{"entity": "researcher", "timestamp": "2026-08-20T21:08:33.014Z", "family": "Vlachos", "given": "Ioannis S", "initials": "IS", "orcid": "0000-0002-8849-808X", "affiliations": ["Spatial Technologies Unit, Harvard Medical School Initiative for RNA Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA.", "Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA.", "Broad Institute of MIT and Harvard, Cambridge, MA, USA."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/486d1c8f0d984011ac065a50699bfa99.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/486d1c8f0d984011ac065a50699bfa99"}}, "publications": [{"entity": "publication", "iuid": "eaa1671d4d2e4f69af8f1d4c38e3dd81", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/eaa1671d4d2e4f69af8f1d4c38e3dd81.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/eaa1671d4d2e4f69af8f1d4c38e3dd81"}}, "title": "snPATHO-seq, a versatile FFPE single-nucleus RNA sequencing method to unlock pathology archives.", "authors": [{"family": "Wang", "given": "Taopeng", "initials": "T", "orcid": "0000-0002-9184-609X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/01e933430f5c4715b4f8551eb21d8158.json"}}, {"family": "Roach", "given": "Michael J", "initials": "MJ", "orcid": "0000-0003-1488-5148", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f8258e46da264256b9735267e451ab6e.json"}}, {"family": "Harvey", "given": "Kate", "initials": "K", "orcid": "0000-0002-2155-5203", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/afb60b0fb41a4fb998ea9fa280bde92d.json"}}, {"family": "Morlanes", "given": "Javier Escudero", "initials": "JE"}, {"family": "Kiedik", "given": "Beata", "initials": "B", "orcid": "0000-0001-8517-5253", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0ee049740d8e4ae7879d456ddcd08ef5.json"}}, {"family": "Al-Eryani", "given": "Ghamdan", "initials": "G"}, {"family": "Greenwald", "given": "Alissa", "initials": "A", "orcid": "0000-0001-5428-9645", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6997859be9f546829facb356d6e9a6d0.json"}}, {"family": "Kalavros", "given": "Nikolaos", "initials": "N", "orcid": "0000-0001-5503-9808", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4839d734d7d04fb08cc1aa05df8da1df.json"}}, {"family": "Dezem", "given": "Felipe Segato", "initials": "FS"}, {"family": "Ma", "given": "Yuling", "initials": "Y"}, {"family": "Pita-Juarez", "given": "Yered H", "initials": "YH"}, {"family": "Wise", "given": "Kellie", "initials": "K"}, {"family": "Degletagne", "given": "Cyril", "initials": "C"}, {"family": "Elz", "given": "Anna", "initials": "A"}, {"family": "Hadadianpour", "given": "Azi", "initials": "A"}, {"family": "Johanneson", "given": "Jack", "initials": "J", "orcid": "0009-0002-7612-1290", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ed3b76d318044ce18d854fa54451fbb9.json"}}, {"family": "Pakiam", "given": "Fiona", "initials": "F"}, {"family": "Ryu", "given": "Heeju", "initials": "H"}, {"family": "Newell", "given": "Evan W", "initials": "EW", "orcid": "0000-0002-2889-243X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/954fa28bfe19491c889a04d9dcdd7fb5.json"}}, {"family": "Tonon", "given": "Laurie", "initials": "L", "orcid": "0009-0005-8794-7276", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/15a0d18b94174c54b565af53459d81d4.json"}}, {"family": "Kohlway", "given": "Andrew", "initials": "A"}, {"family": "Drennon", "given": "Tingsheng", "initials": "T", "orcid": "0000-0002-8106-7981", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2f6bb092530e4ae980f89364447a5457.json"}}, {"family": "Abousoud", "given": "Jawad", "initials": "J"}, {"family": "Stott", "given": "Ryan", "initials": "R"}, {"family": "Lund", "given": "Paul", "initials": "P", "orcid": "0000-0003-0496-1434", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2035bd95fecb47d0a9459a1e7a9df145.json"}}, {"family": "Durruthy", "given": "Jens", "initials": "J"}, {"family": "Vallejo", "given": "Andres F", "initials": "AF", "orcid": "0000-0002-4688-0598", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ac2170668a74079a385db81d2d484ea.json"}}, {"family": "Li", "given": "Wenyan", "initials": "W"}, {"family": "Salomon", "given": "Robert", "initials": "R", "orcid": "0000-0003-4504-2901", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e47860d3ba2747b8baa14a6c55c88d71.json"}}, {"family": "Kaczorowski", "given": "Dominik", "initials": "D", "orcid": "0000-0002-9205-1934", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/283a0caf4e1f4aafbe16338ec9a632f4.json"}}, {"family": "Warren", "given": "Joanna", "initials": "J"}, {"family": "Butler", "given": "Lisa M", "initials": "LM", "orcid": "0000-0003-2698-3220", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e76885407d5c4fd2bdcd4a27e5520217.json"}}, {"family": "O'Toole", "given": "Sandra", "initials": "S"}, {"family": "Plummer", "given": "Jasmine", "initials": "J", "orcid": "0000-0001-7263-350X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/862458ea9eb541d9a9cbfcb74bd2bd37.json"}}, {"family": "Vlachos", "given": "Ioannis S", "initials": "IS", "orcid": "0000-0002-8849-808X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/486d1c8f0d984011ac065a50699bfa99.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d9fa47767cd14ef2b9528c8b998cf095.json"}}, {"family": "Swarbrick", "given": "Alexander", "initials": "A", "orcid": "0000-0002-3051-5676", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/09393c3690dc4ff8b42f5b39ec981a22.json"}}, {"family": "Martelotto", "given": "Luciano G", "initials": "LG", "orcid": "0000-0002-9625-1183", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/87031d582f3c44fc8cb8281fb45ce26f.json"}}], "type": "journal article", "published": "2024-10-16", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "7", "issue": "1", "pages": "1340", "issn-l": "2399-3642"}, "abstract": "Formalin-fixed paraffin-embedded (FFPE) samples are valuable but underutilized in single-cell omics research due to their low RNA quality. In this study, leveraging a recent advance in single-cell genomic technology, we introduce snPATHO-seq, a versatile method to derive high-quality single-nucleus transcriptomic data from FFPE samples. We benchmarked the performance of the snPATHO-seq workflow against existing 10x 3' and Flex assays designed for frozen or fresh samples and highlighted the consistency in snRNA-seq data produced by all workflows. The snPATHO-seq workflow also demonstrated high robustness when tested across a wide range of healthy and diseased FFPE tissue samples. When combined with FFPE spatial transcriptomic technologies such as FFPE Visium, the snPATHO-seq provides a multi-modal sampling approach for FFPE samples, allowing more comprehensive transcriptomic characterization.", "doi": "10.1038/s42003-024-07043-2", "pmid": "39414943", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC11484811"}, {"db": "pii", "key": "10.1038/s42003-024-07043-2"}, {"db": "GEO", "key": "GSE268426"}, {"db": "GEO", "key": "GSE268427"}, {"db": "Dryad", "key": "10.5061/dryad.7m0cfxq4s"}], "notes": [], "created": "2026-08-20T09:25:19.884Z", "modified": "2026-08-20T09:25:20.607Z"}, {"entity": "publication", "iuid": "a03d7d7db4af4dc482c16af3f719109f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a03d7d7db4af4dc482c16af3f719109f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a03d7d7db4af4dc482c16af3f719109f"}}, "title": "Organ Mapping Antibody Panels: a community resource for standardized multiplexed tissue imaging.", "authors": [{"family": "Quardokus", "given": "Ellen M", "initials": "EM", "orcid": "0000-0001-7655-4833", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6f0359f5e2f9438aaf591324f1110f64.json"}}, {"family": "Saunders", "given": "Diane C", "initials": "DC", "orcid": "0000-0002-8849-6746", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/764f92d32a0d4f2d8c62e84e320ea4ba.json"}}, {"family": "McDonough", "given": "Elizabeth", "initials": "E", "orcid": "0000-0001-7524-8260", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/aa249579f8a94bfcadd1431c1e636832.json"}}, {"family": "Hickey", "given": "John W", "initials": "JW", "orcid": "0000-0001-9961-7673", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/674e42e6f0594fd3960adce6260edf93.json"}}, {"family": "Werlein", "given": "Christopher", "initials": "C", "orcid": "0000-0002-7694-4257", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6bc20043daa148b69de69326f6967b10.json"}}, {"family": "Surrette", "given": "Christine", "initials": "C"}, {"family": "Rajbhandari", "given": "Presha", "initials": "P"}, {"family": "Casals", "given": "Anna Martinez", "initials": "AM"}, {"family": "Tian", "given": "Hua", "initials": "H", "orcid": "0000-0002-3598-0219", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cce345ef74b347a7a83076f63c53a23d.json"}}, {"family": "Lowery", "given": "Lisa", "initials": "L"}, {"family": "Neumann", "given": "Elizabeth K", "initials": "EK"}, {"family": "Bj\u00f6rklund", "given": "Frida", "initials": "F"}, {"family": "Neelakantan", "given": "Taruna V", "initials": "TV"}, {"family": "Croteau", "given": "Josh", "initials": "J", "orcid": "0000-0002-8142-0482", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b5a325b6e1504a8186376dfcfe054a0d.json"}}, {"family": "Wiblin", "given": "Anne E", "initials": "AE", "orcid": "0000-0002-6087-5701", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/79355cecf5634e95af8212a4b930782e.json"}}, {"family": "Fisher", "given": "Jeremy", "initials": "J", "orcid": "0000-0002-7296-586X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/165c4a5e54ad4d708f8b2501c71d5e12.json"}}, {"family": "Livengood", "given": "April J", "initials": "AJ"}, {"family": "Dowell", "given": "Karen G", "initials": "KG"}, {"family": "Silverstein", "given": "Jonathan C", "initials": "JC", "orcid": "0000-0002-9252-6039", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9a174aa154fd43619faa4d0f09f15e92.json"}}, {"family": "Spraggins", "given": "Jeffrey M", "initials": "JM", "orcid": "0000-0001-9198-5498", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/20c2567cc66e4915b5536d311961bfbf.json"}}, {"family": "Pryhuber", "given": "Gloria S", "initials": "GS", "orcid": "0000-0002-9185-3994", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7c259a8236344b128624553ee3c91c58.json"}}, {"family": "Deutsch", "given": "Gail", "initials": "G"}, {"family": "Ginty", "given": "Fiona", "initials": "F"}, {"family": "Nolan", "given": "Garry P", "initials": "GP"}, {"family": "Melov", "given": "Simon", "initials": "S", "orcid": "0000-0001-8554-2834", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cdf3f65ef70d402ea2593dc6a93b52db.json"}}, {"family": "Jonigk", "given": "Danny", "initials": "D", "orcid": "0000-0002-5251-2281", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/89891e1c3e104ae88a82c6c147e34c7d.json"}}, {"family": "Caldwell", "given": "Michael A", "initials": "MA"}, {"family": "Vlachos", "given": "Ioannis S", "initials": "IS", "orcid": "0000-0002-8849-808X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/486d1c8f0d984011ac065a50699bfa99.json"}}, {"family": "Muller", "given": "Werner", "initials": "W", "orcid": "0000-0002-1297-9725", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d69ed7ac3f0046369857b4ae1c55ad4b.json"}}, {"family": "Gehlenborg", "given": "Nils", "initials": "N", "orcid": "0000-0003-0327-8297", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/83f7f88927584d80b6b5a5447b20dfdb.json"}}, {"family": "Stockwell", "given": "Brent R", "initials": "BR", "orcid": "0000-0002-3532-3868", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/81510049c217404d9363381818ba6446.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb07e6d0122c4528a927c1fe922e3bc8.json"}}, {"family": "Snyder", "given": "Michael P", "initials": "MP", "orcid": "0000-0003-0784-7987", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ce9e294ff3b64f7caa770c883d12514c.json"}}, {"family": "Germain", "given": "Ronald N", "initials": "RN", "orcid": "0000-0003-1495-9143", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9bc6225f3eef4506a319016701a261d8.json"}}, {"family": "Camarillo", "given": "Jeannie M", "initials": "JM"}, {"family": "Kelleher", "given": "Neil L", "initials": "NL", "orcid": "0000-0002-8815-3372", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/db299d87427049b8972eabe2d9f453a8.json"}}, {"family": "B\u00f6rner", "given": "Katy", "initials": "K", "orcid": "0000-0002-3321-6137", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1b8e7ebf67ae49e3b436a7c1252f7126.json"}}, {"family": "Radtke", "given": "Andrea J", "initials": "AJ", "orcid": "0000-0003-4379-8967", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6c54f64fc7c54f7d9279266878839455.json"}}], "type": "journal article", "published": "2023-08-00", "journal": {"title": "Nat. Methods", "issn": "1548-7105", "volume": "20", "issue": "8", "pages": "1174-1178", "issn-l": "1548-7091"}, "abstract": "Multiplexed antibody-based imaging enables the detailed characterization of molecular and cellular organization in tissues. Advances in the field now allow high-parameter data collection (>60 targets); however, considerable expertise and capital are needed to construct the antibody panels employed by these methods. Organ mapping antibody panels are community-validated resources that save time and money, increase reproducibility, accelerate discovery and support the construction of a Human Reference Atlas.", "doi": "10.1038/s41592-023-01846-7", "pmid": "37468619", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10406602"}, {"db": "pii", "key": "10.1038/s41592-023-01846-7"}], "notes": [], "created": "2026-08-20T09:02:53.512Z", "modified": "2026-08-20T09:02:54.263Z"}]}