{"entity": "researcher", "timestamp": "2026-08-20T21:41:21.757Z", "family": "Kalavros", "given": "Nikolaos", "initials": "N", "orcid": "0000-0001-5503-9808", "affiliations": ["Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA.", "Harvard Medical School, Boston, MA, USA.", "Broad Institute of MIT and Harvard, Cambridge, MA, USA.", "Spatial Technologies Unit, Harvard Medical School Initiative for RNA Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/4839d734d7d04fb08cc1aa05df8da1df.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/4839d734d7d04fb08cc1aa05df8da1df"}}, "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": "23cf806d59d1468c9e25ef36b9f29eef", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/23cf806d59d1468c9e25ef36b9f29eef.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/23cf806d59d1468c9e25ef36b9f29eef"}}, "title": "snPATHO-seq: unlocking the 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": "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", "orcid": "0000-0002-1137-1726", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6869f7a561a443aaac3c157a28f6cb4c.json"}}, {"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"}, {"family": "Pakiam", "given": "Fiona", "initials": "F"}, {"family": "Ryu", "given": "Heeju", "initials": "H"}, {"family": "Newell", "given": "Evan W", "initials": "EW"}, {"family": "Tonon", "given": "Laurie", "initials": "L"}, {"family": "Kohlway", "given": "Andrew", "initials": "A"}, {"family": "Drennon", "given": "Tingsheng", "initials": "T"}, {"family": "Abousoud", "given": "Jawad", "initials": "J"}, {"family": "Stott", "given": "Ryan", "initials": "R"}, {"family": "Lund", "given": "Paul", "initials": "P"}, {"family": "Durruthy", "given": "Jens", "initials": "J"}, {"family": "Vallejo", "given": "Andres F", "initials": "AF"}, {"family": "Kaczorowski", "given": "Dominik", "initials": "D"}, {"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\u2019Toole", "given": "Sandra", "initials": "S", "orcid": "0000-0001-9912-0245", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d16101d8c115471a92b1f2c009881c8e.json"}}, {"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"}, {"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", "initials": "L", "orcid": "0000-0002-9625-1183", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/87031d582f3c44fc8cb8281fb45ce26f.json"}}], "type": "posted-content", "published": "2023-12-08", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2023.12.07.570700", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:50:46.070Z", "modified": "2026-08-20T10:50:46.262Z"}]}