": "T"}, {"family": "Aleixo", "given": "Alexandre", "initials": "A"}, {"family": "Ribas", "given": "Camila Cherem", "initials": "CC"}, {"family": "Antonelli", "given": "Alexandre", "initials": "A"}], "type": "journal article", "published": "2020-01-29", "journal": {"title": "Proc. Biol. Sci.", "issn": "1471-2954", "volume": "287", "issue": "1919", "pages": "20192400", "issn-l": "0962-8452"}, "abstract": "To elucidate the relationships and spatial range evolution across the world of the bird genus Turdus (Aves), we produced a large genomic dataset comprising ca 2 million nucleotides for ca 100 samples representing 53 species, including over 2000 loci. We estimated time-calibrated maximum-likelihood and multispecies coalescent phylogenies and carried out biogeographic analyses. Our results indicate that there have been considerably fewer trans-oceanic dispersals within the genus Turdus than previously suggested, such that the Palaearctic clade did not originate in America and the African clade was not involved in the colonization of the Americas. Instead, our findings suggest that dispersal from the Western Palaearctic via the Antilles to the Neotropics might have occurred in a single event, giving rise to the rich Neotropical diversity of Turdus observed today, with no reverse dispersals to the Palaearctic or Africa. Our large multilocus dataset, combined with dense species-level sampling and analysed under probabilistic methods, brings important insights into historical biogeography and systematics, even in a scenario of fast and spatially complex diversification.", "doi": "10.1098/rspb.2019.2400", "pmid": "31964299", "labels": {"Tobias Andermann": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC7015335"}, {"db": "figshare", "key": "10.6084/m9.figshare.c.4800375"}], "notes": [], "created": "2022-11-11T09:10:40.207Z", "modified": "2022-11-11T09:10:40.234Z"}, {"entity": "publication", "iuid": "04d114f6b56c4f7bbff7b6ce775718dd", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/04d114f6b56c4f7bbff7b6ce775718dd.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/04d114f6b56c4f7bbff7b6ce775718dd"}}, "title": "Boosting Natural Killer Cell-Mediated Targeting of Sarcoma Through DNAM-1 and NKG2D.", "authors": [{"family": "Sayitoglu", "given": "Ece Canan", "initials": "EC"}, {"family": "Georgoudaki", "given": "Anna-Maria", "initials": "AM"}, {"family": "Chrobok", "given": "Michael", "initials": "M"}, {"family": "Ozkazanc", "given": "Didem", "initials": "D"}, {"family": "Josey", "given": "Benjamin J", "initials": "BJ"}, {"family": "Arif", "given": "Muhammad", "initials": "M"}, {"family": "Kusser", "given": "Kim", "initials": "K"}, {"family": "Hartman", "given": "Michelle", "initials": "M"}, {"family": "Chinn", "given": "Tamara M", "initials": "TM"}, {"family": "Potens", "given": "Renee", "initials": "R"}, {"family": "Pamukcu", "given": "Cevriye", "initials": "C"}, {"family": "Krueger", "given": "Robin", "initials": "R"}, {"family": "Zhang", "given": "Cheng", "initials": "C"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Alici", "given": "Evren", "initials": "E"}, {"family": "Temple", "given": "Harry Thomas", "initials": "HT"}, {"family": "Sutlu", "given": "Tolga", "initials": "T"}, {"family": "Duru", "given": "Adil Doganay", "initials": "AD"}], "type": "journal article", "published": "2020-01-28", "journal": {"title": "Front Immunol", "issn": "1664-3224", "issn-l": "1664-3224", "volume": "11", "issue": null, "pages": "40"}, "abstract": "Sarcomas are malignancies of mesenchymal origin that occur in bone and soft tissues. Many are chemo- and radiotherapy resistant, thus conventional treatments fail to increase overall survival. Natural Killer (NK) cells exert anti-tumor activity upon detection of a complex array of tumor ligands, but this has not been thoroughly explored in the context of sarcoma immunotherapy. In this study, we investigated the NK cell receptor/ligand immune profile of primary human sarcoma explants. Analysis of tumors from 32 sarcoma patients identified the proliferative marker PCNA and DNAM-1 ligands CD112 and/or CD155 as commonly expressed antigens that could be efficiently targeted by genetically modified (GM) NK cells. Despite the strong expression of CD112 and CD155 on sarcoma cells, characterization of freshly dissociated sarcomas revealed a general decrease in tumor-infiltrating NK cells compared to the periphery, suggesting a defect in the endogenous NK cell response. We also applied a functional screening approach to identify relevant NK cell receptor/ligand interactions that induce efficient anti-tumor responses using a panel NK-92 cell lines GM to over-express 12 different activating receptors. Using GM NK-92 cells against primary sarcoma explants (n = 12) revealed that DNAM-1 over-expression on NK-92 cells led to efficient degranulation against all tested explants (n = 12). Additionally, NKG2D over-expression showed enhanced responses against 10 out of 12 explants. These results show that DNAM-1+ or NKG2D+ GM NK-92 cells may be an efficient approach in targeting sarcomas. The degranulation capacity of GM NK-92 cell lines was also tested against various established tumor cell lines, including neuroblastoma, Schwannoma, melanoma, myeloma, leukemia, prostate, pancreatic, colon, and lung cancer. Enhanced degranulation of DNAM-1+ or NKG2D+ GM NK-92 cells was observed against the majority of tumor cell lines tested. In conclusion, DNAM-1 or NKG2D over-expression elicited a dynamic increase in NK cell degranulation against all sarcoma explants and cancer cell lines tested, including those that failed to induce a notable response in WT NK-92 cells. These results support the broad therapeutic potential of DNAM-1+ or NKG2D+ GM NK-92 cells and GM human NK cells for the treatment of sarcomas and other malignancies.", "doi": "10.3389/fimmu.2020.00040", "pmid": "32082316", "labels": {"Adil Mardinoglu": "", "SciLifeLab Fellow": "", "DDLS Fellow": "", "Muhammad Arif": ""}, "xrefs": [{"db": "pmc", "key": "PMC7001093"}], "notes": [], "created": "2020-11-30T03:09:41.499Z", "modified": "2026-09-23T08:40:56.056Z"}, {"entity": "publication", "iuid": "ae1b20e7fae94549a77aed22b905f3a1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ae1b20e7fae94549a77aed22b905f3a1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ae1b20e7fae94549a77aed22b905f3a1"}}, "title": "Docking Finds GPCR Ligands in Dark Chemical Matter.", "authors": [{"family": "Ballante", "given": "Flavio", "initials": "F", "orcid": "0000-0002-4831-3423", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8ce9aad230aa414886e3bf519937aad9.json"}}, {"family": "Rudling", "given": "Axel", "initials": "A"}, {"family": "Zeifman", "given": "Alexey", "initials": "A"}, {"family": "Luttens", "given": "Andreas", "initials": "A"}, {"family": "Vo", "given": "Duy Duc", "initials": "DD"}, {"family": "Irwin", "given": "John J", "initials": "JJ"}, {"family": "Kihlberg", "given": "Jan", "initials": "J", "orcid": "0000-0002-4205-6040", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7edb4dfa7c4b4d6c8c4cf0282a9c9a1a.json"}}, {"family": "Brea", "given": "Jose", "initials": "J"}, {"family": "Loza", "given": "Maria Isabel", "initials": "MI"}, {"family": "Carlsson", "given": "Jens", "initials": "J", "orcid": "0000-0003-4623-2977", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/792c1cd4aca248dc94b967115ffa82df.json"}}], "type": "journal article", "published": "2020-01-23", "journal": {"title": "J Med Chem", "issn": "1520-4804", "issn-l": "0022-2623", "volume": "63", "issue": "2", "pages": "613-620"}, "abstract": "High-throughput screening has revealed dark chemical matter, a set of drug-like compounds that has never shown bioactivity despite being extensively assayed. If dark molecules are found active at a therapeutic target, their extraordinary selectivity profiles make excellent starting points for drug development. We explored if ligands of therapeutically relevant G-protein-coupled receptors could be discovered by structure-based virtual screening of the dark chemical matter. Molecular docking screens against crystal structures of the A2A adenosine and the D4 dopamine receptors were carried out, and 53 top-ranked molecules were evaluated experimentally. Two ligands of each receptor were discovered, and the most potent had sub-micromolar affinities. Analysis of bioactivity data showed that the ligands lacked activity at hundreds of off-targets, including several that are associated with adverse effects. Our results demonstrate that virtual screening provides an efficient means to mine the dark chemical space, which could contribute to development of drugs with improved safety profiles.", "doi": "10.1021/acs.jmedchem.9b01560", "pmid": "31846328", "labels": {"Jens Carlsson": "", "SciLifeLab Fellow": "", "Andreas Luttens": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2020-11-30T18:43:42.944Z", "modified": "2026-09-23T11:48:05.377Z"}, {"entity": "publication", "iuid": "5afc72774c7c476086ecf048588acc1d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5afc72774c7c476086ecf048588acc1d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5afc72774c7c476086ecf048588acc1d"}}, "title": "Paenibacillus odorifer, the Predominant Paenibacillus Species Isolated from Milk in the United States, Demonstrates Genetic and Phenotypic Conservation of Psychrotolerance but Clade-Associated Differences in Nitrogen Metabolic Pathways.", "authors": [{"family": "Beno", "given": "Sarah M", "initials": "SM"}, {"family": "Cheng", "given": "Rachel A", "initials": "RA", "orcid": "0000-0002-5932-7011", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c4b1b7638c9c4ec7bad01d1ad6497b6a.json"}}, {"family": "Orsi", "given": "Renato H", "initials": "RH", "orcid": "0000-0003-4933-9817", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/faa4bd30679547898c7bd57690ba18bf.json"}}, {"family": "Duncan", "given": "Diana R", "initials": "DR"}, {"family": "Guo", "given": "Xiaodong", "initials": "X"}, {"family": "Kovac", "given": "Jasna", "initials": "J", "orcid": "0000-0002-9465-4552", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d18e6f5bd24644e18030b59391d1a755.json"}}, {"family": "Carroll", "given": "Laura M", "initials": "LM"}, {"family": "Martin", "given": "Nicole H", "initials": "NH"}, {"family": "Wiedmann", "given": "Martin", "initials": "M"}], "type": "journal article", "published": "2020-01-22", "journal": {"title": "mSphere", "issn": "2379-5042", "volume": "5", "issue": "1", "issn-l": "2379-5042"}, "abstract": "Paenibacillus is a spore-forming bacterial genus that is frequently isolated from fluid milk and is proposed to play a role in spoilage. To characterize the genetic and phenotypic diversity of Paenibacillus spp., we first used rpoB allelic typing data for a preexisting collection of 1,228 Paenibacillus species isolates collected from raw and processed milk, milk products, and dairy environmental sources. Whole-genome sequencing (WGS) and average nucleotide identity by BLAST (ANIb) analyses performed for a subset of 58 isolates representing unique and overrepresented rpoB allelic types in the collection revealed that these isolates represent 21 different Paenibacillus spp., with P. odorifer being the predominant species. Further genomic characterization of P. odorifer isolates identified two distinct phylogenetic clades, clades A and B, which showed significant overrepresentation of 172 and 164 ortholog clusters and 94 and 52 gene ontology (GO) terms, respectively. While nitrogen fixation genes were found in both clades, multiple genes associated with nitrate and nitrite reduction were overrepresented in clade A isolates; additional phenotypic testing demonstrated that nitrate reduction is specific to isolates in clade A. Hidden Markov models detected 9 to 10 different classes of cold shock-associated genetic elements in all P. odorifer isolates. Phenotypic testing revealed that all isolates tested here can grow in skim milk broth at 6\u00b0C, suggesting that psychrotolerance is conserved in P. odorifer Overall, our data suggest that Paenibacillus spp. isolated from milk in the United States represent broad genetic diversity, which may provide challenges for targeted-control strategies aimed at reducing fluid milk spoilage.IMPORTANCE Although Paenibacillus species isolates are frequently isolated from pasteurized fluid milk, the link between the genetic diversity and phenotypic characteristics of these isolates was not well understood, especially as some Bacillales isolated from milk are unable to grow at refrigeration temperatures. Our data demonstrate that Paenibacillus spp. isolated from fluid milk represent tremendous interspecies diversity, with P. odorifer being the predominant Paenibacillus sp. isolated. Furthermore, genetic and phenotypic data support that P. odorifer is well suited to transition from a soil-dwelling environment, where nitrogen fixation (and other nitrate/nitrite reduction pathways present only in clade A) may facilitate growth, to fluid milk, where its multiple cold shock-associated adaptations enable it to grow at refrigeration temperatures throughout the storage of milk. Therefore, efforts to reduce bacterial contamination of milk will require a systematic approach to reduce P. odorifer contamination of raw milk.", "doi": "10.1128/mSphere.00739-19", "pmid": "31969477", "labels": {"Laura Carroll": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC7407005"}, {"db": "pii", "key": "5/1/e00739-19"}], "notes": [], "created": "2025-03-18T17:25:13.299Z", "modified": "2025-03-18T17:25:13.415Z"}, {"entity": "publication", "iuid": "cd5cf48c1645452c84b56f80f60d834a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/cd5cf48c1645452c84b56f80f60d834a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/cd5cf48c1645452c84b56f80f60d834a"}}, "title": "On the Long and Winding Road to a Perfect Membrane Model.", "authors": [{"family": "Doktorova", "given": "Milka", "initials": "M"}], "type": "journal article", "published": "2020-01-21", "journal": {"title": "Biophys. J.", "issn": "1542-0086", "issn-l": "0006-3495", "volume": "118", "issue": "2", "pages": "273-275"}, "abstract": null, "doi": "10.1016/j.bpj.2019.11.3386", "pmid": "31968235", "labels": {"Milka Doktorova": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC6976811"}, {"db": "pii", "key": "S0006-3495(19)34344-9"}], "notes": [], "created": "2024-11-27T12:19:19.726Z", "modified": "2024-11-29T12:16:41.078Z"}, {"entity": "publication", "iuid": "c8385f8f71824af899b09096683dd49e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c8385f8f71824af899b09096683dd49e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c8385f8f71824af899b09096683dd49e"}}, "title": "Evidence of altered mucosa-associated and fecal microbiota composition in patients with Irritable Bowel Syndrome.", "authors": [{"family": "Sundin", "given": "Johanna", "initials": "J"}, {"family": "Aziz", "given": "Imran", "initials": "I"}, {"family": "Nordlander", "given": "Sofia", "initials": "S"}, {"family": "Polster", "given": "Annikka", "initials": "A"}, {"family": "Hu", "given": "Yue O O", "initials": "YOO", "orcid": "0000-0002-2025-2198", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/54d7339204704cb2b511f8ac6c8f0395.json"}}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW", "orcid": "0000-0001-5432-1764", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/246ed7b405dd4c3f9ec5e7ff9f1d3ade.json"}}, {"family": "Pennhag", "given": "Alexandra A L", "initials": "AAL"}, {"family": "Engstrand", "given": "Lars", "initials": "L"}, {"family": "T\u00f6rnblom", "given": "Hans", "initials": "H"}, {"family": "Simr\u00e9n", "given": "Magnus", "initials": "M"}, {"family": "\u00d6hman", "given": "Lena", "initials": "L"}], "type": "journal article", "published": "2020-01-17", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "593", "issn-l": "2045-2322"}, "abstract": "Altered bacterial composition and small intestinal bacterial overgrowth (SIBO) may be associated with irritable bowel syndrome (IBS). This study aimed to determine the fecal and mucosa-associated bacterial composition along the gastrointestinal (GI) tract and to assess SIBO in IBS. Bacterial composition of feces, and mucosa of the duodenum and sigmoid colon was determined by 16S rRNA-amplicon-sequencing. SIBO was evaluated by bacterial culture of duodenal aspirate, glucose and lactulose breath tests. Mucosal antibacterial gene expression was assessed by PCR Array. The bacterial profiles of feces and the mucosa of sigmoid colon, but not duodenum, differed between IBS patients (n = 17) and HS (n = 20). The IBS specific bacterial profiles were linked to the colonic antibacterial gene expression. Fecal bacterial profile differed between IBS subtypes, while the mucosa-associated bacterial profile was associated with IBS symptom severity and breath tests results at baseline (H2 and/or CH4 \u2265 15 ppm). The prevalence of SIBO was similar between IBS patients and HS. This study demonstrates that alterations in the bacterial composition of the sigmoid colon of IBS patients were linked to symptoms and immune activation. While breath tests reflected the mucosa-associated bacterial composition, there was no evidence for high prevalence of SIBO or small intestinal bacterial alterations in IBS.", "doi": "10.1038/s41598-020-57468-y", "pmid": "31953505", "labels": {"Luisa Hugerth": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC6969101"}, {"db": "pii", "key": "10.1038/s41598-020-57468-y"}], "notes": [], "created": "2022-11-08T06:59:06.940Z", "modified": "2023-10-27T09:32:08.890Z"}, {"entity": "publication", "iuid": "03d08ef75f714ba79b4cd3439ed53961", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/03d08ef75f714ba79b4cd3439ed53961.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/03d08ef75f714ba79b4cd3439ed53961"}}, "title": "Publisher Correction: Analysis of the Human Protein Atlas Image Classification competition.", "authors": [{"family": "Ouyang", "given": "Wei", "initials": "W", "orcid": "0000-0002-0291-926X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56f601e1d1c6448aab0c3a1e3cffdbfc.json"}}, {"family": "Winsnes", "given": "Casper F", "initials": "CF", "orcid": "0000-0002-0028-5865", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/edeb3bc6c95d4185bf2098bf1e4a5e3c.json"}}, {"family": "Hjelmare", "given": "Martin", "initials": "M", "orcid": "0000-0001-7375-9681", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b13d6d89bd3a43eab43eee98539ed4ad.json"}}, {"family": "Cesnik", "given": "Anthony J", "initials": "AJ"}, {"family": "\u00c5kesson", "given": "Lovisa", "initials": "L"}, {"family": "Xu", "given": "Hao", "initials": "H"}, {"family": "Sullivan", "given": "Devin P", "initials": "DP"}, {"family": "Dai", "given": "Shubin", "initials": "S", "orcid": "0000-0001-6680-0500", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7f4835d5b16a400b9dd9aaff8a8d49f7.json"}}, 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"https://publications-affiliated.scilifelab.se/researcher/bb07e6d0122c4528a927c1fe922e3bc8.json"}}], "type": "published erratum", "published": "2020-01-00", "journal": {"title": "Nat. Methods", "issn": "1548-7105", "volume": "17", "issue": "1", "pages": "115", "issn-l": "1548-7091"}, "abstract": "An amendment to this paper has been published and can be accessed via a link at the top of the paper.", "doi": "10.1038/s41592-019-0699-x", "pmid": "31822866", "labels": {"DDLS Fellow": "", "Wei Ouyang": ""}, "xrefs": [{"db": "pii", "key": "10.1038/s41592-019-0699-x"}], "notes": [], "created": "2026-08-20T09:02:25.124Z", "modified": "2026-09-23T15:15:35.176Z"}, {"entity": "publication", "iuid": "5f02cd2d2d0449cdaffa6184e3900d09", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5f02cd2d2d0449cdaffa6184e3900d09.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5f02cd2d2d0449cdaffa6184e3900d09"}}, "title": "Association Between Metformin Use and Risk of Esophageal Squamous Cell Carcinoma in a Population-Based Cohort Study.", "authors": [{"family": "Wang", "given": "Qiao-Li", "initials": "QL"}, {"family": "Santoni", "given": "Giola", "initials": "G"}, {"family": "Ness-Jensen", "given": "Eivind", "initials": "E"}, {"family": "Lagergren", "given": "Jesper", "initials": "J"}, {"family": "Xie", "given": "Shao-Hua", "initials": "SH"}], "type": "journal article", "published": "2020-01-00", "journal": {"title": "Am J Gastroenterol", "issn": "1572-0241", "volume": "115", "issue": "1", "pages": "73-78", "issn-l": null}, "abstract": "Esophageal cancer is a highly fatal malignant neoplasm, with 2 etiologically different histological types. A large prospective study is expected to elucidate the specific risk of the 90% subtype of esophageal cancer, esophageal squamous cell carcinoma (ESCC), with metformin therapy. This study aims to determine the association between metformin use and incident ESCC risk.\n\nThis was a nationwide population-based prospective cohort study conducted in Sweden in 2005-2015. Among 8.4 million participants identified in the cohort, 411,603 (5%) were metformin users. The users were compared with 10 times as many frequency-matched nonusers of metformin (n = 4,116,030) by age and sex. Metformin use was treated as a time-varying variate, and multivariable cause-specific proportional hazards model was used to calculate hazard ratios (HR) with 95% confidence intervals (CI) for ESCC, adjusted for age, sex, calendar year, residence area, tobacco smoking, alcohol overconsumption, and use of nonsteroidal anti-inflammatory drugs or statins.\n\nThe incidence rates of ESCC were 3.5 per 100,000 person-years among the metformin users and 5.3 per 100,000 person-years in the nonusers. Metformin users overall were at a decreased risk of ESCC compared with nonusers (HR 0.68, 95% CI 0.54-0.85). The decrease in risk was more pronounced in new metformin users (HR 0.44, 95% CI 0.28-0.64) and participants aged 60-69 years (HR 0.45, 95% CI 0.31-0.66).\n\nMetformin use decreases the risk of developing ESCC.", "doi": "10.14309/ajg.0000000000000478", "pmid": "31821177", "labels": {"DDLS Fellow": null, "Qiaoli Wang": null}, "xrefs": [{"db": "pii", "key": "00000434-202001000-00014"}], "notes": [], "created": "2025-11-27T18:53:29.631Z", "modified": "2025-11-27T18:53:29.648Z"}, {"entity": "publication", "iuid": "be71fe82a6e54d0ab872cb00a39c3fec", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/be71fe82a6e54d0ab872cb00a39c3fec.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/be71fe82a6e54d0ab872cb00a39c3fec"}}, "title": "Discovery of Functional Alternatively Spliced <i>PKM</i> Transcripts in Human Cancers", "authors": [{"family": "Li", "given": "Xiangyu", "initials": "X"}, {"family": "Zhang", "given": "Cheng", 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"0000-0003-0786-8091", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/73a770eb9e614448a046b8e9199052e9.json"}}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/33f2b49a39ed4e54ba77dfe397ed3087.json"}}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ea446aa574042a295d5f69437402f76.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca58bf2d214047e0ae5e38a42a0f2808.json"}}], "type": "posted-content", "published": "2020-00-00", "journal": {"issn-l": null}, "abstract": null, "doi": "10.2139/ssrn.3713513", "pmid": null, "labels": {"SciLifeLab Fellow": "", "DDLS Fellow": "", "Adil Mardinoglu": "", "Muhammad Arif": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T13:00:45.435Z", "modified": "2026-09-23T15:07:56.593Z"}, {"entity": "publication", "iuid": "4c64259401374b34a58ac322599ca919", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4c64259401374b34a58ac322599ca919.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4c64259401374b34a58ac322599ca919"}}, "title": "Circulating miRNA Signature Predicts and Rescues Spaceflight Associated Health Risks", "authors": [{"family": "Malkani", "given": "Sherina", "initials": "S", "orcid": "0000-0001-9041-5848", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/af185b0c757b460c9cecf109b36198a6.json"}}, {"family": "Cekanaviciute", "given": "Egle", "initials": "E", "orcid": "0000-0003-3306-1806", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/44f617fae1ec4a5e93e6e5393d74aa1b.json"}}, {"family": "Mortreux", "given": "Marie", "initials": "M", "orcid": "0000-0001-8567-8184", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/88378e19ebcf4b8aae2ae79ae69948f5.json"}}, {"family": "Okunola", "given": "Hazeem", "initials": "H", "orcid": "0000-0002-9424-8984", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ab077873fbd43cb98562eb46afbf259.json"}}, {"family": "Tarbier", "given": "Marcel", "initials": "M", "orcid": "0000-0003-0556-2531", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9678d0797def441e9870afe6ffbb08d0.json"}}, {"family": "Schreurs", "given": "Ann Sofie", "initials": "AS"}, {"family": "Shirazi-Fard", "given": "Yasaman", "initials": "Y", "orcid": "0000-0002-6520-3824", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1afedae564cd4632ae72e3a6939f4eba.json"}}, {"family": "Tahimic", "given": "Candice G T", "initials": "CGT"}, {"family": 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{"family": "Mason", "given": "Christopher E", "initials": "CE", "orcid": "0000-0002-1850-1642", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0d4b550b1cab4def9302399e8c1cb8e7.json"}}, {"family": "Rutkove", "given": "Seward", "initials": "S", "orcid": "0000-0002-6375-3312", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ec8ac6e27c1142e3aac540f6a70e4e91.json"}}, {"family": "Grabham", "given": "Peter", "initials": "P", "orcid": "0000-0002-1523-0891", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ea612106fc2246ecb4d992220460fe91.json"}}, {"family": "Beheshti", "given": "Afshin", "initials": "A", "orcid": "0000-0003-4643-531X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/88d9eb73d9834a79ab05e6ee30708fba.json"}}], "type": "posted-content", "published": "2020-00-00", "journal": {"issn-l": null}, "abstract": null, "doi": "10.2139/ssrn.3641936", "pmid": null, "labels": {"SciLifeLab Fellow": "", "DDLS Fellow": "", "Marcel Tarbier": "", "Marc Friedl\u00e4nder": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T13:00:41.267Z", "modified": "2026-09-23T14:42:18.361Z"}, {"entity": "publication", "iuid": "e31185798a4d4550ae71b6449b12c327", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e31185798a4d4550ae71b6449b12c327.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e31185798a4d4550ae71b6449b12c327"}}, "title": "A genome-wide transcriptomic analysis of protein-coding genes in human blood cells.", "authors": [{"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ea446aa574042a295d5f69437402f76.json"}}, {"family": "Karlsson", "given": "Max J", "initials": "MJ", "orcid": "0000-0002-7000-4416", "researcher": {"href": 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"initials": "T", "orcid": "0000-0001-7256-5770", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/28e45f00f5f247389409f0411d412da1.json"}}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0002-5248-8568", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a6982072448e4e8889c71fc14d214fed.json"}}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e213b04f8984c8eb00c68f5bc2f6a36.json"}}, {"family": "Odeberg", "given": "Jacob", "initials": "J", "orcid": "0000-0003-0996-1644", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d6abb3fc822a4cacbf1d45224f2442f5.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca58bf2d214047e0ae5e38a42a0f2808.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f46e4161be08458994efddb75ed75874.json"}}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K", "orcid": "0000-0002-0257-7554", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f4c4545bd2324b7d9b6696dab5bcb7dd.json"}}, {"family": "Mulder", "given": "Jan", "initials": "J", "orcid": "0000-0003-3717-5018", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/40ed8170792444b491519e499d51c434.json"}}, {"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E", "orcid": "0000-0002-0327-7377", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ec6fb5a1c88b44798144fd2de255fb00.json"}}, {"family": "Hober", "given": "Andreas", "initials": "A", "orcid": "0000-0001-8947-2562", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/06cbc187628340278395a00ab9dd6c89.json"}}, {"family": "Oksvold", "given": "Per", "initials": "P", "orcid": "0000-0003-3014-5502", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/16beca5822c747128300910b5c74dbfc.json"}}, {"family": "Zwahlen", "given": "Martin", "initials": "M", "orcid": "0000-0002-0064-4776", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/456805fa3f4f47328f3923b78bf66996.json"}}, {"family": "Ponten", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9f5294424542413c9ba4432c839c2b63.json"}}, {"family": "Lindskog", "given": "Cecilia", "initials": "C", "orcid": "0000-0001-5611-1015", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/21610a810a87459c962d6da3f2ad38ad.json"}}, {"family": "Sivertsson", "given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0001-8800-8469", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9397c6e626b1457e8dcd47f037c4cf9d.json"}}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/abbbf8193d5a4376a5c726768d039439.json"}}, {"family": "Brodin", "given": "Petter", "initials": "P"}], "type": "journal article", "published": "2019-12-20", "journal": {"title": "Science (New York, N.Y.)", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "366", "issue": "6472", "pages": "eaax9198"}, "abstract": "Blood is the predominant source for molecular analyses in humans, both in clinical and research settings. It is the target for many therapeutic strategies, emphasizing the need for comprehensive molecular maps of the cells constituting human blood. In this study, we performed a genome-wide transcriptomic analysis of protein-coding genes in sorted blood immune cell populations to characterize the expression levels of each individual gene across the blood cell types. All data are presented in an interactive, open-access Blood Atlas as part of the Human Protein Atlas and are integrated with expression profiles across all major tissues to provide spatial classification of all protein-coding genes. This allows for a genome-wide exploration of the expression profiles across human immune cell populations and all major human tissues and organs.", "doi": "10.1126/science.aax9198", "pmid": "31857451", "labels": {"Adil Mardinoglu": "", "SciLifeLab Fellow": "", "Fredrik Edfors": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pii", "key": "366/6472/eaax9198"}], "notes": [], "created": "2020-09-25T13:04:52.822Z", "modified": "2026-09-23T06:31:18.795Z"}, {"entity": "publication", "iuid": "df7da3689b624e71a18a5d55b5db2c12", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/df7da3689b624e71a18a5d55b5db2c12.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/df7da3689b624e71a18a5d55b5db2c12"}}, "title": "Ancient microRNA profiles of a 14,300-year-old canid are taxonomically informative and give glimpses into gene regulation from the Pleistocene", "authors": [{"family": "Fromm", "given": "Bastian", "initials": "B", "orcid": "0000-0003-0352-3037", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cdc4c42e06604b759dd6225c5f8362b5.json"}}, {"family": "Tarbier", "given": "Marcel", "initials": "M", "orcid": "0000-0003-0556-2531", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9678d0797def441e9870afe6ffbb08d0.json"}}, {"family": "Smith", "given": "Oliver", "initials": "O", "orcid": "0000-0002-0146-9244", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4b114f019dad43c580e985932e10a586.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L"}, {"family": "Gilbert", "given": "M T P", "initials": "MTP"}, {"family": "Friedl\u00e4nder", "given": "Marc R", "initials": "MR"}], "type": "posted-content", "published": "2019-12-17", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2019.12.16.877761", "pmid": null, "labels": {"SciLifeLab Fellow": "", "DDLS Fellow": "", "Marcel Tarbier": "", "Marc Friedl\u00e4nder": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T09:55:12.032Z", "modified": "2026-09-23T14:30:27.598Z"}, {"entity": "publication", "iuid": "76fcc5ddb8994280b0b398c67945f0b3", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/76fcc5ddb8994280b0b398c67945f0b3.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/76fcc5ddb8994280b0b398c67945f0b3"}}, "title": "MPRAscore: robust and non-parametric analysis of massively parallel reporter assays.", "authors": [{"family": "Niroula", "given": "Abhishek", "initials": "A"}, {"family": "Ajore", "given": "Ram", "initials": "R"}, {"family": "Nilsson", "given": "Bj\u00f6rn", "initials": "B"}], "type": "journal article", "published": "2019-12-15", "journal": {"title": "Bioinformatics", "issn": "1367-4811", "volume": "35", "issue": "24", "pages": "5351-5353", "issn-l": "1367-4803"}, "abstract": "Massively parallel reporter assays (MPRA) enable systematic screening of DNA sequence variants for effects on transcriptional activity. However, convenient analysis tools are still needed.\n\nWe introduce MPRAscore, a novel tool to infer allele-specific effects on transcription from MPRA data. MPRAscore uses a weighted, variance-regularized method to calculate variant effect sizes robustly, and a permutation approach to test for significance without assuming normality or independence.\n\nSource code (C++), precompiled binaries and data used in the paper at https://github.com/abhisheknrl/MPRAscore and https://www.ncbi.nlm.nih.gov/bioproject/PRJNA554195.\n\nSupplementary data are available at Bioinformatics online.", "doi": "10.1093/bioinformatics/btz591", "pmid": "31359027", "labels": {"Abhishek Niroula": null, "DDLS Fellow": null}, "xrefs": [{"db": "pii", "key": "5540322"}], "notes": [], "created": "2023-11-20T11:21:46.535Z", "modified": "2023-11-20T11:21:46.554Z"}, {"entity": "publication", "iuid": "f8f5e184773d41eb8585341f7da36cce", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f8f5e184773d41eb8585341f7da36cce.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f8f5e184773d41eb8585341f7da36cce"}}, "title": "ImJoy: an open-source computational platform for the deep learning era.", "authors": [{"family": "Ouyang", "given": "Wei", "initials": "W"}, {"family": "Mueller", "given": "Florian", "initials": "F"}, {"family": "Hjelmare", "given": "Martin", "initials": "M"}, {"family": "Lundberg", "given": "Emma", "initials": "E"}, {"family": "Zimmer", "given": "Christophe", "initials": "C"}], "type": "letter", "published": "2019-12-00", "journal": {"title": "Nat. Methods", "issn": "1548-7105", "volume": "16", "issue": "12", "pages": "1199-1200", "issn-l": "1548-7091"}, "abstract": null, "doi": "10.1038/s41592-019-0627-0", "pmid": "31780825", "labels": {"DDLS Fellow": "", "Wei Ouyang": ""}, "xrefs": [{"db": "pii", "key": "10.1038/s41592-019-0627-0"}], "notes": [], "created": "2026-08-20T09:02:15.762Z", "modified": "2026-09-23T07:27:14.056Z"}, {"entity": "publication", "iuid": "b27d136a1f794f30a08da659234c2fd3", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b27d136a1f794f30a08da659234c2fd3.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b27d136a1f794f30a08da659234c2fd3"}}, "title": "Enrichment of oral microbiota in early cystic precursors to invasive pancreatic cancer.", "authors": [{"family": "Gaiser", "given": "Rogier A\u00e4ron", "initials": "RA", "orcid": "0000-0002-5701-6332", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d85d082016524abcb00e78649a1beabb.json"}}, {"family": "Halimi", "given": "Asif", "initials": "A"}, {"family": "Alkharaan", "given": "Hassan", "initials": "H"}, {"family": "Lu", "given": "Liyan", "initials": "L"}, {"family": "Davanian", "given": "Haleh", "initials": "H"}, {"family": "Healy", "given": "Katie", "initials": "K"}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW"}, {"family": "Ateeb", "given": "Zeeshan", "initials": "Z"}, {"family": "Valente", "given": "Roberto", "initials": "R"}, {"family": "Fern\u00e1ndez Moro", "given": "Carlos", "initials": "C"}, {"family": "Del Chiaro", "given": "Marco", "initials": "M"}, {"family": "S\u00e4llberg Chen", "given": "Margaret", "initials": "M"}], "type": "journal article", "published": "2019-12-00", "journal": {"title": "Gut", "issn": "1468-3288", "volume": "68", "issue": "12", "pages": "2186-2194", "issn-l": "0017-5749"}, "abstract": "Intraductal papillary mucinous neoplasms (IPMNs) are pancreatic cysts that can progress to invasive pancreatic cancer. Associations between oncogenesis and oral microbiome alterations have been reported. This study aims to investigate a potential intracystic pancreatic microbiome in a pancreatic cystic neoplasm (PCN) surgery patient cohort.\n\nPaired cyst fluid and plasma were collected at pancreatic surgery from patients with suspected PCN (n=105). Quantitative and qualitative assessment of bacterial DNA by qPCR, PacBio sequencing (n=35), and interleukin (IL)-1\u03b2 quantification was performed. The data were correlated to diagnosis, lesion severity and clinical and laboratory profile, including proton-pump inhibitor (PPI) usage and history of invasive endoscopy procedures.\n\nIntracystic bacterial 16S DNA copy number and IL-1\u03b2 protein quantity were significantly higher in IPMN with high-grade dysplasia and IPMN with cancer compared with non-IPMN PCNs. Despite high interpersonal variation of intracystic microbiota composition, bacterial network and linear discriminant analysis effect size analyses demonstrated co-occurrence and enrichment of oral bacterial taxa including Fusobacterium nucleatum and Granulicatella adiacens in cyst fluid from IPMN with high-grade dysplasia. The elevated intracystic bacterial DNA is associated with, but not limited to, prior exposure to invasive endoscopic procedures, and is independent from use of PPI and antibiotics.\n\nCollectively, these findings warrant further investigation into the role of oral bacteria in cystic precursors to pancreatic cancer and have added values on the aetiopathology as well as the management of pancreatic cysts.", "doi": "10.1136/gutjnl-2018-317458", "pmid": "30872392", "labels": {"Luisa Hugerth": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC6872446"}, {"db": "pii", "key": "gutjnl-2018-317458"}], "notes": [], "created": "2022-11-08T06:59:21.572Z", "modified": "2026-09-23T06:42:33.960Z"}, {"entity": "publication", "iuid": "b65dc36259594f1e9c22bf1efba3467f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b65dc36259594f1e9c22bf1efba3467f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b65dc36259594f1e9c22bf1efba3467f"}}, "title": "Cardiac expression of the microsomal triglyceride transport protein protects the heart function during ischemia.", "authors": [{"family": "Klevstig", "given": "Martina", "initials": "M"}, {"family": "Arif", "given": "Muhammad", "initials": "M"}, {"family": "Mannila", "given": "Maria", "initials": "M"}, {"family": "Svedlund", "given": "Sara", "initials": "S"}, {"family": "Mardani", "given": "Ismena", "initials": "I"}, {"family": "St\u00e5hlman", "given": "Marcus", "initials": "M"}, {"family": "Andersson", "given": "Linda", "initials": "L"}, {"family": "Lindbom", "given": "Malin", "initials": "M"}, {"family": "Miljanovic", "given": "Azra", "initials": "A"}, {"family": "Franco-Cereceda", "given": "Anders", "initials": "A"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Jeppsson", "given": "Anders", "initials": "A"}, {"family": "Gan", "given": "Li-Ming", "initials": "LM"}, {"family": "Levin", "given": "Malin", "initials": "M"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Ehrenborg", "given": "Ewa", "initials": "E"}, {"family": "Bor\u00e9n", "given": "Jan", "initials": "J", "orcid": "0000-0003-0786-8091", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/73a770eb9e614448a046b8e9199052e9.json"}}], "type": "journal article", "published": "2019-12-00", "journal": {"title": "J. Mol. Cell. Cardiol.", "issn": "1095-8584", "issn-l": "0022-2828", "volume": "137", "issue": null, "pages": "1-8"}, "abstract": "The microsomal triglyceride transport protein (MTTP) is critical for assembly and secretion of apolipoprotein B (apoB)-containing lipoproteins and is most abundant in the liver and intestine. Surprisingly, MTTP is also expressed in the heart. Here we tested the functional relevance of cardiac MTTP expression.\n\nWe combined clinical studies, advanced expression analysis of human heart biopsies and analyses in genetically modified mice lacking cardiac expression of the MTTP-A isoform of MTTP.\n\nOur results indicate that lower cardiac MTTP expression in humans is associated with structural and perfusion abnormalities in patients with ischemic heart disease. MTTP-A deficiency in mice heart does not affect total MTTP expression, activity or lipid concentration in the heart. Despite this, MTTP-A deficient mice displayed impaired cardiac function after a myocardial infarction. Expression analysis of MTTP indicates that MTTP expression is linked to cardiac function and responses in the heart.\n\nOur results indicate that MTTP may play an important role for the heart function in conjunction to ischemic events.", "doi": "10.1016/j.yjmcc.2019.09.003", "pmid": "31533023", "labels": {"Adil Mardinoglu": "", "SciLifeLab Fellow": "", "DDLS Fellow": "", "Muhammad Arif": ""}, "xrefs": [{"db": "pii", "key": "S0022-2828(19)30186-5"}], "notes": [], "created": "2020-09-25T13:14:18.085Z", "modified": "2026-09-23T13:08:55.802Z"}, {"entity": "publication", "iuid": "1f3a270aeb764f7f874a53c92a4f26b7", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1f3a270aeb764f7f874a53c92a4f26b7.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1f3a270aeb764f7f874a53c92a4f26b7"}}, "title": "Analysis of the Human Protein Atlas Image Classification competition.", "authors": [{"family": "Ouyang", "given": "Wei", "initials": "W", "orcid": "0000-0002-0291-926X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56f601e1d1c6448aab0c3a1e3cffdbfc.json"}}, {"family": "Winsnes", "given": "Casper F", "initials": "CF", "orcid": "0000-0002-0028-5865", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/edeb3bc6c95d4185bf2098bf1e4a5e3c.json"}}, {"family": "Hjelmare", "given": "Martin", "initials": "M", "orcid": "0000-0001-7375-9681", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b13d6d89bd3a43eab43eee98539ed4ad.json"}}, {"family": "Cesnik", "given": "Anthony J", "initials": "AJ"}, {"family": "\u00c5kesson", "given": "Lovisa", "initials": "L"}, {"family": "Xu", "given": "Hao", "initials": "H"}, {"family": "Sullivan", "given": "Devin P", "initials": "DP"}, {"family": "Dai", "given": "Shubin", "initials": "S"}, {"family": "Lan", "given": "Jun", "initials": "J"}, {"family": "Jinmo", "given": "Park", "initials": "P"}, {"family": "Galib", "given": "Shaikat M", "initials": "SM"}, {"family": "Henkel", "given": "Christof", "initials": "C"}, {"family": "Hwang", "given": "Kevin", "initials": "K"}, {"family": "Poplavskiy", "given": "Dmytro", "initials": "D"}, {"family": "Tunguz", "given": "Bojan", "initials": "B"}, {"family": "Wolfinger", "given": "Russel D", "initials": "RD"}, {"family": "Gu", "given": "Yinzheng", "initials": "Y"}, {"family": "Li", "given": "Chuanpeng", "initials": "C"}, {"family": "Xie", "given": "Jinbin", "initials": "J"}, {"family": "Buslov", "given": "Dmitry", "initials": "D"}, {"family": "Fironov", "given": "Sergei", "initials": "S"}, {"family": "Kiselev", "given": "Alexander", "initials": "A"}, {"family": "Panchenko", "given": "Dmytro", "initials": "D"}, {"family": "Cao", "given": "Xuan", "initials": "X"}, {"family": "Wei", "given": "Runmin", "initials": "R"}, {"family": "Wu", "given": "Yuanhao", "initials": "Y"}, {"family": "Zhu", "given": "Xun", "initials": "X"}, {"family": "Tseng", "given": "Kuan-Lun", "initials": "KL"}, {"family": "Gao", "given": "Zhifeng", "initials": "Z"}, {"family": "Ju", "given": "Cheng", "initials": "C"}, {"family": "Yi", "given": "Xiaohan", "initials": "X"}, {"family": "Zheng", "given": "Hongdong", "initials": "H"}, {"family": "Kappel", "given": "Constantin", "initials": "C"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb07e6d0122c4528a927c1fe922e3bc8.json"}}], "type": "journal article", "published": "2019-12-00", "journal": {"title": "Nat. Methods", "issn": "1548-7105", "volume": "16", "issue": "12", "pages": "1254-1261", "issn-l": "1548-7091"}, "abstract": "Pinpointing subcellular protein localizations from microscopy images is easy to the trained eye, but challenging to automate. Based on the Human Protein Atlas image collection, we held a competition to identify deep learning solutions to solve this task. Challenges included training on highly imbalanced classes and predicting multiple labels per image. Over 3 months, 2,172 teams participated. Despite convergence on popular networks and training techniques, there was considerable variety among the solutions. Participants applied strategies for modifying neural networks and loss functions, augmenting data and using pretrained networks. The winning models far outperformed our previous effort at multi-label classification of protein localization patterns by ~20%. These models can be used as classifiers to annotate new images, feature extractors to measure pattern similarity or pretrained networks for a wide range of biological applications.", "doi": "10.1038/s41592-019-0658-6", "pmid": "31780840", "labels": {"DDLS Fellow": "", "Wei Ouyang": ""}, "xrefs": [{"db": "pmc", "key": "PMC6976526"}, {"db": "pii", "key": "10.1038/s41592-019-0658-6"}], "notes": [], "created": "2026-08-20T09:02:23.393Z", "modified": "2026-09-23T07:30:34.782Z"}, {"entity": "publication", "iuid": "7a761b56c94c4f4f939ff612982c68f4", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/7a761b56c94c4f4f939ff612982c68f4.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/7a761b56c94c4f4f939ff612982c68f4"}}, "title": "Absolute Quantification of Apolipoproteins Following Treatment with Omega-3 Carboxylic Acids and Fenofibrate Using a High Precision Stable Isotope-labeled Recombinant Protein Fragments Based SRM Assay.", "authors": [{"family": "Hober", "given": "Andreas", "initials": "A"}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Ryaboshapkina", "given": "Maria", "initials": "M"}, {"family": "Malmqvist", "given": "Jonas", "initials": "J"}, {"family": "Rosengren", "given": "Louise", "initials": "L"}, {"family": "Percy", "given": "Andrew J", "initials": "AJ"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Oscarsson", "given": "Jan", "initials": "J"}, {"family": "Miliotis", "given": "Tasso", "initials": "T"}], "type": "journal article", "published": "2019-12-00", "journal": {"title": "Mol. Cell Proteomics", "issn": "1535-9484", "volume": "18", "issue": "12", "pages": "2433-2446", "issn-l": "1535-9476"}, "abstract": "Stable isotope-labeled standard (SIS) peptides are used as internal standards in targeted proteomics to provide robust protein quantification, which is required in clinical settings. However, SIS peptides are typically added post trypsin digestion and, as the digestion efficiency can vary significantly between peptides within a protein, the accuracy and precision of the assay may be compromised. These drawbacks can be remedied by a new class of internal standards introduced by the Human Protein Atlas project, which are based on SIS recombinant protein fragments called SIS PrESTs. SIS PrESTs are added initially to the sample and SIS peptides are released on trypsin digestion. The SIS PrEST technology is promising for absolute quantification of protein biomarkers but has not previously been evaluated in a clinical setting. An automated and scalable solid phase extraction workflow for desalting and enrichment of plasma digests was established enabling simultaneous preparation of up to 96 samples. Robust high-precision quantification of 13 apolipoproteins was achieved using a novel multiplex SIS PrEST-based LC-SRM/MS Tier 2 assay in non-depleted human plasma. The assay exhibited inter-day coefficients of variation between 1.5% and 14.5% (median = 3.5%) and was subsequently used to investigate the effects of omega-3 carboxylic acids (OM3-CA) and fenofibrate on these 13 apolipoproteins in human plasma samples from a randomized placebo-controlled trial, EFFECT I (NCT02354976). No significant changes were observed in the OM3-CA arm, whereas treatment with fenofibrate significantly increased apoAII and reduced apoB, apoCI, apoE and apoCIV levels. The reduction in apoCIV following fenofibrate treatment is a novel finding. The study demonstrates that SIS PrESTs can facilitate the generation of robust multiplexed biomarker Tier 2 assays for absolute quantification of proteins in clinical studies.", "doi": "10.1074/mcp.RA119.001765", "pmid": "31591263", "labels": {"Fredrik Edfors": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC6885709"}, {"db": "pii", "key": "S1535-9476(20)31647-9"}], "notes": [], "created": "2026-08-20T09:32:47.083Z", "modified": "2026-09-23T11:46:46.785Z"}, {"entity": "publication", "iuid": "b88c28292c524760a32c286f42bb228b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b88c28292c524760a32c286f42bb228b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b88c28292c524760a32c286f42bb228b"}}, "title": "The human secretome.", "authors": [{"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ea446aa574042a295d5f69437402f76.json"}}, {"family": "Karlsson", "given": "Max J", "initials": "MJ", "orcid": "0000-0002-7000-4416", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b93284f942e44f1086616357d77267c3.json"}}, {"family": "Hober", "given": "Andreas", "initials": "A", "orcid": "0000-0001-8947-2562", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/06cbc187628340278395a00ab9dd6c89.json"}}, {"family": "Svensson", "given": "Anne-Sophie", "initials": "AS"}, {"family": "Scheffel", "given": "Julia", "initials": "J", "orcid": "0000-0001-8353-3774", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/26054d5035214c8ab2b7e449c8402fc0.json"}}, {"family": "Kotol", "given": "David", "initials": "D"}, {"family": "Zhong", "given": "Wen", "initials": "W", "orcid": "0000-0002-7422-6104", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d6ffb1140aaa42c5ac63fe76653fc63b.json"}}, {"family": "Tebani", "given": "Abdellah", "initials": "A", "orcid": "0000-0002-8901-2678", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/794215a6625b4fe4b652ec08bcab98ec.json"}}, {"family": "Strandberg", "given": "Linn\u00e9a", "initials": "L", "orcid": "0000-0001-5386-5460", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ea4741b77234afe83e92c3dfff0a799.json"}}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e213b04f8984c8eb00c68f5bc2f6a36.json"}}, {"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E", "orcid": "0000-0002-0327-7377", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ec6fb5a1c88b44798144fd2de255fb00.json"}}, {"family": "Mulder", "given": "Jan", "initials": "J", "orcid": "0000-0003-3717-5018", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/40ed8170792444b491519e499d51c434.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca58bf2d214047e0ae5e38a42a0f2808.json"}}, {"family": "Berling", "given": "Anna", "initials": "A"}, {"family": "Ekblad", "given": "Siri", "initials": "S", "orcid": "0000-0002-0582-7141", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/172a0df6d88347b499f6dd25b5602194.json"}}, {"family": "Dannemeyer", "given": "Melanie", "initials": "M", "orcid": "0000-0001-9542-601X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/262cf0a008ac4ced8969d35e33628fe5.json"}}, {"family": "Kanje", "given": "Sara", "initials": "S", "orcid": "0000-0002-4751-2519", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/28e34a13f8f748a38a5ca6241205a878.json"}}, {"family": "Rockberg", "given": "Johan", "initials": "J"}, {"family": "Lundqvist", "given": "Magnus", "initials": "M", "orcid": "0000-0002-7875-2822", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/57ae4837a9a947709093067a0456f715.json"}}, {"family": "Malm", "given": "Magdalena", "initials": "M", "orcid": "0000-0003-1763-9073", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a69f7651977a4b4a92bdf5f9d6408d04.json"}}, {"family": "Volk", "given": "Anna-Luisa", "initials": "AL", "orcid": "0000-0003-1096-9061", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ce3e9610155a4814add604d22b11ae04.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3db33fa3edb94febb8be7927a16838d0.json"}}, {"family": "M\u00e5nberg", "given": "Anna", "initials": "A", "orcid": "0000-0002-0056-1313", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1ccc9581865849c285b687a4670bbf2b.json"}}, {"family": "Dodig-Crnkovic", "given": "Tea", "initials": "T", "orcid": "0000-0002-2875-896X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5365873ed6a7463485fb44550a4826ec.json"}}, {"family": "Pin", "given": "Elisa", "initials": "E", "orcid": "0000-0002-2158-2674", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1533d567ad31481fae15627d3b316382.json"}}, {"family": "Zwahlen", "given": "Martin", "initials": "M", "orcid": "0000-0002-0064-4776", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/456805fa3f4f47328f3923b78bf66996.json"}}, {"family": "Oksvold", "given": "Per", "initials": "P", "orcid": "0000-0003-3014-5502", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/16beca5822c747128300910b5c74dbfc.json"}}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K", "orcid": "0000-0002-0257-7554", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f4c4545bd2324b7d9b6696dab5bcb7dd.json"}}, {"family": "H\u00e4ussler", "given": "Ragna S", "initials": "RS", "orcid": "0000-0003-1664-8875", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7cc0ab2ae97c4f968d6218ca2915389f.json"}}, {"family": "Hong", "given": "Mun-Gwan", "initials": "MG", "orcid": "0000-0001-8603-8293", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d12504acae5c4f31b83f75c3d7786cd4.json"}}, {"family": "Lindskog", "given": "Cecilia", "initials": "C", "orcid": "0000-0001-5611-1015", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/21610a810a87459c962d6da3f2ad38ad.json"}}, {"family": "Ponten", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9f5294424542413c9ba4432c839c2b63.json"}}, {"family": "Katona", "given": "Borbala", "initials": "B"}, {"family": "Vuu", "given": "Jimmy", "initials": "J"}, {"family": "Lindstr\u00f6m", "given": "Emil", "initials": "E"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/33f2b49a39ed4e54ba77dfe397ed3087.json"}}, {"family": "Robinson", "given": "Jonathan", "initials": "J", "orcid": "0000-0001-8567-5960", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/528edd3ba8374bdd8e3187556978c5ef.json"}}, {"family": "Ayoglu", "given": "Burcu", "initials": "B", "orcid": "0000-0001-7843-2960", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4d75c3ce33814d2b961aef643f0d7f0c.json"}}, {"family": "Mahdessian", "given": "Diana", "initials": "D", "orcid": "0000-0003-0750-1070", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7bab301bfb3544e69cf96ae4080fc3e9.json"}}, {"family": "Sullivan", "given": "Devin", "initials": "D", "orcid": "0000-0001-6176-108X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e3bff10128d545ff8323e2a701e73eba.json"}}, {"family": "Thul", "given": "Peter", "initials": "P", "orcid": "0000-0002-6107-1465", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/af9dad977d4649bbbb883a9836dade94.json"}}, {"family": "Danielsson", "given": "Frida", "initials": "F"}, {"family": "Stadler", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-6781-1938", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5aff7e9c1d774b8c8bfee2f09a323ed2.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb07e6d0122c4528a927c1fe922e3bc8.json"}}, {"family": "Bergstr\u00f6m", "given": "G\u00f6ran", "initials": "G"}, {"family": "Gummesson", "given": "Anders", "initials": "A", "orcid": "0000-0003-0024-960X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1703619132e242aaad263d4ecd80a8ae.json"}}, {"family": "Voldborg", "given": "Bj\u00f8rn G", "initials": "BG", "orcid": "0000-0002-7005-1642", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/75368e988b364f2ca5e320e0a2c17f82.json"}}, {"family": "Tegel", "given": "Hanna", "initials": "H", "orcid": "0000-0002-7067-9173", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7b9de19b82b4406d8904cb937a466e8b.json"}}, {"family": "Hober", "given": "Sophia", "initials": "S", "orcid": "0000-0003-0605-8417", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4a1bdfd8500c4dbea343132bc0d8e44c.json"}}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0002-5248-8568", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a6982072448e4e8889c71fc14d214fed.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/022e140799b6466ea123319c3d70c76e.json"}}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/abbbf8193d5a4376a5c726768d039439.json"}}, {"family": "Sivertsson", "given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0001-8800-8469", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9397c6e626b1457e8dcd47f037c4cf9d.json"}}], "type": "journal article", "published": "2019-11-26", "journal": {"title": "Sci Signal", "issn": "1937-9145", "issn-l": "1945-0877", "volume": "12", "issue": "609", "pages": "eaaz0274"}, "abstract": "The proteins secreted by human cells (collectively referred to as the secretome) are important not only for the basic understanding of human biology but also for the identification of potential targets for future diagnostics and therapies. Here, we present a comprehensive analysis of proteins predicted to be secreted in human cells, which provides information about their final localization in the human body, including the proteins actively secreted to peripheral blood. The analysis suggests that a large number of the proteins of the secretome are not secreted out of the cell, but instead are retained intracellularly, whereas another large group of proteins were identified that are predicted to be retained locally at the tissue of expression and not secreted into the blood. Proteins detected in the human blood by mass spectrometry-based proteomics and antibody-based immunoassays are also presented with estimates of their concentrations in the blood. The results are presented in an updated version 19 of the Human Protein Atlas in which each gene encoding a secretome protein is annotated to provide an open-access knowledge resource of the human secretome, including body-wide expression data, spatial localization data down to the single-cell and subcellular levels, and data about the presence of proteins that are detectable in the blood.", "doi": "10.1126/scisignal.aaz0274", "pmid": "31772123", "labels": {"Adil Mardinoglu": "", "SciLifeLab Fellow": "", "Fredrik Edfors": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pii", "key": "12/609/eaaz0274"}], "notes": [], "created": "2020-09-25T13:06:12.633Z", "modified": "2026-09-23T06:32:51.441Z"}, {"entity": "publication", "iuid": "6bec8b54783c46e08477226aee284887", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/6bec8b54783c46e08477226aee284887.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/6bec8b54783c46e08477226aee284887"}}, "title": "Effects of sampling strategy and DNA extraction on human skin microbiome investigations.", "authors": [{"family": "Bjerre", "given": "Rie Dybboe", "initials": "RD", "orcid": "0000-0002-0110-6320", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f928bb58156d40f8b51a5b03714a8bf9.json"}}, {"family": "Hugerth", "given": "Luisa Warchavchik", "initials": "LW", "orcid": "0000-0001-5432-1764", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/246ed7b405dd4c3f9ec5e7ff9f1d3ade.json"}}, {"family": "Boulund", "given": "Fredrik", "initials": "F"}, {"family": "Seifert", "given": "Maike", "initials": "M"}, {"family": "Johansen", "given": "Jeanne Duus", "initials": "JD"}, {"family": "Engstrand", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2019-11-21", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "9", "issue": "1", "pages": "17287", "issn-l": "2045-2322"}, "abstract": "The human skin is colonized by a wide array of microorganisms playing a role in skin disorders. Studying the skin microbiome provides unique obstacles such as low microbial biomass. The objective of this study was to establish methodology for skin microbiome analyses, focusing on sampling technique and DNA extraction. Skin swabs and scrapes were collected from 9 healthy adult subjects, and DNA extracted using 12 commercial kits. All 165 samples were sequenced using the 16S rRNA gene. Comparing the populations captured by eSwabs and scrapes, 99.3% of sequences overlapped. Using eSwabs yielded higher consistency. The success rate of library preparation applying different DNA extraction kits ranged from 39% to 100%. Some kits had higher Shannon alpha-diversity. Metagenomic shotgun analyses were performed on a subset of samples (N = 12). These data indicate that a reduction of human DNA from 90% to 57% is feasible without lowering the success of 16S rRNA library preparation and without introducing taxonomic bias. Using swabs is a reliable technique to investigate the skin microbiome. DNA extraction methodology is crucial for success of sequencing and adds a substantial amount of variation in microbiome analyses. Reduction of host DNA is recommended for interventional studies applying metagenomics.", "doi": "10.1038/s41598-019-53599-z", "pmid": "31754146", "labels": {"Luisa Hugerth": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC6872721"}, {"db": "pii", "key": "10.1038/s41598-019-53599-z"}, {"db": "figshare", "key": "10.6084/m9.figshare.8319842.v1"}], "notes": [], "created": "2022-11-08T06:59:19.169Z", "modified": "2026-09-23T07:34:12.979Z"}, {"entity": "publication", "iuid": "661ab53d108e4bb684084296e0f39d89", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/661ab53d108e4bb684084296e0f39d89.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/661ab53d108e4bb684084296e0f39d89"}}, "title": "Classification of clear cell renal cell carcinoma based on PKM alternative splicing", "authors": [{"family": "Li", "given": "Xiangyu", "initials": "X"}, {"family": "Turanli", "given": "Beste", "initials": "B"}, {"family": "Juszczak", "given": "Kajetan", "initials": "K"}, {"family": "Kim", "given": "Woonghee", "initials": "W"}, {"family": "Arif", "given": "Muhammad", "initials": "M"}, {"family": "Sato", "given": "Yusuke", "initials": "Y"}, {"family": "Ogawa", "given": "Seishi", "initials": "S"}, {"family": "Turkez", "given": "Hasan", "initials": "H"}, {"family": "Nielsen", "given": "Jens", "initials": "J"}, {"family": "Boren", "given": "Jan", "initials": "J"}, {"family": "Uhlen", "given": "Mathias", "initials": "M"}, {"family": "Zhang", "given": "Cheng", "initials": "C"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}], "type": "posted-content", "published": "2019-11-12", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/823336", "pmid": null, "labels": {"SciLifeLab Fellow": "", "DDLS Fellow": "", "Adil Mardinoglu": "", "Muhammad Arif": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T11:15:07.918Z", "modified": "2026-09-23T15:02:03.210Z"}, {"entity": "publication", "iuid": "8d71bb0c8d5a4afea0ba7cdff99bb345", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8d71bb0c8d5a4afea0ba7cdff99bb345.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8d71bb0c8d5a4afea0ba7cdff99bb345"}}, "title": "Complex I is bypassed during high intensity exercise.", "authors": [{"family": "Nilsson", "given": "Avlant", "initials": "A", "orcid": "0000-0002-9476-4516", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f2e21dbc1c624f6a841c59e959e948e4.json"}}, {"family": "Bj\u00f6rnson", "given": "Elias", "initials": "E", "orcid": "0000-0002-0003-6463", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2c5435f61cd24205af6a5d770a9a0451.json"}}, {"family": "Flockhart", "given": "Mikael", "initials": "M", "orcid": "0000-0002-7743-9295", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1490d76702754143a3963b24055f10dd.json"}}, {"family": "Larsen", "given": "Filip J", "initials": "FJ", "orcid": "0000-0002-1343-8656", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/63564df3b52d4e4ebc7ec2d9dd2e49ac.json"}}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/33f2b49a39ed4e54ba77dfe397ed3087.json"}}], "type": "journal article", "published": "2019-11-07", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "10", "issue": "1", "pages": "5072"}, "abstract": "Human muscles are tailored towards ATP synthesis. When exercising at high work rates muscles convert glucose to lactate, which is less nutrient efficient than respiration. There is hence a trade-off between endurance and power. Metabolic models have been developed to study how limited catalytic capacity of enzymes affects ATP synthesis. Here we integrate an enzyme-constrained metabolic model with proteomics data from muscle fibers. We find that ATP synthesis is constrained by several enzymes. A metabolic bypass of mitochondrial complex I is found to increase the ATP synthesis rate per gram of protein compared to full respiration. To test if this metabolic mode occurs in vivo, we conduct a high resolved incremental exercise tests for five subjects. Their gas exchange at different work rates is accurately reproduced by a whole-body metabolic model incorporating complex I bypass. The study therefore shows how proteome allocation influences metabolism during high intensity exercise.", "doi": "10.1038/s41467-019-12934-8", "pmid": "31699973", "labels": {"Avlant Nilsson": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC6838197"}, {"db": "pii", "key": "10.1038/s41467-019-12934-8"}], "notes": [], "created": "2025-03-20T11:09:42.939Z", "modified": "2025-03-21T13:17:16.987Z"}, {"entity": "publication", "iuid": "ed3b15798c0e4a8a9287d7b89caabd2a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ed3b15798c0e4a8a9287d7b89caabd2a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ed3b15798c0e4a8a9287d7b89caabd2a"}}, "title": "ProTstab - predictor for cellular protein stability.", "authors": [{"family": "Yang", "given": "Yang", "initials": "Y"}, {"family": "Ding", "given": "Xuesong", "initials": "X"}, {"family": "Zhu", "given": "Guanchen", "initials": "G"}, {"family": "Niroula", "given": "Abhishek", "initials": "A"}, {"family": "Lv", "given": "Qiang", "initials": "Q"}, {"family": "Vihinen", "given": "Mauno", "initials": "M", "orcid": "0000-0002-9614-7976", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d39c85536a524a2cab1eca8304d37181.json"}}], "type": "journal article", "published": "2019-11-04", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "20", "issue": "1", "pages": "804", "issn-l": "1471-2164"}, "abstract": "Stability is one of the most fundamental intrinsic characteristics of proteins and can be determined with various methods. Characterization of protein properties does not keep pace with increase in new sequence data and therefore even basic properties are not known for far majority of identified proteins. There have been some attempts to develop predictors for protein stabilities; however, they have suffered from small numbers of known examples.\n\nWe took benefit of results from a recently developed cellular stability method, which is based on limited proteolysis and mass spectrometry, and developed a machine learning method using gradient boosting of regression trees. ProTstab method has high performance and is well suited for large scale prediction of protein stabilities.\n\nThe Pearson's correlation coefficient was 0.793 in 10-fold cross validation and 0.763 in independent blind test. The corresponding values for mean absolute error are 0.024 and 0.036, respectively. Comparison with a previously published method indicated ProTstab to have superior performance. We used the method to predict stabilities of all the remaining proteins in the entire human proteome and then correlated the predicted stabilities to protein chain lengths of isoforms and to localizations of proteins.", "doi": "10.1186/s12864-019-6138-7", "pmid": "31684883", "labels": {"Abhishek Niroula": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC6830000"}, {"db": "pii", "key": "10.1186/s12864-019-6138-7"}], "notes": [], "created": "2023-11-20T11:21:48.127Z", "modified": "2023-11-20T11:21:48.183Z"}, {"entity": "publication", "iuid": "1dc6346f86994d9e8fcb327e5eac2020", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1dc6346f86994d9e8fcb327e5eac2020.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1dc6346f86994d9e8fcb327e5eac2020"}}, "title": "Isolates from Colonic Spirochetosis in Humans Show High Genomic Divergence and Potential Pathogenic Features but Are Not Detected Using Standard Primers for the Human Microbiota.", "authors": [{"family": "Thorell", "given": "Kaisa", "initials": "K", "orcid": "0000-0002-4447-8968", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/789d4029a5c14d3c83df7c47b3b514c7.json"}}, {"family": "Ingan\u00e4s", "given": "Linn", "initials": "L"}, {"family": "Backhans", "given": "Annette", "initials": "A"}, {"family": "Agr\u00e9us", "given": "Lars", "initials": "L"}, {"family": "\u00d6st", "given": "\u00c5ke", "initials": "\u00c5"}, {"family": "Walker", "given": "Marjorie M", "initials": "MM"}, {"family": "Talley", "given": "Nicholas J", "initials": "NJ"}, {"family": "Kjellstr\u00f6m", "given": "Lars", "initials": "L"}, {"family": "Andreasson", "given": "Anna", "initials": "A"}, {"family": "Engstrand", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2019-11-01", "journal": {"title": "J. Bacteriol.", "issn": "1098-5530", "volume": "201", "issue": "21", "issn-l": "0021-9193"}, "abstract": "Colonic spirochetosis, diagnosed based on the striking appearance in histological sections, still has an obscure clinical relevance, and only a few bacterial isolates from this condition have been characterized to date. In a randomized, population-based study in Stockholm, Sweden, 745 healthy individuals underwent colonoscopy with biopsy sampling. Of these individuals, 17 (2.3%) had colonic spirochetosis, which was associated with eosinophilic infiltration and a 3-fold-increased risk for irritable bowel syndrome (IBS). We aimed to culture the bacteria and perform whole-genome sequencing of the isolates from this unique representative population sample. From 14 out of 17 individuals with spirochetosis we successfully isolated, cultured, and performed whole-genome sequencing of in total 17 isolates, including the Brachyspira aalborgi type strain, 513A. Also, 16S analysis of the mucosa-associated microbiota was performed in the cases and nonspirochetosis controls. We found one isolate to be of the species Brachyspira pilosicoli; all remaining isolates were of the species Brachyspira aalborgi Besides displaying extensive genetic heterogeneity, the isolates harbored several mucin-degrading enzymes and other virulence-associated genes that could confer a pathogenic potential in the human colon. We also showed that 16S amplicon sequencing using standard primers for human microbiota studies failed to detect Brachyspira due to primer incompatibility.IMPORTANCE This is the first report of whole-genome analysis of clinical isolates from individuals with colonic spirochetosis. This characterization provides new opportunities in understanding the physiology and potentials of these bacteria that densely colonize the gut in the individuals infected. The observation that standard 16S amplicon primers fail to detect colonic spirochetosis may have major implications for studies searching for associations between members of the microbiota and clinical conditions such as irritable bowel syndrome (IBS) and should be taken into consideration in project design and interpretation of gastrointestinal tract microbiota in population-based and clinical settings.", "doi": "10.1128/JB.00272-19", "pmid": "31405919", "labels": {"DDLS Fellow": "", "Kaisa Thorell": ""}, "xrefs": [{"db": "pmc", "key": "PMC6779451"}, {"db": "pii", "key": "JB.00272-19"}], "notes": [], "created": "2026-08-20T12:00:16.178Z", "modified": "2026-09-23T08:52:56.941Z"}, {"entity": "publication", "iuid": "aeb9d78769a1414096b5d2db44d44dbe", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/aeb9d78769a1414096b5d2db44d44dbe.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/aeb9d78769a1414096b5d2db44d44dbe"}}, "title": "Genome Sequence of Segmented Filamentous Bacteria Present in the Human Intestine", "authors": [{"family": "Jonsson", "given": "Hans", "initials": "H"}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW"}, {"family": "Sundh", "given": "John", "initials": "J"}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cc9be99ec6ca47ed8a805ebb4db7c168.json"}}], "type": "posted-content", "published": "2019-10-21", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/813196", "pmid": null, "labels": {"DDLS Fellow": "", "Luisa Hugerth": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T11:15:04.283Z", "modified": "2026-09-23T14:18:56.728Z"}, {"entity": "publication", "iuid": "f89ec060f7f34be7ab0850d93dd84380", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f89ec060f7f34be7ab0850d93dd84380.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f89ec060f7f34be7ab0850d93dd84380"}}, "title": "The importance of study design in the application of artificial intelligence methods in medicine.", "authors": [{"family": "Eklund", "given": "Martin", "initials": "M", "orcid": "0000-0001-5032-5266", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/06721510ebc8462386e0e6fc6c84315b.json"}}, {"family": "Kartasalo", "given": "Kimmo", "initials": "K", "orcid": "0000-0002-9470-4783", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7c6fc97c06ed456c8bdd1f03db8a9b72.json"}}, {"family": "Olsson", "given": "Henrik", "initials": "H", "orcid": "0000-0002-2270-2017", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/da0547e978264d9c88fc6a222dcbfd5f.json"}}, {"family": "Str\u00f6m", "given": "Peter", "initials": "P", "orcid": "0000-0002-1631-806X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2798ea6ef2ed4ae88b78dd04d2f14437.json"}}], "type": "journal article", "published": "2019-10-18", "journal": {"title": "NPJ Digit Med", "issn": "2398-6352", "issn-l": null, "volume": "2", "issue": null, "pages": "101"}, "abstract": null, "doi": "10.1038/s41746-019-0174-1", "pmid": "31646183", "labels": {"Kimmo Kartasalo": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC6802122"}, {"db": "pii", "key": "174"}], "notes": [], "created": "2024-11-05T16:10:25.356Z", "modified": "2024-11-29T09:31:22.619Z"}, {"entity": "publication", "iuid": "616328cd9bb84abf9ffce7d1e4a66d1c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/616328cd9bb84abf9ffce7d1e4a66d1c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/616328cd9bb84abf9ffce7d1e4a66d1c"}}, "title": "DeepImageJ: A user-friendly environment to run deep learning models in ImageJ", "authors": [{"family": "G\u00f3mez-de-Mariscal", "given": "Estibaliz", "initials": "E", "orcid": "0000-0003-2082-3277", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cdcc04b3b1534abc8457380935970dd5.json"}}, {"family": "Garc\u00eda-L\u00f3pez-de-Haro", "given": "Carlos", "initials": "C"}, {"family": "Ouyang", "given": "Wei", "initials": "W", "orcid": "0000-0002-0291-926X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56f601e1d1c6448aab0c3a1e3cffdbfc.json"}}, {"family": "Donati", "given": "Laur\u00e8ne", "initials": "L"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb07e6d0122c4528a927c1fe922e3bc8.json"}}, {"family": "Unser", "given": "Michael", "initials": "M"}, {"family": "Mu\u00f1oz-Barrutia", "given": "Arrate", "initials": "A", "orcid": "0000-0002-1573-1661", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1f71dcceb0284105a7033f2ed195b9c1.json"}}, {"family": "Sage", "given": "Daniel", "initials": "D", "orcid": "0000-0002-1150-1623", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/919b0180005444d88757db8e63b80d83.json"}}], "type": "posted-content", "published": "2019-10-16", "journal": {"title": "bioRxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/799270", "pmid": null, "labels": {"DDLS Fellow": null, "Wei Ouyang": null}, "xrefs": [], "notes": [], "created": "2026-09-23T13:43:14.914Z", "modified": "2026-10-05T07:29:15.352Z"}, {"entity": "publication", "iuid": "67f1cc95200a45eb839a753a8ea2bd4f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/67f1cc95200a45eb839a753a8ea2bd4f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/67f1cc95200a45eb839a753a8ea2bd4f"}}, "title": "Industrial wastewater treatment plant enriches antibiotic resistance genes and alters the structure of microbial communities.", "authors": [{"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Milakovic", "given": "Milena", "initials": "M"}, {"family": "\u0160vecov\u00e1", "given": "Helena", "initials": "H"}, {"family": "Ganjto", "given": "Marin", "initials": "M"}, {"family": "Jonsson", "given": "Viktor", "initials": "V"}, {"family": "Grabic", "given": "Roman", "initials": "R"}, {"family": "Udikovic-Kolic", "given": "Nikolina", "initials": "N"}], "type": "journal article", "published": "2019-10-01", "journal": {"title": "Water Res", "issn": "1879-2448", "volume": "162", "pages": "437-445", "issn-l": null}, "abstract": "Antibiotic resistance is an emerging global health crisis, driven largely by overuse and misuse of antibiotics. However, there are examples in which the production of these antimicrobial agents has polluted the environment with active antibiotic residues, selecting for antibiotic resistant bacteria and the genes they carry. In this work, we have used shotgun metagenomics to investigate the taxonomic structure and resistance gene composition of sludge communities in a treatment plant in Croatia receiving wastewater from production of the macrolide antibiotic azithromycin. We found that the total abundance of antibiotic resistance genes was three times higher in sludge from the treatment plant receiving wastewater from pharmaceutical production than in municipal sludge from a sewage treatment plant in Zagreb. Surprisingly, macrolide resistance genes did not have higher abundances in the industrial sludge, but genes associated with mobile genetic elements such as integrons had. We conclude that at high concentrations of antibiotics, selection may favor taxonomic shifts towards intrinsically resistant species or strains harboring chromosomal resistance mutations rather than acquisition of mobile resistance determinants. Our results underscore the need for regulatory action also within Europe to avoid release of antibiotics into the environment.", "doi": "10.1016/j.watres.2019.06.073", "pmid": "31301473", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pii", "key": "S0043-1354(19)30595-0"}], "notes": [], "created": "2022-11-08T09:28:13.908Z", "modified": "2022-11-08T09:28:13.951Z"}, {"entity": "publication", "iuid": "b5ebaebc5bcf41569099b25b3dc0bc19", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b5ebaebc5bcf41569099b25b3dc0bc19.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b5ebaebc5bcf41569099b25b3dc0bc19"}}, "title": "Nuclear gene proximity and protein interactions shape transcript covariances in mammalian single cells", "authors": [{"family": "Tarbier", "given": "Marcel", "initials": "M"}, {"family": "Mackowiak", "given": "Sebastian D", "initials": "SD"}, {"family": "Frade", "given": "Jo\u00e3o", "initials": "J"}, {"family": "Catuara-Solarz", "given": "Silvina", "initials": "S"}, {"family": "Biryukova", "given": "Inna", "initials": "I"}, {"family": "Gelali", "given": "Eleni", "initials": "E"}, {"family": "Men\u00e9ndez", "given": "Diego B\u00e1rcena", "initials": "DB"}, {"family": "Zapata", "given": "Luis", "initials": "L"}, {"family": "Ossowski", "given": "Stephan", "initials": "S"}, {"family": "Bienko", "given": "Magda", "initials": "M"}, {"family": "Gallant", "given": "Caroline J", "initials": "CJ"}, {"family": "Friedl\u00e4nder", "given": "Marc R", "initials": "MR"}], "type": "posted-content", "published": "2019-09-16", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/771402", "pmid": null, "labels": {"SciLifeLab Fellow": "", "Magda Bienko": "", "DDLS Fellow": "", "Marcel Tarbier": "", "Marc Friedl\u00e4nder": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T11:14:51.704Z", "modified": "2026-09-23T14:23:40.514Z"}, {"entity": "publication", "iuid": "7cc9ceb62973482195d1ed302e5c3ff6", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/7cc9ceb62973482195d1ed302e5c3ff6.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/7cc9ceb62973482195d1ed302e5c3ff6"}}, "title": "Peptide-Induced Lipid Flip-Flop in Asymmetric Liposomes Measured by Small Angle Neutron Scattering.", "authors": [{"family": "Nguyen", "given": "Michael H L", "initials": "MHL"}, {"family": "DiPasquale", "given": "Mitchell", "initials": "M"}, {"family": "Rickeard", "given": "Brett W", "initials": "BW"}, {"family": "Doktorova", "given": "Milka", "initials": "M"}, {"family": "Heberle", "given": "Frederick A", "initials": "FA", "orcid": "0000-0002-0424-3240", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2557f5621a0b4c87b5f4702fbc7b6bdb.json"}}, {"family": "Scott", "given": "Haden L", "initials": "HL"}, {"family": "Barrera", "given": "Francisco N", "initials": "FN"}, {"family": "Taylor", "given": "Graham", "initials": "G"}, {"family": "Collier", "given": "Charles P", "initials": "CP", "orcid": "0000-0002-8198-793X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c9ebfa8b6f4d4fafaccc956166f0a187.json"}}, {"family": "Stanley", "given": "Christopher B", "initials": "CB", "orcid": "0000-0002-4226-7710", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5d6a186b9b434487907f1035cb1c8edf.json"}}, {"family": "Katsaras", "given": "John", "initials": "J"}, {"family": "Marquardt", "given": "Drew", "initials": "D", "orcid": "0000-0001-6848-2497", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/114cdc1c929d46308422b3b587f8e1d6.json"}}], "type": "journal article", "published": "2019-09-10", "journal": {"title": "Langmuir", "issn": "1520-5827", "issn-l": "0743-7463", "volume": "35", "issue": "36", "pages": "11735-11744"}, "abstract": "Despite the prevalence of lipid transbilayer asymmetry in natural plasma membranes, most biomimetic model membranes studied are symmetric. Recent advances have helped to overcome the difficulties in preparing asymmetric liposomes in vitro, allowing for the examination of a larger set of relevant biophysical questions. Here, we investigate the stability of asymmetric bilayers by measuring lipid flip-flop with time-resolved small-angle neutron scattering (SANS). Asymmetric large unilamellar vesicles with inner bilayer leaflets containing predominantly 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and outer leaflets composed mainly of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) displayed slow spontaneous flip-flop at 37 \u25e6C (half-time, t1/2 = 140 h). However, inclusion of peptides, namely, gramicidin, alamethicin, melittin, or pHLIP (i.e., pH-low insertion peptide), accelerated lipid flip-flop. For three of these peptides (i.e., pHLIP, alamethicin, and melittin), each of which was added externally to preformed asymmetric vesicles, we observed a completely scrambled bilayer in less than 2 h. Gramicidin, on the other hand, was preincorporated during the formation of the asymmetric liposomes and showed a time resolvable 8-fold increase in the rate of lipid asymmetry loss. These results point to a membrane surface-related (e.g., adsorption/insertion) event as the primary driver of lipid scrambling in the asymmetric model membranes of this study. We discuss the implications of membrane peptide binding, conformation, and insertion on lipid asymmetry.", "doi": "10.1021/acs.langmuir.9b01625", "pmid": "31408345", "labels": {"Milka Doktorova": null, "DDLS Fellow": null}, "xrefs": [{"db": "mid", "key": "NIHMS1612790"}, {"db": "pmc", "key": "PMC7393738"}], "notes": [], "created": "2024-11-27T12:18:10.589Z", "modified": "2024-11-29T12:16:50.099Z"}, {"entity": "publication", "iuid": "a8b8ad5d0ab74d478b472b6584fa084a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a8b8ad5d0ab74d478b472b6584fa084a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a8b8ad5d0ab74d478b472b6584fa084a"}}, "title": "Strategies to Reduce or Eliminate Resistant Pathogens in the Environment", "authors": [{"family": "Bengtsson\u2010Palme", "given": "Johan", "initials": "J"}, {"family": "He\u00df", "given": "Stefanie", "initials": "S", "orcid": "0000-0002-9293-4622", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/054fe98a937b4e8787c84df52b7c7a76.json"}}], "type": "other", "published": "2019-09-09", "journal": {"title": "Antibiotic Drug Resistance", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": "637-673"}, "abstract": null, "doi": "10.1002/9781119282549.ch24", "pmid": null, "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [], "notes": [], "created": "2022-11-08T09:31:43.533Z", "modified": "2023-06-19T13:59:25.234Z"}, {"entity": "publication", "iuid": "32a39e448d03414198ac66924d0f6095", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/32a39e448d03414198ac66924d0f6095.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/32a39e448d03414198ac66924d0f6095"}}, "title": "Mumame: a software tool for quantifying gene-specific point-mutations in shotgun metagenomic data", "authors": [{"family": "Magesh", "given": "Shruthi", "initials": "S"}, {"family": "Jonsson", "given": "Viktor", "initials": "V"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J", "orcid": "0000-0002-6528-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c666068e9d34939b0252a627007cec7.json"}}], "type": "journal-article", "published": "2019-09-04", "journal": {"title": "MBMG", "issn": "2534-9708", "volume": "3", "issn-l": null}, "abstract": null, "doi": "10.3897/mbmg.3.36236", "pmid": null, "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [], "notes": [], "created": "2022-11-08T09:28:11.614Z", "modified": "2022-11-08T09:28:11.675Z"}, {"entity": "publication", "iuid": "0a560623d69849ff98bc0db49ecd29d0", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0a560623d69849ff98bc0db49ecd29d0.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0a560623d69849ff98bc0db49ecd29d0"}}, "title": "Insights Into Enhanced Complement Activation by Structures of Properdin and Its Complex With the C-Terminal Domain of C3b.", "authors": [{"family": "van den Bos", "given": "Ramon M", "initials": "RM"}, {"family": "Pearce", "given": "Nicholas M", "initials": "NM"}, {"family": "Granneman", "given": "Joke", "initials": "J"}, {"family": "Brondijk", "given": "T Harma C", "initials": "THC"}, {"family": "Gros", "given": "Piet", "initials": "P"}], "type": "journal article", "published": "2019-09-04", "journal": {"title": "Front Immunol", "issn": "1664-3224", "volume": "10", "pages": "2097", "issn-l": "1664-3224"}, "abstract": "Properdin enhances complement-mediated opsonization of targeted cells and particles for immune clearance. Properdin occurs as dimers, trimers and tetramers in human plasma, which recognize C3b-deposited surfaces, promote formation, and prolong the lifetime of C3bBb-enzyme complexes that convert C3 into C3b, thereby enhancing the complement-amplification loop. Here, we report crystal structures of monomerized properdin, which was produced by co-expression of separate N- and C-terminal constructs that yielded monomer-sized properdin complexes that stabilized C3bBb. Consistent with previous low-resolution X-ray and EM data, the crystal structures revealed ring-shaped arrangements that are formed by interactions between thrombospondin type-I repeat (TSR) domains 4 and 6 of one protomer interacting with the N-terminal domain (which adopts a short transforming-growth factor B binding protein-like fold) and domain TSR1 of a second protomer, respectively. Next, a structure of monomerized properdin in complex with the C-terminal domain of C3b showed that properdin-domain TSR5 binds along the C-terminal \u03b1-helix of C3b, while two loops, one from domain TSR5 and one from TSR6, extend and fold around the C3b C-terminus like stirrups. This suggests a mechanistic model in which these TSR5 and TSR6 \"stirrups\" bridge interactions between C3b and factor B or its fragment Bb, and thereby enhance formation of C3bB pro-convertases and stabilize C3bBb convertases. In addition, properdin TSR6 would sterically block binding of the protease factor I to C3b, thus limiting C3b proteolytic degradation. The presence of a valine instead of a third tryptophan in the canonical Trp-ladder of TSR domains in TSR4 allows a remarkable ca. 60\u00b0-domain bending motion of TSR4. Together with variable positioning of TSR2 and, putatively, TSR3, this explains the conformational flexibility required for properdin to form dimers, trimers, and tetramers. In conclusion, the results indicate that binding avidity of oligomeric properdin is needed to distinguish surface-deposited C3b molecules from soluble C3b or C3 and suggest that properdin-mediated interactions bridging C3b-B and C3b-Bb enhance affinity, thus promoting convertase formation and stabilization. These mechanisms explain the enhancement of complement-mediated opsonization of targeted cells and particle for immune clearance.", "doi": "10.3389/fimmu.2019.02097", "pmid": "31552043", "labels": {"Nicholas Pearce": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC6736995"}], "notes": [], "created": "2022-12-05T18:57:33.487Z", "modified": "2022-12-05T18:57:33.505Z"}, {"entity": "publication", "iuid": "a3ed235c77f44594a95e94a4c3a7953f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a3ed235c77f44594a95e94a4c3a7953f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a3ed235c77f44594a95e94a4c3a7953f"}}, "title": "Investigation of the skin microbiome: swabs vs. biopsies.", "authors": [{"family": "Prast-Nielsen", "given": "S", "initials": "S", "orcid": "0000-0001-5877-7988", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fe13dffa03b24588a919b6b028788a6e.json"}}, {"family": "Tobin", "given": "A-M", "initials": "AM", "orcid": "0000-0003-2730-9561", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/be1b7c678a604819a192a67959caf883.json"}}, {"family": "Adamzik", "given": "K", "initials": "K"}, {"family": "Powles", "given": "A", "initials": "A"}, {"family": "Hugerth", "given": "L W", "initials": "LW"}, {"family": "Sweeney", "given": "C", "initials": "C"}, {"family": "Kirby", "given": "B", "initials": "B"}, {"family": "Engstrand", "given": "L", "initials": "L"}, {"family": "Fry", "given": "L", "initials": "L"}], "type": "comparative study", "published": "2019-09-00", "journal": {"title": "Br. J. Dermatol.", "issn": "1365-2133", "volume": "181", "issue": "3", "pages": "572-579", "issn-l": "0007-0963"}, "abstract": "Human skin is populated by diverse bacteria and there is increasing evidence that resident bacteria play a key role initiating immune responses in cutaneous diseases such as atopic dermatitis, psoriasis and hidradenitis suppurativa. Bacteria are present at all layers of the skin but many studies have relied on swabs to profile the skin microbiota.\n\nAs the pathogenesis of many skin conditions is dermal, we wanted to compare the microbiota obtained in swabs (surface) and biopsies (dermis).\n\nUsing 16S rRNA gene sequencing we established the microbial profiles of skin swabs and skin biopsies in 16 patients.\n\nWe found differences in both diversity and taxonomic composition of the microbiome obtained from swabs and biopsies of the same individual. Several taxa were found to be more abundant in the swabs, which displayed significantly higher community richness, but Clostridiales and Bacteroidetes were significantly enriched in the biopsies. Most published research on cutaneous microbiota has been based on skin swabs, which represent the surface of the skin.\n\nOur study demonstrated a clear difference between the microbiome observed from skin swabs and skin biopsies. These findings may be highly relevant in disorders such as psoriasis where pathogenesis arises in the dermis. What's already known about this topic? 16S RNA gene sequencing has facilitated study of the skin microbiome. Several studies have sequenced the microbiome sampled by skin swabs. What does this study add? The microbiome data obtained using swabs and biopsies were different. Diseases that are predominantly dermal should be studied using both swabs and biopsies.", "doi": "10.1111/bjd.17691", "pmid": "30693476", "labels": {"Luisa Hugerth": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2022-11-08T07:01:07.271Z", "modified": "2023-10-27T09:32:21.503Z"}, {"entity": "publication", "iuid": "439e2f9400ed4300846814cd13aaf51f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/439e2f9400ed4300846814cd13aaf51f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/439e2f9400ed4300846814cd13aaf51f"}}, "title": "Combined mRNA and protein single cell analysis in a dynamic cellular system using SPARC", "authors": [{"family": "Reimeg\u00e5rd", "given": "Johan", "initials": "J"}, {"family": "Danielsson", "given": "Marcus", "initials": "M"}, {"family": "Tarbier", "given": "Marcel", "initials": "M"}, {"family": "Schuster", "given": "Jens", "initials": "J"}, {"family": "Baskaran", "given": "Sathishkumar", "initials": "S"}, {"family": "Panagiotou", "given": "Styliani", "initials": "S"}, {"family": "Dahl", "given": "Niklas", "initials": "N"}, {"family": "Friedl\u00e4nder", "given": "Marc R", "initials": "MR"}, {"family": "Gallant", "given": "Caroline J", "initials": "CJ"}], "type": "posted-content", "published": "2019-08-28", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/749473", "pmid": null, "labels": {"SciLifeLab Fellow": "", "DDLS Fellow": "", "Marcel Tarbier": "", "Marc Friedl\u00e4nder": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T11:14:44.305Z", "modified": "2026-09-23T14:10:00.200Z"}, {"entity": "publication", "iuid": "4ae200fc14d242d0a9426b2aa7133bfa", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4ae200fc14d242d0a9426b2aa7133bfa.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4ae200fc14d242d0a9426b2aa7133bfa"}}, "title": "Systematic Development of Sandwich Immunoassays for the Plasma Secretome.", "authors": [{"family": "H\u00e4ussler", "given": "Ragna S", "initials": "RS", "orcid": "0000-0003-1664-8875", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7cc0ab2ae97c4f968d6218ca2915389f.json"}}, {"family": "Bendes", "given": "Annika", "initials": "A"}, {"family": "Iglesias", "given": "MariaJesus", "initials": "M"}, {"family": "Sanchez-Rivera", "given": "Laura", "initials": "L"}, {"family": "Dodig-Crnkovi\u0107", "given": "Tea", "initials": "T"}, {"family": "Bystr\u00f6m", "given": "Sanna", "initials": "S"}, {"family": "Fredolini", "given": "Claudia", "initials": "C"}, {"family": "Birgersson", "given": "Elin", "initials": "E"}, {"family": "Dale", "given": "Matilda", "initials": "M"}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Rockberg", "given": "Johan", "initials": "J"}, {"family": "Tegel", "given": "Hanna", "initials": "H"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Qundos", "given": "Ulrika", "initials": "U"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM"}], "type": "journal article", "published": "2019-08-00", "journal": {"title": "Proteomics", "issn": "1615-9861", "volume": "19", "issue": "15", "pages": "e1900008", "issn-l": "1615-9853"}, "abstract": "The plasma proteome offers a clinically useful window into human health. Recent advances from highly multiplexed assays now call for appropriate pipelines to validate individual candidates. Here, a workflow is developed to build dual binder sandwich immunoassays (SIA) and for proteins predicted to be secreted into plasma. Utilizing suspension bead arrays, \u22481800 unique antibody pairs are first screened against 209 proteins with recombinant proteins as well as EDTA plasma. Employing 624 unique antibodies, dilution-dependent curves in plasma and concentration-dependent curves of full-length proteins for 102 (49%) of the targets are obtained. For 22 protein assays, the longitudinal, interindividual, and technical performance is determined in a set of plasma samples collected from 18 healthy subjects every third month over 1 year. Finally, 14 of these assays are compared with with SIAs composed of other binders, proximity extension assays, and affinity-free targeted mass spectrometry. The workflow provides a multiplexed approach to screen for SIA pairs that suggests using at least three antibodies per target. This design is applicable for a wider range of targets of the plasma proteome, and the assays can be applied for discovery but also to validate emerging candidates derived from other platforms.", "doi": "10.1002/pmic.201900008", "pmid": "31278833", "labels": {"Fredrik Edfors": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2026-09-23T11:07:55.353Z", "modified": "2026-09-23T11:07:55.417Z"}, {"entity": "publication", "iuid": "520616878298403eb711d4ce0b5d21ca", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/520616878298403eb711d4ce0b5d21ca.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/520616878298403eb711d4ce0b5d21ca"}}, "title": "Strategies for increasing the throughput of super-resolution microscopies.", "authors": [{"family": "Mahecic", "given": "Dora", "initials": "D"}, {"family": "Testa", "given": "Ilaria", "initials": "I"}, {"family": "Griffi\u00e9", "given": "Juliette", "initials": "J"}, {"family": "Manley", "given": "Suliana", "initials": "S"}], "type": "journal article", "published": "2019-08-00", "journal": {"title": "Curr Opin Chem Biol", "issn": "1879-0402", "issn-l": "1367-5931", "volume": "51", "issue": null, "pages": "84-91"}, "abstract": "Fluorescence microscopy methods have been developed to circumvent the diffraction limit by exploiting nonlinearities in the interactions between light and fluorophores. Initially, these methods were up to orders of magnitude slower than standard microscopies. In recent years, a wide array of technological advances have increased the throughput of super-resolution microscopies, through parallelization, smart scanning or data processing, and sample expansion. Here, we review recent innovations for increased throughput, some applications that have benefitted from them, and how they could be improved in the future.", "doi": "10.1016/j.cbpa.2019.05.012", "pmid": "31212117", "labels": {"Ilaria Testa": "", "SciLifeLab Fellow": "", "DDLS Fellow": "", "Juliette Griffie": ""}, "xrefs": [{"db": "pii", "key": "S1367-5931(19)30032-8"}], "notes": [], "created": "2020-09-29T10:05:41.034Z", "modified": "2026-09-23T10:41:39.374Z"}, {"entity": "publication", "iuid": "01d5f2288879483eacf0c7e62c866f1a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/01d5f2288879483eacf0c7e62c866f1a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/01d5f2288879483eacf0c7e62c866f1a"}}, "title": "Elucidating the Reprograming of Colorectal Cancer Metabolism Using Genome-Scale Metabolic Modeling.", "authors": [{"family": "Zhang", "given": "Cheng", "initials": "C"}, {"family": "Aldrees", "given": "Mohammed", "initials": "M"}, {"family": "Arif", "given": "Muhammad", "initials": "M"}, {"family": "Li", "given": "Xiangyu", "initials": "X"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Aziz", "given": "Mohammad Azhar", "initials": "MA"}], "type": "journal article", "published": "2019-07-30", "journal": {"title": "Front Oncol", "issn": "2234-943X", "issn-l": "2234-943X", "volume": "9", "issue": null, "pages": "681"}, "abstract": "Colorectal cancer is the third most incidental cancer worldwide, and the response rate of current treatment for colorectal cancer is very low. Genome-scale metabolic models (GEMs) are systems biology platforms, and they had been used to assist researchers in understanding the metabolic alterations in different types of cancer. Here, we reconstructed a generic colorectal cancer GEM by merging 374 personalized GEMs from the Human Pathology Atlas and used it as a platform for systematic investigation of the difference between tumor and normal samples. The reconstructed model revealed the metabolic reprogramming in glutathione as well as the arginine and proline metabolism in response to tumor occurrence. In addition, six genes including ODC1, SMS, SRM, RRM2, SMOX, and SAT1 associated with arginine and proline metabolism were found to be key players in this metabolic alteration. We also investigated these genes in independent colorectal cancer patients and cell lines and found that many of these genes showed elevated level in colorectal cancer and exhibited adverse effect in patients. Therefore, these genes could be promising therapeutic targets for treatment of a specific colon cancer patient group.", "doi": "10.3389/fonc.2019.00681", "pmid": "31417867", "labels": {"Adil Mardinoglu": "", "SciLifeLab Fellow": "", "DDLS Fellow": "", "Muhammad Arif": ""}, "xrefs": [{"db": "pmc", "key": "PMC6682621"}], "notes": [], "created": "2020-09-25T13:21:04.060Z", "modified": "2026-09-23T09:35:16.177Z"}, {"entity": "publication", "iuid": "5600e22f0ffd4eb5a4bd3b2c18f6ec82", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5600e22f0ffd4eb5a4bd3b2c18f6ec82.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5600e22f0ffd4eb5a4bd3b2c18f6ec82"}}, "title": "A validated single-cell-based strategy to identify diagnostic and therapeutic targets in complex diseases.", "authors": [{"family": "Gawel", "given": "Danuta R", "initials": "DR"}, {"family": "Serra-Musach", "given": "Jordi", "initials": "J"}, {"family": "Lilja", "given": "Sandra", "initials": "S"}, {"family": "Aagesen", "given": "Jesper", "initials": "J"}, {"family": "Arenas", "given": "Alex", "initials": "A"}, {"family": "Asking", "given": "Bengt", "initials": "B"}, {"family": "Bengn\u00e9r", "given": "Malin", "initials": "M"}, {"family": "Bj\u00f6rkander", "given": "Janne", "initials": "J"}, {"family": "Biggs", "given": "Sophie", "initials": "S"}, {"family": "Ernerudh", "given": "Jan", "initials": "J"}, {"family": "Hjortswang", "given": "Henrik", "initials": "H"}, {"family": "Karlsson", "given": "Jan-Erik", "initials": "JE"}, {"family": "K\u00f6psen", "given": "Mattias", "initials": "M"}, {"family": "Lee", "given": "Eun Jung", "initials": "EJ"}, {"family": "Lentini", "given": "Antonio", "initials": "A"}, {"family": "Li", "given": "Xinxiu", "initials": "X"}, {"family": "Magnusson", "given": "Mattias", "initials": "M"}, {"family": "Mart\u00ednez-Enguita", "given": "David", "initials": "D"}, {"family": "Matussek", "given": "Andreas", "initials": "A"}, {"family": "Nestor", "given": "Colm E", "initials": "CE"}, {"family": "Sch\u00e4fer", "given": "Samuel", "initials": "S"}, {"family": "Seifert", "given": "Oliver", "initials": "O"}, {"family": "Sonmez", "given": "Ceylan", "initials": "C"}, {"family": "Stjernman", "given": "Henrik", "initials": "H"}, {"family": "Tj\u00e4rnberg", "given": "Andreas", "initials": "A"}, {"family": "Wu", "given": "Simon", "initials": "S"}, {"family": "\u00c5kesson", "given": "Karin", "initials": "K"}, {"family": "Shalek", "given": "Alex K", "initials": "AK"}, {"family": "Stenmarker", "given": "Margaretha", "initials": "M"}, {"family": "Zhang", "given": "Huan", "initials": "H"}, {"family": "Gustafsson", "given": "Mika", "initials": "M"}, {"family": "Benson", "given": "Mikael", "initials": "M", "orcid": "0000-0002-7753-9181", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7d60373e5f0c4c58a9853eb4ca671950.json"}}], "type": "journal article", "published": "2019-07-30", "journal": {"title": "Genome Med", "issn": "1756-994X", "volume": "11", "issue": "1", "pages": "47", "issn-l": "1756-994X"}, "abstract": "Genomic medicine has paved the way for identifying biomarkers and therapeutically actionable targets for complex diseases, but is complicated by the involvement of thousands of variably expressed genes across multiple cell types. Single-cell RNA-sequencing study (scRNA-seq) allows the characterization of such complex changes in whole organs.\n\nThe study is based on applying network tools to organize and analyze scRNA-seq data from a mouse model of arthritis and human rheumatoid arthritis, in order to find diagnostic biomarkers and therapeutic targets. Diagnostic validation studies were performed using expression profiling data and potential protein biomarkers from prospective clinical studies of 13 diseases. A candidate drug was examined by a treatment study of a mouse model of arthritis, using phenotypic, immunohistochemical, and cellular analyses as read-outs.\n\nWe performed the first systematic analysis of pathways, potential biomarkers, and drug targets in scRNA-seq data from a complex disease, starting with inflamed joints and lymph nodes from a mouse model of arthritis. We found the involvement of hundreds of pathways, biomarkers, and drug targets that differed greatly between cell types. Analyses of scRNA-seq and GWAS data from human rheumatoid arthritis (RA) supported a similar dispersion of pathogenic mechanisms in different cell types. Thus, systems-level approaches to prioritize biomarkers and drugs are needed. Here, we present a prioritization strategy that is based on constructing network models of disease-associated cell types and interactions using scRNA-seq data from our mouse model of arthritis, as well as human RA, which we term multicellular disease models (MCDMs). We find that the network centrality of MCDM cell types correlates with the enrichment of genes harboring genetic variants associated with RA and thus could potentially be used to prioritize cell types and genes for diagnostics and therapeutics. We validated this hypothesis in a large-scale study of patients with 13 different autoimmune, allergic, infectious, malignant, endocrine, metabolic, and cardiovascular diseases, as well as a therapeutic study of the mouse arthritis model.\n\nOverall, our results support that our strategy has the potential to help prioritize diagnostic and therapeutic targets in human disease.", "doi": "10.1186/s13073-019-0657-3", "pmid": "31358043", "labels": {"Antonio Lentini": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC6664760"}, {"db": "pii", "key": "10.1186/s13073-019-0657-3"}], "notes": [], "created": "2025-03-28T07:12:03.937Z", "modified": "2025-03-28T07:12:03.993Z"}, {"entity": "publication", "iuid": "b8255350185546aa9deb9805f2b5cede", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b8255350185546aa9deb9805f2b5cede.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b8255350185546aa9deb9805f2b5cede"}}, "title": "Screening a Resource of Recombinant Protein Fragments for Targeted Proteomics.", "authors": [{"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e213b04f8984c8eb00c68f5bc2f6a36.json"}}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Vunk", "given": "Helian", "initials": "H"}, {"family": "Kotol", "given": "David", "initials": "D"}, {"family": "Fredolini", "given": "Claudia", "initials": "C"}, {"family": "Maddalo", "given": "Gianluca", "initials": "G"}, {"family": "Svensson", "given": "Anne-Sophie", "initials": "AS"}, {"family": "Bostr\u00f6m", "given": "Tove", "initials": "T"}, {"family": "Tegel", "given": "Hanna", "initials": "H"}, {"family": "Nilsson", "given": "Peter", "initials": "P"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/022e140799b6466ea123319c3d70c76e.json"}}, {"family": "Uhlen", "given": "Mathias", "initials": "M"}], "type": "journal article", "published": "2019-07-05", "journal": {"title": "J. Proteome Res.", "issn": "1535-3907", "volume": "18", "issue": "7", "pages": "2706-2718", "issn-l": "1535-3893"}, "abstract": "The availability of proteomics resources hosting protein and peptide standards, as well as the data describing their analytical performances, will continue to enhance our current capabilities to develop targeted proteomics methods for quantitative biology. This study describes the analysis of a resource of 26,840 individually purified recombinant protein fragments corresponding to more than 16,000 human protein-coding genes. The resource was screened to identify proteotypic peptides suitable for targeted proteomics efforts, and we report LC-MS/MS assay coordinates for more than 25,000 proteotypic peptides, corresponding to more than 10,000 unique proteins. Additionally, peptide formation and digestion kinetics were, for a subset of the standards, monitored using a time-course protocol involving parallel digestion of isotope-labeled recombinant protein standards and endogenous human plasma proteins. We show that the strategy by adding isotope-labeled recombinant proteins before trypsin digestion enables short digestion protocols (\u226460 min) with robust quantitative precision. In a proof-of-concept study, we quantified 23 proteins in human plasma using assay parameters defined in our study and used the standards to describe distinct clusters of individuals linked to different levels of LPA, APOE, SERPINA5, and TFRC. In summary, we describe the use and utility of a resource of recombinant proteins to identify proteotypic peptides useful for targeted proteomics assay development.", "doi": "10.1021/acs.jproteome.8b00924", "pmid": "31094526", "labels": {"Fredrik Edfors": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2026-09-23T11:49:21.946Z", "modified": "2026-09-23T11:49:21.999Z"}, {"entity": "publication", "iuid": "2df25f96a5b941089c19d9d4ce1e04f7", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/2df25f96a5b941089c19d9d4ce1e04f7.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/2df25f96a5b941089c19d9d4ce1e04f7"}}, "title": "Development of parallel reaction monitoring assays for cerebrospinal fluid proteins associated with Alzheimer's disease.", "authors": [{"family": "Andersson", "given": "Annika", "initials": "A"}, {"family": "Remnest\u00e5l", "given": "Julia", "initials": "J"}, {"family": "Nellg\u00e5rd", "given": "Bengt", "initials": "B"}, {"family": "Vunk", "given": "Helian", "initials": "H"}, {"family": "Kotol", "given": "David", "initials": "D"}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM"}, {"family": "Ilag", "given": "Leopold L", "initials": "LL"}, {"family": "Zetterberg", "given": "Henrik", "initials": "H"}, {"family": "Blennow", "given": "Kaj", "initials": "K"}, {"family": "M\u00e5nberg", "given": "Anna", "initials": "A"}, {"family": "Nilsson", "given": "Peter", "initials": "P"}, {"family": "Fredolini", "given": "Claudia", "initials": "C"}], "type": "journal article", "published": "2019-07-00", "journal": {"title": "Clin Chim Acta", "issn": "1873-3492", "volume": "494", "pages": "79-93", "issn-l": null}, "abstract": "Detailed knowledge of protein changes in cerebrospinal fluid (CSF) across healthy and diseased individuals would provide a better understanding of the onset and progression of neurodegenerative disorders. In this study, we selected 20 brain-enriched proteins previously identified in CSF by antibody suspension bead arrays (SBA) to be potentially biomarkers for Alzheimer's disease (AD) and verified these using an orthogonal approach. We examined the same set of 94 CSF samples from patients affected by AD (including preclinical and prodromal), mild cognitive impairment (MCI), non-AD dementia and healthy individuals, which had previously been analyzed by SBA. Twenty-eight parallel reaction monitoring (PRM) assays were developed and 13 of them could be validated for protein quantification. Antibody profiles were verified by PRM. For seven proteins, the antibody profiles were highly correlated with the PRM results (r > 0.7) and GAP43, VCAM1 and PSAP were identified as potential markers of preclinical AD. In conclusion, we demonstrate the usefulness of targeted mass spectrometry as a tool for the orthogonal verification of antibody profiling data, suggesting that these complementary methods can be successfully applied for comprehensive exploration of CSF protein levels in neurodegenerative disorders.", "doi": "10.1016/j.cca.2019.03.243", "pmid": "30858094", "labels": {"Fredrik Edfors": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pii", "key": "S0009-8981(19)30348-1"}], "notes": [], "created": "2026-09-23T08:35:52.642Z", "modified": "2026-09-23T08:35:52.706Z"}, {"entity": "publication", "iuid": "3324c2681ab64dd1b8433a69b0680265", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3324c2681ab64dd1b8433a69b0680265.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3324c2681ab64dd1b8433a69b0680265"}}, "title": "3D-Printed Whole Prostate Models with Tumor Hotspots Using Dual-Extruder Printer.", "authors": [{"family": "Liimatainen", "given": "Kaisa", "initials": "K"}, {"family": "Latonen", "given": "Leena", "initials": "L"}, {"family": "Kartasalo", "given": "Kimmo", "initials": "K"}, {"family": "Ruusuvuori", "given": "Pekka", "initials": "P"}], "type": "journal article", "published": "2019-07-00", "journal": {"title": "Annu Int Conf IEEE Eng Med Biol Soc", "issn": "2694-0604", "issn-l": null, "volume": "2019", "issue": null, "pages": "2867-2871"}, "abstract": "3D printing has emerged as a popular technology in various biomedical applications. Physical models of anatomical structures concretize the digital representations and can be used for teaching and analysis. In this study we combine 3D histology with 3D printing, creating realistic physical models of tissues with hotspots of interest. As an example we use mouse prostates containing tumors. Surface meshes are created from binary masks of HE-stained serial sections of mouse prostates and manually annotated tumor areas. Sections are interpolated to expand sparse image stacks for smoother results. Fiji, Meshlab and Tinkercad are used for mesh creation and processing. Objects are printed with Prusa-based dual-extruder printer enabling different colors for tumors and the surrounding prostate tissue. Our 3D-printed mouse prostates appear realistic and tumors located at the edges of the organ are clearly visible. When transparent filament is used, the tumor hotspots are visible even when they are inside the prostate.", "doi": "10.1109/EMBC.2019.8857068", "pmid": "31946490", "labels": {"Kimmo Kartasalo": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2024-11-05T16:04:39.384Z", "modified": "2024-11-29T10:45:42.118Z"}, {"entity": "publication", "iuid": "15a934184a3b466da718695f9bcc26a8", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/15a934184a3b466da718695f9bcc26a8.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/15a934184a3b466da718695f9bcc26a8"}}, "title": "Serotype-specific evolutionary patterns of antimicrobial-resistant Salmonella enterica.", "authors": [{"family": "Liao", "given": "Jingqiu", "initials": "J"}, {"family": "Orsi", "given": "Renato Hohl", "initials": "RH"}, {"family": "Carroll", "given": "Laura M", "initials": "LM"}, {"family": "Kovac", "given": "Jasna", "initials": "J"}, {"family": "Ou", "given": "Hongyu", "initials": "H"}, {"family": "Zhang", "given": "Hailong", "initials": "H"}, {"family": "Wiedmann", "given": "Martin", "initials": "M"}], "type": "journal article", "published": "2019-06-21", "journal": {"title": "BMC Evol Biol BMC Evolutionary Biology", "issn": "1471-2148", "volume": "19", "issue": "1", "pages": "132", "issn-l": "1471-2148"}, "abstract": "The emergence of antimicrobial-resistant (AMR) strains of the important human and animal pathogen Salmonella enterica poses a growing threat to public health. Here, we studied the genome-wide evolution of 90 S. enterica AMR isolates, representing one host adapted serotype (S. Dublin) and two broad host range serotypes (S. Newport and S. Typhimurium).\n\nAMR S. Typhimurium had a large effective population size, a large and diverse genome, AMR profiles with high diversity, and frequent positive selection and homologous recombination. AMR S. Newport showed a relatively low level of diversity and a relatively clonal population structure. AMR S. Dublin showed evidence for a recent population bottleneck, and the genomes were characterized by a larger number of genes and gene ontology terms specifically absent from this serotype and a significantly higher number of pseudogenes as compared to other two serotypes. Approximately 50% of accessory genes, including specific AMR and putative prophage genes, were significantly over- or under-represented in a given serotype. Approximately 65% of the core genes showed phylogenetic clustering by serotype, including the AMR gene aac (6')-Iaa. While cell surface proteins were shown to be the main target of positive selection, some proteins with possible functions in AMR and virulence also showed evidence for positive selection. Homologous recombination mainly acted on prophage-associated proteins.\n\nOur data indicates a strong association between genome content of S. enterica and serotype. Evolutionary patterns observed in S. Typhimurium are consistent with multiple emergence events of AMR strains and/or ecological success of this serotype in different hosts or habitats. Evolutionary patterns of S. Newport suggested that antimicrobial resistance emerged in one single lineage, Lineage IIC. A recent population bottleneck and genome decay observed in AMR S. Dublin are congruent with its narrow host range. Finally, our results suggest the potentially important role of positive selection in the evolution of antimicrobial resistance, host adaptation and serotype diversification in S. enterica.", "doi": "10.1186/s12862-019-1457-5", "pmid": "31226931", "labels": {"Laura Carroll": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC6588947"}, {"db": "pii", "key": "10.1186/s12862-019-1457-5"}], "notes": [], "created": "2025-03-18T17:24:58.163Z", "modified": "2025-03-18T17:24:58.167Z"}, {"entity": "publication", "iuid": "10e0b502a55d48469ccb8202a1649d73", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/10e0b502a55d48469ccb8202a1649d73.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/10e0b502a55d48469ccb8202a1649d73"}}, "title": "Colitis-induced colorectal cancer and intestinal epithelial estrogen receptor beta impact gut microbiota diversity.", "authors": [{"family": "Ibrahim", "given": "Ahmed", "initials": "A"}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW"}, {"family": "Hases", "given": "Linnea", "initials": "L"}, {"family": "Saxena", "given": "Ashish", "initials": "A"}, {"family": "Seifert", "given": "Maike", "initials": "M"}, {"family": "Thomas", "given": "Quentin", "initials": "Q"}, {"family": "Gustafsson", "given": "Jan-\u00c5ke", "initials": "J\u00c5"}, {"family": "Engstrand", "given": "Lars", "initials": "L"}, {"family": "Williams", "given": "Cecilia", "initials": "C", "orcid": "0000-0002-0602-2062", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/872c978997c74e89ae75efd90d592b42.json"}}], "type": "journal article", "published": "2019-06-15", "journal": {"title": "Int. J. Cancer", "issn": "1097-0215", "volume": "144", "issue": "12", "pages": "3086-3098", "issn-l": "0020-7136"}, "abstract": "Chronic inflammation of the colon (colitis) is a risk factor for colorectal cancer (CRC). Hormone-replacement therapy reduces CRC incidences, and the estrogen receptor beta (ER\u03b2/ESR2) has been implicated in this protection. Gut microbiota is altered in both colitis and CRC and may influence the severity of both. Here we test the hypothesis that intestinal ER\u03b2 impacts the gut microbiota. Mice with and without intestine-specific deletion of ER\u03b2 (ER\u03b2KOVil ) were generated using the Cre-LoxP system. Colitis and CRC were induced with a single intraperitoneal injection of azoxymethane (AOM) followed by administration of three cycles of dextran sulfate sodium (DSS) in drinking water. The microbiota population were characterized by high-throughput 16S rRNA gene sequencing of DNA extracted from fecal samples (N = 39). Differences in the microbiota due to AOM/DSS and absence of ER\u03b2 were identified through bioinformatic analyses of the 16S-Seq data, and the distribution of bacterial species was corroborated using qPCR. We demonstrate that colitis-induced CRC reduced the gut microbiota diversity and that loss of ER\u03b2 enhanced this process. Further, the Bacteroidetes genus Prevotellaceae_UCG_001 was overrepresented in AOM/DSS mice compared to untreated controls (3.5-fold, p = 0.004), and this was enhanced in females and in ER\u03b2KOVil mice. Overall, AOM/DSS enriched for microbiota impacting immune system diseases and metabolic functions, and lack of ER\u03b2 in combination with AOM/DSS enriched for microbiota impacting carbohydrate metabolism and cell motility, while reducing those impacting the endocrine system. Our data support that intestinal ER\u03b2 contributes to a more favorable microbiome that could attenuate CRC development.", "doi": "10.1002/ijc.32037", "pmid": "30515752", "labels": {"Luisa Hugerth": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC6519213"}], "notes": [], "created": "2022-11-08T06:59:16.768Z", "modified": "2026-09-23T07:29:37.161Z"}, {"entity": "publication", "iuid": "7122797371204e72b6184a986143f8ab", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/7122797371204e72b6184a986143f8ab.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/7122797371204e72b6184a986143f8ab"}}, "title": "iNetModels 2.0: an interactive visualization and database of multi-omics data", "authors": [{"family": "Arif", "given": "Muhammad", "initials": "M", "orcid": "0000-0003-2261-0881", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c8ffc9889ace44e3b992816601b817e2.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C"}, {"family": "Li", "given": "Xiangyu", "initials": "X"}, {"family": "G\u00fcng\u00f6r", "given": "Cem", "initials": "C"}, {"family": "\u00c7akmak", "given": "Bu\u011fra", "initials": "B"}, {"family": "Arslant\u00fcrk", "given": "Metin", "initials": "M"}, {"family": "Tebani", "given": "Abdellah", "initials": "A", "orcid": "0000-0002-8901-2678", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/794215a6625b4fe4b652ec08bcab98ec.json"}}, {"family": "\u00d6zcan", "given": "Berkay", "initials": "B"}, {"family": "Suba\u015f", "given": "O\u011fuzhan", "initials": "O"}, {"family": "Zhou", "given": "Wenyu", "initials": "W", "orcid": "0000-0001-7719-0859", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/adebb996026246a29ed03a9ecb5c6358.json"}}, {"family": "Piening", "given": "Brian", "initials": "B"}, {"family": "Turkez", "given": "Hasan", "initials": "H", "orcid": "0000-0002-7046-8990", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cf2f1748757d45cabfe56fdfaccead6a.json"}}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/abbbf8193d5a4376a5c726768d039439.json"}}, {"family": "Price", "given": "Nathan", "initials": "N", "orcid": "0000-0002-4157-0267", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/071ae2c98fb54fbfbb4e847c54d18c23.json"}}, {"family": "Hood", "given": "Leroy", "initials": "L", "orcid": "0000-0001-7158-3678", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ad7224b8388b49778de38301ad77e60a.json"}}, {"family": "Snyder", "given": "Michael", "initials": "M", "orcid": "0000-0003-0784-7987", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ce9e294ff3b64f7caa770c883d12514c.json"}}, {"family": "Nielsen", "given": "Jens", "initials": "J"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ea446aa574042a295d5f69437402f76.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca58bf2d214047e0ae5e38a42a0f2808.json"}}], "type": "posted-content", "published": "2019-06-08", "journal": {"title": "bioRxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/662502", "pmid": null, "labels": {"SciLifeLab Fellow": null, "DDLS Fellow": null, "Adil Mardinoglu": null, "Muhammad Arif": null}, "xrefs": [], "notes": [], "created": "2026-08-20T11:13:56.955Z", "modified": "2026-10-05T08:42:59.517Z"}, {"entity": "publication", "iuid": "a0e252a585cf43948974491823d3742c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a0e252a585cf43948974491823d3742c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a0e252a585cf43948974491823d3742c"}}, "title": "Assembly and Characterization of a Pathogen Strain Collection for Produce Safety Applications: Pre-growth Conditions Have a Larger Effect on Peroxyacetic Acid Tolerance Than Strain Diversity.", "authors": [{"family": "Harrand", "given": "Anna Sophia", "initials": "AS"}, {"family": "Kovac", "given": "Jasna", "initials": "J"}, {"family": "Carroll", "given": "Laura M", "initials": "LM"}, {"family": "Guariglia-Oropeza", "given": "Veronica", "initials": "V"}, {"family": "Kent", "given": "David J", "initials": "DJ"}, {"family": "Wiedmann", "given": "Martin", "initials": "M"}], "type": "journal article", "published": "2019-05-31", "journal": {"title": "Front Microbiol", "issn": "1664-302X", "volume": "10", "pages": "1223", "issn-l": "1664-302X"}, "abstract": "Effective control of foodborne pathogens on produce requires science-based validation of interventions and control strategies, which typically involves challenge studies with a set of bacterial strains representing the target pathogens or appropriate surrogates. In order to facilitate these types of studies, a produce-relevant strain collection was assembled to represent strains from produce outbreaks or pre-harvest environments, including Listeria monocytogenes (n = 11), Salmonella enterica (n = 23), shiga-toxin producing Escherichia coli (STEC) (n = 13), and possible surrogate organisms (n = 8); all strains were characterized by whole genome sequencing (WGS). Strain diversity was assured by including the 10 most common S. enterica serotypes, L. monocytogenes lineages I-IV, and E. coli O157 as well as selected \"non-O157\" STEC serotypes. As it has previously been shown that strains and genetic lineages of a pathogen may differ in their ability to survive different stress conditions, a subset of representative strains for each \"pathogen group\" (e.g., Salmonella, STEC) was selected and assessed for survival of exposure to peroxyacetic acid (PAA) using strains pre-grown under different conditions including (i) low pH, (ii) high salt, (iii) reduced water activity, (iv) different growth phases, (v) minimal medium, and (vi) different temperatures (21\u00b0C, 37\u00b0C). The results showed that across the three pathogen groups pre-growth conditions had a larger effect on bacterial reduction after PAA exposure as compared to strain diversity. Interestingly, bacteria exposed to salt stress (4.5% NaCl) consistently showed the least reduction after exposure to PAA; however, for STEC, strains pre-grown at 21\u00b0C were as tolerant to PAA exposure as strains pre-grown under salt stress. Overall, our data suggests that challenge studies conducted with multi-strain cocktails (pre-grown under a single specific condition) may not necessarily reflect the relevant phenotypic range needed to appropriately assess different intervention strategies.", "doi": "10.3389/fmicb.2019.01223", "pmid": "31231329", "labels": {"Laura Carroll": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC6558390"}], "notes": [], "created": "2025-03-18T17:24:39.705Z", "modified": "2025-03-18T17:24:39.709Z"}, {"entity": "publication", "iuid": "5cecf57f8c9543e698d89e51283be8e4", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5cecf57f8c9543e698d89e51283be8e4.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5cecf57f8c9543e698d89e51283be8e4"}}, "title": "Sex differences in IL-17 contribute to chronicity in male versus female urinary tract infection.", "authors": [{"family": "Zychlinsky Scharff", "given": "Anna", "initials": "A"}, {"family": "Rousseau", "given": "Matthieu", "initials": "M"}, {"family": "Lacerda Mariano", "given": "Livia", "initials": "L"}, {"family": "Canton", "given": "Tracy", "initials": "T"}, {"family": "Consiglio", "given": "Camila Rosat", "initials": "CR"}, {"family": "Albert", "given": "Matthew L", "initials": "ML"}, {"family": "Fontes", "given": "Magnus", "initials": "M"}, {"family": "Duffy", "given": "Darragh", "initials": "D"}, {"family": "Ingersoll", "given": "Molly A", "initials": "MA"}], "type": "journal article", "published": "2019-05-30", "journal": {"title": "JCI Insight", "issn": "2379-3708", "volume": "5", "issue": "13", "issn-l": null}, "abstract": "Sex-based differences influence incidence and outcome of infectious disease. Women have a significantly greater incidence of urinary tract infection (UTI) than men, yet, conversely, male UTI is more persistent with greater associated morbidity. Mechanisms underlying these sex-based differences are unknown, in part due to a lack of experimental models. We optimized a model to transurethrally infect male mice and directly compared UTI in both sexes. Although both sexes were initially equally colonized by uropathogenic E. coli, only male and testosterone-treated female mice remained chronically infected for up to 4 weeks. Female mice had more robust innate responses, including higher IL-17 expression, and increased \u03b3\u03b4 T cells and group 3 innate lymphoid cells in the bladder following infection. Accordingly, neutralizing IL-17 abolished resolution in female mice, identifying a cytokine pathway necessary for bacterial clearance. Our findings support the concept that sex-based responses to UTI contribute to impaired innate immunity in males and provide a rationale for non-antibiotic-based immune targeting to improve the response to UTI.", "doi": "10.1172/jci.insight.122998", "pmid": "31145099", "labels": {"Camila Consiglio": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC6629110"}, {"db": "pii", "key": "122998"}], "notes": [], "created": "2023-11-22T09:17:16.822Z", "modified": "2023-11-22T09:17:16.867Z"}, {"entity": "publication", "iuid": "cd11ad76b86a4a5fb9a53e840c0fe83b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/cd11ad76b86a4a5fb9a53e840c0fe83b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/cd11ad76b86a4a5fb9a53e840c0fe83b"}}, "title": "Mucosal-associated invariant T cells and oral microbiome in persistent apical periodontitis.", "authors": [{"family": "Davanian", "given": "Haleh", "initials": "H"}, {"family": "Gaiser", "given": "Rogier A\u00e4ron", "initials": "RA", "orcid": "0000-0002-5701-6332", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d85d082016524abcb00e78649a1beabb.json"}}, {"family": "Silfverberg", "given": "Mikael", "initials": "M"}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW"}, {"family": "Sobkowiak", "given": "Micha\u0142 J", "initials": "MJ"}, {"family": "Lu", "given": "Liyan", "initials": "L"}, {"family": "Healy", "given": "Katie", "initials": "K"}, {"family": "Sandberg", "given": "Johan K", "initials": "JK", "orcid": "0000-0002-6275-0750", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d33bfbd945e647ac82e2d2699df02cb9.json"}}, {"family": "N\u00e4sman", "given": "Peggy", "initials": "P"}, {"family": "Karlsson", "given": "J\u00f6rgen", "initials": "J"}, {"family": "Jansson", "given": "Leif", "initials": "L"}, {"family": "Engstrand", "given": "Lars", "initials": "L"}, {"family": "S\u00e4llberg Chen", "given": "Margaret", "initials": "M"}], "type": "journal article", "published": "2019-05-09", "journal": {"title": "Int J Oral Sci", "issn": "2049-3169", "volume": "11", "issue": "2", "pages": "16", "issn-l": null}, "abstract": "Opportunistic bacteria in apical periodontitis (AP) may pose a risk for systemic dissemination. Mucosal-associated invariant T (MAIT) cells are innate-like T cells with a broad and potent antimicrobial activity important for gut mucosal integrity. It was recently shown that MAIT cells are present in the oral mucosal tissue, but the involvement of MAIT cells in AP is unknown. Here, comparison of surgically resected AP and gingival tissues demonstrated that AP tissues express significantly higher levels of V\u03b17.2-J\u03b133, V\u03b17.2-J\u03b120, V\u03b17.2-J\u03b112, C\u03b1 and tumour necrosis factor (TNF), interferon (IFN)-\u03b3 and interleukin (IL)-17A transcripts, resembling a MAIT cell signature. Moreover, in AP tissues the MR1-restricted MAIT cells positive for MR1-5-OP-RU tetramer staining appeared to be of similar levels as in peripheral blood but consisted mainly of CD4+ subset. Unlike gingival tissues, the AP microbiome was quantitatively impacted by factors like fistula and high patient age and had a prominent riboflavin-expressing bacterial feature. When merged in an integrated view, the examined immune and microbiome data in the sparse partial least squares discriminant analysis could identify bacterial relative abundances that negatively correlated with V\u03b17.2-J\u03b133, C\u03b1, and IL-17A transcript expressions in AP, implying that MAIT cells could play a role in the local defence at the oral tissue barrier. In conclusion, we describe the presence of MAIT cells at the oral site where translocation of oral microbiota could take place. These findings have implications for understanding the immune sensing of polymicrobial-related oral diseases.", "doi": "10.1038/s41368-019-0049-y", "pmid": "31068577", "labels": {"Luisa Hugerth": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC6506549"}, {"db": "pii", "key": "10.1038/s41368-019-0049-y"}], "notes": [], "created": "2022-11-08T07:01:09.569Z", "modified": "2026-09-23T10:43:47.513Z"}, {"entity": "publication", "iuid": "3353d6ca6f3c4745a865eb29ee2551f4", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3353d6ca6f3c4745a865eb29ee2551f4.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3353d6ca6f3c4745a865eb29ee2551f4"}}, "title": "Identification of Novel Mobilized Colistin Resistance Gene mcr-9 in a Multidrug-Resistant, Colistin-Susceptible Salmonella enterica Serotype Typhimurium Isolate.", "authors": [{"family": "Carroll", "given": "Laura M", "initials": "LM"}, {"family": "Gaballa", "given": "Ahmed", "initials": "A"}, {"family": "Guldimann", "given": "Claudia", "initials": "C"}, {"family": "Sullivan", "given": "Genevieve", "initials": "G"}, {"family": "Henderson", "given": "Lory O", "initials": "LO"}, {"family": "Wiedmann", "given": "Martin", "initials": "M"}], "type": "journal article", "published": "2019-05-07", "journal": {"title": "MBio", "issn": "2150-7511", "volume": "10", "issue": "3", "issn-l": null}, "abstract": "Mobilized colistin resistance (mcr) genes are plasmid-borne genes that confer resistance to colistin, an antibiotic used to treat severe bacterial infections. To date, eight known mcr homologues have been described (mcr-1 to -8). Here, we describe mcr-9, a novel mcr homologue detected during routine in silico screening of sequenced Salmonella genomes for antimicrobial resistance genes. The amino acid sequence of mcr-9, detected in a multidrug-resistant (MDR) Salmonella enterica serotype Typhimurium (S Typhimurium) strain isolated from a human patient in Washington State in 2010, most closely resembled mcr-3, aligning with 64.5% amino acid identity and 99.5% coverage using Translated Nucleotide BLAST (tblastn). The S. Typhimurium strain was tested for phenotypic resistance to colistin and was found to be sensitive at the 2-mg/liter European Committee on Antimicrobial Susceptibility Testing breakpoint under the tested conditions. mcr-9 was cloned in colistin-susceptible Escherichia coli NEB5\u03b1 under an IPTG (isopropyl-\u03b2-d-thiogalactopyranoside)-induced promoter to determine whether it was capable of conferring resistance to colistin when expressed in a heterologous host. Expression of mcr-9 conferred resistance to colistin in E. coli NEB5\u03b1 at 1, 2, and 2.5 mg/liter colistin, albeit at a lower level than mcr-3 Pairwise comparisons of the predicted protein structures associated with all nine mcr homologues (Mcr-1 to -9) revealed that Mcr-9, Mcr-3, Mcr-4, and Mcr-7 share a high degree of similarity at the structural level. Our results indicate that mcr-9 is capable of conferring phenotypic resistance to colistin in Enterobacteriaceae and should be immediately considered when monitoring plasmid-mediated colistin resistance.IMPORTANCE Colistin is a last-resort antibiotic that is used to treat severe infections caused by MDR and extensively drug-resistant (XDR) bacteria. The World Health Organization (WHO) has designated colistin as a \"highest priority critically important antimicrobial for human medicine\" (WHO, Critically Important Antimicrobials for Human Medicine, 5th revision, 2017, https://www.who.int/foodsafety/publications/antimicrobials-fifth/en/), as it is often one of the only therapies available for treating serious bacterial infections in critically ill patients. Plasmid-borne mcr genes that confer resistance to colistin pose a threat to public health at an international scale, as they can be transmitted via horizontal gene transfer and have the potential to spread globally. Therefore, the establishment of a complete reference of mcr genes that can be used to screen for plasmid-mediated colistin resistance is essential for developing effective control strategies.", "doi": "10.1128/mBio.00853-19", "pmid": "31064835", "labels": {"Laura Carroll": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC6509194"}, {"db": "pii", "key": "mBio.00853-19"}], "notes": [], "created": "2025-03-18T17:24:21.725Z", "modified": "2025-03-18T17:24:21.736Z"}, {"entity": "publication", "iuid": "f67c76cd800b4b24a330aceceaa49752", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f67c76cd800b4b24a330aceceaa49752.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f67c76cd800b4b24a330aceceaa49752"}}, "title": "CoordinateCleaner: Standardized cleaning of occurrence records from biological collection databases", "authors": [{"family": "Zizka", "given": "Alexander", "initials": "A", "orcid": "0000-0002-1680-9192", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c62a905324e94d869ccd715ebbc98828.json"}}, {"family": "Silvestro", "given": "Daniele", "initials": "D", "orcid": "0000-0003-0100-0961", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4870742190514c5b83450c567c11398a.json"}}, {"family": "Andermann", "given": "Tobias", "initials": "T", "orcid": "0000-0002-0932-1623", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dfff478dfcfc43ddbd40bb1bafbcb0a7.json"}}, {"family": "Azevedo", "given": "Josu\u00e9", "initials": "J"}, {"family": "Duarte Ritter", "given": "Camila", "initials": "C"}, {"family": "Edler", "given": "Daniel", "initials": "D", "orcid": "0000-0001-5420-0591", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/10c85cb53c3e4b6e9eb2d2d1764b8ef5.json"}}, {"family": "Farooq", "given": "Harith", "initials": "H", "orcid": "0000-0001-9031-2785", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2df4a4a86585457792924c2c58738407.json"}}, {"family": "Herdean", "given": "Andrei", "initials": "A", "orcid": "0000-0003-2143-0213", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/342d608aae8f48498a9561fa5f32f2f0.json"}}, {"family": "Ariza", "given": "Mar\u00eda", "initials": "M"}, {"family": "Scharn", "given": "Ruud", "initials": "R"}, {"family": "Svantesson", "given": "Sten", "initials": "S"}, {"family": "Wengstr\u00f6m", "given": "Niklas", "initials": "N"}, {"family": "Zizka", "given": "Vera", "initials": "V"}, {"family": "Antonelli", "given": "Alexandre", "initials": "A", "orcid": "0000-0003-1842-9297", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1de98df1bb2140fc9666507cb2fb5614.json"}}], "type": "journal-article", "published": "2019-05-00", "journal": {"title": "Methods Ecol Evol", "issn": "2041-210X", "volume": "10", "issue": "5", "pages": "744-751", "issn-l": null}, "abstract": null, "doi": "10.1111/2041-210x.13152", "pmid": null, "labels": {"Tobias Andermann": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2022-11-11T09:11:49.152Z", "modified": "2025-12-04T16:57:46.944Z"}, {"entity": "publication", "iuid": "f3285123db344c3599c348d56221f00e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f3285123db344c3599c348d56221f00e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f3285123db344c3599c348d56221f00e"}}, "title": "Discovery of functional alternatively spliced PKM transcripts in human cancers", "authors": [{"family": "Li", "given": "Xiangyu", "initials": "X"}, {"family": "Zhang", "given": "Cheng", "initials": "C"}, {"family": "Kim", "given": "Woonghee", "initials": "W"}, {"family": "Arif", "given": "Muhammad", "initials": "M"}, {"family": "Gao", "given": "Chunxia", "initials": "C"}, {"family": "Hober", "given": "Andreas", "initials": "A"}, {"family": "Kotol", "given": "David", "initials": "D"}, {"family": "Strandberg", "given": "Linn\u00e9a", "initials": "L"}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Sivertsson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Oksvold", "given": "Per", "initials": "P"}, {"family": "Gr\u00f8tli", "given": "Morten", "initials": "M"}, {"family": "Sato", "given": "Yusuke", "initials": "Y"}, {"family": "Kume", "given": "Haruki", "initials": "H"}, {"family": "Ogawa", "given": "Seishi", "initials": "S"}, {"family": "Boren", "given": "Jan", "initials": "J"}, {"family": "Nielsen", "given": "Jens", "initials": "J"}, {"family": "Uhlen", "given": "Mathias", "initials": "M"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}], "type": "posted-content", "published": "2019-04-18", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/613364", "pmid": null, "labels": {"SciLifeLab Fellow": "", "DDLS Fellow": "", "Adil Mardinoglu": "", "Muhammad Arif": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T11:13:35.938Z", "modified": "2026-09-23T14:23:26.814Z"}, {"entity": "publication", "iuid": "f42dc647da1440518d7898b359235efd", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f42dc647da1440518d7898b359235efd.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f42dc647da1440518d7898b359235efd"}}, "title": "Prediction of individuals at high absolute risk of esophageal squamous cell carcinoma.", "authors": [{"family": "Wang", "given": "Qiao-Li", "initials": "QL"}, {"family": "Lagergren", "given": "Jesper", "initials": "J"}, {"family": "Xie", "given": "Shao-Hua", "initials": "SH"}], "type": "journal article", "published": "2019-04-00", "journal": {"title": "Gastrointest Endosc", "issn": "1097-6779", "volume": "89", "issue": "4", "pages": "726-732.e2", "issn-l": null}, "abstract": "This study aimed to develop a prediction model for identifying individuals at high absolute risk of esophageal squamous cell carcinoma (ESCC) for endoscopic screening at a curable stage based on readily identifiable risk factors.\n\nThis was a nationwide Swedish population-based, case-control study, including 167 new cases of ESCC and 820 randomly selected control participants. Odds ratios with 95% confidence intervals (CI) were assessed by using multivariable unconditional logistic regression. The discriminative accuracy of the model was assessed by the area under the receiver operating characteristic curve (AUC) with leave-1-out cross validation. Models for projecting individuals' absolute 5-year risk of ESCC were developed by incorporating the age-specific and sex-specific incidence rates and competing risk of death from other causes.\n\nA model including the risk factors age, sex, tobacco smoking, alcohol overconsumption, education, duration of living with a partner, and place of residence during childhood generated an AUC of 0.81 (95% CI, 0.77-0.84). A model based only on age, sex, tobacco smoking, and alcohol overconsumption obtained a similar AUC (0.79; 95% CI, 0.75-0.82). A 5-year follow-up of 355 men aged 70 to 74 years with over 35 years' smoking and alcohol overconsumption history is needed to detect 1 ESCC case. The estimated individuals' absolute 5-year risk of ESCC varied according to the combinations of risk factors.\n\nThis easy-to-use risk prediction model showed a good discriminative accuracy and had the potential to identify individuals at high absolute risk of ESCC who might benefit from tailored endoscopic screening and surveillance.", "doi": "10.1016/j.gie.2018.10.025", "pmid": "30616974", "labels": {"DDLS Fellow": null, "Qiaoli Wang": null}, "xrefs": [{"db": "pii", "key": "S0016-5107(18)33198-5"}], "notes": [], "created": "2025-11-27T18:45:17.366Z", "modified": "2025-11-27T18:45:17.402Z"}, {"entity": "publication", "iuid": "3fab25f2fb434804aa7fd393e0d5e104", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3fab25f2fb434804aa7fd393e0d5e104.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3fab25f2fb434804aa7fd393e0d5e104"}}, "title": "Deep Learning in Image Cytometry: A Review.", "authors": [{"family": "Gupta", "given": "Anindya", "initials": "A", "orcid": "0000-0003-3557-4947", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/57cb44fb9e0a42ba8f91e813e2e45c76.json"}}, {"family": "Harrison", "given": "Philip J", "initials": "PJ", "orcid": "0000-0003-4046-9017", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ef739cc45eff40b98c80ecc77f3afb73.json"}}, {"family": "Wieslander", "given": "H\u00e5kan", "initials": "H", "orcid": "0000-0002-6289-7285", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/72067b4a36de4d68a2200110df7cef4b.json"}}, {"family": "Pielawski", "given": "Nicolas", "initials": "N", "orcid": "0000-0001-8182-0091", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a001a04d47014ba4af7cccb48b669783.json"}}, {"family": "Kartasalo", "given": "Kimmo", "initials": "K", "orcid": "0000-0002-9470-4783", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7c6fc97c06ed456c8bdd1f03db8a9b72.json"}}, {"family": "Partel", "given": "Gabriele", "initials": "G", "orcid": "0000-0002-4482-3119", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d2d38e59d5c840a0a53a4b90690fdc7a.json"}}, {"family": "Solorzano", "given": "Leslie", "initials": "L", "orcid": "0000-0001-8658-6417", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f5c33a5b8cef4cad8b9f57b4510fb0c2.json"}}, {"family": "Suveer", "given": "Amit", "initials": "A", "orcid": "0000-0002-7779-094X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/caf81c0056e8483c9f072e06453ab67d.json"}}, {"family": "Klemm", "given": "Anna H", "initials": "AH", "orcid": "0000-0002-3466-1320", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bda9a501396248b5a7daa41db01518dc.json"}}, {"family": "Spjuth", "given": "Ola", "initials": "O", "orcid": "0000-0002-8083-2864", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2c192389f99d4801b91f3350e07dfb9e.json"}}, {"family": "Sintorn", "given": "Ida-Maria", "initials": "IM", "orcid": "0000-0002-8307-7411", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8dbd58070a9b4985b8bff09c1f965413.json"}}, {"family": "W\u00e4hlby", "given": "Carolina", "initials": "C", "orcid": "0000-0002-4139-7003", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/833afe3444d84c24be12ea1468563bea.json"}}], "type": "journal article", "published": "2019-04-00", "journal": {"title": "Cytometry A", "issn": "1552-4930", "issn-l": "1552-4922", "volume": "95", "issue": "4", "pages": "366-380"}, "abstract": "Artificial intelligence, deep convolutional neural networks, and deep learning are all niche terms that are increasingly appearing in scientific presentations as well as in the general media. In this review, we focus on deep learning and how it is applied to microscopy image data of cells and tissue samples. Starting with an analogy to neuroscience, we aim to give the reader an overview of the key concepts of neural networks, and an understanding of how deep learning differs from more classical approaches for extracting information from image data. We aim to increase the understanding of these methods, while highlighting considerations regarding input data requirements, computational resources, challenges, and limitations. We do not provide a full manual for applying these methods to your own data, but rather review previously published articles on deep learning in image cytometry, and guide the readers toward further reading on specific networks and methods, including new methods not yet applied to cytometry data. \u00a9 2018 The Authors. Cytometry Part A published by Wiley Periodicals, Inc. on behalf of International Society for Advancement of Cytometry.", "doi": "10.1002/cyto.a.23701", "pmid": "30565841", "labels": {"Kimmo Kartasalo": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC6590257"}], "notes": [], "created": "2024-11-05T16:04:36.061Z", "modified": "2026-09-23T06:45:59.062Z"}, {"entity": "publication", "iuid": "11b3f7322b67483ebff16b06ab4b7afe", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/11b3f7322b67483ebff16b06ab4b7afe.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/11b3f7322b67483ebff16b06ab4b7afe"}}, "title": "Gramicidin Increases Lipid Flip-Flop in Symmetric and Asymmetric Lipid Vesicles.", "authors": [{"family": "Doktorova", "given": "Milka", "initials": "M"}, {"family": "Heberle", "given": "Frederick A", "initials": "FA"}, {"family": "Marquardt", "given": "Drew", "initials": "D"}, {"family": "Rusinova", "given": "Radda", "initials": "R"}, {"family": "Sanford", "given": "R Lea", "initials": "RL"}, {"family": "Peyear", "given": "Thasin A", "initials": "TA"}, {"family": "Katsaras", "given": "John", "initials": "J"}, {"family": "Feigenson", "given": "Gerald W", "initials": "GW"}, {"family": "Weinstein", "given": "Harel", "initials": "H"}, {"family": "Andersen", "given": "Olaf S", "initials": "OS"}], "type": "journal article", "published": "2019-03-05", "journal": {"title": "Biophys. J.", "issn": "1542-0086", "issn-l": "0006-3495", "volume": "116", "issue": "5", "pages": "860-873"}, "abstract": "Unlike most transmembrane proteins, phospholipids can migrate from one leaflet of the membrane to the other. Because this spontaneous lipid translocation (flip-flop) tends to be very slow, cells facilitate the process with enzymes that catalyze the transmembrane movement and thereby regulate the transbilayer lipid distribution. Nonenzymatic membrane-spanning proteins with unrelated primary functions have also been found to accelerate lipid flip-flop in a nonspecific manner and by various hypothesized mechanisms. Using deuterated phospholipids, we examined the acceleration of flip-flop by gramicidin channels, which have well-defined structures and known functions, features that make them ideal candidates for probing the protein-membrane interactions underlying lipid flip-flop. To study compositionally and isotopically asymmetric proteoliposomes containing gramicidin, we expanded a recently developed protocol for the preparation and characterization of lipid-only asymmetric vesicles. Channel incorporation, conformation, and function were examined with small angle x-ray scattering, circular dichroism, and a stopped-flow spectrofluorometric assay, respectively. As a measure of lipid scrambling, we used differential scanning calorimetry to monitor the effect of gramicidin on the melting transition temperatures of the two bilayer leaflets. The two calorimetric peaks of the individual leaflets merged into a single peak over time, suggestive of scrambling, and the effect of the channel on the transbilayer lipid distribution in both symmetric 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine and asymmetric 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine/1,2-dimyristoyl-sn-glycero-3-phosphocholine vesicles was quantified from proton NMR measurements. Our results show that gramicidin increases lipid flip-flop in a complex, concentration-dependent manner. To determine the molecular mechanism of the process, we used molecular dynamics simulations and further computational analysis of the trajectories to estimate the extent of membrane deformation. Together, the experimental and computational approaches were found to constitute an effective means for studying the effects of transmembrane proteins on lipid distribution in both symmetric and asymmetric model membranes.", "doi": "10.1016/j.bpj.2019.01.016", "pmid": "30755300", "labels": {"Milka Doktorova": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC6400823"}, {"db": "pii", "key": "S0006-3495(19)30051-7"}], "notes": [], "created": "2024-11-27T12:18:15.867Z", "modified": "2024-11-29T12:16:58.054Z"}, {"entity": "publication", "iuid": "fb746087a9c94556b5a56a862e9e9b1f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/fb746087a9c94556b5a56a862e9e9b1f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/fb746087a9c94556b5a56a862e9e9b1f"}}, "title": "Pyruvate kinase L/R is a regulator of lipid metabolism and mitochondrial function.", "authors": [{"family": "Liu", "given": "Zhengtao", "initials": "Z"}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f46e4161be08458994efddb75ed75874.json"}}, {"family": "Lee", "given": "Sunjae", "initials": "S"}, {"family": "Kim", "given": "Woonghee", "initials": "W"}, {"family": "Klevstig", "given": "Martina", "initials": "M", "orcid": "0000-0001-7563-4161", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eac579cfda084526988ba438919e8b5f.json"}}, {"family": "Harzandi", "given": "Azadeh M", "initials": "AM"}, {"family": "Sikanic", "given": "Natasa", "initials": "N"}, {"family": "Arif", "given": "Muhammad", "initials": "M"}, {"family": "St\u00e5hlman", "given": "Marcus", "initials": "M"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/33f2b49a39ed4e54ba77dfe397ed3087.json"}}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ea446aa574042a295d5f69437402f76.json"}}, {"family": "Boren", "given": "Jan", "initials": "J", "orcid": "0000-0003-0786-8091", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/73a770eb9e614448a046b8e9199052e9.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}], "type": "journal article", "published": "2019-03-00", "journal": {"title": "Metab. Eng.", "issn": "1096-7184", "issn-l": "1096-7176", "volume": "52", "issue": null, "pages": "263-272"}, "abstract": "The pathogenesis of non-alcoholic fatty liver disease (NAFLD) and hepatocellular carcinoma (HCC) has been associated with altered expression of liver-specific genes including pyruvate kinase liver and red blood cell (PKLR), patatin-like phospholipase domain containing 3 (PNPLA3) and proprotein convertase subtilisin/kexin type 9 (PCSK9). Here, we inhibited and overexpressed the expression of these three genes in HepG2 cells, generated RNA-seq data before and after perturbation and revealed the altered global biological functions with the modulation of these genes using integrated network (IN) analysis. We found that modulation of these genes effects the total triglycerides levels within the cells and viability of the cells. Next, we generated IN for HepG2 cells, identified reporter transcription factors based on IN and found that the modulation of these genes affects key metabolic pathways associated with lipid metabolism (steroid biosynthesis, PPAR signalling pathway, fatty acid synthesis and oxidation) and cancer development (DNA replication, cell cycle and p53 signalling) involved in the progression of NAFLD and HCC. Finally, we observed that inhibition of PKLR lead to decreased glucose uptake and decreased mitochondrial activity in HepG2 cells. Hence, our systems level analysis indicated that PKLR can be targeted for development efficient treatment strategy for NAFLD and HCC.", "doi": "10.1016/j.ymben.2019.01.001", "pmid": "30615941", "labels": {"Adil Mardinoglu": "", "SciLifeLab Fellow": "", "DDLS Fellow": "", "Muhammad Arif": ""}, "xrefs": [{"db": "pii", "key": "S1096-7176(18)30318-5"}], "notes": [], "created": "2020-09-25T13:17:30.855Z", "modified": "2026-09-23T07:49:55.288Z"}, {"entity": "publication", "iuid": "fef3a5d364cf48299a854fb7fe8081fa", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/fef3a5d364cf48299a854fb7fe8081fa.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/fef3a5d364cf48299a854fb7fe8081fa"}}, "title": "The long-term prognostic and predictive capacity of cyclin D1 gene amplification in 2305 breast tumours.", "authors": [{"family": "Lundberg", "given": "Arian", "initials": "A", "orcid": "0000-0002-6630-2787", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/baa2c7c8963840bfb6a22d7c5cfe35f9.json"}}, {"family": "Lindstr\u00f6m", "given": "Linda S", "initials": "LS"}, {"family": "Li", "given": "Jingmei", "initials": "J"}, {"family": "Harrell", "given": "J Chuck", "initials": "JC"}, {"family": "Darai-Ramqvist", "given": "Eva", "initials": "E"}, {"family": "Sifakis", "given": "Emmanouil G", "initials": "EG"}, {"family": "Foukakis", "given": "Theodoros", "initials": "T"}, {"family": "Perou", "given": "Charles M", "initials": "CM"}, {"family": "Czene", "given": "Kamila", "initials": "K"}, {"family": "Bergh", "given": "Jonas", "initials": "J"}, {"family": "Tobin", "given": "Nicholas P", "initials": "NP", "orcid": "0000-0003-2343-9772", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b9aa223903694c8399b89adc231facce.json"}}], "type": "journal article", "published": "2019-02-28", "journal": {"title": "Breast Cancer Res.", "issn": "1465-542X", "volume": "21", "issue": "1", "pages": "34", "issn-l": "1465-5411"}, "abstract": "Use of cyclin D1 (CCND1) gene amplification as a breast cancer biomarker has been hampered by conflicting assessments of the relationship between cyclin D1 protein levels and patient survival. Here, we aimed to clarify its prognostic and treatment predictive potential through comprehensive long-term survival analyses.\n\nCCND1 amplification was assessed using SNP arrays from two cohorts of 1965 and 340 patients with matching gene expression array and clinical follow-up data of over 15 years. Kaplan-Meier and multivariable Cox regression analyses were used to determine survival differences between CCND1 amplified vs. non-amplified tumours in clinically relevant patient sets, within PAM50 subtypes and within treatment-specific subgroups. Boxplots and differential gene expression analyses were performed to assess differences between amplified vs. non-amplified tumours within PAM50 subtypes.\n\nWhen combining both cohorts, worse survival was found for patients with CCND1-amplified tumours in luminal A (HR = 1.68; 95% CI, 1.15-2.46), luminal B (1.37; 1.01-1.86) and ER+/LN-/HER2- (1.66; 1.14-2.41) subgroups. In gene expression analysis, CCND1-amplified luminal A tumours showed increased proliferation (P < 0.001) and decreased progesterone (P = 0.002) levels along with a large overlap in differentially expressed genes when comparing luminal A and B-amplified vs. non-amplified tumours.\n\nOur results indicate that CCND1 amplification is associated with worse 15-year survival in ER+/LN-/HER2-, luminal A and luminal B patients. Moreover, luminal A CCND1-amplified tumours display gene expression changes consistent with a more aggressive phenotype. These novel findings highlight the potential of CCND1 to identify patients that could benefit from long-term treatment strategies.", "doi": "10.1186/s13058-019-1121-4", "pmid": "30819233", "labels": {"DDLS Fellow": null, "Arian Lundberg": null}, "xrefs": [{"db": "pmc", "key": "PMC6394106"}, {"db": "pii", "key": "10.1186/s13058-019-1121-4"}], "notes": [], "created": "2025-11-14T07:51:51.389Z", "modified": "2026-01-03T12:43:33.474Z"}, {"entity": "publication", "iuid": "a2a9a20751a647c6bab9f0e9f6d00fee", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a2a9a20751a647c6bab9f0e9f6d00fee.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a2a9a20751a647c6bab9f0e9f6d00fee"}}, "title": "Characterization of Emetic and Diarrheal Bacillus cereus Strains From a 2016 Foodborne Outbreak Using Whole-Genome Sequencing: Addressing the Microbiological, Epidemiological, and Bioinformatic Challenges.", "authors": [{"family": "Carroll", "given": "Laura M", "initials": "LM"}, {"family": "Wiedmann", "given": "Martin", "initials": "M"}, {"family": "Mukherjee", "given": "Manjari", "initials": "M"}, {"family": "Nicholas", "given": "David C", "initials": "DC"}, {"family": "Mingle", "given": "Lisa A", "initials": "LA"}, {"family": "Dumas", "given": "Nellie B", "initials": "NB"}, {"family": "Cole", "given": "Jocelyn A", "initials": "JA"}, {"family": "Kovac", "given": "Jasna", "initials": "J"}], "type": "journal article", "published": "2019-02-12", "journal": {"title": "Front Microbiol", "issn": "1664-302X", "volume": "10", "pages": "144", "issn-l": "1664-302X"}, "abstract": "The Bacillus cereus group comprises multiple species capable of causing emetic or diarrheal foodborne illness. Despite being responsible for tens of thousands of illnesses each year in the U.S. alone, whole-genome sequencing (WGS) is not yet routinely employed to characterize B. cereus group isolates from foodborne outbreaks. Here, we describe the first WGS-based characterization of isolates linked to an outbreak caused by members of the B. cereus group. In conjunction with a 2016 outbreak traced to a supplier of refried beans served by a fast food restaurant chain in upstate New York, a total of 33 B. cereus group isolates were obtained from human cases (n = 7) and food samples (n = 26). Emetic (n = 30) and diarrheal (n = 3) isolates were most closely related to B. paranthracis (group III) and B. cereus sensu stricto (group IV), respectively. WGS indicated that the 30 emetic isolates (24 and 6 from food and humans, respectively) were closely related and formed a well-supported clade distinct from publicly available emetic group III genomes with an identical sequence type (ST 26). The 30 emetic group III isolates from this outbreak differed from each other by a mean of 8.3 to 11.9 core single nucleotide polymorphisms (SNPs), while differing from publicly available emetic group III ST 26 B. cereus group genomes by a mean of 301.7-528.0 core SNPs, depending on the SNP calling methodology used. Using a WST-1 cell proliferation assay, the strains isolated from this outbreak had only mild detrimental effects on HeLa cell metabolic activity compared to reference diarrheal strain B. cereus ATCC 14579. We hypothesize that the outbreak was a single source outbreak caused by emetic group III B. cereus belonging to the B. paranthracis species, although food samples were not tested for presence of the emetic toxin cereulide. In addition to showcasing how WGS can be used to characterize B. cereus group strains linked to a foodborne outbreak, we also discuss potential microbiological and epidemiological challenges presented by B. cereus group outbreaks, and we offer recommendations for analyzing WGS data from the isolates associated with them.", "doi": "10.3389/fmicb.2019.00144", "pmid": "30809204", "labels": {"Laura Carroll": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC6379260"}, {"db": "figshare", "key": "10.6084/m9.figshare.7001525.v1"}], "notes": [], "created": "2025-03-18T17:24:05.329Z", "modified": "2025-03-18T17:24:05.335Z"}, {"entity": "publication", "iuid": "a6fb41a057f142749b93162381fb08e2", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a6fb41a057f142749b93162381fb08e2.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a6fb41a057f142749b93162381fb08e2"}}, "title": "Isolates from colonic spirochaetosis in humans show high genomic divergence and carry potential pathogenic features but are not detected by 16S amplicon sequencing using standard primers for the human microbiota", "authors": [{"family": "Thorell", "given": "Kaisa", "initials": "K", "orcid": "0000-0002-4447-8968", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/789d4029a5c14d3c83df7c47b3b514c7.json"}}, {"family": "Ingan\u00e4s", "given": "Linn", "initials": "L"}, {"family": "Backhans", "given": "Annette", "initials": "A"}, {"family": "Agr\u00e9us", "given": "Lars", "initials": "L"}, {"family": "\u00d6st", "given": "\u00c5ke", "initials": "\u00c5"}, {"family": "Walker", "given": "Marjorie", "initials": "M"}, {"family": "Talley", "given": "Nicholas J", "initials": "NJ"}, {"family": "Kjellstr\u00f6m", "given": "Lars", "initials": "L"}, {"family": "Andreasson", "given": "Anna", "initials": "A"}, {"family": "Engstrand", "given": "Lars", "initials": "L"}], "type": "posted-content", "published": "2019-02-08", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/544502", "pmid": null, "labels": {"DDLS Fellow": "", "Kaisa Thorell": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T11:12:16.846Z", "modified": "2026-09-23T14:59:52.119Z"}, {"entity": "publication", "iuid": "381331e3b38d459399e10de35aa1195b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/381331e3b38d459399e10de35aa1195b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/381331e3b38d459399e10de35aa1195b"}}, "title": "Spatiotemporal dissection of the cell cycle with single-cell proteogenomics", "authors": [{"family": "Mahdessian", "given": "Diana", "initials": "D", "orcid": "0000-0003-0750-1070", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7bab301bfb3544e69cf96ae4080fc3e9.json"}}, {"family": "Cesnik", "given": "Anthony J", "initials": "AJ", "orcid": "0000-0002-5326-7134", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0fda549f3795457fb60ec3372b98e2d5.json"}}, {"family": "Gnann", "given": "Christian", "initials": "C", "orcid": "0000-0001-6566-3559", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ac838ae59a574620bc8c9fb84271ee9c.json"}}, {"family": "Danielsson", "given": "Frida", "initials": "F"}, {"family": "Stenstr\u00f6m", "given": "Lovisa", "initials": "L"}, {"family": "Arif", "given": "Muhammad", "initials": "M", "orcid": "0000-0003-2261-0881", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c8ffc9889ace44e3b992816601b817e2.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C"}, {"family": "Shutten", "given": "Rutger", "initials": "R"}, {"family": "B\u00e4ckstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Thul", "given": "Peter", "initials": "P", "orcid": "0000-0002-6107-1465", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/af9dad977d4649bbbb883a9836dade94.json"}}, {"family": "Cho", "given": "Nathan H", "initials": "NH", "orcid": "0000-0002-0110-1343", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/67e2461debe34aa8903b42000d77084d.json"}}, {"family": "Carja", "given": "Oana", "initials": "O"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ea446aa574042a295d5f69437402f76.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca58bf2d214047e0ae5e38a42a0f2808.json"}}, {"family": "Stadler", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-6781-1938", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5aff7e9c1d774b8c8bfee2f09a323ed2.json"}}, {"family": "Lindskog", "given": "Cecilia", "initials": "C", "orcid": "0000-0001-5611-1015", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/21610a810a87459c962d6da3f2ad38ad.json"}}, {"family": "Ayoglu", "given": "Burcu", "initials": "B"}, {"family": "Leonetti", "given": "Manuel D", "initials": "MD", "orcid": "0000-0002-4881-405X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a7a2148955042f3985f39e11c7558f4.json"}}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9f5294424542413c9ba4432c839c2b63.json"}}, {"family": "Sullivan", "given": "Devin", "initials": "D", "orcid": "0000-0001-6176-108X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e3bff10128d545ff8323e2a701e73eba.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E"}], "type": "posted-content", "published": "2019-02-07", "journal": {"title": "bioRxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/543231", "pmid": null, "labels": {"SciLifeLab Fellow": null, "DDLS Fellow": null, "Adil Mardinoglu": null, "Muhammad Arif": null}, "xrefs": [], "notes": [], "created": "2026-08-20T11:12:14.908Z", "modified": "2026-10-05T07:11:35.403Z"}, {"entity": "publication", "iuid": "0a0fba5c5e124ada8a23d58296828257", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0a0fba5c5e124ada8a23d58296828257.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0a0fba5c5e124ada8a23d58296828257"}}, "title": "A New Computational Method for Membrane Compressibility: Bilayer Mechanical Thickness Revisited.", "authors": [{"family": "Doktorova", "given": "Milka", "initials": "M", "orcid": "0000-0003-4366-2242", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/791384c319f04584bac8ffb21df7271f.json"}}, {"family": "LeVine", "given": "Michael V", "initials": "MV"}, {"family": "Khelashvili", "given": "George", "initials": "G", "orcid": "0000-0001-7235-8579", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/49b73bce7f8541fd8c959b5117bbe668.json"}}, {"family": "Weinstein", "given": "Harel", "initials": "H", "orcid": "0000-0003-3473-9818", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d92af3f7c4bb4ca1abe3d658a824c446.json"}}], "type": "journal article", "published": "2019-02-05", "journal": {"title": "Biophys. J.", "issn": "1542-0086", "issn-l": "0006-3495", "volume": "116", "issue": "3", "pages": "487-502"}, "abstract": "Because lipid bilayers can bend and stretch in ways similar to thin elastic sheets, physical models of bilayer deformation have utilized mechanical constants such as the moduli for bending rigidity (\u03baC) and area compressibility (KA). However, the use of these models to quantify the energetics of membrane deformation associated with protein-membrane interactions, and the membrane response to stress is often hampered by the shortage of experimental data suitable for the estimation of the mechanical constants of various lipid mixtures. Although computational tools such as molecular dynamics simulations can provide alternative means to estimate KA values, current approaches suffer significant technical limitations. Here, we present a novel, to our knowledge, computational framework that allows for a direct estimation of KA values for individual bilayer leaflets. The theory is based on the concept of elasticity and derives KA from real-space analysis of local thickness fluctuations sampled in molecular dynamics simulations. We explore and validate the model on a large set of single and multicomponent bilayers of different lipid compositions and sizes, simulated at different temperatures. The calculated bilayer compressibility moduli agree with values estimated previously from experiments and those obtained from a standard computational method based on a series of constrained tension simulations. We further validate our framework in a comparison with an existing polymer brush model and confirm the polymer brush model's predicted linear relationship with proportionality coefficient of 24, using elastic parameters calculated from the simulation trajectories. The robustness of the results that emerge from the method allows us to revisit the origins of the bilayer mechanical (compressible) thickness and in particular its dependence on acyl-chain unsaturation and the presence of cholesterol.", "doi": "10.1016/j.bpj.2018.12.016", "pmid": "30665693", "labels": {"Milka Doktorova": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC6369663"}, {"db": "pii", "key": "S0006-3495(18)34530-2"}], "notes": "Erratum publication available: A New Computational Method for Membrane Compressibility: Bilayer Mechanical Thickness Revisited. DOI: 10.1016/j.bpj.2019.07.039", "created": "2024-11-27T12:16:10.765Z", "modified": "2024-11-29T10:50:35.970Z"}, {"entity": "publication", "iuid": "5ff2806b13414d1b8788dddbd78e8471", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5ff2806b13414d1b8788dddbd78e8471.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5ff2806b13414d1b8788dddbd78e8471"}}, "title": "How good are pathogenicity predictors in detecting benign variants?", "authors": [{"family": "Niroula", "given": "Abhishek", "initials": "A", "orcid": "0000-0002-5904-0635", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/05df7afc7a494ba5af8a378e5ffa53f0.json"}}, {"family": "Vihinen", "given": "Mauno", "initials": "M", "orcid": "0000-0002-9614-7976", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d39c85536a524a2cab1eca8304d37181.json"}}], "type": "journal article", "published": "2019-02-00", "journal": {"title": "PLoS Comput Biol", "issn": "1553-7358", "volume": "15", "issue": "2", "pages": "e1006481", "issn-l": "1553-734X"}, "abstract": "Computational tools are widely used for interpreting variants detected in sequencing projects. The choice of these tools is critical for reliable variant impact interpretation for precision medicine and should be based on systematic performance assessment. The performance of the methods varies widely in different performance assessments, for example due to the contents and sizes of test datasets. To address this issue, we obtained 63,160 common amino acid substitutions (allele frequency \u22651% and <25%) from the Exome Aggregation Consortium (ExAC) database, which contains variants from 60,706 genomes or exomes. We evaluated the specificity, the capability to detect benign variants, for 10 variant interpretation tools. In addition to overall specificity of the tools, we tested their performance for variants in six geographical populations. PON-P2 had the best performance (95.5%) followed by FATHMM (86.4%) and VEST (83.5%). While these tools had excellent performance, the poorest method predicted more than one third of the benign variants to be disease-causing. The results allow choosing reliable methods for benign variant interpretation, for both research and clinical purposes, as well as provide a benchmark for method developers.", "doi": "10.1371/journal.pcbi.1006481", "pmid": "30742610", "labels": {"Abhishek Niroula": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC6386394"}, {"db": "pii", "key": "PCOMPBIOL-D-18-01511"}], "notes": [], "created": "2023-11-20T11:21:45.204Z", "modified": "2023-11-20T11:21:45.274Z"}, {"entity": "publication", "iuid": "c73fea28a83841639d29567b73892e4c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c73fea28a83841639d29567b73892e4c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c73fea28a83841639d29567b73892e4c"}}, "title": "Characterization of heterogeneous redox responses in hepatocellular carcinoma patients using network analysis.", "authors": [{"family": "Benfeitas", "given": "Rui", "initials": "R", "orcid": "0000-0001-7972-0083", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e2ec344c501496796be3250fd563699.json"}}, {"family": "Bidkhori", "given": "Gholamreza", "initials": "G"}, {"family": "Mukhopadhyay", "given": "Bani", "initials": "B"}, {"family": "Klevstig", "given": "Martina", "initials": "M"}, {"family": "Arif", "given": "Muhammad", "initials": "M", "orcid": "0000-0003-2261-0881", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c8ffc9889ace44e3b992816601b817e2.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f46e4161be08458994efddb75ed75874.json"}}, {"family": "Lee", "given": "Sunjae", "initials": "S", "orcid": "0000-0002-6428-5936", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9c0d15b9219a462a868adab9f428e5fa.json"}}, {"family": "Cinar", "given": "Resat", "initials": "R"}, {"family": "Nielsen", "given": "Jens", "initials": "J"}, {"family": "Uhlen", "given": "Mathias", "initials": "M"}, {"family": "Boren", "given": "Jan", "initials": "J", "orcid": "0000-0003-0786-8091", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/73a770eb9e614448a046b8e9199052e9.json"}}, {"family": "Kunos", "given": "George", "initials": "G"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca58bf2d214047e0ae5e38a42a0f2808.json"}}], "type": "journal article", "published": "2019-02-00", "journal": {"title": "EBioMedicine", "issn": "2352-3964", "issn-l": "2352-3964", "volume": "40", "issue": null, "pages": "471-487"}, "abstract": "Redox metabolism is often considered a potential target for cancer treatment, but a systematic examination of redox responses in hepatocellular carcinoma (HCC) is missing.\n\nHere, we employed systems biology and biological network analyses to reveal key roles of genes associated with redox metabolism in HCC by integrating multi-omics data.\n\nWe found that several redox genes, including 25 novel potential prognostic genes, are significantly co-expressed with liver-specific genes and genes associated with immunity and inflammation. Based on an integrative analysis, we found that HCC tumors display antagonistic behaviors in redox responses. The two HCC groups are associated with altered fatty acid, amino acid, drug and hormone metabolism, differentiation, proliferation, and NADPH-independent vs -dependent antioxidant defenses. Redox behavior varies with known tumor subtypes and progression, affecting patient survival. These antagonistic responses are also displayed at the protein and metabolite level and were validated in several independent cohorts. We finally showed the differential redox behavior using mice transcriptomics in HCC and noncancerous tissues and associated with hypoxic features of the two redox gene groups.\n\nOur integrative approaches highlighted mechanistic differences among tumors and allowed the identification of a survival signature and several potential therapeutic targets for the treatment of HCC.", "doi": "10.1016/j.ebiom.2018.12.057", "pmid": "30606699", "labels": {"Adil Mardinoglu": "", "SciLifeLab Fellow": "", "DDLS Fellow": "", "Muhammad Arif": ""}, "xrefs": [{"db": "pmc", "key": "PMC6412169"}, {"db": "pii", "key": "S2352-3964(18)30635-2"}], "notes": [], "created": "2020-09-25T13:18:08.963Z", "modified": "2026-09-23T09:30:22.891Z"}, {"entity": "publication", "iuid": "251e9bb52a544a7bb8310212aba91139", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/251e9bb52a544a7bb8310212aba91139.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/251e9bb52a544a7bb8310212aba91139"}}, "title": "TCF/LEF dependent and independent transcriptional regulation of Wnt/\u03b2-catenin target genes.", "authors": [{"family": "Doumpas", "given": "Nikolaos", "initials": "N"}, {"family": "Lampart", "given": "Franziska", "initials": "F"}, {"family": "Robinson", "given": "Mark D", "initials": "MD", "orcid": "0000-0002-3048-5518", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f257efcb44304179bb377abee0dd12bb.json"}}, {"family": "Lentini", "given": "Antonio", "initials": "A", "orcid": "0000-0003-1239-5495", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c5042d3005814ad0a2d1eaeee5d2de3b.json"}}, {"family": "Nestor", "given": "Colm E", "initials": "CE"}, {"family": "Cant\u00f9", "given": "Claudio", "initials": "C", "orcid": "0000-0003-1547-5415", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cf8cf56e956942f4baa10f2772c13734.json"}}, {"family": "Basler", "given": "Konrad", "initials": "K", "orcid": "0000-0003-3534-1529", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/687fb3d1c608472f8106a4dacb0e4053.json"}}], "type": "journal article", "published": "2019-01-15", "journal": {"title": "EMBO J.", "issn": "1460-2075", "volume": "38", "issue": "2", "issn-l": "0261-4189"}, "abstract": "During canonical Wnt signalling, the activity of nuclear \u03b2-catenin is largely mediated by the TCF/LEF family of transcription factors. To challenge this view, we used the CRISPR/Cas9 genome editing approach to generate HEK 293T cell clones lacking all four TCF/LEF genes. By performing unbiased whole transcriptome sequencing analysis, we found that a subset of \u03b2-catenin transcriptional targets did not require TCF/LEF factors for their regulation. Consistent with this finding, we observed in a genome-wide analysis that \u03b2-catenin occupied specific genomic regions in the absence of TCF/LEF Finally, we revealed the existence of a transcriptional activity of \u03b2-catenin that specifically appears when TCF/LEF factors are absent, and refer to this as \u03b2-catenin-GHOST response. Collectively, this study uncovers a previously neglected modus operandi of \u03b2-catenin that bypasses the TCF/LEF transcription factors.", "doi": "10.15252/embj.201798873", "pmid": "30425074", "labels": {"Antonio Lentini": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC6331726"}, {"db": "pii", "key": "embj.201798873"}], "notes": [], "created": "2025-03-28T07:12:06.244Z", "modified": "2025-03-28T07:12:06.400Z"}, {"entity": "publication", "iuid": "f2d1c449a7644c4892771cf72d916532", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f2d1c449a7644c4892771cf72d916532.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f2d1c449a7644c4892771cf72d916532"}}, "title": "Diarrheal bacterial pathogens and multi-resistant enterobacteria in the Choqueyapu River in La Paz, Bolivia.", "authors": [{"family": "Guzman-Otazo", "given": "Jessica", "initials": "J", "orcid": "0000-0003-2664-6013", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/45c59c61843841198aa14c6fbf836f8e.json"}}, {"family": "Gonzales-Siles", "given": "Lucia", "initials": "L"}, {"family": "Poma", "given": "Violeta", "initials": "V"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Thorell", "given": "Kaisa", "initials": "K"}, {"family": "Flach", "given": "Carl-Fredrik", "initials": "CF"}, {"family": "I\u00f1iguez", "given": "Volga", "initials": "V"}, {"family": "Sj\u00f6ling", "given": "\u00c5sa", "initials": "\u00c5"}], "type": "journal article", "published": "2019-01-14", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "14", "issue": "1", "pages": "e0210735", "issn-l": "1932-6203"}, "abstract": "Water borne diarrheal pathogens might accumulate in river water and cause contamination of drinking and irrigation water. The La Paz River basin, including the Choqueyapu River, flows through La Paz city in Bolivia where it is receiving sewage, and residues from inhabitants, hospitals, and industry. Using quantitative real-time PCR (qPCR), we determined the quantity and occurrence of diarrheagenic Escherichia coli (DEC), Salmonella enterica, Klebsiella pneumoniae, Shigella spp. and total enterobacteria in river water, downstream agricultural soil, and irrigated crops, during one year of sampling. The most abundant and frequently detected genes were gapA and eltB, indicating presence of enterobacteria and enterotoxigenic E. coli (ETEC) carrying the heat labile toxin, respectively. Pathogen levels in the samples were significantly positively associated with high water conductivity and low water temperature. In addition, a set of bacterial isolates from water, soil and crops were analyzed by PCR for presence of the genes blaCTX-M, blaKPC, blaNDM, blaVIM and blaOXA-48. Four isolates were found to be positive for blaCTX-M genes and whole genome sequencing identified them as E. coli and one Enterobacter cloacae. The E. coli isolates belonged to the emerging, globally disseminated, multi-resistant E. coli lineages ST648, ST410 and ST162. The results indicate not only a high potential risk of transmission of diarrheal diseases by the consumption of contaminated water and vegetables but also the possibility of antibiotic resistance transfer from the environment to the community.", "doi": "10.1371/journal.pone.0210735", "pmid": "30640938", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pii", "key": "PONE-D-18-20728"}, {"db": "pmc", "key": "PMC6331111"}], "notes": [], "created": "2022-11-08T09:28:16.182Z", "modified": "2022-11-08T09:28:16.247Z"}, {"entity": "publication", "iuid": "1fe5190ca482425cbf03f66ba03113ca", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1fe5190ca482425cbf03f66ba03113ca.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1fe5190ca482425cbf03f66ba03113ca"}}, "title": "The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications.", "authors": [{"family": "Nilsson", "given": "Rolf Henrik", "initials": "RH"}, {"family": "Larsson", "given": "Karl-Henrik", "initials": "KH"}, {"family": "Taylor", "given": "Andy F S", "initials": "AFS"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Jeppesen", "given": "Thomas S", "initials": "TS"}, {"family": "Schigel", "given": "Dmitry", "initials": "D"}, {"family": "Kennedy", "given": "Peter", "initials": "P"}, {"family": "Picard", "given": "Kathryn", "initials": "K"}, {"family": "Gl\u00f6ckner", "given": "Frank Oliver", "initials": "FO"}, {"family": "Tedersoo", "given": "Leho", "initials": "L"}, {"family": "Saar", "given": "Irja", "initials": "I"}, {"family": "K\u00f5ljalg", "given": "Urmas", "initials": "U"}, {"family": "Abarenkov", "given": "Kessy", "initials": "K"}], "type": "journal article", "published": "2019-01-08", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "volume": "47", "issue": "D1", "pages": "D259-D264", "issn-l": "0305-1048"}, "abstract": "UNITE (https://unite.ut.ee/) is a web-based database and sequence management environment for the molecular identification of fungi. It targets the formal fungal barcode-the nuclear ribosomal internal transcribed spacer (ITS) region-and offers all \u223c1 000 000 public fungal ITS sequences for reference. These are clustered into \u223c459 000 species hypotheses and assigned digital object identifiers (DOIs) to promote unambiguous reference across studies. In-house and web-based third-party sequence curation and annotation have resulted in more than 275 000 improvements to the data over the past 15 years. UNITE serves as a data provider for a range of metabarcoding software pipelines and regularly exchanges data with all major fungal sequence databases and other community resources. Recent improvements include redesigned handling of unclassifiable species hypotheses, integration with the taxonomic backbone of the Global Biodiversity Information Facility, and support for an unlimited number of parallel taxonomic classification systems.", "doi": "10.1093/nar/gky1022", "pmid": "30371820", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pii", "key": "5146189"}, {"db": "pmc", "key": "PMC6324048"}], "notes": [], "created": "2022-11-08T09:28:21.040Z", "modified": "2022-11-08T09:28:21.067Z"}, {"entity": "publication", "iuid": "de2e468f1d4b4d40a87b33d521760ccb", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/de2e468f1d4b4d40a87b33d521760ccb.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/de2e468f1d4b4d40a87b33d521760ccb"}}, "title": "Systematic Development of Sandwich Immunoassays for the Plasma Secretome", "authors": [{"family": "H\u00e4ussler", "given": "Ragna S", "initials": "RS", "orcid": "0000-0003-1664-8875", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7cc0ab2ae97c4f968d6218ca2915389f.json"}}, {"family": "Bendes", "given": "Annika", "initials": "A"}, {"family": "Iglesias", "given": "MariaJesus", "initials": "M"}, {"family": "Sanchez-Rivera", "given": "Laura", "initials": "L"}, {"family": "Dodig-Crnkovi\u0107", "given": "Tea", "initials": "T"}, {"family": "Bystr\u00f6m", "given": "Sanna", "initials": "S"}, {"family": "Fredolini", "given": "Claudia", "initials": "C"}, {"family": "Birgersson", "given": "Elin", "initials": "E"}, {"family": "Dale", "given": "Matilda", "initials": "M"}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Rockberg", "given": "Johan", "initials": "J"}, {"family": "Tegel", "given": "Hanna", "initials": "H"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Qundos", "given": "Ulrika", "initials": "U"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/022e140799b6466ea123319c3d70c76e.json"}}], "type": "posted-content", "published": "2019-01-08", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/511907", "pmid": null, "labels": {"Fredrik Edfors": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T11:11:58.736Z", "modified": "2026-09-23T14:29:36.726Z"}, {"entity": "publication", "iuid": "72803c5c25c945fcb390f869e028d1f5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/72803c5c25c945fcb390f869e028d1f5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/72803c5c25c945fcb390f869e028d1f5"}}, "title": "Large expert-curated database for benchmarking document similarity detection in biomedical literature search.", "authors": [{"family": "Brown", "given": "Peter", "initials": "P"}, {"family": "RELISH Consortium\n", "given": "", "initials": ""}, {"family": "Zhou", "given": "Yaoqi", "initials": "Y"}], "type": "journal article", "published": "2019-01-01", "journal": {"title": "Database (Oxford)", "issn": "1758-0463", "volume": "2019", "issn-l": "1758-0463"}, "abstract": "Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.", "doi": "10.1093/database/baz085", "pmid": "33326193", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pii", "key": "5608006"}, {"db": "pmc", "key": "PMC7291946"}], "notes": [], "created": "2022-11-08T09:28:09.519Z", "modified": "2022-11-08T09:28:09.522Z"}, {"entity": "publication", "iuid": "0667b6fa8fc443c4b87b2aa2a5839d35", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0667b6fa8fc443c4b87b2aa2a5839d35.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0667b6fa8fc443c4b87b2aa2a5839d35"}}, "title": "Allele Phasing Greatly Improves the Phylogenetic Utility of Ultraconserved Elements.", "authors": [{"family": "Andermann", "given": "Tobias", "initials": "T"}, {"family": "Fernandes", "given": "Alexandre M", "initials": "AM"}, {"family": "Olsson", "given": "Urban", "initials": "U"}, {"family": "T\u00f6pel", "given": "Mats", "initials": "M"}, {"family": "Pfeil", "given": "Bernard", "initials": "B"}, {"family": "Oxelman", "given": "Bengt", "initials": "B"}, {"family": "Aleixo", "given": "Alexandre", "initials": "A"}, {"family": "Faircloth", "given": "Brant C", "initials": "BC"}, {"family": "Antonelli", "given": "Alexandre", "initials": "A"}], "type": "journal article", "published": "2019-01-01", "journal": {"title": "Syst. Biol.", "issn": "1076-836X", "volume": "68", "issue": "1", "pages": "32-46", "issn-l": "1063-5157"}, "abstract": "Advances in high-throughput sequencing techniques now allow relatively easy and affordable sequencing of large portions of the genome, even for nonmodel organisms. Many phylogenetic studies reduce costs by focusing their sequencing efforts on a selected set of targeted loci, commonly enriched using sequence capture. The advantage of this approach is that it recovers a consistent set of loci, each with high sequencing depth, which leads to more confidence in the assembly of target sequences. High sequencing depth can also be used to identify phylogenetically informative allelic variation within sequenced individuals, but allele sequences are infrequently assembled in phylogenetic studies. Instead, many scientists perform their phylogenetic analyses using contig sequences which result from the de novo assembly of sequencing reads into contigs containing only canonical nucleobases, and this may reduce both statistical power and phylogenetic accuracy. Here, we develop an easy-to-use pipeline to recover allele sequences from sequence capture data, and we use simulated and empirical data to demonstrate the utility of integrating these allele sequences to analyses performed under the multispecies coalescent model. Our empirical analyses of ultraconserved element locus data collected from the South American hummingbird genus Topaza demonstrate that phased allele sequences carry sufficient phylogenetic information to infer the genetic structure, lineage divergence, and biogeographic history of a genus that diversified during the last 3 myr. The phylogenetic results support the recognition of two species and suggest a high rate of gene flow across large distances of rainforest habitats but rare admixture across the Amazon River. Our simulations provide evidence that analyzing allele sequences leads to more accurate estimates of tree topology and divergence times than the more common approach of using contig sequences.", "doi": "10.1093/sysbio/syy039", "pmid": "29771371", "labels": {"Tobias Andermann": null, "DDLS Fellow": null}, "xrefs": [{"db": "pii", "key": "4996310"}, {"db": "pmc", "key": "PMC6292485"}, {"db": "Dryad", "key": "10.5061/dryad.hq3vq"}], "notes": [], "created": "2022-11-11T09:08:44.486Z", "modified": "2022-11-11T09:08:44.511Z"}, {"entity": "publication", "iuid": "995c31eea84f4a48bde69d0a66dae0a2", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/995c31eea84f4a48bde69d0a66dae0a2.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/995c31eea84f4a48bde69d0a66dae0a2"}}, "title": "Introducing ribosomal tandem repeat barcoding for fungi.", "authors": [{"family": "Wurzbacher", "given": "Christian", "initials": "C", "orcid": "0000-0001-7418-0831", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a8303415592c4c46b9fcf27904aec4fa.json"}}, {"family": "Larsson", "given": "Ellen", "initials": "E"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Van den Wyngaert", "given": "Silke", "initials": "S"}, {"family": "Svantesson", "given": "Sten", "initials": "S"}, {"family": "Kristiansson", "given": "Erik", "initials": "E"}, {"family": "Kagami", "given": "Maiko", "initials": "M", "orcid": "0000-0003-3086-390X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5feee43ae01d4a7187cba6126e24cf65.json"}}, {"family": "Nilsson", "given": "R Henrik", "initials": "RH", "orcid": "0000-0002-8052-0107", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/74fbd134d83345efa9287939798ad29f.json"}}], "type": "journal article", "published": "2019-01-00", "journal": {"title": "Mol Ecol Resour", "issn": "1755-0998", "volume": "19", "issue": "1", "pages": "118-127", "issn-l": "1755-098X"}, "abstract": "Sequence comparison and analysis of the various ribosomal genetic markers are the dominant molecular methods for identification and description of fungi. However, new environmental fungal lineages known only from DNA data reveal significant gaps in our sampling of the fungal kingdom in terms of both taxonomy and marker coverage in the reference sequence databases. To facilitate the integration of reference data from all of the ribosomal markers, we present three sets of general primers that allow for amplification of the complete ribosomal operon from the ribosomal tandem repeats. The primers cover all ribosomal markers: ETS, SSU, ITS1, 5.8S, ITS2, LSU and IGS. We coupled these primers successfully with third-generation sequencing (PacBio and Nanopore sequencing) to showcase our approach on authentic fungal herbarium specimens (Basidiomycota), aquatic chytrids (Chytridiomycota) and a poorly understood lineage of early diverging fungi (Nephridiophagidae). In particular, we were able to generate high-quality reference data with Nanopore sequencing in a high-throughput manner, showing that the generation of reference data can be achieved on a regular desktop computer without the involvement of any large-scale sequencing facility. The quality of the Nanopore generated sequences was 99.85%, which is comparable with the 99.78% accuracy described for Sanger sequencing. With this work, we hope to stimulate the generation of a new comprehensive standard of ribosomal reference data with the ultimate aim to close the huge gaps in our reference datasets.", "doi": "10.1111/1755-0998.12944", "pmid": "30240145", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [], "notes": [], "created": "2022-11-08T09:28:25.798Z", "modified": "2022-11-08T09:28:25.974Z"}, {"entity": "publication", "iuid": "8c142158f5404cbdbaa3962fe7825832", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8c142158f5404cbdbaa3962fe7825832.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8c142158f5404cbdbaa3962fe7825832"}}, "title": "Host-derived population genomics data provides insights into bacterial and diatom composition of the killer whale skin.", "authors": [{"family": "Hooper", "given": "Rebecca", "initials": "R"}, {"family": "Brealey", "given": "Jaelle C", "initials": "JC", "orcid": "0000-0001-7068-2017", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/94980a28c68b44c8a2c709ac6a4c6dc7.json"}}, {"family": "van der Valk", "given": "Tom", "initials": "T", "orcid": "0000-0001-6582-3452", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/aa0dba3cc12143cba213f7f3a052216c.json"}}, {"family": "Alberdi", "given": "Antton", "initials": "A", "orcid": "0000-0002-2875-6446", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7db6c63c5480449c8791411cffa3b2a5.json"}}, {"family": "Durban", "given": "John W", "initials": "JW"}, {"family": "Fearnbach", "given": "Holly", "initials": "H"}, {"family": "Robertson", "given": "Kelly M", "initials": "KM", "orcid": "0000-0002-0090-8604", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dd34e649cf2148a382009e97594c4d9a.json"}}, {"family": "Baird", "given": "Robin W", "initials": "RW"}, {"family": "Bradley Hanson", "given": "M", "initials": "M"}, {"family": "Wade", "given": "Paul", "initials": "P"}, {"family": "Gilbert", "given": "M Thomas P", "initials": "MTP"}, {"family": "Morin", "given": "Phillip A", "initials": "PA", "orcid": "0000-0002-3279-1519", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6068e888748e4995b6e7f2d39702c8b0.json"}}, {"family": "Wolf", "given": "Jochen B W", "initials": "JBW"}, {"family": "Foote", "given": "Andrew D", "initials": "AD", "orcid": "0000-0001-7384-1634", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d685d768b18a41b6ae4ece4569cb99b7.json"}}, {"family": "Guschanski", "given": "Katerina", "initials": "K", "orcid": "0000-0002-8493-5457", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4e062373c6bc46b98e56215d3ec89eeb.json"}}], "type": "journal article", "published": "2019-01-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "volume": "28", "issue": "2", "pages": "484-502", "issn-l": "0962-1083"}, "abstract": "Recent exploration into the interactions and relationship between hosts and their microbiota has revealed a connection between many aspects of the host's biology, health and associated micro-organisms. Whereas amplicon sequencing has traditionally been used to characterize the microbiome, the increasing number of published population genomics data sets offers an underexploited opportunity to study microbial profiles from the host shotgun sequencing data. Here, we use sequence data originally generated from killer whale Orcinus orca skin biopsies for population genomics, to characterize the skin microbiome and investigate how host social and geographical factors influence the microbial community composition. Having identified 845 microbial taxa from 2.4 million reads that did not map to the killer whale reference genome, we found that both ecotypic and geographical factors influence community composition of killer whale skin microbiomes. Furthermore, we uncovered key taxa that drive the microbiome community composition and showed that they are embedded in unique networks, one of which is tentatively linked to diatom presence and poor skin condition. Community composition differed between Antarctic killer whales with and without diatom coverage, suggesting that the previously reported episodic migrations of Antarctic killer whales to warmer waters associated with skin turnover may control the effects of potentially pathogenic bacteria such as Tenacibaculum dicentrarchi. Our work demonstrates the feasibility of microbiome studies from host shotgun sequencing data and highlights the importance of metagenomics in understanding the relationship between host and microbial ecology.", "doi": "10.1111/mec.14860", "pmid": "30187987", "labels": {"DDLS Fellow": "", "Tom van der Valk": ""}, "xrefs": [{"db": "pmc", "key": "PMC6487819"}, {"db": "GENBANK", "key": "ERS554424"}, {"db": "GENBANK", "key": "ERS554471"}, {"db": "GENBANK", "key": "ANOL00000000.2"}], "notes": [], "created": "2026-08-20T11:18:52.996Z", "modified": "2026-09-23T08:38:59.606Z"}, {"entity": "publication", "iuid": "3a3bd7ad87de4bae890fb0bce58bb7df", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3a3bd7ad87de4bae890fb0bce58bb7df.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3a3bd7ad87de4bae890fb0bce58bb7df"}}, "title": "Next-Generation Sequencing", "authors": [{"family": "Wiedmann", "given": "Martin", "initials": "M"}, {"family": "Carroll", "given": "Laura M", "initials": "LM"}], "type": "book-chapter", "published": "2019-00-00", "journal": {"pages": "376-383", "issn-l": null}, "abstract": null, "doi": "10.1016/b978-0-08-100596-5.21792-7", "pmid": null, "labels": {"Laura Carroll": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2025-03-18T17:23:48.813Z", "modified": "2025-03-18T17:23:48.813Z"}, {"entity": "publication", "iuid": "8bda5a29ea654995a9e48a0d08db1bac", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8bda5a29ea654995a9e48a0d08db1bac.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8bda5a29ea654995a9e48a0d08db1bac"}}, "title": "Assessment and Management of Risks Associated With Antibiotic Resistance in the Environment", "authors": [{"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}], "type": "book-chapter", "published": "2019-00-00", "journal": {"title": "Management of Emerging Public Health Issues and Risks: Multidisciplinary Approaches to the Changing Environment", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": "243-263"}, "abstract": null, "doi": "10.1016/b978-0-12-813290-6.00010-x", "pmid": null, "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [], "notes": [], "created": "2022-11-08T09:31:45.578Z", "modified": "2025-12-04T17:02:41.120Z"}, {"entity": "publication", "iuid": "734cfe2abc1d4591b283e55f4cf214bb", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/734cfe2abc1d4591b283e55f4cf214bb.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/734cfe2abc1d4591b283e55f4cf214bb"}}, "title": "Phenotypic and genomic analyses of bacteriophages targeting environmental and clinical CS3-expressing enterotoxigenic Escherichia coli (ETEC) strains.", "authors": [{"family": "Chakraborty", "given": "Sajib", "initials": "S", "orcid": "0000-0002-8900-503X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bdf8f2d6238f4720baa804128cfc8b50.json"}}, {"family": "von Mentzer", "given": "Astrid", "initials": "A"}, {"family": "Begum", "given": "Yasmin Ara", "initials": "YA"}, {"family": "Manzur", "given": "Mehnaz", "initials": "M"}, {"family": "Hasan", "given": "Mahmudul", "initials": "M"}, {"family": "Ghosh", "given": "Amar N", "initials": "AN"}, {"family": "Hossain", "given": "M Anwar", "initials": "MA"}, {"family": "Camilli", "given": "Andrew", "initials": "A"}, {"family": "Qadri", "given": "Firdausi", "initials": "F"}], "type": "journal article", "published": "2018-12-20", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "13", "issue": "12", "pages": "e0209357", "issn-l": "1932-6203"}, "abstract": "Diarrhea due to infection of enterotoxigenic Escherichia coli (ETEC) is of great concern in several low and middle-income countries. ETEC infection is considered to be the most common cause of diarrhea in Bangladesh and is mainly spread through contaminated water and food. ETEC pathogenesis is mediated by the expression of enterotoxins and colonization factors (CFs) that target the intestinal mucosa. ETEC can survive for extended time periods in water, where they are likely to be attacked by bacteriophages. Antibiotic resistance is common amongst enteric pathogens and therefore is the use of bacteriophages (phage) as a therapeutic tool an interesting approach. This study was designed to identify novel phages that specifically target ETEC virulence factors. In total, 48 phages and 195 ETEC isolates were collected from water sources and stool samples. Amongst the identified ETEC specific phages, an enterobacteria phage T7, designated as IMM-002, showed a significant specificity towards colonization factor CS3-expressing ETEC isolates. Antibody-blocking and phage-neutralization assays revealed that CS3 is used as a host receptor for the IMM-002 phage. The bacterial CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR-associated) defence mechanism can invoke immunity against phages. Genomic analyses coupled with plaque assay experiments indicate that the ETEC CRISPR-Cas system is involved in the resistance against the CS3-specific phage (IMM-002) and the previously identified CS7-specific phage (IMM-001). As environmental water serves as a reservoir for ETEC, it is important to search for new antimicrobial agents such as phages in environmental water as well as the human gut. A better understanding of how the interplay between ETEC-specific phages and ETEC isolates affects the ETEC diversity, both in environmental ecosystems and within the host, is important for the development of new treatments for ETEC infections.", "doi": "10.1371/journal.pone.0209357", "pmid": "30571788", "labels": {"Astrid von Mentzer": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC6301781"}, {"db": "pii", "key": "PONE-D-18-19050"}], "notes": [], "created": "2025-12-02T15:48:50.905Z", "modified": "2025-12-02T15:48:50.948Z"}, {"entity": "publication", "iuid": "57e2e52d7e0e4131b1889404f25b8d40", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/57e2e52d7e0e4131b1889404f25b8d40.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/57e2e52d7e0e4131b1889404f25b8d40"}}, "title": "Next-generation sequencing reveals two populations of damage-induced small RNAs at endogenous DNA double-strand breaks.", "authors": [{"family": "Bonath", "given": "Franziska", "initials": "F"}, {"family": "Domingo-Prim", "given": "Judit", "initials": "J"}, {"family": "Tarbier", "given": "Marcel", "initials": "M"}, {"family": "Friedl\u00e4nder", "given": "Marc R", "initials": "MR", "orcid": "0000-0001-6577-4363", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ac5a2794be7c4cab89d1e4f1570c9417.json"}}, {"family": "Visa", "given": "Neus", "initials": "N", "orcid": "0000-0003-3145-3953", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a4c087f7bdef4eb3b85a7529c46a778f.json"}}], "type": "journal article", "published": "2018-12-14", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "issn-l": "0305-1048", "volume": "46", "issue": "22", "pages": "11869-11882"}, "abstract": "Recent studies suggest that transcription takes place at DNA double-strand breaks (DSBs), that transcripts at DSBs are processed by Drosha and Dicer into damage-induced small RNAs (diRNAs), and that diRNAs are required for DNA repair. However, diRNAs have been mostly detected in reporter constructs or repetitive sequences, and their existence at endogenous loci has been questioned by recent reports. Using the homing endonuclease I-PpoI, we have investigated diRNA production in genetically unperturbed human and mouse cells. I-PpoI is an ideal tool to clarify the requirements for diRNA production because it induces DSBs in different types of loci: the repetitive 28S locus, unique genes and intergenic loci. We show by extensive sequencing that the rDNA locus produces substantial levels of diRNAs, whereas unique genic and intergenic loci do not. Further characterization of diRNAs emerging from the 28S locus reveals the existence of two diRNA subtypes. Surprisingly, Drosha and its partner DGCR8 are dispensable for diRNA production and only one diRNAs subtype depends on Dicer processing. Furthermore, we provide evidence that diRNAs are incorporated into Argonaute. Our findings provide direct evidence for diRNA production at endogenous loci in mammalian cells and give insights into RNA processing at DSBs.", "doi": "10.1093/nar/gky1107", "pmid": "30418607", "labels": {"Marc Friedl\u00e4nder": "", "SciLifeLab Fellow": "", "Marcel Tarbier": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC6294500"}, {"db": "pii", "key": "5168823"}], "notes": [], "created": "2020-10-12T12:02:26.645Z", "modified": "2026-09-23T07:48:54.096Z"}, {"entity": "publication", "iuid": "06b20e7a0cd94350ad7a0d40da8b8e7f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/06b20e7a0cd94350ad7a0d40da8b8e7f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/06b20e7a0cd94350ad7a0d40da8b8e7f"}}, "title": "Metaxa2 Database Builder: enabling taxonomic identification from metagenomic or metabarcoding data using any genetic marker.", "authors": [{"family": "Bengtsson-Palme", "given": "Johan", "initials": "J", "orcid": "0000-0002-6528-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c666068e9d34939b0252a627007cec7.json"}}, {"family": "Richardson", "given": "Rodney T", "initials": "RT", "orcid": "0000-0002-4443-1705", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c82db3acb0b241caa1cbeea98d6ced09.json"}}, {"family": "Meola", "given": "Marco", "initials": "M"}, {"family": "Wurzbacher", "given": "Christian", "initials": "C"}, {"family": "Tremblay", "given": "\u00c9milie D", "initials": "\u00c9D"}, {"family": "Thorell", "given": "Kaisa", "initials": "K"}, {"family": "Kanger", "given": "K\u00e4rt", "initials": "K"}, {"family": "Eriksson", "given": "K Martin", "initials": "KM"}, {"family": "Bilodeau", "given": "Guillaume J", "initials": "GJ"}, {"family": "Johnson", "given": "Reed M", "initials": "RM"}, {"family": "Hartmann", "given": "Martin", "initials": "M"}, {"family": "Nilsson", "given": "R Henrik", "initials": "RH"}], "type": "journal article", "published": "2018-12-01", "journal": {"title": "Bioinformatics", "issn": "1367-4811", "volume": "34", "issue": "23", "pages": "4027-4033", "issn-l": "1367-4803"}, "abstract": "Correct taxonomic identification of DNA sequences is central to studies of biodiversity using both shotgun metagenomic and metabarcoding approaches. However, no genetic marker gives sufficient performance across all the biological kingdoms, hampering studies of taxonomic diversity in many groups of organisms. This has led to the adoption of a range of genetic markers for DNA metabarcoding. While many taxonomic classification software tools can be re-trained on these genetic markers, they are often designed with assumptions that impair their utility on genes other than the SSU and LSU rRNA. Here, we present an update to Metaxa2 that enables the use of any genetic marker for taxonomic classification of metagenome and amplicon sequence data.\n\nWe evaluated the Metaxa2 Database Builder on 11 commonly used barcoding regions and found that while there are wide differences in performance between different genetic markers, our software performs satisfactorily provided that the input taxonomy and sequence data are of high quality.\n\nFreely available on the web as part of the Metaxa2 package at http://microbiology.se/software/metaxa2/.\n\nSupplementary data are available at Bioinformatics online.", "doi": "10.1093/bioinformatics/bty482", "pmid": "29912385", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pii", "key": "5038464"}, {"db": "pmc", "key": "PMC6247927"}], "notes": [], "created": "2022-11-08T09:28:46.434Z", "modified": "2022-11-16T11:34:52.032Z"}, {"entity": "publication", "iuid": "83ee2300b9a74f8e9d22ba7c8dcdfb49", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/83ee2300b9a74f8e9d22ba7c8dcdfb49.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/83ee2300b9a74f8e9d22ba7c8dcdfb49"}}, "title": "Multiscale patterns and drivers of arbuscular mycorrhizal fungal communities in the roots and root-associated soil of a wild perennial herb.", "authors": [{"family": "Rasmussen", "given": "Pil U", "initials": "PU", "orcid": "0000-0003-0607-4230", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/80035ea7380843aa9d2c58a3ebfa3d4b.json"}}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW"}, {"family": "Blanchet", "given": "F Guillaume", "initials": "FG"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}, {"family": "Lindahl", "given": "Bj\u00f6rn D", "initials": "BD"}, {"family": "Tack", "given": "Ayco J M", "initials": "AJM", "orcid": "0000-0002-3550-1070", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/20531f32048b4cd498311138500cc6bc.json"}}], "type": "journal article", "published": "2018-12-00", "journal": {"title": "New Phytol.", "issn": "1469-8137", "volume": "220", "issue": "4", "pages": "1248-1261", "issn-l": "0028-646X"}, "abstract": "Arbuscular mycorrhizal (AM) fungi form diverse communities and are known to influence above-ground community dynamics and biodiversity. However, the multiscale patterns and drivers of AM fungal composition and diversity are still poorly understood. We sequenced DNA markers from roots and root-associated soil from Plantago lanceolata plants collected across multiple spatial scales to allow comparison of AM fungal communities among neighbouring plants, plant subpopulations, nearby plant populations, and regions. We also measured soil nutrients, temperature, humidity, and community composition of neighbouring plants and nonAM root-associated fungi. AM fungal communities were already highly dissimilar among neighbouring plants (c. 30 cm apart), albeit with a high variation in the degree of similarity at this small spatial scale. AM fungal communities were increasingly, and more consistently, dissimilar at larger spatial scales. Spatial structure and environmental drivers explained a similar percentage of the variation, from 7% to 25%. A large fraction of the variation remained unexplained, which may be a result of unmeasured environmental variables, species interactions and stochastic processes. We conclude that AM fungal communities are highly variable among nearby plants. AM fungi may therefore play a major role in maintaining small-scale variation in community dynamics and biodiversity.", "doi": "10.1111/nph.15088", "pmid": "29573431", "labels": {"Luisa Hugerth": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC6282561"}], "notes": [], "created": "2022-11-08T07:01:18.958Z", "modified": "2026-09-23T09:17:40.340Z"}, {"entity": "publication", "iuid": "66308a0abc1b40a7babb2464cf69bf2a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/66308a0abc1b40a7babb2464cf69bf2a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/66308a0abc1b40a7babb2464cf69bf2a"}}, "title": "Control of hepatic gluconeogenesis by Argonaute2.", "authors": [{"family": "Yan", "given": "Xin", "initials": "X", "orcid": "0000-0002-9135-7915", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/64c45d84ade64e3f945873ad5a81f94e.json"}}, {"family": "Wang", "given": "Zhen", "initials": "Z"}, {"family": "Bishop", "given": "Christopher A", "initials": "CA"}, {"family": "Weitkunat", "given": "Karolin", "initials": "K"}, {"family": "Feng", "given": "Xiao", "initials": "X"}, {"family": "Tarbier", "given": "Marcel", "initials": "M"}, {"family": "Luo", "given": "Jiankai", "initials": "J"}, {"family": "Friedl\u00e4nder", "given": "Marc R", "initials": "MR"}, {"family": "Burkhardt", "given": "Ralph", "initials": "R"}, {"family": "Klaus", "given": "Susanne", "initials": "S"}, {"family": "Willnow", "given": "Thomas E", "initials": "TE"}, {"family": "Poy", "given": "Matthew N", "initials": "MN", "orcid": "0000-0002-4904-2426", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/89f1b6fe353445ae94dce345963755af.json"}}], "type": "journal article", "published": "2018-12-00", "journal": {"title": "Mol Metab", "issn": "2212-8778", "issn-l": "2212-8778", "volume": "18", "issue": null, "pages": "15-24"}, "abstract": "The liver performs a central role in regulating energy homeostasis by increasing glucose output during fasting. Recent studies on Argonaute2 (Ago2), a key RNA-binding protein mediating the microRNA pathway, have illustrated its role in adaptive mechanisms according to changes in metabolic demand. Here we sought to characterize the functional role of Ago2 in the liver in the maintenance of systemic glucose homeostasis.\n\nWe first analyzed Ago2 expression in mouse primary hepatocyte cultures after modulating extracellular glucose concentrations and in the presence of activators or inhibitors of glucokinase activity. We then characterized a conditional loss-of-function mouse model of Ago2 in liver for alterations in systemic energy metabolism.\n\nHere we show that Ago2 expression in liver is directly correlated to extracellular glucose concentrations and that modulating glucokinase activity is adequate to affect hepatic Ago2 levels. Conditional deletion of Ago2 in liver resulted in decreased fasting glucose levels in addition to reducing hepatic glucose production. Moreover, loss of Ago2 promoted hepatic expression of AMP-activated protein kinase \u03b11 (AMPK\u03b11) by de-repressing its targeting by miR-148a, an abundant microRNA in the liver. Deletion of Ago2 from hyperglycemic, obese, and insulin-resistant Lepob/ob mice reduced both random and fasted blood glucose levels and body weight and improved insulin sensitivity.\n\nThese data illustrate a central role for Ago2 in the adaptive response of the liver to fasting. Ago2 mediates the suppression of AMPK\u03b11 by miR-148a, thereby identifying a regulatory link between non-coding RNAs and a key stress regulator in the hepatocyte.", "doi": "10.1016/j.molmet.2018.10.003", "pmid": "30348590", "labels": {"Marc Friedl\u00e4nder": "", "SciLifeLab Fellow": "", "Marcel Tarbier": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC6308973"}, {"db": "pii", "key": "S2212-8778(18)30794-4"}], "notes": [], "created": "2020-10-12T12:03:03.002Z", "modified": "2026-09-23T12:49:05.176Z"}, {"entity": "publication", "iuid": "d683b7d3c0504c88b272b1e49cd0d722", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d683b7d3c0504c88b272b1e49cd0d722.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d683b7d3c0504c88b272b1e49cd0d722"}}, "title": "The human secretome \u2013 the proteins secreted from human cells", "authors": [{"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ea446aa574042a295d5f69437402f76.json"}}, {"family": "Tegel", "given": "Hanna", "initials": "H"}, {"family": "Sivertsson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Kuo", "given": "Chih Chung", "initials": "CC"}, {"family": "Gutierrez", "given": "Jahir M", "initials": "JM"}, {"family": "Lewis", "given": "Nathan E", "initials": "NE"}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Dannemeyer", "given": "Melanie", "initials": "M"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Malm", "given": "Magdalena", "initials": "M"}, {"family": "Vunk", "given": "Helian", "initials": "H"}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Hober", "given": "Andreas", "initials": "A"}, {"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E"}, {"family": "Kotol", "given": "David", "initials": "D"}, {"family": "Mulder", "given": "Jan", "initials": "J"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM"}, {"family": "Nilsson", "given": "Peter", "initials": "P"}, {"family": "Zwahlen", "given": "Martin", "initials": "M"}, {"family": "Takanen", "given": "Jenny Ottosson", "initials": "JO"}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K"}, {"family": "Stadler", "given": "Charlotte", "initials": "C"}, {"family": "Lindskog", "given": "Cecilia", "initials": "C"}, {"family": "Ponten", "given": "Fredrik", "initials": "F"}, {"family": "Nielsen", "given": "Jens", "initials": "J"}, {"family": "Palsson", "given": "Bernhard O", "initials": "BO"}, {"family": "Volk", "given": "Anna Luisa", "initials": "AL"}, {"family": "Lundqvist", "given": "Magnus", "initials": "M"}, {"family": "Berling", "given": "Anna", "initials": "A"}, {"family": "Svensson", "given": "Anne Sophie", "initials": "AS"}, {"family": "Kanje", "given": "Sara", "initials": "S"}, {"family": "Enstedt", "given": "Henric", "initials": "H"}, {"family": "Afshari", "given": "Delaram", "initials": "D"}, {"family": "Ekblad", "given": "Siri", "initials": "S"}, {"family": "Scheffel", "given": "Julia", "initials": "J"}, {"family": "Katona", "given": "Borbala", "initials": "B"}, {"family": "Vuu", "given": "Jimmy", "initials": "J"}, {"family": "Lindstr\u00f6m", "given": "Emil", "initials": "E"}, {"family": "Xu", "given": "LanLan", "initials": "L"}, {"family": "Mihai", "given": "Roxana", "initials": "R"}, {"family": "Bremer", "given": "Lucas", "initials": "L"}, {"family": "Westin", "given": "Malin", "initials": "M"}, {"family": "Muse", "given": "Muna", "initials": "M"}, {"family": "Mayr", "given": "Lorenz M", "initials": "LM"}, {"family": "Knight", "given": "Sinead", "initials": "S"}, {"family": "G\u00f6pel", "given": "Sven", "initials": "S"}, {"family": "Davies", "given": "Rick", "initials": "R"}, {"family": "Varley", "given": "Paul", "initials": "P"}, {"family": "Hatton", "given": "Diane", "initials": "D"}, {"family": "Fields", "given": "Ray", "initials": "R"}, {"family": "Voldborg", "given": "Bj\u00f8rn G", "initials": "BG"}, {"family": "Rockberg", "given": "Johan", "initials": "J"}, {"family": "Schiavone", "given": "Lovisa Holmberg", "initials": "LH"}, {"family": "Hober", "given": "Sophia", "initials": "S"}], "type": "posted-content", "published": "2018-11-26", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/465815", "pmid": null, "labels": {"SciLifeLab Fellow": "", "Fredrik Edfors": "", "DDLS Fellow": "", "Adil Mardinoglu": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T11:11:28.538Z", "modified": "2026-09-23T13:47:02.929Z"}, {"entity": "publication", "iuid": "b67466ff3a8143989339ec38284b10b1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b67466ff3a8143989339ec38284b10b1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b67466ff3a8143989339ec38284b10b1"}}, "title": "Screening a Resource of Recombinant Protein Fragments for Targeted Proteomics", "authors": [{"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e213b04f8984c8eb00c68f5bc2f6a36.json"}}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Vunk", "given": "Helian", "initials": "H"}, {"family": "Kotol", "given": "David", "initials": "D"}, {"family": "Fredolini", "given": "Claudia", "initials": "C"}, {"family": "Maddalo", "given": "Gianluca", "initials": "G"}, {"family": "Svensson", "given": "Anne Sophie", "initials": "AS"}, {"family": "Bostr\u00f6m", "given": "Tove", "initials": "T"}, {"family": "Tegel", "given": "Hanna", "initials": "H"}, {"family": "Nilsson", "given": "Peter", "initials": "P"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/022e140799b6466ea123319c3d70c76e.json"}}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ea446aa574042a295d5f69437402f76.json"}}], "type": "posted-content", "published": "2018-11-19", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/472662", "pmid": null, "labels": {"Fredrik Edfors": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T11:11:33.847Z", "modified": "2026-09-23T14:40:04.244Z"}, {"entity": "publication", "iuid": "5195ce1c7147434c92ca57f36caec0e0", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5195ce1c7147434c92ca57f36caec0e0.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5195ce1c7147434c92ca57f36caec0e0"}}, "title": "Profiles of circulating histidine-rich glycoprotein associate with chronological age and risk of all-cause mortality", "authors": [{"family": "Hong", "given": "Mun Gwan", "initials": "MG", "orcid": "0000-0001-8603-8293", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d12504acae5c4f31b83f75c3d7786cd4.json"}}, {"family": "Dodig-Crnkovi\u0107", "given": "Tea", "initials": "T", "orcid": "0000-0002-2875-896X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5365873ed6a7463485fb44550a4826ec.json"}}, {"family": "Chen", "given": "Xu", "initials": "X", "orcid": "0000-0002-7299-3238", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a4e440b72e0f47079dadf74bfd661448.json"}}, {"family": "Drobin", "given": "Kimi", "initials": "K"}, {"family": "Lee", "given": "Woojoo", "initials": "W", "orcid": "0000-0001-7447-7045", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c1f336e0cda240838ba0534f3b454121.json"}}, {"family": "Wang", "given": "Yunzhang", "initials": "Y"}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Kotol", "given": "David", "initials": "D", "orcid": "0000-0002-5388-3826", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c41f8f491c474e6bba2047b5d04b4af5.json"}}, {"family": "Thomas", "given": "Cecilia Engel", "initials": "CE"}, {"family": "Sj\u00f6berg", "given": "Ronald", "initials": "R", "orcid": "0000-0003-1363-5796", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d78ebc1fe5f140dd8a8011d8f7f4d05c.json"}}, {"family": "Odeberg", "given": "Jacob", "initials": "J", "orcid": "0000-0003-0996-1644", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d6abb3fc822a4cacbf1d45224f2442f5.json"}}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Silveira", "given": "Angela", "initials": "A", "orcid": "0000-0003-2063-4935", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2d8cbafcc7f04ac3adda984af7d85a16.json"}}, {"family": "Hall", "given": "Per", "initials": "P", "orcid": "0000-0002-5640-9126", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d59cc296ca1649ceb0d0734d20f1510a.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3db33fa3edb94febb8be7927a16838d0.json"}}, {"family": "Pawitan", "given": "Yudi", "initials": "Y", "orcid": "0000-0003-0324-7052", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c45201523b0d47fc9067d3fbe25ffa17.json"}}, {"family": "H\u00e4gg", "given": "Sara", "initials": "S", "orcid": "0000-0002-2452-1500", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/40186021027c42e4b2ed6daf9c196a29.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ea446aa574042a295d5f69437402f76.json"}}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL", "orcid": "0000-0001-8057-3543", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/db8023b719d54397bc73a795d4f13381.json"}}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE", "orcid": "0000-0002-7315-7899", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d6fa8b01df9f4bf68607603c51c5a106.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/022e140799b6466ea123319c3d70c76e.json"}}], "type": "posted-content", "published": "2018-11-09", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/464909", "pmid": null, "labels": {"Fredrik Edfors": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T11:11:26.556Z", "modified": "2026-09-23T14:30:35.256Z"}, {"entity": "publication", "iuid": "e870a684741f4bbbbd92b5483b04e76f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e870a684741f4bbbbd92b5483b04e76f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e870a684741f4bbbbd92b5483b04e76f"}}, "title": "New tools for automated high-resolution cryo-EM structure determination in RELION-3.", "authors": [{"family": "Zivanov", "given": "Jasenko", "initials": "J", "orcid": "0000-0001-8407-0759", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c558645bdcb34890a1eee8786b3126d8.json"}}, {"family": "Nakane", "given": "Takanori", "initials": "T", "orcid": "0000-0003-2697-2767", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3fa28db5ed51428f85508b6986fa0f72.json"}}, {"family": "Forsberg", "given": "Bj\u00f6rn O", "initials": "BO", "orcid": "0000-0002-6247-4063", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/36ea51bfa66d48b7a43559c3d0eaa59f.json"}}, {"family": "Kimanius", "given": "Dari", "initials": "D", "orcid": "0000-0002-2662-6373", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3a3803ee817a464ca07c849c07096dc2.json"}}, {"family": "Hagen", "given": "Wim Jh", "initials": "WJ", "orcid": "0000-0001-6229-2692", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f90d3efecb1f420e8ba6bf2e2d5f0f91.json"}}, {"family": "Lindahl", "given": "Erik", "initials": "E", "orcid": "0000-0002-2734-2794", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9eb30fa60f9b4b95842ac9d9f3a0eaa9.json"}}, {"family": "Scheres", "given": "Sjors Hw", "initials": "SH", "orcid": "0000-0002-0462-6540", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b64851b999fd42f7bf7b25856946dc62.json"}}], "type": "journal article", "published": "2018-11-09", "journal": {"title": "Elife", "issn": "2050-084X", "volume": "7", "issn-l": "2050-084X"}, "abstract": "Here, we describe the third major release of RELION. CPU-based vector acceleration has been added in addition to GPU support, which provides flexibility in use of resources and avoids memory limitations. Reference-free autopicking with Laplacian-of-Gaussian filtering and execution of jobs from python allows non-interactive processing during acquisition, including 2D-classification, de novo model generation and 3D-classification. Per-particle refinement of CTF parameters and correction of estimated beam tilt provides higher resolution reconstructions when particles are at different heights in the ice, and/or coma-free alignment has not been optimal. Ewald sphere curvature correction improves resolution for large particles. We illustrate these developments with publicly available data sets: together with a Bayesian approach to beam-induced motion correction it leads to resolution improvements of 0.2-0.7 \u00c5 compared to previous RELION versions.", "doi": "10.7554/eLife.42166", "pmid": "30412051", "labels": {"DDLS Fellow": "", "Bj\u00f6rn Forsberg": ""}, "xrefs": [{"db": "pmc", "key": "PMC6250425"}, {"db": "pii", "key": "42166"}], "notes": [], "created": "2026-08-21T13:07:26.149Z", "modified": "2026-09-22T19:57:24.918Z"}, {"entity": "publication", "iuid": "2e88e1a9c4184637bcb630acb69d7a94", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/2e88e1a9c4184637bcb630acb69d7a94.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/2e88e1a9c4184637bcb630acb69d7a94"}}, "title": "Accurate In Silico Modeling of Asymmetric Bilayers Based on Biophysical Principles.", "authors": [{"family": "Doktorova", "given": "Milka", "initials": "M"}, {"family": "Weinstein", "given": "Harel", "initials": "H"}], "type": "journal article", "published": "2018-11-06", "journal": {"title": "Biophys. J.", "issn": "1542-0086", "issn-l": "0006-3495", "volume": "115", "issue": "9", "pages": "1638-1643"}, "abstract": "Technological advances in the last decade have enabled the study of ever more complex and physiologically relevant model membranes to help dispel the mystery surrounding the role of plasma membrane asymmetry in various cellular processes. The slowly accumulating body of experimental data is fueling renewed interest in and the need for computational methods to support interpretations and address a wide range of problems that are still not amenable to direct experimental study. The specific appeal of molecular dynamics simulations for this purpose lies in their ability to access information at atomic resolution, which is useful for the formulation of testable mechanistic hypotheses. But, the range of questions that can be addressed reliably with such simulations is determined by the appropriate construction and simulation of asymmetric bilayer models. One essential way to achieve this goal is to follow rigorous biophysical criteria and principles. In this context, we show that the requirement for a robust comparison between the properties of simulated asymmetric and symmetric model membranes is for the tension in each bilayer leaflet to be zero. Commonly used methods for constructing asymmetric bilayers, including matching the average areas of the leaflets from the corresponding symmetric systems, do not ensure zero leaflet tension, thus precluding physically realistic changes in the areas of the two leaflets. We present, to our knowledge, a new method for identifying the ideal lipid packing in bilayers with different leaflet compositions that achieves the zero-tension goal, and discuss the basic principles underlying the biophysically correct computational study of asymmetric membranes.", "doi": "10.1016/j.bpj.2018.09.008", "pmid": "30297133", "labels": {"Milka Doktorova": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC6224353"}, {"db": "pii", "key": "S0006-3495(18)31059-2"}], "notes": [], "created": "2024-11-27T12:16:14.212Z", "modified": "2024-11-29T12:17:05.276Z"}, {"entity": "publication", "iuid": "aad8fe901d1e4010aef907a85ecd5587", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/aad8fe901d1e4010aef907a85ecd5587.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/aad8fe901d1e4010aef907a85ecd5587"}}, "title": "Author response: New tools for automated high-resolution cryo-EM structure determination in RELION-3", "authors": [{"family": "Zivanov", "given": "Jasenko", "initials": "J", "orcid": "0000-0001-8407-0759", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c558645bdcb34890a1eee8786b3126d8.json"}}, {"family": "Nakane", "given": "Takanori", "initials": "T", "orcid": "0000-0003-2697-2767", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3fa28db5ed51428f85508b6986fa0f72.json"}}, {"family": "Forsberg", "given": "Bj\u00f6rn O", "initials": "BO"}, {"family": "Kimanius", "given": "Dari", "initials": "D"}, {"family": "Hagen", "given": "Wim JH", "initials": "WJ", "orcid": "0000-0001-6229-2692", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f90d3efecb1f420e8ba6bf2e2d5f0f91.json"}}, {"family": "Lindahl", "given": "Erik", "initials": "E", "orcid": "0000-0002-2734-2794", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9eb30fa60f9b4b95842ac9d9f3a0eaa9.json"}}, {"family": "Scheres", "given": "Sjors HW", "initials": "SH", "orcid": "0000-0002-0462-6540", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b64851b999fd42f7bf7b25856946dc62.json"}}], "type": "peer-review", "published": "2018-11-05", "journal": {"issn-l": null}, "abstract": null, "doi": "10.7554/elife.42166.030", "pmid": null, "labels": {"DDLS Fellow": "", "Bj\u00f6rn Forsberg": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T13:52:40.740Z", "modified": "2026-10-05T08:14:51.141Z"}, {"entity": "publication", "iuid": "e289c31695bc4702b2276fddfdf81eed", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e289c31695bc4702b2276fddfdf81eed.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e289c31695bc4702b2276fddfdf81eed"}}, "title": "Nearly Neutral Evolution across the Drosophila melanogaster Genome.", "authors": [{"family": "Castellano", "given": "David", "initials": "D"}, {"family": "James", "given": "Jennifer", "initials": "J", "orcid": "0000-0003-0518-6783", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4b807f7ab8f46f8a5e927e1b090d662.json"}}, {"family": "Eyre-Walker", "given": "Adam", "initials": "A", "orcid": "0000-0001-5527-8729", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/710750d73a5c4e1483168d45dfd0e93f.json"}}], "type": "journal article", "published": "2018-11-01", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "issn-l": "0737-4038", "volume": "35", "issue": "11", "pages": "2685-2694"}, "abstract": "Under the nearly neutral theory of molecular evolution, the proportion of effectively neutral mutations is expected to depend upon the effective population size (Ne). Here, we investigate whether this is the case across the genome of Drosophila melanogaster using polymorphism data from North American and African lines. We show that the ratio of the number of nonsynonymous and synonymous polymorphisms is negatively correlated to the number of synonymous polymorphisms, even when the nonindependence is accounted for. The relationship is such that the proportion of effectively neutral nonsynonymous mutations increases by \u223c45% as Ne is halved. However, we also show that this relationship is steeper than expected from an independent estimate of the distribution of fitness effects from the site frequency spectrum. We investigate a number of potential explanations for this and show, using simulation, that this is consistent with a model of genetic hitchhiking: Genetic hitchhiking depresses diversity at neutral and weakly selected sites, but has little effect on the diversity of strongly selected sites.", "doi": "10.1093/molbev/msy164", "pmid": "30418639", "labels": {"Jennifer James": null, "DDLS Fellow": null}, "xrefs": [{"db": "pii", "key": "5078937"}], "notes": [], "created": "2024-11-27T09:29:05.759Z", "modified": "2025-11-30T11:19:13.619Z"}, {"entity": "publication", "iuid": "8ff453e7337b440f83c79309aed248e1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8ff453e7337b440f83c79309aed248e1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8ff453e7337b440f83c79309aed248e1"}}, "title": "microRNA-205-5p is a modulator of insulin sensitivity that inhibits FOXO function.", "authors": [{"family": "Langlet", "given": "Fanny", "initials": "F"}, {"family": "Tarbier", "given": "Marcel", "initials": "M"}, {"family": "Haeusler", "given": "Rebecca A", "initials": "RA"}, {"family": "Camastra", "given": "Stefania", "initials": "S", "orcid": "0000-0001-9015-7244", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/de900f775eb643bc8884f59b11ef619d.json"}}, {"family": "Ferrannini", "given": "Eleuterio", "initials": "E"}, {"family": "Friedl\u00e4nder", "given": "Marc R", "initials": "MR"}, {"family": "Accili", "given": "Domenico", "initials": "D"}], "type": "journal article", "published": "2018-11-00", "journal": {"title": "Mol Metab", "issn": "2212-8778", "issn-l": "2212-8778", "volume": "17", "issue": null, "pages": "49-60"}, "abstract": "Hepatic insulin resistance is a hallmark of type 2 diabetes and obesity. Insulin receptor signaling through AKT and FOXO has important metabolic effects that have traditionally been ascribed to regulation of gene expression. However, whether all the metabolic effects of FOXO arise from its regulation of protein-encoding mRNAs is unknown.\n\nTo address this question, we obtained expression profiles of FOXO-regulated murine hepatic microRNAs (miRNAs) during fasting and refeeding using mice lacking Foxo1, 3a, and 4 in liver (L-Foxo1,3a, 4).\n\nOut of 439 miRNA analyzed, 175 were differentially expressed in Foxo knockouts. Their functions were associated with insulin, Wnt, Mapk signaling, and aging. Among them, we report a striking increase of miR-205-5p expression in L-Foxo1,3a,4 knockouts, as well as in obese mice. We show that miR-205-5p gain-of-function increases AKT phosphorylation and decreases SHIP2 in primary hepatocytes, resulting in FOXO inhibition. This results in decreased hepatocyte glucose production. Consistent with these observations, miR-205-5p gain-of-function in mice lowered glucose levels and improved pyruvate tolerance.\n\nThese findings reveal a homeostatic miRNA loop regulating insulin signaling, with potential implications for in vivo glucose metabolism.", "doi": "10.1016/j.molmet.2018.08.003", "pmid": "30174230", "labels": {"Marc Friedl\u00e4nder": "", "SciLifeLab Fellow": "", "Marcel Tarbier": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC6197154"}, {"db": "pii", "key": "S2212-8778(18)30754-3"}], "notes": [], "created": "2020-10-12T12:03:05.046Z", "modified": "2026-09-23T10:24:26.735Z"}, {"entity": "publication", "iuid": "0148698226474085bd69d99ddb677319", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0148698226474085bd69d99ddb677319.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0148698226474085bd69d99ddb677319"}}, "title": "First report of an mcr-1-harboring Salmonella enterica subsp. enterica serotype 4,5,12:i:- strain isolated from blood of a patient in Switzerland.", "authors": [{"family": "Carroll", "given": "Laura M", "initials": "LM"}, {"family": "Zurfluh", "given": "Katrin", "initials": "K"}, {"family": "Jang", "given": "Hyein", "initials": "H"}, {"family": "Gopinath", "given": "Gopal", "initials": "G"}, {"family": "N\u00fcesch-Inderbinen", "given": "Magdalena", "initials": "M"}, {"family": "Poirel", "given": "Laurent", "initials": "L"}, {"family": "Nordmann", "given": "Patrice", "initials": "P"}, {"family": "Stephan", "given": "Roger", "initials": "R"}, {"family": "Guldimann", "given": "Claudia", "initials": "C"}], "type": "case reports", "published": "2018-11-00", "journal": {"title": "Int. J. Antimicrob. Agents", "issn": "1872-7913", "volume": "52", "issue": "5", "pages": "740-741", "issn-l": "0924-8579"}, "abstract": null, "doi": "10.1016/j.ijantimicag.2018.08.003", "pmid": "30099057", "labels": {"Laura Carroll": null, "DDLS Fellow": null}, "xrefs": [{"db": "pii", "key": "S0924-8579(18)30229-2"}], "notes": [], "created": "2025-03-18T17:21:46.468Z", "modified": "2025-03-18T17:22:30.528Z"}, {"entity": "publication", "iuid": "d2b6e075a9d94f80bc1a3d4252f086a1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d2b6e075a9d94f80bc1a3d4252f086a1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d2b6e075a9d94f80bc1a3d4252f086a1"}}, "title": "Quantifying point-mutations in shotgun metagenomic data", "authors": [{"family": "Magesh", "given": "Shruthi", "initials": "S"}, {"family": "Jonsson", "given": "Viktor", "initials": "V", "orcid": "0000-0002-1445-5220", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8068fef596794494add13b3a4bc35768.json"}}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J", "orcid": "0000-0002-6528-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c666068e9d34939b0252a627007cec7.json"}}], "type": "posted-content", "published": "2018-10-11", "journal": {"title": "bioRxiv preprint", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/438572", "pmid": null, "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [], "notes": [], "created": "2022-11-08T09:31:21.964Z", "modified": "2025-12-04T17:02:34.870Z"}, {"entity": "publication", "iuid": "69474be543ee4e479cefe50817890bc1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/69474be543ee4e479cefe50817890bc1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/69474be543ee4e479cefe50817890bc1"}}, "title": "Growth of Cyanobacteria Is Constrained by the Abundance of Light and Carbon Assimilation Proteins.", "authors": [{"family": "Jahn", "given": "Michael", "initials": "M"}, {"family": "Vialas", "given": "Vital", "initials": "V"}, {"family": "Karlsen", "given": "Jan", "initials": "J"}, {"family": "Maddalo", "given": "Gianluca", "initials": "G"}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L"}, {"family": "Hudson", "given": "Elton P", "initials": "EP"}], "type": "journal article", "published": "2018-10-09", "journal": {"title": "Cell Reports", "issn": "2211-1247", "issn-l": null, "volume": "25", "issue": "2", "pages": "478-486.e8"}, "abstract": "Cyanobacteria must balance separate demands for energy generation, carbon assimilation, and biomass synthesis. We used shotgun proteomics to investigate proteome allocation strategies in the model cyanobacterium Synechocystis sp. PCC 6803 as it adapted to light and inorganic carbon (Ci) limitation. When partitioning the proteome into seven functional sectors, we find that sector sizes change linearly with growth rate. The sector encompassing ribosomes is significantly smaller than in E. coli, which may explain the lower maximum growth rate in Synechocystis. Limitation of light dramatically affects multiple proteome sectors, whereas the effect of Ci limitation is weak. Carbon assimilation proteins respond more strongly to changes in light intensity than to Ci. A coarse-grained cell economy model generally explains proteome trends. However, deviations from model predictions suggest that the large proteome sectors for carbon and light assimilation are not optimally utilized under some growth conditions and may constrain the proteome space available to ribosomes.", "doi": "10.1016/j.celrep.2018.09.040", "pmid": "30304686", "labels": {"Paul Hudson": "", "SciLifeLab Fellow": "", "Fredrik Edfors": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pii", "key": "S2211-1247(18)31485-2"}], "notes": [], "created": "2020-10-06T14:19:03.144Z", "modified": "2026-09-23T07:30:48.735Z"}, {"entity": "publication", "iuid": "16e1d96d3f3f44e99e9ecd90b38b2f61", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/16e1d96d3f3f44e99e9ecd90b38b2f61.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/16e1d96d3f3f44e99e9ecd90b38b2f61"}}, "title": "Enhanced validation of antibodies for research applications.", "authors": [{"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e213b04f8984c8eb00c68f5bc2f6a36.json"}}, {"family": "Hober", "given": "Andreas", "initials": "A", "orcid": "0000-0001-8947-2562", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/06cbc187628340278395a00ab9dd6c89.json"}}, {"family": "Linderb\u00e4ck", "given": "Klas", "initials": "K"}, {"family": "Maddalo", "given": "Gianluca", "initials": "G"}, {"family": "Azimi", "given": "Alireza", "initials": "A"}, {"family": "Sivertsson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Tegel", "given": "Hanna", "initials": "H", "orcid": "0000-0002-7067-9173", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7b9de19b82b4406d8904cb937a466e8b.json"}}, {"family": "Hober", "given": "Sophia", "initials": "S"}, {"family": "Szigyarto", "given": "Cristina Al-Khalili", "initials": "CA"}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/abbbf8193d5a4376a5c726768d039439.json"}}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K"}, {"family": "Oksvold", "given": "Per", "initials": "P", "orcid": "0000-0003-3014-5502", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/16beca5822c747128300910b5c74dbfc.json"}}, {"family": "Lindskog", "given": "Cecilia", "initials": "C"}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0002-5248-8568", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a6982072448e4e8889c71fc14d214fed.json"}}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ea446aa574042a295d5f69437402f76.json"}}], "type": "journal article", "published": "2018-10-08", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "9", "issue": "1", "pages": "4130", "issn-l": "2041-1723"}, "abstract": "There is a need for standardized validation methods for antibody specificity and selectivity. Recently, five alternative validation pillars were proposed to explore the specificity of research antibodies using methods with no need for prior knowledge about the protein target. Here, we show that these principles can be used in a streamlined manner for enhanced validation of research antibodies in Western blot applications. More than 6,000 antibodies were validated with at least one of these strategies involving orthogonal methods, genetic knockdown, recombinant expression, independent antibodies, and capture mass spectrometry analysis. The results show a path forward for efforts to validate antibodies in an application-specific manner suitable for both providers and users.", "doi": "10.1038/s41467-018-06642-y", "pmid": "30297845", "labels": {"Fredrik Edfors": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC6175901"}, {"db": "pii", "key": "10.1038/s41467-018-06642-y"}], "notes": [], "created": "2026-09-23T07:38:11.276Z", "modified": "2026-09-23T07:38:11.368Z"}, {"entity": "publication", "iuid": "b569b1707b304ebb9c08c89f6a1f5f86", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b569b1707b304ebb9c08c89f6a1f5f86.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b569b1707b304ebb9c08c89f6a1f5f86"}}, "title": "Conceptual and empirical advances in Neotropical biodiversity research.", "authors": [{"family": "Antonelli", "given": "Alexandre", "initials": "A", "orcid": "0000-0003-1842-9297", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1de98df1bb2140fc9666507cb2fb5614.json"}}, {"family": "Ariza", "given": "Mar\u00eda", "initials": "M"}, {"family": "Albert", "given": "James", "initials": "J"}, {"family": "Andermann", "given": "Tobias", "initials": "T", "orcid": "0000-0002-0932-1623", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dfff478dfcfc43ddbd40bb1bafbcb0a7.json"}}, {"family": "Azevedo", "given": "Josu\u00e9", "initials": "J"}, {"family": "Bacon", "given": "Christine", "initials": "C", "orcid": "0000-0003-2341-2705", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/659f1ab881cf4890b80ebbdf23188ebc.json"}}, {"family": "Faurby", "given": "S\u00f8ren", "initials": "S"}, {"family": "Guedes", "given": "Thais", "initials": "T", "orcid": "0000-0003-3318-7193", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8da950be9d6a47978c950d094a8de4a5.json"}}, {"family": "Hoorn", "given": "Carina", "initials": "C"}, {"family": "Lohmann", "given": "L\u00facia G", "initials": "LG", "orcid": "0000-0003-4960-0587", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bce4810871104a18b6c2fc5235680b4b.json"}}, {"family": "Matos-Marav\u00ed", "given": "P\u00e1vel", "initials": "P"}, {"family": "Ritter", "given": "Camila D", "initials": "CD", "orcid": "0000-0002-3371-7425", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/51b184cc48e941a79b499cbacb139705.json"}}, {"family": "Sanmart\u00edn", "given": "Isabel", "initials": "I", "orcid": "0000-0001-6104-9658", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f7e68d7b73f74cfd9f101c0894a1e336.json"}}, {"family": "Silvestro", "given": "Daniele", "initials": "D", "orcid": "0000-0003-0100-0961", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4870742190514c5b83450c567c11398a.json"}}, {"family": "Tejedor", "given": "Marcelo", "initials": "M"}, {"family": "Ter Steege", "given": "Hans", "initials": "H"}, {"family": "Tuomisto", "given": "Hanna", "initials": "H"}, {"family": "Werneck", "given": "Fernanda P", "initials": "FP", "orcid": "0000-0002-8779-2607", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f535695017224d6da66668658bea6618.json"}}, {"family": "Zizka", "given": "Alexander", "initials": "A", "orcid": "0000-0002-1680-9192", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c62a905324e94d869ccd715ebbc98828.json"}}, {"family": "Edwards", "given": "Scott V", "initials": "SV", "orcid": "0000-0003-2535-6217", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/249a83cc8fb240609cd7bd76c6c79e2c.json"}}], "type": "journal article", "published": "2018-10-04", "journal": {"title": "PeerJ", "issn": "2167-8359", "volume": "6", "pages": "e5644", "issn-l": "2167-8359"}, "abstract": "The unparalleled biodiversity found in the American tropics (the Neotropics) has attracted the attention of naturalists for centuries. Despite major advances in recent years in our understanding of the origin and diversification of many Neotropical taxa and biotic regions, many questions remain to be answered. Additional biological and geological data are still needed, as well as methodological advances that are capable of bridging these research fields. In this review, aimed primarily at advanced students and early-career scientists, we introduce the concept of \"trans-disciplinary biogeography,\" which refers to the integration of data from multiple areas of research in biology (e.g., community ecology, phylogeography, systematics, historical biogeography) and Earth and the physical sciences (e.g., geology, climatology, palaeontology), as a means to reconstruct the giant puzzle of Neotropical biodiversity and evolution in space and time. We caution against extrapolating results derived from the study of one or a few taxa to convey general scenarios of Neotropical evolution and landscape formation. We urge more coordination and integration of data and ideas among disciplines, transcending their traditional boundaries, as a basis for advancing tomorrow's ground-breaking research. Our review highlights the great opportunities for studying the Neotropical biota to understand the evolution of life.", "doi": "10.7717/peerj.5644", "pmid": "30310740", "labels": {"Tobias Andermann": null, "DDLS Fellow": null}, "xrefs": [{"db": "pii", "key": "5644"}, {"db": "pmc", "key": "PMC6174874"}], "notes": [], "created": "2022-11-11T09:10:33.135Z", "modified": "2022-11-11T09:10:33.573Z"}, {"entity": "publication", "iuid": "fe0df6a374124b54b9dba430f3fe7edd", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/fe0df6a374124b54b9dba430f3fe7edd.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/fe0df6a374124b54b9dba430f3fe7edd"}}, "title": "Bacteriophages Synergize with the Gut Microbial Community To Combat Salmonella.", "authors": [{"family": "Hu", "given": "Yue O O", "initials": "YOO"}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW"}, {"family": "Bengtsson", "given": "Carina", "initials": "C"}, {"family": "Alisjahbana", "given": "Arlisa", "initials": "A"}, {"family": "Seifert", "given": "Maike", "initials": "M"}, {"family": "Kamal", "given": "Anaga", "initials": "A"}, {"family": "Sj\u00f6ling", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Midtvedt", "given": "Tore", "initials": "T"}, {"family": "Norin", "given": "Elisabeth", "initials": "E"}, {"family": "Du", "given": "Juan", "initials": "J", "orcid": "0000-0001-7649-9571", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f67834a614ca4cd4aff026e5e9a1a1e4.json"}}, {"family": "Engstrand", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2018-10-02", "journal": {"title": "mSystems", "issn": "2379-5077", "volume": "3", "issue": "5", "issn-l": "2379-5077"}, "abstract": "Salmonella infection is one of the main causes of food-borne diarrheal diseases worldwide. Although most Salmonella infections can be cleared without treatment, some cause serious illnesses that require antibiotic treatment. In view of the growing emergence of antibiotic-resistant Salmonella strains, novel treatments are increasingly required. Furthermore, there is a striking paucity of data on how a balanced human gut microbiota responds to Salmonella infection. This study aimed to evaluate whether a balanced gut microbiota protects against Salmonella growth and to compare two antimicrobial approaches for managing Salmonella infection: bacteriophage (phage) treatment and antibiotic treatment. Anaerobically cultivated human intestinal microflora (ACHIM) is a feasible model for the human gut microbiota and naturally inhibits Salmonella infection. By mimicking Salmonella infection in vitro using ACHIM, we observed a large reduction of Salmonella growth by the ACHIM itself. Treatments with phage and antibiotic further inhibited Salmonella growth. However, phage treatment had less impact on the nontargeted bacteria in ACHIM than the antibiotic treatment did. Phage treatment has high specificity when combating Salmonella infection and offers a noninvasive alternative to antibiotic treatment. IMPORTANCE Antibiotic-resistant bacteria are a global threat. Therefore, alternative approaches for combatting bacteria, especially antibiotic-resistant bacteria, are urgently needed. Using a human gut microbiota model, we demonstrate that bacteriophages (phages) are able to substantially decrease pathogenic Salmonella without perturbing the microbiota. Conversely, antibiotic treatment leads to the eradication of close to all commensal bacteria, leaving only antibiotic-resistant bacteria. An unbalanced microbiota has been linked to many diseases both in the gastrointestinal tract or \"nonintestinal\" diseases. In our study, we show that the microbiota provides a protective effect against Salmonella. Since phage treatment preserves the healthy gut microbiota, it is a feasible superior alternative to antibiotic treatment. Furthermore, when combating infections caused by pathogenic bacteria, gut microbiota should be considered.", "doi": "10.1128/mSystems.00119-18", "pmid": "30320220", "labels": {"DDLS Fellow": "", "Luisa Hugerth": ""}, "xrefs": [{"db": "pmc", "key": "PMC6172775"}, {"db": "pii", "key": "mSystems00119-18"}], "notes": [], "created": "2022-11-08T07:01:11.963Z", "modified": "2026-09-23T10:47:08.157Z"}, {"entity": "publication", "iuid": "c4dd05ee7cbe41a89012fe11ccb27f71", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c4dd05ee7cbe41a89012fe11ccb27f71.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c4dd05ee7cbe41a89012fe11ccb27f71"}}, "title": "High Cell Density Perfusion Culture has a Maintained Exoproteome and Metabolome.", "authors": [{"family": "Zamani", "given": "Leila", "initials": "L"}, {"family": "Lundqvist", "given": "Magnus", "initials": "M"}, {"family": "Zhang", "given": "Ye", "initials": "Y"}, {"family": "Aberg", "given": "Magnus", "initials": "M"}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Bidkhori", "given": "Gholamreza", "initials": "G"}, {"family": "Lindahl", "given": "Anna", "initials": "A"}, {"family": "Mie", "given": "Axel", "initials": "A"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Field", "given": "Raymond", "initials": "R"}, {"family": "Turner", "given": "Richard", "initials": "R"}, {"family": "Rockberg", "given": "Johan", "initials": "J"}, {"family": "Chotteau", "given": "Veronique", "initials": "V"}], "type": "journal article", "published": "2018-10-00", "journal": {"title": "Biotechnol J", "issn": "1860-7314", "issn-l": "1860-6768", "volume": "13", "issue": "10", "pages": "e1800036"}, "abstract": "The optimization of bioprocesses for biopharmaceutical manufacturing by Chinese hamster ovary (CHO) cells can be a challenging endeavor and, today, heavily relies on empirical methods treating the bioreactor process and the cells as black boxes. Multi-omics approaches have the potential to reveal otherwise unknown characteristics of these systems and identify culture parameters to more rationally optimize the cultivation process. Here, the authors have applied both metabolomic and proteomic profiling to a perfusion process, using CHO cells for antibody production, to explore how cell biology and reactor environment change as the cell density reaches \u2265200 \u00d7 106 cells mL-1 . The extracellular metabolic composition obtained in perfusion mode shows a markedly more stable profile in comparison to fed-batch, despite a far larger range of viable cell densities in perfusion. This stable profile is confirmed in the extracellular proteosome. Furthermore, the proteomics data shows an increase of structural proteins as cell density increases, which could be due to a higher shear stress and explain the decrease in cell diameter at very high cell densities. Both proteomic and metabolic results shows signs of oxidative stress and changes in glutathione metabolism at very high cell densities. The authors suggest the methodology presented herein to be a powerful tool for optimizing processes of recombinant protein production.", "doi": "10.1002/biot.201800036", "pmid": "29957873", "labels": {"Adil Mardinoglu": "", "SciLifeLab Fellow": "", "Fredrik Edfors": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2020-09-25T13:29:29.121Z", "modified": "2026-09-23T11:42:01.355Z"}, {"entity": "publication", "iuid": "1c619a21890b4a04a96ac708f21c8847", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1c619a21890b4a04a96ac708f21c8847.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1c619a21890b4a04a96ac708f21c8847"}}, "title": "Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes.", "authors": [{"family": "Alneberg", "given": "Johannes", "initials": "J"}, {"family": "Karlsson", "given": "Christofer M G", "initials": "CMG"}, {"family": "Divne", "given": "Anna-Maria", "initials": "AM"}, {"family": "Bergin", "given": "Claudia", "initials": "C"}, {"family": "Homa", "given": "Felix", "initials": "F"}, {"family": "Lindh", "given": "Markus V", "initials": "MV"}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW"}, {"family": "Ettema", "given": "Thijs J G", "initials": "TJG"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}, {"family": "Pinhassi", "given": "Jarone", "initials": "J", "orcid": "0000-0002-6405-1347", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/28b77762086343048e74046a6486caff.json"}}], "type": "journal article", "published": "2018-09-28", "journal": {"title": "Microbiome", "issn": "2049-2618", "volume": "6", "issue": "1", "pages": "173", "issn-l": "2049-2618"}, "abstract": "Prokaryotes dominate the biosphere and regulate biogeochemical processes essential to all life. Yet, our knowledge about their biology is for the most part limited to the minority that has been successfully cultured. Molecular techniques now allow for obtaining genome sequences of uncultivated prokaryotic taxa, facilitating in-depth analyses that may ultimately improve our understanding of these key organisms.\n\nWe compared results from two culture-independent strategies for recovering bacterial genomes: single-amplified genomes and metagenome-assembled genomes. Single-amplified genomes were obtained from samples collected at an offshore station in the Baltic Sea Proper and compared to previously obtained metagenome-assembled genomes from a time series at the same station. Among 16 single-amplified genomes analyzed, seven were found to match metagenome-assembled genomes, affiliated with a diverse set of taxa. Notably, genome pairs between the two approaches were nearly identical (average 99.51% sequence identity; range 98.77-99.84%) across overlapping regions (30-80% of each genome). Within matching pairs, the single-amplified genomes were consistently smaller and less complete, whereas the genetic functional profiles were maintained. For the metagenome-assembled genomes, only on average 3.6% of the bases were estimated to be missing from the genomes due to wrongly binned contigs.\n\nThe strong agreement between the single-amplified and metagenome-assembled genomes emphasizes that both methods generate accurate genome information from uncultivated bacteria. Importantly, this implies that the research questions and the available resources are allowed to determine the selection of genomics approach for microbiome studies.", "doi": "10.1186/s40168-018-0550-0", "pmid": "30266101", "labels": {"Luisa Hugerth": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC6162917"}, {"db": "pii", "key": "10.1186/s40168-018-0550-0"}], "notes": [], "created": "2022-11-08T07:01:16.695Z", "modified": "2026-09-23T07:34:23.943Z"}, {"entity": "publication", "iuid": "fbb24d8a50e743b88a01eb648061d9f9", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/fbb24d8a50e743b88a01eb648061d9f9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/fbb24d8a50e743b88a01eb648061d9f9"}}, "title": "ESS: A Tool for Genome-Scale Quantification of Essentiality Score for Reaction/Genes in Constraint-Based Modeling.", "authors": [{"family": "Zhang", "given": "Cheng", "initials": "C"}, {"family": "Bidkhori", "given": "Gholamreza", "initials": "G"}, {"family": "Benfeitas", "given": "Rui", "initials": "R"}, {"family": "Lee", "given": "Sunjae", "initials": "S"}, {"family": "Arif", "given": "Muhammad", "initials": "M"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}], "type": "journal article", "published": "2018-09-28", "journal": {"title": "Front. Physiol.", "issn": "1664-042X", "issn-l": "1664-042X", "volume": "9", "issue": null, "pages": "1355"}, "abstract": "Genome-scale metabolic models (GEMs) are comprehensive descriptions of cell metabolism and have been extensively used to understand biological responses in health and disease. One such application is in determining metabolic adaptation to the absence of a gene or reaction, i.e., essentiality analysis. However, current methods do not permit efficiently and accurately quantifying reaction/gene essentiality. Here, we present Essentiality Score Simulator (ESS), a tool for quantification of gene/reaction essentialities in GEMs. ESS quantifies and scores essentiality of each reaction/gene and their combinations based on the stoichiometric balance using synthetic lethal analysis. This method provides an option to weight metabolic models which currently rely mostly on topologic parameters, and is potentially useful to investigate the metabolic pathway differences between different organisms, cells, tissues, and/or diseases. We benchmarked the proposed method against multiple network topology parameters, and observed that our method displayed higher accuracy based on experimental evidence. In addition, we demonstrated its application in the wild-type and ldh knock-out E. coli core model, as well as two human cell lines, and revealed the changes of essentiality in metabolic pathways based on the reactions essentiality score. ESS is available without any limitation at https://sourceforge.net/projects/essentiality-score-simulator.", "doi": "10.3389/fphys.2018.01355", "pmid": "30323767", "labels": {"Adil Mardinoglu": "", "SciLifeLab Fellow": "", "DDLS Fellow": "", "Muhammad Arif": ""}, "xrefs": [{"db": "pmc", "key": "PMC6173058"}], "notes": [], "created": "2020-09-25T13:25:54.986Z", "modified": "2026-09-23T12:49:03.302Z"}, {"entity": "publication", "iuid": "e4aae79599bc44388a0e63f893a43113", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e4aae79599bc44388a0e63f893a43113.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e4aae79599bc44388a0e63f893a43113"}}, "title": "Maternal gut and breast milk microbiota affect infant gut antibiotic resistome and mobile genetic elements.", "authors": [{"family": "P\u00e4rn\u00e4nen", "given": "Katariina", "initials": "K"}, {"family": "Karkman", "given": "Antti", "initials": "A"}, {"family": "Hultman", "given": "Jenni", "initials": "J", "orcid": "0000-0002-3431-1785", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4e9c0d6fdfdd4570809812ae7e58b1c5.json"}}, {"family": "Lyra", "given": "Christina", "initials": "C"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J", "orcid": "0000-0002-6528-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c666068e9d34939b0252a627007cec7.json"}}, {"family": "Larsson", "given": "D G Joakim", "initials": "DGJ", "orcid": "0000-0002-5496-0328", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5b42f991b26e48879dacdf815ccafa12.json"}}, {"family": "Rautava", "given": "Samuli", "initials": "S"}, {"family": "Isolauri", "given": "Erika", "initials": "E"}, {"family": "Salminen", "given": "Seppo", "initials": "S"}, {"family": "Kumar", "given": "Himanshu", "initials": "H"}, {"family": "Satokari", "given": "Reetta", "initials": "R"}, {"family": "Virta", "given": "Marko", "initials": "M", "orcid": "0000-0001-5981-7566", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7d4c82f58f4946e693b7d7878ccaea95.json"}}], "type": "journal article", "published": "2018-09-24", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "9", "issue": "1", "pages": "3891", "issn-l": "2041-1723"}, "abstract": "The infant gut microbiota has a high abundance of antibiotic resistance genes (ARGs) compared to adults, even in the absence of antibiotic exposure. Here we study potential sources of infant gut ARGs by performing metagenomic sequencing of breast milk, as well as infant and maternal gut microbiomes. We find that fecal ARG and mobile genetic element (MGE) profiles of infants are more similar to those of their own mothers than to those of unrelated mothers. MGEs in mothers' breast milk are also shared with their own infants. Termination of breastfeeding and intrapartum antibiotic prophylaxis of mothers, which have the potential to affect microbial community composition, are associated with higher abundances of specific ARGs, the composition of which is largely shaped by bacterial phylogeny in the infant gut. Our results suggest that infants inherit the legacy of past antibiotic consumption of their mothers via transmission of genes, but microbiota composition still strongly impacts the overall resistance load.", "doi": "10.1038/s41467-018-06393-w", "pmid": "30250208", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-018-06393-w"}, {"db": "pmc", "key": "PMC6155145"}], "notes": [], "created": "2022-11-08T09:28:23.437Z", "modified": "2022-11-08T09:28:23.601Z"}, {"entity": "publication", "iuid": "0ae9a718b4e946f9be72c32349581e95", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0ae9a718b4e946f9be72c32349581e95.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0ae9a718b4e946f9be72c32349581e95"}}, "title": "Characterization of different fat depots in NAFLD using inflammation-associated proteome, lipidome and metabolome.", "authors": [{"family": "Lovric", "given": "Alen", "initials": "A"}, {"family": "Gran\u00e9r", "given": "Marit", "initials": "M"}, {"family": "Bjornson", "given": "Elias", "initials": "E"}, {"family": "Arif", "given": "Muhammad", "initials": "M"}, {"family": "Benfeitas", "given": "Rui", "initials": "R"}, {"family": "Nyman", "given": "Kristofer", "initials": "K"}, {"family": "St\u00e5hlman", "given": "Marcus", "initials": "M"}, {"family": "Pentik\u00e4inen", "given": "Markku O", "initials": "MO"}, {"family": "Lundbom", "given": "Jesper", "initials": "J"}, {"family": "Hakkarainen", "given": "Antti", "initials": "A", "orcid": "0000-0002-7367-2532", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/265475fc39804ba2b3a1a455ea93bf84.json"}}, {"family": "Sir\u00e9n", "given": "Reijo", "initials": "R", "orcid": "0000-0002-5191-6145", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1273b5f89d2a4c0da5ceb201f24f2457.json"}}, {"family": "Nieminen", "given": "Markku S", "initials": "MS"}, {"family": "Lundbom", "given": "Nina", "initials": "N"}, {"family": "Lauerma", "given": "Kirsi", "initials": "K"}, {"family": "Taskinen", "given": "Marja-Riitta", "initials": "MR"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Boren", "given": "Jan", "initials": "J", "orcid": "0000-0003-0786-8091", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/73a770eb9e614448a046b8e9199052e9.json"}}], "type": "journal article", "published": "2018-09-21", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "8", "issue": "1", "pages": "14200"}, "abstract": "Non-alcoholic fatty liver disease (NAFLD) is recognized as a liver manifestation of metabolic syndrome, accompanied with excessive fat accumulation in the liver and other vital organs. Ectopic fat accumulation was previously associated with negative effects at the systemic and local level in the human body. Thus, we aimed to identify and assess the predictive capability of novel potential metabolic biomarkers for ectopic fat depots in non-diabetic men with NAFLD, using the inflammation-associated proteome, lipidome and metabolome. Myocardial and hepatic triglycerides were measured with magnetic spectroscopy while function of left ventricle, pericardial and epicardial fat, subcutaneous and visceral adipose tissue were measured with magnetic resonance imaging. Measured ectopic fat depots were profiled and predicted using a Random Forest algorithm, and by estimating the Area Under the Receiver Operating Characteristic curves. We have identified distinct metabolic signatures of fat depots in the liver (TAG50:1, glutamate, diSM18:0 and CE20:3), pericardium (N-palmitoyl-sphinganine, HGF, diSM18:0, glutamate, and TNFSF14), epicardium (sphingomyelin, CE20:3, PC38:3 and TNFSF14), and myocardium (CE20:3, LAPTGF-\u03b21, glutamate and glucose). Our analyses highlighted non-invasive biomarkers that accurately predict ectopic fat depots, and reflect their distinct metabolic signatures in subjects with NAFLD.", "doi": "10.1038/s41598-018-31865-w", "pmid": "30242179", "labels": {"Adil Mardinoglu": "", "SciLifeLab Fellow": "", "DDLS Fellow": "", "Muhammad Arif": ""}, "xrefs": [{"db": "pmc", "key": "PMC6155005"}, {"db": "pii", "key": "10.1038/s41598-018-31865-w"}], "notes": [], "created": "2020-11-30T03:17:16.010Z", "modified": "2026-09-23T08:39:38.549Z"}, {"entity": "publication", "iuid": "9c4cbb326ac4478cbf8526a0eee0ca4d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9c4cbb326ac4478cbf8526a0eee0ca4d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9c4cbb326ac4478cbf8526a0eee0ca4d"}}, "title": "RELION-3: new tools for automated high-resolution cryo-EM structure determination", "authors": [{"family": "Zivanov", "given": "Jasenko", "initials": "J", "orcid": "0000-0001-8407-0759", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c558645bdcb34890a1eee8786b3126d8.json"}}, {"family": "Nakane", "given": "Takanori", "initials": "T", "orcid": "0000-0003-2697-2767", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3fa28db5ed51428f85508b6986fa0f72.json"}}, {"family": "Forsberg", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0002-6247-4063", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/36ea51bfa66d48b7a43559c3d0eaa59f.json"}}, {"family": "Kimanius", "given": "Dari", "initials": "D", "orcid": "0000-0002-2662-6373", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3a3803ee817a464ca07c849c07096dc2.json"}}, {"family": "Hagen", "given": "Wim J H", "initials": "WJH", "orcid": "0000-0001-6229-2692", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f90d3efecb1f420e8ba6bf2e2d5f0f91.json"}}, {"family": "Lindahl", "given": "Erik", "initials": "E", "orcid": "0000-0002-2734-2794", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9eb30fa60f9b4b95842ac9d9f3a0eaa9.json"}}, {"family": "Scheres", "given": "Sjors H W", "initials": "SHW", "orcid": "0000-0002-0462-6540", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b64851b999fd42f7bf7b25856946dc62.json"}}], "type": "posted-content", "published": "2018-09-19", "journal": {"title": "bioRxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/421123", "pmid": null, "labels": {"DDLS Fellow": null, "Bj\u00f6rn Forsberg": null}, "xrefs": [], "notes": [], "created": "2026-08-20T11:11:09.289Z", "modified": "2026-10-05T07:22:44.769Z"}, {"entity": "publication", "iuid": "ec5af15c2fcd4fbca0292ec3b72dc5ee", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ec5af15c2fcd4fbca0292ec3b72dc5ee.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ec5af15c2fcd4fbca0292ec3b72dc5ee"}}, "title": "Focal Adhesion Kinase and ROCK Signaling Are Switch-Like Regulators of Human Adipose Stem Cell Differentiation towards Osteogenic and Adipogenic Lineages.", "authors": [{"family": "Hyv\u00e4ri", "given": "Laura", "initials": "L", "orcid": "0000-0002-9893-0323", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/acdbb8ff6f6b4bfdac09534392ae9631.json"}}, {"family": "Ojansivu", "given": "Miina", "initials": "M", "orcid": "0000-0002-5493-3530", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f752fc30ac694e9f9495aa2d8e6df60e.json"}}, {"family": "Juntunen", "given": "Miia", "initials": "M", "orcid": "0000-0001-5282-4376", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0567dd8adccc4f2a86119b3220719106.json"}}, {"family": "Kartasalo", "given": "Kimmo", "initials": "K", "orcid": "0000-0002-9470-4783", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7c6fc97c06ed456c8bdd1f03db8a9b72.json"}}, {"family": "Miettinen", "given": "Susanna", "initials": "S", "orcid": "0000-0002-0647-9556", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ce415c4e4d7419ab3704b4096333c59.json"}}, {"family": "Vanhatupa", "given": "Sari", "initials": "S", "orcid": "0000-0002-2444-9713", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/adadbd28e84a4764be421fe20cf3648b.json"}}], "type": "journal article", "published": "2018-09-12", "journal": {"title": "Stem Cells Int", "issn": "1687-966X", "issn-l": null, "volume": "2018", "issue": null, "pages": "2190657"}, "abstract": "Adipose tissue is an attractive stem cell source for soft and bone tissue engineering applications and stem cell therapies. The adipose-derived stromal/stem cells (ASCs) have a multilineage differentiation capacity that is regulated through extracellular signals. The cellular events related to cell adhesion and cytoskeleton have been suggested as central regulators of differentiation fate decision. However, the detailed knowledge of these molecular mechanisms in human ASCs remains limited. This study examined the significance of focal adhesion kinase (FAK), Rho-Rho-associated protein kinase (Rho-ROCK), and their downstream target extracellular signal-regulated kinase 1/2 (ERK1/2) on hASCs differentiation towards osteoblasts and adipocytes. Analyses of osteogenic markers RUNX2A, alkaline phosphatase, and matrix mineralization revealed an essential role of active FAK, ROCK, and ERK1/2 signaling for the osteogenesis of hASCs. Inhibition of these kinases with specific small molecule inhibitors diminished osteogenesis, while inhibition of FAK and ROCK activity led to elevation of adipogenic marker genes AP2 and LEP and lipid accumulation implicating adipogenesis. This denotes to a switch-like function of FAK and ROCK signaling in the osteogenic and adipogenic fates of hASCs. On the contrary, inhibition of ERK1/2 kinase activity deceased adipogenic differentiation, indicating that activation of ERK signaling is required for both adipogenic and osteogenic potential. Our findings highlight the reciprocal role of cell adhesion mechanisms and actin dynamics in regulation of hASC lineage commitment. This study enhances the knowledge of molecular mechanisms dictating hASC differentiation and thus opens possibilities for more efficient control of hASC differentiation.", "doi": "10.1155/2018/2190657", "pmid": "30275837", "labels": {"Kimmo Kartasalo": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC6157106"}], "notes": [], "created": "2024-11-05T16:04:38.060Z", "modified": "2024-11-29T09:31:50.695Z"}, {"entity": "publication", "iuid": "26eb9a164a0c4b2f80d89fe2e0086e4d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/26eb9a164a0c4b2f80d89fe2e0086e4d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/26eb9a164a0c4b2f80d89fe2e0086e4d"}}, "title": "Comparative analysis of tissue reconstruction algorithms for 3D histology.", "authors": [{"family": "Kartasalo", "given": "Kimmo", "initials": "K"}, {"family": "Latonen", "given": "Leena", "initials": "L"}, {"family": "Vihinen", "given": "Jorma", "initials": "J"}, {"family": "Visakorpi", "given": "Tapio", "initials": "T"}, {"family": "Nykter", "given": "Matti", "initials": "M"}, {"family": "Ruusuvuori", "given": "Pekka", "initials": "P"}], "type": "comparative study", "published": "2018-09-01", "journal": {"title": "Bioinformatics", "issn": "1367-4811", "issn-l": "1367-4803", "volume": "34", "issue": "17", "pages": "3013-3021"}, "abstract": "Digital pathology enables new approaches that expand beyond storage, visualization or analysis of histological samples in digital format. One novel opportunity is 3D histology, where a three-dimensional reconstruction of the sample is formed computationally based on serial tissue sections. This allows examining tissue architecture in 3D, for example, for diagnostic purposes. Importantly, 3D histology enables joint mapping of cellular morphology with spatially resolved omics data in the true 3D context of the tissue at microscopic resolution. Several algorithms have been proposed for the reconstruction task, but a quantitative comparison of their accuracy is lacking.\r\n\r\nWe developed a benchmarking framework to evaluate the accuracy of several free and commercial 3D reconstruction methods using two whole slide image datasets. The results provide a solid basis for further development and application of 3D histology algorithms and indicate that methods capable of compensating for local tissue deformation are superior to simpler approaches.\r\n\r\nCode: https://github.com/BioimageInformaticsTampere/RegBenchmark. Whole slide image datasets: http://urn.fi/urn: nbn: fi: csc-kata20170705131652639702.\r\n\r\nSupplementary data are available at Bioinformatics online.", "doi": "10.1093/bioinformatics/bty210", "pmid": "29684099", "labels": {"Kimmo Kartasalo": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC6129300"}, {"db": "pii", "key": "4978049"}], "notes": [], "created": "2024-11-05T16:04:34.883Z", "modified": "2024-11-29T12:04:50.269Z"}, {"entity": "publication", "iuid": "2f07c62cc1f443868e9a6013aec27ba4", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/2f07c62cc1f443868e9a6013aec27ba4.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/2f07c62cc1f443868e9a6013aec27ba4"}}, "title": "Preparation of asymmetric phospholipid vesicles for use as cell membrane models.", "authors": [{"family": "Doktorova", "given": "Milka", "initials": "M", "orcid": "0000-0003-4366-2242", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/791384c319f04584bac8ffb21df7271f.json"}}, {"family": "Heberle", "given": "Frederick A", "initials": "FA", "orcid": "0000-0002-0424-3240", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2557f5621a0b4c87b5f4702fbc7b6bdb.json"}}, {"family": "Eicher", "given": "Barbara", "initials": "B"}, {"family": "Standaert", "given": "Robert F", "initials": "RF"}, {"family": "Katsaras", "given": "John", "initials": "J", "orcid": "0000-0002-0424-3240", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2557f5621a0b4c87b5f4702fbc7b6bdb.json"}}, {"family": "London", "given": "Erwin", "initials": "E", "orcid": "0000-0002-1295-0113", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/65792417577b43f48d05e1e00ee94415.json"}}, {"family": "Pabst", "given": "Georg", "initials": "G", "orcid": "0000-0003-1967-1536", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ec4ae71525c9411ea39715388b46afee.json"}}, {"family": "Marquardt", "given": "Drew", "initials": "D", "orcid": "0000-0001-6848-2497", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/114cdc1c929d46308422b3b587f8e1d6.json"}}], "type": "journal article", "published": "2018-09-00", "journal": {"title": "Nat Protoc", "issn": "1750-2799", "issn-l": null, "volume": "13", "issue": "9", "pages": "2086-2101"}, "abstract": "Freely suspended liposomes are widely used as model membranes for studying lipid-lipid and protein-lipid interactions. Liposomes prepared by conventional methods have chemically identical bilayer leaflets. By contrast, living cells actively maintain different lipid compositions in the two leaflets of the plasma membrane, resulting in asymmetric membrane properties that are critical for normal cell function. Here, we present a protocol for the preparation of unilamellar asymmetric phospholipid vesicles that better mimic biological membranes. Asymmetry is generated by methyl-\u03b2-cyclodextrin-catalyzed exchange of the outer leaflet lipids between vesicle pools of differing lipid composition. Lipid destined for the outer leaflet of the asymmetric vesicles is provided by heavy-donor multilamellar vesicles containing a dense sucrose core. Donor lipid is exchanged into extruded unilamellar acceptor vesicles that lack the sucrose core, facilitating the post-exchange separation of the donor and acceptor pools by centrifugation because of differences in vesicle size and density. We present two complementary assays allowing quantification of each leaflet's lipid composition: the overall lipid composition is determined by gas chromatography-mass spectrometry, whereas the lipid distribution between the two leaflets is determined by NMR, using the lanthanide shift reagent Pr3+. The preparation protocol and the chromatographic assay can be applied to any type of phospholipid bilayer, whereas the NMR assay is specific to lipids with choline-containing headgroups, such as phosphatidylcholine and sphingomyelin. In ~12 h, the protocol can produce a large yield of asymmetric vesicles (up to 20 mg) suitable for a wide range of biophysical studies.", "doi": "10.1038/s41596-018-0033-6", "pmid": "30190552", "labels": {"Milka Doktorova": null, "DDLS Fellow": null}, "xrefs": [{"db": "mid", "key": "EMS82425"}, {"db": "pmc", "key": "PMC6459367"}, {"db": "pii", "key": "10.1038/s41596-018-0033-6"}], "notes": [], "created": "2024-11-27T12:17:12.634Z", "modified": "2024-11-29T10:50:07.950Z"}, {"entity": "publication", "iuid": "e0a08bc4e8e642c2a51a7f6b8f229208", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e0a08bc4e8e642c2a51a7f6b8f229208.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e0a08bc4e8e642c2a51a7f6b8f229208"}}, "title": "Structure and function of the global topsoil microbiome.", "authors": [{"family": "Bahram", "given": "Mohammad", "initials": "M"}, {"family": "Hildebrand", "given": "Falk", "initials": "F"}, {"family": "Forslund", "given": "Sofia K", "initials": "SK"}, {"family": "Anderson", "given": "Jennifer L", "initials": "JL"}, {"family": "Soudzilovskaia", "given": "Nadejda A", "initials": "NA"}, {"family": "Bodegom", "given": "Peter M", "initials": "PM"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Anslan", "given": "Sten", "initials": "S"}, {"family": "Coelho", "given": "Luis Pedro", "initials": "LP"}, {"family": "Harend", "given": "Helery", "initials": "H"}, {"family": "Huerta-Cepas", "given": "Jaime", "initials": "J"}, {"family": "Medema", "given": "Marnix H", "initials": "MH"}, {"family": "Maltz", "given": "Mia R", "initials": "MR"}, {"family": "Mundra", "given": "Sunil", "initials": "S"}, {"family": "Olsson", "given": "P\u00e5l Axel", "initials": "PA"}, {"family": "Pent", "given": "Mari", "initials": "M"}, {"family": "P\u00f5lme", "given": "Sergei", "initials": "S"}, {"family": "Sunagawa", "given": "Shinichi", "initials": "S"}, {"family": "Ryberg", "given": "Martin", "initials": "M"}, {"family": "Tedersoo", "given": "Leho", "initials": "L"}, {"family": "Bork", "given": "Peer", "initials": "P"}], "type": "journal article", "published": "2018-08-00", "journal": {"title": "Nature", "issn": "1476-4687", "volume": "560", "issue": "7717", "pages": "233-237", "issn-l": "0028-0836"}, "abstract": "Soils harbour some of the most diverse microbiomes on Earth and are essential for both nutrient cycling and carbon storage. To understand soil functioning, it is necessary to model the global distribution patterns and functional gene repertoires of soil microorganisms, as well as the biotic and environmental associations between the diversity and structure of both bacterial and fungal soil communities1-4. Here we show, by leveraging metagenomics and metabarcoding of global topsoil samples (189 sites, 7,560 subsamples), that bacterial, but not fungal, genetic diversity is highest in temperate habitats and that microbial gene composition varies more strongly with environmental variables than with geographic distance. We demonstrate that fungi and bacteria show global niche differentiation that is associated with contrasting diversity responses to precipitation and soil pH. Furthermore, we provide evidence for strong bacterial-fungal antagonism, inferred from antibiotic-resistance genes, in topsoil and ocean habitats, indicating the substantial role of biotic interactions in shaping microbial communities. Our results suggest that both competition and environmental filtering affect the abundance, composition and encoded gene functions of bacterial and fungal communities, indicating that the relative contributions of these microorganisms to global nutrient cycling varies spatially.", "doi": "10.1038/s41586-018-0386-6", "pmid": "30069051", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pii", "key": "10.1038/s41586-018-0386-6"}], "notes": [], "created": "2022-11-08T09:28:28.202Z", "modified": "2022-11-08T09:28:28.227Z"}, {"entity": "publication", "iuid": "62234246e0d04161bcb6d0865f437d5d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/62234246e0d04161bcb6d0865f437d5d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/62234246e0d04161bcb6d0865f437d5d"}}, "title": "Publisher Correction: Structure of the chloroplast ribosome with chl-RRF and hibernation-promoting factor.", "authors": [{"family": "Perez Boerema", "given": "Annemarie", "initials": "A"}, {"family": "Aibara", "given": "Shintaro", "initials": "S"}, {"family": "Paul", "given": "Bijoya", "initials": "B"}, {"family": "Tobiasson", "given": "Victor", "initials": "V"}, {"family": "Kimanius", "given": "Dari", "initials": "D"}, {"family": "Forsberg", "given": "Bj\u00f6rn O", "initials": "BO"}, {"family": "Wallden", "given": "Karin", "initials": "K"}, {"family": "Lindahl", "given": "Erik", "initials": "E"}, {"family": "Amunts", "given": "A", "initials": "A", "orcid": "0000-0002-5302-1740", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6c79bee23e114906bc847dfbd0975139.json"}}], "type": "journal article", "published": "2018-08-00", "journal": {"title": "Nat Plants", "issn": "2055-0278", "volume": "4", "issue": "8", "pages": "615", "issn-l": "2055-0278"}, "abstract": "In the version of this Article originally published, the name of co-author Annemarie Perez Boerema was coded wrongly, resulting in it being incorrect when exported to citation databases. This has been corrected, though no visible changes will be apparent.", "doi": "10.1038/s41477-018-0203-0", "pmid": "30038411", "labels": {"SciLifeLab Fellow": "", "DDLS Fellow": "", "Alexey Amunts": "", "Bj\u00f6rn Forsberg": ""}, "xrefs": [{"db": "pii", "key": "10.1038/s41477-018-0203-0"}], "notes": [], "created": "2026-08-20T08:54:28.954Z", "modified": "2026-09-23T14:39:25.738Z"}, {"entity": "publication", "iuid": "402502cdb74f4693b60287484e4b2cf8", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/402502cdb74f4693b60287484e4b2cf8.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/402502cdb74f4693b60287484e4b2cf8"}}, "title": "DNA methylation as a genomic marker of exposure to chemical and environmental agents.", "authors": [{"family": "Meehan", "given": "Richard R", "initials": "RR"}, {"family": "Thomson", "given": "John P", "initials": "JP"}, {"family": "Lentini", "given": "Antonio", "initials": "A"}, {"family": "Nestor", "given": "Colm E", "initials": "CE"}, {"family": "Pennings", "given": "Sari", "initials": "S"}], "type": "journal article", "published": "2018-08-00", "journal": {"title": "Curr Opin Chem Biol", "issn": "1879-0402", "volume": "45", "pages": "48-56", "issn-l": "1367-5931"}, "abstract": "Recent progress in interpreting comprehensive genetic and epigenetic profiles for human cellular states has contributed new insights into the developmental origins of disease, elucidated novel signalling pathways and enhanced drug discovery programs. A similar comprehensive approach to decoding the epigenetic readouts from chemical challenges in vivo would yield new paradigms for monitoring and assessing environmental exposure in model systems and humans.", "doi": "10.1016/j.cbpa.2018.02.006", "pmid": "29505975", "labels": {"Antonio Lentini": null, "DDLS Fellow": null}, "xrefs": [{"db": "pii", "key": "S1367-5931(17)30206-5"}], "notes": [], "created": "2025-03-28T07:12:08.408Z", "modified": "2025-03-28T07:12:08.431Z"}, {"entity": "publication", "iuid": "e2897397a00a415bb58be6c6c8cd748f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e2897397a00a415bb58be6c6c8cd748f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e2897397a00a415bb58be6c6c8cd748f"}}, "title": "Critical knowledge gaps and research needs related to the environmental dimensions of antibiotic resistance.", "authors": [{"family": "Larsson", "given": "D G Joakim", "initials": "DGJ"}, {"family": "Andremont", "given": "Antoine", "initials": "A"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Brandt", "given": "Kristian Koefoed", "initials": "KK"}, {"family": "de Roda Husman", "given": "Ana Maria", "initials": "AM"}, {"family": "Fagerstedt", "given": "Patriq", "initials": "P"}, {"family": "Fick", "given": "Jerker", "initials": "J"}, {"family": "Flach", "given": "Carl-Fredrik", "initials": "CF"}, {"family": "Gaze", "given": "William H", "initials": "WH"}, {"family": "Kuroda", "given": "Makoto", "initials": "M"}, {"family": "Kvint", "given": "Kristian", "initials": "K"}, {"family": "Laxminarayan", "given": "Ramanan", "initials": "R"}, {"family": "Manaia", "given": "Celia M", "initials": "CM"}, {"family": "Nielsen", "given": "Kaare Magne", "initials": "KM"}, {"family": "Plant", "given": "Laura", "initials": "L"}, {"family": "Ploy", "given": "Marie-C\u00e9cile", "initials": "MC"}, {"family": "Segovia", "given": "Carlos", "initials": "C"}, {"family": "Simonet", "given": "Pascal", "initials": "P"}, {"family": "Smalla", "given": "Kornelia", "initials": "K"}, {"family": "Snape", "given": "Jason", "initials": "J"}, {"family": "Topp", "given": "Edward", "initials": "E"}, {"family": "van Hengel", "given": "Arjon J", "initials": "AJ"}, {"family": "Verner-Jeffreys", "given": "David W", "initials": "DW"}, {"family": "Virta", "given": "Marko P J", "initials": "MPJ"}, {"family": "Wellington", "given": "Elizabeth M", "initials": "EM"}, {"family": "Wernersson", "given": "Ann-Sofie", "initials": "AS"}], "type": "journal article", "published": "2018-08-00", "journal": {"title": "Environ Int", "issn": "1873-6750", "volume": "117", "pages": "132-138", "issn-l": "0160-4120"}, "abstract": "There is growing understanding that the environment plays an important role both in the transmission of antibiotic resistant pathogens and in their evolution. Accordingly, researchers and stakeholders world-wide seek to further explore the mechanisms and drivers involved, quantify risks and identify suitable interventions. There is a clear value in establishing research needs and coordinating efforts within and across nations in order to best tackle this global challenge. At an international workshop in late September 2017, scientists from 14 countries with expertise on the environmental dimensions of antibiotic resistance gathered to define critical knowledge gaps. Four key areas were identified where research is urgently needed: 1) the relative contributions of different sources of antibiotics and antibiotic resistant bacteria into the environment; 2) the role of the environment, and particularly anthropogenic inputs, in the evolution of resistance; 3) the overall human and animal health impacts caused by exposure to environmental resistant bacteria; and 4) the efficacy and feasibility of different technological, social, economic and behavioral interventions to mitigate environmental antibiotic resistance.1.", "doi": "10.1016/j.envint.2018.04.041", "pmid": "29747082", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pii", "key": "S0160-4120(18)30098-9"}], "notes": [], "created": "2022-11-08T09:28:48.727Z", "modified": "2022-11-08T09:28:48.751Z"}, {"entity": "publication", "iuid": "d7dfb2dc45294753ace4915621c9d0af", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d7dfb2dc45294753ace4915621c9d0af.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d7dfb2dc45294753ace4915621c9d0af"}}, "title": "BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea.", "authors": [{"family": "Alneberg", "given": "Johannes", "initials": "J"}, {"family": "Sundh", "given": "John", "initials": "J"}, {"family": "Bennke", "given": "Christin", "initials": "C"}, {"family": "Beier", "given": "Sara", "initials": "S"}, {"family": "Lundin", "given": "Daniel", "initials": "D"}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW"}, {"family": "Pinhassi", "given": "Jarone", "initials": "J", "orcid": "0000-0002-6405-1347", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/28b77762086343048e74046a6486caff.json"}}, {"family": "Kisand", "given": "Veljo", "initials": "V"}, {"family": "Riemann", "given": "Lasse", "initials": "L", "orcid": "0000-0001-9207-2543", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a666f6ec1a584756ab4c725b7ace3d3a.json"}}, {"family": "J\u00fcrgens", "given": "Klaus", "initials": "K"}, {"family": "Labrenz", "given": "Matthias", "initials": "M"}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cc9be99ec6ca47ed8a805ebb4db7c168.json"}}], "type": "dataset", "published": "2018-07-31", "journal": {"title": "Sci Data", "issn": "2052-4463", "volume": "5", "pages": "180146", "issn-l": "2052-4463"}, "abstract": "The Baltic Sea is one of the world's largest brackish water bodies and is characterised by pronounced physicochemical gradients where microbes are the main biogeochemical catalysts. Meta-omic methods provide rich information on the composition of, and activities within, microbial ecosystems, but are computationally heavy to perform. We here present the Baltic Sea Reference Metagenome (BARM), complete with annotated genes to facilitate further studies with much less computational effort. The assembly is constructed using 2.6 billion metagenomic reads from 81 water samples, spanning both spatial and temporal dimensions, and contains 6.8 million genes that have been annotated for function and taxonomy. The assembly is useful as a reference, facilitating taxonomic and functional annotation of additional samples by simply mapping their reads against the assembly. This capability is demonstrated by the successful mapping and annotation of 24 external samples. In addition, we present a public web interface, BalticMicrobeDB, for interactive exploratory analysis of the dataset.", "doi": "10.1038/sdata.2018.146", "pmid": "30063227", "labels": {"Luisa Hugerth": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC6067050"}, {"db": "pii", "key": "sdata2018146"}, {"db": "figshare", "key": "10.6084/m9.figshare.c.3831631"}], "notes": [], "created": "2022-11-08T07:01:14.252Z", "modified": "2026-09-23T13:42:02.745Z"}, {"entity": "publication", "iuid": "238538acd04446b193d8d700570d326f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/238538acd04446b193d8d700570d326f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/238538acd04446b193d8d700570d326f"}}, "title": "Metabolic Network-Based Identification and Prioritization of Anticancer Targets Based on Expression Data in Hepatocellular Carcinoma.", "authors": [{"family": "Bidkhori", "given": "Gholamreza", "initials": "G"}, {"family": "Benfeitas", "given": "Rui", "initials": "R"}, {"family": "Elmas", "given": "Ezgi", "initials": "E"}, {"family": "Kararoudi", "given": "Meisam Naeimi", "initials": "MN"}, {"family": "Arif", "given": "Muhammad", "initials": "M"}, {"family": "Uhlen", "given": "Mathias", "initials": "M"}, {"family": "Nielsen", "given": "Jens", "initials": "J"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}], "type": "journal article", "published": "2018-07-17", "journal": {"title": "Front. Physiol.", "issn": "1664-042X", "issn-l": "1664-042X", "volume": "9", "issue": null, "pages": "916"}, "abstract": "Hepatocellular carcinoma (HCC) is a deadly form of liver cancer with high mortality worldwide. Unfortunately, the large heterogeneity of this disease makes it difficult to develop effective treatment strategies. Cellular network analyses have been employed to study heterogeneity in cancer, and to identify potential therapeutic targets. However, the existing approaches do not consider metabolic growth requirements, i.e., biological network functionality, to rank candidate targets while preventing toxicity to non-cancerous tissues. Here, we developed an algorithm to overcome these issues based on integration of gene expression data, genome-scale metabolic models, network controllability, and dispensability, as well as toxicity analysis. This method thus predicts and ranks potential anticancer non-toxic controlling metabolite and gene targets. Our algorithm encompasses both objective-driven and-independent tasks, and uses network topology to finally rank the predicted therapeutic targets. We employed this algorithm to the analysis of transcriptomic data for 50 HCC patients with both cancerous and non-cancerous samples. We identified several potential targets that would prevent cell growth, including 74 anticancer metabolites, and 3 gene targets (PRKACA, PGS1, and CRLS1). The predicted anticancer metabolites showed good agreement with existing FDA-approved cancer drugs, and the 3 genes were experimentally validated by performing experiments in HepG2 and Hep3B liver cancer cell lines. Our observations indicate that our novel approach successfully identifies therapeutic targets for effective treatment of cancer. This approach may also be applied to any cancer type that has tumor and non-tumor gene or protein expression data.", "doi": "10.3389/fphys.2018.00916", "pmid": "30065658", "labels": {"Affiliated researcher": "", "Adil Mardinoglu": "", "SciLifeLab Fellow": "", "DDLS Fellow": "", "Muhammad Arif": ""}, "xrefs": [{"db": "pmc", "key": "PMC6056771"}], "notes": [], "created": "2019-01-17T13:55:20.897Z", "modified": "2026-09-23T09:31:30.250Z"}, {"entity": "publication", "iuid": "8c50144a05fe4c89a83415339102f038", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8c50144a05fe4c89a83415339102f038.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8c50144a05fe4c89a83415339102f038"}}, "title": "SECAPR-a bioinformatics pipeline for the rapid and user-friendly processing of targeted enriched Illumina sequences, from raw reads to alignments.", "authors": [{"family": "Andermann", "given": "Tobias", "initials": "T"}, {"family": "Cano", "given": "\u00c1ngela", "initials": "\u00c1"}, {"family": "Zizka", "given": "Alexander", "initials": "A"}, {"family": "Bacon", "given": "Christine", "initials": "C"}, {"family": "Antonelli", "given": "Alexandre", "initials": "A"}], "type": "journal article", "published": "2018-07-13", "journal": {"title": "PeerJ", "issn": "2167-8359", "volume": "6", "pages": "e5175", "issn-l": "2167-8359"}, "abstract": "Evolutionary biology has entered an era of unprecedented amounts of DNA sequence data, as new sequencing technologies such as Massive Parallel Sequencing (MPS) can generate billions of nucleotides within less than a day. The current bottleneck is how to efficiently handle, process, and analyze such large amounts of data in an automated and reproducible way. To tackle these challenges we introduce the Sequence Capture Processor (SECAPR) pipeline for processing raw sequencing data into multiple sequence alignments for downstream phylogenetic and phylogeographic analyses. SECAPR is user-friendly and we provide an exhaustive empirical data tutorial intended for users with no prior experience with analyzing MPS output. SECAPR is particularly useful for the processing of sequence capture (synonyms: target or hybrid enrichment) datasets for non-model organisms, as we demonstrate using an empirical sequence capture dataset of the palm genus Geonoma (Arecaceae). Various quality control and plotting functions help the user to decide on the most suitable settings for even challenging datasets. SECAPR is an easy-to-use, free, and versatile pipeline, aimed to enable efficient and reproducible processing of MPS data for many samples in parallel.", "doi": "10.7717/peerj.5175", "pmid": "30023140", "labels": {"Tobias Andermann": null, "DDLS Fellow": null}, "xrefs": [{"db": "pii", "key": "5175"}, {"db": "pmc", "key": "PMC6047508"}], "notes": [], "created": "2022-11-11T09:08:37.730Z", "modified": "2022-11-11T09:08:37.753Z"}, {"entity": "publication", "iuid": "60ac528c470a45b7bbd3760ebd37cd06", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/60ac528c470a45b7bbd3760ebd37cd06.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/60ac528c470a45b7bbd3760ebd37cd06"}}, "title": "The diversity of uncharacterized antibiotic resistance genes can be predicted from known gene variants-but not always.", "authors": [{"family": "Bengtsson-Palme", "given": "Johan", "initials": "J", "orcid": "0000-0002-6528-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c666068e9d34939b0252a627007cec7.json"}}], "type": "journal article", "published": "2018-07-07", "journal": {"title": "Microbiome", "issn": "2049-2618", "volume": "6", "issue": "1", "pages": "125", "issn-l": "2049-2618"}, "abstract": "Antibiotic resistance is considered one of the most urgent threats to modern healthcare, and the role of the environment in resistance development is increasingly recognized. It is often assumed that the abundance and diversity of known resistance genes are representative also for the non-characterized fraction of the resistome in a given environment, but this assumption has not been verified. In this study, this hypothesis is tested, using the resistance gene profiles of 1109 metagenomes from various environments.\n\nThis study shows that the diversity and abundance of known antibiotic resistance genes can generally predict the diversity and abundance of undescribed resistance genes. However, the extent of this predictability is dependent on the type of environment investigated. Furthermore, it is shown that carefully selected small sets of resistance genes can describe total resistance gene diversity remarkably well.\n\nThe results of this study suggest that knowledge gained from large-scale quantifications of known resistance genes can be utilized as a proxy for unknown resistance factors. This is important for current and proposed monitoring efforts for environmental antibiotic resistance and has implications for the design of risk ranking strategies and the choices of measures and methods for describing resistance gene abundance and diversity in the environment.", "doi": "10.1186/s40168-018-0508-2", "pmid": "29981578", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pii", "key": "10.1186/s40168-018-0508-2"}, {"db": "pmc", "key": "PMC6035801"}], "notes": [], "created": "2022-11-08T09:28:30.629Z", "modified": "2022-11-08T09:28:30.678Z"}, {"entity": "publication", "iuid": "4db2dbd5fb1444109d0c5d2374732bc3", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4db2dbd5fb1444109d0c5d2374732bc3.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4db2dbd5fb1444109d0c5d2374732bc3"}}, "title": "Selective concentration for ciprofloxacin resistance in Escherichia coli grown in complex aquatic bacterial biofilms.", "authors": [{"family": "Kraupner", "given": "Nadine", "initials": "N"}, {"family": "Ebmeyer", "given": "Stefan", "initials": "S"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Fick", "given": "Jerker", "initials": "J"}, {"family": "Kristiansson", "given": "Erik", "initials": "E"}, {"family": "Flach", "given": "Carl-Fredrik", "initials": "CF"}, {"family": "Larsson", "given": "D G Joakim", "initials": "DGJ"}], "type": "journal article", "published": "2018-07-00", "journal": {"title": "Environ Int", "issn": "1873-6750", "volume": "116", "pages": "255-268", "issn-l": "0160-4120"}, "abstract": "There is concern that antibiotics in the environment can select for and enrich bacteria carrying acquired antibiotic resistance genes, thus increasing the potential of those genes to emerge in a clinical context. A critical question for understanding and managing such risks is what levels of antibiotics are needed to select for resistance in complex bacterial communities. Here, we address this question by examining the phenotypic and genotypic profiles of aquatic communities exposed to ciprofloxacin, also evaluating the within-species selection of resistant E. coli in complex communities. The taxonomic composition was significantly altered at ciprofloxacin exposure concentrations down to 1 \u03bcg/L. Shotgun metagenomic analysis indicated that mobile quinolone resistance determinants (qnrD, qnrS and qnrB) were enriched as a direct consequence of ciprofloxacin exposure from 1 \u03bcg/L or higher. Only at 5-10 \u03bcg/L resistant E.coli increased relative to their sensitive counterparts. These resistant E. coli predominantly harbored non-transferrable, chromosomal triple mutations (gyrA S83 L, D87N and parC S80I), which confer high-level resistance. In a controlled experimental setup such as this, we interpret effects on taxonomic composition and enrichment of mobile quinolone resistance genes as relevant indicators of risk. Hence, the lowest observed effect concentration for resistance selection in complex communities by ciprofloxacin was 1 \u03bcg/L and the corresponding no observed effect concentration 0.1 \u03bcg/L. These findings can be used to define and implement discharge or surface water limits to reduce risks for selection of antibiotic resistance in the environment.", "doi": "10.1016/j.envint.2018.04.029", "pmid": "29704804", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pii", "key": "S0160-4120(18)30080-1"}], "notes": [], "created": "2022-11-08T09:28:53.631Z", "modified": "2022-11-08T09:28:53.657Z"}, {"entity": "publication", "iuid": "330d27dd418540418ade2ded8f31f2ef", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/330d27dd418540418ade2ded8f31f2ef.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/330d27dd418540418ade2ded8f31f2ef"}}, "title": "A reassessment of DNA-immunoprecipitation-based genomic profiling.", "authors": [{"family": "Lentini", "given": "Antonio", "initials": "A", "orcid": "0000-0003-1239-5495", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c5042d3005814ad0a2d1eaeee5d2de3b.json"}}, {"family": "Lagerwall", "given": "Cathrine", "initials": "C"}, {"family": "Vikingsson", "given": "Svante", "initials": "S"}, {"family": "Mjoseng", "given": "Heidi K", "initials": "HK"}, {"family": "Douvlataniotis", "given": "Karolos", "initials": "K", "orcid": "0000-0002-5511-2232", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b82c735ba61d4862b373683f1210ce19.json"}}, {"family": "Vogt", "given": "Hartmut", "initials": "H"}, {"family": "Green", "given": "Henrik", "initials": "H"}, {"family": "Meehan", "given": "Richard R", "initials": "RR", "orcid": "0000-0001-6471-6882", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/833674ddef544afbad1f7ad70456e0e7.json"}}, {"family": "Benson", "given": "Mikael", "initials": "M"}, {"family": "Nestor", "given": "Colm E", "initials": "CE", "orcid": "0000-0001-5853-1769", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/53da1d2e5d714a368bcb61c4001abd0f.json"}}], "type": "journal article", "published": "2018-07-00", "journal": {"title": "Nat. Methods", "issn": "1548-7105", "volume": "15", "issue": "7", "pages": "499-504", "issn-l": "1548-7091"}, "abstract": "DNA immunoprecipitation followed by sequencing (DIP-seq) is a common enrichment method for profiling DNA modifications in mammalian genomes. However, the results of independent DIP-seq studies often show considerable variation between profiles of the same genome and between profiles obtained by alternative methods. Here we show that these differences are primarily due to the intrinsic affinity of IgG for short unmodified DNA repeats. This pervasive experimental error accounts for 50-99% of regions identified as 'enriched' for DNA modifications in DIP-seq data. Correction of this error profoundly altered DNA-modification profiles for numerous cell types, including mouse embryonic stem cells, and subsequently revealed novel associations among DNA modifications, chromatin modifications and biological processes. We conclude that both matched input and IgG controls are essential in order for the results of DIP-based assays to be interpreted correctly, and that complementary, non-antibody-based techniques should be used to validate DIP-based findings to avoid further misinterpretation of genome-wide profiling data.", "doi": "10.1038/s41592-018-0038-7", "pmid": "29941872", "labels": {"Antonio Lentini": null, "DDLS Fellow": null}, "xrefs": [{"db": "mid", "key": "EMS83565"}, {"db": "pmc", "key": "PMC6625966"}, {"db": "pii", "key": "10.1038/s41592-018-0038-7"}], "notes": [], "created": "2025-03-28T07:14:42.349Z", "modified": "2025-03-28T07:14:42.427Z"}, {"entity": "publication", "iuid": "e8b81de513944c37a2a8e2335fa7d9b7", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e8b81de513944c37a2a8e2335fa7d9b7.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e8b81de513944c37a2a8e2335fa7d9b7"}}, "title": "A reference cytochrome c oxidase subunit I database curated for hierarchical classification of arthropod metabarcoding data", "authors": [{"family": "Richardson", "given": "Rodney T", "initials": "RT", "orcid": "0000-0002-4443-1705", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c82db3acb0b241caa1cbeea98d6ced09.json"}}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J", "orcid": "0000-0002-6528-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c666068e9d34939b0252a627007cec7.json"}}, {"family": "Gardiner", "given": "Mary M", "initials": "MM"}, {"family": "Johnson", "given": "Reed M", "initials": "RM"}], "type": "journal-article", "published": "2018-06-26", "journal": {"title": "PeerJ", "issn": "2167-8359", "volume": "6", "pages": "e5126", "issn-l": "2167-8359"}, "abstract": "Metabarcoding is a popular application which warrants continued methods optimization. To maximize barcoding inferences, hierarchy-based sequence classification methods are increasingly common. We present methods for the construction and curation of a database designed for hierarchical classification of a 157 bp barcoding region of the arthropod cytochrome c oxidase subunit I (COI) locus. We produced a comprehensive arthropod COI amplicon dataset including annotated arthropod COI sequences and COI sequences extracted from arthropod whole mitochondrion genomes, the latter of which provided the only source of representation for Zoraptera, Callipodida and Holothyrida. The database contains extracted sequences of the target amplicon from all major arthropod clades, including all insect orders, all arthropod classes and Onychophora, Tardigrada and Mollusca outgroups. During curation, we extracted the COI region of interest from approximately 81 percent of the input sequences, corresponding to 73 percent of the genus-level diversity found in the input data. Further, our analysis revealed a high degree of sequence redundancy within the NCBI nucleotide database, with a mean of approximately 11 sequence entries per species in the input data. The curated, low-redundancy database is included in the Metaxa2 sequence classification software (http://microbiology.se/software/metaxa2/). Using this database with the Metaxa2 classifier, we performed a cross-validation analysis to characterize the relationship between the Metaxa2 reliability score, an estimate of classification confidence, and classification error probability. We used this analysis to select a reliability score threshold which minimized error. We then estimated classification sensitivity, false discovery rate and overclassification, the propensity to classify sequences from taxa not represented in the reference database. Our work will help researchers design and evaluate classification databases and conduct metabarcoding on arthropods and alternate taxa.", "doi": "10.7717/peerj.5126", "pmid": "29967752", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pii", "key": "5126"}, {"db": "pmc", "key": "PMC6025149"}], "notes": [], "created": "2022-11-08T09:28:44.221Z", "modified": "2022-11-16T11:34:04.084Z"}, {"entity": "publication", "iuid": "d53bdab822d54bb2bb935f9f851a398c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d53bdab822d54bb2bb935f9f851a398c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d53bdab822d54bb2bb935f9f851a398c"}}, "title": "Global time trends in the incidence of esophageal squamous cell carcinoma.", "authors": [{"family": "Wang", "given": "Qiao-Li", "initials": "QL"}, {"family": "Xie", "given": "Shao-Hua", "initials": "SH"}, {"family": "Wahlin", "given": "Karl", "initials": "K"}, {"family": "Lagergren", "given": "Jesper", "initials": "J"}], "type": "journal article", "published": "2018-06-19", "journal": {"title": "Clin Epidemiol", "issn": "1179-1349", "volume": "10", "pages": "717-728", "issn-l": "1179-1349"}, "abstract": "Esophageal squamous cell carcinoma (ESCC) is the dominant histological type of esophageal cancer worldwide (90%). We aimed to provide an update of the global temporal trends in the incidence of ESCC.\n\nIncidence data for ESCC were collected from 30 well-established cancer registries from 20 countries in Europe, Northern America, Australia, or Asia for 1970-2015. Time trends in annual age-standardized incidence rates of ESCC were assessed using joinpoint analysis and log-linear regression. Age-period-cohort analysis was used to estimate the influence of age, calendar-period, and birth-cohort on the observed time trends in incidence.\n\nThe age-standardized incidence rates of ESCC varied more than eightfold in men and sevenfold in women across populations. In 2012, the highest rate of ESCC in men was observed in Nagasaki, Japan (9.7/100,000 person-years) and in women in Scotland (2.7/100,000 person-years). In men, the incidence decreased globally during the study period, as well as during the last few years. In women, the incidence increased in Japan (three regions), the Netherlands, New Zealand, Norway, and Switzerland, whereas it stabilized or decreased in other populations. Among ethnic groups in the United States, black men and women had more pronounced decreases in incidence than other groups. Generally, birth-cohort effects were stronger determinants of incidence trends than calendar-period effects.\n\nIn men, the global ESCC incidence has decreased over time. In women, the incidence trends vary across populations, and the rates have increased in some countries. Changes in the prevalence of tobacco smoking and alcohol consumption may have contributed to these time trends.", "doi": "10.2147/CLEP.S166078", "pmid": "29950901", "labels": {"DDLS Fellow": null, "Qiaoli Wang": null}, "xrefs": [{"db": "pmc", "key": "PMC6016013"}, {"db": "pii", "key": "clep-10-717"}], "notes": [], "created": "2025-11-27T18:45:16.282Z", "modified": "2025-11-27T18:45:16.297Z"}, {"entity": "publication", "iuid": "fbac514e63244e01a9b3cfe502e173fe", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/fbac514e63244e01a9b3cfe502e173fe.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/fbac514e63244e01a9b3cfe502e173fe"}}, "title": "An expanded allosteric network in PTP1B by multitemperature crystallography, fragment screening, and covalent tethering.", "authors": [{"family": "Keedy", "given": "Daniel A", "initials": "DA", "orcid": "0000-0002-9184-7586", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7fd571647a0e4ba9a85a1d339765f0c4.json"}}, {"family": "Hill", "given": "Zachary B", "initials": "ZB"}, {"family": "Biel", "given": "Justin T", "initials": "JT", "orcid": "0000-0002-0935-8362", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/884e784334ee4e67b1a985f90ef32821.json"}}, {"family": "Kang", "given": "Emily", "initials": "E"}, {"family": "Rettenmaier", "given": "T Justin", "initials": "TJ"}, {"family": "Brand\u00e3o-Neto", "given": "Jos\u00e9", "initials": "J", "orcid": "0000-0001-6015-320X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8692b60d7100483fa2fe0ecdc908f77b.json"}}, {"family": "Pearce", "given": "Nicholas M", "initials": "NM", "orcid": "0000-0002-6693-8603", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/07d6d5de91cc4120b2bf996ca578a13e.json"}}, {"family": "von Delft", "given": "Frank", "initials": "F", "orcid": "0000-0003-0378-0017", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/51e35baa89fe49ada5a9dcbc2c2e1e20.json"}}, {"family": "Wells", "given": "James A", "initials": "JA", "orcid": "0000-0001-8267-5519", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f0c1fc2f2b584824bd489884424e333c.json"}}, {"family": "Fraser", "given": "James S", "initials": "JS", "orcid": "0000-0002-5080-2859", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c95b7a3dcf1545ff87da0c64abdd0f68.json"}}], "type": "journal article", "published": "2018-06-07", "journal": {"title": "Elife", "issn": "2050-084X", "volume": "7", "issn-l": "2050-084X"}, "abstract": "Allostery is an inherent feature of proteins, but it remains challenging to reveal the mechanisms by which allosteric signals propagate. A clearer understanding of this intrinsic circuitry would afford new opportunities to modulate protein function. Here, we have identified allosteric sites in protein tyrosine phosphatase 1B (PTP1B) by combining multiple-temperature X-ray crystallography experiments and structure determination from hundreds of individual small-molecule fragment soaks. New modeling approaches reveal 'hidden' low-occupancy conformational states for protein and ligands. Our results converge on allosteric sites that are conformationally coupled to the active-site WPD loop and are hotspots for fragment binding. Targeting one of these sites with covalently tethered molecules or mutations allosterically inhibits enzyme activity. Overall, this work demonstrates how the ensemble nature of macromolecular structure, revealed here by multitemperature crystallography, can elucidate allosteric mechanisms and open new doors for long-range control of protein function.", "doi": "10.7554/eLife.36307", "pmid": "29877794", "labels": {"Nicholas Pearce": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC6039181"}, {"db": "pii", "key": "36307"}], "notes": [], "created": "2022-12-05T18:57:35.912Z", "modified": "2022-12-05T18:57:36.084Z"}, {"entity": "publication", "iuid": "d152e4bd8f164fdfac57ab4d6199fd13", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d152e4bd8f164fdfac57ab4d6199fd13.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d152e4bd8f164fdfac57ab4d6199fd13"}}, "title": "Metabolite Depletion Affects Flux Profiling of Cell Lines.", "authors": [{"family": "Nilsson", "given": "A", "initials": "A", "orcid": "0000-0002-9476-4516", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f2e21dbc1c624f6a841c59e959e948e4.json"}}, {"family": "Haanstra", "given": "J R", "initials": "JR", "orcid": "0000-0001-9652-0219", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3bf355cfa5a040d180c267a9a917552f.json"}}, {"family": "Teusink", "given": "B", "initials": "B", "orcid": "0000-0003-3929-0423", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/68e4ce6dd53d40428d44d8490060b6a6.json"}}, {"family": "Nielsen", "given": "J", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/33f2b49a39ed4e54ba77dfe397ed3087.json"}}], "type": "journal article", "published": "2018-06-00", "journal": {"title": "Trends Biochem. Sci.", "issn": "0968-0004", "issn-l": null, "volume": "43", "issue": "6", "pages": "395-397"}, "abstract": "Quantifying the rate of consumption and release of metabolites (i.e., flux profiling) has become integral to the study of cancer. The fluxes as well as the growth of the cells may be affected by metabolite depletion during cultivation.", "doi": "10.1016/j.tibs.2018.03.009", "pmid": "29656822", "labels": {"Avlant Nilsson": null, "DDLS Fellow": null}, "xrefs": [{"db": "pii", "key": "S0968-0004(18)30063-X"}], "notes": [], "created": "2025-03-20T11:09:45.269Z", "modified": "2025-03-21T13:17:37.372Z"}, {"entity": "publication", "iuid": "741564be6ba84d349d61110cbfafd9bd", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/741564be6ba84d349d61110cbfafd9bd.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/741564be6ba84d349d61110cbfafd9bd"}}, "title": "A Protein Standard That Emulates Homology for the Characterization of Protein Inference Algorithms.", "authors": [{"family": "The", "given": "Matthew", "initials": "M", "orcid": "0000-0002-5401-5553", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9d8d7d850ed24f92b9506b203ca63ed1.json"}}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e213b04f8984c8eb00c68f5bc2f6a36.json"}}, {"family": "Perez-Riverol", "given": "Yasset", "initials": "Y", "orcid": "0000-0001-6579-6941", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cb4449bad29741b195a7593fc39a769d.json"}}, {"family": "Payne", "given": "Samuel H", "initials": "SH", "orcid": "0000-0002-8351-1994", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fe701ec4cf24456980c1902ec61a0ab1.json"}}, {"family": "Hoopmann", "given": "Michael R", "initials": "MR", "orcid": "0000-0001-7029-7792", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/04f75056428f499d9806d2fd85d50e9a.json"}}, {"family": "Palmblad", "given": "Magnus", "initials": "M", "orcid": "0000-0002-5865-8994", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/80053e2256cd4e55afc7ba916821602c.json"}}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0002-5248-8568", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a6982072448e4e8889c71fc14d214fed.json"}}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L", "orcid": "0000-0001-5689-9797", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4464f2bf868498fa6d149a4a6d60e8b.json"}}], "type": "journal article", "published": "2018-05-04", "journal": {"title": "J. Proteome Res.", "issn": "1535-3907", "volume": "17", "issue": "5", "pages": "1879-1886", "issn-l": "1535-3893"}, "abstract": "A natural way to benchmark the performance of an analytical experimental setup is to use samples of known composition and see to what degree one can correctly infer the content of such a sample from the data. For shotgun proteomics, one of the inherent problems of interpreting data is that the measured analytes are peptides and not the actual proteins themselves. As some proteins share proteolytic peptides, there might be more than one possible causative set of proteins resulting in a given set of peptides and there is a need for mechanisms that infer proteins from lists of detected peptides. A weakness of commercially available samples of known content is that they consist of proteins that are deliberately selected for producing tryptic peptides that are unique to a single protein. Unfortunately, such samples do not expose any complications in protein inference. Hence, for a realistic benchmark of protein inference procedures, there is a need for samples of known content where the present proteins share peptides with known absent proteins. Here, we present such a standard, that is based on E. coli expressed human protein fragments. To illustrate the application of this standard, we benchmark a set of different protein inference procedures on the data. We observe that inference procedures excluding shared peptides provide more accurate estimates of errors compared to methods that include information from shared peptides, while still giving a reasonable performance in terms of the number of identified proteins. We also demonstrate that using a sample of known protein content without proteins with shared tryptic peptides can give a false sense of accuracy for many protein inference methods.", "doi": "10.1021/acs.jproteome.7b00899", "pmid": "29631402", "labels": {"Fredrik Edfors": "", "DDLS Fellow": ""}, "xrefs": [{"db": "mid", "key": "NIHMS1016465"}, {"db": "pmc", "key": "PMC6474350"}], "notes": [], "created": "2018-12-05T12:41:06.410Z", "modified": "2026-09-23T10:32:00.062Z"}, {"entity": "publication", "iuid": "2a03c2be4c3d4d59a30f26a1891010fe", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/2a03c2be4c3d4d59a30f26a1891010fe.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/2a03c2be4c3d4d59a30f26a1891010fe"}}, "title": "Substrate-bound outward-open structure of a Na+-coupled sialic acid symporter reveals a new Na+ site.", "authors": [{"family": "Wahlgren", "given": "Weixiao Y", "initials": "WY"}, {"family": "Dunevall", "given": "Elin", "initials": "E", "orcid": "0000-0002-9781-200X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1355fba8090e4c67b266cd4350c8adf8.json"}}, {"family": "North", "given": "Rachel A", "initials": "RA"}, {"family": "Paz", "given": "Aviv", "initials": "A"}, {"family": "Scalise", "given": "Mariafrancesca", "initials": "M"}, {"family": "Bisignano", "given": "Paola", "initials": "P", "orcid": "0000-0003-1789-762X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8d5cb57214c84d7bb8eaf55fa3804985.json"}}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J", "orcid": "0000-0002-6528-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c666068e9d34939b0252a627007cec7.json"}}, {"family": "Goyal", "given": "Parveen", "initials": "P"}, {"family": "Claesson", "given": "Elin", "initials": "E"}, {"family": "Caing-Carlsson", "given": "Rhawnie", "initials": "R", "orcid": "0000-0002-8530-856X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3b2850ccc240424db40253b08bf24701.json"}}, {"family": "Andersson", "given": "Rebecka", "initials": "R"}, {"family": "Beis", "given": "Konstantinos", "initials": "K", "orcid": "0000-0001-5727-4721", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ee8b1ddc19e74747810405886609cd26.json"}}, {"family": "Nilsson", "given": "Ulf J", "initials": "UJ", "orcid": "0000-0001-5815-9522", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e867c9a9f4004f35bb1685ecfa6a671e.json"}}, {"family": "Farewell", "given": "Anne", "initials": "A"}, {"family": "Pochini", "given": "Lorena", "initials": "L"}, {"family": "Indiveri", "given": "Cesare", "initials": "C"}, {"family": "Grabe", "given": "Michael", "initials": "M"}, {"family": "Dobson", "given": "Renwick C J", "initials": "RCJ"}, {"family": "Abramson", "given": "Jeff", "initials": "J"}, {"family": "Ramaswamy", "given": "S", "initials": "S"}, {"family": "Friemann", "given": "Rosmarie", "initials": "R", "orcid": "0000-0002-5633-2894", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2c62276885624e95b672a625a8121b51.json"}}], "type": "journal article", "published": "2018-05-01", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "9", "issue": "1", "pages": "1753", "issn-l": "2041-1723"}, "abstract": "Many pathogenic bacteria utilise sialic acids as an energy source or use them as an external coating to evade immune detection. As such, bacteria that colonise sialylated environments deploy specific transporters to mediate import of scavenged sialic acids. Here, we report a substrate-bound 1.95 \u00c5 resolution structure and subsequent characterisation of SiaT, a sialic acid transporter from Proteus mirabilis. SiaT is a secondary active transporter of the sodium solute symporter (SSS) family, which use Na+ gradients to drive the uptake of extracellular substrates. SiaT adopts the LeuT-fold and is in an outward-open conformation in complex with the sialic acid N-acetylneuraminic acid and two Na+ ions. One Na+ binds to the conserved Na2 site, while the second Na+ binds to a new position, termed Na3, which is conserved in many SSS family members. Functional and molecular dynamics studies validate the substrate-binding site and demonstrate that both Na+ sites regulate N-acetylneuraminic acid transport.", "doi": "10.1038/s41467-018-04045-7", "pmid": "29717135", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-018-04045-7"}, {"db": "pmc", "key": "PMC5931594"}], "notes": [], "created": "2022-11-08T09:28:51.143Z", "modified": "2022-11-08T09:28:51.425Z"}, {"entity": "publication", "iuid": "8826ab998feb4ae1961c8c63ee398ce1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8826ab998feb4ae1961c8c63ee398ce1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8826ab998feb4ae1961c8c63ee398ce1"}}, "title": "Estimating Age-Dependent Extinction: Contrasting Evidence from Fossils and Phylogenies.", "authors": [{"family": "Hagen", "given": "Oskar", "initials": "O"}, {"family": "Andermann", "given": "Tobias", "initials": "T"}, {"family": "Quental", "given": "Tiago B", "initials": "TB"}, {"family": "Antonelli", "given": "Alexandre", "initials": "A"}, {"family": "Silvestro", "given": "Daniele", "initials": "D"}], "type": "journal article", "published": "2018-05-01", "journal": {"title": "Syst. Biol.", "issn": "1076-836X", "volume": "67", "issue": "3", "pages": "458-474", "issn-l": "1063-5157"}, "abstract": "The estimation of diversification rates is one of the most vividly debated topics in modern systematics, with considerable controversy surrounding the power of phylogenetic and fossil-based approaches in estimating extinction. Van Valen's seminal work from 1973 proposed the \"Law of constant extinction,\" which states that the probability of extinction of taxa is not dependent on their age. This assumption of age-independent extinction has prevailed for decades with its assessment based on survivorship curves, which, however, do not directly account for the incompleteness of the fossil record, and have rarely been applied at the species level. Here, we present a Bayesian framework to estimate extinction rates from the fossil record accounting for age-dependent extinction (ADE). Our approach, unlike previous implementations, explicitly models unobserved species and accounts for the effects of fossil preservation on the observed longevity of sampled lineages. We assess the performance and robustness of our method through extensive simulations and apply it to a fossil data set of terrestrial Carnivora spanning the past 40 myr. We find strong evidence of ADE, as we detect the extinction rate to be highest in young species and declining with increasing species age. For comparison, we apply a recently developed analogous ADE model to a dated phylogeny of extant Carnivora. Although the phylogeny-based analysis also infers ADE, it indicates that the extinction rate, instead, increases with increasing taxon age. The estimated mean species longevity also differs substantially, with the fossil-based analyses estimating 2.0 myr, in contrast to 9.8 myr derived from the phylogeny-based inference. Scrutinizing these discrepancies, we find that both fossil and phylogeny-based ADE models are prone to high error rates when speciation and extinction rates increase or decrease through time. However, analyses of simulated and empirical data show that fossil-based inferences are more robust. This study shows that an accurate estimation of ADE from incomplete fossil data is possible when the effects of preservation are jointly modeled, thus allowing for a reassessment of Van Valen's model as a general rule in macroevolution.", "doi": "10.1093/sysbio/syx082", "pmid": "29069434", "labels": {"Tobias Andermann": null, "DDLS Fellow": null}, "xrefs": [{"db": "pii", "key": "4563320"}, {"db": "pmc", "key": "PMC5920349"}, {"db": "Dryad", "key": "10.5061/dryad.r5f70"}], "notes": [], "created": "2022-11-11T09:10:49.491Z", "modified": "2022-11-11T09:10:49.522Z"}, {"entity": "publication", "iuid": "93077511f3ff417c971fdc21f47f3f6b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/93077511f3ff417c971fdc21f47f3f6b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/93077511f3ff417c971fdc21f47f3f6b"}}, "title": "Introducing ribosomal tandem repeat barcoding for fungi", "authors": [{"family": "Wurzbacher", "given": "Christian", "initials": "C", "orcid": "0000-0001-7418-0831", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a8303415592c4c46b9fcf27904aec4fa.json"}}, {"family": "Larsson", "given": "Ellen", "initials": "E"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J", "orcid": "0000-0002-6528-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c666068e9d34939b0252a627007cec7.json"}}, {"family": "den Wyngaert", "given": "Silke Van", "initials": "SV"}, {"family": "Svantesson", "given": "Sten", "initials": "S"}, {"family": "Kristiansson", "given": "Erik", "initials": "E", "orcid": "0000-0002-8609-2414", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/18d5538c8c0749199a6f1b51d15eec69.json"}}, {"family": "Kagami", "given": "Maiko", "initials": "M", "orcid": "0000-0003-3086-390X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5feee43ae01d4a7187cba6126e24cf65.json"}}, {"family": "Henrik Nilsson", "given": "R", "initials": "R"}], "type": "posted-content", "published": "2018-04-28", "journal": {"title": "bioRxiv preprint", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/310540", "pmid": null, "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [], "notes": [], "created": "2022-11-08T09:31:24.051Z", "modified": "2025-12-04T17:02:22.119Z"}, {"entity": "publication", "iuid": "1f3b363ef193467690a01579a4ff3b49", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1f3b363ef193467690a01579a4ff3b49.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1f3b363ef193467690a01579a4ff3b49"}}, "title": "The multiple myeloma risk allele at 5q15 lowers ELL2 expression and increases ribosomal gene expression.", "authors": [{"family": "Ali", "given": "Mina", "initials": "M"}, {"family": "Ajore", "given": "Ram", "initials": "R"}, {"family": "Wihlborg", "given": "Anna-Karin", "initials": "AK"}, {"family": "Niroula", "given": "Abhishek", "initials": "A", "orcid": "0000-0002-5904-0635", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/05df7afc7a494ba5af8a378e5ffa53f0.json"}}, {"family": "Swaminathan", "given": "Bhairavi", "initials": "B"}, {"family": "Johnsson", "given": "Ellinor", "initials": "E"}, {"family": "Stephens", "given": "Owen W", "initials": "OW"}, {"family": "Morgan", "given": "Gareth", "initials": "G"}, {"family": "Meissner", "given": "Tobias", "initials": "T"}, {"family": "Turesson", "given": "Ingemar", "initials": "I"}, {"family": "Goldschmidt", "given": "Hartmut", "initials": "H"}, {"family": "Mellqvist", "given": "Ulf-Henrik", "initials": "UH"}, {"family": "Gullberg", "given": "Urban", "initials": "U"}, {"family": "Hansson", "given": "Markus", "initials": "M", "orcid": "0000-0002-7715-4548", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9aabef8e26ba40d9abd8e229d954795d.json"}}, {"family": "Hemminki", "given": "Kari", "initials": "K"}, {"family": "Nahi", "given": "Hareth", "initials": "H"}, {"family": "Waage", "given": "Anders", "initials": "A"}, {"family": "Weinhold", "given": "Niels", "initials": "N"}, {"family": "Nilsson", "given": "Bj\u00f6rn", "initials": "B"}], "type": "journal article", "published": "2018-04-25", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "9", "issue": "1", "pages": "1649", "issn-l": "2041-1723"}, "abstract": "Recently, we identified ELL2 as a susceptibility gene for multiple myeloma (MM). To understand its mechanism of action, we performed expression quantitative trait locus analysis in CD138+ plasma cells from 1630 MM patients from four populations. We show that the MM risk allele lowers ELL2 expression in these cells (Pcombined = 2.5 \u00d7 10-27; \u03b2combined = -0.24 SD), but not in peripheral blood or other tissues. Consistent with this, several variants representing the MM risk allele map to regulatory genomic regions, and three yield reduced transcriptional activity in plasmocytoma cell lines. One of these (rs3777189-C) co-locates with the best-supported lead variants for ELL2 expression and MM risk, and reduces binding of MAFF/G/K family transcription factors. Moreover, further analysis reveals that the MM risk allele associates with upregulation of gene sets related to ribosome biogenesis, and knockout/knockdown and rescue experiments in plasmocytoma cell lines support a cause-effect relationship. Our results provide mechanistic insight into MM predisposition.", "doi": "10.1038/s41467-018-04082-2", "pmid": "29695719", "labels": {"Abhishek Niroula": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC5917026"}, {"db": "pii", "key": "10.1038/s41467-018-04082-2"}], "notes": [], "created": "2023-11-20T11:21:43.002Z", "modified": "2023-11-20T11:21:43.218Z"}, {"entity": "publication", "iuid": "b40b2019bf28426aa3186ecf1506150b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b40b2019bf28426aa3186ecf1506150b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b40b2019bf28426aa3186ecf1506150b"}}, "title": "The challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing technologies.", "authors": [{"family": "Angers-Loustau", "given": "Alexandre", "initials": "A", "orcid": "0000-0003-1425-4143", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d5d3dc0d500f4a72a45e2688c3c62582.json"}}, {"family": "Petrillo", "given": "Mauro", "initials": "M", "orcid": "0000-0002-6782-4704", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ee3cb672d7584081ae0ca267e6da6526.json"}}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J", "orcid": "0000-0002-6528-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c666068e9d34939b0252a627007cec7.json"}}, {"family": "Berendonk", "given": "Thomas", "initials": "T"}, {"family": "Blais", "given": "Burton", "initials": "B"}, {"family": "Chan", "given": "Kok-Gan", "initials": "KG", "orcid": "0000-0002-1883-1115", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/440e1455ad55403287a36e98ca7d59b8.json"}}, {"family": "Coque", "given": "Teresa M", "initials": "TM"}, {"family": "Hammer", "given": "Paul", "initials": "P"}, {"family": "He\u00df", "given": "Stefanie", "initials": "S", "orcid": "0000-0002-9293-4622", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/054fe98a937b4e8787c84df52b7c7a76.json"}}, {"family": "Kagkli", "given": "Dafni M", "initials": "DM"}, {"family": "Krumbiegel", "given": "Carsten", "initials": "C"}, {"family": "Lanza", "given": "Val F", "initials": "VF"}, {"family": "Madec", "given": "Jean-Yves", "initials": "JY"}, {"family": "Naas", "given": "Thierry", "initials": "T"}, {"family": "O'Grady", "given": "Justin", "initials": "J"}, {"family": "Paracchini", "given": "Valentina", "initials": "V"}, {"family": "Rossen", "given": "John W A", "initials": "JWA", "orcid": "0000-0002-7167-8623", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e94f9b8f85ab46909633011e11e9e670.json"}}, {"family": "Rupp\u00e9", "given": "Etienne", "initials": "E"}, {"family": "Vamathevan", "given": "Jessica", "initials": "J", "orcid": "0000-0003-2016-9754", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2e8ec4f83b434e4381804d969ee69b6e.json"}}, {"family": "Venturi", "given": "Vittorio", "initials": "V"}, {"family": "Van den Eede", "given": "Guy", "initials": "G"}], "type": "journal article", "published": "2018-04-13", "journal": {"title": "F1000Res", "issn": "2046-1402", "volume": "7", "pages": "459", "issn-l": "2046-1402"}, "abstract": "Next-Generation Sequencing (NGS) technologies are expected to play a crucial role in the surveillance of infectious diseases, with their unprecedented capabilities for the characterisation of genetic information underlying the virulence and antimicrobial resistance (AMR) properties of microorganisms. In the implementation of any novel technology for regulatory purposes, important considerations such as harmonisation, validation and quality assurance need to be addressed. NGS technologies pose unique challenges in these regards, in part due to their reliance on bioinformatics for the processing and proper interpretation of the data produced. Well-designed benchmark resources are thus needed to evaluate, validate and ensure continued quality control over the bioinformatics component of the process. This concept was explored as part of a workshop on \"Next-generation sequencing technologies and antimicrobial resistance\" held October 4-5 2017. Challenges involved in the development of such a benchmark resource, with a specific focus on identifying the molecular determinants of AMR, were identified. For each of the challenges, sets of unsolved questions that will need to be tackled for them to be properly addressed were compiled. These take into consideration the requirement for monitoring of AMR bacteria in humans, animals, food and the environment, which is aligned with the principles of a \"One Health\" approach.", "doi": "10.12688/f1000research.14509.2", "pmid": "30026930", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pmc", "key": "PMC6039958"}, {"db": "pii", "key": "ISCB Comm J-459"}], "notes": [], "created": "2022-11-08T09:28:18.460Z", "modified": "2023-06-19T13:59:25.251Z"}, {"entity": "publication", "iuid": "f1230a53d9da48bfa961fd15f738177c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f1230a53d9da48bfa961fd15f738177c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f1230a53d9da48bfa961fd15f738177c"}}, "title": "Structure of the chloroplast ribosome with chl-RRF and hibernation-promoting factor.", "authors": [{"family": "Perez Boerema", "given": "Annemarie", "initials": "A"}, {"family": "Aibara", "given": "Shintaro", "initials": "S"}, {"family": "Paul", "given": "Bijoya", "initials": "B"}, {"family": "Tobiasson", "given": "Victor", "initials": "V"}, {"family": "Kimanius", "given": "Dari", "initials": "D"}, {"family": "Forsberg", "given": "Bj\u00f6rn O", "initials": "BO"}, {"family": "Wallden", "given": "Karin", "initials": "K"}, {"family": "Lindahl", "given": "Erik", "initials": "E"}, {"family": "Amunts", "given": "A", "initials": "A", "orcid": "0000-0002-5302-1740", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6c79bee23e114906bc847dfbd0975139.json"}}], "type": "journal article", "published": "2018-04-00", "journal": {"title": "Nat Plants", "issn": "2055-0278", "issn-l": "2055-0278", "volume": "4", "issue": "4", "pages": "212-217"}, "abstract": "Oxygenic photosynthesis produces oxygen and builds a variety of organic compounds, changing the chemistry of the air, the sea and fuelling the food chain on our planet. The photochemical reactions underpinning this process in plants take place in the chloroplast. Chloroplasts evolved ~1.2 billion years ago from an engulfed primordial diazotrophic cyanobacterium, and chlororibosomes are responsible for synthesis of the core proteins driving photochemical reactions. Chlororibosomal activity is spatiotemporally coupled to the synthesis and incorporation of functionally essential co-factors, implying the presence of chloroplast-specific regulatory mechanisms and structural adaptation of the chlororibosome1,2. Despite recent structural information3-6, some of these aspects remained elusive. To provide new insights into the structural specialities and evolution, we report a comprehensive analysis of the 2.9-3.1 \u00c5 resolution electron cryo-microscopy structure of the spinach chlororibosome in complex with its recycling factor and hibernation-promoting factor. The model reveals a prominent channel extending from the exit tunnel to the chlororibosome exterior, structural re-arrangements that lead to increased surface area for translocon binding, and experimental evidence for parallel and convergent evolution of chloro- and mitoribosomes.", "doi": "10.1038/s41477-018-0129-6", "pmid": "29610536", "labels": {"Affiliated researcher": "", "Alexey Amunts": "", "SciLifeLab Fellow": "", "DDLS Fellow": "", "Bj\u00f6rn Forsberg": ""}, "xrefs": [{"db": "pii", "key": "10.1038/s41477-018-0129-6"}], "notes": [], "created": "2018-12-05T12:22:11.946Z", "modified": "2026-09-23T07:48:44.543Z"}, {"entity": "publication", "iuid": "3212e0a605d845f2989db0c187452bc0", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3212e0a605d845f2989db0c187452bc0.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3212e0a605d845f2989db0c187452bc0"}}, "title": "PON-tstab: Protein Variant Stability Predictor. Importance of Training Data Quality.", "authors": [{"family": "Yang", "given": "Yang", "initials": "Y"}, {"family": "Urolagin", "given": "Siddhaling", "initials": "S"}, {"family": "Niroula", "given": "Abhishek", "initials": "A"}, {"family": "Ding", "given": "Xuesong", "initials": "X"}, {"family": "Shen", "given": "Bairong", "initials": "B"}, {"family": "Vihinen", "given": "Mauno", "initials": "M", "orcid": "0000-0002-9614-7976", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d39c85536a524a2cab1eca8304d37181.json"}}], "type": "journal article", "published": "2018-03-28", "journal": {"title": "Int J Mol Sci", "issn": "1422-0067", "volume": "19", "issue": "4", "issn-l": null}, "abstract": "Several methods have been developed to predict effects of amino acid substitutions on protein stability. Benchmark datasets are essential for method training and testing and have numerous requirements including that the data is representative for the investigated phenomenon. Available machine learning algorithms for variant stability have all been trained with ProTherm data. We noticed a number of issues with the contents, quality and relevance of the database. There were errors, but also features that had not been clearly communicated. Consequently, all machine learning variant stability predictors have been trained on biased and incorrect data. We obtained a corrected dataset and trained a random forests-based tool, PON-tstab, applicable to variants in any organism. Our results highlight the importance of the benchmark quality, suitability and appropriateness. Predictions are provided for three categories: stability decreasing, increasing and those not affecting stability.", "doi": "10.3390/ijms19041009", "pmid": "29597263", "labels": {"Abhishek Niroula": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC5979465"}, {"db": "pii", "key": "ijms19041009"}], "notes": [], "created": "2023-11-20T11:21:40.394Z", "modified": "2023-11-20T11:21:40.565Z"}, {"entity": "publication", "iuid": "df609e686bc04cbdb9ab9ae70a886049", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/df609e686bc04cbdb9ab9ae70a886049.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/df609e686bc04cbdb9ab9ae70a886049"}}, "title": "A comprehensive automated pipeline for human microbiome sampling, 16S rRNA gene sequencing and bioinformatics processing", "authors": [{"family": "Hugerth", "given": "LW", "initials": "L", "orcid": "0000-0001-5432-1764", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/246ed7b405dd4c3f9ec5e7ff9f1d3ade.json"}}, {"family": "Seifert", "given": "M", "initials": "M"}, {"family": "Pennhag", "given": "AAL", "initials": "A"}, {"family": "Du", "given": "J", "initials": "J"}, {"family": "Hamsten", "given": "MC", "initials": "M"}, {"family": "Schuppe-Koistinen", "given": "I", "initials": "I", "orcid": "0000-0002-4742-448X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6dac4f7100004bdda67980875909478d.json"}}, {"family": "Engstrand", "given": "L", "initials": "L", "orcid": "0000-0002-7713-2373", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02d8684df81e42169e613de803446fbf.json"}}], "type": "posted-content", "published": "2018-03-21", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/286526", "pmid": null, "labels": {"DDLS Fellow": "", "Luisa Hugerth": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T11:09:52.115Z", "modified": "2026-09-23T13:42:48.284Z"}, {"entity": "publication", "iuid": "1c415b98149c497a95e0c101be84c863", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1c415b98149c497a95e0c101be84c863.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1c415b98149c497a95e0c101be84c863"}}, "title": "Host-derived population genomics data provides insights into bacterial and diatom composition of the killer whale skin", "authors": [{"family": "Hooper", "given": "Rebecca", "initials": "R"}, {"family": "Brealey", "given": "Jaelle C", "initials": "JC"}, {"family": "van der Valk", "given": "Tom", "initials": "T", "orcid": "0000-0001-6582-3452", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/aa0dba3cc12143cba213f7f3a052216c.json"}}, {"family": "Alberdi", "given": "Antton", "initials": "A"}, {"family": "Durban", "given": "John W", "initials": "JW"}, {"family": "Fearnbach", "given": "Holly", "initials": "H"}, {"family": "Robertson", "given": "Kelly M", "initials": "KM"}, {"family": "Baird", "given": "Robin W", "initials": "RW"}, {"family": "Hanson", "given": "M Bradley", "initials": "MB"}, {"family": "Wade", "given": "Paul", "initials": "P"}, {"family": "Thomas", "given": "M", "initials": "M"}, {"family": "Gilbert", "given": "P", "initials": "P"}, {"family": "Morin", "given": "Phillip A", "initials": "PA"}, {"family": "Wolf", "given": "Jochen B W", "initials": "JBW", "orcid": "0000-0002-2958-5183", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d1004f304db34314a61ca1fa0ee028b2.json"}}, {"family": "Foote", "given": "Andrew D", "initials": "AD"}, {"family": "Guschanski", "given": "Katerina", "initials": "K", "orcid": "0000-0002-8493-5457", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4e062373c6bc46b98e56215d3ec89eeb.json"}}], "type": "posted-content", "published": "2018-03-14", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/282038", "pmid": null, "labels": {"DDLS Fellow": "", "Tom van der Valk": ""}, "xrefs": [], "notes": [], "created": "2026-10-01T08:31:10.556Z", "modified": "2026-10-01T08:31:10.592Z"}, {"entity": "publication", "iuid": "ab2c4bdaf8e947f3a6d6aa3e2b078b9f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ab2c4bdaf8e947f3a6d6aa3e2b078b9f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ab2c4bdaf8e947f3a6d6aa3e2b078b9f"}}, "title": "Targeting CDK2 overcomes melanoma resistance against BRAF and Hsp90 inhibitors.", "authors": [{"family": "Azimi", "given": "Alireza", "initials": "A"}, {"family": "Caramuta", "given": "Stefano", "initials": "S"}, {"family": "Seashore-Ludlow", "given": "Brinton", "initials": "B"}, {"family": "Bostr\u00f6m", "given": "Johan", "initials": "J", "orcid": "0000-0001-5252-4023", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6e6b3b2450f0498f9d0be4d9af615e89.json"}}, {"family": "Robinson", "given": "Jonathan L", "initials": "JL"}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Tuominen", "given": "Rainer", "initials": "R"}, {"family": "Kemper", "given": "Kristel", "initials": "K"}, {"family": "Krijgsman", "given": "Oscar", "initials": "O", "orcid": "0000-0003-0825-3291", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cec664f6fc7f43c8a31035b29b58d29f.json"}}, {"family": "Peeper", "given": "Daniel S", "initials": "DS", "orcid": "0000-0003-1293-3177", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bcbcd40701b546fbb9a343ecaca928b3.json"}}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/33f2b49a39ed4e54ba77dfe397ed3087.json"}}, {"family": "Hansson", "given": "Johan", "initials": "J"}, {"family": "Egyhazi Brage", "given": "Suzanne", "initials": "S"}, {"family": "Altun", "given": "Mikael", "initials": "M", "orcid": "0000-0002-6937-6124", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d77b74fe6e7d44f4800fe8bb4404ad8f.json"}}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ea446aa574042a295d5f69437402f76.json"}}, {"family": "Maddalo", "given": "Gianluca", "initials": "G", "orcid": "0000-0003-2297-6488", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3fbe53488c7848c582122063ecad8e2b.json"}}], "type": "journal article", "published": "2018-03-05", "journal": {"title": "Mol Syst Biol", "issn": "1744-4292", "volume": "14", "issue": "3", "pages": "e7858", "issn-l": "1744-4292"}, "abstract": "Novel therapies are undergoing clinical trials, for example, the Hsp90 inhibitor, XL888, in combination with BRAF inhibitors for the treatment of therapy-resistant melanomas. Unfortunately, our data show that this combination elicits a heterogeneous response in a panel of melanoma cell lines including PDX-derived models. We sought to understand the mechanisms underlying the differential responses and suggest a patient stratification strategy. Thermal proteome profiling (TPP) identified the protein targets of XL888 in a pair of sensitive and unresponsive cell lines. Unbiased proteomics and phosphoproteomics analyses identified CDK2 as a driver of resistance to both BRAF and Hsp90 inhibitors and its expression is regulated by the transcription factor MITF upon XL888 treatment. The CDK2 inhibitor, dinaciclib, attenuated resistance to both classes of inhibitors and combinations thereof. Notably, we found that MITF expression correlates with CDK2 upregulation in patients; thus, dinaciclib would warrant consideration for treatment of patients unresponsive to BRAF-MEK and/or Hsp90 inhibitors and/or harboring MITF amplification/overexpression.", "doi": "10.15252/msb.20177858", "pmid": "29507054", "labels": {"Fredrik Edfors": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC5836539"}], "notes": [], "created": "2018-12-05T12:44:14.490Z", "modified": "2026-09-23T09:15:19.735Z"}, {"entity": "publication", "iuid": "ab66e18f57f8433ab18944aad96feabe", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ab66e18f57f8433ab18944aad96feabe.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ab66e18f57f8433ab18944aad96feabe"}}, "title": "Recon3D enables a three-dimensional view of gene variation in human metabolism.", "authors": [{"family": "Brunk", "given": "Elizabeth", "initials": "E", "orcid": "0000-0001-8578-8658", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f2f4ccbbc0a44a928c52fe9b0a4b272f.json"}}, {"family": "Sahoo", "given": "Swagatika", "initials": "S"}, {"family": "Zielinski", "given": "Daniel C", "initials": "DC"}, {"family": "Altunkaya", "given": "Ali", "initials": "A", "orcid": "0000-0002-0430-6715", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6b07813fc65a4eb8872e41b17f576f6e.json"}}, {"family": "Dr\u00e4ger", "given": "Andreas", "initials": "A", "orcid": "0000-0002-1240-5553", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/abdb1c71e95f451ab6f9cfbaba479769.json"}}, {"family": "Mih", "given": "Nathan", "initials": "N"}, {"family": "Gatto", "given": "Francesco", "initials": "F", "orcid": "0000-0002-9031-9562", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c6245aca43db4408b4617e781a34c0f9.json"}}, {"family": "Nilsson", "given": "Avlant", "initials": "A", "orcid": "0000-0002-9476-4516", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f2e21dbc1c624f6a841c59e959e948e4.json"}}, {"family": "Preciat Gonzalez", "given": "German Andres", "initials": "GA", "orcid": "0000-0003-4903-9515", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1c4ad33f19df469ab788d5e6cbe2fefc.json"}}, {"family": "Aurich", "given": "Maike Kathrin", "initials": "MK"}, {"family": "Prli\u0107", "given": "Andreas", "initials": "A"}, {"family": "Sastry", "given": "Anand", "initials": "A"}, {"family": "Danielsdottir", "given": "Anna D", "initials": "AD"}, {"family": "Heinken", "given": "Almut", "initials": "A"}, {"family": "Noronha", "given": "Alberto", "initials": "A"}, {"family": "Rose", "given": "Peter W", "initials": "PW"}, {"family": "Burley", "given": "Stephen K", "initials": "SK"}, {"family": "Fleming", "given": "Ronan M T", "initials": "RMT", "orcid": "0000-0001-5346-9812", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/96874bc1f1ba4cd19be4400037f1e191.json"}}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/33f2b49a39ed4e54ba77dfe397ed3087.json"}}, {"family": "Thiele", "given": "Ines", "initials": "I", "orcid": "0000-0002-8071-7110", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/da328416c189424fa633a30c43893b04.json"}}, {"family": "Palsson", "given": "Bernhard O", "initials": "BO", "orcid": "0000-0003-2357-6785", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fd602b497a2f48f39452f55f1fc28ac9.json"}}], "type": "journal article", "published": "2018-03-00", "journal": {"title": "Nat. Biotechnol.", "issn": "1546-1696", "issn-l": "1087-0156", "volume": "36", "issue": "3", "pages": "272-281"}, "abstract": "Genome-scale network reconstructions have helped uncover the molecular basis of metabolism. Here we present Recon3D, a computational resource that includes three-dimensional (3D) metabolite and protein structure data and enables integrated analyses of metabolic functions in humans. We use Recon3D to functionally characterize mutations associated with disease, and identify metabolic response signatures that are caused by exposure to certain drugs. Recon3D represents the most comprehensive human metabolic network model to date, accounting for 3,288 open reading frames (representing 17% of functionally annotated human genes), 13,543 metabolic reactions involving 4,140 unique metabolites, and 12,890 protein structures. These data provide a unique resource for investigating molecular mechanisms of human metabolism. Recon3D is available at http://vmh.life.", "doi": "10.1038/nbt.4072", "pmid": "29457794", "labels": {"Avlant Nilsson": null, "DDLS Fellow": null}, "xrefs": [{"db": "mid", "key": "NIHMS934074"}, {"db": "pmc", "key": "PMC5840010"}, {"db": "pii", "key": "nbt.4072"}], "notes": [], "created": "2025-03-20T11:09:47.269Z", "modified": "2025-03-21T13:17:48.747Z"}, {"entity": "publication", "iuid": "7865d0ae7f704fbba6ee25c516e9ef25", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/7865d0ae7f704fbba6ee25c516e9ef25.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/7865d0ae7f704fbba6ee25c516e9ef25"}}, "title": "Protection goals must guide risk assessment for antibiotics.", "authors": [{"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Larsson", "given": "D G Joakim", "initials": "DGJ"}], "type": "letter", "published": "2018-02-00", "journal": {"title": "Environ Int", "issn": "1873-6750", "volume": "111", "pages": "352-353", "issn-l": "0160-4120"}, "abstract": null, "doi": "10.1016/j.envint.2017.10.019", "pmid": "29097053", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pii", "key": "S0160-4120(17)31844-5"}], "notes": [], "created": "2022-11-08T09:30:38.013Z", "modified": "2022-11-08T09:30:38.035Z"}, {"entity": "publication", "iuid": "f4ef3556e5f847eea33a5e6076be2afa", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f4ef3556e5f847eea33a5e6076be2afa.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f4ef3556e5f847eea33a5e6076be2afa"}}, "title": "Impacts of feeding preweaned calves milk containing drug residues on the functional profile of the fecal microbiota.", "authors": [{"family": "Pereira", "given": "Richard Van Vleck", "initials": "RVV", "orcid": "0000-0003-2028-8761", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/259babf68c9e4d738c0a088d0ea27c0d.json"}}, {"family": "Carroll", "given": "Laura M", "initials": "LM"}, {"family": "Lima", "given": "Svetlana", "initials": "S"}, {"family": "Foditsch", "given": "Carla", "initials": "C"}, {"family": "Siler", "given": "Julie D", "initials": "JD"}, {"family": "Bicalho", "given": "Rodrigo Carvalho", "initials": "RC"}, {"family": "Warnick", "given": "Lorin D", "initials": "LD"}], "type": "journal article", "published": "2018-01-11", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "8", "issue": "1", "pages": "554", "issn-l": "2045-2322"}, "abstract": "Feeding drug residue-containing milk to calves is common worldwide and no information is currently available on the impact on the functional profile of the fecal microbiota. Our objective was to characterize the functional profile of the fecal microbiota of preweaned dairy calves fed raw milk with residual concentrations of antimicrobials commonly found in waste milk from birth to weaning. Calves were assigned to a controlled feeding trial being fed milk with no drug residues or milk with antibiotic residues. Fecal samples collected from each calf once a week starting at birth, prior to the first feeding in the trial, until 6 weeks of age. Antibiotic residues resulted in a significant difference in relative abundance of microbial cell functions, especially with genes linked with stress response, regulation and cell signaling, and nitrogen metabolism. These changes could directly impacts selection and dissemination of virulence and antimicrobial. Our data also identified a strong association between age in weeks and abundance of Resistance to Antibiotics and Toxic Compounds. Findings from this study support the hypothesis that drug residues, even at very low concentrations, impact the gut microbiota of calves and result in changes in the functional profile of microbial populations.", "doi": "10.1038/s41598-017-19021-2", "pmid": "29323259", "labels": {"Laura Carroll": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC5764986"}, {"db": "pii", "key": "10.1038/s41598-017-19021-2"}], "notes": [], "created": "2025-03-18T17:21:44.239Z", "modified": "2025-03-18T17:22:28.532Z"}, {"entity": "publication", "iuid": "6514a583e1c647dd8869971e52a8281c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/6514a583e1c647dd8869971e52a8281c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/6514a583e1c647dd8869971e52a8281c"}}, "title": "Taxonomic annotation of public fungal ITS sequences from the built environment - a report from an April 10-11, 2017 workshop (Aberdeen, UK).", "authors": [{"family": "Nilsson", "given": "R Henrik", "initials": "RH"}, {"family": "Taylor", "given": "Andy F S", "initials": "AFS"}, {"family": "Adams", "given": "Rachel I", "initials": "RI"}, {"family": "Baschien", "given": "Christiane", "initials": "C"}, {"family": "Cangren", "given": "Patrik", "initials": "P"}, {"family": "Coleine", "given": "Claudia", "initials": "C"}, {"family": "Glassman", "given": "Sydney I", "initials": "SI"}, {"family": "Hirooka", "given": "Yuuri", "initials": "Y"}, {"family": "Irinyi", "given": "Laszlo", "initials": "L"}, {"family": "Meyer", "given": "Wieland", "initials": "W"}, {"family": "Seifert", "given": "Keith A", "initials": "KA"}, {"family": "Sklen\u00e1\u0159", "given": "Frantisek", "initials": "F"}, {"family": "Suh", "given": "Sung-Oui", "initials": "SO"}, {"family": "Summerbell", "given": "Richard", "initials": "R"}, {"family": "Svantesson", "given": "Sten", "initials": "S"}, {"family": "Weiss", "given": "Michael", "initials": "M"}, {"family": "Woudenberg", "given": "Joyce Hc", "initials": "JH"}, {"family": "den Wyngaert", "given": "Silke Van", "initials": "SV"}, {"family": "Yilmaz", "given": "Neriman", "initials": "N"}, {"family": "K\u00f5ljalg", "given": "Urmas", "initials": "U"}, {"family": "Abarenkov", "given": "Kessy", "initials": "K"}], "type": "journal article", "published": "2018-01-08", "journal": {"title": "MycoKeys", "issn": "1314-4057", "issue": "28", "pages": "65-82", "issn-l": null}, "abstract": "Recent DNA-based studies have shown that the built environment is surprisingly rich in fungi. These indoor fungi - whether transient visitors or more persistent residents - may hold clues to the rising levels of human allergies and other medical and building-related health problems observed globally. The taxonomic identity of these fungi is crucial in such pursuits. Molecular identification of the built mycobiome is no trivial undertaking, however, given the large number of unidentified, misidentified, and technically compromised fungal sequences in public sequence databases. In addition, the sequence metadata required to make informed taxonomic decisions - such as country and host/substrate of collection - are often lacking even from reference and ex-type sequences. Here we report on a taxonomic annotation workshop (April 10-11, 2017) organized at the James Hutton Institute/University of Aberdeen (UK) to facilitate reproducible studies of the built mycobiome. The 32 participants went through public fungal ITS barcode sequences related to the built mycobiome for taxonomic and nomenclatural correctness, technical quality, and metadata availability. A total of 19,508 changes - including 4,783 name changes, 14,121 metadata annotations, and the removal of 99 technically compromised sequences - were implemented in the UNITE database for molecular identification of fungi (https://unite.ut.ee/) and shared with a range of other databases and downstream resources. Among the genera that saw the largest number of changes were Penicillium, Talaromyces, Cladosporium, Acremonium, and Alternaria, all of them of significant importance in both culture-based and culture-independent surveys of the built environment.", "doi": "10.3897/mycokeys.28.20887", "pmid": "29559822", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pmc", "key": "PMC5804120"}], "notes": [], "created": "2022-11-08T09:28:56.059Z", "modified": "2022-11-08T09:28:56.105Z"}, {"entity": "publication", "iuid": "be4ba12fc09e4e498fa9b24607327c08", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/be4ba12fc09e4e498fa9b24607327c08.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/be4ba12fc09e4e498fa9b24607327c08"}}, "title": "TCSBN: a database of tissue and cancer specific biological networks.", "authors": [{"family": "Lee", "given": "Sunjae", "initials": "S"}, {"family": "Zhang", "given": "Cheng", "initials": "C"}, {"family": "Arif", "given": "Muhammad", "initials": "M"}, {"family": "Liu", "given": "Zhengtao", "initials": "Z"}, {"family": "Benfeitas", "given": "Rui", "initials": "R"}, {"family": "Bidkhori", "given": "Gholamreza", "initials": "G"}, {"family": "Deshmukh", "given": "Sumit", "initials": "S"}, {"family": "Al Shobky", "given": "Mohamed", "initials": "M"}, {"family": "Lovric", "given": "Alen", "initials": "A"}, {"family": "Boren", "given": "Jan", "initials": "J"}, {"family": "Nielsen", "given": "Jens", "initials": "J"}, {"family": "Uhlen", "given": "Mathias", "initials": "M"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}], "type": "journal article", "published": "2018-01-04", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "issn-l": "0305-1048", "volume": "46", "issue": "D1", "pages": "D595-D600"}, "abstract": "Biological networks provide new opportunities for understanding the cellular biology in both health and disease states. We generated tissue specific integrated networks (INs) for liver, muscle and adipose tissues by integrating metabolic, regulatory and protein-protein interaction networks. We also generated human co-expression networks (CNs) for 46 normal tissues and 17 cancers to explore the functional relationships between genes as well as their relationships with biological functions, and investigate the overlap between functional and physical interactions provided by CNs and INs, respectively. These networks can be employed in the analysis of omics data, provide detailed insight into disease mechanisms by identifying the key biological components and eventually can be used in the development of efficient treatment strategies. Moreover, comparative analysis of the networks may allow for the identification of tissue-specific targets that can be used in the development of drugs with the minimum toxic effect to other human tissues. These context-specific INs and CNs are presented in an interactive website http://inetmodels.com without any limitation.", "doi": "10.1093/nar/gkx994", "pmid": "29069445", "labels": {"Affiliated researcher": "", "Adil Mardinoglu": "", "SciLifeLab Fellow": "", "DDLS Fellow": "", "Muhammad Arif": ""}, "xrefs": [{"db": "pmc", "key": "PMC5753183"}, {"db": "pii", "key": "4563312"}], "notes": [], "created": "2018-12-03T14:44:14.889Z", "modified": "2026-09-23T09:18:43.523Z"}, {"entity": "publication", "iuid": "4fab96c2c4624044b4419d7bc2502863", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4fab96c2c4624044b4419d7bc2502863.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4fab96c2c4624044b4419d7bc2502863"}}, "title": "Environmental factors influencing the development and spread of antibiotic resistance.", "authors": [{"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Kristiansson", "given": "Erik", "initials": "E"}, {"family": "Larsson", "given": "D G Joakim", "initials": "DGJ"}], "type": "journal article", "published": "2018-01-01", "journal": {"title": "FEMS Microbiol Rev", "issn": "1574-6976", "volume": "42", "issue": "1", "issn-l": null}, "abstract": "Antibiotic resistance and its wider implications present us with a growing healthcare crisis. Recent research points to the environment as an important component for the transmission of resistant bacteria and in the emergence of resistant pathogens. However, a deeper understanding of the evolutionary and ecological processes that lead to clinical appearance of resistance genes is still lacking, as is knowledge of environmental dispersal barriers. This calls for better models of how resistance genes evolve, are mobilized, transferred and disseminated in the environment. Here, we attempt to define the ecological and evolutionary environmental factors that contribute to resistance development and transmission. Although mobilization of resistance genes likely occurs continuously, the great majority of such genetic events do not lead to the establishment of novel resistance factors in bacterial populations, unless there is a selection pressure for maintaining them or their fitness costs are negligible. To enable preventative measures it is therefore critical to investigate under what conditions and to what extent environmental selection for resistance takes place. In addition, understanding dispersal barriers is not only key to evaluate risks, but also to prevent resistant pathogens, as well as novel resistance genes, from reaching humans.", "doi": "10.1093/femsre/fux053", "pmid": "29069382", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pii", "key": "4563583"}, {"db": "pmc", "key": "PMC5812547"}], "notes": [], "created": "2022-11-08T09:29:00.786Z", "modified": "2022-11-08T09:29:00.810Z"}, {"entity": "publication", "iuid": "1cda564baaa54443b948773ec8cb5a30", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1cda564baaa54443b948773ec8cb5a30.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1cda564baaa54443b948773ec8cb5a30"}}, "title": "Can branding and price of pharmaceuticals guide informed choices towards improved pollution control during manufacturing?", "authors": [{"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Gunnarsson", "given": "Lina", "initials": "L"}, {"family": "Larsson", "given": "D G Joakim", "initials": "DGJ"}], "type": "journal-article", "published": "2018-01-00", "journal": {"title": "Journal of Cleaner Production", "issn": "0959-6526", "volume": "171", "pages": "137-146", "issn-l": null}, "abstract": null, "doi": "10.1016/j.jclepro.2017.09.247", "pmid": null, "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [], "notes": [], "created": "2022-11-08T09:29:05.177Z", "modified": "2022-11-08T09:29:05.225Z"}, {"entity": "publication", "iuid": "9292dc92a9844c4c90b94d8e0827972b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9292dc92a9844c4c90b94d8e0827972b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9292dc92a9844c4c90b94d8e0827972b"}}, "title": "Strategies for Taxonomic and Functional Annotation of Metagenomes", "authors": [{"family": "Bengtsson-Palme", "given": "Johan", "initials": "J", "orcid": "0000-0002-6528-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c666068e9d34939b0252a627007cec7.json"}}], "type": "book-chapter", "published": "2018-00-00", "journal": {"title": "Metagenomics: Perspectives, Methods, and Applications", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": "55-79"}, "abstract": null, "doi": "10.1016/b978-0-08-102268-9.00003-3", "pmid": null, "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [], "notes": [], "created": "2022-11-08T09:31:47.635Z", "modified": "2025-12-04T19:43:45.606Z"}, {"entity": "publication", "iuid": "f86978282116465a8ef9b30eb9ba1db9", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f86978282116465a8ef9b30eb9ba1db9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f86978282116465a8ef9b30eb9ba1db9"}}, "title": "Network Analysis Reveals Heterogeneous Response of Redox Metabolism in Hepatocellular Carcinoma Patients", "authors": [{"family": "Benfeitas", "given": "Rui", "initials": "R"}, {"family": "Bidkhori", "given": "Gholamreza", "initials": "G"}, {"family": "Mukhopadhyay", "given": "Bani", "initials": "B"}, {"family": "Klevstig", "given": "Martina", "initials": "M"}, {"family": "Arif", "given": "Muhammad", "initials": "M"}, {"family": "Zhang", "given": "Cheng", "initials": "C"}, {"family": "Lee", "given": "Sunjae", "initials": "S"}, {"family": "Cinar", "given": "Resat", "initials": "R"}, {"family": "Nielsen", "given": "Jens", "initials": "J"}, {"family": "Uhlen", "given": "Mathias", "initials": "M"}, {"family": "Boren", "given": "Jan", "initials": "J"}, {"family": "Kunos", "given": "George", "initials": "G"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}], "type": "journal-article", "published": "2018-00-00", "journal": {"title": "SSRN Journal", "issn": "1556-5068", "issn-l": null}, "abstract": null, "doi": "10.2139/ssrn.3215903", "pmid": null, "labels": {"SciLifeLab Fellow": "", "DDLS Fellow": "", "Adil Mardinoglu": "", "Muhammad Arif": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T13:00:22.881Z", "modified": "2026-09-23T15:06:21.270Z"}, {"entity": "publication", "iuid": "d90e8d5ac14a4580872688e5ccee81c1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d90e8d5ac14a4580872688e5ccee81c1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d90e8d5ac14a4580872688e5ccee81c1"}}, "title": "Metabolic Models of Protein Allocation Call for the Kinetome.", "authors": [{"family": "Nilsson", "given": "Avlant", "initials": "A", "orcid": "0000-0002-9476-4516", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f2e21dbc1c624f6a841c59e959e948e4.json"}}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/33f2b49a39ed4e54ba77dfe397ed3087.json"}}, {"family": "Palsson", "given": "Bernhard O", "initials": "BO", "orcid": "0000-0003-2357-6785", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fd602b497a2f48f39452f55f1fc28ac9.json"}}], "type": "journal article", "published": "2017-12-27", "journal": {"title": "Cell Systems", "issn": "2405-4712", "issn-l": null, "volume": "5", "issue": "6", "pages": "538-541"}, "abstract": "The flux of metabolites in the living cell depend on enzyme activities. Recently, many metabolic phenotypes have been explained by computer models that incorporate enzyme activity data. To move further, the scientific community needs to measure the kinetics of all enzymes in a systematic way.", "doi": "10.1016/j.cels.2017.11.013", "pmid": "29284126", "labels": {"Avlant Nilsson": null, "DDLS Fellow": null}, "xrefs": [{"db": "pii", "key": "S2405-4712(17)30541-0"}], "notes": [], "created": "2025-03-20T11:00:14.681Z", "modified": "2025-03-21T13:14:43.640Z"}, {"entity": "publication", "iuid": "bcc3ce0b92d346ef938cd492f9ee633e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/bcc3ce0b92d346ef938cd492f9ee633e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/bcc3ce0b92d346ef938cd492f9ee633e"}}, "title": "A protein standard that emulates homology for the characterization of protein inference algorithms", "authors": [{"family": "The", "given": "Matthew", "initials": "M", "orcid": "0000-0002-5401-5553", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9d8d7d850ed24f92b9506b203ca63ed1.json"}}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e213b04f8984c8eb00c68f5bc2f6a36.json"}}, {"family": "Perez-Riverol", "given": "Yasset", "initials": "Y", "orcid": "0000-0001-6579-6941", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cb4449bad29741b195a7593fc39a769d.json"}}, {"family": "Payne", "given": "Samuel H", "initials": "SH", "orcid": "0000-0002-8351-1994", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fe701ec4cf24456980c1902ec61a0ab1.json"}}, {"family": "Hoopmann", "given": "Michael R", "initials": "MR", "orcid": "0000-0001-7029-7792", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/04f75056428f499d9806d2fd85d50e9a.json"}}, {"family": "Palmblad", "given": "Magnus", "initials": "M", "orcid": "0000-0002-5865-8994", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/80053e2256cd4e55afc7ba916821602c.json"}}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L", "orcid": "0000-0001-5689-9797", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4464f2bf868498fa6d149a4a6d60e8b.json"}}], "type": "posted-content", "published": "2017-12-19", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/236471", "pmid": null, "labels": {"Fredrik Edfors": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T11:08:00.975Z", "modified": "2026-09-23T14:23:28.675Z"}, {"entity": "publication", "iuid": "0fece34fa5164ddb89f593377f685db3", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0fece34fa5164ddb89f593377f685db3.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0fece34fa5164ddb89f593377f685db3"}}, "title": "Gene Expression Signatures and Immunohistochemical Subtypes Add Prognostic Value to Each Other in Breast Cancer Cohorts.", "authors": [{"family": "Lundberg", "given": "Arian", "initials": "A", "orcid": "0000-0002-6630-2787", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/baa2c7c8963840bfb6a22d7c5cfe35f9.json"}}, {"family": "Lindstr\u00f6m", "given": "Linda S", "initials": "LS"}, {"family": "Harrell", "given": "J Chuck", "initials": "JC"}, {"family": "Falato", "given": "Claudette", "initials": "C"}, {"family": "Carlson", "given": "Joseph W", "initials": "JW"}, {"family": "Wright", "given": "Paul K", "initials": "PK"}, {"family": "Foukakis", "given": "Theodoros", "initials": "T"}, {"family": "Perou", "given": "Charles M", "initials": "CM"}, {"family": "Czene", "given": "Kamila", "initials": "K"}, {"family": "Bergh", "given": "Jonas", "initials": "J"}, {"family": "Tobin", "given": "Nicholas P", "initials": "NP"}], "type": "journal article", "published": "2017-12-15", "journal": {"title": "Clin. Cancer Res.", "issn": "1557-3265", "volume": "23", "issue": "24", "pages": "7512-7520", "issn-l": "1078-0432"}, "abstract": "Purpose: Gene signatures and Ki67 stratify the same breast tumor into opposing good/poor prognosis groups in approximately 20% of patients. Given this discrepancy, we hypothesized that the combination of a clinically relevant signature and IHC markers may provide more prognostic information than either classifier alone.Experimental Design: We assessed Ki67 alone or combined with ER, PR and HER2 (forming IHC subtypes), and the research versions of the Genomic Grade Index, 70-gene, cell-cycle score, recurrence score (RS), and PAM50 signatures on matching TMA/whole tumor sections and microarray data in two Swedish breast cancer cohorts of 379 and 209 patients, with median follow-up of 12.4 and 12.5 years, respectively. First, we fit Cox proportional hazards models and used the change in likelihood ratio (\u0394 LR) to determine the additional prognostic information provided by signatures beyond that of (i) Ki67 and (ii) IHC subtypes. Second and uniquely, we then assessed whether signatures could compete well with pathology-based IHC classifiers by calculating the additional prognostic information of Ki67/IHC subtypes beyond signatures.Results: In cohort 1, only RS and PAM50 provided additional prognostic information beyond Ki67 and IHC subtypes (\u0394 LR-\u03c72 Ki67: RS = 12.8, PAM50 = 20.7, IHC subtypes: RS = 12.9, PAM50 = 11.7). Conversely, IHC subtypes added prognostic information beyond all signatures except PAM50. Similar results were observed in cohort 2.Conclusions: RS and PAM50 provided more prognostic information than the IHC subtypes in all breast cancer patients; however, the IHC subtypes did not add any prognostic information to PAM50. Clin Cancer Res; 23(24); 7512-20. \u00a92017 AACR.", "doi": "10.1158/1078-0432.CCR-17-1535", "pmid": "28972043", "labels": {"DDLS Fellow": null, "Arian Lundberg": null}, "xrefs": [{"db": "mid", "key": "NIHMS943047"}, {"db": "pmc", "key": "PMC5822691"}, {"db": "pii", "key": "1078-0432.CCR-17-1535"}], "notes": [], "created": "2025-11-14T07:51:52.611Z", "modified": "2026-01-03T12:25:29.300Z"}, {"entity": "publication", "iuid": "6ab7bdcfdabd41909c1deb91458f37d0", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/6ab7bdcfdabd41909c1deb91458f37d0.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/6ab7bdcfdabd41909c1deb91458f37d0"}}, "title": "Diagnostic Assessment of Deep Learning Algorithms for Detection of Lymph Node Metastases in Women With Breast Cancer.", "authors": [{"family": "Ehteshami Bejnordi", "given": "Babak", "initials": "B"}, {"family": "Veta", "given": "Mitko", "initials": "M"}, {"family": "Johannes van Diest", "given": "Paul", "initials": "P"}, {"family": "van Ginneken", "given": "Bram", "initials": "B"}, {"family": "Karssemeijer", "given": "Nico", "initials": "N"}, {"family": "Litjens", "given": "Geert", "initials": "G"}, {"family": "van der Laak", "given": "Jeroen A W M", "initials": "JAWM"}, {"family": "the CAMELYON16 Consortium", "given": "", "initials": ""}, {"family": "Hermsen", "given": "Meyke", "initials": "M"}, {"family": "Manson", "given": "Quirine F", "initials": "QF"}, {"family": "Balkenhol", "given": "Maschenka", "initials": "M"}, {"family": "Geessink", "given": "Oscar", "initials": "O"}, {"family": "Stathonikos", "given": "Nikolaos", "initials": "N"}, {"family": "van Dijk", "given": "Marcory Crf", "initials": "MC"}, {"family": "Bult", "given": "Peter", "initials": "P"}, {"family": "Beca", "given": "Francisco", "initials": "F"}, {"family": "Beck", "given": "Andrew H", "initials": "AH"}, {"family": "Wang", "given": "Dayong", "initials": "D"}, {"family": "Khosla", "given": "Aditya", "initials": "A"}, {"family": "Gargeya", "given": "Rishab", "initials": "R"}, {"family": "Irshad", "given": "Humayun", "initials": "H"}, {"family": "Zhong", "given": "Aoxiao", "initials": "A"}, {"family": "Dou", "given": "Qi", "initials": "Q"}, {"family": "Li", "given": "Quanzheng", "initials": "Q"}, {"family": "Chen", "given": "Hao", "initials": "H"}, {"family": "Lin", "given": "Huang-Jing", "initials": "H"}, {"family": "Heng", "given": "Pheng-Ann", "initials": "P"}, {"family": "Ha\u00df", "given": "Christian", "initials": "C"}, {"family": "Bruni", "given": "Elia", "initials": "E"}, {"family": "Wong", "given": "Quincy", "initials": "Q"}, {"family": "Halici", "given": "Ugur", "initials": "U"}, {"family": "\u00d6ner", "given": "Mustafa \u00dcmit", "initials": "M\u00dc"}, {"family": "Cetin-Atalay", "given": "Rengul", "initials": "R"}, {"family": "Berseth", "given": "Matt", "initials": "M"}, {"family": "Khvatkov", "given": "Vitali", "initials": "V"}, {"family": "Vylegzhanin", "given": "Alexei", "initials": "A"}, {"family": "Kraus", "given": "Oren", "initials": "O"}, {"family": "Shaban", "given": "Muhammad", "initials": "M"}, {"family": "Rajpoot", "given": "Nasir", "initials": "N"}, {"family": "Awan", "given": "Ruqayya", "initials": "R"}, {"family": "Sirinukunwattana", "given": "Korsuk", "initials": "K"}, {"family": "Qaiser", "given": "Talha", "initials": "T"}, {"family": "Tsang", "given": "Yee-Wah", "initials": "Y"}, {"family": "Tellez", "given": "David", "initials": "D"}, {"family": "Annuscheit", "given": "Jonas", "initials": "J"}, {"family": "Hufnagl", "given": "Peter", "initials": "P"}, {"family": "Valkonen", "given": "Mira", "initials": "M"}, {"family": "Kartasalo", "given": "Kimmo", "initials": "K"}, {"family": "Latonen", "given": "Leena", "initials": "L"}, {"family": "Ruusuvuori", "given": "Pekka", "initials": "P"}, {"family": "Liimatainen", "given": "Kaisa", "initials": "K"}, {"family": "Albarqouni", "given": "Shadi", "initials": "S"}, {"family": "Mungal", "given": "Bharti", "initials": "B"}, {"family": "George", "given": "Ami", "initials": "A"}, {"family": "Demirci", "given": "Stefanie", "initials": "S"}, {"family": "Navab", "given": "Nassir", "initials": "N"}, {"family": "Watanabe", "given": "Seiryo", "initials": "S"}, {"family": "Seno", "given": "Shigeto", "initials": "S"}, {"family": "Takenaka", "given": "Yoichi", "initials": "Y"}, {"family": "Matsuda", "given": "Hideo", "initials": "H"}, {"family": "Ahmady Phoulady", "given": "Hady", "initials": "H"}, {"family": "Kovalev", "given": "Vassili", "initials": "V"}, {"family": "Kalinovsky", "given": "Alexander", "initials": "A"}, {"family": "Liauchuk", "given": "Vitali", "initials": "V"}, {"family": "Bueno", "given": "Gloria", "initials": "G"}, {"family": "Fernandez-Carrobles", "given": "M Milagro", "initials": "MM"}, {"family": "Serrano", "given": "Ismael", "initials": "I"}, {"family": "Deniz", "given": "Oscar", "initials": "O"}, {"family": "Racoceanu", "given": "Daniel", "initials": "D"}, {"family": "Ven\u00e2ncio", "given": "Rui", "initials": "R"}], "type": "comparative study", "published": "2017-12-12", "journal": {"title": "JAMA", "issn": "1538-3598", "issn-l": null, "volume": "318", "issue": "22", "pages": "2199-2210"}, "abstract": "Application of deep learning algorithms to whole-slide pathology images can potentially improve diagnostic accuracy and efficiency.\r\n\r\nAssess the performance of automated deep learning algorithms at detecting metastases in hematoxylin and eosin-stained tissue sections of lymph nodes of women with breast cancer and compare it with pathologists' diagnoses in a diagnostic setting.\r\n\r\nResearcher challenge competition (CAMELYON16) to develop automated solutions for detecting lymph node metastases (November 2015-November 2016). A training data set of whole-slide images from 2 centers in the Netherlands with (n = 110) and without (n = 160) nodal metastases verified by immunohistochemical staining were provided to challenge participants to build algorithms. Algorithm performance was evaluated in an independent test set of 129 whole-slide images (49 with and 80 without metastases). The same test set of corresponding glass slides was also evaluated by a panel of 11 pathologists with time constraint (WTC) from the Netherlands to ascertain likelihood of nodal metastases for each slide in a flexible 2-hour session, simulating routine pathology workflow, and by 1 pathologist without time constraint (WOTC).\r\n\r\nDeep learning algorithms submitted as part of a challenge competition or pathologist interpretation.\r\n\r\nThe presence of specific metastatic foci and the absence vs presence of lymph node metastasis in a slide or image using receiver operating characteristic curve analysis. The 11 pathologists participating in the simulation exercise rated their diagnostic confidence as definitely normal, probably normal, equivocal, probably tumor, or definitely tumor.\r\n\r\nThe area under the receiver operating characteristic curve (AUC) for the algorithms ranged from 0.556 to 0.994. The top-performing algorithm achieved a lesion-level, true-positive fraction comparable with that of the pathologist WOTC (72.4% [95% CI, 64.3%-80.4%]) at a mean of 0.0125 false-positives per normal whole-slide image. For the whole-slide image classification task, the best algorithm (AUC, 0.994 [95% CI, 0.983-0.999]) performed significantly better than the pathologists WTC in a diagnostic simulation (mean AUC, 0.810 [range, 0.738-0.884]; P < .001). The top 5 algorithms had a mean AUC that was comparable with the pathologist interpreting the slides in the absence of time constraints (mean AUC, 0.960 [range, 0.923-0.994] for the top 5 algorithms vs 0.966 [95% CI, 0.927-0.998] for the pathologist WOTC).\r\n\r\nIn the setting of a challenge competition, some deep learning algorithms achieved better diagnostic performance than a panel of 11 pathologists participating in a simulation exercise designed to mimic routine pathology workflow; algorithm performance was comparable with an expert pathologist interpreting whole-slide images without time constraints. Whether this approach has clinical utility will require evaluation in a clinical setting.", "doi": "10.1001/jama.2017.14585", "pmid": "29234806", "labels": {"Kimmo Kartasalo": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC5820737"}, {"db": "pii", "key": "2665774"}], "notes": [], "created": "2024-11-05T16:04:33.743Z", "modified": "2024-11-29T12:04:56.431Z"}, {"entity": "publication", "iuid": "1032389c85734af89d4e7acec34a6b2a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1032389c85734af89d4e7acec34a6b2a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1032389c85734af89d4e7acec34a6b2a"}}, "title": "The relation between Blastocystis and the intestinal microbiota in Swedish travellers.", "authors": [{"family": "Forsell", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4250-113X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/70af6582ea49444aa7ae4682d07787d6.json"}}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Angelin", "given": "Martin", "initials": "M"}, {"family": "Johansson", "given": "Anders", "initials": "A"}, {"family": "Eveng\u00e5rd", "given": "Birgitta", "initials": "B"}, {"family": "Granlund", "given": "Margareta", "initials": "M"}], "type": "journal article", "published": "2017-12-11", "journal": {"title": "BMC Microbiol.", "issn": "1471-2180", "volume": "17", "issue": "1", "pages": "231", "issn-l": "1471-2180"}, "abstract": "Blastocystis sp. is a unicellular eukaryote that is commonly found in the human intestine. Its ability to cause disease is debated and a subject for ongoing research. In this study, faecal samples from 35 Swedish university students were examined through shotgun metagenomics before and after travel to the Indian peninsula or Central Africa. We aimed at assessing the impact of travel on Blastocystis carriage and seek associations between Blastocystis and the bacterial microbiota.\n\nWe found a prevalence of Blastocystis of 16/35 (46%) before travel and 15/35 (43%) after travel. The two most commonly Blastocystis subtypes (STs) found were ST3 and ST4, accounting for 20 of the 31 samples positive for Blastocystis. No mixed subtype carriage was detected. All ten individuals with a typable ST before and after travel maintained their initial ST. The composition of the gut bacterial community was not significantly different between Blastocystis-carriers and non-carriers. Interestingly, the presence of Blastocystis was accompanied with higher abundances of the bacterial genera Sporolactobacillus and Candidatus Carsonella. Blastocystis carriage was positively associated with high bacterial genus richness, and negatively correlated to the Bacteroides-driven enterotype. These associations were both largely dependent on ST4 - a subtype commonly described from Europe - while the globally prevalent ST3 did not show such significant relationships.\n\nThe high rate of Blastocystis subtype persistence found during travel indicates that long-term carriage of Blastocystis is common. The associations between Blastocystis and the bacterial microbiota found in this study could imply a link between Blastocystis and a healthy microbiota as well as with diets high in vegetables. Whether the associations between Blastocystis and the microbiota are resulting from the presence of Blastocystis, or are a prerequisite for colonization with Blastocystis, are interesting questions for further studies.", "doi": "10.1186/s12866-017-1139-7", "pmid": "29228901", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pii", "key": "10.1186/s12866-017-1139-7"}, {"db": "pmc", "key": "PMC5725903"}], "notes": [], "created": "2022-11-08T09:28:58.311Z", "modified": "2022-11-08T09:28:58.388Z"}, {"entity": "publication", "iuid": "be41190a4e9847b1a5d5ea4ec7a7d2af", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/be41190a4e9847b1a5d5ea4ec7a7d2af.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/be41190a4e9847b1a5d5ea4ec7a7d2af"}}, "title": "Smoking Cessation and Risk of Esophageal Cancer by Histological Type: Systematic Review and Meta-analysis.", "authors": [{"family": "Wang", "given": "Qiao-Li", "initials": "QL"}, {"family": "Xie", "given": "Shao-Hua", "initials": "SH"}, {"family": "Li", "given": "Wen-Tao", "initials": "WT"}, {"family": "Lagergren", "given": "Jesper", "initials": "J"}], "type": "journal article", "published": "2017-12-01", "journal": {"title": "J. Natl. Cancer Inst.", "issn": "1460-2105", "volume": "109", "issue": "12", "issn-l": "0027-8874"}, "abstract": "Tobacco smoking strongly increases risk of esophageal squamous cell carcinoma and moderately increases risk of esophageal adenocarcinoma. How smoking cessation influences esophageal cancer risk across histological subtypes, time latencies, and geographic regions is not clear.\n\nStudies were systematically searched on Medline, Embase, Web of Science, Cochrane Library, and ClinicalTrials.gov. Pooled estimates of risk ratios (RRs) were derived using a random effects model. Cochran's Q test and I2 statistic were used to detect heterogeneity.\n\nAmong 15 009 studies, 52 fulfilled the inclusion criteria. Using nonsmokers as a reference, risk of esophageal squamous cell carcinoma was lower among former smokers (RR = 2.05, 95% confidence interval [CI] = 1.71 to 2.45) than among current smokers (RR = 4.18, 95% CI = 3.42 to 5.12). Compared with current smokers, a strong risk reduction was evident after five or more years (RR = 0.59, 95% CI = 0.47 to 0.75), and became stronger after 10 or more years (RR = 0.42, 95% CI = 0.34 to 0.51) and 20 or more years (RR = 0.34, 95% CI = 0.25 to 0.47) following smoking cessation. The risk reduction was strong in Western populations, while weak in Asian populations. Using nonsmokers as reference, the risk of esophageal adenocarcinoma was only slightly lower among former smokers (RR = 1.66, 95% CI = 1.48 to 1.85) than among current smokers (RR = 2.34, 95% CI = 2.04 to 2.69). The risk of esophageal adenocarcinoma did not show any clear reduction over time after smoking cessation, with a risk ratio of 0.72 (95% CI = 0.52 to 1.01) 20 or more years after smoking cessation, compared with current smokers.\n\nSmoking cessation time-dependently decreases risk of esophageal squamous cell carcinoma, particularly in Western populations, while it has limited influence on the risk of esophageal adenocarcinoma.", "doi": "10.1093/jnci/djx115", "pmid": "29933436", "labels": {"DDLS Fellow": null, "Qiaoli Wang": null}, "xrefs": [{"db": "pii", "key": "4064131"}], "notes": [], "created": "2025-11-27T18:45:15.230Z", "modified": "2025-11-27T18:45:15.233Z"}, {"entity": "publication", "iuid": "46aa415bd1c44874a382cfcf1d72822c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/46aa415bd1c44874a382cfcf1d72822c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/46aa415bd1c44874a382cfcf1d72822c"}}, "title": "PAM50 Provides Prognostic Information When Applied to the Lymph Node Metastases of Advanced Breast Cancer Patients.", "authors": [{"family": "Tobin", "given": "Nicholas P", "initials": "NP"}, {"family": "Lundberg", "given": "Arian", "initials": "A", "orcid": "0000-0002-6630-2787", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/baa2c7c8963840bfb6a22d7c5cfe35f9.json"}}, {"family": "Lindstr\u00f6m", "given": "Linda S", "initials": "LS"}, {"family": "Harrell", "given": "J Chuck", "initials": "JC"}, {"family": "Foukakis", "given": "Theodoros", "initials": "T"}, {"family": "Carlsson", "given": "Lena", "initials": "L"}, {"family": "Einbeigi", "given": "Zakaria", "initials": "Z"}, {"family": "Linderholm", "given": "Barbro K", "initials": "BK"}, {"family": "Loman", "given": "Niklas", "initials": "N"}, {"family": "Malmberg", "given": "Martin", "initials": "M"}, {"family": "Fern\u00f6", "given": "M\u00e5rten", "initials": "M"}, {"family": "Czene", "given": "Kamila", "initials": "K"}, {"family": "Perou", "given": "Charles M", "initials": "CM"}, {"family": "Bergh", "given": "Jonas", "initials": "J"}, {"family": "Hatschek", "given": "Thomas", "initials": "T"}, {"family": "TEX Trialists Group", "given": "", "initials": ""}], "type": "journal article", "published": "2017-12-01", "journal": {"title": "Clin. Cancer Res.", "issn": "1557-3265", "volume": "23", "issue": "23", "pages": "7225-7231", "issn-l": "1078-0432"}, "abstract": "Purpose: Transcriptional pathway activity and the molecular subtypes of breast cancer metastases have been shown to significantly influence patient postrelapse survival. Here, we further determine the relevance of clinically employed gene signatures in the advanced breast cancer (ABC) setting.Experimental Design: Sufficient RNA for expression profiling was obtained from distant metastatic or inoperable loco-regional relapse tissue by fine-needle aspiration from 109 patients of the Swedish TEX clinical trial. Gene signatures (GGI, 70 gene, recurrence score, cell-cycle score, risk of recurrence score, and PAM50) were applied to all metastases, and their relationship to long- (5-year) and short-term (1.5-year) postrelapse survival at all and locoregional lymph nodes (n = 40) versus other metastatic sites (n = 69) combined was assessed using Kaplan-Meier and/or multivariate Cox regression analyses.Results: The majority of metastases were classified into intermediate or high-risk groups by all signatures, and a significant association was found between metastatic signature subgroups and primary tumor estrogen receptor status and histologic grade (P < 0.05). When considering all sites of metastasis, only PAM50 was statistically significant in Kaplan-Meier analysis (Log-rank P = 0.008 and 0.008 for long- and short-term postrelapse breast cancer-specific survival, respectively). This significance remained in both uni- and multivariate models when restricting analyses to lymph node metastases only, and a similar trend was observed in other metastatic sites combined, but did not reach formal significance.Conclusions: Our findings are the first to demonstrate that the PAM50 signature can provide prognostic information from the lymph node metastases of ABC patients. Clin Cancer Res; 23(23); 7225-31. \u00a92017 AACR.", "doi": "10.1158/1078-0432.CCR-17-2301", "pmid": "28972041", "labels": {"DDLS Fellow": null, "Arian Lundberg": null}, "xrefs": [{"db": "mid", "key": "NIHMS943057"}, {"db": "pmc", "key": "PMC5822712"}, {"db": "pii", "key": "1078-0432.CCR-17-2301"}], "notes": [], "created": "2025-11-14T07:51:53.765Z", "modified": "2026-01-03T12:43:49.366Z"}, {"entity": "publication", "iuid": "6d7655c5b65948fea35e3a6b0d38b220", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/6d7655c5b65948fea35e3a6b0d38b220.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/6d7655c5b65948fea35e3a6b0d38b220"}}, "title": "Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes", "authors": [{"family": "Alneberg", "given": "Johannes", "initials": "J", "orcid": "0000-0002-2467-008X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/339963840ba84d45a027d6229fef75a1.json"}}, {"family": "Karlsson", "given": "Christofer M G", "initials": "CMG"}, {"family": "Divne", "given": "Anna Maria", "initials": "AM"}, {"family": "Bergin", "given": "Claudia", "initials": "C", "orcid": "0000-0001-7960-1789", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3df040286ae04a76b419b510ad56b56c.json"}}, {"family": "Homa", "given": "Felix", "initials": "F", "orcid": "0000-0003-0852-707X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bd724f67502140f497cf068b2dd4a2a1.json"}}, {"family": "Lindh", "given": "Markus V", "initials": "MV"}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW", "orcid": "0000-0001-5432-1764", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/246ed7b405dd4c3f9ec5e7ff9f1d3ade.json"}}, {"family": "Ettema", "given": "Thijs JG", "initials": "TJ", "orcid": "0000-0002-6898-6377", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a7921cec2bb45a7a7b0454f41b5f1aa.json"}}, {"family": "Bertilsson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-4265-1835", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4fd9423637a54230892379a5b50cf47f.json"}}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cc9be99ec6ca47ed8a805ebb4db7c168.json"}}, {"family": "Pinhassi", "given": "Jarone", "initials": "J", "orcid": "0000-0002-6405-1347", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/28b77762086343048e74046a6486caff.json"}}], "type": "posted-content", "published": "2017-11-14", "journal": {"title": "bioRxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/219295", "pmid": null, "labels": {"DDLS Fellow": null, "Luisa Hugerth": null}, "xrefs": [], "notes": [], "created": "2026-08-20T11:07:53.717Z", "modified": "2026-10-05T08:45:08.941Z"}, {"entity": "publication", "iuid": "1b83df4c2d9b40f7a010dc90d26f4ff7", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1b83df4c2d9b40f7a010dc90d26f4ff7.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1b83df4c2d9b40f7a010dc90d26f4ff7"}}, "title": "Cholesterol Promotes Protein Binding by Affecting Membrane Electrostatics and Solvation Properties.", "authors": [{"family": "Doktorova", "given": "Milka", "initials": "M"}, {"family": "Heberle", "given": "Frederick A", "initials": "FA"}, {"family": "Kingston", "given": "Richard L", "initials": "RL"}, {"family": "Khelashvili", "given": "George", "initials": "G"}, {"family": "Cuendet", "given": "Michel A", "initials": "MA"}, {"family": "Wen", "given": "Yi", "initials": "Y"}, {"family": "Katsaras", "given": "John", "initials": "J"}, {"family": "Feigenson", "given": "Gerald W", "initials": "GW"}, {"family": "Vogt", "given": "Volker M", "initials": "VM"}, {"family": "Dick", "given": "Robert A", "initials": "RA"}], "type": "journal article", "published": "2017-11-07", "journal": {"title": "Biophys. J.", "issn": "1542-0086", "issn-l": "0006-3495", "volume": "113", "issue": "9", "pages": "2004-2015"}, "abstract": "Binding of the retroviral structural protein Gag to the cellular plasma membrane is mediated by the protein's matrix (MA) domain. Prominent among MA-PM interactions is electrostatic attraction between the positively charged MA domain and the negatively charged plasma membrane inner leaflet. Previously, we reported that membrane association of HIV-1 Gag, as well as purified Rous sarcoma virus (RSV) MA and Gag, depends strongly on the presence of acidic lipids and is enhanced by cholesterol (Chol). The mechanism underlying this enhancement was unclear. Here, using a broad set of in vitro and in silico techniques we addressed molecular mechanisms of association between RSV MA and model membranes, and investigated how Chol enhances this association. In neutron scattering experiments with liposomes in the presence or absence of Chol, MA preferentially interacted with preexisting POPS-rich clusters formed by nonideal lipid mixing, binding peripherally to the lipid headgroups with minimal perturbation to the bilayer structure. Molecular dynamics simulations showed a stronger MA-bilayer interaction in the presence of Chol, and a large Chol-driven increase in lipid packing and membrane surface charge density. Although in vitro MA-liposome association is influenced by disparate variables, including ionic strength and concentrations of Chol and charged lipids, continuum electrostatic theory revealed an underlying dependence on membrane surface potential. Together, these results conclusively show that Chol affects RSV MA-membrane association by making the electrostatic potential at the membrane surface more negative, while decreasing the penalty for lipid headgroup desolvation. The presented approach can be applied to other viral and nonviral proteins.", "doi": "10.1016/j.bpj.2017.08.055", "pmid": "29117524", "labels": {"Milka Doktorova": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC5685651"}, {"db": "pii", "key": "S0006-3495(17)30987-6"}], "notes": [], "created": "2024-11-27T12:16:09.556Z", "modified": "2024-11-29T12:17:12.234Z"}, {"entity": "publication", "iuid": "87166ee413de4b4d9c1d2a9812bd6062", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/87166ee413de4b4d9c1d2a9812bd6062.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/87166ee413de4b4d9c1d2a9812bd6062"}}, "title": "Cryo-EM reconstruction of the chlororibosome to 3.2 \u00c5 resolution within 24 h.", "authors": [{"family": "Forsberg", "given": "Bj\u00f6rn O", "initials": "BO", "orcid": "0000-0002-6247-4063", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/36ea51bfa66d48b7a43559c3d0eaa59f.json"}}, {"family": "Aibara", "given": "Shintaro", "initials": "S"}, {"family": "Kimanius", "given": "Dari", "initials": "D", "orcid": "0000-0002-2662-6373", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3a3803ee817a464ca07c849c07096dc2.json"}}, {"family": "Paul", "given": "Bijoya", "initials": "B"}, {"family": "Lindahl", "given": "Erik", "initials": "E", "orcid": "0000-0003-1333-5398", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/35c127f97e0e4d0c9fbbb401cbe8a4f9.json"}}, {"family": "Amunts", "given": "Alexey", "initials": "A", "orcid": "0000-0002-5302-1740", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6c79bee23e114906bc847dfbd0975139.json"}}], "type": "journal article", "published": "2017-11-01", "journal": {"title": "IUCrJ", "issn": "2052-2525", "issn-l": "2052-2525", "volume": "4", "issue": "Pt 6", "pages": "723-727"}, "abstract": "The introduction of direct detectors and the automation of data collection in cryo-EM have led to a surge in data, creating new opportunities for advancing computational processing. In particular, on-the-fly workflows that connect data collection with three-dimensional reconstruction would be valuable for more efficient use of cryo-EM and its application as a sample-screening tool. Here, accelerated on-the-fly analysis is reported with optimized organization of the data-processing tools, image acquisition and particle alignment that make it possible to reconstruct the three-dimensional density of the 70S chlororibosome to 3.2 \u00c5 resolution within 24 h of tissue harvesting. It is also shown that it is possible to achieve even faster processing at comparable quality by imposing some limits to data use, as illustrated by a 3.7 \u00c5 resolution map that was obtained in only 80 min on a desktop computer. These on-the-fly methods can be employed as an assessment of data quality from small samples and extended to high-throughput approaches.", "doi": "10.1107/S205225251701226X", "pmid": "29123673", "labels": {"Alexey Amunts": "", "SciLifeLab Fellow": "", "DDLS Fellow": "", "Bj\u00f6rn Forsberg": ""}, "xrefs": [{"db": "pmc", "key": "PMC5668856"}, {"db": "pii", "key": "kf5004"}], "notes": [], "created": "2018-12-05T12:54:15.165Z", "modified": "2026-09-23T12:54:49.989Z"}, {"entity": "publication", "iuid": "72d1bb4c78864f3d9b072582389a5420", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/72d1bb4c78864f3d9b072582389a5420.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/72d1bb4c78864f3d9b072582389a5420"}}, "title": "Precision food safety: A systems approach to food safety facilitated by genomics tools", "authors": [{"family": "Kovac", "given": "Jasna", "initials": "J"}, {"family": "Bakker", "given": "Henk den", "initials": "Hd"}, {"family": "Carroll", "given": "Laura M", "initials": "LM"}, {"family": "Wiedmann", "given": "Martin", "initials": "M"}], "type": "journal-article", "published": "2017-11-00", "journal": {"title": "TrAC Trends in Analytical Chemistry", "issn": "0165-9936", "volume": "96", "pages": "52-61", "issn-l": null}, "abstract": null, "doi": "10.1016/j.trac.2017.06.001", "pmid": null, "labels": {"Laura Carroll": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2025-03-18T17:21:42.034Z", "modified": "2025-03-18T17:22:26.077Z"}, {"entity": "publication", "iuid": "62ce46f9bd544109b71d54435029b753", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/62ce46f9bd544109b71d54435029b753.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/62ce46f9bd544109b71d54435029b753"}}, "title": "Identification of 76 novel B1 metallo-\u03b2-lactamases through large-scale screening of genomic and metagenomic data.", "authors": [{"family": "Berglund", "given": "Fanny", "initials": "F"}, {"family": "Marathe", "given": "Nachiket P", "initials": "NP"}, {"family": "\u00d6sterlund", "given": "Tobias", "initials": "T"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Kotsakis", "given": "Stathis", "initials": "S"}, {"family": "Flach", "given": "Carl-Fredrik", "initials": "CF"}, {"family": "Larsson", "given": "D G Joakim", "initials": "DGJ"}, {"family": "Kristiansson", "given": "Erik", "initials": "E", "orcid": "0000-0002-8609-2414", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/18d5538c8c0749199a6f1b51d15eec69.json"}}], "type": "journal article", "published": "2017-10-12", "journal": {"title": "Microbiome", "issn": "2049-2618", "volume": "5", "issue": "1", "pages": "134", "issn-l": "2049-2618"}, "abstract": "Metallo-\u03b2-lactamases are bacterial enzymes that provide resistance to carbapenems, the most potent class of antibiotics. These enzymes are commonly encoded on mobile genetic elements, which, together with their broad substrate spectrum and lack of clinically useful inhibitors, make them a particularly problematic class of antibiotic resistance determinants. We hypothesized that there is a large and unexplored reservoir of unknown metallo-\u03b2-lactamases, some of which may spread to pathogens, thereby threatening public health. The aim of this study was to identify novel metallo-\u03b2-lactamases of class B1, the most clinically important subclass of these enzymes.\n\nBased on a new computational method using an optimized hidden Markov model, we analyzed over 10,000 bacterial genomes and plasmids together with more than 5 terabases of metagenomic data to identify novel metallo-\u03b2-lactamase genes. In total, 76 novel genes were predicted, forming 59 previously undescribed metallo-\u03b2-lactamase gene families. The ability to hydrolyze imipenem in an Escherichia coli host was experimentally confirmed for 18 of the 21 tested genes. Two of the novel B1 metallo-\u03b2-lactamase genes contained atypical zinc-binding motifs in their active sites, which were previously undescribed for metallo-\u03b2-lactamases. Phylogenetic analysis showed that B1 metallo-\u03b2-lactamases could be divided into five major groups based on their evolutionary origin. Our results also show that, except for one, all of the previously characterized mobile B1 \u03b2-lactamases are likely to have originated from chromosomal genes present in Shewanella spp. and other Proteobacterial species.\n\nThis study more than doubles the number of known B1 metallo-\u03b2-lactamases. The findings have further elucidated the diversity and evolutionary history of this important class of antibiotic resistance genes and prepare us for some of the challenges that may be faced in clinics in the future.", "doi": "10.1186/s40168-017-0353-8", "pmid": "29020980", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pii", "key": "10.1186/s40168-017-0353-8"}, {"db": "pmc", "key": "PMC5637372"}], "notes": [], "created": "2022-11-08T09:29:03.058Z", "modified": "2022-11-08T09:29:03.139Z"}, {"entity": "publication", "iuid": "195336cf7a984cc5b01bb8012babc3dd", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/195336cf7a984cc5b01bb8012babc3dd.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/195336cf7a984cc5b01bb8012babc3dd"}}, "title": "Identification and characterization of the novel colonization factor CS30 based on whole genome sequencing in enterotoxigenic Escherichia coli (ETEC).", "authors": [{"family": "von Mentzer", "given": "Astrid", "initials": "A"}, {"family": "Tobias", "given": "Joshua", "initials": "J"}, {"family": "Wiklund", "given": "Gudrun", "initials": "G"}, {"family": "Nordqvist", "given": "Stefan", "initials": "S"}, {"family": "Aslett", "given": "Martin", "initials": "M"}, {"family": "Dougan", "given": "Gordon", "initials": "G"}, {"family": "Sj\u00f6ling", "given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0003-1529-1720", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6b817fe2e55b4acf860ff498a650bb94.json"}}, {"family": "Svennerholm", "given": "Ann-Mari", "initials": "AM"}], "type": "journal article", "published": "2017-10-02", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "7", "issue": "1", "pages": "12514", "issn-l": "2045-2322"}, "abstract": "The ability to colonize the small intestine is essential for enterotoxigenic Escherichia coli (ETEC) to cause diarrhea. Although 22 antigenically different colonization factors (CFs) have been identified and characterized in ETEC at least 30% of clinical ETEC isolates lack known CFs. Ninety-four whole genome sequenced \"CF negative\" isolates were searched for novel CFs using a reverse genetics approach followed by phenotypic analyses. We identified a novel CF, CS30, encoded by a set of seven genes, csmA-G, related to the human CF operon CS18 and the porcine CF operon 987P (F6). CS30 was shown to be thermo-regulated, expressed at 37 \u00b0C, but not at 20 \u00b0C, by SDS-page and mass spectrometry analyses as well as electron microscopy imaging. Bacteria expressing CS30 were also shown to bind to differentiated human intestinal Caco-2 cells. The genes encoding CS30 were located on a plasmid (E873p3) together with the genes encoding LT and STp. PCR screening of ETEC isolates revealed that 8.6% (n = 13) of \"CF negative\" (n = 152) and 19.4% (n = 13) of \"CF negative\" LT + STp (n = 67) expressing isolates analyzed harbored CS30. Hence, we conclude that CS30 is common among \"CF negative\" LT + STp isolates and is associated with ETEC that cause diarrhea.", "doi": "10.1038/s41598-017-12743-3", "pmid": "28970563", "labels": {"Astrid von Mentzer": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC5624918"}, {"db": "pii", "key": "10.1038/s41598-017-12743-3"}], "notes": [], "created": "2025-12-02T15:48:52.979Z", "modified": "2025-12-02T15:48:53.038Z"}, {"entity": "publication", "iuid": "1b50cc6371f742dab55fa3484aaa04e7", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1b50cc6371f742dab55fa3484aaa04e7.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1b50cc6371f742dab55fa3484aaa04e7"}}, "title": "Using metagenomics to investigate human and environmental resistomes.", "authors": [{"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Larsson", "given": "D G Joakim", "initials": "DGJ"}, {"family": "Kristiansson", "given": "Erik", "initials": "E"}], "type": "journal article", "published": "2017-10-01", "journal": {"title": "J Antimicrob Chemother", "issn": "1460-2091", "volume": "72", "issue": "10", "pages": "2690-2703", "issn-l": null}, "abstract": "Antibiotic resistance is a global health concern declared by the WHO as one of the largest threats to modern healthcare. In recent years, metagenomic DNA sequencing has started to be applied as a tool to study antibiotic resistance in different environments, including the human microbiota. However, a multitude of methods exist for metagenomic data analysis, and not all methods are suitable for the investigation of resistance genes, particularly if the desired outcome is an assessment of risks to human health. In this review, we outline the current state of methods for sequence handling, mapping to databases of resistance genes, statistical analysis and metagenomic assembly. In addition, we provide an overview of important considerations related to the analysis of resistance genes, and recommend some of the currently used tools and methods that are best equipped to inform research and clinical practice related to antibiotic resistance.", "doi": "10.1093/jac/dkx199", "pmid": "28673041", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pii", "key": "3904526"}], "notes": [], "created": "2022-11-08T09:29:23.090Z", "modified": "2022-11-08T09:29:23.142Z"}, {"entity": "publication", "iuid": "57def0bc0a3a4045aadac7e748b61ed4", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/57def0bc0a3a4045aadac7e748b61ed4.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/57def0bc0a3a4045aadac7e748b61ed4"}}, "title": "Differential Impact of Glucose Administered Intravenously and Orally on Circulating miR-375 Levels in Human Subjects.", "authors": [{"family": "Yan", "given": "Xin", "initials": "X"}, {"family": "Wang", "given": "Zhen", "initials": "Z"}, {"family": "Westberg-Rasmussen", "given": "Sidse", "initials": "S"}, {"family": "Tarbier", "given": "Marcel", "initials": "M"}, {"family": "Rathjen", "given": "Thomas", "initials": "T"}, {"family": "Tattikota", "given": "Sudhir G", "initials": "SG"}, {"family": "Peck", "given": "Bailey C E", "initials": "BCE"}, {"family": "Kanke", "given": "Matt", "initials": "M"}, {"family": "Oxvig", "given": "Claus", "initials": "C"}, {"family": "Frystyk", "given": "Jan", "initials": "J"}, {"family": "Starup-Linde", "given": "Jakob", "initials": "J"}, {"family": "Sethupathy", "given": "Praveen", "initials": "P"}, {"family": "Friedl\u00e4nder", "given": "Marc R", "initials": "MR"}, {"family": "Gregersen", "given": "S\u00f8ren", "initials": "S"}, {"family": "Poy", "given": "Matthew N", "initials": "MN"}], "type": "clinical trial", "published": "2017-10-01", "journal": {"title": "J. Clin. Endocrinol. Metab.", "issn": "1945-7197", "issn-l": "0021-972X", "volume": "102", "issue": "10", "pages": "3749-3755"}, "abstract": "To date, numerous nucleic acid species have been detected in the systemic circulation including microRNAs (miRNAs); however, their functional role in this compartment remains unclear.\n\nThe aim of this study was to determine whether systemic levels of miRNAs abundant in blood, including the neuroendocrine tissue-enriched miR-375, are altered in response to a glucose challenge.\n\nTwelve healthy males were recruited for an acute crossover study that consisted of two tests each following an 8-hour fasting period. An oral glucose tolerance test (OGTT) was performed, and blood samples were collected over a 3-hour period. Following a period of at least 1 week, the same participants were administered an isoglycemic intravenous glucose infusion (IIGI) with the same blood-collection protocol.\n\nThe glucose response curve following the IIGI mimicked that obtained after the OGTT, but as expected, systemic insulin levels were lower during the IIGI compared with the OGTT (P < 0.05). miR-375 levels in circulation were increased only in response to an OGTT and not during an IIGI. In addition, the response to the OGTT also coincided with the transient increase of circulating glucagon-like peptide (GLP)-1, GLP-2, and glucose-dependent insulinotropic polypeptide.\n\nThe present findings show levels of miR-375 increase following administration of an OGTT and, in light of its enrichment in cells of the gut, suggest that the gastrointestinal tract may play an important role in the abundance and function of this miRNA in the blood.", "doi": "10.1210/jc.2017-01365", "pmid": "28973164", "labels": {"Affiliated researcher": "", "Marc Friedl\u00e4nder": "", "SciLifeLab Fellow": "", "Marcel Tarbier": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pii", "key": "4049504"}, {"db": "ClinicalTrials.gov", "key": "NCT02213276"}], "notes": [], "created": "2018-12-03T14:41:54.319Z", "modified": "2026-09-23T13:26:30.550Z"}, {"entity": "publication", "iuid": "9da3c468d20a487b99ddb51744b01a10", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9da3c468d20a487b99ddb51744b01a10.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9da3c468d20a487b99ddb51744b01a10"}}, "title": "In Vivo Analysis of the Viable Microbiota and Helicobacter pylori Transcriptome in Gastric Infection and Early Stages of Carcinogenesis.", "authors": [{"family": "Thorell", "given": "Kaisa", "initials": "K", "orcid": "0000-0002-4447-8968", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/789d4029a5c14d3c83df7c47b3b514c7.json"}}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Liu", "given": "Oscar Hsin-Fu", "initials": "OH"}, {"family": "Palacios Gonzales", "given": "Reyna Victoria", "initials": "RV"}, {"family": "Nookaew", "given": "Intawat", "initials": "I"}, {"family": "Rabeneck", "given": "Linda", "initials": "L"}, {"family": "Paszat", "given": "Lawrence", "initials": "L"}, {"family": "Graham", "given": "David Y", "initials": "DY"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/33f2b49a39ed4e54ba77dfe397ed3087.json"}}, {"family": "Lundin", "given": "Samuel B", "initials": "SB"}, {"family": "Sj\u00f6ling", "given": "\u00c5sa", "initials": "\u00c5"}], "type": "journal article", "published": "2017-10-00", "journal": {"title": "Infect. Immun.", "issn": "1098-5522", "volume": "85", "issue": "10", "issn-l": "0019-9567"}, "abstract": "Emerging evidence shows that the human microbiota plays a larger role in disease progression and health than previously anticipated. Helicobacter pylori, the causative agent of gastric cancer and duodenal and gastric ulcers, was early associated with gastric disease, but it has also been proposed that the accompanying microbiota in Helicobacter pylori-infected individuals might affect disease progression and gastric cancer development. In this study, the composition of the transcriptionally active microbial community and H. pylori gene expression were determined using metatranscriptomic RNA sequencing of stomach biopsy specimens from individuals with different H. pylori infection statuses and premalignant tissue changes. The results show that H. pylori completely dominates the microbiota not only in infected individuals but also in most individuals classified as H. pylori uninfected using conventional methods. Furthermore, H. pylori abundance is positively correlated with the presence of Campylobacter, Deinococcus, and Sulfurospirillum Finally, we quantified the expression of a large number of Helicobacter pylori genes and found high expression of genes involved in pH regulation and nickel transport. Our study is the first to dissect the viable microbiota of the human stomach by metatranscriptomic analysis, and it shows that metatranscriptomic analysis of the gastric microbiota is feasible and can provide new insights into how bacteria respond in vivo to variations in the stomach microenvironment and at different stages of disease progression.", "doi": "10.1128/IAI.00031-17", "pmid": "28694295", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pii", "key": "IAI.00031-17"}, {"db": "pmc", "key": "PMC5607399"}], "notes": [], "created": "2022-11-08T09:29:20.716Z", "modified": "2022-11-08T09:29:20.850Z"}, {"entity": "publication", "iuid": "07a064cf641a4412a579ff6aa8015841", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/07a064cf641a4412a579ff6aa8015841.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/07a064cf641a4412a579ff6aa8015841"}}, "title": "Dual Structured Convolutional Neural Network with Feature Augmentation for Quantitative Characterization of Tissue Histology", "authors": [{"family": "Valkonen", "given": "Mira", "initials": "M"}, {"family": "Kartasalo", "given": "Kimmo", "initials": "K"}, {"family": "Liimatainen", "given": "Kaisa", "initials": "K"}, {"family": "Nykter", "given": "Matti", "initials": "M"}, {"family": "Latonen", "given": "Leena", "initials": "L"}, {"family": "Ruusuvuori", "given": "Pekka", "initials": "P"}], "type": "proceedings-article", "published": "2017-10-00", "journal": {"title": null, "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": "27-35"}, "abstract": null, "doi": "10.1109/iccvw.2017.10", "pmid": null, "labels": {"Kimmo Kartasalo": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2024-11-05T16:04:28.827Z", "modified": "2024-11-29T12:05:14.216Z"}, {"entity": "publication", "iuid": "a7625226b60f4eb982847f2a1564cb97", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a7625226b60f4eb982847f2a1564cb97.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a7625226b60f4eb982847f2a1564cb97"}}, "title": "Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing.", "authors": [{"family": "Hugerth", "given": "Luisa W", "initials": "LW"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}], "type": "journal article", "published": "2017-09-04", "journal": {"title": "Front Microbiol", "issn": "1664-302X", "volume": "8", "issue": null, "pages": "1561", "issn-l": "1664-302X"}, "abstract": "Microbial ecology as a scientific field is fundamentally driven by technological advance. The past decade's revolution in DNA sequencing cost and throughput has made it possible for most research groups to map microbial community composition in environments of interest. However, the computational and statistical methodology required to analyse this kind of data is often not part of the biologist training. In this review, we give a historical perspective on the use of sequencing data in microbial ecology and restate the current need for this method; but also highlight the major caveats with standard practices for handling these data, from sample collection and library preparation to statistical analysis. Further, we outline the main new analytical tools that have been developed in the past few years to bypass these caveats, as well as highlight the major requirements of common statistical practices and the extent to which they are applicable to microbial data. Besides delving into the meaning of select alpha- and beta-diversity measures, we give special consideration to techniques for finding the main drivers of community dissimilarity and for interaction network construction. While every project design has specific needs, this review should serve as a starting point for considering what options are available.", "doi": "10.3389/fmicb.2017.01561", "pmid": "28928718", "labels": {"Affiliated researcher": "", "Luisa Hugerth": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC5591341"}], "notes": [], "created": "2018-12-05T12:09:18.835Z", "modified": "2026-09-23T06:34:54.301Z"}, {"entity": "publication", "iuid": "5d5fe5fc2e1840a7b9fef3c23229c8b0", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5d5fe5fc2e1840a7b9fef3c23229c8b0.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5d5fe5fc2e1840a7b9fef3c23229c8b0"}}, "title": "Computational discovery and functional validation of novel fluoroquinolone resistance genes in public metagenomic data sets.", "authors": [{"family": "Boulund", "given": "Fredrik", "initials": "F"}, {"family": "Berglund", "given": "Fanny", "initials": "F"}, {"family": "Flach", "given": "Carl-Fredrik", "initials": "CF"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Marathe", "given": "Nachiket P", "initials": "NP"}, {"family": "Larsson", "given": "D G Joakim", "initials": "DGJ"}, {"family": "Kristiansson", "given": "Erik", "initials": "E"}], "type": "journal article", "published": "2017-09-02", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "18", "issue": "1", "pages": "682", "issn-l": "1471-2164"}, "abstract": "Fluoroquinolones are broad-spectrum antibiotics used to prevent and treat a wide range of bacterial infections. Plasmid-mediated qnr genes provide resistance to fluoroquinolones in many bacterial species and are increasingly encountered in clinical settings. Over the last decade, several families of qnr genes have been discovered and characterized, but their true prevalence and diversity still remain unclear. In particular, environmental and host-associated bacterial communities have been hypothesized to maintain a large and unknown collection of qnr genes that could be mobilized into pathogens.\n\nIn this study we used computational methods to screen genomes and metagenomes for novel qnr genes. In contrast to previous studies, we analyzed an almost 20-fold larger dataset comprising almost 13 terabases of sequence data. In total, 362,843 potential qnr gene fragments were identified, from which 611 putative qnr genes were reconstructed. These gene sequences included all previously described plasmid-mediated qnr gene families. Fifty-two of the 611 identified qnr genes were reconstructed from metagenomes, and 20 of these were previously undescribed. All of the novel qnr genes were assembled from metagenomes associated with aquatic environments. Nine of the novel genes were selected for validation, and six of the tested genes conferred consistently decreased susceptibility to ciprofloxacin when expressed in Escherichia coli.\n\nThe results presented in this study provide additional evidence for the ubiquitous presence of qnr genes in environmental microbial communities, expand the number of known qnr gene variants and further elucidate the diversity of this class of resistance genes. This study also strengthens the hypothesis that environmental bacterial communities act as sources of previously uncharacterized qnr genes.", "doi": "10.1186/s12864-017-4064-0", "pmid": "28865446", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-017-4064-0"}, {"db": "pmc", "key": "PMC5581476"}], "notes": [], "created": "2022-11-08T09:29:16.036Z", "modified": "2022-11-08T09:29:16.040Z"}, {"entity": "publication", "iuid": "20bd4bc29d8a41ef891e70e19d4f1ac6", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/20bd4bc29d8a41ef891e70e19d4f1ac6.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/20bd4bc29d8a41ef891e70e19d4f1ac6"}}, "title": "Rapid, High-Throughput Identification of Anthrax-Causing and Emetic Bacillus cereus Group Genome Assemblies via BTyper, a Computational Tool for Virulence-Based Classification of Bacillus cereus Group Isolates by Using Nucleotide Sequencing Data.", "authors": [{"family": "Carroll", "given": "Laura M", "initials": "LM"}, {"family": "Kovac", "given": "Jasna", "initials": "J"}, {"family": "Miller", "given": "Rachel A", "initials": "RA"}, {"family": "Wiedmann", "given": "Martin", "initials": "M"}], "type": "journal article", "published": "2017-09-01", "journal": {"title": "Applied and environmental microbiology", "issn": "1098-5336", "volume": "83", "issue": "17", "issn-l": "0099-2240"}, "abstract": "The Bacillus cereus group comprises nine species, several of which are pathogenic. Differentiating between isolates that may cause disease and those that do not is a matter of public health and economic importance, but it can be particularly challenging due to the high genomic similarity within the group. To this end, we have developed BTyper, a computational tool that employs a combination of (i) virulence gene-based typing, (ii) multilocus sequence typing (MLST), (iii) panC clade typing, and (iv) rpoB allelic typing to rapidly classify B. cereus group isolates using nucleotide sequencing data. BTyper was applied to a set of 662 B. cereus group genome assemblies to (i) identify anthrax-associated genes in non-B. anthracis members of the B. cereus group, and (ii) identify assemblies from B. cereus group strains with emetic potential. With BTyper, the anthrax toxin genes cya, lef, and pagA were detected in 8 genomes classified by the NCBI as B. cereus that clustered into two distinct groups using k-medoids clustering, while either the B. anthracis poly-\u03b3-d-glutamate capsule biosynthesis genes capABCDE or the hyaluronic acid capsule hasA gene was detected in an additional 16 assemblies classified as either B. cereus or Bacillus thuringiensis isolated from clinical, environmental, and food sources. The emetic toxin genes cesABCD were detected in 24 assemblies belonging to panC clades III and VI that had been isolated from food, clinical, and environmental settings. The command line version of BTyper is available at https://github.com/lmc297/BTyper In addition, BMiner, a companion application for analyzing multiple BTyper output files in aggregate, can be found at https://github.com/lmc297/BMinerIMPORTANCE Bacillus cereus is a foodborne pathogen that is estimated to cause tens of thousands of illnesses each year in the United States alone. Even with molecular methods, it can be difficult to distinguish nonpathogenic B. cereus group isolates from their pathogenic counterparts, including the human pathogen Bacillus anthracis, which is responsible for anthrax, as well as the insect pathogen B. thuringiensis By using the variety of typing schemes employed by BTyper, users can rapidly classify, characterize, and assess the virulence potential of any isolate using its nucleotide sequencing data.", "doi": "10.1128/AEM.01096-17", "pmid": "28625989", "labels": {"Laura Carroll": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC5561296"}, {"db": "pii", "key": "AEM.01096-17"}], "notes": [], "created": "2025-03-18T17:21:39.987Z", "modified": "2025-03-18T17:22:23.988Z"}, {"entity": "publication", "iuid": "aa7318a48c314f4d91e0ea9c9128a310", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/aa7318a48c314f4d91e0ea9c9128a310.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/aa7318a48c314f4d91e0ea9c9128a310"}}, "title": "Working toward precision medicine: Predicting phenotypes from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges.", "authors": [{"family": "Daneshjou", "given": "Roxana", "initials": "R", "orcid": "0000-0001-7988-9356", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f3cdccf2b26c4825a9d4420c407266c0.json"}}, {"family": "Wang", "given": "Yanran", "initials": "Y"}, {"family": "Bromberg", "given": "Yana", "initials": "Y"}, {"family": "Bovo", "given": "Samuele", "initials": "S"}, {"family": "Martelli", "given": "Pier L", "initials": "PL"}, {"family": "Babbi", "given": "Giulia", "initials": "G"}, {"family": "Lena", "given": "Pietro Di", "initials": "PD"}, {"family": "Casadio", "given": "Rita", "initials": "R"}, {"family": "Edwards", "given": "Matthew", "initials": "M", "orcid": "0000-0002-5845-748X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/61ce728f30544d628b8edd1bcd349b6a.json"}}, {"family": "Gifford", "given": "David", "initials": "D"}, {"family": "Jones", "given": "David T", "initials": "DT"}, {"family": "Sundaram", "given": "Laksshman", "initials": "L"}, {"family": "Bhat", "given": "Rajendra Rana", "initials": "RR"}, {"family": "Li", "given": "Xiaolin", "initials": "X"}, {"family": "Pal", "given": "Lipika R", "initials": "LR"}, {"family": "Kundu", "given": "Kunal", "initials": "K"}, {"family": "Yin", "given": "Yizhou", "initials": "Y"}, {"family": "Moult", "given": "John", "initials": "J", "orcid": "0000-0002-3012-2282", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eecbcb5d519340c786c29125d8ee994d.json"}}, {"family": "Jiang", "given": "Yuxiang", "initials": "Y"}, {"family": "Pejaver", "given": "Vikas", "initials": "V"}, {"family": "Pagel", "given": "Kymberleigh A", "initials": "KA"}, {"family": "Li", "given": "Biao", "initials": "B"}, {"family": "Mooney", "given": "Sean D", "initials": "SD", "orcid": "0000-0003-2654-0833", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/13d8f4ee95304bf49d0a62c6381ba168.json"}}, {"family": "Radivojac", "given": "Predrag", "initials": "P"}, {"family": "Shah", "given": "Sohela", "initials": "S"}, {"family": "Carraro", "given": "Marco", "initials": "M"}, {"family": "Gasparini", "given": "Alessandra", "initials": "A"}, {"family": "Leonardi", "given": "Emanuela", "initials": "E"}, {"family": "Giollo", "given": "Manuel", "initials": "M"}, {"family": "Ferrari", "given": "Carlo", "initials": "C"}, {"family": "Tosatto", "given": "Silvio C E", "initials": "SCE", "orcid": "0000-0003-4525-7793", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/152b8eca864e44f1954ee4952c60aa0d.json"}}, {"family": "Bachar", "given": "Eran", "initials": "E"}, {"family": "Azaria", "given": "Johnathan R", "initials": "JR"}, {"family": "Ofran", "given": "Yanay", "initials": "Y"}, {"family": "Unger", "given": "Ron", "initials": "R"}, {"family": "Niroula", "given": "Abhishek", "initials": "A", "orcid": "0000-0002-5904-0635", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/05df7afc7a494ba5af8a378e5ffa53f0.json"}}, {"family": "Vihinen", "given": "Mauno", "initials": "M"}, {"family": "Chang", "given": "Billy", "initials": "B"}, {"family": "Wang", "given": "Maggie H", "initials": "MH", "orcid": "0000-0003-1223-4595", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/839870522504426ebb2831d9a52ba8fb.json"}}, {"family": "Franke", "given": "Andre", "initials": "A"}, {"family": "Petersen", "given": "Britt-Sabina", "initials": "BS"}, {"family": "Pirooznia", "given": "Mehdi", "initials": "M"}, {"family": "Zandi", "given": "Peter", "initials": "P"}, {"family": "McCombie", "given": "Richard", "initials": "R"}, {"family": "Potash", "given": "James B", "initials": "JB"}, {"family": "Altman", "given": "Russ B", "initials": "RB"}, {"family": "Klein", "given": "Teri E", "initials": "TE"}, {"family": "Hoskins", "given": "Roger A", "initials": "RA"}, {"family": "Repo", "given": "Susanna", "initials": "S"}, {"family": "Brenner", "given": "Steven E", "initials": "SE"}, {"family": "Morgan", "given": "Alexander A", "initials": "AA"}], "type": "journal article", "published": "2017-09-00", "journal": {"title": "Hum. Mutat.", "issn": "1098-1004", "volume": "38", "issue": "9", "pages": "1182-1192", "issn-l": "1059-7794"}, "abstract": "Precision medicine aims to predict a patient's disease risk and best therapeutic options by using that individual's genetic sequencing data. The Critical Assessment of Genome Interpretation (CAGI) is a community experiment consisting of genotype-phenotype prediction challenges; participants build models, undergo assessment, and share key findings. For CAGI 4, three challenges involved using exome-sequencing data: Crohn's disease, bipolar disorder, and warfarin dosing. Previous CAGI challenges included prior versions of the Crohn's disease challenge. Here, we discuss the range of techniques used for phenotype prediction as well as the methods used for assessing predictive models. Additionally, we outline some of the difficulties associated with making predictions and evaluating them. The lessons learned from the exome challenges can be applied to both research and clinical efforts to improve phenotype prediction from genotype. In addition, these challenges serve as a vehicle for sharing clinical and research exome data in a secure manner with scientists who have a broad range of expertise, contributing to a collaborative effort to advance our understanding of genotype-phenotype relationships.", "doi": "10.1002/humu.23280", "pmid": "28634997", "labels": {"Abhishek Niroula": null, "DDLS Fellow": null}, "xrefs": [{"db": "mid", "key": "NIHMS885554"}, {"db": "pmc", "key": "PMC5600620"}], "notes": [], "created": "2023-11-20T10:43:39.086Z", "modified": "2023-11-20T10:43:39.629Z"}, {"entity": "publication", "iuid": "3640b43712bb4610b77a737f0fee2c3a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3640b43712bb4610b77a737f0fee2c3a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3640b43712bb4610b77a737f0fee2c3a"}}, "title": "Performance of in silico tools for the evaluation of p16INK4a (CDKN2A) variants in CAGI.", "authors": [{"family": "Carraro", "given": "Marco", "initials": "M"}, {"family": "Minervini", "given": "Giovanni", "initials": "G"}, {"family": "Giollo", "given": "Manuel", "initials": "M"}, {"family": "Bromberg", "given": "Yana", "initials": "Y"}, {"family": "Capriotti", "given": "Emidio", "initials": "E"}, {"family": "Casadio", "given": "Rita", "initials": "R"}, {"family": "Dunbrack", "given": "Roland", "initials": "R", "orcid": "0000-0001-7674-6667", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/699c3665247f42ae802d5d2c010b8076.json"}}, {"family": "Elefanti", "given": "Lisa", "initials": "L"}, {"family": "Fariselli", "given": "Pietro", "initials": "P"}, {"family": "Ferrari", "given": "Carlo", "initials": "C"}, {"family": "Gough", "given": "Julian", "initials": "J"}, {"family": "Katsonis", "given": "Panagiotis", "initials": "P", "orcid": "0000-0002-7172-1644", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a3584cc414864b3aa35b01ccae57d49c.json"}}, {"family": "Leonardi", "given": "Emanuela", "initials": "E"}, {"family": "Lichtarge", "given": "Olivier", "initials": "O"}, {"family": "Menin", "given": "Chiara", "initials": "C"}, {"family": "Martelli", "given": "Pier Luigi", "initials": "PL"}, {"family": "Niroula", "given": "Abhishek", "initials": "A", "orcid": "0000-0002-5904-0635", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/05df7afc7a494ba5af8a378e5ffa53f0.json"}}, {"family": "Pal", "given": "Lipika R", "initials": "LR"}, {"family": "Repo", "given": "Susanna", "initials": "S"}, {"family": "Scaini", "given": "Maria Chiara", "initials": "MC"}, {"family": "Vihinen", "given": "Mauno", "initials": "M"}, {"family": "Wei", "given": "Qiong", "initials": "Q"}, {"family": "Xu", "given": "Qifang", "initials": "Q"}, {"family": "Yang", "given": "Yuedong", "initials": "Y"}, {"family": "Yin", "given": "Yizhou", "initials": "Y"}, {"family": "Zaucha", "given": "Jan", "initials": "J"}, {"family": "Zhao", "given": "Huiying", "initials": "H"}, {"family": "Zhou", "given": "Yaoqi", "initials": "Y"}, {"family": "Brenner", "given": "Steven E", "initials": "SE"}, {"family": "Moult", "given": "John", "initials": "J", "orcid": "0000-0002-3012-2282", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eecbcb5d519340c786c29125d8ee994d.json"}}, {"family": "Tosatto", "given": "Silvio C E", "initials": "SCE", "orcid": "0000-0003-4525-7793", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/152b8eca864e44f1954ee4952c60aa0d.json"}}], "type": "journal article", "published": "2017-09-00", "journal": {"title": "Hum. Mutat.", "issn": "1098-1004", "volume": "38", "issue": "9", "pages": "1042-1050", "issn-l": "1059-7794"}, "abstract": "Correct phenotypic interpretation of variants of unknown significance for cancer-associated genes is a diagnostic challenge as genetic screenings gain in popularity in the next-generation sequencing era. The Critical Assessment of Genome Interpretation (CAGI) experiment aims to test and define the state of the art of genotype-phenotype interpretation. Here, we present the assessment of the CAGI p16INK4a challenge. Participants were asked to predict the effect on cellular proliferation of 10 variants for the p16INK4a tumor suppressor, a cyclin-dependent kinase inhibitor encoded by the CDKN2A gene. Twenty-two pathogenicity predictors were assessed with a variety of accuracy measures for reliability in a medical context. Different assessment measures were combined in an overall ranking to provide more robust results. The R scripts used for assessment are publicly available from a GitHub repository for future use in similar assessment exercises. Despite a limited test-set size, our findings show a variety of results, with some methods performing significantly better. Methods combining different strategies frequently outperform simpler approaches. The best predictor, Yang&Zhou lab, uses a machine learning method combining an empirical energy function measuring protein stability with an evolutionary conservation term. The p16INK4a challenge highlights how subtle structural effects can neutralize otherwise deleterious variants.", "doi": "10.1002/humu.23235", "pmid": "28440912", "labels": {"Abhishek Niroula": null, "DDLS Fellow": null}, "xrefs": [{"db": "mid", "key": "NIHMS871420"}, {"db": "pmc", "key": "PMC5561474"}], "notes": [], "created": "2023-11-20T10:43:36.769Z", "modified": "2023-11-20T10:43:37.420Z"}, {"entity": "publication", "iuid": "ba3f265efaa0454391b830f16ed11279", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ba3f265efaa0454391b830f16ed11279.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ba3f265efaa0454391b830f16ed11279"}}, "title": "PON-P and PON-P2 predictor performance in CAGI challenges: Lessons learned.", "authors": [{"family": "Niroula", "given": "Abhishek", "initials": "A"}, {"family": "Vihinen", "given": "Mauno", "initials": "M"}], "type": "journal article", "published": "2017-09-00", "journal": {"title": "Hum. Mutat.", "issn": "1098-1004", "volume": "38", "issue": "9", "pages": "1085-1091", "issn-l": "1059-7794"}, "abstract": "Computational tools are widely used for ranking and prioritizing variants for characterizing their disease relevance. Since numerous tools have been developed, they have to be properly assessed before being applied. Critical Assessment of Genome Interpretation (CAGI) experiments have significantly contributed toward the assessment of prediction methods for various tasks. Within and outside the CAGI, we have addressed several questions that facilitate development and assessment of variation interpretation tools. These areas include collection and distribution of benchmark datasets, their use for systematic large-scale method assessment, and the development of guidelines for reporting methods and their performance. For us, CAGI has provided a chance to experiment with new ideas, test the application areas of our methods, and network with other prediction method developers. In this article, we discuss our experiences and lessons learned from the various CAGI challenges. We describe our approaches, their performance, and impact of CAGI on our research. Finally, we discuss some of the possibilities that CAGI experiments have opened up and make some suggestions for future experiments.", "doi": "10.1002/humu.23199", "pmid": "28224672", "labels": {"Abhishek Niroula": null, "DDLS Fellow": null}, "xrefs": [{"db": "mid", "key": "NIHMS854618"}, {"db": "pmc", "key": "PMC5561442"}], "notes": [], "created": "2023-11-20T10:43:35.367Z", "modified": "2023-11-20T10:43:35.370Z"}, {"entity": "publication", "iuid": "3dd620737efa46b0bd712c488765d3b8", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3dd620737efa46b0bd712c488765d3b8.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3dd620737efa46b0bd712c488765d3b8"}}, "title": "Genome scale metabolic modeling of cancer.", "authors": [{"family": "Nilsson", "given": "Avlant", "initials": "A", "orcid": "0000-0002-9476-4516", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f2e21dbc1c624f6a841c59e959e948e4.json"}}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/33f2b49a39ed4e54ba77dfe397ed3087.json"}}], "type": "journal article", "published": "2017-09-00", "journal": {"title": "Metab. Eng.", "issn": "1096-7184", "issn-l": "1096-7176", "volume": "43", "issue": "Pt B", "pages": "103-112"}, "abstract": "Cancer cells reprogram metabolism to support rapid proliferation and survival. Energy metabolism is particularly important for growth and genes encoding enzymes involved in energy metabolism are frequently altered in cancer cells. A genome scale metabolic model (GEM) is a mathematical formalization of metabolism which allows simulation and hypotheses testing of metabolic strategies. It has successfully been applied to many microorganisms and is now used to study cancer metabolism. Generic models of human metabolism have been reconstructed based on the existence of metabolic genes in the human genome. Cancer specific models of metabolism have also been generated by reducing the number of reactions in the generic model based on high throughput expression data, e.g. transcriptomics and proteomics. Targets for drugs and bio markers for diagnostics have been identified using these models. They have also been used as scaffolds for analysis of high throughput data to allow mechanistic interpretation of changes in expression. Finally, GEMs allow quantitative flux predictions using flux balance analysis (FBA). Here we critically review the requirements for successful FBA simulations of cancer cells and discuss the symmetry between the methods used for modeling of microbial and cancer metabolism. GEMs have great potential for translational research on cancer and will therefore become of increasing importance in the future.", "doi": "10.1016/j.ymben.2016.10.022", "pmid": "27825806", "labels": {"Avlant Nilsson": null, "DDLS Fellow": null}, "xrefs": [{"db": "pii", "key": "S1096-7176(16)30212-9"}], "notes": [], "created": "2025-03-20T11:06:20.312Z", "modified": "2025-03-21T13:15:02.826Z"}, {"entity": "publication", "iuid": "e93a106b33454cf6997416df80d12c91", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e93a106b33454cf6997416df80d12c91.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e93a106b33454cf6997416df80d12c91"}}, "title": "An untypeable enterotoxigenic Escherichia coli represents one of the dominant types causing human disease.", "authors": [{"family": "Iguchi", "given": "Atsushi", "initials": "A"}, {"family": "von Mentzer", "given": "Astrid", "initials": "A"}, {"family": "Kikuchi", "given": "Taisei", "initials": "T"}, {"family": "Thomson", "given": "Nicholas R", "initials": "NR"}], "type": "journal article", "published": "2017-09-00", "journal": {"title": "Microb Genom", "issn": "2057-5858", "volume": "3", "issue": "9", "pages": "e000121", "issn-l": null}, "abstract": "Enterotoxigenic Escherichia coli (ETEC) is a major cause of diarrhoea in children below 5 years of age in endemic areas, and is a primary cause of diarrhoea in travellers visiting developing countries. Epidemiological analysis of E. coli pathovars is traditionally carried out based on the results of serotyping. However, genomic analysis of a global ETEC collection of 362 isolates taken from patients revealed nine novel O-antigen biosynthesis gene clusters that were previously unrecognized, and have collectively been called unclassified. When put in the context of all isolates sequenced, one of the novel O-genotypes, OgN5, was found to be the second most common ETEC O-genotype causing disease, after O6, in a globally representative ETEC collection. It's also clear that ETEC OgN5 isolates have spread globally. These novel O-genotypes have now been included in our comprehensive O-genotyping scheme, and can be detected using a PCR-based and an in silico typing method. This will assist in epidemiological studies, as well as in ETEC vaccine development.", "doi": "10.1099/mgen.0.000121", "pmid": "29114400", "labels": {"Astrid von Mentzer": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC5643014"}], "notes": [], "created": "2025-12-02T15:48:54.975Z", "modified": "2025-12-02T15:48:54.993Z"}, {"entity": "publication", "iuid": "96c1d5dbe4a04df893cb0a04749db0bb", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/96c1d5dbe4a04df893cb0a04749db0bb.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/96c1d5dbe4a04df893cb0a04749db0bb"}}, "title": "A pathology atlas of the human cancer transcriptome.", "authors": [{"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ea446aa574042a295d5f69437402f76.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f46e4161be08458994efddb75ed75874.json"}}, {"family": "Lee", "given": "Sunjae", "initials": "S", "orcid": "0000-0002-6428-5936", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9c0d15b9219a462a868adab9f428e5fa.json"}}, {"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E", "orcid": "0000-0002-0327-7377", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ec6fb5a1c88b44798144fd2de255fb00.json"}}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/abbbf8193d5a4376a5c726768d039439.json"}}, {"family": "Bidkhori", "given": "Gholamreza", "initials": "G", "orcid": "0000-0001-5232-6094", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4cfd96c1edb4b7abfc0f25949b9e4ef.json"}}, {"family": "Benfeitas", "given": "Rui", "initials": "R", "orcid": "0000-0001-7972-0083", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e2ec344c501496796be3250fd563699.json"}}, {"family": "Arif", "given": "Muhammad", "initials": "M", "orcid": "0000-0003-2261-0881", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c8ffc9889ace44e3b992816601b817e2.json"}}, {"family": "Liu", "given": "Zhengtao", "initials": "Z", "orcid": "0000-0001-7803-6044", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9fa0caee72804459be90af5793c7326b.json"}}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e213b04f8984c8eb00c68f5bc2f6a36.json"}}, {"family": "Sanli", "given": "Kemal", "initials": "K"}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K", "orcid": "0000-0002-0257-7554", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f4c4545bd2324b7d9b6696dab5bcb7dd.json"}}, {"family": "Oksvold", "given": "Per", "initials": "P", "orcid": "0000-0003-3014-5502", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/16beca5822c747128300910b5c74dbfc.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb07e6d0122c4528a927c1fe922e3bc8.json"}}, {"family": "Hober", "given": "Sophia", "initials": "S", "orcid": "0000-0003-0605-8417", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4a1bdfd8500c4dbea343132bc0d8e44c.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3db33fa3edb94febb8be7927a16838d0.json"}}, {"family": "Mattsson", "given": "Johanna", "initials": "J", "orcid": "0000-0002-2266-7629", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5077c51b610a49cb9e628fb1e02d6daa.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/022e140799b6466ea123319c3d70c76e.json"}}, {"family": "Brunnstr\u00f6m", "given": "Hans", "initials": "H", "orcid": "0000-0001-7402-138X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1b51d0768d1a4c31bba8cf898f962a09.json"}}, {"family": "Glimelius", "given": "Bengt", "initials": "B", "orcid": "0000-0002-5440-791X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0a4a4dfe9cc6478baaaae4672181691c.json"}}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T", "orcid": "0000-0001-6668-4140", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/851b95a56b3244fb9bc7cec8294e7ae7.json"}}, {"family": "Edqvist", "given": "Per-Henrik", "initials": "PH", "orcid": "0000-0002-8330-0134", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5219527c2dc6480da474f3c47dff9318.json"}}, {"family": "Djureinovic", "given": "Dijana", "initials": "D", "orcid": "0000-0002-1852-5409", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f2806baba4d6477a89ffd4100ae6ea5e.json"}}, {"family": "Micke", "given": "Patrick", "initials": "P", "orcid": "0000-0003-1210-5961", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8b4b9d0f748440e19db93d4543bbe25f.json"}}, {"family": "Lindskog", "given": "Cecilia", "initials": "C", "orcid": "0000-0001-5611-1015", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/21610a810a87459c962d6da3f2ad38ad.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca58bf2d214047e0ae5e38a42a0f2808.json"}}, {"family": "Ponten", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9f5294424542413c9ba4432c839c2b63.json"}}], "type": "journal article", "published": "2017-08-18", "journal": {"title": "Science (New York, N.Y.)", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "357", "issue": "6352", "pages": "eaan2507"}, "abstract": "Cancer is one of the leading causes of death, and there is great interest in understanding the underlying molecular mechanisms involved in the pathogenesis and progression of individual tumors. We used systems-level approaches to analyze the genome-wide transcriptome of the protein-coding genes of 17 major cancer types with respect to clinical outcome. A general pattern emerged: Shorter patient survival was associated with up-regulation of genes involved in cell growth and with down-regulation of genes involved in cellular differentiation. Using genome-scale metabolic models, we show that cancer patients have widespread metabolic heterogeneity, highlighting the need for precise and personalized medicine for cancer treatment. All data are presented in an interactive open-access database (www.proteinatlas.org/pathology) to allow genome-wide exploration of the impact of individual proteins on clinical outcomes.", "doi": "10.1126/science.aan2507", "pmid": "28818916", "labels": {"Affiliated researcher": "", "Adil Mardinoglu": "", "SciLifeLab Fellow": "", "Fredrik Edfors": "", "DDLS Fellow": "", "Muhammad Arif": ""}, "xrefs": [{"db": "pii", "key": "357/6352/eaan2507"}], "notes": [], "created": "2018-12-03T14:43:54.058Z", "modified": "2026-09-22T19:57:42.190Z"}, {"entity": "publication", "iuid": "12bfd0e40d794da6aab1921cd13e5888", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/12bfd0e40d794da6aab1921cd13e5888.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/12bfd0e40d794da6aab1921cd13e5888"}}, "title": "The complete mitochondrial genome of the copepod Calanus glacialis.", "authors": [{"family": "Choquet", "given": "Marvin", "initials": "M", "orcid": "0000-0001-6719-2332", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/82aa1d0fa21743698c6746b667391028.json"}}, {"family": "Alves Monteiro", "given": "Hom\u00e8re J", "initials": "HJ"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Hoarau", "given": "Galice", "initials": "G"}], "type": "journal article", "published": "2017-08-06", "journal": {"title": "Mitochondrial DNA B Resour", "issn": "2380-2359", "volume": "2", "issue": "2", "pages": "506-507", "issn-l": null}, "abstract": "Calanus glacialis, a marine planktonic copepod, is a keystone species in the Arctic Ocean. In this study, we shotgun sequenced the total DNA of one C. glacialis individual, using the NextSeq\u00ae Illumina platform, in order to determine its mitochondrial genome sequence. We successfully assembled and annotated this 20,674 bp long sequence, which included 13 protein-coding genes, 2 rRNA genes and 22 tRNA genes. Common gene-coding regions of 19 other species were used to reconstruct a phylogenetic tree, using mitogenomes of the phylogenetically closest copepods available. The new resource described here constitutes a tool of interest for better understanding the structure and dynamics of C. glacialis populations.", "doi": "10.1080/23802359.2017.1361357", "pmid": "33473877", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pii", "key": "1361357"}, {"db": "pmc", "key": "PMC7799568"}], "notes": [], "created": "2022-11-08T09:29:18.301Z", "modified": "2022-11-08T09:29:18.376Z"}, {"entity": "publication", "iuid": "bbf556784ee1423cbf2af439d2dc824c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/bbf556784ee1423cbf2af439d2dc824c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/bbf556784ee1423cbf2af439d2dc824c"}}, "title": "Improving the phenotype predictions of a yeast genome-scale metabolic model by incorporating enzymatic constraints.", "authors": [{"family": "S\u00e1nchez", "given": "Benjam\u00edn J", "initials": "BJ", "orcid": "0000-0001-6093-4110", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d5c008a0fbd646fab02156701275efbc.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f46e4161be08458994efddb75ed75874.json"}}, {"family": "Nilsson", "given": "Avlant", "initials": "A", "orcid": "0000-0002-9476-4516", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f2e21dbc1c624f6a841c59e959e948e4.json"}}, {"family": "Lahtvee", "given": "Petri-Jaan", "initials": "PJ", "orcid": "0000-0002-3327-3190", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/14e86c856a2e4b03a61e0285aee2166d.json"}}, {"family": "Kerkhoven", "given": "Eduard J", "initials": "EJ", "orcid": "0000-0002-3593-5792", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/182c8731b6744479864cc75ced13d229.json"}}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/33f2b49a39ed4e54ba77dfe397ed3087.json"}}], "type": "journal article", "published": "2017-08-03", "journal": {"title": "Mol Syst Biol", "issn": "1744-4292", "volume": "13", "issue": "8", "pages": "935", "issn-l": "1744-4292"}, "abstract": "Genome-scale metabolic models (GEMs) are widely used to calculate metabolic phenotypes. They rely on defining a set of constraints, the most common of which is that the production of metabolites and/or growth are limited by the carbon source uptake rate. However, enzyme abundances and kinetics, which act as limitations on metabolic fluxes, are not taken into account. Here, we present GECKO, a method that enhances a GEM to account for enzymes as part of reactions, thereby ensuring that each metabolic flux does not exceed its maximum capacity, equal to the product of the enzyme's abundance and turnover number. We applied GECKO to a Saccharomyces cerevisiae GEM and demonstrated that the new model could correctly describe phenotypes that the previous model could not, particularly under high enzymatic pressure conditions, such as yeast growing on different carbon sources in excess, coping with stress, or overexpressing a specific pathway. GECKO also allows to directly integrate quantitative proteomics data; by doing so, we significantly reduced flux variability of the model, in over 60% of metabolic reactions. Additionally, the model gives insight into the distribution of enzyme usage between and within metabolic pathways. The developed method and model are expected to increase the use of model-based design in metabolic engineering.", "doi": "10.15252/msb.20167411", "pmid": "28779005", "labels": {"Avlant Nilsson": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC5572397"}], "notes": [], "created": "2018-12-05T11:16:03.593Z", "modified": "2026-09-23T06:32:56.109Z"}, {"entity": "publication", "iuid": "49447c9046ef4ccc9f8574176dfe5c65", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/49447c9046ef4ccc9f8574176dfe5c65.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/49447c9046ef4ccc9f8574176dfe5c65"}}, "title": "p16(Ink4a) and senescence-associated \u03b2-galactosidase can be induced in macrophages as part of a reversible response to physiological stimuli.", "authors": [{"family": "Hall", "given": "Brandon M", "initials": "BM"}, {"family": "Balan", "given": "Vitaly", "initials": "V"}, {"family": "Gleiberman", "given": "Anatoli S", "initials": "AS"}, {"family": "Strom", "given": "Evguenia", "initials": "E"}, {"family": "Krasnov", "given": "Peter", "initials": "P"}, {"family": "Virtuoso", "given": "Lauren P", "initials": "LP"}, {"family": "Rydkina", "given": "Elena", "initials": "E"}, {"family": "Vujcic", "given": "Slavoljub", "initials": "S"}, {"family": "Balan", "given": "Karina", "initials": "K"}, {"family": "Gitlin", "given": "Ilya I", "initials": "II"}, {"family": "Leonova", "given": "Katerina I", "initials": "KI"}, {"family": "Consiglio", "given": "Camila R", "initials": "CR"}, {"family": "Gollnick", "given": "Sandra O", "initials": "SO"}, {"family": "Chernova", "given": "Olga B", "initials": "OB"}, {"family": "Gudkov", "given": "Andrei V", "initials": "AV"}], "type": "comparative study", "published": "2017-08-02", "journal": {"title": "Aging (Albany NY)", "issn": "1945-4589", "volume": "9", "issue": "8", "pages": "1867-1884", "issn-l": null}, "abstract": "Constitutive p16 expression, along with senescence-associated \u03b2-galactosidase (SA\u03b2G), are commonly accepted biomarkers of senescent cells (SCs). Recent reports attributed improvement of the healthspan of aged mice following Ink4ap16-positive cell killing to the eradication of accumulated SCs. However, detection of Ink4ap16/SA\u03b2G-positive macrophages in the adipose tissue of old mice and in the peritoneal cavity of young animals following injection of alginate-encapsulated SCs has raised concerns about the exclusivity of these markers for SCs. Here we report that expression of Ink4ap16 and SA\u03b2G in macrophages is acquired as part of a physiological response to immune stimuli rather than through senescence, consistent with reports that p16Ink4aInk4a plays a role in macrophage polarization and response. Unlike SCs, p16/SA\u03b2G-positive macrophages can be induced in p53-null mice. Macrophages, but not mesenchymal SCs, lose both markers in response to M1- [LPS, IFN-\u03b1, Poly(I:C)] and increase their expression in response to M2-inducing stimuli (IL-4, IL-13). Moreover, interferon-inducing agent Poly(I:C) dramatically reduced Ink4ap16 expression Ink4ain vivo in our alginate bead model and in the adipose tissue of aged mice. These observations suggest that the antiaging effects following eradication of p16-positive cells may not be solely attributed to SCs but also to non-senescent Ink4ap16/SA\u03b2G-positive macrophages.Ink4a", "doi": "10.18632/aging.101268", "pmid": "28768895", "labels": {"Camila Consiglio": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC5611982"}, {"db": "pii", "key": "101268"}], "notes": [], "created": "2023-11-22T09:17:49.398Z", "modified": "2023-11-22T09:17:49.446Z"}, {"entity": "publication", "iuid": "7a505a055f614a3bba6c459da4c80894", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/7a505a055f614a3bba6c459da4c80894.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/7a505a055f614a3bba6c459da4c80894"}}, "title": "Does antifouling paint select for antibiotic resistance?", "authors": [{"family": "Flach", "given": "Carl-Fredrik", "initials": "CF"}, {"family": "Pal", "given": "Chandan", "initials": "C"}, {"family": "Svensson", "given": "Carl Johan", "initials": "CJ"}, {"family": "Kristiansson", "given": "Erik", "initials": "E"}, {"family": "\u00d6stman", "given": "Marcus", "initials": "M"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Tysklind", "given": "Mats", "initials": "M"}, {"family": "Larsson", "given": "D G Joakim", "initials": "DGJ"}], "type": "journal article", "published": "2017-07-15", "journal": {"title": "Sci. Total Environ.", "issn": "1879-1026", "volume": "590-591", "pages": "461-468", "issn-l": "0048-9697"}, "abstract": "There is concern that heavy metals and biocides contribute to the development of antibiotic resistance via co-selection. Most antifouling paints contain high amounts of such substances, which risks turning painted ship hulls into highly mobile refuges and breeding grounds for antibiotic-resistant bacteria. The objectives of this study were to start investigate if heavy-metal based antifouling paints can pose a risk for co-selection of antibiotic-resistant bacteria and, if so, identify the underlying genetic basis. Plastic panels with one side painted with copper and zinc-containing antifouling paint were submerged in a Swedish marina and biofilms from both sides of the panels were harvested after 2.5-4weeks. DNA was isolated from the biofilms and subjected to metagenomic sequencing. Biofilm bacteria were cultured on marine agar supplemented with tetracycline, gentamicin, copper sulfate or zinc sulfate. Biofilm communities from painted surfaces displayed lower taxonomic diversity and enrichment of Gammaproteobacteria. Bacteria from these communities showed increased resistance to both heavy metals and tetracycline but not to gentamicin. Significantly higher abundance of metal and biocide resistance genes was observed, whereas mobile antibiotic resistance genes were not enriched in these communities. In contrast, we found an enrichment of chromosomal RND efflux system genes, including such with documented ability to confer decreased susceptibility to both antibiotics and biocides/heavy metals. This was paralleled by increased abundances of integron-associated integrase and ISCR transposase genes. The results show that the heavy metal-based antifouling paint exerts a strong selection pressure on marine bacterial communities and can co-select for certain antibiotic-resistant bacteria, likely by favoring species and strains carrying genes that provide cross-resistance. Although this does not indicate an immediate risk for promotion of mobile antibiotic resistance, the clear increase of genes involved in mobilizing DNA provides a foundation for increased opportunities for gene transfer in such communities, which might also involve yet unknown resistance mechanisms.", "doi": "10.1016/j.scitotenv.2017.01.213", "pmid": "28284638", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pii", "key": "S0048-9697(17)30230-9"}], "notes": [], "created": "2022-11-08T09:29:25.463Z", "modified": "2022-11-08T09:29:25.490Z"}, {"entity": "publication", "iuid": "ad0fda02bf0b4d2b9d39efae19bc03e9", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ad0fda02bf0b4d2b9d39efae19bc03e9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ad0fda02bf0b4d2b9d39efae19bc03e9"}}, "title": "Mineral Type Structures Soil Microbial Communities", "authors": [{"family": "Ahmed", "given": "Engy", "initials": "E", "orcid": "0000-0002-1386-134X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4d72646279dd40e1a5549232e3dbce5a.json"}}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW", "orcid": "0000-0001-5432-1764", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/246ed7b405dd4c3f9ec5e7ff9f1d3ade.json"}}, {"family": "Logue", "given": "J\u00fcrg B", "initials": "JB"}, {"family": "Br\u00fcchert", "given": "Volker", "initials": "V"}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cc9be99ec6ca47ed8a805ebb4db7c168.json"}}, {"family": "Holmstr\u00f6m", "given": "Sara J M", "initials": "SJM"}], "type": "journal-article", "published": "2017-07-03", "journal": {"title": "Geomicrobiology Journal", "issn": "0149-0451", "volume": "34", "issue": "6", "pages": "538-545", "issn-l": null}, "abstract": null, "doi": "10.1080/01490451.2016.1225868", "pmid": null, "labels": {"Affiliated researcher": "", "Luisa Hugerth": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2018-12-05T13:16:09.801Z", "modified": "2026-09-23T11:42:21.908Z"}, {"entity": "publication", "iuid": "995f674f4df942efa5673b3eb84f9581", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/995f674f4df942efa5673b3eb84f9581.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/995f674f4df942efa5673b3eb84f9581"}}, "title": "Evaluating and optimizing the performance of software commonly used for the taxonomic classification of DNA metabarcoding sequence data.", "authors": [{"family": "Richardson", "given": "Rodney T", "initials": "RT"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Johnson", "given": "Reed M", "initials": "RM"}], "type": "journal article", "published": "2017-07-00", "journal": {"title": "Mol Ecol Resour", "issn": "1755-0998", "volume": "17", "issue": "4", "pages": "760-769", "issn-l": "1755-098X"}, "abstract": "The taxonomic classification of DNA sequences has become a critical component of numerous ecological research applications; however, few studies have evaluated the strengths and weaknesses of commonly used sequence classification approaches. Further, the methods and software available for sequence classification are diverse, creating an environment in which it may be difficult to determine the best course of action and the trade-offs made using different classification approaches. Here, we provide an in silico evaluation of three DNA sequence classifiers, the rdp Na\u00efve Bayesian Classifier, rtax and utax. Further, we discuss the results, merits and limitations of both the classifiers and our method of classifier evaluation. Our methods of comparison are simple, yet robust, and will provide researchers a methodological and conceptual foundation for making such evaluations in a variety of research situations. Generally, we found a considerable trade-off between accuracy and sensitivity for the classifiers tested, indicating a need for further improvement of sequence classification tools.", "doi": "10.1111/1755-0998.12628", "pmid": "27797448", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [], "notes": [], "created": "2022-11-08T09:29:27.698Z", "modified": "2022-11-08T09:29:27.723Z"}, {"entity": "publication", "iuid": "8f80e77b96e2483b808be44ddc39ce2e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8f80e77b96e2483b808be44ddc39ce2e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8f80e77b96e2483b808be44ddc39ce2e"}}, "title": "A durable and biocompatible ascorbic acid-based covalent coating method of polydimethylsiloxane for dynamic cell culture.", "authors": [{"family": "Leivo", "given": "Joni", "initials": "J"}, {"family": "Virjula", "given": "Sanni", "initials": "S", "orcid": "0000-0002-3950-472X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/85ef10e4b79546df8ce63252cfaf5869.json"}}, {"family": "Vanhatupa", "given": "Sari", "initials": "S"}, {"family": "Kartasalo", "given": "Kimmo", "initials": "K"}, {"family": "Kreutzer", "given": "Joose", "initials": "J"}, {"family": "Miettinen", "given": "Susanna", "initials": "S"}, {"family": "Kallio", "given": "Pasi", "initials": "P", "orcid": "0000-0002-2890-6782", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d51a1d33f2c347deba15f9cbc0a3e8b5.json"}}], "type": "journal article", "published": "2017-07-00", "journal": {"title": "J R Soc Interface", "issn": "1742-5662", "issn-l": null, "volume": "14", "issue": "132", "pages": null}, "abstract": "Polydimethylsiloxane (PDMS) is widely used in dynamic biological microfluidic applications. As a highly hydrophobic material, native PDMS does not support cell attachment and culture, especially in dynamic conditions. Previous covalent coating methods use glutaraldehyde (GA) which, however, is cytotoxic. This paper introduces a novel and simple method for binding collagen type I covalently on PDMS using ascorbic acid (AA) as a cross-linker instead of GA. We compare the novel method against physisorption and GA cross-linker-based methods. The coatings are characterized by immunostaining, contact angle measurement, atomic force microscopy and infrared spectroscopy, and evaluated in static and stretched human adipose stem cell (hASC) cultures up to 13 days. We found that AA can replace GA as a cross-linker in the covalent coating method and that the coating is durable after sonication and after 6 days of stretching. Furthermore, we show that hASCs attach and proliferate better on AA cross-linked samples compared with physisorbed or GA-based methods. Thus, in this paper, we provide a new PDMS coating method for studying cells, such as hASCs, in static and dynamic conditions. The proposed method is an important step in the development of PDMS-based devices in cell and tissue engineering applications.", "doi": "10.1098/rsif.2017.0318", "pmid": "28747398", "labels": {"Kimmo Kartasalo": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC5550978"}, {"db": "pii", "key": "rsif.2017.0318"}], "notes": [], "created": "2024-11-05T16:04:32.172Z", "modified": "2024-11-29T12:05:48.640Z"}, {"entity": "publication", "iuid": "598e70b0ae3843ccbbb5b8118161f802", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/598e70b0ae3843ccbbb5b8118161f802.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/598e70b0ae3843ccbbb5b8118161f802"}}, "title": "Determination of bending rigidity and tilt modulus of lipid membranes from real-space fluctuation analysis of molecular dynamics simulations.", "authors": [{"family": "Doktorova", "given": "M", "initials": "M"}, {"family": "Harries", "given": "D", "initials": "D"}, {"family": "Khelashvili", "given": "G", "initials": "G"}], "type": "journal article", "published": "2017-06-28", "journal": {"title": "Phys Chem Chem Phys", "issn": "1463-9084", "issn-l": "1463-9076", "volume": "19", "issue": "25", "pages": "16806-16818"}, "abstract": "We have recently developed a novel computational methodology (termed RSF for Real-Space Fluctuations) to quantify the bending rigidity and tilt modulus of lipid membranes from real-space analysis of fluctuations in the tilt and splay degrees of freedom as sampled in molecular dynamics (MD) simulations. In this article, we present a comprehensive study that combines results from the application of the RSF method to a wide range of lipid bilayer systems that encompass membranes of different fluidities and sizes, including lipids with saturated and unsaturated lipid tails, single and multi-component lipid systems, as well as non-standard lipids such as the four-tailed cardiolipin. By comparing the material properties calculated with the RSF method to those obtained from experimental data and from other computational methodologies, we rigorously demonstrate the validity of our approach and show its robustness. This should allow for future applications of even more complex lipidic assemblies, whose material properties are not tractable by other computational techniques. In addition, we discuss the relationship between different definitions of the tilt modulus appearing in current literature to address some important unresolved discrepancies in the field.", "doi": "10.1039/c7cp01921a", "pmid": "28627570", "labels": {"Milka Doktorova": null, "DDLS Fellow": null}, "xrefs": [{"db": "mid", "key": "NIHMS886135"}, {"db": "pmc", "key": "PMC5538590"}], "notes": [], "created": "2024-11-27T12:29:35.347Z", "modified": "2024-11-29T12:17:18.795Z"}, {"entity": "publication", "iuid": "3ba86a1fe87745c3af23bfd6d76dcf76", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3ba86a1fe87745c3af23bfd6d76dcf76.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3ba86a1fe87745c3af23bfd6d76dcf76"}}, "title": "Whole-Genome Sequencing of Drug-Resistant Salmonella enterica Isolates from Dairy Cattle and Humans in New York and Washington States Reveals Source and Geographic Associations.", "authors": [{"family": "Carroll", "given": "Laura M", "initials": "LM"}, {"family": "Wiedmann", "given": "Martin", "initials": "M"}, {"family": "den Bakker", "given": "Henk", "initials": "H"}, {"family": "Siler", "given": "Julie", "initials": "J"}, {"family": "Warchocki", "given": "Steven", "initials": "S"}, {"family": "Kent", "given": "David", "initials": "D"}, {"family": "Lyalina", "given": "Svetlana", "initials": "S"}, {"family": "Davis", "given": "Margaret", "initials": "M"}, {"family": "Sischo", "given": "William", "initials": "W"}, {"family": "Besser", "given": "Thomas", "initials": "T"}, {"family": "Warnick", "given": "Lorin D", "initials": "LD"}, {"family": "Pereira", "given": "Richard V", "initials": "RV", "orcid": "0000-0003-2028-8761", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/259babf68c9e4d738c0a088d0ea27c0d.json"}}], "type": "journal article", "published": "2017-06-15", "journal": {"title": "Applied and environmental microbiology", "issn": "1098-5336", "volume": "83", "issue": "12", "issn-l": "0099-2240"}, "abstract": "Multidrug-resistant (MDR) Salmonella enterica can be spread from cattle to humans through direct contact with animals shedding Salmonella as well as through the food chain, making MDR Salmonella a serious threat to human health. The objective of this study was to use whole-genome sequencing to compare antimicrobial-resistant (AMR) Salmonella enterica serovars Typhimurium, Newport, and Dublin isolated from dairy cattle and humans in Washington State and New York State at the genotypic and phenotypic levels. A total of 90 isolates were selected for the study (37 S Typhimurium, 32 S Newport, and 21 S Dublin isolates). All isolates were tested for phenotypic antibiotic resistance to 12 drugs using Kirby-Bauer disk diffusion. AMR genes were detected in the assembled genome of each isolate using nucleotide BLAST and ARG-ANNOT. Genotypic prediction of phenotypic resistance resulted in a mean sensitivity of 97.2 and specificity of 85.2. Sulfamethoxazole-trimethoprim resistance was observed only in human isolates (P < 0.05), while resistance to quinolones and fluoroquinolones was observed only in 6 S Typhimurium isolates from humans in Washington State. S Newport isolates showed a high degree of AMR profile similarity, regardless of source. S Dublin isolates from New York State differed from those from Washington State based on the presence/absence of plasmid replicons, as well as phenotypic AMR susceptibility/nonsusceptibility (P < 0.05). The results of this study suggest that distinct factors may contribute to the emergence and dispersal of AMR S. enterica in humans and farm animals in different regions.IMPORTANCE The use of antibiotics in food-producing animals has been hypothesized to select for AMR Salmonella enterica and associated AMR determinants, which can be transferred to humans through different routes. Previous studies have sought to assess the degree to which AMR livestock- and human-associated Salmonella strains overlap, as well as the spatial distribution of Salmonella's associated AMR determinants, but have often been limited by the degree of resolution at which isolates can be compared. Here, a comparative genomics study of livestock- and human-associated Salmonella strains from different regions of the United States shows that while many AMR genes and phenotypes were confined to human isolates, overlaps between the resistomes of bovine and human-associated Salmonella isolates were observed on numerous occasions, particularly for S Newport. We have also shown that whole-genome sequencing can be used to reliably predict phenotypic resistance across Salmonella isolated from bovine sources.", "doi": "10.1128/AEM.00140-17", "pmid": "28389536", "labels": {"Laura Carroll": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC5452826"}, {"db": "pii", "key": "AEM.00140-17"}], "notes": [], "created": "2025-03-18T17:21:37.659Z", "modified": "2025-03-18T17:22:21.870Z"}, {"entity": "publication", "iuid": "8807f96189f64482a07e8a097e39e1cf", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8807f96189f64482a07e8a097e39e1cf.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8807f96189f64482a07e8a097e39e1cf"}}, "title": "Metastasis detection from whole slide images using local features and random forests.", "authors": [{"family": "Valkonen", "given": "Mira", "initials": "M"}, {"family": "Kartasalo", "given": "Kimmo", "initials": "K"}, {"family": "Liimatainen", "given": "Kaisa", "initials": "K"}, {"family": "Nykter", "given": "Matti", "initials": "M"}, {"family": "Latonen", "given": "Leena", "initials": "L"}, {"family": "Ruusuvuori", "given": "Pekka", "initials": "P"}], "type": "journal article", "published": "2017-06-00", "journal": {"title": "Cytometry A", "issn": "1552-4930", "issn-l": "1552-4922", "volume": "91", "issue": "6", "pages": "555-565"}, "abstract": "Digital pathology has led to a demand for automated detection of regions of interest, such as cancerous tissue, from scanned whole slide images. With accurate methods using image analysis and machine learning, significant speed-up, and savings in costs through increased throughput in histological assessment could be achieved. This article describes a machine learning approach for detection of cancerous tissue from scanned whole slide images. Our method is based on feature engineering and supervised learning with a random forest model. The features extracted from the whole slide images include several local descriptors related to image texture, spatial structure, and distribution of nuclei. The method was evaluated in breast cancer metastasis detection from lymph node samples. Our results show that the method detects metastatic areas with high accuracy (AUC = 0.97-0.98 for tumor detection within whole image area, AUC = 0.84-0.91 for tumor vs. normal tissue detection) and that the method generalizes well for images from more than one laboratory. Further, the method outputs an interpretable classification model, enabling the linking of individual features to differences between tissue types. \u00a9 2017 International Society for Advancement of Cytometry.", "doi": "10.1002/cyto.a.23089", "pmid": "28426134", "labels": {"Kimmo Kartasalo": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2024-11-05T16:04:31.056Z", "modified": "2024-11-29T12:05:56.034Z"}, {"entity": "publication", "iuid": "33d9812163c94901a2f9abd174eef32c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/33d9812163c94901a2f9abd174eef32c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/33d9812163c94901a2f9abd174eef32c"}}, "title": "Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life.", "authors": [{"family": "Wampach", "given": "Linda", "initials": "L"}, {"family": "Heintz-Buschart", "given": "Anna", "initials": "A"}, {"family": "Hogan", "given": "Angela", "initials": "A"}, {"family": "Muller", "given": "Emilie E L", "initials": "EEL"}, {"family": "Narayanasamy", "given": "Shaman", "initials": "S"}, {"family": "Laczny", "given": "Cedric C", "initials": "CC"}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW"}, {"family": "Bindl", "given": "Lutz", "initials": "L"}, {"family": "Bottu", "given": "Jean", "initials": "J"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}, {"family": "de Beaufort", "given": "Carine", "initials": "C"}, {"family": "Wilmes", "given": "Paul", "initials": "P"}], "type": "journal article", "published": "2017-05-02", "journal": {"title": "Front Microbiol", "issn": "1664-302X", "volume": "8", "issue": null, "pages": "738", "issn-l": "1664-302X"}, "abstract": "Perturbations to the colonization process of the human gastrointestinal tract have been suggested to result in adverse health effects later in life. Although much research has been performed on bacterial colonization and succession, much less is known about the other two domains of life, archaea, and eukaryotes. Here we describe colonization and succession by bacteria, archaea and microeukaryotes during the first year of life (samples collected around days 1, 3, 5, 28, 150, and 365) within the gastrointestinal tract of infants delivered either vaginally or by cesarean section and using a combination of quantitative real-time PCR as well as 16S and 18S rRNA gene amplicon sequencing. Sequences from organisms belonging to all three domains of life were detectable in all of the collected meconium samples. The microeukaryotic community composition fluctuated strongly over time and early diversification was delayed in infants receiving formula milk. Cesarean section-delivered (CSD) infants experienced a delay in colonization and succession, which was observed for all three domains of life. Shifts in prokaryotic succession in CSD infants compared to vaginally delivered (VD) infants were apparent as early as days 3 and 5, which were characterized by increased relative abundances of the genera Streptococcus and Staphylococcus, and a decrease in relative abundance for the genera Bifidobacterium and Bacteroides. Generally, a depletion in Bacteroidetes was detected as early as day 5 postpartum in CSD infants, causing a significantly increased Firmicutes/Bacteroidetes ratio between days 5 and 150 when compared to VD infants. Although the delivery mode appeared to have the strongest influence on differences between the infants, other factors such as a younger gestational age or maternal antibiotics intake likely contributed to the observed patterns as well. Our findings complement previous observations of a delay in colonization and succession of CSD infants, which affects not only bacteria but also archaea and microeukaryotes. This further highlights the need for resolving bacterial, archaeal, and microeukaryotic dynamics in future longitudinal studies of microbial colonization and succession within the neonatal gastrointestinal tract.", "doi": "10.3389/fmicb.2017.00738", "pmid": "28512451", "labels": {"Affiliated researcher": "", "Luisa Hugerth": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC5411419"}], "notes": [], "created": "2018-12-05T10:09:14.775Z", "modified": "2026-09-23T06:39:43.671Z"}, {"entity": "publication", "iuid": "582a51ea009447c784cef8d795486a28", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/582a51ea009447c784cef8d795486a28.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/582a51ea009447c784cef8d795486a28"}}, "title": "Temporal Genomic Phylogeny Reconstruction Indicates a Geospatial Transmission Path of Salmonella Cerro in the United States and a Clade-Specific Loss of Hydrogen Sulfide Production.", "authors": [{"family": "Kovac", "given": "Jasna", "initials": "J"}, {"family": "Cummings", "given": "Kevin J", "initials": "KJ"}, {"family": "Rodriguez-Rivera", "given": "Lorraine D", "initials": "LD"}, {"family": "Carroll", "given": "Laura M", "initials": "LM"}, {"family": "Thachil", "given": "Anil", "initials": "A"}, {"family": "Wiedmann", "given": "Martin", "initials": "M"}], "type": "journal article", "published": "2017-05-01", "journal": {"title": "Front Microbiol", "issn": "1664-302X", "volume": "8", "pages": "737", "issn-l": "1664-302X"}, "abstract": "Salmonella Cerro has become one of the most prevalent Salmonella serotypes isolated from dairy cattle in several U.S. states, including New York where it represented 36% of all Salmonella isolates of bovine origin in 2015. This serotype is commonly isolated from dairy cattle with clinical signs of salmonellosis, including diarrhea and fever, although it has also been identified in herds without evidence of clinical disease or decreased production. To better understand the transmission patterns and drivers of its geographic spread, we have studied the genomic similarity and microevolution of S. Cerro isolates from the northeast U.S. and Texas. Eighty-three out of 86 isolates were confirmed as multilocus sequence type 367. We identified core genome SNPs in 57 upstate New York (NY), 2 Pennsylvania (PA), and 27 Texas S. Cerro isolates from dairy cattle, farm environments, raw milk, and one human clinical case and used them to construct a tip-dated phylogeny. S. Cerro isolates clustered in three distinct clades, including (i) clade I (n = 3; 2013) comprising isolates from northwest Texas (NTX), (ii) clade II (n = 14; 2009-2011, 2014) comprising isolates from NY, and (iii) clade III comprising isolates from NY, PA, and central Texas (CTX) in subclade IIIa (n = 45; 2008-2014), and only CTX isolates in subclade IIIb (n = 24; 2013). Temporal phylogenetic analysis estimated the divergence of these three clades from the most recent common ancestor in approximately 1980. The CTX clade IIIb was estimated to have evolved and diverged from the NY ancestor around 2004. Furthermore, gradual temporal loss of genes encoding a D-alanine transporter, involved in virulence, was observed. These genes were present in the isolates endemic to NTX clade I and were gradually lost in clades II and III. The virulence gene orgA, which is part of the Salmonella Pathogenicity Island 1, was lost in a subgroup of Texas isolates in clades I and IIIb. All S. Cerro isolates had an additional cytosine inserted in a cytosine-rich region of the virulence gene sopA, resulting in premature termination of translation likely responsible for loss of pathogenic capacity in humans. A group of closely related NY isolates was characterized by the loss of hydrogen sulfide production due to the truncation or complete loss of phsA. Our data suggest the ability of Salmonella to rapidly diverge and adapt to specific niches (e.g., bovine niche), and to modify virulence-related characteristics such as the ability to utilize tetrathionate as an alternative electron acceptor, which is commonly used to detect Salmonella. Overall, our results show that clinical outcome data and genetic data for S. Cerro isolates, such as truncations in virulence genes leading to novel pheno- and pathotypes, should be correlated to allow for accurate risk assessment.", "doi": "10.3389/fmicb.2017.00737", "pmid": "28507536", "labels": {"Laura Carroll": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC5410586"}], "notes": [], "created": "2025-03-18T17:21:34.483Z", "modified": "2025-03-18T17:22:19.744Z"}, {"entity": "publication", "iuid": "a6d2c6238fdf43b383d5be6eda65f06c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a6d2c6238fdf43b383d5be6eda65f06c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a6d2c6238fdf43b383d5be6eda65f06c"}}, "title": "Ten simple rules for surviving an interdisciplinary PhD.", "authors": [{"family": "Demharter", "given": "Samuel", "initials": "S", "orcid": "0000-0001-7352-3994", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/88cc93b8315144c59d88ce19b585fc83.json"}}, {"family": "Pearce", "given": "Nicholas", "initials": "N", "orcid": "0000-0002-6693-8603", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/07d6d5de91cc4120b2bf996ca578a13e.json"}}, {"family": "Beattie", "given": "Kylie", "initials": "K"}, {"family": "Frost", "given": "Isabel", "initials": "I"}, {"family": "Leem", "given": "Jinwoo", "initials": "J", "orcid": "0000-0002-7817-3644", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4960217f023347039e979a6c422af4ca.json"}}, {"family": "Martin", "given": "Alistair", "initials": "A"}, {"family": "Oppenheimer", "given": "Robert", "initials": "R", "orcid": "0000-0001-5384-3261", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6dd7bfed793c4d669625f9de41a3580c.json"}}, {"family": "Regep", "given": "Cristian", "initials": "C"}, {"family": "Rukat", "given": "Tammo", "initials": "T", "orcid": "0000-0002-6186-0077", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/63f41563075541678184d19310eaa68d.json"}}, {"family": "Skates", "given": "Alexander", "initials": "A"}, {"family": "Trendel", "given": "Nicola", "initials": "N", "orcid": "0000-0002-8078-5068", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8ad9acc70a194b3f943ab081c8b06bf7.json"}}, {"family": "Gavaghan", "given": "David J", "initials": "DJ"}, {"family": "Deane", "given": "Charlotte M", "initials": "CM", "orcid": "0000-0003-1388-2252", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a6e9c69dd1dc47bfad3b72dccfb836c0.json"}}, {"family": "Knapp", "given": "Bernhard", "initials": "B", "orcid": "0000-0002-5714-7105", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ff749c1f41fa4f6280c0a7ae319b8ea9.json"}}], "type": "editorial", "published": "2017-05-00", "journal": {"title": "PLoS Comput Biol", "issn": "1553-7358", "volume": "13", "issue": "5", "pages": "e1005512", "issn-l": "1553-734X"}, "abstract": null, "doi": "10.1371/journal.pcbi.1005512", "pmid": "28542231", "labels": {"Nicholas Pearce": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC5444598"}, {"db": "pii", "key": "PCOMPBIOL-D-16-02078"}], "notes": [], "created": "2022-12-05T18:57:40.964Z", "modified": "2022-12-05T18:57:41.197Z"}, {"entity": "publication", "iuid": "e35ed1238d2c467ba9b93c70c85faff1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e35ed1238d2c467ba9b93c70c85faff1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e35ed1238d2c467ba9b93c70c85faff1"}}, "title": "Partial-occupancy binders identified by the Pan-Dataset Density Analysis method offer new chemical opportunities and reveal cryptic binding sites.", "authors": [{"family": "Pearce", "given": "Nicholas M", "initials": "NM"}, {"family": "Bradley", "given": "Anthony R", "initials": "AR"}, {"family": "Krojer", "given": "Tobias", "initials": "T"}, {"family": "Marsden", "given": "Brian D", "initials": "BD"}, {"family": "Deane", "given": "Charlotte M", "initials": "CM"}, {"family": "von Delft", "given": "Frank", "initials": "F"}], "type": "journal article", "published": "2017-05-00", "journal": {"title": "Struct Dyn", "issn": "2329-7778", "volume": "4", "issue": "3", "pages": "032104", "issn-l": null}, "abstract": "Crystallographic fragment screening uses low molecular weight compounds to probe the protein surface and although individual protein-fragment interactions are high quality, fragments commonly bind at low occupancy, historically making identification difficult. However, our new Pan-Dataset Density Analysis method readily identifies binders missed by conventional analysis: for fragment screening data of lysine-specific demethylase 4D (KDM4D), the hit rate increased from 0.9% to 10.6%. Previously unidentified fragments reveal multiple binding sites and demonstrate: the versatility of crystallographic fragment screening; that surprisingly large conformational changes are possible in crystals; and that low crystallographic occupancy does not by itself reflect a protein-ligand complex's significance.", "doi": "10.1063/1.4974176", "pmid": "28345007", "labels": {"Nicholas Pearce": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC5336473"}, {"db": "pii", "key": "1.4974176"}], "notes": [], "created": "2022-12-05T18:57:38.528Z", "modified": "2022-12-05T18:57:38.555Z"}, {"entity": "publication", "iuid": "f079c771c50442d1ac7072c0a6d77bd8", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f079c771c50442d1ac7072c0a6d77bd8.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f079c771c50442d1ac7072c0a6d77bd8"}}, "title": "A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density.", "authors": [{"family": "Pearce", "given": "Nicholas M", "initials": "NM"}, {"family": "Krojer", "given": "Tobias", "initials": "T"}, {"family": "Bradley", "given": "Anthony R", "initials": "AR"}, {"family": "Collins", "given": "Patrick", "initials": "P", "orcid": "0000-0002-6265-9922", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/67ac751ea9d9407db6de2b5ace3a2c22.json"}}, {"family": "Nowak", "given": "Rados\u0142aw P", "initials": "RP"}, {"family": "Talon", "given": "Romain", "initials": "R"}, {"family": "Marsden", "given": "Brian D", "initials": "BD"}, {"family": "Kelm", "given": "Sebastian", "initials": "S"}, {"family": "Shi", "given": "Jiye", "initials": "J"}, {"family": "Deane", "given": "Charlotte M", "initials": "CM", "orcid": "0000-0003-1388-2252", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a6e9c69dd1dc47bfad3b72dccfb836c0.json"}}, {"family": "von Delft", "given": "Frank", "initials": "F", "orcid": "0000-0003-0378-0017", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/51e35baa89fe49ada5a9dcbc2c2e1e20.json"}}], "type": "journal article", "published": "2017-04-24", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "8", "pages": "15123", "issn-l": "2041-1723"}, "abstract": "In macromolecular crystallography, the rigorous detection of changed states (for example, ligand binding) is difficult unless signal is strong. Ambiguous ('weak' or 'noisy') density is experimentally common, since molecular states are generally only fractionally present in the crystal. Existing methodologies focus on generating maximally accurate maps whereby minor states become discernible; in practice, such map interpretation is disappointingly subjective, time-consuming and methodologically unsound. Here we report the PanDDA method, which automatically reveals clear electron density for the changed state-even from inaccurate maps-by subtracting a proportion of the confounding 'ground state'; changed states are objectively identified from statistical analysis of density distributions. The method is completely general, implying new best practice for all changed-state studies, including the routine collection of multiple ground-state crystals. More generally, these results demonstrate: the incompleteness of atomic models; that single data sets contain insufficient information to model them fully; and that accuracy requires further map-deconvolution approaches.", "doi": "10.1038/ncomms15123", "pmid": "28436492", "labels": {"Nicholas Pearce": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC5413968"}, {"db": "pii", "key": "ncomms15123"}], "notes": [], "created": "2022-12-05T18:57:43.605Z", "modified": "2022-12-05T18:57:43.661Z"}, {"entity": "publication", "iuid": "bc32b56d21e6495f8f1fea6ae226e2e3", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/bc32b56d21e6495f8f1fea6ae226e2e3.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/bc32b56d21e6495f8f1fea6ae226e2e3"}}, "title": "Direct evidence for a polygenic etiology in familial multiple myeloma.", "authors": [{"family": "Halvarsson", "given": "Britt-Marie", "initials": "BM"}, {"family": "Wihlborg", "given": "Anna-Karin", "initials": "AK"}, {"family": "Ali", "given": "Mina", "initials": "M"}, {"family": "Lemonakis", "given": "Konstantinos", "initials": "K"}, {"family": "Johnsson", "given": "Ellinor", "initials": "E"}, {"family": "Niroula", "given": "Abhishek", "initials": "A"}, {"family": "Cibulskis", "given": "Carrie", "initials": "C"}, {"family": "Weinhold", "given": "Niels", "initials": "N"}, {"family": "F\u00f6rsti", "given": "Asta", "initials": "A"}, {"family": "Alici", "given": "Evren", "initials": "E"}, {"family": "Langer", "given": "Christian", "initials": "C"}, {"family": "Pfreundschuh", "given": "Michael", "initials": "M"}, {"family": "Goldschmidt", "given": "Hartmut", "initials": "H"}, {"family": "Mellqvist", "given": "Ulf-Henrik", "initials": "UH"}, {"family": "Turesson", "given": "Ingemar", "initials": "I"}, {"family": "Waage", "given": "Anders", "initials": "A"}, {"family": "Hemminki", "given": "Kari", "initials": "K"}, {"family": "Golub", "given": "Todd", "initials": "T"}, {"family": "Nahi", "given": "Hareth", "initials": "H"}, {"family": "Gullberg", "given": "Urban", "initials": "U"}, {"family": "Hansson", "given": "Markus", "initials": "M"}, {"family": "Nilsson", "given": "Bj\u00f6rn", "initials": "B"}], "type": "journal article", "published": "2017-04-11", "journal": {"title": "Blood Adv", "issn": "2473-9529", "volume": "1", "issue": "10", "pages": "619-623", "issn-l": null}, "abstract": "Although common risk alleles for multiple myeloma (MM) were recently identified, their contribution to familial MM is unknown. Analyzing 38 familial cases identified primarily by linking Swedish nationwide registries, we demonstrate an enrichment of common MM risk alleles in familial compared with 1530 sporadic cases (P = 4.8 \u00d7 10-2 and 6.0 \u00d7 10-2, respectively, for 2 different polygenic risk scores) and 10 171 population-based controls (P = 1.5 \u00d7 10-4 and 1.3 \u00d7 10-4, respectively). Using mixture modeling, we estimate that about one-third of familial cases result from such enrichments. Our results provide the first direct evidence for a polygenic etiology in a familial hematologic malignancy.", "doi": "10.1182/bloodadvances.2016003111", "pmid": "29296704", "labels": {"Abhishek Niroula": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC5728350"}, {"db": "pii", "key": "2016/003111"}], "notes": [], "created": "2023-11-20T11:21:38.858Z", "modified": "2023-11-20T11:21:38.882Z"}, {"entity": "publication", "iuid": "972d3dd3cfdf40b2a7bfaa07ac389afc", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/972d3dd3cfdf40b2a7bfaa07ac389afc.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/972d3dd3cfdf40b2a7bfaa07ac389afc"}}, "title": "Predicting Severity of Disease-Causing Variants.", "authors": [{"family": "Niroula", "given": "Abhishek", "initials": "A"}, {"family": "Vihinen", "given": "Mauno", "initials": "M"}], "type": "journal article", "published": "2017-04-00", "journal": {"title": "Hum. Mutat.", "issn": "1098-1004", "volume": "38", "issue": "4", "pages": "357-364", "issn-l": "1059-7794"}, "abstract": "Most diseases, including those of genetic origin, express a continuum of severity. Clinical interventions for numerous diseases are based on the severity of the phenotype. Predicting severity due to genetic variants could facilitate diagnosis and choice of therapy. Although computational predictions have been used as evidence for classifying the disease relevance of genetic variants, special tools for predicting disease severity in large scale are missing. Here, we manually curated a dataset containing variants leading to severe and less severe phenotypes and studied the abilities of variation impact predictors to distinguish between them. We found that these tools cannot separate the two groups of variants. Then, we developed a novel machine-learning-based method, PON-PS (http://structure.bmc.lu.se/PON-PS), for the classification of amino acid substitutions associated with benign, severe, and less severe phenotypes. We tested the method using an independent test dataset and variants in four additional proteins. For distinguishing severe and nonsevere variants, PON-PS showed an accuracy of 61% in the test dataset, which is higher than for existing tolerance prediction methods. PON-PS is the first generic tool developed for this task. The tool can be used together with other evidence for improving diagnosis and prognosis and for prioritization of preventive interventions, clinical monitoring, and molecular tests.", "doi": "10.1002/humu.23173", "pmid": "28070986", "labels": {"Abhishek Niroula": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2023-11-20T10:43:33.851Z", "modified": "2023-11-20T10:43:33.898Z"}, {"entity": "publication", "iuid": "a66f7912aa7349d39c71bdf38bdf8387", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a66f7912aa7349d39c71bdf38bdf8387.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a66f7912aa7349d39c71bdf38bdf8387"}}, "title": "Antibiotic resistance in the food supply chain: where can sequencing and metagenomics aid risk assessment?", "authors": [{"family": "Bengtsson-Palme", "given": "Johan", "initials": "J", "orcid": "0000-0002-6528-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c666068e9d34939b0252a627007cec7.json"}}], "type": "journal-article", "published": "2017-04-00", "journal": {"title": "Current Opinion in Food Science", "issn": "2214-7993", "volume": "14", "pages": "66-71", "issn-l": null}, "abstract": null, "doi": "10.1016/j.cofs.2017.01.010", "pmid": null, "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [], "notes": [], "created": "2022-11-08T09:31:06.661Z", "modified": "2025-12-04T19:43:51.799Z"}, {"entity": "publication", "iuid": "4fb82992f713481e8951282648fa75c2", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4fb82992f713481e8951282648fa75c2.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4fb82992f713481e8951282648fa75c2"}}, "title": "Analysis of spatial heterogeneity in normal epithelium and preneoplastic alterations in mouse prostate tumor models.", "authors": [{"family": "Valkonen", "given": "Mira", "initials": "M"}, {"family": "Ruusuvuori", "given": "Pekka", "initials": "P"}, {"family": "Kartasalo", "given": "Kimmo", "initials": "K"}, {"family": "Nykter", "given": "Matti", "initials": "M"}, {"family": "Visakorpi", "given": "Tapio", "initials": "T"}, {"family": "Latonen", "given": "Leena", "initials": "L"}], "type": "journal article", "published": "2017-03-20", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "7", "issue": null, "pages": "44831"}, "abstract": "Cancer involves histological changes in tissue, which is of primary importance in pathological diagnosis and research. Automated histological analysis requires ability to computationally separate pathological alterations from normal tissue with all its variables. On the other hand, understanding connections between genetic alterations and histological attributes requires development of enhanced analysis methods suitable also for small sample sizes. Here, we set out to develop computational methods for early detection and distinction of prostate cancer-related pathological alterations. We use analysis of features from HE stained histological images of normal mouse prostate epithelium, distinguishing the descriptors for variability between ventral, lateral, and dorsal lobes. In addition, we use two common prostate cancer models, Hi-Myc and Pten+/- mice, to build a feature-based machine learning model separating the early pathological lesions provoked by these genetic alterations. This work offers a set of computational methods for separation of early neoplastic lesions in the prostates of model mice, and provides proof-of-principle for linking specific tumor genotypes to quantitative histological characteristics. The results obtained show that separation between different spatial locations within the organ, as well as classification between histologies linked to different genetic backgrounds, can be performed with very high specificity and sensitivity.", "doi": "10.1038/srep44831", "pmid": "28317907", "labels": {"Kimmo Kartasalo": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC5357939"}, {"db": "pii", "key": "srep44831"}], "notes": [], "created": "2024-11-05T16:04:29.995Z", "modified": "2024-11-29T12:06:02.492Z"}, {"entity": "publication", "iuid": "18b08b603a034922a2182d8fb1efb8a1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/18b08b603a034922a2182d8fb1efb8a1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/18b08b603a034922a2182d8fb1efb8a1"}}, "title": "The XChemExplorer graphical workflow tool for routine or large-scale protein-ligand structure determination.", "authors": [{"family": "Krojer", "given": "Tobias", "initials": "T"}, {"family": "Talon", "given": "Romain", "initials": "R"}, {"family": "Pearce", "given": "Nicholas", "initials": "N"}, {"family": "Collins", "given": "Patrick", "initials": "P"}, {"family": "Douangamath", "given": "Alice", "initials": "A"}, {"family": "Brandao-Neto", "given": "Jose", "initials": "J"}, {"family": "Dias", "given": "Alexandre", "initials": "A"}, {"family": "Marsden", "given": "Brian", "initials": "B"}, {"family": "von Delft", "given": "Frank", "initials": "F"}], "type": "journal article", "published": "2017-03-01", "journal": {"title": "Acta Crystallogr D Struct Biol", "issn": "2059-7983", "volume": "73", "issue": "Pt 3", "pages": "267-278", "issn-l": "2059-7983"}, "abstract": "XChemExplorer (XCE) is a data-management and workflow tool to support large-scale simultaneous analysis of protein-ligand complexes during structure-based ligand discovery (SBLD). The user interfaces of established crystallographic software packages such as CCP4 [Winn et al. (2011), Acta Cryst. D67, 235-242] or PHENIX [Adams et al. (2010), Acta Cryst. D66, 213-221] have entrenched the paradigm that a `project' is concerned with solving one structure. This does not hold for SBLD, where many almost identical structures need to be solved and analysed quickly in one batch of work. Functionality to track progress and annotate structures is essential. XCE provides an intuitive graphical user interface which guides the user from data processing, initial map calculation, ligand identification and refinement up until data dissemination. It provides multiple entry points depending on the need of each project, enables batch processing of multiple data sets and records metadata, progress and annotations in an SQLite database. XCE is freely available and works on any Linux and Mac OS X system, and the only dependency is to have the latest version of CCP4 installed. The design and usage of this tool are described here, and its usefulness is demonstrated in the context of fragment-screening campaigns at the Diamond Light Source. It is routinely used to analyse projects comprising 1000 data sets or more, and therefore scales well to even very large ligand-design projects.", "doi": "10.1107/S2059798316020234", "pmid": "28291762", "labels": {"Nicholas Pearce": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC5349439"}, {"db": "pii", "key": "S2059798316020234"}], "notes": [], "created": "2022-12-05T19:25:09.779Z", "modified": "2022-12-05T19:25:09.782Z"}, {"entity": "publication", "iuid": "8d6ada2aca454044907cc88985866711", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8d6ada2aca454044907cc88985866711.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8d6ada2aca454044907cc88985866711"}}, "title": "Proper modelling of ligand binding requires an ensemble of bound and unbound states.", "authors": [{"family": "Pearce", "given": "Nicholas M", "initials": "NM"}, {"family": "Krojer", "given": "Tobias", "initials": "T"}, {"family": "von Delft", "given": "Frank", "initials": "F"}], "type": "journal article", "published": "2017-03-01", "journal": {"title": "Acta Crystallogr D Struct Biol", "issn": "2059-7983", "volume": "73", "issue": "Pt 3", "pages": "256-266", "issn-l": "2059-7983"}, "abstract": "Although noncovalent binding by small molecules cannot be assumed a priori to be stoichiometric in the crystal lattice, occupancy refinement of ligands is often avoided by convention. Occupancies tend to be set to unity, requiring the occupancy error to be modelled by the B factors, and residual weak density around the ligand is necessarily attributed to `disorder'. Where occupancy refinement is performed, the complementary, superposed unbound state is rarely modelled. Here, it is shown that superior accuracy is achieved by modelling the ligand as partially occupied and superposed on a ligand-free `ground-state' model. Explicit incorporation of this model of the crystal, obtained from a reference data set, allows constrained occupancy refinement with minimal fear of overfitting. Better representation of the crystal also leads to more meaningful refined atomic parameters such as the B factor, allowing more insight into dynamics in the crystal. An outline of an approach for algorithmically generating ensemble models of crystals is presented, assuming that data sets representing the ground state are available. The applicability of various electron-density metrics to the validation of the resulting models is assessed, and it is concluded that ensemble models consistently score better than the corresponding single-state models. Furthermore, it appears that ignoring the superposed ground state becomes the dominant source of model error, locally, once the overall model is accurate enough; modelling the local ground state properly is then more meaningful than correcting all remaining model errors globally, especially for low-occupancy ligands. Implications for the simultaneous refinement of B factors and occupancies, and for future evaluation of the limits of the approach, in particular its behaviour at lower data resolution, are discussed.", "doi": "10.1107/S2059798317003412", "pmid": "28291761", "labels": {"Nicholas Pearce": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC5349438"}, {"db": "pii", "key": "S2059798317003412"}], "notes": [], "created": "2022-12-05T19:25:12.071Z", "modified": "2022-12-05T19:25:12.086Z"}, {"entity": "publication", "iuid": "5647f45f04c34c22a184d048fd8b5503", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5647f45f04c34c22a184d048fd8b5503.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5647f45f04c34c22a184d048fd8b5503"}}, "title": "Gentle, fast and effective crystal soaking by acoustic dispensing.", "authors": [{"family": "Collins", "given": "Patrick M", "initials": "PM"}, {"family": "Ng", "given": "Jia Tsing", "initials": "JT"}, {"family": "Talon", "given": "Romain", "initials": "R"}, {"family": "Nekrosiute", "given": "Karolina", "initials": "K"}, {"family": "Krojer", "given": "Tobias", "initials": "T"}, {"family": "Douangamath", "given": "Alice", "initials": "A"}, {"family": "Brandao-Neto", "given": "Jose", "initials": "J"}, {"family": "Wright", "given": "Nathan", "initials": "N"}, {"family": "Pearce", "given": "Nicholas M", "initials": "NM"}, {"family": "von Delft", "given": "Frank", "initials": "F"}], "type": "journal article", "published": "2017-03-01", "journal": {"title": "Acta Crystallogr D Struct Biol", "issn": "2059-7983", "volume": "73", "issue": "Pt 3", "pages": "246-255", "issn-l": "2059-7983"}, "abstract": "The steady expansion in the capacity of modern beamlines for high-throughput data collection, enabled by increasing X-ray brightness, capacity of robotics and detector speeds, has pushed the bottleneck upstream towards sample preparation. Even in ligand-binding studies using crystal soaking, the experiment best able to exploit beamline capacity, a primary limitation is the need for gentle and nontrivial soaking regimens such as stepwise concentration increases, even for robust and well characterized crystals. Here, the use of acoustic droplet ejection for the soaking of protein crystals with small molecules is described, and it is shown that it is both gentle on crystals and allows very high throughput, with 1000 unique soaks easily performed in under 10 min. In addition to having very low compound consumption (tens of nanolitres per sample), the positional precision of acoustic droplet ejection enables the targeted placement of the compound/solvent away from crystals and towards drop edges, allowing gradual diffusion of solvent across the drop. This ensures both an improvement in the reproducibility of X-ray diffraction and increased solvent tolerance of the crystals, thus enabling higher effective compound-soaking concentrations. The technique is detailed here with examples from the protein target JMJD2D, a histone lysine demethylase with roles in cancer and the focus of active structure-based drug-design efforts.", "doi": "10.1107/S205979831700331X", "pmid": "28291760", "labels": {"Nicholas Pearce": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC5349437"}, {"db": "pii", "key": "S205979831700331X"}], "notes": [], "created": "2022-12-05T19:25:07.397Z", "modified": "2022-12-05T19:25:07.400Z"}, {"entity": "publication", "iuid": "5dd1b690eb724f25a6b7d6af56fa1815", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5dd1b690eb724f25a6b7d6af56fa1815.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5dd1b690eb724f25a6b7d6af56fa1815"}}, "title": "Metapopulation theory identifies biogeographical patterns among core and satellite marine bacteria scaling from tens to thousands of kilometers.", "authors": [{"family": "Lindh", "given": "Markus V", "initials": "MV"}, {"family": "Sj\u00f6stedt", "given": "Johanna", "initials": "J"}, {"family": "Ekstam", "given": "B\u00f6rje", "initials": "B"}, {"family": "Casini", "given": "Michele", "initials": "M"}, {"family": "Lundin", "given": "Daniel", "initials": "D", "orcid": "0000-0002-8779-6464", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/290a3bc9eb554620906b93d7f1d57184.json"}}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW"}, {"family": "Hu", "given": "Yue O O", "initials": "YO"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}, {"family": "Andersson", "given": "Agneta", "initials": "A"}, {"family": "Legrand", "given": "Catherine", "initials": "C"}, {"family": "Pinhassi", "given": "Jarone", "initials": "J", "orcid": "0000-0002-6405-1347", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/28b77762086343048e74046a6486caff.json"}}], "type": "journal article", "published": "2017-03-00", "journal": {"title": "Environ. Microbiol.", "issn": "1462-2920", "volume": "19", "issue": "3", "pages": "1222-1236", "issn-l": "1462-2912"}, "abstract": "Metapopulation theory developed in terrestrial ecology provides applicable frameworks for interpreting the role of local and regional processes in shaping species distribution patterns. Yet, empirical testing of metapopulation models on microbial communities is essentially lacking. We determined regional bacterioplankton dynamics from monthly transect sampling in the Baltic Sea Proper using 16S rRNA gene sequencing. A strong positive trend was found between local relative abundance and occupancy of populations. Notably, the occupancy-frequency distributions were significantly bimodal with a satellite mode of rare endemic populations and a core mode of abundant cosmopolitan populations (e.g. Synechococcus, SAR11 and SAR86 clade members). Temporal changes in population distributions supported several theoretical frameworks. Still, bimodality was found among bacterioplankton communities across the entire Baltic Sea, and was also frequent in globally distributed datasets. Datasets spanning waters with widely different physicochemical characteristics or environmental gradients typically lacked significant bimodal patterns. When such datasets were divided into subsets with coherent environmental conditions, bimodal patterns emerged, highlighting the importance of positive feedbacks between local abundance and occupancy within specific biomes. Thus, metapopulation theory applied to microbial biogeography can provide novel insights into the mechanisms governing shifts in biodiversity resulting from natural or anthropogenically induced changes in the environment.", "doi": "10.1111/1462-2920.13650", "pmid": "28028880", "labels": {"Affiliated researcher": "", "Luisa Hugerth": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2018-12-05T12:12:42.674Z", "modified": "2026-09-23T10:23:58.404Z"}, {"entity": "publication", "iuid": "68f649c063774b5994f17a469ce9b9c6", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/68f649c063774b5994f17a469ce9b9c6.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/68f649c063774b5994f17a469ce9b9c6"}}, "title": "Concomitant underexpression of TGFBR2 and overexpression of hTERT are associated with poor prognosis in cervical cancer.", "authors": [{"family": "Yang", "given": "Hui", "initials": "H"}, {"family": "Zhang", "given": "Hongyan", "initials": "H"}, {"family": "Zhong", "given": "Yahua", "initials": "Y"}, {"family": "Wang", "given": "Qiaoli", "initials": "Q"}, {"family": "Yang", "given": "Lei", "initials": "L"}, {"family": "Kang", "given": "Hong", "initials": "H"}, {"family": "Gao", "given": "Xiaojia", "initials": "X"}, {"family": "Yu", "given": "Haijun", "initials": "H"}, {"family": "Xie", "given": "Conghua", "initials": "C"}, {"family": "Zhou", "given": "Fuxiang", "initials": "F"}, {"family": "Zhou", "given": "Yunfeng", "initials": "Y"}], "type": "journal article", "published": "2017-02-14", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "7", "pages": "41670", "issn-l": "2045-2322"}, "abstract": "The human telomerase reverse transcriptase (hTERT) is highly expressed in a variety of tumors. The transforming growth factor beta receptor type II (TGFBR2) is a downstream protein of transforming growth factor beta (TGF-\u03b2) which suppresses telomerase activity. However, the relevance of survival to the expression of TGFBR2, hTERT or TGFBR2/hTERT has not been previously investigated in cervical cancer tissues. Our study showed that patients with low level of TGFBR2 were associated with poor prognosis (HR = 1.704, P = 0.021), but no significant relevance between hTERT expression and survival (HR = 1.390, P = 0.181). However, a combination of low level of TGFBR2 and high level of hTERT was associated with a worse survival (HR = 1.892, P = 0.020), which had higher impact of hazard ratio (HR) on the overall survival (OS) than the low TGFBR2 expression alone. Knockdown of TGFBR2 expression by shRNA in Hela cells increased cell proliferation, cell invasion, G1/S transition and telomere homeostasis but decreased cell apoptosis. Overexpressing TGFBR2 and inhibiting hTERT suppressed Hela cell growth. These results would lead us to further explore whether a phenotype of TGFBR2low/hTERThigh could be considered as a predictor of poor prognosis, and whether simultaneous use of TGFBR2 agonist and hTERT inhibitor could be developed as a therapeutic strategy.", "doi": "10.1038/srep41670", "pmid": "28195144", "labels": {"DDLS Fellow": null, "Qiaoli Wang": null}, "xrefs": [{"db": "pmc", "key": "PMC5307321"}, {"db": "pii", "key": "srep41670"}], "notes": [], "created": "2025-11-27T18:45:13.894Z", "modified": "2025-11-27T18:45:13.897Z"}, {"entity": "publication", "iuid": "4c128b79642e48dcb06de187c7adf844", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4c128b79642e48dcb06de187c7adf844.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4c128b79642e48dcb06de187c7adf844"}}, "title": "Potential Involvement of Type I Interferon Signaling in Immunotherapy in Seasonal Allergic Rhinitis.", "authors": [{"family": "Mattson", "given": "Lina", "initials": "L"}, {"family": "Lentini", "given": "Antonio", "initials": "A"}, {"family": "Gawel", "given": "Danuta R", "initials": "DR"}, {"family": "Badam", "given": "Tejaswi V S", "initials": "TV"}, {"family": "Benson", "given": "Mikael", "initials": "M"}, {"family": "Ledin", "given": "Torbjorn", "initials": "T"}, {"family": "Nestor", "given": "Colm E", "initials": "CE"}, {"family": "Gustafsson", "given": "Mika", "initials": "M"}, {"family": "Serra-Musach", "given": "Jordi", "initials": "J"}, {"family": "Bjorkander", "given": "Janne", "initials": "J"}, {"family": "Xiang", "given": "Zou", "initials": "Z"}, {"family": "Zhang", "given": "Huan", "initials": "H", "orcid": "0000-0001-9339-7999", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d199a695b85a48f2be0a57682dcd043b.json"}}], "type": "journal article", "published": "2016-12-19", "journal": {"title": "J Immunol Res", "issn": "2314-7156", "volume": "2016", "pages": "5153184", "issn-l": null}, "abstract": "Specific immunotherapy (SIT) reverses the symptoms of seasonal allergic rhinitis (SAR) in most patients. Recent studies report type I interferons shifting the balance between type I T helper cell (Th1) and type II T helper cells (Th2) towards Th2 dominance by inhibiting the differentiation of naive T cells into Th1 cells. As SIT is thought to cause a shift towards Th1 dominance, we hypothesized that SIT would alter interferon type I signaling. To test this, allergen and diluent challenged CD4+ T cells from healthy controls and patients from different time points were analyzed. The initial experiments focused on signature genes of the pathway and found complex changes following immunotherapy, which were consistent with our hypothesis. As interferon signaling involves multiple genes, expression profiling studies were performed, showing altered expression of the pathway. These findings require validation in a larger group of patients in further studies.", "doi": "10.1155/2016/5153184", "pmid": "28097155", "labels": {"Antonio Lentini": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC5209614"}], "notes": [], "created": "2025-03-28T07:14:48.673Z", "modified": "2025-03-28T07:14:48.742Z"}, {"entity": "publication", "iuid": "c97ce6033231499580f03f5320cd6343", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c97ce6033231499580f03f5320cd6343.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c97ce6033231499580f03f5320cd6343"}}, "title": "FARAO: the flexible all-round annotation organizer.", "authors": [{"family": "Hammar\u00e9n", "given": "Rickard", "initials": "R"}, {"family": "Pal", "given": "Chandan", "initials": "C"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2016-12-01", "journal": {"title": "Bioinformatics", "issn": "1367-4811", "volume": "32", "issue": "23", "pages": "3664-3666", "issn-l": "1367-4803"}, "abstract": "With decreasing costs of generating DNA sequence data, genome and metagenome projects have become accessible to a wider scientific community. However, to extract meaningful information and visualize the data remain challenging. We here introduce FARAO, a highly scalable software for organization, visualization and integration of annotation and read coverage data that can also combine output data from several bioinformatics tools. The capabilities of FARAO can greatly aid analyses of genomic and metagenomic datasets.\n\nFARAO is implemented in Perl and is supported under Unix-like operative systems, including Linux and macOS. The Perl source code is freely available for download under the MIT License from http://microbiology.se/software/farao/ CONTACT: johan.bengtsson-palme@microbiology.seSupplementary information: Supplementary data are available at Bioinformatics online.", "doi": "10.1093/bioinformatics/btw499", "pmid": "27493193", "labels": {"Affiliated researcher": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pii", "key": "btw499"}], "notes": [], "created": "2018-12-05T13:02:10.221Z", "modified": "2026-09-23T13:03:58.520Z"}, {"entity": "publication", "iuid": "58a77ebdf8dc4cff9eb1c4f5d5a0c33b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/58a77ebdf8dc4cff9eb1c4f5d5a0c33b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/58a77ebdf8dc4cff9eb1c4f5d5a0c33b"}}, "title": "Elucidating selection processes for antibiotic resistance in sewage treatment plants using metagenomics.", "authors": [{"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Hammar\u00e9n", "given": "Rickard", "initials": "R"}, {"family": "Pal", "given": "Chandan", "initials": "C"}, {"family": "\u00d6stman", "given": "Marcus", "initials": "M"}, {"family": "Bj\u00f6rlenius", "given": "Berndt", "initials": "B"}, {"family": "Flach", "given": "Carl-Fredrik", "initials": "CF"}, {"family": "Fick", "given": "Jerker", "initials": "J"}, {"family": "Kristiansson", "given": "Erik", "initials": "E"}, {"family": "Tysklind", "given": "Mats", "initials": "M"}, {"family": "Larsson", "given": "D G Joakim", "initials": "DGJ"}], "type": "journal article", "published": "2016-12-01", "journal": {"title": "Sci. Total Environ.", "issn": "1879-1026", "volume": "572", "issue": null, "pages": "697-712", "issn-l": "0048-9697"}, "abstract": "Sewage treatment plants (STPs) have repeatedly been suggested as \"hotspots\" for the emergence and dissemination of antibiotic-resistant bacteria. A critical question still unanswered is if selection pressures within STPs, caused by residual antibiotics or other co-selective agents, are sufficient to specifically promote resistance. To address this, we employed shotgun metagenomic sequencing of samples from different steps of the treatment process in three Swedish STPs. In parallel, concentrations of selected antibiotics, biocides and metals were analyzed. We found that concentrations of tetracycline and ciprofloxacin in the influent were above predicted concentrations for resistance selection, however, there was no consistent enrichment of resistance genes to any particular class of antibiotics in the STPs, neither for biocide and metal resistance genes. The most substantial change of the bacterial communities compared to human feces occurred already in the sewage pipes, manifested by a strong shift from obligate to facultative anaerobes. Through the treatment process, resistance genes against antibiotics, biocides and metals were not reduced to the same extent as fecal bacteria. The OXA-48 gene was consistently enriched in surplus and digested sludge. We find this worrying as OXA-48, still rare in Swedish clinical isolates, provides resistance to carbapenems, one of our most critically important classes of antibiotics. Taken together, metagenomics analyses did not provide clear support for specific antibiotic resistance selection. However, stronger selective forces affecting gross taxonomic composition, and with that resistance gene abundances, limit interpretability. Comprehensive analyses of resistant/non-resistant strains within relevant species are therefore warranted.", "doi": "10.1016/j.scitotenv.2016.06.228", "pmid": "27542633", "labels": {"Affiliated researcher": null, "DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pii", "key": "S0048-9697(16)31417-6"}], "notes": [], "created": "2018-12-05T09:16:55.877Z", "modified": "2022-11-08T09:29:34.460Z"}, {"entity": "publication", "iuid": "3e3db83f40c04049bf6258cd7aafb9a0", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3e3db83f40c04049bf6258cd7aafb9a0.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3e3db83f40c04049bf6258cd7aafb9a0"}}, "title": "Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2.", "authors": [{"family": "Kimanius", "given": "Dari", "initials": "D"}, {"family": "Forsberg", "given": "Bj\u00f6rn O", "initials": "BO"}, {"family": "Scheres", "given": "Sjors Hw", "initials": "SH", "orcid": "0000-0002-0462-6540", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b64851b999fd42f7bf7b25856946dc62.json"}}, {"family": "Lindahl", "given": "Erik", "initials": "E", "orcid": "0000-0002-2734-2794", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9eb30fa60f9b4b95842ac9d9f3a0eaa9.json"}}], "type": "journal article", "published": "2016-11-15", "journal": {"title": "Elife", "issn": "2050-084X", "volume": "5", "issue": null, "issn-l": "2050-084X"}, "abstract": "By reaching near-atomic resolution for a wide range of specimens, single-particle cryo-EM structure determination is transforming structural biology. However, the necessary calculations come at large computational costs, which has introduced a bottleneck that is currently limiting throughput and the development of new methods. Here, we present an implementation of the RELION image processing software that uses graphics processors (GPUs) to address the most computationally intensive steps of its cryo-EM structure determination workflow. Both image classification and high-resolution refinement have been accelerated more than an order-of-magnitude, and template-based particle selection has been accelerated well over two orders-of-magnitude on desktop hardware. Memory requirements on GPUs have been reduced to fit widely available hardware, and we show that the use of single precision arithmetic does not adversely affect results. This enables high-resolution cryo-EM structure determination in a matter of days on a single workstation.", "doi": "10.7554/eLife.18722", "pmid": "27845625", "labels": {"DDLS Fellow": "", "Bj\u00f6rn Forsberg": ""}, "xrefs": [{"db": "pmc", "key": "PMC5310839"}, {"db": "pii", "key": "e18722"}], "notes": [], "created": "2018-12-05T08:35:33.055Z", "modified": "2026-09-22T19:59:18.095Z"}, {"entity": "publication", "iuid": "009fb006e53e4337bf4773f3bd5999ba", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/009fb006e53e4337bf4773f3bd5999ba.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/009fb006e53e4337bf4773f3bd5999ba"}}, "title": "Identification of new heat-stable (STa) enterotoxin allele variants produced by human enterotoxigenic Escherichia coli (ETEC).", "authors": [{"family": "Joffr\u00e9", "given": "Enrique", "initials": "E"}, {"family": "von Mentzer", "given": "Astrid", "initials": "A"}, {"family": "Svennerholm", "given": "Ann-Mari", "initials": "AM"}, {"family": "Sj\u00f6ling", "given": "\u00c5sa", "initials": "\u00c5"}], "type": "journal article", "published": "2016-11-00", "journal": {"title": "Int J Med Microbiol", "issn": "1618-0607", "volume": "306", "issue": "7", "pages": "586-594", "issn-l": null}, "abstract": "We describe natural variants of the heat stable toxin (STa) produced by enterotoxigenic Escherichia coli (ETEC) isolates collected worldwide. Previous studies of ETEC isolated from human diarrheal cases have reported the existence of three natural STa gene variants estA1, estA2 and estA3/4 where the first variant encodes STp (porcine, bovine, and human origin) and the two latter ones encode STh (human origin). We identified STa sequences by BLASTn and profiled ST amino acid polymorphisms in a collection of 118 clinical ETEC isolates from children and adults from Asia, Africa and, Latin America that were characterized by whole genome sequencing. Three novel variants of STp and STh were found and designated STa5 and STa6, and STa7, respectively. Presence of glucose significantly decreased the production of STh and STp toxin variants (p<0.05) as well as downregulated the gene expression (STh: p<0.001, STp: p<0.05). We found that the ETEC isolates producing the most common STp variant, STa5, co-expressed coli surface antigen CS6 and was significantly associated with disease in adults in this data set (p<0.001). Expression of mature STa5 peptide as well as gene expression of tolC, involved in ST secretion, increased in response to bile (p<0.05). ETEC expressing the common STh variant STa3/4 was associated with disease in children (p<0.05). The crp gene, that positively regulate estA3/4 encoding STa3/4, and estA3/4 itself had decreased transcriptional levels in presence of bile. Since bile levels in the intestine are lower in children than adults, these results may suggest differences in pathogenicity of ETEC in children and adult populations.", "doi": "10.1016/j.ijmm.2016.05.016", "pmid": "27350142", "labels": {"Astrid von Mentzer": null, "DDLS Fellow": null}, "xrefs": [{"db": "pii", "key": "S1438-4221(16)30096-0"}], "notes": [], "created": "2025-12-02T15:48:56.921Z", "modified": "2025-12-02T15:48:56.959Z"}, {"entity": "publication", "iuid": "575c6c6e2d7a45a09189ee0139ab6d31", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/575c6c6e2d7a45a09189ee0139ab6d31.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/575c6c6e2d7a45a09189ee0139ab6d31"}}, "title": "Heteroplasmy of mutant mitochondrial DNA A10398G and analysis of its prognostic value in non-small cell lung cancer.", "authors": [{"family": "Qi", "given": "Yuexiao", "initials": "Y"}, {"family": "Wei", "given": "Yuehua", "initials": "Y"}, {"family": "Wang", "given": "Qiaoli", "initials": "Q"}, {"family": "Xu", "given": "Hui", "initials": "H"}, {"family": "Wang", "given": "You", "initials": "Y"}, {"family": "Yao", "given": "Anqi", "initials": "A"}, {"family": "Yang", "given": "Hui", "initials": "H"}, {"family": "Gao", "given": "Yan", "initials": "Y"}, {"family": "Zhou", "given": "Fuxiang", "initials": "F"}], "type": "journal article", "published": "2016-11-00", "journal": {"title": "Oncol Lett", "issn": "1792-1074", "volume": "12", "issue": "5", "pages": "3081-3088", "issn-l": null}, "abstract": "Mitochondrial dysfunction is associated with pathogenic mitochondrial (mt)DNA mutations. The majority of mtDNA point mutations have a heteroplasmic status, which is defined as the coexistence of wild-type and mutated DNA within a cell or tissue. Previous findings demonstrated that certain mtDNA heteroplasmic mutations contribute to widely spread chronic diseases, including cancer, and alterations in the heteroplasmy level are associated with the clinical phenotype and severity of cancer. In the present study, the proportions of mutant mtDNA 10398G were assessed using amplification-refractory mutation system-quantitative polymerase chain reaction (PCR) assay in 129 non-small cell lung cancer (NSCLC) tissue samples. Wild-type and mutant sequences were separately amplified using allele-specific primers and, subsequently, the PCR products containing the mtDNA 10398 site were ligated into vectors to construct a standard plasmid DNA construct. The association between mtDNA A10398G and the prognosis of patients was analyzed by survival analysis and Cox proportional hazards model. For the patient cohort, the median follow-up time and overall survival time were 20.6 and 26.3 months, respectively. The ratios of mutant heteroplasmy ranged between 0.31 and 97.04%. Patients with a high degree of mutant mtDNA 10398G had a significantly longer overall survival time compared with those with a low degree of mutant mtDNA 10398G (28.7 vs. 22.5 months, respectively; P<0.05). In addition, multivariate analysis demonstrated that epidermal growth factor receptor mutation status, tumor stage and the possession of a low degree of mutant 10398G were the three most independent prognostic factors. In conclusion, the present study suggests that, among NSCLC patients, there are large shifts in mutant mtDNA 10398G heteroplasmy and a low degree of mutant mtDNA 10398G heteroplasmy may be a marker of poor prognosis in patients with NSCLC.", "doi": "10.3892/ol.2016.5086", "pmid": "27899967", "labels": {"DDLS Fellow": null, "Qiaoli Wang": null}, "xrefs": [{"db": "pmc", "key": "PMC5103904"}, {"db": "pii", "key": "OL-0-0-5086"}], "notes": [], "created": "2025-11-27T18:45:12.800Z", "modified": "2025-11-27T18:45:12.803Z"}, {"entity": "publication", "iuid": "575ff6c91e364540ba70a9e1de28a70b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/575ff6c91e364540ba70a9e1de28a70b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/575ff6c91e364540ba70a9e1de28a70b"}}, "title": "Bacillus wiedmannii sp. nov., a psychrotolerant and cytotoxic Bacillus cereus group species isolated from dairy foods and dairy environments.", "authors": [{"family": "Miller", "given": "Rachel A", "initials": "RA"}, {"family": "Beno", "given": "Sarah M", "initials": "SM"}, {"family": "Kent", "given": "David J", "initials": "DJ"}, {"family": "Carroll", "given": "Laura M", "initials": "LM"}, {"family": "Martin", "given": "Nicole H", "initials": "NH"}, {"family": "Boor", "given": "Kathryn J", "initials": "KJ"}, {"family": "Kovac", "given": "Jasna", "initials": "J"}], "type": "journal article", "published": "2016-11-00", "journal": {"title": "Int. J. Syst. Evol. Microbiol.", "issn": "1466-5034", "volume": "66", "issue": "11", "pages": "4744-4753", "issn-l": "1466-5026"}, "abstract": "A facultatively anaerobic, spore-forming Bacillus strain, FSL W8-0169T, collected from raw milk stored in a silo at a dairy powder processing plant in the north-eastern USA was initially identified as a Bacillus cereus group species based on a partial sequence of the rpoB gene and 16S rRNA gene sequence. Analysis of core genome single nucleotide polymorphisms clustered this strain separately from known B. cereus group species. Pairwise average nucleotide identity blast values obtained for FSL W8-0169T compared to the type strains of existing B. cereus group species were <95 % and predicted DNA-DNA hybridization values were <70 %, suggesting that this strain represents a novel B. cereus group species. We characterized 10 additional strains with the same or closely related rpoB allelic type, by whole genome sequencing and phenotypic analyses. Phenotypic characterization identified a higher content of iso-C16 : 0 fatty acid and the combined inability to ferment sucrose or to hydrolyse arginine as the key characteristics differentiating FSL W8-0169T from other B. cereus group species. FSL W8-0169T is psychrotolerant, produces haemolysin BL and non-haemolytic enterotoxin, and is cytotoxic in a HeLa cell model. The name Bacillus wiedmannii sp. nov. is proposed for the novel species represented by the type strain FSL W8-0169T (=DSM 102050T=LMG 29269T).", "doi": "10.1099/ijsem.0.001421", "pmid": "27520992", "labels": {"Laura Carroll": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC5381181"}], "notes": [], "created": "2025-03-18T17:21:32.404Z", "modified": "2025-03-18T17:22:17.642Z"}, {"entity": "publication", "iuid": "a312a6b4d15e44d68e262ca34ba1ec8f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a312a6b4d15e44d68e262ca34ba1ec8f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a312a6b4d15e44d68e262ca34ba1ec8f"}}, "title": "Gene-specific correlation of RNA and protein levels in human cells and tissues.", "authors": [{"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Danielsson", "given": "Frida", "initials": "F"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L"}, {"family": "Lundberg", "given": "Emma", "initials": "E"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9f5294424542413c9ba4432c839c2b63.json"}}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ea446aa574042a295d5f69437402f76.json"}}], "type": "comparative study", "published": "2016-10-20", "journal": {"title": "Mol Syst Biol", "issn": "1744-4292", "volume": "12", "issue": "10", "pages": "883", "issn-l": "1744-4292"}, "abstract": "An important issue for molecular biology is to establish whether transcript levels of a given gene can be used as proxies for the corresponding protein levels. Here, we have developed a targeted proteomics approach for a set of human non-secreted proteins based on parallel reaction monitoring to measure, at steady-state conditions, absolute protein copy numbers across human tissues and cell lines and compared these levels with the corresponding mRNA levels using transcriptomics. The study shows that the transcript and protein levels do not correlate well unless a gene-specific RNA-to-protein (RTP) conversion factor independent of the tissue type is introduced, thus significantly enhancing the predictability of protein copy numbers from RNA levels. The results show that the RTP ratio varies significantly with a few hundred copies per mRNA molecule for some genes to several hundred thousands of protein copies per mRNA molecule for others. In conclusion, our data suggest that transcriptome analysis can be used as a tool to predict the protein copy numbers per cell, thus forming an attractive link between the field of genomics and proteomics.", "doi": "10.15252/msb.20167144", "pmid": "27951527", "labels": {"Fredrik Edfors": "", "DDLS Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC5081484"}], "notes": [], "created": "2018-12-05T09:05:24.526Z", "modified": "2026-09-23T06:32:53.749Z"}, {"entity": "publication", "iuid": "3f65caaf36df4efa949a725983b14502", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3f65caaf36df4efa949a725983b14502.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3f65caaf36df4efa949a725983b14502"}}, "title": "Author response: Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2", "authors": [{"family": "Kimanius", "given": "Dari", "initials": "D"}, {"family": "Forsberg", "given": "Bj\u00f6rn O", "initials": "BO"}, {"family": "Scheres", "given": "Sjors HW", "initials": "SH", "orcid": "0000-0002-0462-6540", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b64851b999fd42f7bf7b25856946dc62.json"}}, {"family": "Lindahl", "given": "Erik", "initials": "E", "orcid": "0000-0002-2734-2794", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9eb30fa60f9b4b95842ac9d9f3a0eaa9.json"}}], "type": "peer-review", "published": "2016-10-16", "journal": {"issn-l": null}, "abstract": null, "doi": "10.7554/elife.18722.024", "pmid": null, "labels": {"DDLS Fellow": "", "Bj\u00f6rn Forsberg": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T13:51:51.527Z", "modified": "2026-09-23T13:47:50.222Z"}, {"entity": "publication", "iuid": "19cadf1ebb5f494fbd2820f03f143563", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/19cadf1ebb5f494fbd2820f03f143563.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/19cadf1ebb5f494fbd2820f03f143563"}}, "title": "The structure and diversity of human, animal and environmental resistomes.", "authors": [{"family": "Pal", "given": "Chandan", "initials": "C"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Kristiansson", "given": "Erik", "initials": "E"}, {"family": "Larsson", "given": "D G Joakim", "initials": "DG"}], "type": "journal article", "published": "2016-10-07", "journal": {"title": "Microbiome", "issn": "2049-2618", "volume": "4", "issue": "1", "pages": "54", "issn-l": "2049-2618"}, "abstract": "Antibiotic resistance genes (ARGs) are widespread but cause problems only when present in pathogens. Environments where selection and transmission of antibiotic resistance frequently take place are likely to be characterized by high abundance and diversity of horizontally transferable ARGs. Large-scale quantitative data on ARGs is, however, lacking for most types of environments, including humans and animals, as is data on resistance genes to potential co-selective agents, such as biocides and metals. This paucity prevents efficient identification of risk environments.\n\nWe provide a comprehensive characterization of resistance genes, mobile genetic elements (MGEs) and bacterial taxonomic compositions for 864 metagenomes from humans (n = 350), animals (n = 145) and external environments (n = 369), all deeply sequenced using Illumina technology. Environment types showed clear differences in both resistance profiles and bacterial community compositions. Human and animal microbial communities were characterized by limited taxonomic diversity and low abundance and diversity of biocide/metal resistance genes and MGEs but a relatively high abundance of ARGs. In contrast, external environments showed consistently high taxonomic diversity which in turn was linked to high diversity of both biocide/metal resistance genes and MGEs. Water, sediment and soil generally carried low relative abundance and few varieties of known ARGs, whereas wastewater/sludge was on par with the human gut. The environments with the largest relative abundance and/or diversity of ARGs, including genes encoding resistance to last resort antibiotics, were those subjected to industrial antibiotic pollution and a limited set of deeply sequenced air samples from a Beijing smog event.\n\nOur study identifies air and antibiotic-polluted environments as under-investigated transmission routes and reservoirs for antibiotic resistance. The high taxonomic and genetic diversity of external environments supports the hypothesis that these also form vast sources of unknown resistance genes, with potential to be transferred to pathogens in the future.", "doi": "10.1186/s40168-016-0199-5", "pmid": "27717408", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pii", "key": "10.1186/s40168-016-0199-5"}, {"db": "pmc", "key": "PMC5055678"}], "notes": [], "created": "2022-11-08T09:29:30.040Z", "modified": "2022-11-08T09:29:30.065Z"}, {"entity": "publication", "iuid": "fd4e6306695e49a785e552a8fe7e4692", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/fd4e6306695e49a785e552a8fe7e4692.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/fd4e6306695e49a785e552a8fe7e4692"}}, "title": "An introduction to plant phylogenomics with a focus on palms", "authors": [{"family": "Barrett", "given": "Craig F", "initials": "CF"}, {"family": "Bacon", "given": "Christine D", "initials": "CD"}, {"family": "Antonelli", "given": "Alexandre", "initials": "A"}, {"family": "Cano", "given": "\u00c1ngela", "initials": "\u00c1"}, {"family": "Hofmann", "given": "Tobias", "initials": "T"}], "type": "journal-article", "published": "2016-10-00", "journal": {"title": "Bot. J. Linn. Soc.", "issn": "0024-4074", "volume": "182", "issue": "2", "pages": "234-255", "issn-l": null}, "abstract": null, "doi": "10.1111/boj.12399", "pmid": null, "labels": {"Tobias Andermann": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2022-11-11T09:10:37.742Z", "modified": "2025-12-04T16:58:28.958Z"}, {"entity": "publication", "iuid": "1893720707a144e38951bbf8db6bf57c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1893720707a144e38951bbf8db6bf57c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1893720707a144e38951bbf8db6bf57c"}}, "title": "Annotating public fungal ITS sequences from the built environment according to the MIxS-Built Environment standard \u2013 a report from a May 23-24, 2016 workshop (Gothenburg, Sweden)", "authors": [{"family": "Abarenkov", "given": "Kessy", "initials": "K"}, {"family": "Adams", "given": "Rachel I", "initials": "RI"}, {"family": "Laszlo", "given": "Irinyi", "initials": "I"}, {"family": "Agan", "given": "Ahto", "initials": "A"}, {"family": "Ambrosio", "given": "Elia", "initials": "E"}, {"family": "Antonelli", "given": "Alexandre", "initials": "A"}, {"family": "Bahram", "given": "Mohammad", "initials": "M"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Bok", "given": "Gunilla", "initials": "G"}, {"family": "Cangren", "given": "Patrik", "initials": "P"}, {"family": "Coimbra", "given": "Victor", "initials": "V"}, {"family": "Coleine", "given": "Claudia", "initials": "C"}, {"family": "Gustafsson", "given": "Claes", "initials": "C"}, {"family": "He", "given": "Jinhong", "initials": "J"}, {"family": "Hofmann", "given": "Tobias", "initials": "T"}, {"family": "Kristiansson", "given": "Erik", "initials": "E"}, {"family": "Larsson", "given": "Ellen", "initials": "E"}, {"family": "Larsson", "given": "Tomas", "initials": "T"}, {"family": "Liu", "given": "Yingkui", "initials": "Y"}, {"family": "Martinsson", "given": "Svante", "initials": "S"}, {"family": "Meyer", "given": "Wieland", "initials": "W"}, {"family": "Panova", "given": "Marina", "initials": "M"}, {"family": "Pombubpa", "given": "Nuttapon", "initials": "N"}, {"family": "Ritter", "given": "Camila", "initials": "C"}, {"family": "Ryberg", "given": "Martin", "initials": "M"}, {"family": "Svantesson", "given": "Sten", "initials": "S"}, {"family": "Scharn", "given": "Ruud", "initials": "R"}, {"family": "Svensson", "given": "Ola", "initials": "O"}, {"family": "T\u00f6pel", "given": "Mats", "initials": "M"}, {"family": "Unterseher", "given": "Martin", "initials": "M"}, {"family": "Visagie", "given": "Cobus", "initials": "C"}, {"family": "Wurzbacher", "given": "Christian", "initials": "C"}, {"family": "Taylor", "given": "Andy F S", "initials": "AFS"}, {"family": "K\u00f5ljalg", "given": "Urmas", "initials": "U"}, {"family": "Schriml", "given": "Lynn", "initials": "L"}, {"family": "Nilsson", "given": "R Henrik", "initials": "RH"}], "type": "journal-article", "published": "2016-09-26", "journal": {"title": "MykoKeys", "issn": "1314-4049", "issn-l": null, "volume": "16", "issue": null, "pages": "1-15"}, "abstract": null, "doi": "10.3897/mycokeys.16.10000", "pmid": null, "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [], "notes": [], "created": "2022-11-08T09:29:32.172Z", "modified": "2025-12-04T17:01:55.738Z"}, {"entity": "publication", "iuid": "566e17fe9b114125b6726dca6e114ea5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/566e17fe9b114125b6726dca6e114ea5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/566e17fe9b114125b6726dca6e114ea5"}}, "title": "Strategies to improve usability and preserve accuracy in biological sequence databases.", "authors": [{"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Boulund", "given": "Fredrik", "initials": "F"}, {"family": "Edstr\u00f6m", "given": "Robert", "initials": "R"}, {"family": "Feizi", "given": "Amir", "initials": "A"}, {"family": "Johnning", "given": "Anna", "initials": "A"}, {"family": "Jonsson", "given": "Viktor A", "initials": "VA"}, {"family": "Karlsson", "given": "Fredrik H", "initials": "FH"}, {"family": "Pal", "given": "Chandan", "initials": "C"}, {"family": "Pereira", "given": "Mariana Buongermino", "initials": "MB"}, {"family": "Rehammar", "given": "Anna", "initials": "A"}, {"family": "Sanchez", "given": "Jos\u00e9", "initials": "J"}, {"family": "Sanli", "given": "Kemal", "initials": "K"}, {"family": "Thorell", "given": "Kaisa", "initials": "K"}], "type": "journal article", "published": "2016-09-00", "journal": {"title": "Proteomics", "issn": "1615-9861", "volume": "16", "issue": "18", "pages": "2454-2460", "issn-l": "1615-9853"}, "abstract": "Biology is increasingly dependent on large-scale analysis, such as proteomics, creating a requirement for efficient bioinformatics. Bioinformatic predictions of biological functions rely upon correctly annotated database sequences, and the presence of inaccurately annotated or otherwise poorly described sequences introduces noise and bias to biological analyses. Accurate annotations are, for example, pivotal for correct identification of polypeptide fragments. However, standards for how sequence databases are organized and presented are currently insufficient. Here, we propose five strategies to address fundamental issues in the annotation of sequence databases: (i) to clearly separate experimentally verified and unverified sequence entries; (ii) to enable a system for tracing the origins of annotations; (iii) to separate entries with high-quality, informative annotation from less useful ones; (iv) to integrate automated quality-control software whenever such tools exist; and (v) to facilitate postsubmission editing of annotations and metadata associated with sequences. We believe that implementation of these strategies, for example as requirements for publication of database papers, would enable biology to better take advantage of large-scale data.", "doi": "10.1002/pmic.201600034", "pmid": "27528420", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [], "notes": [], "created": "2022-11-08T09:31:08.898Z", "modified": "2022-11-08T09:31:08.924Z"}, {"entity": "publication", "iuid": "7d189d83f25f45579a08612309e0cdb9", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/7d189d83f25f45579a08612309e0cdb9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/7d189d83f25f45579a08612309e0cdb9"}}, "title": "Proteomic Screening and Lasso Regression Reveal Differential Signaling in Insulin and Insulin-like Growth Factor I (IGF1) Pathways.", "authors": [{"family": "Erdem", "given": "Cemal", "initials": "C"}, {"family": "Nagle", "given": "Alison M", "initials": "AM"}, {"family": "Casa", "given": "Angelo J", "initials": "AJ"}, {"family": "Litzenburger", "given": "Beate C", "initials": "BC"}, {"family": "Wang", "given": "Yu-Fen", "initials": "YF"}, {"family": "Taylor", "given": "D Lansing", "initials": "DL"}, {"family": "Lee", "given": "Adrian V", "initials": "AV"}, {"family": "Lezon", "given": "Timothy R", "initials": "TR"}], "type": "journal article", "published": "2016-09-00", "journal": {"title": "Mol. Cell Proteomics", "issn": "1535-9484", "volume": "15", "issue": "9", "pages": "3045-3057", "issn-l": "1535-9476"}, "abstract": "Insulin and insulin-like growth factor I (IGF1) influence cancer risk and progression through poorly understood mechanisms. To better understand the roles of insulin and IGF1 signaling in breast cancer, we combined proteomic screening with computational network inference to uncover differences in IGF1 and insulin induced signaling. Using reverse phase protein array, we measured the levels of 134 proteins in 21 breast cancer cell lines stimulated with IGF1 or insulin for up to 48 h. We then constructed directed protein expression networks using three separate methods: (i) lasso regression, (ii) conventional matrix inversion, and (iii) entropy maximization. These networks, named here as the time translation models, were analyzed and the inferred interactions were ranked by differential magnitude to identify pathway differences. The two top candidates, chosen for experimental validation, were shown to regulate IGF1/insulin induced phosphorylation events. First, acetyl-CoA carboxylase (ACC) knock-down was shown to increase the level of mitogen-activated protein kinase (MAPK) phosphorylation. Second, stable knock-down of E-Cadherin increased the phospho-Akt protein levels. Both of the knock-down perturbations incurred phosphorylation responses stronger in IGF1 stimulated cells compared with insulin. Overall, the time-translation modeling coupled to wet-lab experiments has proven to be powerful in inferring differential interactions downstream of IGF1 and insulin signaling, in vitro.", "doi": "10.1074/mcp.M115.057729", "pmid": "27364358", "labels": {"DDLS Fellow": null, "Cemal Erdem": null}, "xrefs": [{"db": "pmc", "key": "PMC5013316"}, {"db": "pii", "key": "S1535-9476(20)33378-8"}], "notes": [], "created": "2023-10-27T08:53:51.548Z", "modified": "2023-10-27T08:53:51.570Z"}, {"entity": "publication", "iuid": "18e71103fef345b89e3fd6b06e73ec45", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/18e71103fef345b89e3fd6b06e73ec45.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/18e71103fef345b89e3fd6b06e73ec45"}}, "title": "Benchmarking of algorithms for 3D tissue reconstruction", "authors": [{"family": "Kartasalo", "given": "Kimmo", "initials": "K"}, {"family": "Latonen", "given": "Leena", "initials": "L"}, {"family": "Visakorpi", "given": "Tapio", "initials": "T"}, {"family": "Nykter", "given": "Matti", "initials": "M"}, {"family": "Ruusuvuori", "given": "Pekka", "initials": "P"}], "type": "proceedings-article", "published": "2016-09-00", "journal": {"title": null, "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": "2360-2364"}, "abstract": null, "doi": "10.1109/icip.2016.7532781", "pmid": null, "labels": {"Kimmo Kartasalo": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2024-11-05T16:04:26.892Z", "modified": "2024-11-29T12:06:09.011Z"}, {"entity": "publication", "iuid": "c94b83cf9f3a49aca7799f1ffea4ee1a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c94b83cf9f3a49aca7799f1ffea4ee1a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c94b83cf9f3a49aca7799f1ffea4ee1a"}}, "title": "A software tool for studying the size and shape of human cardiomyocytes", "authors": [{"family": "Rasku", "given": "Jyrki", "initials": "J"}, {"family": "Ojala", "given": "Marisa", "initials": "M"}, {"family": "P\u00f6l\u00f6nen", "given": "Risto Pekka", "initials": "RP"}, {"family": "Joutsijoki", "given": "Henry", "initials": "H"}, {"family": "Gizatdinova", "given": "Yulia", "initials": "Y"}, {"family": "Laurikkala", "given": "Jorma", "initials": "J"}, {"family": "Kartasalo", "given": "Kimmo", "initials": "K"}, {"family": "Aalto-Set\u00e4l\u00e4", "given": "Katriina", "initials": "K"}, {"family": "Juhola", "given": "Martti", "initials": "M"}], "type": "journal-article", "published": "2016-09-00", "journal": {"title": "Biomedical Signal Processing and Control", "issn": "1746-8094", "issn-l": null, "volume": "30", "issue": null, "pages": "134-139"}, "abstract": null, "doi": "10.1016/j.bspc.2016.06.011", "pmid": null, "labels": {"Kimmo Kartasalo": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2024-11-05T16:03:07.826Z", "modified": "2024-11-29T12:06:20.360Z"}, {"entity": "publication", "iuid": "17237a40c3fc42ce8f2ef9ac3c599bb6", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/17237a40c3fc42ce8f2ef9ac3c599bb6.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/17237a40c3fc42ce8f2ef9ac3c599bb6"}}, "title": "Production of hemolysin BL by Bacillus cereus group isolates of dairy origin is associated with whole-genome phylogenetic clade.", "authors": [{"family": "Kovac", "given": "Jasna", "initials": "J"}, {"family": "Miller", "given": "Rachel A", "initials": "RA"}, {"family": "Carroll", "given": "Laura M", "initials": "LM"}, {"family": "Kent", "given": "David J", "initials": "DJ"}, {"family": "Jian", "given": "Jiahui", "initials": "J"}, {"family": "Beno", "given": "Sarah M", "initials": "SM"}, {"family": "Wiedmann", "given": "Martin", "initials": "M"}], "type": "journal article", "published": "2016-08-09", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "17", "pages": "581", "issn-l": "1471-2164"}, "abstract": "Bacillus cereus group isolates that produce diarrheal or emetic toxins are frequently isolated from raw milk and, in spore form, can survive pasteurization. Several species within the B. cereus group are closely related and cannot be reliably differentiated by established taxonomical criteria. While B. cereus is traditionally recognized as the principal causative agent of foodborne disease in this group, there is a need to better understand the distribution and expression of different toxin and virulence genes among B. cereus group food isolates to facilitate reliable characterization that allows for assessment of the likelihood of a given isolate to cause a foodborne disease.\n\nWe performed whole genome sequencing of 22 B. cereus group dairy isolates, which represented considerable genetic diversity not covered by other isolates characterized to date. Maximum likelihood analysis of these genomes along with 47 reference genomes representing eight validly published species revealed nine phylogenetic clades. Three of these clades were represented by a single species (B. toyonensis -clade V, B. weihenstephanensis - clade VI, B. cytotoxicus - VII), one by two dairy-associated isolates (clade II; representing a putative new species), one by two species (B. mycoides, B. pseudomycoides - clade I) and four by three species (B. cereus, B. thuringiensis, B. anthracis - clades III-a, b, c and IV). Homologues of genes encoding a principal diarrheal enterotoxin (hemolysin BL) were distributed across all, except the B. cytotoxicus clade. Using a lateral flow immunoassay, hemolysin BL was detected in 13 out of 18 isolates that carried hblACD genes. Isolates from clade III-c (which included B. cereus and B. thuringiensis) consistently did not carry hblACD and did not produce hemolysin BL. Isolates from clade IV (B. cereus, B. thuringiensis) consistently carried hblACD and produced hemolysin BL. Compared to others, clade IV was significantly (p = 0.0001) more likely to produce this toxin. Isolates from clade VI (B. weihenstephanensis) carried hblACD homologues, but did not produce hemolysin BL, possibly due to amino acid substitutions in different toxin-encoding genes.\n\nOur results demonstrate that production of diarrheal enterotoxin hemolysin BL is neither inclusive nor exclusive to B. cereus sensu stricto, and that phylogenetic classification of isolates may be better than taxonomic identification for assessment of B. cereus group isolates risk for causing a diarrheal foodborne disease.", "doi": "10.1186/s12864-016-2883-z", "pmid": "27507015", "labels": {"Laura Carroll": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC4979109"}, {"db": "pii", "key": "10.1186/s12864-016-2883-z"}, {"db": "figshare", "key": "/s/7f5965d498bd33ccaac4"}], "notes": [], "created": "2025-03-18T17:21:30.227Z", "modified": "2025-03-18T17:22:14.948Z"}, {"entity": "publication", "iuid": "67db7e9cbf9d41aba727869210e364dd", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/67db7e9cbf9d41aba727869210e364dd.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/67db7e9cbf9d41aba727869210e364dd"}}, "title": "5-Hydroxymethylcytosine Remodeling Precedes Lineage Specification during Differentiation of Human CD4(+) T Cells.", "authors": [{"family": "Nestor", "given": "Colm E", "initials": "CE"}, {"family": "Lentini", "given": "Antonio", "initials": "A"}, {"family": "H\u00e4gg Nilsson", "given": "Cathrine", "initials": "C"}, {"family": "Gawel", "given": "Danuta R", "initials": "DR"}, {"family": "Gustafsson", "given": "Mika", "initials": "M"}, {"family": "Mattson", "given": "Lina", "initials": "L"}, {"family": "Wang", "given": "Hui", "initials": "H"}, {"family": "Rundquist", "given": "Olof", "initials": "O"}, {"family": "Meehan", "given": "Richard R", "initials": "RR"}, {"family": "Klocke", "given": "Bernward", "initials": "B"}, {"family": "Seifert", "given": "Martin", "initials": "M"}, {"family": "Hauck", "given": "Stefanie M", "initials": "SM"}, {"family": "Laumen", "given": "Helmut", "initials": "H"}, {"family": "Zhang", "given": "Huan", "initials": "H"}, {"family": "Benson", "given": "Mikael", "initials": "M"}], "type": "journal article", "published": "2016-07-12", "journal": {"title": "Cell Reports", "issn": "2211-1247", "volume": "16", "issue": "2", "pages": "559-570", "issn-l": null}, "abstract": "5-methylcytosine (5mC) is converted to 5-hydroxymethylcytosine (5hmC) by the TET family of enzymes as part of a recently discovered active DNA de-methylation pathway. 5hmC plays important roles in regulation of gene expression and differentiation and has been implicated in T cell malignancies and autoimmunity. Here, we report early and widespread 5mC/5hmC remodeling during human CD4(+) T cell differentiation ex vivo at genes and cell-specific enhancers with known T cell function. We observe similar DNA de-methylation in CD4(+) memory T cells in vivo, indicating that early remodeling events persist long term in differentiated cells. Underscoring their important function, 5hmC loci were highly enriched for genetic variants associated with T cell diseases and T-cell-specific chromosomal interactions. Extensive functional validation of 22 risk variants revealed potentially pathogenic mechanisms in diabetes and multiple sclerosis. Our results support 5hmC-mediated DNA de-methylation as a key component of CD4(+) T cell biology in humans, with important implications for gene regulation and lineage commitment.", "doi": "10.1016/j.celrep.2016.05.091", "pmid": "27346350", "labels": {"Antonio Lentini": null, "DDLS Fellow": null}, "xrefs": [{"db": "mid", "key": "EMS76499"}, {"db": "pmc", "key": "PMC5868728"}, {"db": "pii", "key": "S2211-1247(16)30704-5"}], "notes": [], "created": "2025-03-28T07:14:46.632Z", "modified": "2025-03-28T07:14:46.655Z"}, {"entity": "publication", "iuid": "f51bf9b567714a3da0ee16ca1c433d6c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f51bf9b567714a3da0ee16ca1c433d6c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f51bf9b567714a3da0ee16ca1c433d6c"}}, "title": "Molecular Evolutionary Consequences of Island Colonization.", "authors": [{"family": "James", "given": "Jennifer E", "initials": "JE"}, {"family": "Lanfear", "given": "Robert", "initials": "R"}, {"family": "Eyre-Walker", "given": "Adam", "initials": "A", "orcid": "0000-0001-5527-8729", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/710750d73a5c4e1483168d45dfd0e93f.json"}}], "type": "journal article", "published": "2016-07-02", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "issn-l": "1759-6653", "volume": "8", "issue": "6", "pages": "1876-1888"}, "abstract": "Island endemics are expected to have low effective population sizes (Ne), first because some may experience population bottlenecks when they are founded, and second because they have restricted ranges. Therefore, we expect island species to have reduced genetic diversity, inefficient selection, and reduced adaptive potential compared with their mainland counterparts. We used both polymorphism and substitution data to address these predictions, improving on the approach of recent studies that only used substitution data. This allowed us to directly test the assumption that island species have small values of Ne We found that island species had significantly less genetic diversity than mainland species; however, this pattern could be attributed to a subset of island species that appeared to have undergone a recent population bottleneck. When these species were excluded from the analysis, island and mainland species had similar levels of genetic diversity, despite island species occupying considerably smaller areas than their mainland counterparts. We also found no overall difference between island and mainland species in terms of the effectiveness of selection or the mutation rate. Our evidence suggests that island colonization has no lasting impact on molecular evolution. This surprising result highlights gaps in our knowledge of the relationship between census and effective population size.", "doi": "10.1093/gbe/evw120", "pmid": "27358424", "labels": {"Jennifer James": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC4943191"}, {"db": "pii", "key": "evw120"}], "notes": [], "created": "2024-11-27T09:29:09.889Z", "modified": "2025-11-30T11:20:37.566Z"}, {"entity": "publication", "iuid": "582af57f49224d9bb8c79d86ede6968d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/582af57f49224d9bb8c79d86ede6968d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/582af57f49224d9bb8c79d86ede6968d"}}, "title": "PON-Sol: prediction of effects of amino acid substitutions on protein solubility.", "authors": [{"family": "Yang", "given": "Yang", "initials": "Y"}, {"family": "Niroula", "given": "Abhishek", "initials": "A"}, {"family": "Shen", "given": "Bairong", "initials": "B"}, {"family": "Vihinen", "given": "Mauno", "initials": "M"}], "type": "journal article", "published": "2016-07-01", "journal": {"title": "Bioinformatics", "issn": "1367-4811", "volume": "32", "issue": "13", "pages": "2032-2034", "issn-l": "1367-4803"}, "abstract": "Solubility is one of the fundamental protein properties. It is of great interest because of its relevance to protein expression. Reduced solubility and protein aggregation are also associated with many diseases.\n\nWe collected from literature the largest experimentally verified solubility affecting amino acid substitution (AAS) dataset and used it to train a predictor called PON-Sol. The predictor can distinguish both solubility decreasing and increasing variants from those not affecting solubility. PON-Sol has normalized correct prediction ratio of 0.491 on cross-validation and 0.432 for independent test set. The performance of the method was compared both to solubility and aggregation predictors and found to be superior. PON-Sol can be used for the prediction of effects of disease-related substitutions, effects on heterologous recombinant protein expression and enhanced crystallizability. One application is to investigate effects of all possible AASs in a protein to aid protein engineering.\n\nPON-Sol is freely available at http://structure.bmc.lu.se/PON-Sol The training and test data are available at http://structure.bmc.lu.se/VariBench/ponsol.php\n\nmauno.vihinen@med.lu.se\n\nSupplementary data are available at Bioinformatics online.", "doi": "10.1093/bioinformatics/btw066", "pmid": "27153720", "labels": {"Abhishek Niroula": null, "DDLS Fellow": null}, "xrefs": [{"db": "pii", "key": "btw066"}], "notes": [], "created": "2023-11-20T10:43:31.965Z", "modified": "2023-11-20T10:43:31.970Z"}, {"entity": "publication", "iuid": "85f248dbcf274f7085d3904ac12efa67", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/85f248dbcf274f7085d3904ac12efa67.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/85f248dbcf274f7085d3904ac12efa67"}}, "title": "Application of a Nonlinear Model to Transcript Levels of Upregulated Stress Response Gene ibpA in Stationary-Phase Salmonella enterica Subjected to Sublethal Heat Stress.", "authors": [{"family": "Carroll", "given": "Laura M", "initials": "LM"}, {"family": "Bergholz", "given": "Teresa M", "initials": "TM"}, {"family": "Hildebrandt", "given": "Ian M", "initials": "IM"}, {"family": "Marks", "given": "Bradley P", "initials": "BP"}], "type": "journal article", "published": "2016-07-00", "journal": {"title": "J Food Prot", "issn": "1944-9097", "volume": "79", "issue": "7", "pages": "1089-1096", "issn-l": null}, "abstract": "Sublethal heating, which can occur during slow cooking of meat products, is known to induce increased thermal resistance in Salmonella. However, very few studies have addressed the kinetics of this response. Although several recent studies have reported improved thermal inactivation models that include the effect of prior sublethal history on subsequent thermal resistance, none of these models were based on cellular-level responses to sublethal thermal stress. The goal of this study was to determine whether a nonlinear model could accurately portray the response of Salmonella to heat stress induced by prolonged exposure to sublethal temperatures. To accomplish this, stationary-phase Salmonella Montevideo cultures were subjected to various heating profiles (held at either 40 or 45\u00b0C for 0, 5, 10, 15, 30, 60, 90, 180, or 240 min) using a PCR thermal cycler. Differential plating on selective and nonselective media was used to confirm the presence of cellular injury. Reverse transcription quantitative PCR was used to screen the transcript levels of six heat stress-related genes to find candidate genes for nonlinear modeling. Injury was detected in populations of Salmonella held at 45\u00b0C for 30, 60, and 90 min and at 40\u00b0C for 0, 5, and 90 min (P < 0.05), whereas no significant injury was found at 180 and 240 min (P > 0.05). The transcript levels of ibpA, which codes for a small heat shock protein associated with the ClpB and DnaK-DnaJ-GrpE chaperone systems, showed the greatest increase relative to the transcript levels at 0 min, which was significant at 5, 10, 15, 30, 60, 90, and 180 min at 45\u00b0C and at 5, 10, 15, 30, 60, and 90 min at 40\u00b0C (P < 0.05). Using ibpA transcript levels as an indicator of adaptation to thermal stress, a nonlinear model for sublethal injury is proposed. The use of variables indicating the physiological state of the pathogen during stress has the potential to increase the accuracy of thermal inactivation models that must account for prolonged exposure to sublethal temperatures.", "doi": "10.4315/0362-028X.JFP-15-377", "pmid": "27357027", "labels": {"Laura Carroll": null, "DDLS Fellow": null}, "xrefs": [{"db": "pii", "key": "S0362-028X(22)09264-X"}], "notes": [], "created": "2025-03-18T17:21:27.934Z", "modified": "2025-03-18T17:22:12.787Z"}, {"entity": "publication", "iuid": "691c13865e6549abadb77db55d7e473f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/691c13865e6549abadb77db55d7e473f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/691c13865e6549abadb77db55d7e473f"}}, "title": "Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2", "authors": [{"family": "Kimanius", "given": "Dari", "initials": "D", "orcid": "0000-0002-2662-6373", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3a3803ee817a464ca07c849c07096dc2.json"}}, {"family": "Forsberg", "given": "Bj\u00f6rn O", "initials": "BO", "orcid": "0000-0002-6247-4063", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/36ea51bfa66d48b7a43559c3d0eaa59f.json"}}, {"family": "Scheres", "given": "Sjors HW", "initials": "SH", "orcid": "0000-0002-0462-6540", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b64851b999fd42f7bf7b25856946dc62.json"}}, {"family": "Lindahl", "given": "Erik", "initials": "E"}], "type": "posted-content", "published": "2016-06-19", "journal": {"title": "bioRxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/059717", "pmid": null, "labels": {"DDLS Fellow": null, "Bj\u00f6rn Forsberg": null}, "xrefs": [], "notes": [], "created": "2026-08-20T09:53:20.608Z", "modified": "2026-10-05T08:18:01.082Z"}, {"entity": "publication", "iuid": "fb3a33ef298b4b48bc2dff576302310d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/fb3a33ef298b4b48bc2dff576302310d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/fb3a33ef298b4b48bc2dff576302310d"}}, "title": "Draft Genome Sequence of Moraxella catarrhalis Type Strain CCUG 353T.", "authors": [{"family": "Jakobsson", "given": "Hedvig E", "initials": "HE"}, {"family": "Salv\u00e0-Serra", "given": "Francisco", "initials": "F", "orcid": "0000-0003-0173-560X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fd8b67169228469b913ff8da0ad5f2a0.json"}}, {"family": "Thorell", "given": "Kaisa", "initials": "K", "orcid": "0000-0002-4447-8968", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/789d4029a5c14d3c83df7c47b3b514c7.json"}}, {"family": "Gonzales-Siles", "given": "Lucia", "initials": "L"}, {"family": "Boulund", "given": "Fredrik", "initials": "F"}, {"family": "Karlsson", "given": "Roger", "initials": "R"}, {"family": "Sikora", "given": "Per", "initials": "P"}, {"family": "Engstrand", "given": "Lars", "initials": "L", "orcid": "0000-0002-7713-2373", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02d8684df81e42169e613de803446fbf.json"}}, {"family": "Kristiansson", "given": "Erik", "initials": "E"}, {"family": "Moore", "given": "Edward R B", "initials": "ER", "orcid": "0000-0001-7693-924X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6862c4ac13144c25ae08f822671f62e4.json"}}], "type": "journal article", "published": "2016-06-16", "journal": {"title": "Genome Announc", "issn": "2169-8287", "volume": "4", "issue": "3", "issn-l": null}, "abstract": "Moraxella catarrhalis is a Gram-negative commensal and pathogenic bacterium found in the human respiratory tract. It is associated with otitis media and respiratory tract infections. Here, we report the draft genome sequence of M. catarrhalis type strain CCUG 353(T), composed of 18 contigs and a total size of 1.89 Mb.", "doi": "10.1128/genomeA.00552-16", "pmid": "27313296", "labels": {"DDLS Fellow": "", "Kaisa Thorell": ""}, "xrefs": [{"db": "pmc", "key": "PMC4911475"}, {"db": "pii", "key": "4/3/e00552-16"}], "notes": [], "created": "2026-08-20T12:00:10.020Z", "modified": "2026-09-23T13:10:11.482Z"}, {"entity": "publication", "iuid": "00aacd724d4043a58ce3cc544cbdb0c3", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/00aacd724d4043a58ce3cc544cbdb0c3.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/00aacd724d4043a58ce3cc544cbdb0c3"}}, "title": "Variation Interpretation Predictors: Principles, Types, Performance, and Choice.", "authors": [{"family": "Niroula", "given": "Abhishek", "initials": "A"}, {"family": "Vihinen", "given": "Mauno", "initials": "M"}], "type": "journal article", "published": "2016-06-00", "journal": {"title": "Hum. Mutat.", "issn": "1098-1004", "volume": "37", "issue": "6", "pages": "579-597", "issn-l": "1059-7794"}, "abstract": "Next-generation sequencing methods have revolutionized the speed of generating variation information. Sequence data have a plethora of applications and will increasingly be used for disease diagnosis. Interpretation of the identified variants is usually not possible with experimental methods. This has caused a bottleneck that many computational methods aim at addressing. Fast and efficient methods for explaining the significance and mechanisms of detected variants are required for efficient precision/personalized medicine. Computational prediction methods have been developed in three areas to address the issue. There are generic tolerance (pathogenicity) predictors for filtering harmful variants. Gene/protein/disease-specific tools are available for some applications. Mechanism and effect-specific computer programs aim at explaining the consequences of variations. Here, we discuss the different types of predictors and their applications. We review available variation databases and prediction methods useful for variation interpretation. We discuss how the performance of methods is assessed and summarize existing assessment studies. A brief introduction is provided to the principles of the methods developed for variation interpretation as well as guidelines for how to choose the optimal tools and where the field is heading in the future.", "doi": "10.1002/humu.22987", "pmid": "26987456", "labels": {"Abhishek Niroula": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2023-11-20T10:43:30.706Z", "modified": "2023-11-20T10:43:30.709Z"}, {"entity": "publication", "iuid": "6fb9e09a19d742f2ba5a885cde207515", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/6fb9e09a19d742f2ba5a885cde207515.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/6fb9e09a19d742f2ba5a885cde207515"}}, "title": "Subnanometer Structure of an Asymmetric Model Membrane: Interleaflet Coupling Influences Domain Properties.", "authors": [{"family": "Heberle", "given": "Frederick A", "initials": "FA"}, {"family": "Marquardt", "given": "Drew", "initials": "D"}, {"family": "Doktorova", "given": "Milka", "initials": "M"}, {"family": "Geier", "given": "Barbara", "initials": "B"}, {"family": "Standaert", "given": "Robert F", "initials": "RF"}, {"family": "Heftberger", "given": "Peter", "initials": "P"}, {"family": "Kollmitzer", "given": "Benjamin", "initials": "B"}, {"family": "Nickels", "given": "Jonathan D", "initials": "JD"}, {"family": "Dick", "given": "Robert A", "initials": "RA"}, {"family": "Feigenson", "given": "Gerald W", "initials": "GW"}, {"family": "Katsaras", "given": "John", "initials": "J"}, {"family": "London", "given": "Erwin", "initials": "E"}, {"family": "Pabst", "given": "Georg", "initials": "G"}], "type": "journal article", "published": "2016-05-24", "journal": {"title": "Langmuir", "issn": "1520-5827", "issn-l": "0743-7463", "volume": "32", "issue": "20", "pages": "5195-5200"}, "abstract": "Cell membranes possess a complex three-dimensional architecture, including nonrandom lipid lateral organization within the plane of a bilayer leaflet, and compositional asymmetry between the two leaflets. As a result, delineating the membrane structure-function relationship has been a highly challenging task. Even in simplified model systems, the interactions between bilayer leaflets are poorly understood, due in part to the difficulty of preparing asymmetric model membranes that are free from the effects of residual organic solvent or osmotic stress. To address these problems, we have modified a technique for preparing asymmetric large unilamellar vesicles (aLUVs) via cyclodextrin-mediated lipid exchange in order to produce tensionless, solvent-free aLUVs suitable for a range of biophysical studies. Leaflet composition and structure were characterized using isotopic labeling strategies, which allowed us to avoid the use of bulky labels. NMR and gas chromatography provided precise quantification of the extent of lipid exchange and bilayer asymmetry, while small-angle neutron scattering (SANS) was used to resolve bilayer structural features with subnanometer resolution. Isotopically asymmetric POPC vesicles were found to have the same bilayer thickness and area per lipid as symmetric POPC vesicles, demonstrating that the modified exchange protocol preserves native bilayer structure. Partial exchange of DPPC into the outer leaflet of POPC vesicles produced chemically asymmetric vesicles with a gel/fluid phase-separated outer leaflet and a uniform, POPC-rich inner leaflet. SANS was able to separately resolve the thicknesses and areas per lipid of coexisting domains, revealing reduced lipid packing density of the outer leaflet DPPC-rich phase compared to typical gel phases. Our finding that a disordered inner leaflet can partially fluidize ordered outer leaflet domains indicates some degree of interleaflet coupling, and invites speculation on a role for bilayer asymmetry in modulating membrane lateral organization.", "doi": "10.1021/acs.langmuir.5b04562", "pmid": "27128636", "labels": {"Milka Doktorova": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC4910133"}], "notes": [], "created": "2024-11-27T12:16:13.156Z", "modified": "2024-11-29T12:17:26.421Z"}, {"entity": "publication", "iuid": "93d4a8f263994dc89713e799f11f8140", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/93d4a8f263994dc89713e799f11f8140.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/93d4a8f263994dc89713e799f11f8140"}}, "title": "Minimal selective concentrations of tetracycline in complex aquatic bacterial biofilms.", "authors": [{"family": "Lundstr\u00f6m", "given": "Sara V", "initials": "SV"}, {"family": "\u00d6stman", "given": "Marcus", "initials": "M"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Rutgersson", "given": "Carolin", "initials": "C"}, {"family": "Thoudal", "given": "Malin", "initials": "M"}, {"family": "Sircar", "given": "Triranta", "initials": "T"}, {"family": "Blanck", "given": "Hans", "initials": "H"}, {"family": "Eriksson", "given": "K Martin", "initials": "KM"}, {"family": "Tysklind", "given": "Mats", "initials": "M"}, {"family": "Flach", "given": "Carl-Fredrik", "initials": "CF"}, {"family": "Larsson", "given": "D G Joakim", "initials": "DGJ"}], "type": "journal article", "published": "2016-05-15", "journal": {"title": "Sci. Total Environ.", "issn": "1879-1026", "volume": "553", "pages": "587-595", "issn-l": "0048-9697"}, "abstract": "Selection pressure generated by antibiotics released into the environment could enrich for antibiotic resistance genes and antibiotic resistant bacteria, thereby increasing the risk for transmission to humans and animals. Tetracyclines comprise an antibiotic class of great importance to both human and animal health. Accordingly, residues of tetracycline are commonly detected in aquatic environments. To assess if tetracycline pollution in aquatic environments promotes development of resistance, we determined minimal selective concentrations (MSCs) in biofilms of complex aquatic bacterial communities using both phenotypic and genotypic assays. Tetracycline significantly increased the relative abundance of resistant bacteria at 10 \u03bcg/L, while specific tet genes (tetA and tetG) increased significantly at the lowest concentration tested (1 \u03bcg/L). Taxonomic composition of the biofilm communities was altered with increasing tetracycline concentrations. Metagenomic analysis revealed a concurrent increase of several tet genes and a range of other genes providing resistance to different classes of antibiotics (e.g. cmlA, floR, sul1, and mphA), indicating potential for co-selection. Consequently, MSCs for the tet genes of \u2264 1 \u03bcg/L suggests that current exposure levels in e.g. sewage treatment plants could be sufficient to promote resistance. The methodology used here to assess MSCs could be applied in risk assessment of other antibiotics as well.", "doi": "10.1016/j.scitotenv.2016.02.103", "pmid": "26938321", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pii", "key": "S0048-9697(16)30314-X"}], "notes": [], "created": "2022-11-08T09:29:50.289Z", "modified": "2022-11-08T09:29:50.311Z"}, {"entity": "publication", "iuid": "a0a74d9b96644c34a5d4ba46ca19994e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a0a74d9b96644c34a5d4ba46ca19994e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a0a74d9b96644c34a5d4ba46ca19994e"}}, "title": "Metaxa2 Diversity Tools: Easing microbial community analysis with Metaxa2", "authors": [{"family": "Bengtsson-Palme", "given": "Johan", "initials": "J", "orcid": "0000-0002-6528-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c666068e9d34939b0252a627007cec7.json"}}, {"family": "Thorell", "given": "Kaisa", "initials": "K"}, {"family": "Wurzbacher", "given": "Christian", "initials": "C"}, {"family": "Sj\u00f6ling", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Nilsson", "given": "R Henrik", "initials": "RH"}], "type": "journal-article", "published": "2016-05-00", "journal": {"title": "Ecological Informatics", "issn": "1574-9541", "volume": "33", "pages": "45-50", "issn-l": null}, "abstract": null, "doi": "10.1016/j.ecoinf.2016.04.004", "pmid": null, "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [], "notes": [], "created": "2022-11-08T09:29:48.001Z", "modified": "2025-12-04T17:03:10.263Z"}, {"entity": "publication", "iuid": "8476d10b661e4130932a608647657c40", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8476d10b661e4130932a608647657c40.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8476d10b661e4130932a608647657c40"}}, "title": "Stability of the Encoding Plasmids and Surface Expression of CS6 Differs in Enterotoxigenic Escherichia coli (ETEC) Encoding Different Heat-Stable (ST) Enterotoxins (STh and STp).", "authors": [{"family": "Tobias", "given": "Joshua", "initials": "J"}, {"family": "Von Mentzer", "given": "Astrid", "initials": "A"}, {"family": "Loayza Frykberg", "given": "Patricia", "initials": "P"}, {"family": "Aslett", "given": "Martin", "initials": "M"}, {"family": "Page", "given": "Andrew J", "initials": "AJ"}, {"family": "Sj\u00f6ling", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Svennerholm", "given": "Ann-Mari", "initials": "AM"}], "type": "journal article", "published": "2016-04-07", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "11", "issue": "4", "pages": "e0152899", "issn-l": "1932-6203"}, "abstract": "Enterotoxigenic Escherichia coli (ETEC), one of the most common reasons of diarrhea among infants and children in developing countries, causes disease by expression of either or both of the enterotoxins heat-labile (LT) and heat-stable (ST; divided into human-type [STh] and porcine-type [STp] variants), and colonization factors (CFs) among which CS6 is one of the most prevalent ETEC CFs. In this study we show that ETEC isolates expressing CS6+STh have higher copy numbers of the cssABCD operon encoding CS6 than those expressing CS6+STp. Long term cultivation of up to ten over-night passages of ETEC isolates harboring CS6+STh (n = 10) or CS6+STp (n = 15) showed instability of phenotypic expression of CS6 in a majority of the CS6+STp isolates, whereas most of the CS6+STh isolates retained CS6 expression. The observed instability was a correlated with loss of genes cssA and cssD as examined by PCR. Mobilization of the CS6 plasmid from an unstable CS6+STp isolate into a laboratory E. coli strain resulted in loss of the plasmid after a single over-night passage whereas the plasmid from an CS6+STh strain was retained in the laboratory strain during 10 passages. A sequence comparison between the CS6 plasmids from a stable and an unstable ETEC isolate revealed that genes necessary for plasmid stabilization, for example pemI, pemK, stbA, stbB and parM, were not present in the unstable ETEC isolate. Our results indicate that stable retention of CS6 may in part be affected by the stability of the plasmid on which both CS6 and STp or STh are located.", "doi": "10.1371/journal.pone.0152899", "pmid": "27054573", "labels": {"Astrid von Mentzer": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC4824445"}, {"db": "pii", "key": "PONE-D-15-55751"}], "notes": [], "created": "2025-12-02T15:48:58.957Z", "modified": "2025-12-02T15:48:58.974Z"}, {"entity": "publication", "iuid": "71c3e763ae31489196284b5da84b6cf0", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/71c3e763ae31489196284b5da84b6cf0.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/71c3e763ae31489196284b5da84b6cf0"}}, "title": "Draft Genome Sequence of Streptococcus gordonii Type Strain CCUG 33482T.", "authors": [{"family": "Salv\u00e0-Serra", "given": "Francisco", "initials": "F", "orcid": "0000-0003-0173-560X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fd8b67169228469b913ff8da0ad5f2a0.json"}}, {"family": "Jakobsson", "given": "Hedvig E", "initials": "HE"}, {"family": "Thorell", "given": "Kaisa", "initials": "K", "orcid": "0000-0002-4447-8968", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/789d4029a5c14d3c83df7c47b3b514c7.json"}}, {"family": "Gonzales-Siles", "given": "Lucia", "initials": "L"}, {"family": "Hallb\u00e4ck", "given": "Erika T", "initials": "ET"}, {"family": "Ja\u00e9n-Luchoro", "given": "Daniel", "initials": "D"}, {"family": "Boulund", "given": "Fredrik", "initials": "F"}, {"family": "Sikora", "given": "Per", "initials": "P"}, {"family": "Karlsson", "given": "Roger", "initials": "R"}, {"family": "Svensson", "given": "Liselott", "initials": "L"}, {"family": "Bennasar", "given": "Antoni", "initials": "A"}, {"family": "Engstrand", "given": "Lars", "initials": "L"}, {"family": "Kristiansson", "given": "Erik", "initials": "E"}, {"family": "Moore", "given": "Edward R B", "initials": "ER", "orcid": "0000-0001-7693-924X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6862c4ac13144c25ae08f822671f62e4.json"}}], "type": "journal article", "published": "2016-03-24", "journal": {"title": "Genome Announc", "issn": "2169-8287", "volume": "4", "issue": "2", "issn-l": null}, "abstract": "Streptococcus gordoniitype strain CCUG 33482(T)is a member of theStreptococcus mitisgroup, isolated from a case of subacute bacterial endocarditis. Here, we report the draft genome sequence ofS. gordoniiCCUG 33482(T), composed of 41 contigs of a total size of 2.15 Mb with 2,061 annotated coding sequences.", "doi": "10.1128/genomeA.00175-16", "pmid": "27013051", "labels": {"DDLS Fellow": "", "Kaisa Thorell": ""}, "xrefs": [{"db": "pmc", "key": "PMC4807240"}, {"db": "pii", "key": "4/2/e00175-16"}], "notes": [], "created": "2026-08-20T12:00:07.480Z", "modified": "2026-09-23T13:31:31.342Z"}, {"entity": "publication", "iuid": "d78eb9c1bf864d88abb677dc6714ba9c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d78eb9c1bf864d88abb677dc6714ba9c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d78eb9c1bf864d88abb677dc6714ba9c"}}, "title": "PON-mt-tRNA: a multifactorial probability-based method for classification of mitochondrial tRNA variations.", "authors": [{"family": "Niroula", "given": "Abhishek", "initials": "A"}, {"family": "Vihinen", "given": "Mauno", "initials": "M"}], "type": "journal article", "published": "2016-03-18", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "volume": "44", "issue": "5", "pages": "2020-2027", "issn-l": "0305-1048"}, "abstract": "Transfer RNAs (tRNAs) are essential for encoding the transcribed genetic information from DNA into proteins. Variations in the human tRNAs are involved in diverse clinical phenotypes. Interestingly, all pathogenic variations in tRNAs are located in mitochondrial tRNAs (mt-tRNAs). Therefore, it is crucial to identify pathogenic variations in mt-tRNAs for disease diagnosis and proper treatment. We collected mt-tRNA variations using a classification based on evidence from several sources and used the data to develop a multifactorial probability-based prediction method, PON-mt-tRNA, for classification of mt-tRNA single nucleotide substitutions. We integrated a machine learning-based predictor and an evidence-based likelihood ratio for pathogenicity using evidence of segregation, biochemistry and histochemistry to predict the posterior probability of pathogenicity of variants. The accuracy and Matthews correlation coefficient (MCC) of PON-mt-tRNA are 1.00 and 0.99, respectively. In the absence of evidence from segregation, biochemistry and histochemistry, PON-mt-tRNA classifies variations based on the machine learning method with an accuracy and MCC of 0.69 and 0.39, respectively. We classified all possible single nucleotide substitutions in all human mt-tRNAs using PON-mt-tRNA. The variations in the loops are more often tolerated compared to the variations in stems. The anticodon loop contains comparatively more predicted pathogenic variations than the other loops. PON-mt-tRNA is available at http://structure.bmc.lu.se/PON-mt-tRNA/.", "doi": "10.1093/nar/gkw046", "pmid": "26843426", "labels": {"Abhishek Niroula": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC4797295"}, {"db": "pii", "key": "gkw046"}], "notes": [], "created": "2023-11-20T10:43:28.840Z", "modified": "2023-11-20T10:43:28.846Z"}, {"entity": "publication", "iuid": "d3767b516fcd4d71b3a8062f21049254", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d3767b516fcd4d71b3a8062f21049254.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d3767b516fcd4d71b3a8062f21049254"}}, "title": "Metabolic Trade-offs in Yeast are Caused by F1F0-ATP synthase.", "authors": [{"family": "Nilsson", "given": "Avlant", "initials": "A", "orcid": "0000-0002-9476-4516", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f2e21dbc1c624f6a841c59e959e948e4.json"}}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/33f2b49a39ed4e54ba77dfe397ed3087.json"}}], "type": "journal article", "published": "2016-03-01", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "6", "issue": null, "pages": "22264"}, "abstract": "Intermediary metabolism provides living cells with free energy and precursor metabolites required for synthesizing proteins, lipids, RNA and other cellular constituents, and it is highly conserved among living species. Only a fraction of cellular protein can, however, be allocated to enzymes of intermediary metabolism and consequently metabolic trade-offs may take place. One such trade-off, aerobic fermentation, occurs in both yeast (the Crabtree effect) and cancer cells (the Warburg effect) and has been a scientific challenge for decades. Here we show, using flux balance analysis combined with in vitro measured enzyme specific activities, that fermentation is more catalytically efficient than respiration, i.e. it produces more ATP per protein mass. And that the switch to fermentation at high growth rates therefore is a consequence of a high ATP production rate, provided by a limited pool of enzymes. The catalytic efficiency is also higher for cells grown on glucose compared to galactose and ethanol, which may explain the observed differences in their growth rates. The enzyme F1F0-ATP synthase (Complex V) was found to have flux control over respiration in the model, and since it is evolutionary conserved, we expect the trade-off to occur in organisms from all kingdoms of life.", "doi": "10.1038/srep22264", "pmid": "26928598", "labels": {"Avlant Nilsson": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC4772093"}, {"db": "pii", "key": "srep22264"}], "notes": [], "created": "2025-03-20T11:00:19.432Z", "modified": "2025-03-21T13:15:39.319Z"}, {"entity": "publication", "iuid": "35783800bbcd4277ac4415fc8adcd702", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/35783800bbcd4277ac4415fc8adcd702.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/35783800bbcd4277ac4415fc8adcd702"}}, "title": "Bimodal occupancy-frequency distributions uncover the importance of regional dynamics in shaping marine microbial biogeography", "authors": [{"family": "Lindh", "given": "Markus V", "initials": "MV"}, {"family": "Sj\u00f6stedt", "given": "Johanna", "initials": "J"}, {"family": "Ekstam", "given": "B\u00f6rje", "initials": "B"}, {"family": "Casini", "given": "Michele", "initials": "M"}, {"family": "Lundin", "given": "Daniel", "initials": "D"}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW"}, {"family": "Hu", "given": "Yue O O", "initials": "YOO"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}, {"family": "Andersson", "given": "Agneta", "initials": "A"}, {"family": "Legrand", "given": "Catherine", "initials": "C"}, {"family": "Pinhassi", "given": "Jarone", "initials": "J"}], "type": "posted-content", "published": "2016-02-18", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/039883", "pmid": null, "labels": {"DDLS Fellow": "", "Luisa Hugerth": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T09:53:10.558Z", "modified": "2026-09-23T14:15:08.180Z"}, {"entity": "publication", "iuid": "f7fc10b81a7b416686c84dcc21001be0", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f7fc10b81a7b416686c84dcc21001be0.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f7fc10b81a7b416686c84dcc21001be0"}}, "title": "The rate of adaptive evolution in animal mitochondria.", "authors": [{"family": "James", "given": "Jennifer E", "initials": "JE"}, {"family": "Piganeau", "given": "Gwenael", "initials": "G"}, {"family": "Eyre-Walker", "given": "Adam", "initials": "A", "orcid": "0000-0001-5527-8729", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/710750d73a5c4e1483168d45dfd0e93f.json"}}], "type": "journal article", "published": "2016-01-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "issn-l": "0962-1083", "volume": "25", "issue": "1", "pages": "67-78"}, "abstract": "We have investigated whether there is adaptive evolution in mitochondrial DNA, using an extensive data set containing over 500 animal species from a wide range of taxonomic groups. We apply a variety of McDonald-Kreitman style methods to the data. We find that the evolution of mitochondrial DNA is dominated by slightly deleterious mutations, a finding which is supported by a number of previous studies. However, when we control for the presence of deleterious mutations using a new method, we find that mitochondria undergo a significant amount of adaptive evolution, with an estimated 26% (95% confidence intervals: 5.7-45%) of nonsynonymous substitutions fixed by adaptive evolution. We further find some weak evidence that the rate of adaptive evolution is correlated to synonymous diversity. We interpret this as evidence that at least some adaptive evolution is limited by the supply of mutations.", "doi": "10.1111/mec.13475", "pmid": "26578312", "labels": {"Jennifer James": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC4737298"}, {"db": "figshare", "key": "10.6084/M9.FIGSHARE.1408490"}], "notes": [], "created": "2024-11-27T09:29:11.932Z", "modified": "2025-11-30T11:18:43.689Z"}, {"entity": "publication", "iuid": "5f4a143bd1da49deac86ee498f6e24de", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5f4a143bd1da49deac86ee498f6e24de.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5f4a143bd1da49deac86ee498f6e24de"}}, "title": "Concentrations of antibiotics predicted to select for resistant bacteria: Proposed limits for environmental regulation.", "authors": [{"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Larsson", "given": "D G Joakim", "initials": "DG"}], "type": "journal article", "published": "2016-01-00", "journal": {"title": "Environ Int", "issn": "1873-6750", "volume": "86", "pages": "140-149", "issn-l": "0160-4120"}, "abstract": "There are concerns that selection pressure from antibiotics in the environment may accelerate the evolution and dissemination of antibiotic-resistant pathogens. Nevertheless, there is currently no regulatory system that takes such risks into account. In part, this is due to limited knowledge of environmental concentrations that might exert selection for resistant bacteria. To experimentally determine minimal selective concentrations in complex microbial ecosystems for all antibiotics would involve considerable effort. In this work, our aim was to estimate upper boundaries for selective concentrations for all common antibiotics, based on the assumption that selective concentrations a priori need to be lower than those completely inhibiting growth. Data on Minimal Inhibitory Concentrations (MICs) were obtained for 111 antibiotics from the public EUCAST database. The 1% lowest observed MICs were identified, and to compensate for limited species coverage, predicted lowest MICs adjusted for the number of tested species were extrapolated through modeling. Predicted No Effect Concentrations (PNECs) for resistance selection were then assessed using an assessment factor of 10 to account for differences between MICs and minimal selective concentrations. The resulting PNECs ranged from 8 ng/L to 64 \u03bcg/L. Furthermore, the link between taxonomic similarity between species and lowest MIC was weak. This work provides estimated upper boundaries for selective concentrations (lowest MICs) and PNECs for resistance selection for all common antibiotics. In most cases, PNECs for selection of resistance were below available PNECs for ecotoxicological effects. The generated PNECs can guide implementation of compound-specific emission limits that take into account risks for resistance promotion.", "doi": "10.1016/j.envint.2015.10.015", "pmid": "26590482", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pii", "key": "S0160-4120(15)30081-7"}], "notes": [], "created": "2022-11-08T09:29:52.650Z", "modified": "2022-11-08T09:29:52.673Z"}, {"entity": "publication", "iuid": "3df73ce48a5d4ad09e6abb69fc80c249", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3df73ce48a5d4ad09e6abb69fc80c249.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3df73ce48a5d4ad09e6abb69fc80c249"}}, "title": "The European technical report on aquatic effect-based monitoring tools under the water framework directive", "authors": [{"family": "Wernersson", "given": "Ann Sofie", "initials": "AS"}, {"family": "Carere", "given": "Mario", "initials": "M"}, {"family": "Maggi", "given": "Chiara", "initials": "C"}, {"family": "Tusil", "given": "Petr", "initials": "P"}, {"family": "Soldan", "given": "Premysl", "initials": "P"}, {"family": "James", "given": "Alice", "initials": "A"}, {"family": "Sanchez", "given": "Wilfried", "initials": "W"}, {"family": "Dulio", "given": "Valeria", "initials": "V"}, {"family": "Broeg", "given": "Katja", "initials": "K"}, {"family": "Reifferscheid", "given": "Georg", "initials": "G"}, {"family": "Buchinger", "given": "Sebastian", "initials": "S"}, {"family": "Maas", "given": "Hannie", "initials": "H"}, {"family": "Van Der Grinten", "given": "Esther", "initials": "E"}, {"family": "O\u2019Toole", "given": "Simon", "initials": "S"}, {"family": "Ausili", "given": "Antonella", "initials": "A"}, {"family": "Manfra", "given": "Loredana", "initials": "L"}, {"family": "Marziali", "given": "Laura", "initials": "L"}, {"family": "Polesello", "given": "Stefano", "initials": "S"}, {"family": "Lacchetti", "given": "Ines", "initials": "I"}, {"family": "Mancini", "given": "Laura", "initials": "L"}, {"family": "Lilja", "given": "Karl", "initials": "K"}, {"family": "Linderoth", "given": "Maria", "initials": "M"}, {"family": "Lundeberg", "given": "Tove", "initials": "T"}, {"family": "Fj\u00e4llborg", "given": "Bengt", "initials": "B"}, {"family": "Porsbring", "given": "Tobias", "initials": "T"}, {"family": "Larsson", "given": "DG Joakim", "initials": "DJ"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J", "orcid": "0000-0002-6528-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c666068e9d34939b0252a627007cec7.json"}}, {"family": "F\u00f6rlin", "given": "Lars", "initials": "L"}, {"family": "Kienle", "given": "Cornelia", "initials": "C"}, {"family": "Kunz", "given": "Petra", "initials": "P"}, {"family": "Vermeirssen", "given": "Etienne", "initials": "E"}, {"family": "Werner", "given": "Inge", "initials": "I"}, {"family": "Robinson", "given": "Craig D", "initials": "CD"}, {"family": "Lyons", "given": "Brett", "initials": "B"}, {"family": "Katsiadaki", "given": "Ioanna", "initials": "I"}, {"family": "Whalley", "given": "Caroline", "initials": "C"}, {"family": "den Haan", "given": "Klaas", "initials": "K"}, {"family": "Messiaen", "given": "Marlies", "initials": "M"}, {"family": "Clayton", "given": "Helen", "initials": "H"}, {"family": "Lettieri", "given": "Teresa", "initials": "T"}, {"family": "Carvalho", "given": "Raquel Negr\u00e3o", "initials": "RN"}, {"family": "Gawlik", "given": "Bernd Manfred", "initials": "BM"}, {"family": "Hollert", "given": "Henner", "initials": "H"}, {"family": "Di Paolo", "given": "Carolina", "initials": "C"}, {"family": "Brack", "given": "Werner", "initials": "W"}, {"family": "Kammann", "given": "Ulrike", "initials": "U"}, {"family": "Kase", "given": "Robert", "initials": "R"}], "type": "journal-article", "published": "2015-12-00", "journal": {"title": "Environ Sci Eur", "issn": "2190-4707", "volume": "27", "issue": "1", "issn-l": null}, "abstract": null, "doi": "10.1186/s12302-015-0039-4", "pmid": null, "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [], "notes": [], "created": "2022-11-08T09:30:04.077Z", "modified": "2025-12-04T19:43:56.165Z"}, {"entity": "publication", "iuid": "802a56137f7b41f2acab4f2d20495b08", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/802a56137f7b41f2acab4f2d20495b08.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/802a56137f7b41f2acab4f2d20495b08"}}, "title": "Classification of Amino Acid Substitutions in Mismatch Repair Proteins Using PON-MMR2.", "authors": [{"family": "Niroula", "given": "Abhishek", "initials": "A"}, {"family": "Vihinen", "given": "Mauno", "initials": "M"}], "type": "journal article", "published": "2015-12-00", "journal": {"title": "Hum. Mutat.", "issn": "1098-1004", "volume": "36", "issue": "12", "pages": "1128-1134", "issn-l": "1059-7794"}, "abstract": "Variations in mismatch repair (MMR) system genes are causative of Lynch syndrome and other cancers. Thousands of variants have been identified in MMR genes, but the clinical relevance is known for only a small proportion. Recently, the InSiGHT group classified 2,360 MMR variants into five classes. One-third of variants, majority of which is nonsynonymous variants, remain to be of uncertain clinical relevance. Computational tools can be used to prioritize variants for disease relevance investigations. Previously, we classified 248 MMR variants as likely pathogenic and likely benign using PON-MMR. We have developed a novel tool, PON-MMR2, which is trained on a larger and more reliable dataset. In performance comparison, PON-MMR2 outperforms both generic tolerance prediction methods as well as methods optimized for MMR variants. It achieves accuracy and MCC of 0.89 and 0.78, respectively, in cross-validation and 0.86 and 0.69, respectively, on an independent test dataset. We classified 354 class 3 variants in InSiGHT database as well as all possible amino acid substitutions in four MMR proteins. Likely harmful variants mainly appear in the protein core, whereas likely benign variants are on the surface. PON-MMR2 is a highly reliable tool to prioritize variants for functional analysis. It is freely available at http://structure.bmc.lu.se/PON-MMR2/.", "doi": "10.1002/humu.22900", "pmid": "26333163", "labels": {"Abhishek Niroula": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2023-11-20T10:43:27.140Z", "modified": "2023-11-20T10:43:27.144Z"}, {"entity": "publication", "iuid": "fd4f41085ff14063ab747d7fb63ff1cd", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/fd4f41085ff14063ab747d7fb63ff1cd.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/fd4f41085ff14063ab747d7fb63ff1cd"}}, "title": "Co-occurrence of resistance genes to antibiotics, biocides and metals reveals novel insights into their co-selection potential.", "authors": [{"family": "Pal", "given": "Chandan", "initials": "C"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Kristiansson", "given": "Erik", "initials": "E"}, {"family": "Larsson", "given": "D G Joakim", "initials": "DG"}], "type": "journal article", "published": "2015-11-17", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "16", "pages": "964", "issn-l": "1471-2164"}, "abstract": "Antibacterial biocides and metals can co-select for antibiotic resistance when bacteria harbour resistance or tolerance genes towards both types of compounds. Despite numerous case studies, systematic and quantitative data on co-occurrence of such genes on plasmids and chromosomes is lacking, as is knowledge on environments and bacterial taxa that tend to carry resistance genes to such compounds. This effectively prevents identification of risk scenarios. Therefore, we aimed to identify general patterns for which biocide/metal resistance genes (BMRGs) and antibiotic resistance genes (ARGs) that tend to occur together. We also aimed to quantify co-occurrence of resistance genes in different environments and taxa, and investigate to what extent plasmids carrying both types of genes are conjugative and/or are carrying toxin-antitoxin systems.\n\nCo-occurrence patterns of resistance genes were derived from publicly available, fully sequenced bacterial genomes (n = 2522) and plasmids (n = 4582). The only BMRGs commonly co-occurring with ARGs on plasmids were mercury resistance genes and the qacE\u22061 gene that provides low-level resistance to quaternary ammonium compounds. Novel connections between cadmium/zinc and macrolide/aminoglycoside resistance genes were also uncovered. Several clinically important bacterial taxa were particularly prone to carry both BMRGs and ARGs. Bacteria carrying BMRGs more often carried ARGs compared to bacteria without (p < 0.0001). BMRGs were found in 86 % of bacterial genomes, and co-occurred with ARGs in 17 % of the cases. In contrast, co-occurrences of BMRGs and ARGs were rare on plasmids from all external environments (<0.7 %) but more common on those of human and domestic animal origin (5 % and 7 %, respectively). Finally, plasmids with both BMRGs and ARGs were more likely to be conjugative (p < 0.0001) and carry toxin-antitoxin systems (p < 0.0001) than plasmids without resistance genes.\n\nThis is the first large-scale identification of compounds, taxa and environments of particular concern for co-selection of resistance against antibiotics, biocides and metals. Genetic co-occurrences suggest that plasmids provide limited opportunities for biocides and metals to promote horizontal transfer of antibiotic resistance through co-selection, whereas ample possibilities exist for indirect selection via chromosomal BMRGs. Taken together, the derived patterns improve our understanding of co-selection potential between biocides, metals and antibiotics, and thereby provide guidance for risk-reducing actions.", "doi": "10.1186/s12864-015-2153-5", "pmid": "26576951", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-015-2153-5"}, {"db": "pmc", "key": "PMC4650350"}], "notes": [], "created": "2022-11-08T09:29:54.977Z", "modified": "2022-11-08T09:29:55.001Z"}, {"entity": "publication", "iuid": "5f7c22e3a42c43a4985ca9871d14a705", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5f7c22e3a42c43a4985ca9871d14a705.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5f7c22e3a42c43a4985ca9871d14a705"}}, "title": "A validated gene regulatory network and GWAS identifies early regulators of T cell-associated diseases.", "authors": [{"family": "Gustafsson", "given": "Mika", "initials": "M"}, {"family": "Gawel", "given": "Danuta R", "initials": "DR"}, {"family": "Alfredsson", "given": "Lars", "initials": "L"}, {"family": "Baranzini", "given": "Sergio", "initials": "S"}, {"family": "Bj\u00f6rkander", "given": "Janne", "initials": "J"}, {"family": "Blomgran", "given": "Robert", "initials": "R"}, {"family": "Hellberg", "given": "Sandra", "initials": "S"}, {"family": "Eklund", "given": "Daniel", "initials": "D"}, {"family": "Ernerudh", "given": "Jan", "initials": "J"}, {"family": "Kockum", "given": "Ingrid", "initials": "I"}, {"family": "Konstantinell", "given": "Aelita", "initials": "A"}, {"family": "Lahesmaa", "given": "Riita", "initials": "R"}, {"family": "Lentini", "given": "Antonio", "initials": "A"}, {"family": "Liljenstr\u00f6m", "given": "H Robert I", "initials": "HR"}, {"family": "Mattson", "given": "Lina", "initials": "L"}, {"family": "Matussek", "given": "Andreas", "initials": "A"}, {"family": "Mellerg\u00e5rd", "given": "Johan", "initials": "J"}, {"family": "Mendez", "given": "Melissa", "initials": "M"}, {"family": "Olsson", "given": "Tomas", "initials": "T"}, {"family": "Pujana", "given": "Miguel A", "initials": "MA"}, {"family": "Rasool", "given": "Omid", "initials": "O"}, {"family": "Serra-Musach", "given": "Jordi", "initials": "J"}, {"family": "Stenmarker", "given": "Margaretha", "initials": "M"}, {"family": "Tripathi", "given": "Subhash", "initials": "S"}, {"family": "Viitala", "given": "Miro", "initials": "M"}, {"family": "Wang", "given": "Hui", "initials": "H"}, {"family": "Zhang", "given": "Huan", "initials": "H"}, {"family": "Nestor", "given": "Colm E", "initials": "CE"}, {"family": "Benson", "given": "Mikael", "initials": "M"}], "type": "journal article", "published": "2015-11-11", "journal": {"title": "Sci Transl Med", "issn": "1946-6242", "volume": "7", "issue": "313", "pages": "313ra178", "issn-l": "1946-6234"}, "abstract": "Early regulators of disease may increase understanding of disease mechanisms and serve as markers for presymptomatic diagnosis and treatment. However, early regulators are difficult to identify because patients generally present after they are symptomatic. We hypothesized that early regulators of T cell-associated diseases could be found by identifying upstream transcription factors (TFs) in T cell differentiation and by prioritizing hub TFs that were enriched for disease-associated polymorphisms. A gene regulatory network (GRN) was constructed by time series profiling of the transcriptomes and methylomes of human CD4(+) T cells during in vitro differentiation into four helper T cell lineages, in combination with sequence-based TF binding predictions. The TFs GATA3, MAF, and MYB were identified as early regulators and validated by ChIP-seq (chromatin immunoprecipitation sequencing) and small interfering RNA knockdowns. Differential mRNA expression of the TFs and their targets in T cell-associated diseases supports their clinical relevance. To directly test if the TFs were altered early in disease, T cells from patients with two T cell-mediated diseases, multiple sclerosis and seasonal allergic rhinitis, were analyzed. Strikingly, the TFs were differentially expressed during asymptomatic stages of both diseases, whereas their targets showed altered expression during symptomatic stages. This analytical strategy to identify early regulators of disease by combining GRNs with genome-wide association studies may be generally applicable for functional and clinical studies of early disease development.", "doi": "10.1126/scitranslmed.aad2722", "pmid": "26560356", "labels": {"Antonio Lentini": null, "DDLS Fellow": null}, "xrefs": [{"db": "pii", "key": "7/313/313ra178"}, {"db": "GEO", "key": "GSE60680"}], "notes": [], "created": "2025-03-28T07:14:53.297Z", "modified": "2025-03-28T07:14:53.312Z"}, {"entity": "publication", "iuid": "06a924aaeadb4e21a623a6de50323180", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/06a924aaeadb4e21a623a6de50323180.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/06a924aaeadb4e21a623a6de50323180"}}, "title": "METAXA2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data.", "authors": [{"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Hartmann", "given": "Martin", "initials": "M"}, {"family": "Eriksson", "given": "Karl Martin", "initials": "KM"}, {"family": "Pal", "given": "Chandan", "initials": "C"}, {"family": "Thorell", "given": "Kaisa", "initials": "K"}, {"family": "Larsson", "given": "Dan G\u00f6ran Joakim", "initials": "DG"}, {"family": "Nilsson", "given": "Rolf Henrik", "initials": "RH"}], "type": "comparative study", "published": "2015-11-00", "journal": {"title": "Mol Ecol Resour", "issn": "1755-0998", "volume": "15", "issue": "6", "pages": "1403-1414", "issn-l": "1755-098X"}, "abstract": "The ribosomal rRNA genes are widely used as genetic markers for taxonomic identification of microbes. Particularly the small subunit (SSU; 16S/18S) rRNA gene is frequently used for species- or genus-level identification, but also the large subunit (LSU; 23S/28S) rRNA gene is employed in taxonomic assignment. The METAXA software tool is a popular utility for extracting partial rRNA sequences from large sequencing data sets and assigning them to an archaeal, bacterial, nuclear eukaryote, mitochondrial or chloroplast origin. This study describes a comprehensive update to METAXA - METAXA2 - that extends the capabilities of the tool, introducing support for the LSU rRNA gene, a greatly improved classifier allowing classification down to genus or species level, as well as enhanced support for short-read (100 bp) and paired-end sequences, among other changes. The performance of METAXA2 was compared to other commonly used taxonomic classifiers, showing that METAXA2 often outperforms previous methods in terms of making correct predictions while maintaining a low misclassification rate. METAXA2 is freely available from http://microbiology.se/software/metaxa2/.", "doi": "10.1111/1755-0998.12399", "pmid": "25732605", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [], "notes": [], "created": "2022-11-08T09:30:06.396Z", "modified": "2022-11-08T09:30:06.420Z"}, {"entity": "publication", "iuid": "1472910fee63425e8e183d732cfb69cf", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1472910fee63425e8e183d732cfb69cf.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1472910fee63425e8e183d732cfb69cf"}}, "title": "Metagenomic sequencing of marine periphyton: taxonomic and functional insights into biofilm communities.", "authors": [{"family": "Sanli", "given": "Kemal", "initials": "K"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Nilsson", "given": "R Henrik", "initials": "RH"}, {"family": "Kristiansson", "given": "Erik", "initials": "E"}, {"family": "Alm Rosenblad", "given": "Magnus", "initials": "M"}, {"family": "Blanck", "given": "Hans", "initials": "H"}, {"family": "Eriksson", "given": "Karl M", "initials": "KM"}], "type": "journal article", "published": "2015-10-30", "journal": {"title": "Front Microbiol", "issn": "1664-302X", "volume": "6", "pages": "1192", "issn-l": "1664-302X"}, "abstract": "Periphyton communities are complex phototrophic, multispecies biofilms that develop on surfaces in aquatic environments. These communities harbor a large diversity of organisms comprising viruses, bacteria, algae, fungi, protozoans, and metazoans. However, thus far the total biodiversity of periphyton has not been described. In this study, we use metagenomics to characterize periphyton communities from the marine environment of the Swedish west coast. Although we found approximately ten times more eukaryotic rRNA marker gene sequences compared to prokaryotic, the whole metagenome-based similarity searches showed that bacteria constitute the most abundant phyla in these biofilms. We show that marine periphyton encompass a range of heterotrophic and phototrophic organisms. Heterotrophic bacteria, including the majority of proteobacterial clades and Bacteroidetes, and eukaryotic macro-invertebrates were found to dominate periphyton. The phototrophic groups comprise Cyanobacteria and the alpha-proteobacterial genus Roseobacter, followed by different micro- and macro-algae. We also assess the metabolic pathways that predispose these communities to an attached lifestyle. Functional indicators of the biofilm form of life in periphyton involve genes coding for enzymes that catalyze the production and degradation of extracellular polymeric substances, mainly in the form of complex sugars such as starch and glycogen-like meshes together with chitin. Genes for 278 different transporter proteins were detected in the metagenome, constituting the most abundant protein complexes. Finally, genes encoding enzymes that participate in anaerobic pathways, such as denitrification and methanogenesis, were detected suggesting the presence of anaerobic or low-oxygen micro-zones within the biofilms.", "doi": "10.3389/fmicb.2015.01192", "pmid": "26579098", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pmc", "key": "PMC4626570"}], "notes": [], "created": "2022-11-08T09:29:57.322Z", "modified": "2022-11-08T09:29:57.347Z"}, {"entity": "publication", "iuid": "0b55ebb2323a4bdd8fe51e40737fbd26", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0b55ebb2323a4bdd8fe51e40737fbd26.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0b55ebb2323a4bdd8fe51e40737fbd26"}}, "title": "CytoSpectre: a tool for spectral analysis of oriented structures on cellular and subcellular levels.", "authors": [{"family": "Kartasalo", "given": "Kimmo", "initials": "K"}, {"family": "P\u00f6l\u00f6nen", "given": "Risto-Pekka", "initials": "R"}, {"family": "Ojala", "given": "Marisa", "initials": "M"}, {"family": "Rasku", "given": "Jyrki", "initials": "J"}, {"family": "Lekkala", "given": "Jukka", "initials": "J"}, {"family": "Aalto-Set\u00e4l\u00e4", "given": "Katriina", "initials": "K"}, {"family": "Kallio", "given": "Pasi", "initials": "P"}], "type": "journal article", "published": "2015-10-26", "journal": {"title": "BMC Bioinformatics", "issn": "1471-2105", "issn-l": "1471-2105", "volume": "16", "issue": null, "pages": "344"}, "abstract": "Orientation and the degree of isotropy are important in many biological systems such as the sarcomeres of cardiomyocytes and other fibrillar structures of the cytoskeleton. Image based analysis of such structures is often limited to qualitative evaluation by human experts, hampering the throughput, repeatability and reliability of the analyses. Software tools are not readily available for this purpose and the existing methods typically rely at least partly on manual operation.\r\n\r\nWe developed CytoSpectre, an automated tool based on spectral analysis, allowing the quantification of orientation and also size distributions of structures in microscopy images. CytoSpectre utilizes the Fourier transform to estimate the power spectrum of an image and based on the spectrum, computes parameter values describing, among others, the mean orientation, isotropy and size of target structures. The analysis can be further tuned to focus on targets of particular size at cellular or subcellular scales. The software can be operated via a graphical user interface without any programming expertise. We analyzed the performance of CytoSpectre by extensive simulations using artificial images, by benchmarking against FibrilTool and by comparisons with manual measurements performed for real images by a panel of human experts. The software was found to be tolerant against noise and blurring and superior to FibrilTool when analyzing realistic targets with degraded image quality. The analysis of real images indicated general good agreement between computational and manual results while also revealing notable expert-to-expert variation. Moreover, the experiment showed that CytoSpectre can handle images obtained of different cell types using different microscopy techniques. Finally, we studied the effect of mechanical stretching on cardiomyocytes to demonstrate the software in an actual experiment and observed changes in cellular orientation in response to stretching.\r\n\r\nCytoSpectre, a versatile, easy-to-use software tool for spectral analysis of microscopy images was developed. The tool is compatible with most 2D images and can be used to analyze targets at different scales. We expect the tool to be useful in diverse applications dealing with structures whose orientation and size distributions are of interest. While designed for the biological field, the software could also be useful in non-biological applications.", "doi": "10.1186/s12859-015-0782-y", "pmid": "26503371", "labels": {"Kimmo Kartasalo": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC4624586"}, {"db": "pii", "key": "10.1186/s12859-015-0782-y"}], "notes": [], "created": "2024-11-05T16:03:05.768Z", "modified": "2024-11-29T12:06:27.278Z"}, {"entity": "publication", "iuid": "854144235f174f9e8e86d87ed2d424ab", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/854144235f174f9e8e86d87ed2d424ab.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/854144235f174f9e8e86d87ed2d424ab"}}, "title": "Transcriptome Sequencing Reveals PCAT5 as a Novel ERG-Regulated Long Noncoding RNA in Prostate Cancer.", "authors": [{"family": "Ylip\u00e4\u00e4", "given": "Antti", "initials": "A"}, {"family": "Kivinummi", "given": "Kati", "initials": "K"}, {"family": "Kohvakka", "given": "Annika", "initials": "A"}, {"family": "Annala", "given": "Matti", "initials": "M"}, {"family": "Latonen", "given": "Leena", "initials": "L"}, {"family": "Scaravilli", "given": "Mauro", "initials": "M"}, {"family": "Kartasalo", "given": "Kimmo", "initials": "K"}, {"family": "Lepp\u00e4nen", "given": "Simo-Pekka", "initials": "S"}, {"family": "Karakurt", "given": "Serdar", "initials": "S"}, {"family": "Sepp\u00e4l\u00e4", "given": "Janne", "initials": "J"}, {"family": "Yli-Harja", "given": "Olli", "initials": "O"}, {"family": "Tammela", "given": "Teuvo L J", "initials": "TLJ"}, {"family": "Zhang", "given": "Wei", "initials": "W"}, {"family": "Visakorpi", "given": "Tapio", "initials": "T"}, {"family": "Nykter", "given": "Matti", "initials": "M"}], "type": "comparative study", "published": "2015-10-01", "journal": {"title": "Cancer Res.", "issn": "1538-7445", "issn-l": "0008-5472", "volume": "75", "issue": "19", "pages": "4026-4031"}, "abstract": "Castration-resistant prostate cancers (CRPC) that arise after the failure of androgen-blocking therapies cause most of the deaths from prostate cancer, intensifying the need to fully understand CRPC pathophysiology. In this study, we characterized the transcriptomic differences between untreated prostate cancer and locally recurrent CRPC. Here, we report the identification of 145 previously unannotated intergenic long noncoding RNA transcripts (lncRNA) or isoforms that are associated with prostate cancer or CRPC. Of the one third of these transcripts that were specific for CRPC, we defined a novel lncRNA termed PCAT5 as a regulatory target for the transcription factor ERG, which is activated in approximately 50% of human prostate cancer. Genome-wide expression analysis of a PCAT5-positive prostate cancer after PCAT5 silencing highlighted alterations in cell proliferation pathways. Strikingly, an in vitro validation of these alterations revealed a complex integrated phenotype affecting cell growth, migration, invasion, colony-forming potential, and apoptosis. Our findings reveal a key molecular determinant of differences between prostate cancer and CRPC at the level of the transcriptome. Furthermore, they establish PCAT5 as a novel oncogenic lncRNA in ERG-positive prostate cancers, with implications for defining CRPC biomarkers and new therapeutic interventions.", "doi": "10.1158/0008-5472.CAN-15-0217", "pmid": "26282172", "labels": {"Kimmo Kartasalo": null, "DDLS Fellow": null}, "xrefs": [{"db": "pii", "key": "0008-5472.CAN-15-0217"}], "notes": [], "created": "2024-11-05T16:03:04.600Z", "modified": "2024-11-29T12:06:33.844Z"}, {"entity": "publication", "iuid": "f91f34ba481d417ba8021b11a169a07f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f91f34ba481d417ba8021b11a169a07f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f91f34ba481d417ba8021b11a169a07f"}}, "title": "Harmful somatic amino acid substitutions affect key pathways in cancers.", "authors": [{"family": "Niroula", "given": "Abhishek", "initials": "A"}, {"family": "Vihinen", "given": "Mauno", "initials": "M"}], "type": "journal article", "published": "2015-08-19", "journal": {"title": "BMC Med Genomics", "issn": "1755-8794", "volume": "8", "pages": "53", "issn-l": "1755-8794"}, "abstract": "Cancer is characterized by the accumulation of large numbers of genetic variations and alterations of multiple biological phenomena. Cancer genomics has largely focused on the identification of such genetic alterations and the genes containing them, known as 'cancer genes'. However, the non-functional somatic variations out-number functional variations and remain as a major challenge. Recurrent somatic variations are thought to be cancer drivers but they are present in only a small fraction of patients.\n\nWe performed an extensive analysis of amino acid substitutions (AASs) from 6,861 cancer samples (whole genome or exome sequences) classified into 30 cancer types and performed pathway enrichment analysis. We also studied the overlap between the cancers based on proteins containing harmful AASs and pathways affected by them.\n\nWe found that only a fraction of AASs (39.88 %) are harmful even in known cancer genes. In addition, we found that proteins containing harmful AASs in cancers are often centrally located in protein interaction networks. Based on the proteins containing harmful AASs, we identified significantly affected pathways in 28 cancer types and indicate that proteins containing harmful AASs can affect pathways despite the frequency of AASs in them. Our cross-cancer overlap analysis showed that it would be more beneficial to identify affected pathways in cancers rather than individual genes and variations.\n\nPathways affected by harmful AASs reveal key processes involved in cancer development. Our approach filters out the putative benign AASs thus reducing the list of cancer variations allowing reliable identification of affected pathways. The pathways identified in individual cancer and overlap between cancer types open avenues for further experimental research and for developing targeted therapies and interventions.", "doi": "10.1186/s12920-015-0125-x", "pmid": "26282678", "labels": {"Abhishek Niroula": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC4539680"}, {"db": "pii", "key": "10.1186/s12920-015-0125-x"}], "notes": [], "created": "2023-11-20T10:43:25.467Z", "modified": "2023-11-20T10:43:25.474Z"}, {"entity": "publication", "iuid": "a62bb2eeb4394512aa59a750769c2200", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a62bb2eeb4394512aa59a750769c2200.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a62bb2eeb4394512aa59a750769c2200"}}, "title": "Clinical significance of expression of DNA Helicase RecQL1 in cervical carcinoma", "authors": [{"family": "Wu", "given": "L", "initials": "L"}, {"family": "Yang", "given": "H", "initials": "H"}, {"family": "Gao", "given": "X", "initials": "X"}, {"family": "Wang", "given": "QL", "initials": "Q"}, {"family": "Yang", "given": "L", "initials": "L"}, {"family": "Zhou", "given": "F", "initials": "F"}, {"family": "Zhou", "given": "Y", "initials": "Y"}], "type": null, "published": "2015-06-24", "journal": {"title": "Medical Journal of Wuhan University", "issn": "1671-8852", "issn-l": null, "volume": "36", "issue": "4", "pages": "506-509"}, "abstract": null, "doi": "10.14188/j.1671-8852.2015.04.002", "pmid": null, "labels": {"DDLS Fellow": null, "Qiaoli Wang": null}, "xrefs": [], "notes": [], "created": "2025-11-27T18:51:26.769Z", "modified": "2025-11-27T18:51:53.810Z"}, {"entity": "publication", "iuid": "ab2b1c67df634f0f8ae340fa81b555eb", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ab2b1c67df634f0f8ae340fa81b555eb.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ab2b1c67df634f0f8ae340fa81b555eb"}}, "title": "Treg-cell depletion promotes chemokine production and accumulation of CXCR3(+) conventional T cells in intestinal tumors.", "authors": [{"family": "Akeus", "given": "Paulina", "initials": "P"}, {"family": "Langenes", "given": "Veronica", "initials": "V"}, {"family": "Kristensen", "given": "Jonas", "initials": "J"}, {"family": "von Mentzer", "given": "Astrid", "initials": "A"}, {"family": "Sparwasser", "given": "Tim", "initials": "T"}, {"family": "Raghavan", "given": "Sukanya", "initials": "S"}, {"family": "Quiding-J\u00e4rbrink", "given": "Marianne", "initials": "M"}], "type": "journal article", "published": "2015-06-00", "journal": {"title": "Eur. J. Immunol.", "issn": "1521-4141", "volume": "45", "issue": "6", "pages": "1654-1666", "issn-l": "0014-2980"}, "abstract": "Colorectal cancer (CRC) is one of the most prevalent tumor types worldwide and tumor-infiltrating T cells are crucial for anti-tumor immunity. We previously demonstrated that Treg cells from CRC patients inhibit transendothelial migration of conventional T cells. However, it remains unclear if local Treg cells affect lymphocyte migration into colonic tumors. By breeding APC(Min/+) mice with depletion of regulatory T cells mice, expressing the diphtheria toxin receptor under the control of the FoxP3 promoter, we were able to selectively deplete Treg cells in tumor-bearing mice, and investigate the impact of these cells on the infiltration of conventional T cells into intestinal tumors. Short-term Treg-cell depletion led to a substantial increase in the frequencies of T cells in the tumors, attributed by both increased infiltration and proliferation of T cells in the Treg-cell-depleted tumors. We also demonstrate a selective increase of the chemokines CXCL9 and CXCL10 in Treg-cell-depleted tumors, which were accompanied by accumulation of CXCR3(+) T cells, and increased IFN-\u03b3 mRNA expression. In conclusion, Treg-cell depletion increases the accumulation of conventional T cells in intestinal tumors, and targeting Treg cells could be a possible anti-tumor immunotherapy, which not only affects T-cell effector functions, but also their recruitment to tumors.", "doi": "10.1002/eji.201445058", "pmid": "25754875", "labels": {"Astrid von Mentzer": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2025-12-02T15:51:18.144Z", "modified": "2025-12-02T15:51:18.147Z"}, {"entity": "publication", "iuid": "04e7100398184489af69b85b9f5dd4cf", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/04e7100398184489af69b85b9f5dd4cf.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/04e7100398184489af69b85b9f5dd4cf"}}, "title": "MATHEMATICAL MODELING OF BEH\u00c7ET'S DISEASE: A DYNAMICAL SYSTEMS APPROACH", "authors": [{"family": "ERDEM", "given": "CEMAL", "initials": "C"}, {"family": "BOZKURT", "given": "YASEMIN", "initials": "Y"}, {"family": "ERMAN", "given": "BURAK", "initials": "B"}, {"family": "G\u00dcL", "given": "AHMET", "initials": "A"}, {"family": "DEMIR", "given": "ALPER", "initials": "A"}], "type": "journal-article", "published": "2015-06-00", "journal": {"title": "J. Biol. Syst.", "issn": "0218-3390", "volume": "23", "issue": "02", "pages": "231-257", "issn-l": null}, "abstract": null, "doi": "10.1142/s0218339015500126", "pmid": null, "labels": {"DDLS Fellow": null, "Cemal Erdem": null}, "xrefs": [], "notes": [], "created": "2023-10-27T08:53:53.912Z", "modified": "2025-12-04T16:54:55.690Z"}, {"entity": "publication", "iuid": "4529cda4b8924f209668ddcd90e17ca7", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4529cda4b8924f209668ddcd90e17ca7.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4529cda4b8924f209668ddcd90e17ca7"}}, "title": "Antibiotic resistance genes in the environment: prioritizing risks.", "authors": [{"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Larsson", "given": "D G Joakim", "initials": "DG"}], "type": "letter", "published": "2015-06-00", "journal": {"title": "Nat. Rev. Microbiol.", "issn": "1740-1534", "volume": "13", "issue": "6", "pages": "396", "issn-l": "1740-1526"}, "abstract": null, "doi": "10.1038/nrmicro3399-c1", "pmid": "25915637", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pii", "key": "nrmicro3399-c1"}], "notes": [], "created": "2022-11-08T09:31:11.123Z", "modified": "2022-11-08T09:31:11.149Z"}, {"entity": "publication", "iuid": "632e5ed6844f49e896b1661edc704ab8", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/632e5ed6844f49e896b1661edc704ab8.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/632e5ed6844f49e896b1661edc704ab8"}}, "title": "ITS1: a DNA barcode better than ITS2 in eukaryotes?", "authors": [{"family": "Wang", "given": "Xin-Cun", "initials": "XC"}, {"family": "Liu", "given": "Chang", "initials": "C"}, {"family": "Huang", "given": "Liang", "initials": "L"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Chen", "given": "Haimei", "initials": "H"}, {"family": "Zhang", "given": "Jian-Hui", "initials": "JH"}, {"family": "Cai", "given": "Dayong", "initials": "D"}, {"family": "Li", "given": "Jian-Qin", "initials": "JQ"}], "type": "comparative study", "published": "2015-05-00", "journal": {"title": "Mol Ecol Resour", "issn": "1755-0998", "volume": "15", "issue": "3", "pages": "573-586", "issn-l": "1755-098X"}, "abstract": "A DNA barcode is a short piece of DNA sequence used for species determination and discovery. The internal transcribed spacer (ITS/ITS2) region has been proposed as the standard DNA barcode for fungi and seed plants and has been widely used in DNA barcoding analyses for other biological groups, for example algae, protists and animals. The ITS region consists of both ITS1 and ITS2 regions. Here, a large-scale meta-analysis was carried out to compare ITS1 and ITS2 from three aspects: PCR amplification, DNA sequencing and species discrimination, in terms of the presence of DNA barcoding gaps, species discrimination efficiency, sequence length distribution, GC content distribution and primer universality. In total, 85 345 sequence pairs in 10 major groups of eukaryotes, including ascomycetes, basidiomycetes, liverworts, mosses, ferns, gymnosperms, monocotyledons, eudicotyledons, insects and fishes, covering 611 families, 3694 genera, and 19 060 species, were analysed. Using similarity-based methods, we calculated species discrimination efficiencies for ITS1 and ITS2 in all major groups, families and genera. Using Fisher's exact test, we found that ITS1 has significantly higher efficiencies than ITS2 in 17 of the 47 families and 20 of the 49 genera, which are sample-rich. By in silico PCR amplification evaluation, primer universality of the extensively applied ITS1 primers was found superior to that of ITS2 primers. Additionally, shorter length of amplification product and lower GC content was discovered to be two other advantages of ITS1 for sequencing. In summary, ITS1 represents a better DNA barcode than ITS2 for eukaryotic species.", "doi": "10.1111/1755-0998.12325", "pmid": "25187125", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "Dryad", "key": "10.5061/dryad.N56T9"}], "notes": [], "created": "2022-11-08T09:30:17.345Z", "modified": "2022-11-08T09:30:17.371Z"}, {"entity": "publication", "iuid": "d174c14df4d9479eb2f530d40ce77da8", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d174c14df4d9479eb2f530d40ce77da8.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d174c14df4d9479eb2f530d40ce77da8"}}, "title": "Electrolyte disorders assessment in solid tumor patients treated with anti-EGFR monoclonal antibodies: a pooled analysis of 25 randomized clinical trials.", "authors": [{"family": "Wang", "given": "Qiaoli", "initials": "Q"}, {"family": "Qi", "given": "Yuexiao", "initials": "Y"}, {"family": "Zhang", "given": "Di", "initials": "D"}, {"family": "Gong", "given": "Caifeng", "initials": "C"}, {"family": "Yao", "given": "Anqi", "initials": "A"}, {"family": "Xiao", "given": "Yi", "initials": "Y"}, {"family": "Yang", "given": "Jie", "initials": "J"}, {"family": "Zhou", "given": "Fuxiang", "initials": "F"}, {"family": "Zhou", "given": "Yunfeng", "initials": "Y"}], "type": "journal article", "published": "2015-05-00", "journal": {"title": "Tumour Biol.", "issn": "1423-0380", "volume": "36", "issue": "5", "pages": "3471-3482", "issn-l": "1010-4283"}, "abstract": "The role of anti-epithelial growth factor receptor monoclonal antibodies (anti-EGFR MoAbs) in treatment-related electrolyte disorders is still controversial. Therefore, we conducted a meta-analysis of published randomized controlled trials (RCTs) to evaluate the incidences and overall risks of all-grade and grade 3/4 electrolyte disorder events. We searched relevant clinical trials from PubMed, EMBASE, and Web of Knowledge databases, meeting proceedings of American Society of Clinical Oncology and the European Society of Medical Oncology, as well as ClinicalTrials.gov. Eligible studies included phases II, III, and IV RCTs. Statistical analysis was performed to calculate the summary incidence, relative risk (RR), and 95 % confidence intervals (CIs) using fixed effects or random effects models based on the heterogeneity of included studies. A total of 16,411 patients from 25 RCTs were included in this meta-analysis. The all-grade incidence of hypomagnesemia related to anti-EGFR MoAbs was 34.0 % (95 % CI 28.0-40.5 %), and that for hypokalemia and hypocalcemia were 14.5 % (95 % CI 8.2-24.4 %) and 16.8 % (95 % CI 14.2-19.7 %), respectively. Compared with chemotherapy alone in colorectal cancer, addition of cetuximab increased the risk of grade 3/4 hypomagnesemia and grade 3/4 hypokalemia with RRs of 7.14 (95 % CI 3.13-16.27, p < 0.001) and 2.19 (95 % CI 1.14-4.23, p = 0.019). Additionally, colorectal cancer patients in panitumumab cases were more vulnerable to grade 3/4 hypomagnesemia and hypokalemia (RR 18.29, 95 % CI 7.29-48.41, p < 0.001, and RR 3.3, 95 % CI 1.32-8.25, p = .011). Treatment with anti-EGFR MoAbs is associated with significantly higher risks of electrolyte disorders such as hypomagnesemia, hypomagnesemia, and hypocalcemia, especially in colorectal cancer. Rigorous monitoring and early treatment of electrolyte disorders are proposed.", "doi": "10.1007/s13277-014-2983-9", "pmid": "25542231", "labels": {"DDLS Fellow": null, "Qiaoli Wang": null}, "xrefs": [{"db": "pmc", "key": "PMC4445483"}], "notes": [], "created": "2025-11-27T18:45:11.796Z", "modified": "2025-11-27T18:45:11.816Z"}, {"entity": "publication", "iuid": "e95b8e3c0fae4dc281a9dd863e736cd1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e95b8e3c0fae4dc281a9dd863e736cd1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e95b8e3c0fae4dc281a9dd863e736cd1"}}, "title": "Computational modeling of the N-terminus of the human dopamine transporter and its interaction with PIP2 -containing membranes.", "authors": [{"family": "Khelashvili", "given": "George", "initials": "G"}, {"family": "Doktorova", "given": "Milka", "initials": "M"}, {"family": "Sahai", "given": "Michelle A", "initials": "MA"}, {"family": "Johner", "given": "Niklaus", "initials": "N"}, {"family": "Shi", "given": "Lei", "initials": "L"}, {"family": "Weinstein", "given": "Harel", "initials": "H"}], "type": "journal article", "published": "2015-05-00", "journal": {"title": "Proteins", "issn": "1097-0134", "issn-l": "0887-3585", "volume": "83", "issue": "5", "pages": "952-969"}, "abstract": "The dopamine transporter (DAT) is a transmembrane protein belonging to the family of neurotransmitter:sodium symporters (NSS). Members of the NSS are responsible for the clearance of neurotransmitters from the synaptic cleft, and for their translocation back into the presynaptic nerve terminal. The DAT contains long intracellular N- and C-terminal domains that are strongly implicated in the transporter function. The N-terminus (N-term), in particular, regulates the reverse transport (efflux) of the substrate through DAT. Currently, the molecular mechanisms of the efflux remain elusive in large part due to lack of structural information on the N-terminal segment. Here we report a computational model of the N-term of the human DAT (hDAT), obtained through an ab initio structure prediction, in combination with extensive atomistic molecular dynamics (MD) simulations in the context of a lipid membrane. Our analysis reveals that whereas the N-term is a highly dynamic domain, it contains secondary structure elements that remain stable in the long MD trajectories of interactions with the bilayer (totaling >2.2 \u03bcs). Combining MD simulations with continuum mean-field modeling we found that the N-term engages with lipid membranes through electrostatic interactions with the charged lipids PIP2 (phosphatidylinositol 4,5-Biphosphate) or PS (phosphatidylserine) that are present in these bilayers. We identify specific motifs along the N-term implicated in such interactions and show that differential modes of N-term/membrane association result in differential positioning of the structured segments on the membrane surface. These results will inform future structure-based studies that will elucidate the mechanistic role of the N-term in DAT function.", "doi": "10.1002/prot.24792", "pmid": "25739722", "labels": {"Milka Doktorova": null, "DDLS Fellow": null}, "xrefs": [{"db": "mid", "key": "NIHMS671635"}, {"db": "pmc", "key": "PMC4400265"}], "notes": [], "created": "2024-11-27T12:14:07.081Z", "modified": "2024-11-29T12:17:34.362Z"}, {"entity": "publication", "iuid": "87d3ba72b703443fbc9e6928b26f5caf", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/87d3ba72b703443fbc9e6928b26f5caf.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/87d3ba72b703443fbc9e6928b26f5caf"}}, "title": "UBE2D3 is a positive prognostic factor and is negatively correlated with hTERT expression in esophageal cancer.", "authors": [{"family": "Guan", "given": "Ge Ge", "initials": "GG"}, {"family": "Wang", "given": "Wen Bo", "initials": "WB"}, {"family": "Lei", "given": "Bing Xin", "initials": "BX"}, {"family": "Wang", "given": "Qiao Li", "initials": "QL"}, {"family": "Wu", "given": "Lin", "initials": "L"}, {"family": "Fu", "given": "Zhen Ming", "initials": "ZM"}, {"family": "Zhou", "given": "Fu Xiang", "initials": "FX"}, {"family": "Zhou", "given": "Yun Feng", "initials": "YF"}], "type": "journal article", "published": "2015-04-00", "journal": {"title": "Oncol Lett", "issn": "1792-1074", "volume": "9", "issue": "4", "pages": "1567-1574", "issn-l": null}, "abstract": "Human telomerase reverse transcriptase (hTERT) is a critical factor in unlimited cell proliferation and immortalization, with numerous studies demonstrating that high expression of hTERT is a poor prognostic factor in various types of cancer. Ubiquitin-conjugating enzyme E2D 3 (UBE2D3) is a member of the E2 family, and participates in the ubiquitin proteasome pathway to regulate basic cellular activities, such as cell cycle control, the DNA damage response, apoptosis, and tumorigenesis. Our previous study initially determined that downregulation of UBE2D3 expression increases hTERT expression and cell proliferation, however, the association between the expression of these two proteins and their functions in cancer tissues remains unknown. Therefore, the protein expression levels of hTERT and UBE2D3 were evaluated in 150 esophageal cancer and 30 adjacent healthy tissue samples by performing immunohistochemical analysis. Concurrently, the clinicopathological data of the enrolled patients were obtained to allow correlation analysis. It was identified that the expression of hTERT in the esophageal cancer tissues was significantly higher compared with that of the adjacent tissues (P=0.015), however, the expression of UBE2D3 was significantly lower in esophageal cancer tissues than the adjacent tissues (P=0.001). Additionally, the study demonstrated that hTERT was significantly upregulated in poorly-differentiated, advanced tumor-node-metastasis (TNM) stage cancer tissues (P<0.05 for all), however, UBE2D3 expression was downregulated in poorly-differentiated, lymph node invaded cancer tissues and recurrent cases. It was also identified that traditional factors, including tumor location, T stage, lymph node status, TNM stage, and molecular factors of hTERT and UBE2D3, were significantly associated with overall survival time (P<0.05 for all). Furthermore, UBE2D3, lymph node status and tumor location were independent prognostic factors for esophageal cancer in multivariate analysis. Most notably, hTERT and UBE2D3 expression were negatively correlated with each other. In conclusion, the findings of the present study indicated that hTERT and UBE2D3 proteins appear to be involved in the development of esophageal cancer, that UBE2D3 may a positive prognostic factor for esophageal cancer, and that UBE2D3 and hTERT expression levels are inversely correlated.", "doi": "10.3892/ol.2015.2926", "pmid": "25789002", "labels": {"DDLS Fellow": null, "Qiaoli Wang": null}, "xrefs": [{"db": "pmc", "key": "PMC4356423"}, {"db": "pii", "key": "ol-09-04-1567"}], "notes": [], "created": "2025-11-27T18:45:10.609Z", "modified": "2025-11-27T18:45:10.627Z"}, {"entity": "publication", "iuid": "ad6b4b507c3c4ffcb0d010e62ff0fa3a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ad6b4b507c3c4ffcb0d010e62ff0fa3a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ad6b4b507c3c4ffcb0d010e62ff0fa3a"}}, "title": "Regulation of cerebral CYP2D alters tramadol metabolism in the brain: interactions of tramadol with propranolol and nicotine.", "authors": [{"family": "Wang", "given": "Qiaoli", "initials": "Q"}, {"family": "Han", "given": "Xiaotong", "initials": "X"}, {"family": "Li", "given": "Jian", "initials": "J"}, {"family": "Gao", "given": "Xinghui", "initials": "X"}, {"family": "Wang", "given": "Yan", "initials": "Y"}, {"family": "Liu", "given": "Mingzhou", "initials": "M"}, {"family": "Dong", "given": "Guicheng", "initials": "G"}, {"family": "Yue", "given": "Jiang", "initials": "J"}], "type": "journal article", "published": "2015-04-00", "journal": {"title": "Xenobiotica", "issn": "1366-5928", "volume": "45", "issue": "4", "pages": "335-344", "issn-l": "0049-8254"}, "abstract": "1. Cytochrome P450 2D (CYP2D) protein is widely expressed across brain regions in human and rodents. We investigated the interactions between tramadol, a clinically used analgesic, and brain CYP2D regulators, by establishing concentration-time curves of tramadol and O-desmethyltramadol (M1) in rat cerebrospinal fluid (CSF) and plasma, as well as by analyzing the analgesia-time course of tramadol. 2. Propranolol (20 \u03bcg, intracerebroventricular injection), CYP2D inhibitor, prolonged the elimination t1/2 of tramadol (40 mg/kg, intraperitoneal injection) in the CSF; meanwhile, lower Cmax and AUC0-\u221e values of M1 were observed. Nicotine (1 mg base/kg, subcutaneous injection, seven days), brain CYP2D inducer, induced a shorter Tmax and elevated Cmax of M1 in CSF. No differences in the peripheral metabolism of tramadol were observed following propranolol and nicotine pretreatment. Nicotine increased areas under the analgesia-time curve (AUC) for 0-45 min and 0-90 min of tramadol, which was attenuated by propranolol administration. The analgesic actions of tramadol positively correlated with cerebral M1 concentration. 3. The results suggest that the regulation of brain CYP2D by xenobiotics may cause drug-drug interactions (DDIs) of tramadol. Brain CYPs may play an important role in DDIs of centrally active substances.", "doi": "10.3109/00498254.2014.981609", "pmid": "25387586", "labels": {"DDLS Fellow": null, "Qiaoli Wang": null}, "xrefs": [], "notes": [], "created": "2025-11-27T18:45:07.061Z", "modified": "2025-11-27T18:45:07.064Z"}, {"entity": "publication", "iuid": "e31009ccbb944416823a520aa3859d41", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e31009ccbb944416823a520aa3859d41.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e31009ccbb944416823a520aa3859d41"}}, "title": "Implications of enterotoxigenic Escherichia coli genomics for vaccine development.", "authors": [{"family": "Sj\u00f6ling", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "von Mentzer", "given": "Astrid", "initials": "A"}, {"family": "Svennerholm", "given": "Ann-Mari", "initials": "AM"}], "type": "journal article", "published": "2015-04-00", "journal": {"title": "Expert Rev Vaccines", "issn": "1744-8395", "volume": "14", "issue": "4", "pages": "551-560", "issn-l": null}, "abstract": "Enterotoxigenic Escherichia coli (ETEC) is a major cause of morbidity and mortality caused by diarrhea in children less than 5 years of age in low- and middle-income countries. Despite a wealth of research elucidating the mechanisms of disease, the immunological responses and vaccine development, ETEC is still relatively uncharacterized when it comes to regulation of virulence and detailed immune mechanisms. The recent emergence of next-generation sequencing now offers the possibility to screen genomes of ETEC strains isolated globally to identify novel vaccine targets in addition to those already established. In this review, we discuss how recent findings on ETEC genomics using novel sequencing techniques will aid in finding novel protective antigens that can be used in vaccine approaches.", "doi": "10.1586/14760584.2015.996553", "pmid": "25540974", "labels": {"Astrid von Mentzer": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2025-12-02T15:51:20.050Z", "modified": "2025-12-02T15:51:20.068Z"}, {"entity": "publication", "iuid": "2542ce734d914c91a93ea7110b29c698", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/2542ce734d914c91a93ea7110b29c698.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/2542ce734d914c91a93ea7110b29c698"}}, "title": "A Comprehensive, Automatically Updated Fungal ITS Sequence Dataset for Reference-Based Chimera Control in Environmental Sequencing Efforts.", "authors": [{"family": "Nilsson", "given": "R Henrik", "initials": "RH"}, {"family": "Tedersoo", "given": "Leho", "initials": "L"}, {"family": "Ryberg", "given": "Martin", "initials": "M"}, {"family": "Kristiansson", "given": "Erik", "initials": "E"}, {"family": "Hartmann", "given": "Martin", "initials": "M"}, {"family": "Unterseher", "given": "Martin", "initials": "M"}, {"family": "Porter", "given": "Teresita M", "initials": "TM"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Walker", "given": "Donald M", "initials": "DM"}, {"family": "de Sousa", "given": "Filipe", "initials": "F"}, {"family": "Gamper", "given": "Hannes Andres", "initials": "HA"}, {"family": "Larsson", "given": "Ellen", "initials": "E"}, {"family": "Larsson", "given": "Karl-Henrik", "initials": "KH"}, {"family": "K\u00f5ljalg", "given": "Urmas", "initials": "U"}, {"family": "Edgar", "given": "Robert C", "initials": "RC"}, {"family": "Abarenkov", "given": "Kessy", "initials": "K"}], "type": "journal article", "published": "2015-03-19", "journal": {"title": "Microbes Environ", "issn": "1347-4405", "volume": "30", "issue": "2", "pages": "145-150", "issn-l": null}, "abstract": "The nuclear ribosomal internal transcribed spacer (ITS) region is the most commonly chosen genetic marker for the molecular identification of fungi in environmental sequencing and molecular ecology studies. Several analytical issues complicate such efforts, one of which is the formation of chimeric-artificially joined-DNA sequences during PCR amplification or sequence assembly. Several software tools are currently available for chimera detection, but rely to various degrees on the presence of a chimera-free reference dataset for optimal performance. However, no such dataset is available for use with the fungal ITS region. This study introduces a comprehensive, automatically updated reference dataset for fungal ITS sequences based on the UNITE database for the molecular identification of fungi. This dataset supports chimera detection throughout the fungal kingdom and for full-length ITS sequences as well as partial (ITS1 or ITS2 only) datasets. The performance of the dataset on a large set of artificial chimeras was above 99.5%, and we subsequently used the dataset to remove nearly 1,000 compromised fungal ITS sequences from public circulation. The dataset is available at http://unite.ut.ee/repository.php and is subject to web-based third-party curation.", "doi": "10.1264/jsme2.ME14121", "pmid": "25786896", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pmc", "key": "PMC4462924"}], "notes": [], "created": "2022-11-08T09:30:01.967Z", "modified": "2022-11-08T09:30:02.005Z"}, {"entity": "publication", "iuid": "9dbd618d46f44d3f9caf571d0ac54852", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9dbd618d46f44d3f9caf571d0ac54852.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9dbd618d46f44d3f9caf571d0ac54852"}}, "title": "Rapid reprogramming of epigenetic and transcriptional profiles in mammalian culture systems.", "authors": [{"family": "Nestor", "given": "Colm E", "initials": "CE"}, {"family": "Ottaviano", "given": "Raffaele", "initials": "R"}, {"family": "Reinhardt", "given": "Diana", "initials": "D"}, {"family": "Cruickshanks", "given": "Hazel A", "initials": "HA"}, {"family": "Mjoseng", "given": "Heidi K", "initials": "HK"}, {"family": "McPherson", "given": "Rhoanne C", "initials": "RC"}, {"family": "Lentini", "given": "Antonio", "initials": "A"}, {"family": "Thomson", "given": "John P", "initials": "JP"}, {"family": "Dunican", "given": "Donncha S", "initials": "DS"}, {"family": "Pennings", "given": "Sari", "initials": "S"}, {"family": "Anderton", "given": "Stephen M", "initials": "SM"}, {"family": "Benson", "given": "Mikael", "initials": "M"}, {"family": "Meehan", "given": "Richard R", "initials": "RR"}], "type": "journal article", "published": "2015-02-04", "journal": {"title": "Genome Biol.", "issn": "1474-760X", "volume": "16", "issue": "1", "pages": "11", "issn-l": "1474-7596"}, "abstract": "The DNA methylation profiles of mammalian cell lines differ from those of the primary tissues from which they were derived, exhibiting increasing divergence from the in vivo methylation profile with extended time in culture. Few studies have directly examined the initial epigenetic and transcriptional consequences of adaptation of primary mammalian cells to culture, and the potential mechanisms through which this epigenetic dysregulation occurs is unknown.\n\nWe demonstrate that adaptation of mouse embryonic fibroblasts to cell culture results in a rapid reprogramming of epigenetic and transcriptional states. We observed global 5-hydroxymethylcytosine (5hmC) erasure within three days of culture initiation. Loss of genic 5hmC was independent of global 5-methylcytosine (5mC) levels and could be partially rescued by addition of vitamin C. Significantly, 5hmC loss was not linked to concomitant changes in transcription. Discrete promoter-specific gains of 5mC were also observed within seven days of culture initiation. Against this background of global 5hmC loss we identified a handful of developmentally important genes that maintained their 5hmC profile in culture, including the imprinted loci Gnas and H19. Similar outcomes were identified in the adaption of CD4(+) T cells to culture.\n\nWe report a dramatic and novel consequence of adaptation of mammalian cells to culture in which global loss of 5hmC occurs, suggesting rapid concomitant loss of methylcytosine dioxygenase activity. The observed epigenetic and transcriptional re-programming occurs much earlier than previously assumed, and has significant implications for the use of cell lines as faithful mimics of in vivo epigenetic and physiological processes.", "doi": "10.1186/s13059-014-0576-y", "pmid": "25648825", "labels": {"Antonio Lentini": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC4334405"}, {"db": "pii", "key": "s13059-014-0576-y"}], "notes": [], "created": "2025-03-28T07:14:51.097Z", "modified": "2025-03-28T07:14:51.101Z"}, {"entity": "publication", "iuid": "49ba5d08adc34f389c89bba1d7c450cd", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/49ba5d08adc34f389c89bba1d7c450cd.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/49ba5d08adc34f389c89bba1d7c450cd"}}, "title": "PON-P2: prediction method for fast and reliable identification of harmful variants.", "authors": [{"family": "Niroula", "given": "Abhishek", "initials": "A"}, {"family": "Urolagin", "given": "Siddhaling", "initials": "S"}, {"family": "Vihinen", "given": "Mauno", "initials": "M"}], "type": "journal article", "published": "2015-02-03", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "10", "issue": "2", "pages": "e0117380", "issn-l": "1932-6203"}, "abstract": "More reliable and faster prediction methods are needed to interpret enormous amounts of data generated by sequencing and genome projects. We have developed a new computational tool, PON-P2, for classification of amino acid substitutions in human proteins. The method is a machine learning-based classifier and groups the variants into pathogenic, neutral and unknown classes, on the basis of random forest probability score. PON-P2 is trained using pathogenic and neutral variants obtained from VariBench, a database for benchmark variation datasets. PON-P2 utilizes information about evolutionary conservation of sequences, physical and biochemical properties of amino acids, GO annotations and if available, functional annotations of variation sites. Extensive feature selection was performed to identify 8 informative features among altogether 622 features. PON-P2 consistently showed superior performance in comparison to existing state-of-the-art tools. In 10-fold cross-validation test, its accuracy and MCC are 0.90 and 0.80, respectively, and in the independent test, they are 0.86 and 0.71, respectively. The coverage of PON-P2 is 61.7% in the 10-fold cross-validation and 62.1% in the test dataset. PON-P2 is a powerful tool for screening harmful variants and for ranking and prioritizing experimental characterization. It is very fast making it capable of analyzing large variant datasets. PON-P2 is freely available at http://structure.bmc.lu.se/PON-P2/.", "doi": "10.1371/journal.pone.0117380", "pmid": "25647319", "labels": {"Abhishek Niroula": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC4315405"}, {"db": "pii", "key": "PONE-D-14-43010"}], "notes": [], "created": "2023-11-20T10:43:23.292Z", "modified": "2023-11-20T10:43:23.298Z"}, {"entity": "publication", "iuid": "aaeb9c4e3c83413c973b5e4314f40f62", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/aaeb9c4e3c83413c973b5e4314f40f62.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/aaeb9c4e3c83413c973b5e4314f40f62"}}, "title": "Allele variants of enterotoxigenic Escherichia coli heat-labile toxin are globally transmitted and associated with colonization factors.", "authors": [{"family": "Joffr\u00e9", "given": "Enrique", "initials": "E"}, {"family": "von Mentzer", "given": "Astrid", "initials": "A"}, {"family": "Abd El Ghany", "given": "Moataz", "initials": "M"}, {"family": "Oezguen", "given": "Numan", "initials": "N"}, {"family": "Savidge", "given": "Tor", "initials": "T"}, {"family": "Dougan", "given": "Gordon", "initials": "G"}, {"family": "Svennerholm", "given": "Ann-Mari", "initials": "AM"}, {"family": "Sj\u00f6ling", "given": "\u00c5sa", "initials": "\u00c5"}], "type": "journal article", "published": "2015-01-00", "journal": {"title": "J. Bacteriol.", "issn": "1098-5530", "volume": "197", "issue": "2", "pages": "392-403", "issn-l": "0021-9193"}, "abstract": "Enterotoxigenic Escherichia coli (ETEC) is a significant cause of morbidity and mortality in the developing world. ETEC-mediated diarrhea is orchestrated by heat-labile toxin (LT) and heat-stable toxins (STp and STh), acting in concert with a repertoire of more than 25 colonization factors (CFs). LT, the major virulence factor, induces fluid secretion after delivery of a monomeric ADP-ribosylase (LTA) and its pentameric carrier B subunit (LTB). A study of ETEC isolates from humans in Brazil reported the existence of natural LT variants. In the present study, analysis of predicted amino acid sequences showed that the LT amino acid polymorphisms are associated with a geographically and temporally diverse set of 192 clinical ETEC strains and identified 12 novel LT variants. Twenty distinct LT amino acid variants were observed in the globally distributed strains, and phylogenetic analysis showed these to be associated with different CF profiles. Notably, the most prevalent LT1 allele variants were correlated with major ETEC lineages expressing CS1 + CS3 or CS2 + CS3, and the most prevalent LT2 allele variants were correlated with major ETEC lineages expressing CS5 + CS6 or CFA/I. LTB allele variants generally exhibited more-stringent amino acid sequence conservation (2 substitutions identified) than LTA allele variants (22 substitutions identified). The functional impact of LT1 and LT2 polymorphisms on virulence was investigated by measuring total-toxin production, secretion, and stability using GM1-enzyme-linked immunosorbent assays (GM1-ELISA) and in silico protein modeling. Our data show that LT2 strains produce 5-fold more toxin than LT1 strains (P < 0.001), which may suggest greater virulence potential for this genetic variant. Our data suggest that functionally distinct LT-CF variants with increased fitness have persisted during the evolution of ETEC and have spread globally.", "doi": "10.1128/JB.02050-14", "pmid": "25404692", "labels": {"Astrid von Mentzer": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC4272596"}, {"db": "pii", "key": "JB.02050-14"}], "notes": [], "created": "2025-12-02T15:51:22.102Z", "modified": "2025-12-02T15:51:22.116Z"}, {"entity": "publication", "iuid": "92aebe898a1a4acab761aabe6b5e7bb3", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/92aebe898a1a4acab761aabe6b5e7bb3.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/92aebe898a1a4acab761aabe6b5e7bb3"}}, "title": "Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India.", "authors": [{"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Boulund", "given": "Fredrik", "initials": "F"}, {"family": "Fick", "given": "Jerker", "initials": "J"}, {"family": "Kristiansson", "given": "Erik", "initials": "E"}, {"family": "Larsson", "given": "D G Joakim", "initials": "DG"}], "type": "journal article", "published": "2014-12-02", "journal": {"title": "Front Microbiol", "issn": "1664-302X", "volume": "5", "pages": "648", "issn-l": "1664-302X"}, "abstract": "There is increasing evidence for an environmental origin of many antibiotic resistance genes. Consequently, it is important to identify environments of particular risk for selecting and maintaining such resistance factors. In this study, we described the diversity of antibiotic resistance genes in an Indian lake subjected to industrial pollution with fluoroquinolone antibiotics. We also assessed the genetic context of the identified resistance genes, to try to predict their genetic transferability. The lake harbored a wide range of resistance genes (81 identified gene types) against essentially every major class of antibiotics, as well as genes responsible for mobilization of genetic material. Resistance genes were estimated to be 7000 times more abundant than in a Swedish lake included for comparison, where only eight resistance genes were found. The sul2 and qnrD genes were the most common resistance genes in the Indian lake. Twenty-six known and 21 putative novel plasmids were recovered in the Indian lake metagenome, which, together with the genes found, indicate a large potential for horizontal gene transfer through conjugation. Interestingly, the microbial community of the lake still included a wide range of taxa, suggesting that, across most phyla, bacteria has adapted relatively well to this highly polluted environment. Based on the wide range and high abundance of known resistance factors we have detected, it is plausible that yet unrecognized resistance genes are also present in the lake. Thus, we conclude that environments polluted with waste from antibiotic manufacturing could be important reservoirs for mobile antibiotic resistance genes.", "doi": "10.3389/fmicb.2014.00648", "pmid": "25520706", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pmc", "key": "PMC4251439"}], "notes": [], "created": "2022-11-08T09:30:09.396Z", "modified": "2022-11-08T09:30:09.420Z"}, {"entity": "publication", "iuid": "79089d62a5df43279ed92eddcee19da6", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/79089d62a5df43279ed92eddcee19da6.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/79089d62a5df43279ed92eddcee19da6"}}, "title": "Predictive value of excision repair cross-complementation group 1 expression for platinum-based chemotherapy and survival in gastric cancer: a meta-analysis.", "authors": [{"family": "Yao", "given": "Anqi", "initials": "A"}, {"family": "Wang", "given": "You", "initials": "Y"}, {"family": "Peng", "given": "Xiaohong", "initials": "X"}, {"family": "Ye", "given": "Rong", "initials": "R"}, {"family": "Wang", "given": "Qiaoli", "initials": "Q"}, {"family": "Qi", "given": "Yuexiao", "initials": "Y"}, {"family": "Zhou", "given": "Fuxiang", "initials": "F"}], "type": "journal article", "published": "2014-12-00", "journal": {"title": "J. Cancer Res. Clin. Oncol.", "issn": "1432-1335", "volume": "140", "issue": "12", "pages": "2107-2117", "issn-l": "0171-5216"}, "abstract": "The predictive value of excision repair cross-complementation group 1 (ERCC1) gene for survival and response to platinum-based chemotherapy in gastric cancer (GC) remains controversial. We performed a meta-analysis to clarify the precise estimation of the prognostic and predictive effect of ERCC1.\n\nA systematic literature search was conducted using PubMed, ScienceDirect, Wiley and American Society of Clinical Oncology (ASCO) before March 2014. Studies analyzing survival data and/or chemotherapy response in GC by ERCC1 status were identified. The principal outcome measures were hazard ratios (HRs) for survival and relative risks (RRs) for chemotherapy response. Pooled HRs and RRs were calculated using fixed- or random-effects models according to the heterogeneity.\n\nTwenty-one studies involving 1,628 patients met our inclusion criteria. High ERCC1 expression was significantly associated with shorter overall survival (OS) and lower response to chemotherapy in advanced GC patients receiving palliative chemotherapy (HR 1.83; 95 % CI 1.45-2.31; P < 0.001; RR 0.49; 95 % CI 0.38-0.62; P < 0.001). There was no significant difference in survival between high and low ERCC1 expression in adjuvant setting (OS: HR 1.38; 95 % CI 0.77-2.45; P = 0.276; EFS 0.72; 95 % CI 0.38-1.33; P = 0.291). Some evidence of heterogeneity and possible publication bias were discovered in few meta-analyses.\n\nHigh ERCC1 expression might be an adverse prognostic and a drug-resistance predictive factor for advanced GC patients. However, further studies with consistent ERCC1 assessment methodology are needed.", "doi": "10.1007/s00432-014-1758-4", "pmid": "24994039", "labels": {"DDLS Fellow": null, "Qiaoli Wang": null}, "xrefs": [{"db": "pmc", "key": "PMC11824066"}], "notes": [], "created": "2025-11-27T18:45:05.996Z", "modified": "2025-11-27T18:45:06.000Z"}, {"entity": "publication", "iuid": "6e5bd2161c4943d4bb11d058bc19adc2", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/6e5bd2161c4943d4bb11d058bc19adc2.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/6e5bd2161c4943d4bb11d058bc19adc2"}}, "title": "Identification of enterotoxigenic Escherichia coli (ETEC) clades with long-term global distribution.", "authors": [{"family": "von Mentzer", "given": "Astrid", "initials": "A"}, {"family": "Connor", "given": "Thomas R", "initials": "TR"}, {"family": "Wieler", "given": "Lothar H", "initials": "LH"}, {"family": "Semmler", "given": "Torsten", "initials": "T"}, {"family": "Iguchi", "given": "Atsushi", "initials": "A"}, {"family": "Thomson", "given": "Nicholas R", "initials": "NR"}, {"family": "Rasko", "given": "David A", "initials": "DA"}, {"family": "Joffre", "given": "Enrique", "initials": "E"}, {"family": "Corander", "given": "Jukka", "initials": "J"}, {"family": "Pickard", "given": "Derek", "initials": "D"}, {"family": "Wiklund", "given": "Gudrun", "initials": "G"}, {"family": "Svennerholm", "given": "Ann-Mari", "initials": "AM"}, {"family": "Sj\u00f6ling", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Dougan", "given": "Gordon", "initials": "G"}], "type": "journal article", "published": "2014-12-00", "journal": {"title": "Nat. Genet.", "issn": "1546-1718", "volume": "46", "issue": "12", "pages": "1321-1326", "issn-l": "1061-4036"}, "abstract": "Enterotoxigenic Escherichia coli (ETEC), a major cause of infectious diarrhea, produce heat-stable and/or heat-labile enterotoxins and at least 25 different colonization factors that target the intestinal mucosa. The genes encoding the enterotoxins and most of the colonization factors are located on plasmids found across diverse E. coli serogroups. Whole-genome sequencing of a representative collection of ETEC isolated between 1980 and 2011 identified globally distributed lineages characterized by distinct colonization factor and enterotoxin profiles. Contrary to current notions, these relatively recently emerged lineages might harbor chromosome and plasmid combinations that optimize fitness and transmissibility. These data have implications for understanding, tracking and possibly preventing ETEC disease.", "doi": "10.1038/ng.3145", "pmid": "25383970", "labels": {"Astrid von Mentzer": null, "DDLS Fellow": null}, "xrefs": [{"db": "pii", "key": "ng.3145"}], "notes": [], "created": "2025-12-02T15:51:24.126Z", "modified": "2025-12-02T15:51:24.142Z"}, {"entity": "publication", "iuid": "483cfb89195e4bd197c46cb3f75bb91d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/483cfb89195e4bd197c46cb3f75bb91d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/483cfb89195e4bd197c46cb3f75bb91d"}}, "title": "Metagenomics reveals that detoxification systems are underrepresented in marine bacterial communities.", "authors": [{"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Alm Rosenblad", "given": "Magnus", "initials": "M"}, {"family": "Molin", "given": "Mikael", "initials": "M"}, {"family": "Blomberg", "given": "Anders", "initials": "A"}], "type": "journal article", "published": "2014-09-01", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "15", "pages": "749", "issn-l": "1471-2164"}, "abstract": "Environmental shotgun sequencing (metagenomics) provides a new way to study communities in microbial ecology. We here use sequence data from the Global Ocean Sampling (GOS) expedition to investigate toxicant selection pressures revealed by the presence of detoxification genes in marine bacteria. To capture a broad range of potential toxicants we selected detoxification protein families representing systems protecting microorganisms from a variety of stressors, such as metals, organic compounds, antibiotics and oxygen radicals.\n\nUsing a bioinformatics procedure based on comparative analysis to finished bacterial genomes we found that the amount of detoxification genes present in marine microorganisms seems surprisingly small. The underrepresentation is particularly evident for toxicant transporters and proteins involved in detoxifying metals. Exceptions are enzymes involved in oxidative stress defense where peroxidase enzymes are more abundant in marine bacteria compared to bacteria in general. In contrast, catalases are almost completely absent from the open ocean environment, suggesting that peroxidases and peroxiredoxins constitute a core line of defense against reactive oxygen species (ROS) in the marine milieu.\n\nWe found no indication that detoxification systems would be generally more abundant close to the coast compared to the open ocean. On the contrary, for several of the protein families that displayed a significant geographical distribution, like peroxidase, penicillin binding transpeptidase and divalent ion transport protein, the open ocean samples showed the highest abundance. Along the same lines, the abundance of most detoxification proteins did not increase with estimated pollution. The low level of detoxification systems in marine bacteria indicate that the majority of marine bacteria have a low capacity to adapt to increased pollution. Our study exemplifies the use of metagenomics data in ecotoxicology, and in particular how anthropogenic consequences on life in the sea can be examined.", "doi": "10.1186/1471-2164-15-749", "pmid": "25179155", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pii", "key": "1471-2164-15-749"}, {"db": "pmc", "key": "PMC4161860"}], "notes": [], "created": "2022-11-08T09:30:19.678Z", "modified": "2022-11-08T09:30:19.701Z"}, {"entity": "publication", "iuid": "3d2157abeedf4ea08ca7db8f79ba6d69", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3d2157abeedf4ea08ca7db8f79ba6d69.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3d2157abeedf4ea08ca7db8f79ba6d69"}}, "title": "Altered chemokine production and accumulation of regulatory T cells in intestinal adenomas of APC(Min/+) mice.", "authors": [{"family": "Akeus", "given": "Paulina", "initials": "P"}, {"family": "Langenes", "given": "Veronica", "initials": "V"}, {"family": "von Mentzer", "given": "Astrid", "initials": "A"}, {"family": "Yrlid", "given": "Ulf", "initials": "U"}, {"family": "Sj\u00f6ling", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Saksena", "given": "Pushpa", "initials": "P"}, {"family": "Raghavan", "given": "Sukanya", "initials": "S"}, {"family": "Quiding-J\u00e4rbrink", "given": "Marianne", "initials": "M"}], "type": "journal article", "published": "2014-08-00", "journal": {"title": "Cancer Immunol. Immunother.", "issn": "1432-0851", "volume": "63", "issue": "8", "pages": "807-819", "issn-l": "0340-7004"}, "abstract": "Tumor progression in the colon moves from aberrant crypt foci to adenomatous polyps to invasive carcinomas. The composition of the tumor-infiltrating leukocyte population affects the ability of the immune system to fight the tumor. T cell infiltration into colorectal adenocarcinomas, particularly T helper 1 (Th1) type T cells as well as increased regulatory T cell (Treg) frequencies, is correlated with improved prognosis. However, whether Th1 cells and Tregs are already present at the adenoma stage is not known. In this study, the APC(Min/+) mouse model of intestinal adenomatous polyposis was used to investigate tumor-associated lymphocyte subsets and the mechanisms of their accumulation into gastrointestinal adenomas. Compared to unaffected tissue, adenomas accumulated CD4(+)FoxP3(+) putative Treg in parallel with lower frequencies of conventional T cells and B cells. The accumulation of Treg was also observed in human adenomatous polyps. Despite high Treg numbers, the function of conventional T cells present in the APC(Min/+) adenomas was not different from those in the unaffected tissue. Adenomas displayed an altered chemokine balance, with higher CCL17 and lower CXCL11 and CCL25 expression than in the unaffected tissue. In parallel, CXCR3(+) Tregs were largely absent from adenomas. The data indicate that already in early stages of tumor development, the balance of lymphocyte-recruiting chemokines is altered possibly contributing to the observed shift toward higher frequencies of Treg.", "doi": "10.1007/s00262-014-1555-6", "pmid": "24777614", "labels": {"Astrid von Mentzer": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC11028549"}], "notes": [], "created": "2025-12-02T15:51:26.168Z", "modified": "2025-12-02T15:51:26.185Z"}, {"entity": "publication", "iuid": "64e58711b93a4ccb8927ba2aa1fc3fc2", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/64e58711b93a4ccb8927ba2aa1fc3fc2.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/64e58711b93a4ccb8927ba2aa1fc3fc2"}}, "title": "Computational prediction of hinge axes in proteins.", "authors": [{"family": "Shamsuddin", "given": "Rittika", "initials": "R"}, {"family": "Doktorova", "given": "Milka", "initials": "M"}, {"family": "Jaswal", "given": "Sheila", "initials": "S"}, {"family": "Lee-St John", "given": "Audrey", "initials": "A"}, {"family": "McMenimen", "given": "Kathryn", "initials": "K"}], "type": "evaluation study", "published": "2014-07-14", "journal": {"title": "BMC Bioinformatics", "issn": "1471-2105", "issn-l": "1471-2105", "volume": "15 Suppl 8", "issue": "Suppl 8", "pages": "S2"}, "abstract": "A protein's function is determined by the wide range of motions exhibited by its 3D structure. However, current experimental techniques are not able to reliably provide the level of detail required for elucidating the exact mechanisms of protein motion essential for effective drug screening and design. Computational tools are instrumental in the study of the underlying structure-function relationship. We focus on a special type of proteins called \"hinge proteins\" which exhibit a motion that can be interpreted as a rotation of one domain relative to another.\r\n\r\nThis work proposes a computational approach that uses the geometric structure of a single conformation to predict the feasible motions of the protein and is founded in recent work from rigidity theory, an area of mathematics that studies flexibility properties of general structures. Given a single conformational state, our analysis predicts a relative axis of motion between two specified domains. We analyze a dataset of 19 structures known to exhibit this hinge-like behavior. For 15, the predicted axis is consistent with a motion to a second, known conformation. We present a detailed case study for three proteins whose dynamics have been well-studied in the literature: calmodulin, the LAO binding protein and the Bence-Jones protein.\r\n\r\nOur results show that incorporating rigidity-theoretic analyses can lead to effective computational methods for understanding hinge motions in macromolecules. This initial investigation is the first step towards a new tool for probing the structure-dynamics relationship in proteins.", "doi": "10.1186/1471-2105-15-S8-S2", "pmid": "25080829", "labels": {"Milka Doktorova": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC4120148"}, {"db": "pii", "key": "1471-2105-15-S8-S2"}], "notes": [], "created": "2024-11-27T12:19:20.819Z", "modified": "2024-11-29T12:17:42.004Z"}, {"entity": "publication", "iuid": "b8f1ec8c5d584d898d8c103f4e9a98bb", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b8f1ec8c5d584d898d8c103f4e9a98bb.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b8f1ec8c5d584d898d8c103f4e9a98bb"}}, "title": "A dedicated database system for handling multi-level data in systems biology.", "authors": [{"family": "Pornputtapong", "given": "Natapol", "initials": "N"}, {"family": "Wanichthanarak", "given": "Kwanjeera", "initials": "K"}, {"family": "Nilsson", "given": "Avlant", "initials": "A", "orcid": "0000-0002-9476-4516", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f2e21dbc1c624f6a841c59e959e948e4.json"}}, {"family": "Nookaew", "given": "Intawat", "initials": "I"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/33f2b49a39ed4e54ba77dfe397ed3087.json"}}], "type": "journal article", "published": "2014-07-10", "journal": {"title": "Source Code Biol Med", "issn": "1751-0473", "issn-l": null, "volume": "9", "issue": null, "pages": "17"}, "abstract": "Advances in high-throughput technologies have enabled extensive generation of multi-level omics data. These data are crucial for systems biology research, though they are complex, heterogeneous, highly dynamic, incomplete and distributed among public databases. This leads to difficulties in data accessibility and often results in errors when data are merged and integrated from varied resources. Therefore, integration and management of systems biological data remain very challenging.\r\n\r\nTo overcome this, we designed and developed a dedicated database system that can serve and solve the vital issues in data management and hereby facilitate data integration, modeling and analysis in systems biology within a sole database. In addition, a yeast data repository was implemented as an integrated database environment which is operated by the database system. Two applications were implemented to demonstrate extensibility and utilization of the system. Both illustrate how the user can access the database via the web query function and implemented scripts. These scripts are specific for two sample cases: 1) Detecting the pheromone pathway in protein interaction networks; and 2) Finding metabolic reactions regulated by Snf1 kinase.\r\n\r\nIn this study we present the design of database system which offers an extensible environment to efficiently capture the majority of biological entities and relations encountered in systems biology. Critical functions and control processes were designed and implemented to ensure consistent, efficient, secure and reliable transactions. The two sample cases on the yeast integrated data clearly demonstrate the value of a sole database environment for systems biology research.", "doi": "10.1186/1751-0473-9-17", "pmid": "25053973", "labels": {"Avlant Nilsson": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC4106218"}, {"db": "pii", "key": "1751-0473-9-17"}], "notes": [], "created": "2025-03-20T11:00:21.693Z", "modified": "2025-03-21T13:15:19.899Z"}, {"entity": "publication", "iuid": "9dbfc2c550be4bf6996e32ca8a5dc1f4", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9dbfc2c550be4bf6996e32ca8a5dc1f4.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9dbfc2c550be4bf6996e32ca8a5dc1f4"}}, "title": "SIRT1 promoter polymorphisms as clinical modifiers on systemic lupus erythematosus.", "authors": [{"family": "Consiglio", "given": "Camila Rosat", "initials": "CR"}, {"family": "Juliana da Silveira", "given": "Schauren", "initials": "S"}, {"family": "Monticielo", "given": "Odirlei Andr\u00e9", "initials": "OA"}, {"family": "Xavier", "given": "Ricardo Machado", "initials": "RM"}, {"family": "Brenol", "given": "Jo\u00e3o Carlos Tavares", "initials": "JC"}, {"family": "Chies", "given": "Jos\u00e9 Artur Bogo", "initials": "JA"}], "type": "journal article", "published": "2014-07-00", "journal": {"title": "Mol. Biol. Rep.", "issn": "1573-4978", "volume": "41", "issue": "7", "pages": "4233-4239", "issn-l": "0301-4851"}, "abstract": "Silent mating type Information Regulator 2 homolog 1 (SIRT1) is a deacetylase protein that participates in several physiological processes with importance in transcriptional silencing, apoptosis, immune system regulation and inflammation. Systemic lupus erythematosus (SLE) is an inflammatory autoimmune disease in which upregulated expression of SIRT1 on CD4+ T lymphocytes of active patients has been reported. Also, global hypoacetylation of histones H3 and H4, with H3 hypoacetylation was correlated with a higher disease activity index. SIRT1 promoter rs12778366 and rs3758391 may account for differential expression of this molecule and the role of these variants was investigated in SLE susceptibility and morbidity. Genomic DNA was extracted from peripheral blood of 367 SLE patients and 290 healthy controls of a Southern Brazilian population. SIRT1 rs12778366 and rs3758391 were amplified through PCR and genotyped through sequencing. No statistically significant differences were observed between patients and controls for allelic, genotypic or haplotypic frequencies. Nevertheless, SIRT1 rs3758391 was not in Hardy-Weinberg equilibrium, presenting a paucity of CT heterozygous both in patients and controls. SLE patients with TT and CT genotypes displayed a higher chance of developing lupus nephritis (Pc = 0.012, OR = 2.04 95 % CI 1.32-3.14) and presented a higher disease activity index (Mean rank 170.95 vs 137.26, Pc = 0.006) when compared with CC homozygous patients. Our results suggest that SIRT1 rs3758391 modifies SLE morbidity, with rs3758391 T allele being a risk factor for nephritis and a higher SLEDAI. Nevertheless, it remains to be elucidated how SIRT1 rs3758391 functionally influences SLE severity.", "doi": "10.1007/s11033-014-3294-3", "pmid": "24570024", "labels": {"Camila Consiglio": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2023-11-22T09:17:35.974Z", "modified": "2023-11-22T09:17:35.990Z"}, {"entity": "publication", "iuid": "3797c7eea788441b8caf49bb34d03341", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3797c7eea788441b8caf49bb34d03341.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3797c7eea788441b8caf49bb34d03341"}}, "title": "Improving ITS sequence data for identification of plant pathogenic fungi", "authors": [{"family": "Nilsson", "given": "R Henrik", "initials": "RH", "orcid": "0000-0002-8052-0107", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/74fbd134d83345efa9287939798ad29f.json"}}, {"family": "Hyde", "given": "Kevin D", "initials": "KD"}, {"family": "Paw\u0142owska", "given": "Julia", "initials": "J"}, {"family": "Ryberg", "given": "Martin", "initials": "M"}, {"family": "Tedersoo", "given": "Leho", "initials": "L"}, {"family": "Aas", "given": "Anders Bj\u00f8rnsgard", "initials": "AB"}, {"family": "Alias", "given": "Siti A", "initials": "SA"}, {"family": "Alves", "given": "Artur", "initials": "A"}, {"family": "Anderson", "given": "Cajsa Lisa", "initials": "CL"}, {"family": "Antonelli", "given": "Alexandre", "initials": "A", "orcid": "0000-0003-1842-9297", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1de98df1bb2140fc9666507cb2fb5614.json"}}, {"family": "Arnold", "given": "A Elizabeth", "initials": "AE"}, {"family": "Bahnmann", "given": "Barbara", "initials": "B"}, {"family": "Bahram", "given": "Mohammad", "initials": "M"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J", "orcid": "0000-0002-6528-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c666068e9d34939b0252a627007cec7.json"}}, {"family": "Berlin", "given": "Anna", "initials": "A"}, {"family": "Branco", "given": "Sara", "initials": "S"}, {"family": "Chomnunti", "given": "Putarak", "initials": "P"}, {"family": "Dissanayake", "given": "Asha", "initials": "A"}, {"family": "Drenkhan", "given": "Rein", "initials": "R"}, {"family": "Friberg", "given": "Hanna", "initials": "H"}, {"family": "Fr\u00f8slev", "given": "Tobias Guldberg", "initials": "TG"}, {"family": "Halwachs", "given": "Bettina", "initials": "B"}, {"family": "Hartmann", "given": "Martin", "initials": "M"}, {"family": "Henricot", "given": "Beatrice", "initials": "B"}, {"family": "Jayawardena", "given": "Ruvishika", "initials": "R"}, {"family": "Jumpponen", "given": "Ari", "initials": "A"}, {"family": "Kauserud", "given": "H\u00e5vard", "initials": "H"}, {"family": "Koskela", "given": "Sonja", "initials": "S"}, {"family": "Kulik", "given": "Tomasz", "initials": "T"}, {"family": "Liimatainen", "given": "Kare", "initials": "K"}, {"family": "Lindahl", "given": "Bj\u00f6rn D", "initials": "BD"}, {"family": "Lindner", "given": "Daniel", "initials": "D"}, {"family": "Liu", "given": "Jian Kui", "initials": "JK"}, {"family": "Maharachchikumbura", "given": "Sajeewa", "initials": "S"}, {"family": "Manamgoda", "given": "Dimuthu", "initials": "D"}, {"family": "Martinsson", "given": "Svante", "initials": "S"}, {"family": "Neves", "given": "Maria Alice", "initials": "MA"}, {"family": "Niskanen", "given": "Tuula", "initials": "T"}, {"family": "Nylinder", "given": "Stephan", "initials": "S"}, {"family": "Pereira", "given": "Olinto Liparini", "initials": "OL"}, {"family": "Pinho", "given": "Danilo Batista", "initials": "DB"}, {"family": "Porter", "given": "Teresita M", "initials": "TM"}, {"family": "Queloz", "given": "Valentin", "initials": "V"}, {"family": "Riit", "given": "Taavi", "initials": "T"}, {"family": "S\u00e1nchez-Garc\u00eda", "given": "Marisol", "initials": "M"}, {"family": "de Sousa", "given": "Filipe", "initials": "F"}, {"family": "Stefa\u0144czyk", "given": "Emil", "initials": "E"}, {"family": "Tadych", "given": "Mariusz", "initials": "M"}, {"family": "Takamatsu", "given": "Susumu", "initials": "S"}, {"family": "Tian", "given": "Qing", "initials": "Q"}, {"family": "Udayanga", "given": "Dhanushka", "initials": "D"}, {"family": "Unterseher", "given": "Martin", "initials": "M"}, {"family": "Wang", "given": "Zheng", "initials": "Z"}, {"family": "Wikee", "given": "Saowanee", "initials": "S"}, {"family": "Yan", "given": "Jiye", "initials": "J"}, {"family": "Larsson", "given": "Ellen", "initials": "E"}, {"family": "Larsson", "given": "Karl Henrik", "initials": "KH"}, {"family": "K\u00f5ljalg", "given": "Urmas", "initials": "U"}, {"family": "Abarenkov", "given": "Kessy", "initials": "K"}], "type": "journal-article", "published": "2014-07-00", "journal": {"title": "Fungal Diversity", "issn": "1560-2745", "volume": "67", "issue": "1", "pages": "11-19", "issn-l": null}, "abstract": null, "doi": "10.1007/s13225-014-0291-8", "pmid": null, "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [], "notes": [], "created": "2022-11-08T09:30:21.744Z", "modified": "2025-12-09T13:44:38.343Z"}, {"entity": "publication", "iuid": "726690559d6f4f27a8a188ff58efe4f7", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/726690559d6f4f27a8a188ff58efe4f7.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/726690559d6f4f27a8a188ff58efe4f7"}}, "title": "BioMet Toolbox 2.0: genome-wide analysis of metabolism and omics data.", "authors": [{"family": "Garcia-Albornoz", "given": "Manuel", "initials": "M"}, {"family": "Thankaswamy-Kosalai", "given": "Subazini", "initials": "S"}, {"family": "Nilsson", "given": "Avlant", "initials": "A", "orcid": "0000-0002-9476-4516", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f2e21dbc1c624f6a841c59e959e948e4.json"}}, {"family": "V\u00e4remo", "given": "Leif", "initials": "L"}, {"family": "Nookaew", "given": "Intawat", "initials": "I"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/33f2b49a39ed4e54ba77dfe397ed3087.json"}}], "type": "journal article", "published": "2014-07-00", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "issn-l": "0305-1048", "volume": "42", "issue": "Web Server issue", "pages": "W175-W181"}, "abstract": "Analysis of large data sets using computational and mathematical tools have become a central part of biological sciences. Large amounts of data are being generated each year from different biological research fields leading to a constant development of software and algorithms aimed to deal with the increasing creation of information. The BioMet Toolbox 2.0 integrates a number of functionalities in a user-friendly environment enabling the user to work with biological data in a web interface. The unique and distinguishing feature of the BioMet Toolbox 2.0 is to provide a web user interface to tools for metabolic pathways and omics analysis developed under different platform-dependent environments enabling easy access to these computational tools.", "doi": "10.1093/nar/gku371", "pmid": "24792167", "labels": {"Avlant Nilsson": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC4086127"}, {"db": "pii", "key": "gku371"}], "notes": [], "created": "2025-03-20T11:44:18.653Z", "modified": "2025-03-21T10:37:01.406Z"}, {"entity": "publication", "iuid": "0b800ddc5c5244269df904615e7815d5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0b800ddc5c5244269df904615e7815d5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0b800ddc5c5244269df904615e7815d5"}}, "title": "DNA methylation changes separate allergic patients from healthy controls and may reflect altered CD4+ T-cell population structure.", "authors": [{"family": "Nestor", "given": "Colm E", "initials": "CE"}, {"family": "Barren\u00e4s", "given": "Fredrik", "initials": "F"}, {"family": "Wang", "given": "Hui", "initials": "H"}, {"family": "Lentini", "given": "Antonio", "initials": "A"}, {"family": "Zhang", "given": "Huan", "initials": "H"}, {"family": "Bruhn", "given": "S\u00f6ren", "initials": "S"}, {"family": "J\u00f6rnsten", "given": "Rebecka", "initials": "R"}, {"family": "Langston", "given": "Michael A", "initials": "MA"}, {"family": "Rogers", "given": "Gary", "initials": "G"}, {"family": "Gustafsson", "given": "Mika", "initials": "M"}, {"family": "Benson", "given": "Mikael", "initials": "M"}], "type": "journal article", "published": "2014-01-00", "journal": {"title": "PLoS Genet", "issn": "1553-7404", "volume": "10", "issue": "1", "pages": "e1004059", "issn-l": "1553-7390"}, "abstract": "Altered DNA methylation patterns in CD4(+) T-cells indicate the importance of epigenetic mechanisms in inflammatory diseases. However, the identification of these alterations is complicated by the heterogeneity of most inflammatory diseases. Seasonal allergic rhinitis (SAR) is an optimal disease model for the study of DNA methylation because of its well-defined phenotype and etiology. We generated genome-wide DNA methylation (N(patients) = 8, N(controls) = 8) and gene expression (N(patients) = 9, Ncontrols = 10) profiles of CD4(+) T-cells from SAR patients and healthy controls using Illumina's HumanMethylation450 and HT-12 microarrays, respectively. DNA methylation profiles clearly and robustly distinguished SAR patients from controls, during and outside the pollen season. In agreement with previously published studies, gene expression profiles of the same samples failed to separate patients and controls. Separation by methylation (N(patients) = 12, N(controls) = 12), but not by gene expression (N(patients) = 21, N(controls) = 21) was also observed in an in vitro model system in which purified PBMCs from patients and healthy controls were challenged with allergen. We observed changes in the proportions of memory T-cell populations between patients (N(patients) = 35) and controls (N(controls) = 12), which could explain the observed difference in DNA methylation. Our data highlight the potential of epigenomics in the stratification of immune disease and represents the first successful molecular classification of SAR using CD4(+) T cells.", "doi": "10.1371/journal.pgen.1004059", "pmid": "24391521", "labels": {"Antonio Lentini": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC3879208"}, {"db": "pii", "key": "PGENETICS-D-12-03039"}], "notes": [], "created": "2025-03-28T07:14:55.629Z", "modified": "2025-03-28T07:14:55.644Z"}, {"entity": "publication", "iuid": "dd6d4a6d41b048bcbbe2fd67db322b7a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/dd6d4a6d41b048bcbbe2fd67db322b7a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/dd6d4a6d41b048bcbbe2fd67db322b7a"}}, "title": "BacMet: antibacterial biocide and metal resistance genes database.", "authors": [{"family": "Pal", "given": "Chandan", "initials": "C"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Rensing", "given": "Christopher", "initials": "C"}, {"family": "Kristiansson", "given": "Erik", "initials": "E"}, {"family": "Larsson", "given": "D G Joakim", "initials": "DG"}], "type": "journal article", "published": "2014-01-00", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "volume": "42", "issue": "Database issue", "pages": "D737-D743", "issn-l": "0305-1048"}, "abstract": "Antibiotic resistance has become a major human health concern due to widespread use, misuse and overuse of antibiotics. In addition to antibiotics, antibacterial biocides and metals can contribute to the development and maintenance of antibiotic resistance in bacterial communities through co-selection. Information on metal and biocide resistance genes, including their sequences and molecular functions, is, however, scattered. Here, we introduce BacMet (http://bacmet.biomedicine.gu.se)--a manually curated database of antibacterial biocide- and metal-resistance genes based on an in-depth review of the scientific literature. The BacMet database contains 470 experimentally verified resistance genes. In addition, the database also contains 25 477 potential resistance genes collected from public sequence repositories. All resistance genes in the BacMet database have been organized according to their molecular function and induced resistance phenotype.", "doi": "10.1093/nar/gkt1252", "pmid": "24304895", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pii", "key": "gkt1252"}, {"db": "pmc", "key": "PMC3965030"}], "notes": [], "created": "2022-11-08T09:30:24.068Z", "modified": "2022-11-08T09:30:24.102Z"}, {"entity": "publication", "iuid": "75535e72f05c465eaedfa698795c9f90", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/75535e72f05c465eaedfa698795c9f90.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/75535e72f05c465eaedfa698795c9f90"}}, "title": "Metaxa, Overview", "authors": [{"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Hartmann", "given": "Martin", "initials": "M"}, {"family": "Eriksson", "given": "K Martin", "initials": "KM"}, {"family": "Nilsson", "given": "R Henrik", "initials": "RH"}], "type": "book-chapter", "published": "2014-00-00", "journal": {"title": "Encyclopedia of Metagenomics", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": "1-5"}, "abstract": null, "doi": "10.1007/978-1-4614-6418-1_239-6", "pmid": null, "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [], "notes": [], "created": "2022-11-08T09:31:49.680Z", "modified": "2025-12-04T17:01:49.308Z"}, {"entity": "publication", "iuid": "495c73e30669430d8e678638813da9dd", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/495c73e30669430d8e678638813da9dd.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/495c73e30669430d8e678638813da9dd"}}, "title": "Towards a unified paradigm for sequence-based identification of fungi.", "authors": [{"family": "K\u00f5ljalg", "given": "Urmas", "initials": "U"}, {"family": "Nilsson", "given": "R Henrik", "initials": "RH"}, {"family": "Abarenkov", "given": "Kessy", "initials": "K"}, {"family": "Tedersoo", "given": "Leho", "initials": "L"}, {"family": "Taylor", "given": "Andy F S", "initials": "AF"}, {"family": "Bahram", "given": "Mohammad", "initials": "M"}, {"family": "Bates", "given": "Scott T", "initials": "ST"}, {"family": "Bruns", "given": "Thomas D", "initials": "TD"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Callaghan", "given": "Tony M", "initials": "TM"}, {"family": "Douglas", "given": "Brian", "initials": "B"}, {"family": "Drenkhan", "given": "Tiia", "initials": "T"}, {"family": "Eberhardt", "given": "Ursula", "initials": "U"}, {"family": "Due\u00f1as", "given": "Margarita", "initials": "M"}, {"family": "Grebenc", "given": "Tine", "initials": "T"}, {"family": "Griffith", "given": "Gareth W", "initials": "GW"}, {"family": "Hartmann", "given": "Martin", "initials": "M"}, {"family": "Kirk", "given": "Paul M", "initials": "PM"}, {"family": "Kohout", "given": "Petr", "initials": "P"}, {"family": "Larsson", "given": "Ellen", "initials": "E"}, {"family": "Lindahl", "given": "Bj\u00f6rn D", "initials": "BD"}, {"family": "L\u00fccking", "given": "Robert", "initials": "R"}, {"family": "Mart\u00edn", "given": "Mar\u00eda P", "initials": "MP"}, {"family": "Matheny", "given": "P Brandon", "initials": "PB"}, {"family": "Nguyen", "given": "Nhu H", "initials": "NH"}, {"family": "Niskanen", "given": "Tuula", "initials": "T"}, {"family": "Oja", "given": "Jane", "initials": "J"}, {"family": "Peay", "given": "Kabir G", "initials": "KG"}, {"family": "Peintner", "given": "Ursula", "initials": "U"}, {"family": "Peterson", "given": "Marko", "initials": "M"}, {"family": "P\u00f5ldmaa", "given": "Kadri", "initials": "K"}, {"family": "Saag", "given": "Lauri", "initials": "L"}, {"family": "Saar", "given": "Irja", "initials": "I"}, {"family": "Sch\u00fc\u00dfler", "given": "Arthur", "initials": "A"}, {"family": "Scott", "given": "James A", "initials": "JA"}, {"family": "Sen\u00e9s", "given": "Carolina", "initials": "C"}, {"family": "Smith", "given": "Matthew E", "initials": "ME"}, {"family": "Suija", "given": "Ave", "initials": "A"}, {"family": "Taylor", "given": "D Lee", "initials": "DL"}, {"family": "Telleria", "given": "M Teresa", "initials": "MT"}, {"family": "Weiss", "given": "Michael", "initials": "M"}, {"family": "Larsson", "given": "Karl-Henrik", "initials": "KH"}], "type": "journal article", "published": "2013-11-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "volume": "22", "issue": "21", "pages": "5271-5277", "issn-l": "0962-1083"}, "abstract": "The nuclear ribosomal internal transcribed spacer (ITS) region is the formal fungal barcode and in most cases the marker of choice for the exploration of fungal diversity in environmental samples. Two problems are particularly acute in the pursuit of satisfactory taxonomic assignment of newly generated ITS sequences: (i) the lack of an inclusive, reliable public reference data set and (ii) the lack of means to refer to fungal species, for which no Latin name is available in a standardized stable way. Here, we report on progress in these regards through further development of the UNITE database (http://unite.ut.ee) for molecular identification of fungi. All fungal species represented by at least two ITS sequences in the international nucleotide sequence databases are now given a unique, stable name of the accession number type (e.g. Hymenoscyphus pseudoalbidus|GU586904|SH133781.05FU), and their taxonomic and ecological annotations were corrected as far as possible through a distributed, third-party annotation effort. We introduce the term 'species hypothesis' (SH) for the taxa discovered in clustering on different similarity thresholds (97-99%). An automatically or manually designated sequence is chosen to represent each such SH. These reference sequences are released (http://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and in the QIIME pipeline. The system and the data will be updated automatically as the number of public fungal ITS sequences grows. We invite everybody in the position to improve the annotation or metadata associated with their particular fungal lineages of expertise to do so through the new Web-based sequence management system in UNITE.", "doi": "10.1111/mec.12481", "pmid": "24112409", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [], "notes": [], "created": "2022-11-08T09:36:12.374Z", "modified": "2022-11-08T09:36:12.377Z"}, {"entity": "publication", "iuid": "d7f0cee2686d4f198d9b7910476b8d0c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d7f0cee2686d4f198d9b7910476b8d0c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d7f0cee2686d4f198d9b7910476b8d0c"}}, "title": "Hybrid and nonhybrid lipids exert common effects on membrane raft size and morphology.", "authors": [{"family": "Heberle", "given": "Frederick A", "initials": "FA"}, {"family": "Doktorova", "given": "Milka", "initials": "M"}, {"family": "Goh", "given": "Shih Lin", "initials": "SL"}, {"family": "Standaert", "given": "Robert F", "initials": "RF"}, {"family": "Katsaras", "given": "John", "initials": "J"}, {"family": "Feigenson", "given": "Gerald W", "initials": "GW"}], "type": "journal article", "published": "2013-10-09", "journal": {"title": "Journal of the American Chemical Society", "issn": "1520-5126", "issn-l": "0002-7863", "volume": "135", "issue": "40", "pages": "14932-14935"}, "abstract": "Nanometer-scale domains in cholesterol-rich model membranes emulate lipid rafts in cell plasma membranes (PMs). The physicochemical mechanisms that maintain a finite, small domain size are, however, not well understood. A special role has been postulated for chain-asymmetric or hybrid lipids having a saturated sn-1 chain and an unsaturated sn-2 chain. Hybrid lipids generate nanodomains in some model membranes and are also abundant in the PM. It was proposed that they align in a preferred orientation at the boundary of ordered and disordered phases, lowering the interfacial energy and thus reducing domain size. We used small-angle neutron scattering and fluorescence techniques to detect nanoscopic and modulated liquid phase domains in a mixture composed entirely of nonhybrid lipids and cholesterol. Our results are indistinguishable from those obtained previously for mixtures containing hybrid lipids, conclusively showing that hybrid lipids are not required for the formation of nanoscopic liquid domains and strongly implying a common mechanism for the overall control of raft size and morphology. We discuss implications of these findings for theoretical descriptions of nanodomains.", "doi": "10.1021/ja407624c", "pmid": "24041024", "labels": {"Milka Doktorova": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2024-11-27T12:13:41.592Z", "modified": "2024-11-29T12:17:49.514Z"}, {"entity": "publication", "iuid": "2505fffa36b64238bf2e8dbebf0417f1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/2505fffa36b64238bf2e8dbebf0417f1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/2505fffa36b64238bf2e8dbebf0417f1"}}, "title": "Profiling of human CD4+ T-cell subsets identifies the TH2-specific noncoding RNA GATA3-AS1.", "authors": [{"family": "Zhang", "given": "Huan", "initials": "H"}, {"family": "Nestor", "given": "Colm E", "initials": "CE"}, {"family": "Zhao", "given": "Shuli", "initials": "S"}, {"family": "Lentini", "given": "Antonio", "initials": "A"}, {"family": "Bohle", "given": "Barbara", "initials": "B"}, {"family": "Benson", "given": "Mikael", "initials": "M"}, {"family": "Wang", "given": "Hui", "initials": "H"}], "type": "letter", "published": "2013-10-00", "journal": {"title": "J. Allergy Clin. Immunol.", "issn": "1097-6825", "volume": "132", "issue": "4", "pages": "1005-1008", "issn-l": "0091-6749"}, "abstract": null, "doi": "10.1016/j.jaci.2013.05.033", "pmid": "23870669", "labels": {"Antonio Lentini": null, "DDLS Fellow": null}, "xrefs": [{"db": "pii", "key": "S0091-6749(13)00908-1"}], "notes": [], "created": "2025-03-28T07:14:57.742Z", "modified": "2025-03-28T07:14:57.758Z"}, {"entity": "publication", "iuid": "36371351bbd24891904ab1352c4bc46d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/36371351bbd24891904ab1352c4bc46d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/36371351bbd24891904ab1352c4bc46d"}}, "title": "Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data", "authors": [{"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Ryberg", "given": "Martin", "initials": "M"}, {"family": "Hartmann", "given": "Martin", "initials": "M"}, {"family": "Branco", "given": "Sara", "initials": "S"}, {"family": "Wang", "given": "Zheng", "initials": "Z"}, {"family": "Godhe", "given": "Anna", "initials": "A"}, {"family": "De Wit", "given": "Pierre", "initials": "P"}, {"family": "S\u00e1nchez-Garc\u00eda", "given": "Marisol", "initials": "M"}, {"family": "Ebersberger", "given": "Ingo", "initials": "I"}, {"family": "de Sousa", "given": "Filipe", "initials": "F"}, {"family": "Amend", "given": "Anthony S", "initials": "AS"}, {"family": "Jumpponen", "given": "Ari", "initials": "A"}, {"family": "Unterseher", "given": "Martin", "initials": "M"}, {"family": "Kristiansson", "given": "Erik", "initials": "E"}, {"family": "Abarenkov", "given": "Kessy", "initials": "K"}, {"family": "Bertrand", "given": "Yann J K", "initials": "YJK"}, {"family": "Sanli", "given": "Kemal", "initials": "K"}, {"family": "Eriksson", "given": "K Martin", "initials": "KM"}, {"family": "Vik", "given": "Unni", "initials": "U"}, {"family": "Veldre", "given": "Vilmar", "initials": "V"}, {"family": "Nilsson", "given": "R Henrik", "initials": "RH"}], "type": "journal-article", "published": "2013-07-00", "journal": {"title": "Methods Ecol Evol", "issn": "2041-210X", "pages": "n/a-n/a", "issn-l": null}, "abstract": null, "doi": "10.1111/2041-210x.12073", "pmid": null, "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [], "notes": [], "created": "2022-11-08T09:30:29.159Z", "modified": "2022-11-08T09:30:29.206Z"}, {"entity": "publication", "iuid": "57ce964a2b2b4b9d95d4557f1ed1f3cb", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/57ce964a2b2b4b9d95d4557f1ed1f3cb.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/57ce964a2b2b4b9d95d4557f1ed1f3cb"}}, "title": "Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences", "authors": [{"family": "Nilsson", "given": "R Henrik", "initials": "RH", "orcid": "0000-0002-8052-0107", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/74fbd134d83345efa9287939798ad29f.json"}}, {"family": "Tedersoo", "given": "Leho", "initials": "L"}, {"family": "Abarenkov", "given": "Kessy", "initials": "K"}, {"family": "Ryberg", "given": "Martin", "initials": "M"}, {"family": "Kristiansson", "given": "Erik", "initials": "E", "orcid": "0000-0002-8609-2414", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/18d5538c8c0749199a6f1b51d15eec69.json"}}, {"family": "Hartmann", "given": "Martin", "initials": "M"}, {"family": "Schoch", "given": "Conrad L", "initials": "CL"}, {"family": "Nylander", "given": "Johan A A", "initials": "JAA"}, {"family": "Bergsten", "given": "Johannes", "initials": "J"}, {"family": "Porter", "given": "Teresita M", "initials": "TM"}, {"family": "Jumpponen", "given": "Ari", "initials": "A"}, {"family": "Vaishampayan", "given": "Parag", "initials": "P"}, {"family": "Ovaskainen", "given": "Otso", "initials": "O", "orcid": "0000-0001-9750-4421", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9c73c582d24a44bd895c5ee7084487a4.json"}}, {"family": "Hallenberg", "given": "Nils", "initials": "N"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J", "orcid": "0000-0002-6528-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c666068e9d34939b0252a627007cec7.json"}}, {"family": "Eriksson", "given": "K Martin", "initials": "KM"}, {"family": "Larsson", "given": "Karl Henrik", "initials": "KH"}, {"family": "Larsson", "given": "Ellen", "initials": "E"}, {"family": "K\u00f5ljalg", "given": "Urmas", "initials": "U"}], "type": "journal-article", "published": "2012-09-05", "journal": {"title": "MykoKeys", "issn": "1314-4049", "issn-l": null, "volume": "4", "issue": null, "pages": "37-63"}, "abstract": null, "doi": "10.3897/mycokeys.4.3606", "pmid": null, "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [], "notes": [], "created": "2022-11-08T09:30:31.247Z", "modified": "2025-12-04T17:01:38.967Z"}, {"entity": "publication", "iuid": "464352d011364923ac43d023f4961687", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/464352d011364923ac43d023f4961687.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/464352d011364923ac43d023f4961687"}}, "title": "Megraft: a software package to graft ribosomal small subunit (16S/18S) fragments onto full-length sequences for accurate species richness and sequencing depth analysis in pyrosequencing-length metagenomes and similar environmental datasets.", "authors": [{"family": "Bengtsson", "given": "Johan", "initials": "J"}, {"family": "Hartmann", "given": "Martin", "initials": "M"}, {"family": "Unterseher", "given": "Martin", "initials": "M"}, {"family": "Vaishampayan", "given": "Parag", "initials": "P"}, {"family": "Abarenkov", "given": "Kessy", "initials": "K"}, {"family": "Durso", "given": "Lisa", "initials": "L"}, {"family": "Bik", "given": "Elisabeth M", "initials": "EM"}, {"family": "Garey", "given": "James R", "initials": "JR"}, {"family": "Eriksson", "given": "K Martin", "initials": "KM"}, {"family": "Nilsson", "given": "R Henrik", "initials": "RH"}], "type": "journal article", "published": "2012-07-00", "journal": {"title": "Res. Microbiol.", "issn": "1769-7123", "volume": "163", "issue": "6-7", "pages": "407-412", "issn-l": "0923-2508"}, "abstract": "Metagenomic libraries represent subsamples of the total DNA found at a study site and offer unprecedented opportunities to study ecological and functional aspects of microbial communities. To examine the depth of a community sequencing effort, rarefaction analysis of the ribosomal small subunit (SSU/16S/18S) gene in the metagenome is usually performed. The fragmentary, non-overlapping nature of SSU sequences in metagenomic libraries poses a problem for this analysis, however. We introduce a software package - Megraft - that grafts SSU fragments onto full-length SSU sequences, accounting for observed and unobserved variability, for accurate assessment of species richness and sequencing depth in metagenomics endeavors.", "doi": "10.1016/j.resmic.2012.07.001", "pmid": "22824070", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pii", "key": "S0923-2508(12)00096-4"}], "notes": [], "created": "2022-11-08T09:30:33.474Z", "modified": "2022-11-08T09:30:33.499Z"}, {"entity": "publication", "iuid": "d47bd17accf842e995e947e473e372de", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d47bd17accf842e995e947e473e372de.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d47bd17accf842e995e947e473e372de"}}, "title": "Expression of colonization factor CS5 of enterotoxigenic Escherichia coli (ETEC) is enhanced in vivo and by the bile component Na glycocholate hydrate.", "authors": [{"family": "Nicklasson", "given": "Matilda", "initials": "M"}, {"family": "Sj\u00f6ling", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "von Mentzer", "given": "Astrid", "initials": "A"}, {"family": "Qadri", "given": "Firdausi", "initials": "F"}, {"family": "Svennerholm", "given": "Ann-Mari", "initials": "AM"}], "type": "journal article", "published": "2012-04-30", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "7", "issue": "4", "pages": "e35827", "issn-l": "1932-6203"}, "abstract": "Enterotoxigenic Escherichia coli (ETEC) is an important cause of acute watery diarrhoea in developing countries. Colonization factors (CFs) on the bacterial surface mediate adhesion to the small intestinal epithelium. Two of the most common CFs worldwide are coli surface antigens 5 and 6 (CS5, CS6). In this study we investigated the expression of CS5 and CS6 in vivo, and the effects of bile and sodium bicarbonate, present in the human gut, on the expression of CS5. Five CS5+CS6 ETEC isolates from adult Bangladeshi patients with acute diarrhoea were studied. The level of transcription from the CS5 operon was approximately 100-fold higher than from the CS6 operon in ETEC bacteria recovered directly from diarrhoeal stool without sub-culturing (in vivo). The glyco-conjugated primary bile salt sodium glycocholate hydrate (NaGCH) induced phenotypic expression of CS5 in a dose-dependent manner and caused a 100-fold up-regulation of CS5 mRNA levels; this is the first description of NaGCH as an enteropathogenic virulence inducer. The relative transcription levels from the CS5 and CS6 operons in the presence of bile or NaGCH in vitro were similar to those in vivo. Another bile salt, sodium deoxycholate (NaDC), previously reported to induce enteropathogenic virulence, also induced expression of CS5, whereas sodium bicarbonate did not.", "doi": "10.1371/journal.pone.0035827", "pmid": "22563407", "labels": {"Astrid von Mentzer": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC3342736"}, {"db": "pii", "key": "PONE-D-12-01872"}], "notes": [], "created": "2025-12-02T15:51:28.884Z", "modified": "2025-12-02T15:51:28.898Z"}, {"entity": "publication", "iuid": "692dd2b057b8436fa7f559976b7bea46", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/692dd2b057b8436fa7f559976b7bea46.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/692dd2b057b8436fa7f559976b7bea46"}}, "title": "Metaxa: a software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets.", "authors": [{"family": "Bengtsson", "given": "Johan", "initials": "J"}, {"family": "Eriksson", "given": "K Martin", "initials": "KM"}, {"family": "Hartmann", "given": "Martin", "initials": "M"}, {"family": "Wang", "given": "Zheng", "initials": "Z"}, {"family": "Shenoy", "given": "Belle Damodara", "initials": "BD"}, {"family": "Grelet", "given": "Gwen-A\u00eblle", "initials": "GA"}, {"family": "Abarenkov", "given": "Kessy", "initials": "K"}, {"family": "Petri", "given": "Anna", "initials": "A"}, {"family": "Rosenblad", "given": "Magnus Alm", "initials": "MA"}, {"family": "Nilsson", "given": "R Henrik", "initials": "RH"}], "type": "evaluation study", "published": "2011-10-00", "journal": {"title": "Antonie Van Leeuwenhoek", "issn": "1572-9699", "volume": "100", "issue": "3", "pages": "471-475", "issn-l": null}, "abstract": "The ribosomal small subunit (SSU) rRNA gene has emerged as an important genetic marker for taxonomic identification in environmental sequencing datasets. In addition to being present in the nucleus of eukaryotes and the core genome of prokaryotes, the gene is also found in the mitochondria of eukaryotes and in the chloroplasts of photosynthetic eukaryotes. These three sets of genes are conceptually paralogous and should in most situations not be aligned and analyzed jointly. To identify the origin of SSU sequences in complex sequence datasets has hitherto been a time-consuming and largely manual undertaking. However, the present study introduces Metaxa ( http://microbiology.se/software/metaxa/ ), an automated software tool to extract full-length and partial SSU sequences from larger sequence datasets and assign them to an archaeal, bacterial, nuclear eukaryote, mitochondrial, or chloroplast origin. Using data from reference databases and from full-length organelle and organism genomes, we show that Metaxa detects and scores SSU sequences for origin with very low proportions of false positives and negatives. We believe that this tool will be useful in microbial and evolutionary ecology as well as in metagenomics.", "doi": "10.1007/s10482-011-9598-6", "pmid": "21674231", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [], "notes": [], "created": "2022-11-08T09:30:35.750Z", "modified": "2022-11-08T09:30:35.789Z"}, {"entity": "publication", "iuid": "6546b4241e6540cfb4d7b809db6c4fa6", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/6546b4241e6540cfb4d7b809db6c4fa6.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/6546b4241e6540cfb4d7b809db6c4fa6"}}, "title": "Association of the HLA-G gene +3142C>G polymorphism with systemic lupus erythematosus.", "authors": [{"family": "Consiglio", "given": "C R", "initials": "CR"}, {"family": "Veit", "given": "T D", "initials": "TD"}, {"family": "Monticielo", "given": "O A", "initials": "OA"}, {"family": "Mucenic", "given": "T", "initials": "T"}, {"family": "Xavier", "given": "R M", "initials": "RM"}, {"family": "Brenol", "given": "J C T", "initials": "JC"}, {"family": "Chies", "given": "J A B", "initials": "JA"}], "type": "journal article", "published": "2011-06-00", "journal": {"title": "Tissue Antigens", "issn": "1399-0039", "volume": "77", "issue": "6", "pages": "540-545", "issn-l": null}, "abstract": "Systemic lupus erythematosus (SLE) is an inflammatory autoimmune disease that affects several organs and systems. Its etiology remains unknown, although it is probably multifactorial. The human leukocyte antigen G (HLA-G) is a nonclassic major histocompatibility complex I molecule characterized by restricted expression and low DNA polymorphism. HLA-G plays a role in immunosuppression through different mechanisms. In inflammatory diseases, it has been postulated that HLA-G expression may be a possible mechanism of tissue protection against exacerbated inflammatory response. On the 3' untranslated region (3' UTR) of the HLA-G gene, there is an insertion/deletion polymorphism of 14 bp (rs1704) that was shown to influence the mRNA stability. The influence of this polymorphism in disease susceptibility is controversial. Also in the 3' UTR there is a single nucleotide polymorphism C/G (rs1063320) on the position +3142, at a possible binding site for microRNAs (miRNAs) and having an influence on miRNA affinity. In this study, we analyzed the +3142C>G and the 14 bp polymorphisms in 195 SLE European-derived female patients. Our findings show a significant increase of the +3142G allele frequency among patients as compared with controls (0.58 vs 0.47, P = 0.011). Also, patients presented a higher frequency of the GG genotype (OR = 1.90, 95% CI: 1.08-3.42). Double heterozygotes for the two polymorphisms presented a milder mean systemic lupus erythematosus disease activity index (SLEDAI) than heterozygotes for only one of the variants or non-heterozygous individuals (1.56 vs 3.15 and 3.26, respectively, corrected P = 0.044). These results suggest the involvement of the HLA-G molecule on SLE susceptibility and outcome.", "doi": "10.1111/j.1399-0039.2011.01635.x", "pmid": "21395561", "labels": {"Camila Consiglio": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2023-11-22T09:17:41.855Z", "modified": "2023-11-22T09:17:41.875Z"}]}