{"entity": "researcher", "timestamp": "2026-08-20T21:18:48.383Z", "family": "Harvey", "given": "Kate", "initials": "K", "orcid": "0000-0002-2155-5203", "affiliations": ["The Kinghorn Cancer Centre and Cancer Research Theme, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/afb60b0fb41a4fb998ea9fa280bde92d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/afb60b0fb41a4fb998ea9fa280bde92d"}}, "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"}, {"entity": "publication", "iuid": "74ebdb69517d4624b3d496303d69ca45", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/74ebdb69517d4624b3d496303d69ca45.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/74ebdb69517d4624b3d496303d69ca45"}}, "title": "A single-cell and spatially resolved atlas of human breast cancers.", "authors": [{"family": "Wu", "given": "Sunny Z", "initials": "SZ", "orcid": "0000-0002-6153-0449", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e49f02dfb8b94361819cdd575f15aecc.json"}}, {"family": "Al-Eryani", "given": "Ghamdan", "initials": "G"}, {"family": "Roden", "given": "Daniel Lee", "initials": "DL", "orcid": "0000-0003-2393-5805", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5c0bcc65d24948d69d80dd9a19e727b8.json"}}, {"family": "Junankar", "given": "Simon", "initials": "S", "orcid": "0000-0002-3965-8278", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f51460ede83842c2b5dd65b5f366ceed.json"}}, {"family": "Harvey", "given": "Kate", "initials": "K", "orcid": "0000-0002-2155-5203", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/afb60b0fb41a4fb998ea9fa280bde92d.json"}}, {"family": "Andersson", "given": "Alma", "initials": "A"}, {"family": "Thennavan", "given": "Aatish", "initials": "A"}, {"family": "Wang", "given": "Chenfei", "initials": "C"}, {"family": "Torpy", "given": "James R", "initials": "JR", "orcid": "0000-0002-5392-1642", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/360078a57ebd48038a14aff958147ef1.json"}}, {"family": "Bartonicek", "given": "Nenad", "initials": "N", "orcid": "0000-0003-2144-1887", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/25da7ac0b3504d52b54a7daae6b47f69.json"}}, {"family": "Wang", "given": "Taopeng", "initials": "T"}, {"family": "Larsson", "given": "Ludvig", "initials": "L", "orcid": "0000-0003-4209-2911", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/36ad34c94b64432ab74d61fbc6d16905.json"}}, {"family": "Kaczorowski", "given": "Dominik", "initials": "D", "orcid": "0000-0002-9205-1934", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/283a0caf4e1f4aafbe16338ec9a632f4.json"}}, {"family": "Weisenfeld", "given": "Neil I", "initials": "NI"}, {"family": "Uytingco", "given": "Cedric R", "initials": "CR"}, {"family": "Chew", "given": "Jennifer G", "initials": "JG"}, {"family": "Bent", "given": "Zachary W", "initials": "ZW"}, {"family": "Chan", "given": "Chia-Ling", "initials": "CL"}, {"family": "Gnanasambandapillai", "given": "Vikkitharan", "initials": "V"}, {"family": "Dutertre", "given": "Charles-Antoine", "initials": "CA"}, {"family": "Gluch", "given": "Laurence", "initials": "L"}, {"family": "Hui", "given": "Mun N", "initials": "MN"}, {"family": "Beith", "given": "Jane", "initials": "J"}, {"family": "Parker", "given": "Andrew", "initials": "A"}, {"family": "Robbins", "given": "Elizabeth", "initials": "E"}, {"family": "Segara", "given": "Davendra", "initials": "D"}, {"family": "Cooper", "given": "Caroline", "initials": "C", "orcid": "0000-0002-3630-0019", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bc4526d4776245f5b96695ecd55e8f8d.json"}}, {"family": "Mak", "given": "Cindy", "initials": "C"}, {"family": "Chan", "given": "Belinda", "initials": "B"}, {"family": "Warrier", "given": "Sanjay", "initials": "S"}, {"family": "Ginhoux", "given": "Florent", "initials": "F", "orcid": "0000-0002-2857-7755", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4ad567556a8741b4aa1172dbe8ec5e46.json"}}, {"family": "Millar", "given": "Ewan", "initials": "E"}, {"family": "Powell", "given": "Joseph E", "initials": "JE"}, {"family": "Williams", "given": "Stephen R", "initials": "SR"}, {"family": "Liu", "given": "X Shirley", "initials": "XS", "orcid": "0000-0003-4736-7339", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5769961bb4b14625822435b54b2f009f.json"}}, {"family": "O'Toole", "given": "Sandra", "initials": "S"}, {"family": "Lim", "given": "Elgene", "initials": "E", "orcid": "0000-0001-8065-8838", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ac94e0cecb86495b8ff5f8dae6563f45.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d9fa47767cd14ef2b9528c8b998cf095.json"}}, {"family": "Perou", "given": "Charles M", "initials": "CM", "orcid": "0000-0001-9827-2247", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3f7179d8a91d4703ae5bdfa3e003f941.json"}}, {"family": "Swarbrick", "given": "Alexander", "initials": "A", "orcid": "0000-0002-3051-5676", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/09393c3690dc4ff8b42f5b39ec981a22.json"}}], "type": "journal article", "published": "2021-09-00", "journal": {"title": "Nat. Genet.", "issn": "1546-1718", "volume": "53", "issue": "9", "pages": "1334-1347", "issn-l": "1061-4036"}, "abstract": "Breast cancers are complex cellular ecosystems where heterotypic interactions play central roles in disease progression and response to therapy. However, our knowledge of their cellular composition and organization is limited. Here we present a single-cell and spatially resolved transcriptomics analysis of human breast cancers. We developed a single-cell method of intrinsic subtype classification (SCSubtype) to reveal recurrent neoplastic cell heterogeneity. Immunophenotyping using cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) provides high-resolution immune profiles, including new PD-L1/PD-L2+ macrophage populations associated with clinical outcome. Mesenchymal cells displayed diverse functions and cell-surface protein expression through differentiation within three major lineages. Stromal-immune niches were spatially organized in tumors, offering insights into antitumor immune regulation. Using single-cell signatures, we deconvoluted large breast cancer cohorts to stratify them into nine clusters, termed 'ecotypes', with unique cellular compositions and clinical outcomes. This study provides a comprehensive transcriptional atlas of the cellular architecture of breast cancer.", "doi": "10.1038/s41588-021-00911-1", "pmid": "34493872", "labels": [], "xrefs": [{"db": "mid", "key": "NIHMS1793222"}, {"db": "pmc", "key": "PMC9044823"}, {"db": "pii", "key": "10.1038/s41588-021-00911-1"}], "notes": [], "created": "2026-08-20T08:59:52.153Z", "modified": "2026-08-20T08:59:52.737Z"}]}