{"entity": "researcher", "timestamp": "2026-07-12T09:21:54.520Z", "family": "Theis", "given": "Fabian J", "initials": "FJ", "orcid": "0000-0002-2419-1943", "affiliations": [], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/15139e290953411590201d9bb402da1f.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/15139e290953411590201d9bb402da1f"}}, "publications": [{"entity": "publication", "iuid": "7754d49a002a45ea96c366c1cf61c7fb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7754d49a002a45ea96c366c1cf61c7fb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7754d49a002a45ea96c366c1cf61c7fb"}}, "title": "A combinatorial transcription factor screening platform for immune cell reprogramming.", "authors": [{"family": "Kurochkin", "given": "Ilia", "initials": "I", "orcid": "0000-0003-3100-0903", "researcher": {"href": "https://publications.scilifelab.se/researcher/215e3195c7a943578f6fc51e367fb3af.json"}}, {"family": "Altman", "given": "Abigail R", "initials": "AR"}, {"family": "Caiado", "given": "In\u00eas", "initials": "I", "orcid": "0000-0001-5015-2705", "researcher": {"href": "https://publications.scilifelab.se/researcher/cef853aaa15943f7ac12a225fc590d84.json"}}, {"family": "P\u00e9rtiga-Cabral", "given": "Diogo", "initials": "D"}, {"family": "Halitzki", "given": "Evelyn", "initials": "E"}, {"family": "Minaeva", "given": "Mariia", "initials": "M"}, {"family": "Zimmermannov\u00e1", "given": "Olga", "initials": "O", "orcid": "0000-0002-5706-8124", "researcher": {"href": "https://publications.scilifelab.se/researcher/19ffa427694b45e4800bf54cc457bd3d.json"}}, {"family": "Henriques-Oliveira", "given": "Lu\u00eds", "initials": "L"}, {"family": "Klein", "given": "Dominik", "initials": "D"}, {"family": "Nair", "given": "Malavika", "initials": "M"}, {"family": "Oliveira", "given": "Daniel", "initials": "D", "orcid": "0000-0003-0622-2934", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a7d211d1bfb41c28c667db817d8a7fb.json"}}, {"family": "Cajal", "given": "Laura Rabanal", "initials": "LR"}, {"family": "Knittel", "given": "Ramin", "initials": "R"}, {"family": "Feick", "given": "Cora", "initials": "C"}, {"family": "Ringn\u00e9r", "given": "Markus", "initials": "M", "orcid": "0000-0001-5469-8940", "researcher": {"href": "https://publications.scilifelab.se/researcher/c0308e6d9c534033b431d2552cfe2af6.json"}}, {"family": "Martin", "given": "Marcel", "initials": "M"}, {"family": "Cirovic", "given": "Branko", "initials": "B"}, {"family": "Pires", "given": "Cristiana F", "initials": "CF", "orcid": "0000-0003-2985-6323", "researcher": {"href": "https://publications.scilifelab.se/researcher/9dde1908f0e8470dbfac54d3202e0515.json"}}, {"family": "Rosa", "given": "Fabio F", "initials": "FF", "orcid": "0000-0002-7714-5852", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d6242040a284b6c9a2ee37f773e9adb.json"}}, {"family": "Sitnicka", "given": "Ewa", "initials": "E"}, {"family": "Theis", "given": "Fabian J", "initials": "FJ", "orcid": "0000-0002-2419-1943", "researcher": {"href": "https://publications.scilifelab.se/researcher/15139e290953411590201d9bb402da1f.json"}}, {"family": "Pereira", "given": "Carlos-Filipe", "initials": "CF", "orcid": "0000-0002-9724-1382", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b298bb485b744fdb87f51ad579d0a79.json"}}], "type": "journal article", "published": "2026-01-14", "journal": {"title": "Cell Syst", "issn": "2639-5460", "pages": "101457", "issn-l": "2405-4712"}, "abstract": "Direct reprogramming of immune cells holds promise for immunotherapy but is constrained by limited knowledge of transcription factor (TF) networks. Here, we developed REPROcode, a combinatorial single-cell screening platform to identify TF combinations for immune cell reprogramming. We first validated REPROcode by inducing type-1 conventional dendritic cells (cDC1s) with multiplexed sets of 9, 22, and 42 factors. With cDC1-enriched TFs, REPROcode enabled identification of optimal TF stoichiometry, fidelity enhancers, and regulators of cDC1 states. We then constructed an arrayed lentiviral library of 408 barcoded immune TFs to explore broader reprogramming capacity. Screening 48 TFs enriched in dendritic cell subsets yielded myeloid and lymphoid phenotypes and enabled the construction of a TF hierarchy map to guide immune reprogramming. Finally, we validated REPROcode's discovery power by inducing natural killer (NK)-like cells. This study deepens our understanding of immune transcriptional control and provides a versatile toolbox for engineering immune cells to advance immunotherapy.", "doi": "10.1016/j.cels.2025.101457", "pmid": "41539305", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S2405-4712(25)00290-X"}], "notes": [], "created": "2026-01-15T13:40:34.207Z", "modified": "2026-01-20T07:55:14.966Z"}, {"entity": "publication", "iuid": "91db8e6db9aa49efbc40237fa90ee147", "links": {"self": {"href": "https://publications.scilifelab.se/publication/91db8e6db9aa49efbc40237fa90ee147.json"}, "display": {"href": "https://publications.scilifelab.se/publication/91db8e6db9aa49efbc40237fa90ee147"}}, "title": "Spatial single-cell atlas reveals regional variations in healthy and diseased human lung.", "authors": [{"family": "Firsova", "given": "Alexandra B", "initials": "AB", "orcid": "0000-0002-7345-7429", "researcher": {"href": "https://publications.scilifelab.se/researcher/32fc885aa10d48cebd772ad1470def0c.json"}}, {"family": "Marco Salas", "given": "Sergio", "initials": "S", "orcid": "0000-0002-4636-0322", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db8123d7b0f47afbb06b0559fcd79ff.json"}}, {"family": "Kuemmerle", "given": "Louis B", "initials": "LB"}, {"family": "Abalo", "given": "Xes\u00fas M", "initials": "XM", "orcid": "0000-0002-1643-0705", "researcher": {"href": "https://publications.scilifelab.se/researcher/944b78e930df40ee8cd5d590638cd4d9.json"}}, {"family": "Sountoulidis", "given": "Alexandros", "initials": "A", "orcid": "0000-0002-8837-4642", "researcher": {"href": "https://publications.scilifelab.se/researcher/f49f693f406b4ba28faf373fa67ee683.json"}}, {"family": "Larsson", "given": "Ludvig", "initials": "L"}, {"family": "Mahbubani", "given": "Krishnaa T", "initials": "KT", "orcid": "0000-0002-1327-2334", "researcher": {"href": "https://publications.scilifelab.se/researcher/1f378366e0594e8da4d56704215fc31c.json"}}, {"family": "Theelke", "given": "Jonas", "initials": "J", "orcid": "0000-0002-5074-1793", "researcher": {"href": "https://publications.scilifelab.se/researcher/9bfd9c1f49b24c9e8dc5c22bc4288543.json"}}, {"family": "Andrusivova", "given": "Zaneta", "initials": "Z"}, {"family": "Alonso Galicia", "given": "Leire", "initials": "L"}, {"family": "Liontos", "given": "Andreas", "initials": "A"}, {"family": "Balassa", "given": "Tam\u00e1s", "initials": "T"}, {"family": "Kovacs", "given": "Ferenc", "initials": "F", "orcid": "0000-0003-4512-4448", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8d63cee27914cc19796e7c6502d5f01.json"}}, {"family": "Horvath", "given": "Peter", "initials": "P"}, {"family": "Chen", "given": "Yuexin", "initials": "Y"}, {"family": "Gote-Schniering", "given": "Janine", "initials": "J", "orcid": "0000-0001-7869-4936", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e3e12bc834b4699b4675e3ff6043f5b.json"}}, {"family": "Stoleriu", "given": "Mircea-Gabriel", "initials": "MG"}, {"family": "Behr", "given": "J\u00fcrgen", "initials": "J"}, {"family": "Meyer", "given": "Kerstin B", "initials": "KB", "orcid": "0000-0001-5906-1498", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc26138d52fe4534a58ed24165e3370d.json"}}, {"family": "Timens", "given": "Wim", "initials": "W", "orcid": "0000-0002-4146-6363", "researcher": {"href": "https://publications.scilifelab.se/researcher/f29a8a5f02a14b3095d02444ad631598.json"}}, {"family": "Schiller", "given": "Herbert B", "initials": "HB"}, {"family": "Luecken", "given": "Malte D", "initials": "MD", "orcid": "0000-0001-7464-7921", "researcher": {"href": "https://publications.scilifelab.se/researcher/40b82068719d43448992741da54e00bd.json"}}, {"family": "Theis", "given": "Fabian J", "initials": "FJ", "orcid": "0000-0002-2419-1943", "researcher": {"href": "https://publications.scilifelab.se/researcher/15139e290953411590201d9bb402da1f.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}, {"family": "Nawijn", "given": "Martijn C", "initials": "MC", "orcid": "0000-0003-3372-6521", "researcher": {"href": "https://publications.scilifelab.se/researcher/61646a2dcd43478d955d0e9c5a3e5025.json"}}, {"family": "Samakovlis", "given": "Christos", "initials": "C", "orcid": "0000-0002-9153-6040", "researcher": {"href": "https://publications.scilifelab.se/researcher/004a4a166cb34d59ba054055658425f6.json"}}], "type": "journal article", "published": "2025-11-05", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "9745", "issn-l": "2041-1723"}, "abstract": "Integration of scRNA-seq data from millions of cells revealed a high diversity of cell types in the healthy and diseased human lung. In a large and complex organ, constantly exposed to external agents, it is crucial to understand the influence of lung tissue topography or external factors on gene expression variability within cell types. Here, we apply three spatial transcriptomics approaches, to: (i) localize the majority of lung cell types, including rare epithelial cells within the tissue topography, (ii) describe consistent anatomical and regional gene expression variability within and across cell types, and (iii) reveal distinct cellular neighborhoods in specific anatomical regions and examine gene expression variations in them. We thus provide a spatially resolved tissue reference atlas in three representative regions of the healthy human lung. We further demonstrate its utility by defining previously unknown imbalances of epithelial cell type compositions in chronic obstructive pulmonary disease lungs. Our topographic atlas enables a precise description of characteristic regional cellular responses upon experimental perturbations or during disease progression.", "doi": "10.1038/s41467-025-65704-0", "pmid": "41193468", "labels": {"In Situ Sequencing": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12589588"}, {"db": "pii", "key": "10.1038/s41467-025-65704-0"}], "notes": [], "created": "2025-11-28T06:52:42.945Z", "modified": "2025-11-28T06:52:43.158Z"}, {"entity": "publication", "iuid": "87266d8a6f284e2198986f59a2abeff9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/87266d8a6f284e2198986f59a2abeff9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/87266d8a6f284e2198986f59a2abeff9"}}, "title": "Optimizing Xenium In Situ data utility by quality assessment and best-practice analysis workflows.", "authors": [{"family": "Marco Salas", "given": "Sergio", "initials": "S", "orcid": "0000-0002-4636-0322", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db8123d7b0f47afbb06b0559fcd79ff.json"}}, {"family": "Kuemmerle", "given": "Louis B", "initials": "LB", "orcid": "0000-0002-9193-1243", "researcher": {"href": "https://publications.scilifelab.se/researcher/4d339771ed9a4559ad56a63e9e4e9e80.json"}}, {"family": "Mattsson-Langseth", "given": "Christoffer", "initials": "C"}, {"family": "Tismeyer", "given": "Sebastian", "initials": "S"}, {"family": "Avenel", "given": "Christophe", "initials": "C", "orcid": "0000-0002-1835-921X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5471168acdf94b63b1eab431fd1e8442.json"}}, {"family": "Hu", "given": "Taobo", "initials": "T", "orcid": "0000-0001-5124-7167", "researcher": {"href": "https://publications.scilifelab.se/researcher/b693c14571864cfcb6f3b36cce183f12.json"}}, {"family": "Rehman", "given": "Habib", "initials": "H", "orcid": "0000-0002-8671-982X", "researcher": {"href": "https://publications.scilifelab.se/researcher/dff0d9994c0f4237a5afbcd66d706dbf.json"}}, {"family": "Grillo", "given": "Marco", "initials": "M", "orcid": "0000-0003-2155-0645", "researcher": {"href": "https://publications.scilifelab.se/researcher/bcd8bec6567444558acbcbd1b3d28f7a.json"}}, {"family": "Czarnewski", "given": "Paulo", "initials": "P"}, {"family": "Helgadottir", "given": "Saga", "initials": "S"}, {"family": "Tiklova", "given": "Katarina", "initials": "K"}, {"family": "Andersson", "given": "Axel", "initials": "A", "orcid": "0000-0002-4714-3127", "researcher": {"href": "https://publications.scilifelab.se/researcher/34027f6b47684ff4be205e2d547c5f8a.json"}}, {"family": "Rafati", "given": "Nima", "initials": "N"}, {"family": "Chatzinikolaou", "given": "Maria", "initials": "M"}, {"family": "Theis", "given": "Fabian J", "initials": "FJ", "orcid": "0000-0002-2419-1943", "researcher": {"href": "https://publications.scilifelab.se/researcher/15139e290953411590201d9bb402da1f.json"}}, {"family": "Luecken", "given": "Malte D", "initials": "MD", "orcid": "0000-0001-7464-7921", "researcher": {"href": "https://publications.scilifelab.se/researcher/40b82068719d43448992741da54e00bd.json"}}, {"family": "W\u00e4hlby", "given": "Carolina", "initials": "C", "orcid": "0000-0002-4139-7003", "researcher": {"href": "https://publications.scilifelab.se/researcher/c50194fbc8524d95b7152663ccf17f29.json"}}, {"family": "Ishaque", "given": "Naveed", "initials": "N", "orcid": "0000-0002-8426-901X", "researcher": {"href": "https://publications.scilifelab.se/researcher/38be333e07614a13bf8c559e7935381a.json"}}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}], "type": "journal article", "published": "2025-04-00", "journal": {"title": "Nat. Methods", "issn": "1548-7105", "volume": "22", "issue": "4", "pages": "813-823", "issn-l": "1548-7091"}, "abstract": "The Xenium In Situ platform is a new spatial transcriptomics product commercialized by 10x Genomics, capable of mapping hundreds of genes in situ at subcellular resolution. Given the multitude of commercially available spatial transcriptomics technologies, recommendations in choice of platform and analysis guidelines are increasingly important. Herein, we explore 25 Xenium datasets generated from multiple tissues and species, comparing scalability, resolution, data quality, capacities and limitations with eight other spatially resolved transcriptomics technologies and commercial platforms. In addition, we benchmark the performance of multiple open-source computational tools, when applied to Xenium datasets, in tasks including preprocessing, cell segmentation, selection of spatially variable features and domain identification. This study serves as an independent analysis of the performance of Xenium, and provides best practices and recommendations for analysis of such datasets.", "doi": "10.1038/s41592-025-02617-2", "pmid": "40082609", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "BioImage Informatics": "Collaborative", "In Situ Sequencing": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC11978515"}, {"db": "pii", "key": "10.1038/s41592-025-02617-2"}], "notes": [], "created": "2025-11-21T12:56:02.504Z", "modified": "2025-11-28T06:50:06.581Z"}, {"entity": "publication", "iuid": "a237e9490a124d4eaa61f77c64c90f5b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a237e9490a124d4eaa61f77c64c90f5b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a237e9490a124d4eaa61f77c64c90f5b"}}, "title": "A topographic lung cell atlas reveals regional variation in cell-type specific gene programs and identifies healthy and diseased cellular neighborhoods", "authors": [{"family": "Samakovlis", "given": "Christos", "initials": "C", "orcid": "0000-0002-9153-6040", "researcher": {"href": "https://publications.scilifelab.se/researcher/004a4a166cb34d59ba054055658425f6.json"}}, {"family": "Firsova", "given": "Alexandra", "initials": "A", "orcid": "0000-0002-7345-7429", "researcher": {"href": "https://publications.scilifelab.se/researcher/32fc885aa10d48cebd772ad1470def0c.json"}}, {"family": "Salas", "given": "Sergio Marco", "initials": "SM", "orcid": "0000-0002-4636-0322", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db8123d7b0f47afbb06b0559fcd79ff.json"}}, {"family": "K\u00fcmmerle", "given": "Louis", "initials": "L"}, {"family": "Abalo", "given": "Xesus", "initials": "X", "orcid": "0000-0002-1643-0705", "researcher": {"href": "https://publications.scilifelab.se/researcher/944b78e930df40ee8cd5d590638cd4d9.json"}}, {"family": "Larsson", "given": "Ludvig", "initials": "L"}, {"family": "Mahbubani", "given": "Krishna", "initials": "K", "orcid": "0000-0002-1327-2334", "researcher": {"href": "https://publications.scilifelab.se/researcher/1f378366e0594e8da4d56704215fc31c.json"}}, {"family": "Sountoulidis", "given": "Alexandros", "initials": "A"}, {"family": "Theelke", "given": "Jonas", "initials": "J", "orcid": "0000-0002-5074-1793", "researcher": {"href": "https://publications.scilifelab.se/researcher/9bfd9c1f49b24c9e8dc5c22bc4288543.json"}}, {"family": "Andrusivova", "given": "Zaneta", "initials": "Z", "orcid": "0000-0002-4350-2524", "researcher": {"href": "https://publications.scilifelab.se/researcher/f89be535ddfa4c6ab46201fb383f4a2b.json"}}, {"family": "Galicia", "given": "Leire Alonso", "initials": "LA"}, {"family": "Liontos", "given": "Andreas", "initials": "A", "orcid": "0000-0003-0838-3571", "researcher": {"href": "https://publications.scilifelab.se/researcher/af0596d61a794c188112ba7b256efac6.json"}}, {"family": "Balassa", "given": "Tamas", "initials": "T"}, {"family": "Kovacs", "given": "Ferenc", "initials": "F", "orcid": "0000-0003-4512-4448", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8d63cee27914cc19796e7c6502d5f01.json"}}, {"family": "Horvath", "given": "Peter", "initials": "P"}, {"family": "Chen", "given": "Yuexin", "initials": "Y"}, {"family": "Gote-Schniering", "given": "Janine", "initials": "J"}, {"family": "Stoleriu", "given": "Mircea Gabriel", "initials": "MG"}, {"family": "Behr", "given": "J\u00fcrgen", "initials": "J"}, {"family": "Meyer", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-5906-1498", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc26138d52fe4534a58ed24165e3370d.json"}}, {"family": "Timens", "given": "Wim", "initials": "W", "orcid": "0000-0002-4146-6363", "researcher": {"href": 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