{"entity": "researcher", "timestamp": "2026-10-10T11:22:59.711Z", "family": "Levander", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0710-9792", "affiliations": ["Department of Immunotechnology, Lund University, Lund, Sweden.", "National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Lund University, Lund, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/d3aaa3dcdb4f4e9f9b4bd44097d85d0c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/d3aaa3dcdb4f4e9f9b4bd44097d85d0c"}}, "publications": [{"entity": "publication", "iuid": "2691943b505045888090b9a21c80fda0", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/2691943b505045888090b9a21c80fda0.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/2691943b505045888090b9a21c80fda0"}}, "title": "Effects of acute cold and heat shocks on the protein profile of crayfish hemolymph: Implications for crustacean adaptation to thermal stress", "authors": [{"family": "Mengal", "given": "Kifayatullah", "initials": "K"}, {"family": "Kor", "given": "Golara", "initials": "G"}, {"family": "Siino", "given": "Valentina", "initials": "V"}, {"family": "Levander", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0710-9792", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d3aaa3dcdb4f4e9f9b4bd44097d85d0c.json"}}, {"family": "Niksirat", "given": "Hamid", "initials": "H", "orcid": "0000-0003-3782-4954", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/04537c6d5bbd494dac909ea633c3dc20.json"}}], "type": "journal-article", "published": "2026-03-00", "journal": {"title": "Aquaculture Reports", "issn": "2352-5134", "volume": "46", "pages": "103265", "issn-l": null}, "abstract": null, "doi": "10.1016/j.aqrep.2025.103265", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T06:42:29.797Z", "modified": "2026-09-23T11:38:41.811Z"}, {"entity": "publication", "iuid": "df100137fe8a4b0b81792feff847a5fe", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/df100137fe8a4b0b81792feff847a5fe.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/df100137fe8a4b0b81792feff847a5fe"}}, "title": "Pharmacological activation of p53 induces dose-dependent changes in endothelial cell fate during angiogenic sprouting.", "authors": [{"family": "Al-Radi", "given": "Omayma", "initials": "O"}, {"family": "Ingelshed", "given": "Katrine", "initials": "K"}, {"family": "Eichhorn", "given": "Lisa", "initials": "L"}, {"family": "Josefsson", "given": "Heidi", "initials": "H", "orcid": "0009-0001-0493-4877", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dd6373e0099e4367aa92190ba9f4f86e.json"}}, {"family": "Krkoska", "given": "Martin", "initials": "M"}, {"family": "Br\u00e4utigam", "given": "Lars", "initials": "L"}, {"family": "Lindstr\u00f6m", "given": "Susanne", "initials": "S"}, {"family": "V\u00e9gv\u00e1ri", "given": "\u00c1kos", "initials": "\u00c1", "orcid": "0000-0002-1287-0906", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/724d65ef088147c4988093b2b6b5f318.json"}}, {"family": "Kheder", "given": "Sania", "initials": "S"}, {"family": "Cerrato", "given": "Carmine P", "initials": "CP"}, {"family": "Ferm\u00e9", "given": "Suzon", "initials": "S"}, {"family": "Bosdotter", "given": "Cecilia", "initials": "C"}, {"family": "Allalou", "given": "Amin", "initials": "A"}, {"family": "Levander", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0710-9792", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d3aaa3dcdb4f4e9f9b4bd44097d85d0c.json"}}, {"family": "Vojtesek", "given": "Borivoj", "initials": "B"}, {"family": "Lane", "given": "David P", "initials": "DP"}, {"family": "Kannan", "given": "Pavitra", "initials": "P", "orcid": "0000-0002-9170-6062", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/75906b5633ed430da575e2e7df893252.json"}}], "type": "journal article", "published": "2025-12-08", "journal": {"title": "Cell Death Dis", "issn": "2041-4889", "volume": "16", "issue": "1", "pages": "883", "issn-l": "2041-4889"}, "abstract": "The cell cycle is a key regulator of endothelial cell specification into tip and stalk cell phenotypes, which are essential for angiogenesis in both normal development and pathological conditions. While the tumor suppressor p53 is known to regulate the cell cycle and influence cell fate, its role in modulating the cell fate of these phenotypes remains unclear. Using non-genotoxic small molecule and stapled peptide compounds to pharmacologically activate p53 via MDM2 inhibition, we demonstrate that graded levels of p53 induce distinct cellular fates in normal endothelial cells. Low levels of p53 induce reversible cell cycle arrest by reducing DNA replication, while high levels induce senescence and cell death. Surprisingly, all tested levels of p53 activation reduced the growth of venous blood vessels in vitro and in zebrafish embryo models. This reduction in sprouting may stem from distinct cellular responses in tip-like and non-tip-like cells to pharmacological p53 activation: low p53 levels primarily reduced proliferation in non-tip-like cells, whereas high levels decreased the frequency of tip-like cells and the expression of genes associated with tip and stalk cell identities. Our findings show for the first time that pharmacological p53 activation modulates endothelial cell fate in a dose-dependent manner during sprouting angiogenesis. They also highlight the potential of using graded p53 modulation as a therapeutic strategy to target abnormal tip or stalk cell development in pathological angiogenesis, such as in cancer.", "doi": "10.1038/s41419-025-08292-7", "pmid": "41360924", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC12698774"}, {"db": "pii", "key": "10.1038/s41419-025-08292-7"}], "notes": [], "created": "2026-09-23T15:55:51.197Z", "modified": "2026-09-23T15:55:51.304Z"}, {"entity": "publication", "iuid": "c71c4efd6da042d3a605ae0b9a03e558", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c71c4efd6da042d3a605ae0b9a03e558.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c71c4efd6da042d3a605ae0b9a03e558"}}, "title": "Considerations and Software for Successful Immune Cell Deconvolution Using Proteomics Data.", "authors": [{"family": "Zamore", "given": "M\u00e5ns", "initials": "M", "orcid": "0000-0002-8108-1097", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/07cf9b490bd94f01acb56bcfac8cd0da.json"}}, {"family": "Junior", "given": "Sergio Mosquim", "initials": "SM"}, {"family": "Andree", "given": "Sebastian L", "initials": "SL"}, {"family": "Altunbulakli", "given": "Can", "initials": "C"}, {"family": "Lindstedt", "given": "Malin", "initials": "M"}, {"family": "Levander", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0710-9792", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d3aaa3dcdb4f4e9f9b4bd44097d85d0c.json"}}], "type": "journal article", "published": "2025-08-01", "journal": {"title": "J. Proteome Res.", "issn": "1535-3907", "volume": "24", "issue": "8", "pages": "3751-3761", "issn-l": "1535-3893"}, "abstract": "Inferring the cell-type composition of bulk samples can provide biological insight. While bulk transcriptomics data has been extensively used for this purpose, the use of proteomics data has remained unexplored until recently. This study evaluates computational approaches for estimating immune cell composition using bulk sample proteomics data. Leveraging defined immune cell populations and simulated mixtures, we assess the impact of preprocessing methods and software tools on cell deconvolution outcomes. Our findings demonstrate the feasibility of using proteomics data for cell-type deconvolution, with Pearson correlations for estimated proportions in simulated sample mixtures above 0.9 when employing optimal missing value imputation and reference matrix generation parameters. We further provide an R package, proteoDeconv, to facilitate the preprocessing of proteomics data for deconvolution and parsing of results. This study highlights the feasibility of using proteomics for analyzing cell-type composition in biological samples.", "doi": "10.1021/acs.jproteome.4c00868", "pmid": "40657748", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC12322953"}], "notes": [], "created": "2026-08-20T08:11:58.900Z", "modified": "2026-09-23T12:31:01.348Z"}, {"entity": "publication", "iuid": "f4d8d306cc8340e09e37b45ecd1cd98e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f4d8d306cc8340e09e37b45ecd1cd98e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f4d8d306cc8340e09e37b45ecd1cd98e"}}, "title": "Sex programs functional protein level dimorphism in the zebrafish gastrointestinal tract", "authors": [{"family": "Niksirat", "given": "Hamid", "initials": "H"}, {"family": "Siino", "given": "Valentina", "initials": "V"}, {"family": "Steinbach", "given": "Christoph", "initials": "C"}, {"family": "Levander", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0710-9792", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d3aaa3dcdb4f4e9f9b4bd44097d85d0c.json"}}], "type": "journal-article", "published": "2025-07-00", "journal": {"title": "Aquaculture Reports", "issn": "2352-5134", "volume": "42", "pages": "102775", "issn-l": null}, "abstract": null, "doi": "10.1016/j.aqrep.2025.102775", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T06:42:27.840Z", "modified": "2026-09-23T13:37:05.697Z"}, {"entity": "publication", "iuid": "9ff913d912d34f9a8d8e78ea5577c8bd", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9ff913d912d34f9a8d8e78ea5577c8bd.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9ff913d912d34f9a8d8e78ea5577c8bd"}}, "title": "Multiomic profiling of metastatic potential in estrogen receptor-positive human epidermal growth factor-negative breast cancer", "authors": [{"family": "Mosquim", "given": "Sergio", "initials": "S", "orcid": "0000-0002-1537-7252", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/08836688b1b74eeab88cda7b3ed3e488.json"}}, {"family": "Zamore", "given": "M\u00e5ns", "initials": "M"}, {"family": "Vallon-Christersson", "given": "Johan", "initials": "J", "orcid": "0000-0002-2195-0385", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5a79aa63d75d4ffbb4228bc7c3e16ac4.json"}}, {"family": "Ryd\u00e9n", "given": "Lisa", "initials": "L", "orcid": "0000-0001-7515-3130", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e40f8cbccd87481991010cc506b901fa.json"}}, {"family": "Levander", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0710-9792", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d3aaa3dcdb4f4e9f9b4bd44097d85d0c.json"}}], "type": "posted-content", "published": "2025-01-23", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2025.01.22.25320944", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T11:00:36.538Z", "modified": "2026-09-23T15:44:21.282Z"}, {"entity": "publication", "iuid": "62a99fdbaecc406ba1c205c490123d10", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/62a99fdbaecc406ba1c205c490123d10.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/62a99fdbaecc406ba1c205c490123d10"}}, "title": "Automated multiplexed affinity-based enrichment of peptides for LC-MS/MS plasma proteomics.", "authors": [{"family": "Junior", "given": "Sergio Mosquim", "initials": "SM"}, {"family": "Levander", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0710-9792", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d3aaa3dcdb4f4e9f9b4bd44097d85d0c.json"}}], "type": "journal article", "published": "2024-11-00", "journal": {"title": "Proteomics", "issn": "1615-9861", "volume": "24", "issue": "21-22", "pages": "e2400049", "issn-l": "1615-9853"}, "abstract": "Plasma proteomics offers high potential for biomarker discovery, as plasma is collected through a minimally invasive procedure and constitutes the most complex human-derived proteome. However, the wide dynamic range poses a significant challenge. Here, we propose a semi-automated method based on the use of multiple single chain variable fragment antibodies, each enriching for peptides found in up to a few hundred proteins. This approach allows for the analysis of a complementary fraction compared to full proteome analysis. Proteins from pooled plasma were extracted and digested before testing the performance of 29 different antibodies with the aim of reproducibly maximizing peptide enrichment. Our results demonstrate the enrichment of 3662 peptides not detected in neat plasma or negative controls. Moreover, most antibodies were able to enrich for at least 155 peptides across different levels of abundance in plasma. To further reduce analysis time, a combination of antibodies was used in a multiplexed setting. Repeated sample analyses showed low coefficients of variation, and the method is flexible in terms of affinity binders. It does not impose drastic increases in instrument time, thus showing excellent potential for usage in large scale discovery projects.", "doi": "10.1002/pmic.202400049", "pmid": "39192483", "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T06:34:53.004Z", "modified": "2026-09-23T15:40:45.627Z"}, {"entity": "publication", "iuid": "13ecf5a6bdbd480c993fe7cff54f2c25", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/13ecf5a6bdbd480c993fe7cff54f2c25.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/13ecf5a6bdbd480c993fe7cff54f2c25"}}, "title": "LRPPRC and SLIRP synergize to maintain sufficient and orderly mammalian mitochondrial translation.", "authors": [{"family": "Rubalcava-Gracia", "given": "Diana", "initials": "D", "orcid": "0000-0002-4615-7375", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cdb2286b21364ad795f691aad005a4e1.json"}}, {"family": "Bubb", "given": "Kristina", "initials": "K"}, {"family": "Levander", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0710-9792", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d3aaa3dcdb4f4e9f9b4bd44097d85d0c.json"}}, {"family": "Burr", "given": "Stephen P", "initials": "SP"}, {"family": "August", "given": "Amelie V", "initials": "AV"}, {"family": "Chinnery", "given": "Patrick F", "initials": "PF"}, {"family": "Koolmeister", "given": "Camilla", "initials": "C"}, {"family": "Larsson", "given": "Nils-G\u00f6ran", "initials": "NG", "orcid": "0000-0001-5100-996X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a457478920e048b59b225f2561d3e07a.json"}}], "type": "journal article", "published": "2024-10-14", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "volume": "52", "issue": "18", "pages": "11266-11282", "issn-l": "0305-1048"}, "abstract": "In mammals, the leucine-rich pentatricopeptide repeat protein (LRPPRC) and the stem-loop interacting RNA-binding protein (SLIRP) form a complex in the mitochondrial matrix that is required throughout the life cycle of most mitochondrial mRNAs. Although pathogenic mutations in the LRPPRC and SLIRP genes cause devastating human mitochondrial diseases, the in vivo function of the corresponding proteins is incompletely understood. We show here that loss of SLIRP in mice causes a decrease of complex I levels whereas other OXPHOS complexes are unaffected. We generated knock-in mice to study the in vivo interdependency of SLIRP and LRPPRC by mutating specific amino acids necessary for protein complex formation. When protein complex formation is disrupted, LRPPRC is partially degraded and SLIRP disappears. Livers from Lrpprc knock-in mice had impaired mitochondrial translation except for a marked increase in the synthesis of ATP8. Furthermore, the introduction of a heteroplasmic pathogenic mtDNA mutation (m.C5024T of the tRNAAla gene) into Slirp knockout mice causes an additive effect on mitochondrial translation leading to embryonic lethality and reduced growth of mouse embryonic fibroblasts. To summarize, we report that the LRPPRC/SLIRP protein complex is critical for maintaining normal complex I levels and that it also coordinates mitochondrial translation in a tissue-specific manner.", "doi": "10.1093/nar/gkae662", "pmid": "39087558", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC11472161"}, {"db": "pii", "key": "7725477"}], "notes": [], "created": "2026-09-23T09:08:01.732Z", "modified": "2026-09-23T09:08:01.908Z"}, {"entity": "publication", "iuid": "29f9bd60f9ba4469b1e0a71246022d47", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/29f9bd60f9ba4469b1e0a71246022d47.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/29f9bd60f9ba4469b1e0a71246022d47"}}, "title": "WOMBAT-P: Benchmarking Label-Free Proteomics Data Analysis Workflows.", "authors": [{"family": "Bouyssi\u00e9", "given": "David", "initials": "D", "orcid": "0000-0002-0847-4759", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/877b0a0677fb463b829241dc4fc52203.json"}}, {"family": "Alt\u0131ner", "given": "P\u0131nar", "initials": "P"}, {"family": "Capella-Gutierrez", "given": "Salvador", "initials": "S"}, {"family": "Fern\u00e1ndez", "given": "Jos\u00e9 M", "initials": "JM", "orcid": "0000-0002-4806-5140", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3511b21fa18645df8da018bd490e3d20.json"}}, {"family": "Hagemeijer", "given": "Yanick Paco", "initials": "YP", "orcid": "0000-0001-6036-3741", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/76b2c76095b149a89e349830770c5cc7.json"}}, {"family": "Horvatovich", "given": "Peter", "initials": "P", "orcid": "0000-0003-2218-1140", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/15ce5ebac4b546679244f69fbcb5f379.json"}}, {"family": "Hub\u00e1lek", "given": "Martin", "initials": "M", "orcid": "0000-0003-0247-7956", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b9f36f0a91f548a6b1013f619e139c9a.json"}}, {"family": "Levander", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0710-9792", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d3aaa3dcdb4f4e9f9b4bd44097d85d0c.json"}}, {"family": "Mauri", "given": "Pierluigi", "initials": "P"}, {"family": "Palmblad", "given": "Magnus", "initials": "M", "orcid": "0000-0002-5865-8994", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/80053e2256cd4e55afc7ba916821602c.json"}}, {"family": "Raffelsberger", "given": "Wolfgang", "initials": "W"}, {"family": "Rodr\u00edguez-Navas", "given": "Laura", "initials": "L"}, {"family": "Di Silvestre", "given": "Dario", "initials": "D"}, {"family": "Kunkli", "given": "Bal\u00e1zs Tibor", "initials": "BT", "orcid": "0000-0003-1266-2792", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bc333a7d2db94a4baa1a05cad9080753.json"}}, {"family": "Uszkoreit", "given": "Julian", "initials": "J", "orcid": "0000-0001-7522-4007", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/97c6efaaa4f045a7a718ca2ba376f641.json"}}, {"family": "Vandenbrouck", "given": "Yves", "initials": "Y", "orcid": "0000-0002-1292-373X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1ed616edf97c454aa6b79c56e565ce64.json"}}, {"family": "Vizca\u00edno", "given": "Juan Antonio", "initials": "JA", "orcid": "0000-0002-3905-4335", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/81245410f3234e658147bc94f6b3dad2.json"}}, {"family": "Winkelhardt", "given": "Dirk", "initials": "D", "orcid": "0000-0001-8770-2221", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0bc906f12f834e4f8e909a0b8426e0af.json"}}, {"family": "Schw\u00e4mmle", "given": "Veit", "initials": "V", "orcid": "0000-0002-9708-6722", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/158e08b0cfd34f90882f66142d8e62b7.json"}}], "type": "journal article", "published": "2024-01-05", "journal": {"title": "J. Proteome Res.", "issn": "1535-3907", "volume": "23", "issue": "1", "pages": "418-429", "issn-l": "1535-3893"}, "abstract": "The inherent diversity of approaches in proteomics research has led to a wide range of software solutions for data analysis. These software solutions encompass multiple tools, each employing different algorithms for various tasks such as peptide-spectrum matching, protein inference, quantification, statistical analysis, and visualization. To enable an unbiased comparison of commonly used bottom-up label-free proteomics workflows, we introduce WOMBAT-P, a versatile platform designed for automated benchmarking and comparison. WOMBAT-P simplifies the processing of public data by utilizing the sample and data relationship format for proteomics (SDRF-Proteomics) as input. This feature streamlines the analysis of annotated local or public ProteomeXchange data sets, promoting efficient comparisons among diverse outputs. Through an evaluation using experimental ground truth data and a realistic biological data set, we uncover significant disparities and a limited overlap in the quantified proteins. WOMBAT-P not only enables rapid execution and seamless comparison of workflows but also provides valuable insights into the capabilities of different software solutions. These benchmarking metrics are a valuable resource for researchers in selecting the most suitable workflow for their specific data sets. The modular architecture of WOMBAT-P promotes extensibility and customization. The software is available at https://github.com/wombat-p/WOMBAT-Pipelines.", "doi": "10.1021/acs.jproteome.3c00636", "pmid": "38038272", "labels": [], "xrefs": [], "notes": [], "created": "2026-09-23T13:33:30.019Z", "modified": "2026-09-23T13:33:30.315Z"}, {"entity": "publication", "iuid": "b5cd727f95f64f7987ad923d5d234a30", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b5cd727f95f64f7987ad923d5d234a30.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b5cd727f95f64f7987ad923d5d234a30"}}, "title": "PLK1 as a cooperating partner for BCL2-mediated antiapoptotic program in leukemia.", "authors": [{"family": "Shah", "given": "Kinjal", "initials": "K"}, {"family": "Nasimian", "given": "Ahmad", "initials": "A"}, {"family": "Ahmed", "given": "Mehreen", "initials": "M", "orcid": "0000-0002-0422-2343", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/82d8491f507146d296d2729f8f749538.json"}}, {"family": "Al Ashiri", "given": "Lina", "initials": "L"}, {"family": "Denison", "given": "Linn", "initials": "L"}, {"family": "Sime", "given": "Wondossen", "initials": "W", "orcid": "0000-0001-9518-2457", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f63dc2cdaf684332986f4d514522f2a0.json"}}, {"family": "Bendak", "given": "Katerina", "initials": "K"}, {"family": "Kolosenko", "given": "Iryna", "initials": "I"}, {"family": "Siino", "given": "Valentina", "initials": "V"}, {"family": "Levander", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0710-9792", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d3aaa3dcdb4f4e9f9b4bd44097d85d0c.json"}}, {"family": "Palm-Apergi", "given": "Caroline", "initials": "C"}, {"family": "Massoumi", "given": "Ramin", "initials": "R"}, {"family": "Lock", "given": "Richard B", "initials": "RB"}, {"family": "Kazi", "given": "Julhash U", "initials": "JU", "orcid": "0000-0002-0719-5336", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0028666b14dd4763a8d505cb0592aa1a.json"}}], "type": "journal article", "published": "2023-09-07", "journal": {"title": "Blood Cancer J", "issn": "2044-5385", "volume": "13", "issue": "1", "pages": "139", "issn-l": null}, "abstract": "The deregulation of BCL2 family proteins plays a crucial role in leukemia development. Therefore, pharmacological inhibition of this family of proteins is becoming a prevalent treatment method. However, due to the emergence of primary and acquired resistance, efficacy is compromised in clinical or preclinical settings. We developed a drug sensitivity prediction model utilizing a deep tabular learning algorithm for the assessment of venetoclax sensitivity in T-cell acute lymphoblastic leukemia (T-ALL) patient samples. Through analysis of predicted venetoclax-sensitive and resistant samples, PLK1 was identified as a cooperating partner for the BCL2-mediated antiapoptotic program. This finding was substantiated by additional data obtained through phosphoproteomics and high-throughput kinase screening. Concurrent treatment using venetoclax with PLK1-specific inhibitors and PLK1 knockdown demonstrated a greater therapeutic effect on T-ALL cell lines, patient-derived xenografts, and engrafted mice compared with using each treatment separately. Mechanistically, the attenuation of PLK1 enhanced BCL2 inhibitor sensitivity through upregulation of BCL2L13 and PMAIP1 expression. Collectively, these findings underscore the dependency of T-ALL on PLK1 and postulate a plausible regulatory mechanism.", "doi": "10.1038/s41408-023-00914-7", "pmid": "37679323", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10484999"}, {"db": "pii", "key": "10.1038/s41408-023-00914-7"}], "notes": [], "created": "2026-09-23T11:22:18.869Z", "modified": "2026-09-23T11:22:19.007Z"}, {"entity": "publication", "iuid": "0aa05b85298d4a05befb40be22063e8f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0aa05b85298d4a05befb40be22063e8f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0aa05b85298d4a05befb40be22063e8f"}}, "title": "An mTRAN-mRNA interaction mediates mitochondrial translation initiation in plants.", "authors": [{"family": "Tran", "given": "Huy Cuong", "initials": "HC", "orcid": "0000-0002-7670-2215", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e76543b392594e1eb774530c16be45ce.json"}}, {"family": "Schmitt", "given": "Vivian", "initials": "V", "orcid": "0000-0001-9260-4853", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/018e49a9f23946ab8271c5adb3c95653.json"}}, {"family": "Lama", "given": "Sbatie", "initials": "S", "orcid": "0000-0003-0093-8915", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3ba65b049edd46e889585bdc162e6948.json"}}, {"family": "Wang", "given": "Chuande", "initials": "C", "orcid": "0000-0002-3102-0931", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/705243873508474187ec8089fefccee1.json"}}, {"family": "Launay-Avon", "given": "Alexandra", "initials": "A", "orcid": "0000-0002-1993-313X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a8a46fb422d04148ac4e66296798787b.json"}}, {"family": "Bernfur", "given": "Katja", "initials": "K", "orcid": "0000-0002-7927-9563", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9de098f285774da583545f697f7032cf.json"}}, {"family": "Sultan", "given": "Kristin", "initials": "K", "orcid": "0009-0002-5619-517X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6c74258423194f769a20304ce161fe5f.json"}}, {"family": "Khan", "given": "Kasim", "initials": "K", "orcid": "0000-0001-7336-2764", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/768432365858446ea3afe0a28621e16a.json"}}, {"family": "Brunaud", "given": "V\u00e9ronique", "initials": "V", "orcid": "0000-0002-6246-3161", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0e63007c181541d7bf6b612875aed497.json"}}, {"family": "Liehrmann", "given": "Arnaud", "initials": "A", "orcid": "0000-0002-4936-1056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a8156c29daad4b5db25e51df022ac30c.json"}}, {"family": "Castandet", "given": "Beno\u00eet", "initials": "B", "orcid": "0000-0003-1948-8651", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8d0e103bf6394ceda5ff8ea44c7b5eed.json"}}, {"family": "Levander", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0710-9792", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d3aaa3dcdb4f4e9f9b4bd44097d85d0c.json"}}, {"family": "Rasmusson", "given": "Allan G", "initials": "AG", "orcid": "0000-0003-0734-5020", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8714d6bebceb440f9b4d0bb8130ee9f9.json"}}, {"family": "Mireau", "given": "Hakim", "initials": "H", "orcid": "0000-0002-2299-5139", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f272fa0851b8496faf77735ad1513853.json"}}, {"family": "Delannoy", "given": "Etienne", "initials": "E", "orcid": "0000-0002-0866-2063", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/99cbd34b74334565814f4a89a4a0f892.json"}}, {"family": "Van Aken", "given": "Olivier", "initials": "O", "orcid": "0000-0003-4024-968X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/95b452d731194dbf9e04b63a1a22abd8.json"}}], "type": "journal article", "published": "2023-09-00", "journal": {"title": "Science (New York, N.Y.)", "issn": "1095-9203", "volume": "381", "issue": "6661", "pages": "eadg0995", "issn-l": "0036-8075"}, "abstract": "Plant mitochondria represent the largest group of respiring organelles on the planet. Plant mitochondrial messenger RNAs (mRNAs) lack Shine-Dalgarno-like ribosome-binding sites, so it is unknown how plant mitoribosomes recognize mRNA. We show that \"mitochondrial translation factors\" mTRAN1 and mTRAN2 are land plant-specific proteins, required for normal mitochondrial respiration chain biogenesis. Our studies suggest that mTRANs are noncanonical pentatricopeptide repeat (PPR)-like RNA binding proteins of the mitoribosomal \"small\" subunit. We identified conserved Adenosine (A)/Uridine (U)-rich motifs in the 5' regions of plant mitochondrial mRNAs. mTRAN1 binds this motif, suggesting that it is a mitoribosome homing factor to identify mRNAs. We demonstrate that mTRANs are likely required for translation of all plant mitochondrial mRNAs. Plant mitochondrial translation initiation thus appears to use a protein-mRNA interaction that is divergent from bacteria or mammalian mitochondria.", "doi": "10.1126/science.adg0995", "pmid": "37651534", "labels": [], "xrefs": [], "notes": [], "created": "2026-09-23T10:59:21.737Z", "modified": "2026-09-23T10:59:22.568Z"}, {"entity": "publication", "iuid": "7fb050f27f2f4dd29948c98014445db6", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/7fb050f27f2f4dd29948c98014445db6.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/7fb050f27f2f4dd29948c98014445db6"}}, "title": "Choice of High-Throughput Proteomics Method Affects Data Integration with Transcriptomics and the Potential Use in Biomarker Discovery.", "authors": [{"family": "Mosquim Junior", "given": "Sergio", "initials": "S", "orcid": "0000-0002-1537-7252", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/08836688b1b74eeab88cda7b3ed3e488.json"}}, {"family": "Siino", "given": "Valentina", "initials": "V", "orcid": "0000-0002-0489-6380", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b03ef29e68614191b1cd56f3f8606be9.json"}}, {"family": "Ryd\u00e9n", "given": "Lisa", "initials": "L", "orcid": "0000-0001-7515-3130", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e40f8cbccd87481991010cc506b901fa.json"}}, {"family": "Vallon-Christersson", "given": "Johan", "initials": "J", "orcid": "0000-0002-2195-0385", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5a79aa63d75d4ffbb4228bc7c3e16ac4.json"}}, {"family": "Levander", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0710-9792", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d3aaa3dcdb4f4e9f9b4bd44097d85d0c.json"}}], "type": "journal article", "published": "2022-11-23", "journal": {"title": "Cancers (Basel)", "issn": "2072-6694", "volume": "14", "issue": "23", "issn-l": "2072-6694"}, "abstract": "In recent years, several advances have been achieved in breast cancer (BC) classification and treatment. However, overdiagnosis, overtreatment, and recurrent disease are still significant causes of complication and death. Here, we present the development of a protocol aimed at parallel transcriptome and proteome analysis of BC tissue samples using mass spectrometry, via Data Dependent and Independent Acquisitions (DDA and DIA). Protein digestion was semi-automated and performed on flowthroughs after RNA extraction. Data for 116 samples were acquired in DDA and DIA modes and processed using MaxQuant, EncyclopeDIA, or DIA-NN. DIA-NN showed an increased number of identified proteins, reproducibility, and correlation with matching RNA-seq data, therefore representing the best alternative for this setup. Gene Set Enrichment Analysis pointed towards complementary information being found between transcriptomic and proteomic data. A decision tree model, designed to predict the intrinsic subtypes based on differentially abundant proteins across different conditions, selected protein groups that recapitulate important clinical features, such as estrogen receptor status, HER2 status, proliferation, and aggressiveness. Taken together, our results indicate that the proposed protocol performed well for the application. Additionally, the relevance of the selected proteins points to the possibility of using such data as a biomarker discovery tool for personalized medicine.", "doi": "10.3390/cancers14235761", "pmid": "36497242", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC9736226"}, {"db": "pii", "key": "cancers14235761"}], "notes": [], "created": "2026-09-23T12:11:41.112Z", "modified": "2026-09-23T12:11:41.163Z"}, {"entity": "publication", "iuid": "19cc4919ae204388904fdae4fb3c21d8", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/19cc4919ae204388904fdae4fb3c21d8.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/19cc4919ae204388904fdae4fb3c21d8"}}, "title": "Plasma proteome profiling of healthy individuals across the life span in a Sicilian cohort with long-lived individuals.", "authors": [{"family": "Siino", "given": "Valentina", "initials": "V", "orcid": "0000-0002-0489-6380", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b03ef29e68614191b1cd56f3f8606be9.json"}}, {"family": "Ali", "given": "Ashfaq", "initials": "A", "orcid": "0000-0002-0164-2166", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ee7617286a8c47f9b1ac9343a417ab71.json"}}, {"family": "Accardi", "given": "Giulia", "initials": "G", "orcid": "0000-0003-3565-9529", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5c4a1133c0d64cb086c82df6f2f71b6a.json"}}, {"family": "Aiello", "given": "Anna", "initials": "A", "orcid": "0000-0003-2593-3221", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/df0abb04e1654814929411a55c845387.json"}}, {"family": "Ligotti", "given": "Mattia E", "initials": "ME"}, {"family": "Mosquim Junior", "given": "Sergio", "initials": "S"}, {"family": "Candore", "given": "Giuseppina", "initials": "G", "orcid": "0000-0002-9966-934X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7319de1ea5914c59a30a493cde505b07.json"}}, {"family": "Caruso", "given": "Calogero", "initials": "C", "orcid": "0000-0001-8004-2363", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a6ba0026e36643679376f7552240c3da.json"}}, {"family": "Levander", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0710-9792", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d3aaa3dcdb4f4e9f9b4bd44097d85d0c.json"}}, {"family": "Vasto", "given": "Sonya", "initials": "S", "orcid": "0000-0002-6033-4745", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/624a61c7e0cd43c4ade30bf7ca0e7dda.json"}}], "type": "journal article", "published": "2022-09-00", "journal": {"title": "Aging Cell", "issn": "1474-9726", "volume": "21", "issue": "9", "pages": "e13684", "issn-l": "1474-9718"}, "abstract": "The study of healthy human aging is important for shedding light on the molecular mechanisms behind aging to promote well-being and to possibly predict and/or avoid the development of age-related disorders such as atherosclerosis and diabetes. Herein, we have employed an untargeted mass spectrometry-based approach to study age-related protein changes in a healthy Sicilian plasma cohort including long-lived individuals. This approach confirmed some of the previously known proteins correlated with age including fibulin-1, dystroglycan, and gamma-glutamyl hydrolase. Furthermore, our findings include novel proteins that correlate with age and/or with location and uric acid, which could represent a unique signature for healthy aging.", "doi": "10.1111/acel.13684", "pmid": "35932462", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC9470904"}], "notes": [], "created": "2026-09-23T10:08:03.919Z", "modified": "2026-09-23T10:46:09.830Z"}, {"entity": "publication", "iuid": "363043c4289941499ab1c31c5c9a486f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/363043c4289941499ab1c31c5c9a486f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/363043c4289941499ab1c31c5c9a486f"}}, "title": "Leaf Apoplast of Field-Grown Potato Analyzed by Quantitative Proteomics and Activity-Based Protein Profiling.", "authors": [{"family": "Abreha", "given": "Kibrom B", "initials": "KB", "orcid": "0000-0001-8084-8340", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/30c88290bd9c40c4a0ff1a8f5bf30950.json"}}, {"family": "Alexandersson", "given": "Erik", "initials": "E", "orcid": "0000-0001-6320-2492", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f69d28b493fe4cf4ac56b0c2f3c0e4fb.json"}}, {"family": "Resj\u00f6", "given": "Svante", "initials": "S"}, {"family": "Lankinen", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Sueldo", "given": "Daniela", "initials": "D"}, {"family": "Kaschani", "given": "Farnusch", "initials": "F"}, {"family": "Kaiser", "given": "Markus", "initials": "M"}, {"family": "van der Hoorn", "given": "Renier A L", "initials": "RAL"}, {"family": "Levander", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0710-9792", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d3aaa3dcdb4f4e9f9b4bd44097d85d0c.json"}}, {"family": "Andreasson", "given": "Erik", "initials": "E", "orcid": "0000-0003-0666-7204", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/af7248cae3a54a8ba4624ccf8b59df41.json"}}], "type": "journal article", "published": "2021-11-06", "journal": {"title": "Int J Mol Sci", "issn": "1422-0067", "volume": "22", "issue": "21", "issn-l": null}, "abstract": "Multiple biotic and abiotic stresses challenge plants growing in agricultural fields. Most molecular studies have aimed to understand plant responses to challenges under controlled conditions. However, studies on field-grown plants are scarce, limiting application of the findings in agricultural conditions. In this study, we investigated the composition of apoplastic proteomes of potato cultivar Bintje grown under field conditions, i.e., two field sites in June-August across two years and fungicide treated and untreated, using quantitative proteomics, as well as its activity using activity-based protein profiling (ABPP). Samples were clustered and some proteins showed significant intensity and activity differences, based on their field site and sampling time (June-August), indicating differential regulation of certain proteins in response to environmental or developmental factors. Peroxidases, class II chitinases, pectinesterases, and osmotins were among the proteins more abundant later in the growing season (July-August) as compared to early in the season (June). We did not detect significant differences between fungicide Shirlan treated and untreated field samples in two growing seasons. Using ABPP, we showed differential activity of serine hydrolases and \u03b2-glycosidases under greenhouse and field conditions and across a growing season. Furthermore, the activity of serine hydrolases and \u03b2-glycosidases, including proteins related to biotic stress tolerance, decreased as the season progressed. The generated proteomics data would facilitate further studies aiming at understanding mechanisms of molecular plant physiology in agricultural fields and help applying effective strategies to mitigate biotic and abiotic stresses.", "doi": "10.3390/ijms222112033", "pmid": "34769464", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC8584485"}, {"db": "pii", "key": "ijms222112033"}], "notes": [], "created": "2026-09-23T12:59:02.467Z", "modified": "2026-09-23T12:59:02.629Z"}, {"entity": "publication", "iuid": "bed7acd1d73543e987fff2a1492a3dfd", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/bed7acd1d73543e987fff2a1492a3dfd.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/bed7acd1d73543e987fff2a1492a3dfd"}}, "title": "High-Resolution Proteomic Profiling Shows Sexual Dimorphism in Zebrafish Heart-Associated Proteins.", "authors": [{"family": "Niksirat", "given": "Hamid", "initials": "H", "orcid": "0000-0003-3782-4954", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/04537c6d5bbd494dac909ea633c3dc20.json"}}, {"family": "Siino", "given": "Valentina", "initials": "V"}, {"family": "Steinbach", "given": "Christoph", "initials": "C"}, {"family": "Levander", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0710-9792", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d3aaa3dcdb4f4e9f9b4bd44097d85d0c.json"}}], "type": "journal article", "published": "2021-08-06", "journal": {"title": "J. Proteome Res.", "issn": "1535-3907", "volume": "20", "issue": "8", "pages": "4075-4088", "issn-l": "1535-3893"}, "abstract": "Understanding the molecular basis of sexual dimorphism in the cardiovascular system may contribute to the improvement of the outcome in biological, pharmacological, and toxicological studies as well as on the development of sex-based drugs and therapeutic approaches. Label-free protein quantification using high-resolution mass spectrometry was applied to detect sex-based proteome differences in the heart of zebrafish Danio rerio. Out of almost 3000 unique identified proteins in the heart, 79 showed significant abundance differences between male and female fish. The functional differences were mapped using enrichment analyses. Our results suggest that a large amount of materials needed for reproduction (e.g., sugars, lipids, proteins, etc.) may impose extra pressure on blood, vessels, and heart on their way toward the ovaries. In the present study, the female's heart shows a clear sexual dimorphism by changing abundance levels of numerous proteins, which could be a way to safely overcome material-induced elevated pressures. These proteins belong to the immune system, oxidative stress response, drug metabolization, detoxification, energy, metabolism, and so on. In conclusion, we showed that sex can induce dimorphism at the molecular level in nonsexual organs such as heart and must be considered as an important factor in cardiovascular research. Data are available via ProteomeXchange with identifier PXD023506.", "doi": "10.1021/acs.jproteome.1c00387", "pmid": "34185526", "labels": [], "xrefs": [], "notes": [], "created": "2026-09-23T11:53:00.208Z", "modified": "2026-09-23T11:53:00.246Z"}, {"entity": "publication", "iuid": "facc17ad591043bdb1af83e97b11a4fb", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/facc17ad591043bdb1af83e97b11a4fb.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/facc17ad591043bdb1af83e97b11a4fb"}}, "title": "OmicLoupe: facilitating biological discovery by interactive exploration of multiple omic datasets and statistical comparisons.", "authors": [{"family": "Willforss", "given": "Jakob", "initials": "J"}, {"family": "Siino", "given": "Valentina", "initials": "V"}, {"family": "Levander", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0710-9792", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d3aaa3dcdb4f4e9f9b4bd44097d85d0c.json"}}], "type": "journal article", "published": "2021-03-04", "journal": {"title": "BMC Bioinformatics", "issn": "1471-2105", "volume": "22", "issue": "1", "pages": "107", "issn-l": "1471-2105"}, "abstract": "Visual exploration of gene product behavior across multiple omic datasets can pinpoint technical limitations in data and reveal biological trends. Still, such exploration is challenging as there is a need for visualizations that are tailored for the purpose.\n\nThe OmicLoupe software was developed to facilitate visual data exploration and provides more than 15 interactive cross-dataset visualizations for omics data. It expands visualizations to multiple datasets for quality control, statistical comparisons and overlap and correlation analyses, while allowing for rapid inspection and downloading of selected features. The usage of OmicLoupe is demonstrated in three different studies, where it allowed for detection of both technical data limitations and biological trends across different omic layers. An example is an analysis of SARS-CoV-2 infection based on two previously published studies, where OmicLoupe facilitated the identification of gene products with consistent expression changes across datasets at both the transcript and protein levels.\n\nOmicLoupe provides fast exploration of omics data with tailored visualizations for comparisons within and across data layers. The interactive visualizations are highly informative and are expected to be useful in various analyses of both newly generated and previously published data. OmicLoupe is available at quantitativeproteomics.org/omicloupe.", "doi": "10.1186/s12859-021-04043-5", "pmid": "33663372", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC7931979"}, {"db": "pii", "key": "10.1186/s12859-021-04043-5"}], "notes": [], "created": "2026-09-23T11:00:35.763Z", "modified": "2026-09-23T11:00:35.825Z"}, {"entity": "publication", "iuid": "3bdf9df99988436aa514c33ba81f0de5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3bdf9df99988436aa514c33ba81f0de5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3bdf9df99988436aa514c33ba81f0de5"}}, "title": "OmicLoupe: Facilitating biological discovery by interactive exploration of multiple omic datasets and statistical comparisons", "authors": [{"family": "Willforss", "given": "Jakob", "initials": "J"}, {"family": "Siino", "given": "Valentina", "initials": "V"}, {"family": "Levander", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0710-9792", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d3aaa3dcdb4f4e9f9b4bd44097d85d0c.json"}}], "type": "posted-content", "published": "2020-10-22", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2020.10.22.349944", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T09:59:36.844Z", "modified": "2026-09-23T14:31:01.669Z"}, {"entity": "publication", "iuid": "cca4db03747946478f4549164d9eb849", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/cca4db03747946478f4549164d9eb849.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/cca4db03747946478f4549164d9eb849"}}, "title": "Towards a standardized bioinformatics infrastructure for N- and O-glycomics.", "authors": [{"family": "Rojas-Macias", "given": "Miguel A", "initials": "MA"}, {"family": "Mariethoz", "given": "Julien", "initials": "J", "orcid": "0000-0001-8974-4417", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/950dfb0f623241b194cbc73353c2cbcd.json"}}, {"family": "Andersson", "given": "Peter", "initials": "P"}, {"family": "Jin", "given": "Chunsheng", "initials": "C"}, {"family": "Venkatakrishnan", "given": "Vignesh", "initials": "V", "orcid": "0000-0001-5671-1547", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/14e0a16d5fa24934a7c3579ef6ff0bf3.json"}}, {"family": "Aoki", "given": "Nobuyuki P", "initials": "NP"}, {"family": "Shinmachi", "given": "Daisuke", "initials": "D", "orcid": "0000-0002-2591-3987", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4ce8f794aed74c649b554dc3f4314be4.json"}}, {"family": "Ashwood", "given": "Christopher", "initials": "C", "orcid": "0000-0001-5944-6179", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ccff636a2ca4e78a920d5b708ca710f.json"}}, {"family": "Madunic", "given": "Katarina", "initials": "K", "orcid": "0000-0002-9310-4110", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7a592cb9d7214c97a076eee799cf24c6.json"}}, {"family": "Zhang", "given": "Tao", "initials": "T"}, {"family": "Miller", "given": "Rebecca L", "initials": "RL", "orcid": "0000-0001-8574-1948", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1841c5b27fd54915a28cf8f044c94aa8.json"}}, {"family": "Horlacher", "given": "Oliver", "initials": "O"}, {"family": "Struwe", "given": "Weston B", "initials": "WB"}, {"family": "Watanabe", "given": "Yu", "initials": "Y"}, {"family": "Okuda", "given": "Shujiro", "initials": "S", "orcid": "0000-0002-7704-8104", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a5e1a0e6688d40d899b2e11349a1f406.json"}}, {"family": "Levander", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0710-9792", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d3aaa3dcdb4f4e9f9b4bd44097d85d0c.json"}}, {"family": "Kolarich", "given": "Daniel", "initials": "D", "orcid": "0000-0002-8452-1350", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/14374e53213348daa0598b92d87219de.json"}}, {"family": "Rudd", "given": "Pauline M", "initials": "PM"}, {"family": "Wuhrer", "given": "Manfred", "initials": "M"}, {"family": "Kettner", "given": "Carsten", "initials": "C", "orcid": "0000-0002-8697-6842", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b462e7906cbd494488035045e227c6e0.json"}}, {"family": "Packer", "given": "Nicolle H", "initials": "NH", "orcid": "0000-0002-7532-4021", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9f88f96eb06e40718d01e4ae2d01916f.json"}}, {"family": "Aoki-Kinoshita", "given": "Kiyoko F", "initials": "KF", "orcid": "0000-0002-6662-8015", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ac843f0320cc48948f948928d2149add.json"}}, {"family": "Lisacek", "given": "Fr\u00e9d\u00e9rique", "initials": "F", "orcid": "0000-0002-0948-4537", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/76908c4fa6f8427d84e5edfc56f49b0a.json"}}, {"family": "Karlsson", "given": "Niclas G", "initials": "NG", "orcid": "0000-0002-3045-2628", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1c08a75b6d56459bbd00e8e3fe8004bf.json"}}], "type": "journal article", "published": "2019-07-22", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "10", "issue": "1", "pages": "3275", "issn-l": "2041-1723"}, "abstract": "The mass spectrometry (MS)-based analysis of free polysaccharides and glycans released from proteins, lipids and proteoglycans increasingly relies on databases and software. Here, we review progress in the bioinformatics analysis of protein-released N- and O-linked glycans (N- and O-glycomics) and propose an e-infrastructure to overcome current deficits in data and experimental transparency. This workflow enables the standardized submission of MS-based glycomics information into the public repository UniCarb-DR. It implements the MIRAGE (Minimum Requirement for A Glycomics Experiment) reporting guidelines, storage of unprocessed MS data in the GlycoPOST repository and glycan structure registration using the GlyTouCan registry, thereby supporting the development and extension of a glycan structure knowledgebase.", "doi": "10.1038/s41467-019-11131-x", "pmid": "31332201", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC6796180"}, {"db": "pii", "key": "10.1038/s41467-019-11131-x"}], "notes": [], "created": "2026-09-23T07:39:01.722Z", "modified": "2026-09-23T07:39:02.353Z"}, {"entity": "publication", "iuid": "8a0c5479a86f415a96cf2384d4b45e48", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8a0c5479a86f415a96cf2384d4b45e48.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8a0c5479a86f415a96cf2384d4b45e48"}}, "title": "NormalyzerDE: Online Tool for Improved Normalization of Omics Expression Data and High-Sensitivity Differential Expression Analysis.", "authors": [{"family": "Willforss", "given": "Jakob", "initials": "J"}, {"family": "Chawade", "given": "Aakash", "initials": "A"}, {"family": "Levander", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0710-9792", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d3aaa3dcdb4f4e9f9b4bd44097d85d0c.json"}}], "type": "journal article", "published": "2019-02-01", "journal": {"title": "J. Proteome Res.", "issn": "1535-3907", "volume": "18", "issue": "2", "pages": "732-740", "issn-l": "1535-3893"}, "abstract": "Technical biases are introduced in omics data sets during data generation and interfere with the ability to study biological mechanisms. Several normalization approaches have been proposed to minimize the effects of such biases, but fluctuations in the electrospray current during liquid chromatography-mass spectrometry gradients cause local and sample-specific bias not considered by most approaches. Here we introduce a software named NormalyzerDE that includes a generic retention time (RT)-segmented approach compatible with a wide range of global normalization approaches to reduce the effects of time-resolved bias. The software offers straightforward access to multiple normalization methods, allows for data set evaluation and normalization quality assessment as well as subsequent or independent differential expression analysis using the empirical Bayes Limma approach. When evaluated on two spike-in data sets the RT-segmented approaches outperformed conventional approaches by detecting more peptides (8-36%) without loss of precision. Furthermore, differential expression analysis using the Limma approach consistently increased recall (2-35%) compared to analysis of variance. The combination of RT-normalization and Limma was in one case able to distinguish 108% (2597 vs 1249) more spike-in peptides compared to traditional approaches. NormalyzerDE provides widely usable tools for performing normalization and evaluating the outcome and makes calculation of subsequent differential expression statistics straightforward. The program is available as a web server at http://quantitativeproteomics.org/normalyzerde .", "doi": "10.1021/acs.jproteome.8b00523", "pmid": "30277078", "labels": [], "xrefs": [], "notes": [], "created": "2026-09-23T06:40:41.352Z", "modified": "2026-09-23T06:40:41.371Z"}]}