{"entity": "researcher", "timestamp": "2026-10-05T21:15:19.995Z", "family": "Regev", "given": "Aviv", "initials": "A", "orcid": "0000-0003-3293-3158", "affiliations": ["Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.", "Koch Institute of Integrative Cancer Research, MIT, Cambridge, MA, USA.", "Howard Hughes Medical Institute, Department of Biology, MIT, Cambridge, MA, USA."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/36ee05b2a25d42769587c29b909ba9db.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/36ee05b2a25d42769587c29b909ba9db"}}, "publications": [{"entity": "publication", "iuid": "b1a6f3fb64d34dc5b599349bc378a722", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b1a6f3fb64d34dc5b599349bc378a722.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b1a6f3fb64d34dc5b599349bc378a722"}}, "title": "Three-dimensional spatial transcriptomics uncovers cell type localizations in the human rheumatoid arthritis synovium.", "authors": [{"family": "Vickovic", "given": "Sanja", "initials": "S", "orcid": "0000-0003-0985-9885", "researcher": {"href": "https://publications.scilifelab.se/researcher/1fc02717a5784908b583ef5bbf09a910.json"}}, {"family": "Schapiro", "given": "Denis", "initials": "D", "orcid": "0000-0002-9391-5722", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ebb422a68344362a76e1bd23bfb5b49.json"}}, {"family": "Carlberg", "given": "Konstantin", "initials": "K", "orcid": "0000-0002-1774-6058", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e018cce30794ae08a4d7b5096914169.json"}}, {"family": "L\u00f6tstedt", "given": "Britta", "initials": "B"}, {"family": "Larsson", "given": "Ludvig", "initials": "L", "orcid": "0000-0003-4209-2911", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9ffc7de05a040c48011a6ba639d5851.json"}}, {"family": "Hildebrandt", "given": "Franziska", "initials": "F"}, {"family": "Korotkova", "given": "Marina", "initials": "M"}, {"family": "Hensvold", "given": "Aase H", "initials": "AH"}, {"family": "Catrina", "given": "Anca I", "initials": "AI"}, {"family": "Sorger", "given": "Peter K", "initials": "PK", "orcid": "0000-0002-3364-1838", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c63ad2d92e943b89ea7590c8a928ad9.json"}}, {"family": "Malmstr\u00f6m", "given": "Vivianne", "initials": "V", "orcid": "0000-0001-9251-8082", "researcher": {"href": "https://publications.scilifelab.se/researcher/34027fbf97444632a470b33e446d4d67.json"}}, {"family": "Regev", "given": "Aviv", "initials": "A", "orcid": "0000-0003-3293-3158", "researcher": {"href": "https://publications.scilifelab.se/researcher/36ee05b2a25d42769587c29b909ba9db.json"}}, {"family": "St\u00e5hl", "given": "Patrik L", "initials": "PL", "orcid": "0000-0002-2207-7370", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ea50cf03c6748c086846c3a28882979.json"}}], "type": "journal article", "published": "2022-02-11", "journal": {"title": "Commun Biol", "issn": "2399-3642", "issn-l": "2399-3642", "volume": "5", "issue": "1", "pages": "129"}, "abstract": "The inflamed rheumatic joint is a highly heterogeneous and complex tissue with dynamic recruitment and expansion of multiple cell types that interact in multifaceted ways within a localized area. Rheumatoid arthritis synovium has primarily been studied either by immunostaining or by molecular profiling after tissue homogenization. Here, we use Spatial Transcriptomics, where tissue-resident RNA is spatially labeled in situ with barcodes in a transcriptome-wide fashion, to study local tissue interactions at the site of chronic synovial inflammation. We report comprehensive spatial RNA-Seq data coupled to cell type-specific localization patterns at and around organized structures of infiltrating leukocyte cells in the synovium. Combining morphological features and high-throughput spatially resolved transcriptomics may be able to provide higher statistical power and more insights into monitoring disease severity and treatment-specific responses in seropositive and seronegative rheumatoid arthritis.", "doi": "10.1038/s42003-022-03050-3", "pmid": "35149753", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Spatial omics": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-022-03050-3"}, {"db": "pmc", "key": "PMC8837632"}], "notes": [], "created": "2022-03-29T13:47:26.413Z", "modified": "2022-08-19T09:06:49.671Z"}, {"entity": "publication", "iuid": "e9ac0b2c4b374062801e674f1f395db0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e9ac0b2c4b374062801e674f1f395db0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e9ac0b2c4b374062801e674f1f395db0"}}, "title": "A roadmap for the Human Developmental Cell Atlas.", "authors": [{"family": "Haniffa", "given": "Muzlifah", "initials": "M", "orcid": "0000-0002-3927-2084", "researcher": {"href": "https://publications.scilifelab.se/researcher/317351d4c2454dc8b1398ee76676721f.json"}}, {"family": "Taylor", "given": "Deanne", "initials": "D", "orcid": "0000-0002-3302-4610", "researcher": {"href": "https://publications.scilifelab.se/researcher/862bf6178eaf4d96a9b87be21231c0be.json"}}, {"family": "Linnarsson", "given": "Sten", "initials": "S", "orcid": "0000-0002-3491-3444", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c0d35942ce042688ea07f23902a8d46.json"}}, {"family": "Aronow", "given": "Bruce J", "initials": "BJ", "orcid": "0000-0001-5109-6514", "researcher": {"href": "https://publications.scilifelab.se/researcher/098dde45f6b24b6ab365a126caec6c34.json"}}, {"family": "Bader", "given": "Gary D", "initials": "GD", "orcid": "0000-0003-0185-8861", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d74ad4af0ca460597907e2c71e99d26.json"}}, {"family": "Barker", "given": "Roger A", "initials": "RA"}, {"family": "Camara", "given": "Pablo G", "initials": "PG"}, {"family": "Camp", "given": "J Gray", "initials": "JG", "orcid": "0000-0003-3295-1225", "researcher": {"href": "https://publications.scilifelab.se/researcher/acf9aad6c720461d89cc23a3456685b8.json"}}, {"family": "Ch\u00e9dotal", "given": "Alain", "initials": "A", "orcid": "0000-0001-7577-3794", "researcher": {"href": "https://publications.scilifelab.se/researcher/8cc388d646e8402eb35adc72394cf5a8.json"}}, {"family": "Copp", "given": "Andrew", "initials": "A", "orcid": "0000-0002-2544-9117", "researcher": {"href": "https://publications.scilifelab.se/researcher/52bdb03bc72e487ebb2a0f300bc89399.json"}}, {"family": "Etchevers", "given": "Heather C", "initials": "HC", "orcid": "0000-0003-0201-3799", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8402df6fdd3486b8b5c0b68b2cea895.json"}}, {"family": "Giacobini", "given": "Paolo", "initials": "P", "orcid": "0000-0002-3075-1441", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae0b5091f1f4460ea169c95a1f4876be.json"}}, {"family": "G\u00f6ttgens", "given": "Berthold", "initials": "B", "orcid": "0000-0001-6302-5705", "researcher": {"href": "https://publications.scilifelab.se/researcher/1e2290ec698049ccb7193839604c61fe.json"}}, {"family": "Guo", "given": "Guoji", "initials": "G", "orcid": "0000-0002-1716-4621", "researcher": {"href": "https://publications.scilifelab.se/researcher/8031189c673741ad87a68b332a313f33.json"}}, {"family": "Hupalowska", "given": "Ania", "initials": "A"}, {"family": "James", "given": "Kylie R", "initials": "KR"}, {"family": "Kirby", "given": "Emily", "initials": "E"}, {"family": "Kriegstein", "given": "Arnold", "initials": "A", "orcid": "0000-0001-5742-2990", "researcher": {"href": "https://publications.scilifelab.se/researcher/ea66a8a3999545a0bc54ba18f68c0aa6.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Marioni", "given": "John C", "initials": "JC", "orcid": "0000-0001-9092-0852", "researcher": {"href": "https://publications.scilifelab.se/researcher/d5ae59c4c62847929fb647bcb402ecc1.json"}}, {"family": "Meyer", "given": "Kerstin B", "initials": "KB", "orcid": "0000-0001-5906-1498", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc26138d52fe4534a58ed24165e3370d.json"}}, {"family": "Niakan", "given": "Kathy K", "initials": "KK", "orcid": "0000-0003-1646-4734", "researcher": {"href": "https://publications.scilifelab.se/researcher/20c361a9e9654169bea286571ab44b08.json"}}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}, {"family": "Olabi", "given": "Bayanne", "initials": "B"}, {"family": "Pe'er", "given": "Dana", "initials": "D", "orcid": "0000-0002-9259-8817", "researcher": {"href": "https://publications.scilifelab.se/researcher/76ce08d6ee014482994ec93d3d0244e5.json"}}, {"family": "Regev", "given": "Aviv", "initials": "A", "orcid": "0000-0003-3293-3158", "researcher": {"href": "https://publications.scilifelab.se/researcher/36ee05b2a25d42769587c29b909ba9db.json"}}, {"family": "Rood", "given": "Jennifer", "initials": "J"}, {"family": "Rozenblatt-Rosen", "given": "Orit", "initials": "O", "orcid": "0000-0001-6313-3570", "researcher": {"href": "https://publications.scilifelab.se/researcher/5f15f7a222ae4a72afe524493fdf0d2d.json"}}, {"family": "Satija", "given": "Rahul", "initials": "R", "orcid": "0000-0001-9448-8833", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab2ddbdc294a45b2840762c4c5e2fc8f.json"}}, {"family": "Teichmann", "given": "Sarah A", "initials": "SA", "orcid": "0000-0002-6294-6366", "researcher": {"href": "https://publications.scilifelab.se/researcher/bfc70e2496c94912ac19d32a54d32a2c.json"}}, {"family": "Treutlein", "given": "Barbara", "initials": "B", "orcid": "0000-0002-3299-5597", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6ddef8507fa4a068aa5a98d269db004.json"}}, {"family": "Vento-Tormo", "given": "Roser", "initials": "R", "orcid": "0000-0002-9870-8474", "researcher": {"href": "https://publications.scilifelab.se/researcher/542ebc8ed70a46e680540c8d6534a22a.json"}}, {"family": "Webb", "given": "Simone", "initials": "S", "orcid": "0000-0003-3058-8952", "researcher": {"href": "https://publications.scilifelab.se/researcher/a0d8e263ca654aa599955a029808b32c.json"}}, {"family": "Human Cell Atlas Developmental Biological Network", "given": "", "initials": ""}], "type": "journal article", "published": "2021-09-00", "journal": {"title": "Nature", "issn": "1476-4687", "volume": "597", "issue": "7875", "pages": "196-205", "issn-l": "0028-0836"}, "abstract": "The Human Developmental Cell Atlas (HDCA) initiative, which is part of the Human Cell Atlas, aims to create a comprehensive reference map of cells during development. This will be critical to understanding normal organogenesis, the effect of mutations, environmental factors and infectious agents on human development, congenital and childhood disorders, and the cellular basis of ageing, cancer and regenerative medicine. Here we outline the HDCA initiative and the challenges of mapping and modelling human development using state-of-the-art technologies to create a reference atlas across gestation. Similar to the Human Genome Project, the HDCA will integrate the output from a growing community of scientists who are mapping human development into a unified atlas. We describe the early milestones that have been achieved and the use of human stem-cell-derived cultures, organoids and animal models to inform the HDCA, especially for prenatal tissues that are hard to acquire. Finally, we provide a roadmap towards a complete atlas of human development.", "doi": "10.1038/s41586-021-03620-1", "pmid": "34497388", "labels": {"Spatial Proteomics": null, "In Situ Sequencing": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41586-021-03620-1"}], "notes": [], "created": "2021-12-09T09:49:39.501Z", "modified": "2025-10-17T13:02:17.805Z"}, {"entity": "publication", "iuid": "41bcf2ce98a54d95bd77cb57d287490b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/41bcf2ce98a54d95bd77cb57d287490b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/41bcf2ce98a54d95bd77cb57d287490b"}}, "title": "Building a high-quality Human Cell Atlas.", "authors": [{"family": "Rozenblatt-Rosen", "given": "Orit", "initials": "O"}, {"family": "Shin", "given": "Jay W", "initials": "JW", "orcid": "0000-0003-4037-3533", "researcher": {"href": "https://publications.scilifelab.se/researcher/d036e3b029d54dad9a678b47f138def3.json"}}, {"family": "Rood", "given": "Jennifer E", "initials": "JE"}, {"family": "Hupalowska", "given": "Anna", "initials": "A"}, {"family": "Human Cell Atlas Standards and Technology Working Group", "given": "", "initials": ""}, {"family": "Regev", "given": "Aviv", "initials": "A", "orcid": "0000-0003-3293-3158", "researcher": {"href": "https://publications.scilifelab.se/researcher/36ee05b2a25d42769587c29b909ba9db.json"}}, {"family": "Heyn", "given": "Holger", "initials": "H", "orcid": "0000-0002-3276-1889", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7f8103bc9af4fb5a3bd1d544648e588.json"}}], "type": "letter", "published": "2021-02-00", "journal": {"title": "Nat. Biotechnol.", "issn": "1546-1696", "volume": "39", "issue": "2", "pages": "149-153", "issn-l": "1087-0156"}, "abstract": null, "doi": "10.1038/s41587-020-00812-4", "pmid": "33500565", "labels": {"Spatial Proteomics": "Technology development"}, "xrefs": [{"db": "pii", "key": "10.1038/s41587-020-00812-4"}], "notes": [], "created": "2021-12-09T09:50:46.803Z", "modified": "2021-12-09T09:50:46.886Z"}, {"entity": "publication", "iuid": "ed70a147175843f5a31852a576f105bc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ed70a147175843f5a31852a576f105bc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ed70a147175843f5a31852a576f105bc"}}, "title": "Benchmarking single-cell RNA-sequencing protocols for cell atlas projects.", "authors": [{"family": "Mereu", "given": "Elisabetta", "initials": "E"}, {"family": "Lafzi", "given": "Atefeh", "initials": "A"}, {"family": "Moutinho", "given": "Catia", "initials": "C"}, {"family": "Ziegenhain", "given": "Christoph", "initials": "C", "orcid": "0000-0003-2208-4877", "researcher": {"href": "https://publications.scilifelab.se/researcher/3297f21f1a174cd388ac586eda2b5177.json"}}, {"family": "McCarthy", "given": "Davis J", "initials": "DJ"}, {"family": "\u00c1lvarez-Varela", "given": "Adri\u00e1n", "initials": "A"}, {"family": "Batlle", "given": "Eduard", "initials": "E"}, {"family": "Gr\u00fcn", "given": "Dominic", "initials": "D", "orcid": "0000-0002-3364-5898", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ee67aea7fd94e56a66d33a92c32863b.json"}}, {"family": "Lau", "given": "Julia K", "initials": "JK"}, {"family": "Boutet", "given": "St\u00e9phane C", "initials": "SC"}, {"family": "Sanada", "given": "Chad", "initials": "C"}, {"family": "Ooi", "given": "Aik", "initials": "A"}, {"family": "Jones", "given": "Robert C", "initials": "RC", "orcid": "0000-0001-7235-9854", "researcher": {"href": "https://publications.scilifelab.se/researcher/4fc0262d6f154970914dce5fa42fa83f.json"}}, {"family": "Kaihara", "given": "Kelly", "initials": "K"}, {"family": "Brampton", "given": "Chris", "initials": "C"}, {"family": "Talaga", "given": "Yasha", "initials": "Y"}, {"family": "Sasagawa", "given": "Yohei", "initials": "Y"}, {"family": "Tanaka", "given": "Kaori", "initials": "K"}, {"family": "Hayashi", "given": "Tetsutaro", "initials": "T"}, {"family": "Braeuning", "given": "Caroline", "initials": "C"}, {"family": "Fischer", "given": "Cornelius", "initials": "C", "orcid": "0000-0003-0329-2435", "researcher": {"href": "https://publications.scilifelab.se/researcher/7dcb9bf2b11a45a9a95219a0e456388e.json"}}, {"family": "Sauer", "given": "Sascha", "initials": "S"}, {"family": "Trefzer", "given": "Timo", "initials": "T"}, {"family": "Conrad", "given": "Christian", "initials": "C"}, {"family": "Adiconis", "given": "Xian", "initials": "X"}, {"family": "Nguyen", "given": "Lan T", "initials": "LT"}, {"family": "Regev", "given": "Aviv", "initials": "A", "orcid": "0000-0003-3293-3158", "researcher": {"href": "https://publications.scilifelab.se/researcher/36ee05b2a25d42769587c29b909ba9db.json"}}, {"family": "Levin", "given": "Joshua Z", "initials": "JZ", "orcid": "0000-0002-0170-3598", "researcher": {"href": "https://publications.scilifelab.se/researcher/6aab17c0401f44df98fa2df56e8ddcae.json"}}, {"family": "Parekh", "given": "Swati", "initials": "S", "orcid": "0000-0002-4826-1651", "researcher": {"href": "https://publications.scilifelab.se/researcher/aeed2ef091514d25aa845563f9c41687.json"}}, {"family": "Janjic", "given": "Aleksandar", "initials": "A", "orcid": "0000-0001-7180-5381", "researcher": {"href": "https://publications.scilifelab.se/researcher/38aaef51d88e4c6795f38fb6e8cee5d5.json"}}, {"family": "Wange", "given": "Lucas E", "initials": "LE", "orcid": "0000-0002-3275-9156", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d25e9c8662444ecaad76339843df61e.json"}}, {"family": "Bagnoli", "given": "Johannes W", "initials": "JW"}, {"family": "Enard", "given": "Wolfgang", "initials": "W", "orcid": "0000-0002-4056-0550", "researcher": {"href": "https://publications.scilifelab.se/researcher/5bc85b7ab2ce48408c3d9e00895a7cbf.json"}}, {"family": "Gut", "given": "Marta", "initials": "M"}, {"family": "Sandberg", "given": "Rickard", "initials": "R", "orcid": "0000-0001-6473-1740", "researcher": {"href": "https://publications.scilifelab.se/researcher/048c7c9b9edb4366bac7873daad461cd.json"}}, {"family": "Nikaido", "given": "Itoshi", "initials": "I", "orcid": "0000-0002-7261-2570", "researcher": {"href": "https://publications.scilifelab.se/researcher/c5c5e9ef375146618fb7fbe1c95c2104.json"}}, {"family": "Gut", "given": "Ivo", "initials": "I", "orcid": "0000-0001-7219-632X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c14600c4e0d54a7aae393c728d9af088.json"}}, {"family": "Stegle", "given": "Oliver", "initials": "O"}, {"family": "Heyn", "given": "Holger", "initials": "H", "orcid": "0000-0002-3276-1889", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7f8103bc9af4fb5a3bd1d544648e588.json"}}], "type": "journal article", "published": "2020-06-00", "journal": {"title": "Nat. Biotechnol.", "issn": "1546-1696", "volume": "38", "issue": "6", "pages": "747-755", "issn-l": "1087-0156"}, "abstract": "Single-cell RNA sequencing (scRNA-seq) is the leading technique for characterizing the transcriptomes of individual cells in a sample. The latest protocols are scalable to thousands of cells and are being used to compile cell atlases of tissues, organs and organisms. However, the protocols differ substantially with respect to their RNA capture efficiency, bias, scale and costs, and their relative advantages for different applications are unclear. In the present study, we generated benchmark datasets to systematically evaluate protocols in terms of their power to comprehensively describe cell types and states. We performed a multicenter study comparing 13 commonly used scRNA-seq and single-nucleus RNA-seq protocols applied to a heterogeneous reference sample resource. Comparative analysis revealed marked differences in protocol performance. The protocols differed in library complexity and their ability to detect cell-type markers, impacting their predictive value and suitability for integration into reference cell atlases. These results provide guidance both for individual researchers and for consortium projects such as the Human Cell Atlas.", "doi": "10.1038/s41587-020-0469-4", "pmid": "32518403", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41587-020-0469-4"}], "notes": [], "created": "2020-07-08T13:04:12.225Z", "modified": "2021-11-10T12:50:42.946Z"}]}