{"entity": "researcher", "timestamp": "2026-08-20T20:50:11.564Z", "family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "affiliations": ["Science for Life Laboratory Department of Biochemistry and Biophysics Stockholm University  Box 1031 Se-171 21 Solna Sweden"], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/3311155f09a64b4f88d673da2a40627b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/3311155f09a64b4f88d673da2a40627b"}}, "publications": [{"entity": "publication", "iuid": "ea277b458a2b4444aef52213bc5d355e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ea277b458a2b4444aef52213bc5d355e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ea277b458a2b4444aef52213bc5d355e"}}, "title": "A dual genetic constraint underlies the conservation of early brains in vertebrates", "authors": [{"family": "Senovilla-Ganzo", "given": "Rodrigo", "initials": "R", "orcid": "0000-0001-6615-0923", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9378f3be005344eab9287605a6cc8352.json"}}, {"family": "Bekiari", "given": "Christina", "initials": "C"}, {"family": "Rueda-Ala\u00f1a", "given": "Eneritz", "initials": "E", "orcid": "0000-0003-3045-4970", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/53052de34774443d922c19887a8aa0f5.json"}}, {"family": "Yamada", "given": "Tetsuya", "initials": "T", "orcid": "0000-0001-8601-737X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1abdce0223ba4e2baf064c88a10161e1.json"}}, {"family": "Zaremba", "given": "Bastienne", "initials": "B", "orcid": "0000-0002-2195-5135", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b49f1217d7524fc78fdf70856dcb9868.json"}}, {"family": "Aransay", "given": "Ana Mar\u00eda", "initials": "AM", "orcid": "0000-0002-8271-612X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c8a11379529b4769a5f8b5a989e99330.json"}}, {"family": "Escobar", "given": "Laura", "initials": "L", "orcid": "0000-0003-0955-2015", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a0de21df1c024eca98c19c758f61e93e.json"}}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3311155f09a64b4f88d673da2a40627b.json"}}, {"family": "Grillo", "given": "Marco", "initials": "M", "orcid": "0000-0003-2155-0645", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c1e82de1e6bb4c738b8e9868419e59bf.json"}}, {"family": "Kaessmann", "given": "Henrik", "initials": "H", "orcid": "0000-0001-7563-839X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/81746d8b287e4ed88957c347af706125.json"}}, {"family": "Garc\u00eda-Moreno", "given": "Fernando", "initials": "F", "orcid": "0000-0001-9048-4237", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/829813abf875418a8aa1d59c47e41355.json"}}], "type": "posted-content", "published": "2025-10-29", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2025.10.29.684766", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T11:07:21.097Z", "modified": "2026-08-20T11:07:21.305Z"}, {"entity": "publication", "iuid": "017b47745d074ea3a0a865050f8fce96", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/017b47745d074ea3a0a865050f8fce96.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/017b47745d074ea3a0a865050f8fce96"}}, "title": "Charting the single-cell and spatial landscape of IDH-wild-type glioblastoma with GBmap.", "authors": [{"family": "Ruiz-Moreno", "given": "Cristian", "initials": "C", "orcid": "0000-0001-9689-7964", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/32b30077d80d49d1a69e1619bbadcdff.json"}}, {"family": "Salas", "given": "Sergio Marco", "initials": "SM"}, {"family": "Samuelsson", "given": "Erik", "initials": "E"}, {"family": "Minaeva", "given": "Mariia", "initials": "M"}, {"family": "Ibarra", "given": "Ignacio", "initials": "I"}, {"family": "Grillo", "given": "Marco", "initials": "M"}, {"family": "Brandner", "given": "Sebastian", "initials": "S", "orcid": "0000-0002-8635-7195", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/84649d36adbc4e088c2c7362b9fb3b61.json"}}, {"family": "Roy", "given": "Ananya", "initials": "A"}, {"family": "Forsberg-Nilsson", "given": "Karin", "initials": "K", "orcid": "0000-0003-0692-6245", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6636b7d9d0e24ac2a15ccd0e9f631ed1.json"}}, {"family": "Kranendonk", "given": "Mariette E G", "initials": "MEG"}, {"family": "Theis", "given": "Fabian J", "initials": "FJ"}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3311155f09a64b4f88d673da2a40627b.json"}}, {"family": "Stunnenberg", "given": "Hendrik G", "initials": "HG", "orcid": "0000-0002-0066-1576", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5cadcfd26eea4310a8d2cdcffcd15627.json"}}], "type": "journal article", "published": "2025-10-14", "journal": {"title": "Neuro-oncology", "issn": "1523-5866", "volume": "27", "issue": "9", "pages": "2281-2295", "issn-l": "1522-8517"}, "abstract": "Glioblastoma (GB), particularly IDH-wild type, is the most aggressive brain malignancy with a dismal prognosis. Despite advances in molecular profiling, the complexity of its tumor microenvironment and spatial organization remains poorly understood. This study aimed to create a comprehensive single-cell and spatial atlas of GB to unravel its cellular heterogeneity, spatial architecture, and clinical relevance.\n\nWe integrated single-cell RNA sequencing data from 26 datasets, encompassing over 1.1 million cells from 240 patients, to construct GBmap, a harmonized single-cell atlas. High-resolution spatial transcriptomics was employed to map the spatial organization of GB tissues. We developed the Tumor Structure Score (TSS) to quantify tumor organization and correlated it with patient outcomes.\n\nWe showcase the applications of GBmap for reference mapping, transfer learning, and biological discoveries. GBmap revealed extensive cellular heterogeneity, identifying rare populations such as tumor-associated neutrophils and homeostatic microglia. Spatial analysis uncovered 7 distinct tumor niches, with hypoxia-dependent niches strongly associated with poor prognosis. The TSS demonstrated that highly organized tumors, characterized by well-defined vasculature and hypoxic niches, correlated with worse survival outcomes.\n\nThis study provides a comprehensive resource for understanding glioblastoma heterogeneity and spatial organization. GBmap and the TSS provide an integrative view of tumor architecture in GB, highlighting hypoxia-driven niches that may represent avenues for further investigation. Our resource can facilitate exploratory analyses and hypothesis generation to better understand disease progression.", "doi": "10.1093/neuonc/noaf113", "pmid": "40312969", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC12526130"}, {"db": "pii", "key": "8123663"}], "notes": [], "created": "2026-08-20T09:51:15.109Z", "modified": "2026-08-20T09:51:15.250Z"}, {"entity": "publication", "iuid": "b2c6bf3eb7e541a69181519aa0f55db5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b2c6bf3eb7e541a69181519aa0f55db5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b2c6bf3eb7e541a69181519aa0f55db5"}}, "title": "Spatial miRNomics: towards the integration of microRNAs in spatial biology.", "authors": [{"family": "Robles-Remacho", "given": "Agust\u00edn", "initials": "A", "orcid": "0000-0002-8442-9749", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/83af64a989f148328cf1f5df3661459c.json"}}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3311155f09a64b4f88d673da2a40627b.json"}}], "type": "journal article", "published": "2025-05-00", "journal": {"title": "Nat. Rev. Genet.", "issn": "1471-0064", "volume": "26", "issue": "5", "pages": "291-292", "issn-l": "1471-0056"}, "abstract": null, "doi": "10.1038/s41576-025-00819-0", "pmid": "39915688", "labels": [], "xrefs": [{"db": "pii", "key": "10.1038/s41576-025-00819-0"}], "notes": [], "created": "2026-08-20T08:55:44.126Z", "modified": "2026-08-20T08:55:44.234Z"}, {"entity": "publication", "iuid": "c27f8ba354134aad9f87675dfe5b98b9", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c27f8ba354134aad9f87675dfe5b98b9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c27f8ba354134aad9f87675dfe5b98b9"}}, "title": "Oligodendroglia vulnerability in the human dorsal striatum in Parkinson\u2019s disease", "authors": [{"family": "Barba-Reyes", "given": "Juan M", "initials": "JM", "orcid": "0000-0003-2955-6005", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/59f73b96a3fa4f3b9c2815e5b4401812.json"}}, {"family": "Harder", "given": "Lisbeth", "initials": "L", "orcid": "0000-0002-0637-720X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/681ed4cd72fc41709b33cdcfb30d81e1.json"}}, {"family": "Salas", "given": "Sergio Marco", "initials": "SM", "orcid": "0000-0002-4636-0322", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/68b3baa22ffe41c0aa352075c6ea70b9.json"}}, {"family": "Jaisa-aad", "given": "Methasit", "initials": "M", "orcid": "0000-0003-2994-2416", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cb364e2fc21f4f91accb2e12b8794fb0.json"}}, {"family": "Mu\u00f1oz-Castro", "given": "Clara", "initials": "C", "orcid": "0000-0002-4484-9802", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e5019283d2e42f3bdef23af5ded1a39.json"}}, {"family": "Rafati", "given": "Nima", "initials": "N", "orcid": "0000-0002-3687-9745", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0210ddd9d2c74696ae194924182e09d7.json"}}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3311155f09a64b4f88d673da2a40627b.json"}}, {"family": "Hyman", "given": "Bradley T", "initials": "BT", "orcid": "0000-0002-7959-9401", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9c757e4b540d490e80960dca4d90ef5d.json"}}, {"family": "Serrano-Pozo", "given": "Alberto", "initials": "A", "orcid": "0000-0003-0899-7530", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/30f468ad4acc4fc890841b5d4ac1d3c6.json"}}, {"family": "Mu\u00f1oz-Manchado", "given": "Ana B", "initials": "AB", "orcid": "0000-0002-1121-6072", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4bce0de777144d7389fbb29bb3e246bb.json"}}], "type": "posted-content", "published": "2025-01-20", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2025.01.15.633167", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:59:49.905Z", "modified": "2026-08-20T10:59:50.205Z"}, {"entity": "publication", "iuid": "eb35d0943db84a02b9c0d6ff9edf202d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/eb35d0943db84a02b9c0d6ff9edf202d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/eb35d0943db84a02b9c0d6ff9edf202d"}}, "title": "Spatial Transcriptome Mapping of the Desmoplastic Growth Pattern of Colorectal Liver Metastases by In Situ Sequencing Reveals a Biologically Relevant Zonation of the Desmoplastic Rim.", "authors": [{"family": "Andersson", "given": "Axel", "initials": "A", "orcid": "0000-0002-4714-3127", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/914750c9b0b74160a2c114cfd8e89a22.json"}}, {"family": "Escriva Conde", "given": "Maria", "initials": "M", "orcid": "0009-0005-3891-8794", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ced4721da9964547a0bb4d3a93110e9d.json"}}, {"family": "Surova", "given": "Olga", "initials": "O", "orcid": "0009-0004-8554-9779", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bcfcc2f0d55d4949bbd3eaf9e5c54564.json"}}, {"family": "Vermeulen", "given": "Peter", "initials": "P", "orcid": "0000-0002-5676-3141", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fee9f1031386431899759ebb5112e56a.json"}}, {"family": "W\u00e4hlby", "given": "Carolina", "initials": "C", "orcid": "0000-0002-4139-7003", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/833afe3444d84c24be12ea1468563bea.json"}}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3311155f09a64b4f88d673da2a40627b.json"}}, {"family": "Nystr\u00f6m", "given": "Hanna", "initials": "H", "orcid": "0000-0003-4595-5399", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/51cf5be83afc418ca83a322aad23808b.json"}}], "type": "journal article", "published": "2024-10-01", "journal": {"title": "Clin. Cancer Res.", "issn": "1557-3265", "volume": "30", "issue": "19", "pages": "4517-4529", "issn-l": "1078-0432"}, "abstract": "We describe the fibrotic rim formed in the desmoplastic histopathologic growth pattern (DHGP) of colorectal cancer liver metastasis (CLM) using in situ sequencing (ISS). The origin of the desmoplastic rim is still a matter of debate, and the detailed cellular organization has not yet been fully elucidated. Understanding the biology of the DHGP in CLM can lead to targeted treatment and improve survival.\n\nWe used ISS, targeting 150 genes, to characterize the desmoplastic rim by unsupervised clustering of gene coexpression patterns. The cohort comprised 10 chemo-na\u00efve liver metastasis resection samples with a DHGP.\n\nUnsupervised clustering of spatially mapped genes revealed molecular and cellular diversity within the desmoplastic rim. We confirmed the presence of the ductular reaction and cancer-associated fibroblasts. Importantly, we discovered angiogenesis and outer and inner zonation in the rim, characterized by nerve growth factor receptor and periostin expression.\n\nISS enabled the analysis of the cellular organization of the fibrous rim surrounding CLM with a DHGP and suggests a transition from the outer part of the rim, with nonspecific liver injury response, into the inner part, with gene expression indicating collagen synthesis and extracellular matrix remodeling influenced by the interaction with cancer cells, creating a cancer cell-supportive environment. Moreover, we found angiogenic processes in the rim. Our results provide a potential explanation of the origin of the rim in DHGP and lead to exploring novel targeted treatments for patients with CLM to improve survival.", "doi": "10.1158/1078-0432.CCR-23-3461", "pmid": "39052239", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC11443209"}, {"db": "pii", "key": "746698"}], "notes": [], "created": "2026-08-20T12:12:22.807Z", "modified": "2026-08-20T12:12:23.056Z"}, {"entity": "publication", "iuid": "a5455ddff2c44fe496143a36a2371e3e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a5455ddff2c44fe496143a36a2371e3e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a5455ddff2c44fe496143a36a2371e3e"}}, "title": "Open-source, high-throughput targeted in situ transcriptomics for developmental and tissue biology.", "authors": [{"family": "Lee", "given": "Hower", "initials": "H", "orcid": "0000-0002-8781-3623", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3fd12772d55148518ab8944c401d3820.json"}}, {"family": "Langseth", "given": "Christoffer Mattsson", "initials": "CM", "orcid": "0000-0003-2230-8594", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4d73b090432c4a5397dfe4d8433c72cf.json"}}, {"family": "Salas", "given": "Sergio Marco", "initials": "SM", "orcid": "0000-0002-4636-0322", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/68b3baa22ffe41c0aa352075c6ea70b9.json"}}, {"family": "Sariyar", "given": "Sanem", "initials": "S", "orcid": "0000-0003-0735-5595", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/218ce8c5fb3348f9b04304b811808d4b.json"}}, {"family": "Metousis", "given": "Andreas", "initials": "A", "orcid": "0000-0002-1043-6591", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/beef3eed629e4d11adeb46fc5af35799.json"}}, {"family": "Rueda-Ala\u00f1a", "given": "Eneritz", "initials": "E", "orcid": "0000-0003-3045-4970", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/53052de34774443d922c19887a8aa0f5.json"}}, {"family": "Bekiari", "given": "Christina", "initials": "C", "orcid": "0009-0006-7735-9830", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/200a07e0a1b04f1983c34b7ad54e7cb5.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb07e6d0122c4528a927c1fe922e3bc8.json"}}, {"family": "Garc\u0131 A-Moreno", "given": "Fernando", "initials": "F", "orcid": "0000-0001-9048-4237", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/829813abf875418a8aa1d59c47e41355.json"}}, {"family": "Grillo", "given": "Marco", "initials": "M", "orcid": "0000-0003-2155-0645", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c1e82de1e6bb4c738b8e9868419e59bf.json"}}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3311155f09a64b4f88d673da2a40627b.json"}}], "type": "journal article", "published": "2024-08-15", "journal": {"title": "Development", "issn": "1477-9129", "volume": "151", "issue": "16", "issn-l": "0950-1991"}, "abstract": "Multiplexed spatial profiling of mRNAs has recently gained traction as a tool to explore the cellular diversity and the architecture of tissues. We propose a sensitive, open-source, simple and flexible method for the generation of in situ expression maps of hundreds of genes. We use direct ligation of padlock probes on mRNAs, coupled with rolling circle amplification and hybridization-based in situ combinatorial barcoding, to achieve high detection efficiency, high-throughput and large multiplexing. We validate the method across a number of species and show its use in combination with orthogonal methods such as antibody staining, highlighting its potential value for developmental and tissue biology studies. Finally, we provide an end-to-end computational workflow that covers the steps of probe design, image processing, data extraction, cell segmentation, clustering and annotation of cell types. 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{"family": "Wang", "given": "Su", "initials": "S"}, {"family": "Castillo", "given": "David", "initials": "D"}, {"family": "Langseth", "given": "Christoffer Mattsson", "initials": "CM"}, {"family": "Nguyen", "given": "Huy", "initials": "H"}, {"family": "Chattoraj", "given": "Shyamtanu", "initials": "S", "orcid": "0000-0001-8596-296X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c2dab4c0bc5b4541af2cb9fffd1bd03a.json"}}, {"family": "Casals", "given": "Anna Martinez", "initials": "AM"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb07e6d0122c4528a927c1fe922e3bc8.json"}}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3311155f09a64b4f88d673da2a40627b.json"}}, {"family": "Marti-Renom", "given": "Marc", "initials": "M", "orcid": "0000-0002-0151-4279", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/62d556042a4d4bbb98fcd1919c30ab80.json"}}, {"family": "Wu", "given": "Chao ting", "initials": "Ct"}, {"family": "Crosetto", "given": "Nicola", "initials": "N", "orcid": "0000-0002-3019-6978", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0b1cef698ae749749b4017dbacb9e3db.json"}}, {"family": "Bienko", "given": "Magda", "initials": "M", "orcid": "0000-0002-6499-9082", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4b8da7a1f8524d0e812c83b1f5e20ef6.json"}}], "type": "posted-content", "published": "2022-02-02", "journal": {"issn-l": null}, "abstract": null, "doi": "10.21203/rs.3.rs-1303463/v1", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T12:58:10.026Z", "modified": "2026-08-20T12:58:10.148Z"}, {"entity": "publication", "iuid": "fe982b67c3ab4f9fb2b22f04a23442d6", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/fe982b67c3ab4f9fb2b22f04a23442d6.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/fe982b67c3ab4f9fb2b22f04a23442d6"}}, "title": "Rolling Circle Amplification in Integrated Microsystems: An Uncut Gem toward Massively Multiplexed Pathogen Diagnostics and Genotyping.", "authors": [{"family": "Soares", "given": "Ruben R G", "initials": "RRG", "orcid": "0000-0001-5958-5232", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fef4d913e9e74505a000d8d8488cb62b.json"}}, {"family": "Madaboosi", "given": "Narayanan", "initials": "N"}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3311155f09a64b4f88d673da2a40627b.json"}}], "type": "journal article", "published": "2021-11-02", "journal": {"title": "Acc. Chem. Res.", "issn": "1520-4898", "volume": "54", "issue": "21", "pages": "3979-3990", "issn-l": "0001-4842"}, "abstract": "The development of robust methods allowing the precise detection of specific nucleic acid sequences is of major societal relevance, paving the way for significant advances in biotechnology and biomedical engineering. These range from a better understanding of human disease at a molecular level, allowing the discovery and development of novel biopharmaceuticals and vaccines, to the improvement of biotechnological processes providing improved food quality and safety, efficient green fuels, and smart textiles. Among these applications, the significance of pathogen diagnostics as the main focus of this Account has become particularly clear during the recent SARS-CoV-2 pandemic. In this context, while RT-PCR is the gold standard method for unambiguous detection of genetic material from pathogens, other isothermal amplification alternatives circumventing rapid heating-cooling cycles up to \u223c95 \u00b0C are appealing to facilitate the translation of the assay into point-of-care (PoC) analytical platforms. Furthermore, the possibility of routinely multiplexing the detection of tens to hundreds of target sequences with single base pair specificity, currently not met by state-of-the-art methods available in clinical laboratories, would be instrumental along the path to tackle emergent viral variants and antimicrobial resistance genes. Here, we advocate that padlock probes (PLPs), first reported by Nilsson et al. in 1994, coupled with rolling circle amplification (RCA), termed here as PLP-RCA, is an underexploited technology in current arena of isothermal nucleic acid amplification tests (NAATs) providing an unprecedented degree of multiplexing, specificity, versatility, and amenability to integration in miniaturized PoC platforms. Furthermore, the intrinsically digital amplification of PLP-RCA retains spatial information and opens new avenues in the exploration of pathogenesis with spatial multiomics analysis of infected cells and tissue.The Account starts by introducing PLP-RCA in a nutshell focusing individually on the three main assay steps, namely, (1) PLP design and ligation mechanism, (2) RCA after probe ligation, and (3) detection of the RCA products. Each subject is touched upon succinctly but with sufficient detail for the reader to appreciate some assay intricacies and degree of versatility depending on the analytical challenge at hand. After familiarizing the reader with the method, we discuss specific examples of research in our group and others using PLP-RCA for viral, bacterial, and fungal diagnostics in a variety of clinical contexts, including the genotyping of antibiotic resistance genes and viral subtyping. Then, we dissect key developments in the miniaturization and integration of PLP-RCA to minimize user input, maximize analysis throughput, and expedite the time to results, ultimately aiming at PoC applications. These developments include molecular enrichment for maximum sensitivity, spatial arrays to maximize analytical throughput, automation of liquid handling to streamline the analytical workflow in miniaturized devices, and seamless integration of signal transduction to translate RCA product titers (and ideally spatial information) into a readable output. Finally, we position PLP-RCA in the current landscape of NAATs and furnish a systematic Strengths, Weaknesses, Opportunities and Threats analysis to shine light upon unpolished edges to uncover the gem with potential for ubiquitous, precise, and unbiased pathogen diagnostics.", "doi": "10.1021/acs.accounts.1c00438", "pmid": "34637281", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC8567418"}], "notes": [], "created": "2026-08-20T08:08:18.152Z", "modified": "2026-08-20T08:08:18.220Z"}, {"entity": "publication", "iuid": "68ced44a3aed497697ffaaa5ee1c3f49", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/68ced44a3aed497697ffaaa5ee1c3f49.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/68ced44a3aed497697ffaaa5ee1c3f49"}}, "title": "Correction to 'Hybridization-based in situ sequencing (HybISS) for spatially resolved transcriptomics in human and mouse brain tissue'.", "authors": [{"family": "Gyllborg", "given": "Daniel", "initials": "D", "orcid": "0000-0002-1429-6426", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8a6778b611eb4a62a76b763daa8955f5.json"}}, {"family": "Langseth", "given": "Christoffer Mattsson", "initials": "CM"}, {"family": "Qian", "given": "Xiaoyan", "initials": "X"}, {"family": "Choi", "given": "Eunkyoung", "initials": "E"}, {"family": "Salas", "given": "Sergio Marco", "initials": "SM"}, {"family": "Hilscher", "given": "Markus M", "initials": "MM"}, {"family": "Lein", "given": "Ed S", "initials": "ES"}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3311155f09a64b4f88d673da2a40627b.json"}}], "type": "published erratum", "published": "2021-09-07", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "volume": "49", "issue": "15", "pages": "9002", "issn-l": "0305-1048"}, "abstract": null, "doi": "10.1093/nar/gkab630", "pmid": "34331448", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC8421205"}, {"db": "pii", "key": "6332814"}], "notes": [], "created": "2026-08-20T09:49:39.152Z", "modified": "2026-08-20T09:49:39.264Z"}, {"entity": "publication", "iuid": "ce719f5592a847b8af1f67bfaa7388dd", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ce719f5592a847b8af1f67bfaa7388dd.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ce719f5592a847b8af1f67bfaa7388dd"}}, "title": "Developmental landscape of human forebrain at a single-cell level unveils early waves of oligodendrogenesis", "authors": [{"family": "van Bruggen", "given": "David", "initials": "D"}, {"family": "Pohl", "given": "Fabio", "initials": "F"}, {"family": "Langseth", "given": "Christoffer Mattsson", "initials": "CM", "orcid": "0000-0003-2230-8594", "researcher": {"href": 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"given": "Gon\u00e7alo", "initials": "G", "orcid": "0000-0003-2247-9393", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/50ede6d74fde420f8139cef3f0a1ff5e.json"}}], "type": "posted-content", "published": "2021-07-22", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2021.07.22.453317", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:05:55.099Z", "modified": "2026-08-20T10:05:55.137Z"}, {"entity": "publication", "iuid": "2d13b3d0c12746d4ae79b24d6cab10fc", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/2d13b3d0c12746d4ae79b24d6cab10fc.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/2d13b3d0c12746d4ae79b24d6cab10fc"}}, "title": "De novo spatiotemporal modelling of cell-type signatures identifies novel cell populations in the developmental human heart", "authors": [{"family": "Salas", "given": "Sergio Marco", "initials": "SM", "orcid": "0000-0002-4636-0322", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/68b3baa22ffe41c0aa352075c6ea70b9.json"}}, {"family": "Yuan", "given": "Xiao", "initials": "X"}, {"family": "Sylven", "given": "Christer", "initials": "C", "orcid": "0000-0003-1017-7849", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f591fecdc169450ab14c52f383dece39.json"}}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3311155f09a64b4f88d673da2a40627b.json"}}, {"family": "W\u00e4hlby", "given": "Carolina", "initials": "C", "orcid": "0000-0002-4139-7003", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/833afe3444d84c24be12ea1468563bea.json"}}, {"family": "Partel", "given": "Gabriele", "initials": "G", "orcid": "0000-0002-4482-3119", "researcher": {"href": 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{"family": "Svedlund", "given": "Jessica", "initials": "J"}, {"family": "Strell", "given": "Carina", "initials": "C", "orcid": "0000-0002-3783-7256", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f288539ea7eb406480c84ec1a5605a91.json"}}, {"family": "Gataric", "given": "Milana", "initials": "M", "orcid": "0000-0003-3915-2266", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ce92971066b746b88cf04f47ea9d31ea.json"}}, {"family": "Shmatko", "given": "Artem", "initials": "A", "orcid": "0000-0002-2184-0856", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6865b190ea864bf5a70fb0eba4c3a42f.json"}}, {"family": "Park", "given": "Jun Sung", "initials": "JS"}, {"family": "Ju", "given": "Young Seok", "initials": "YS", "orcid": "0000-0002-5514-4189", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/722d6f64a2dc4b629fa0bb20caa57783.json"}}, {"family": "Dentro", "given": 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"https://publications-affiliated.scilifelab.se/researcher/0210ed780da34fca951333f262b7a9b5.json"}}, {"family": "Pinder", "given": "Sarah", "initials": "S"}, {"family": "Richardson", "given": "Andrea L", "initials": "AL"}, {"family": "Campbell", "given": "Peter J", "initials": "PJ"}, {"family": "Gerstung", "given": "Moritz", "initials": "M", "orcid": "0000-0001-6709-963X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/47c705bf905d4578b2dcb44ad0307a81.json"}}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3311155f09a64b4f88d673da2a40627b.json"}}, {"family": "Yates", "given": "Lucy R", "initials": "LR", "orcid": "0000-0003-4519-7794", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6201b7f172fb4c7d9e8892d953710873.json"}}], "type": "posted-content", "published": "2021-04-16", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2021.04.16.439912", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:04:02.037Z", "modified": "2026-08-20T10:04:02.446Z"}, {"entity": "publication", "iuid": "a529f552547241cb8e8bad79afc9ed06", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a529f552547241cb8e8bad79afc9ed06.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a529f552547241cb8e8bad79afc9ed06"}}, "title": "Comprehensive in situ mapping of human cortical transcriptomic cell types", "authors": [{"family": "Langseth", "given": "Christoffer Mattsson", "initials": "CM", "orcid": "0000-0003-2230-8594", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4d73b090432c4a5397dfe4d8433c72cf.json"}}, {"family": "Gyllborg", "given": "Daniel", "initials": "D", "orcid": "0000-0002-1429-6426", "researcher": {"href": 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"initials": "MM", "orcid": "0000-0001-7782-0830", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ec435b1759284c98aa17c7dfd11c3617.json"}}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3311155f09a64b4f88d673da2a40627b.json"}}], "type": "posted-content", "published": "2021-01-28", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2021.01.28.428548", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:01:21.305Z", "modified": "2026-08-20T10:01:21.534Z"}, {"entity": "publication", "iuid": "850dfd898fe04091b094d635a7e78f01", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/850dfd898fe04091b094d635a7e78f01.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/850dfd898fe04091b094d635a7e78f01"}}, "title": "Human Developmental 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"created": "2026-08-20T09:57:45.464Z", "modified": "2026-08-20T09:57:45.719Z"}, {"entity": "publication", "iuid": "9c33bdfb53214af0a4dba29f6385f0ed", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9c33bdfb53214af0a4dba29f6385f0ed.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9c33bdfb53214af0a4dba29f6385f0ed"}}, "title": "SCRINSHOT, a spatial method for single-cell resolution mapping of cell states in tissue sections", "authors": [{"family": "Sountoulidis", "given": "Alexandros", "initials": "A", "orcid": "0000-0002-8837-4642", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/618bb4684ceb4d839a2a83d4a7bca479.json"}}, {"family": "Liontos", "given": "Andreas", "initials": "A", "orcid": "0000-0003-0838-3571", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b5690cc0920d42aaae3dae9eaaedd2e6.json"}}, {"family": "Nguyen", "given": "Hong Phuong", 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"https://publications-affiliated.scilifelab.se/researcher/3311155f09a64b4f88d673da2a40627b.json"}}, {"family": "Samakovlis", "given": "Christos", "initials": "C", "orcid": "0000-0002-9153-6040", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d8ef864cc7c34dba830faa9caeafc3e7.json"}}], "type": "posted-content", "published": "2020-02-07", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2020.02.07.938571", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T09:55:54.959Z", "modified": "2026-08-20T09:55:55.187Z"}, {"entity": "publication", "iuid": "ad7aba7289a748fca7f620bd52b784ee", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ad7aba7289a748fca7f620bd52b784ee.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ad7aba7289a748fca7f620bd52b784ee"}}, "title": "Identification of spatial compartments in tissue from in situ sequencing data", "authors": [{"family": "Partel", "given": "Gabriele", "initials": "G", "orcid": "0000-0002-4482-3119", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d2d38e59d5c840a0a53a4b90690fdc7a.json"}}, {"family": "Hilscher", "given": "Markus M", "initials": "MM", "orcid": "0000-0001-7782-0830", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ec435b1759284c98aa17c7dfd11c3617.json"}}, {"family": "Milli", "given": "Giorgia", "initials": "G", "orcid": "0000-0002-1679-7523", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1410f82f8e964effa797ca06fcae1827.json"}}, {"family": "Solorzano", "given": "Leslie", "initials": "L", "orcid": "0000-0001-8658-6417", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f5c33a5b8cef4cad8b9f57b4510fb0c2.json"}}, {"family": "Klemm", "given": "Anna H", "initials": "AH", "orcid": "0000-0002-3466-1320", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bda9a501396248b5a7daa41db01518dc.json"}}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3311155f09a64b4f88d673da2a40627b.json"}}, {"family": "W\u00e4hlby", "given": "Carolina", "initials": "C", "orcid": "0000-0002-4139-7003", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/833afe3444d84c24be12ea1468563bea.json"}}], "type": "posted-content", "published": "2019-09-18", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/765842", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T11:14:49.776Z", "modified": "2026-08-20T11:14:49.897Z"}, {"entity": "publication", "iuid": "c869d16781b64399b8d26dba978d2b04", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c869d16781b64399b8d26dba978d2b04.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c869d16781b64399b8d26dba978d2b04"}}, "title": "Smartphone-based clinical diagnostics: towards democratization of evidence-based health care.", "authors": [{"family": "Hern\u00e1ndez-Neuta", "given": "I", "initials": "I", "orcid": "0000-0001-7727-1712", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ef52c05a4439406a86419de6426b2f48.json"}}, {"family": "Neumann", "given": "F", "initials": "F"}, {"family": "Brightmeyer", "given": "J", "initials": "J"}, {"family": "Ba Tis", "given": "T", "initials": "T"}, {"family": "Madaboosi", "given": "N", "initials": "N"}, {"family": "Wei", "given": "Q", "initials": "Q", "orcid": "0000-0003-1214-010X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c7ee45fc417240f5ab7bb5b0d3602240.json"}}, {"family": "Ozcan", "given": "A", "initials": "A", "orcid": "0000-0002-0717-683X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/28fe0cb50624443eb2815042c14f8ff4.json"}}, {"family": "Nilsson", "given": "M", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3311155f09a64b4f88d673da2a40627b.json"}}], "type": "journal article", "published": "2019-01-00", "journal": {"title": "J. Intern. Med.", "issn": "1365-2796", "volume": "285", "issue": "1", "pages": "19-39", "issn-l": "0954-6820"}, "abstract": "Recent advancements in bioanalytical techniques have led to the development of novel and robust diagnostic approaches that hold promise for providing optimal patient treatment, guiding prevention programs and widening the scope of personalized medicine. However, these advanced diagnostic techniques are still complex, expensive and limited to centralized healthcare facilities or research laboratories. This significantly hinders the use of evidence-based diagnostics for resource-limited settings and the primary care, thus creating a gap between healthcare providers and patients, leaving these populations without access to precision and quality medicine. Smartphone-based imaging and sensing platforms are emerging as promising alternatives for bridging this gap and decentralizing diagnostic tests offering practical features such as portability, cost-effectiveness and connectivity. Moreover, towards simplifying and automating bioanalytical techniques, biosensors and lab-on-a-chip technologies have become essential to interface and integrate these assays, bringing together the high precision and sensitivity of diagnostic techniques with the connectivity and computational power of smartphones. Here, we provide an overview of the emerging field of clinical smartphone diagnostics and its contributing technologies, as well as their wide range of areas of application, which span from haematology to digital pathology and rapid infectious disease diagnostics.", "doi": "10.1111/joim.12820", "pmid": "30079527", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC6334517"}], "notes": [], "created": "2026-08-20T11:18:19.386Z", "modified": "2026-08-20T11:18:19.615Z"}]}