{"entity": "researcher", "timestamp": "2026-05-17T09:36:49.176Z", "family": "Regev", "given": "Aviv", "initials": "A", "orcid": "0000-0003-3293-3158", "affiliations": ["Broad Institute of MIT and Harvard, Cambridge, United States", "Department of Biology, Massachusetts Institute of Technology, Cambridge, United States", "Howard Hughes Medical Institute, Chevy Chase, United States"], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca26c12602774846b5d8156baf52dfb6.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca26c12602774846b5d8156baf52dfb6"}}, "publications": [{"entity": "publication", "iuid": "ae2005392bb1435d82f88df1dfd6bbe4", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ae2005392bb1435d82f88df1dfd6bbe4.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ae2005392bb1435d82f88df1dfd6bbe4"}}, "title": "Tissue and cellular spatiotemporal dynamics in colon aging", "authors": [{"family": "Daly", "given": "Aidan C", "initials": "AC"}, {"family": "Cambuli", "given": "Francesco", "initials": "F"}, {"family": "\u00c4ij\u00f6", "given": "Tarmo", "initials": "T", "orcid": "0000-0002-3008-4634", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d1b52cf5dea442c6bbee87f3507cadb4.json"}}, {"family": "L\u00f6tstedt", "given": "Britta", "initials": "B", "orcid": "0000-0003-3545-5489", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5865e21892fd48e09972aca7b3d11d9b.json"}}, {"family": "Marjanovic", "given": "Nemanja Despot", "initials": "ND"}, {"family": "Fernandez", "given": "Sara", "initials": "S", "orcid": "0000-0003-2281-4526", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f642f817ac8342f7a8987c27fa061f6a.json"}}, {"family": "Kuksenko", "given": "Olena", "initials": "O"}, {"family": "Smith-Erb", "given": "Matthew", "initials": "M"}, {"family": "Domovic", "given": "Daniel", "initials": "D", "orcid": "0000-0003-4576-7988", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5f1072e5f9e44a23b79151629a1c7312.json"}}, {"family": "Van Wittenberghe", "given": "Nicholas", "initials": "N"}, {"family": "Drokhlyansky", "given": "Eugene", "initials": "E"}, {"family": "Griffin", "given": "Gabriel K", "initials": "GK", "orcid": "0000-0002-4042-6757", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f6153204e19d4660b640dc4467605973.json"}}, {"family": "Phatnani", "given": "Hemali", "initials": "H", "orcid": "0000-0002-6571-3891", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4495ea85d87a45878b4e14c5e23bd361.json"}}, {"family": "Bonneau", "given": "Richard", "initials": "R", "orcid": "0000-0003-4354-7906", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c7a43f8ee4a542cea7ecb8dcb23d170b.json"}}, {"family": "Regev", "given": "Aviv", "initials": "A", "orcid": "0000-0003-3293-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca26c12602774846b5d8156baf52dfb6.json"}}, {"family": "Vickovic", "given": "Sanja", "initials": "S", "orcid": "0000-0003-0985-9885", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2d4188f01ed74ba499ef845e0ad9fe97.json"}}], "type": "journal-article", "published": "2025-10-22", "journal": {"title": "Nat Biotechnol", "issn": "1087-0156", "issn-l": "1087-0156"}, "abstract": "Tissue structure and molecular circuitry in the colon can be profoundly impacted by systemic age-related effects but many of the underlying molecular cues remain unclear. Here, we build a cellular and spatial atlas of the colon across three anatomical regions and 11 age groups, encompassing ~1,500 mouse gut tissues profiled by spatial transcriptomics and ~400,000 single nucleus RNA-sequencing profiles. We develop a computational framework, cSplotch, which learns a hierarchical Bayesian model of spatially resolved cellular expression associated with age, tissue region and sex by leveraging histological features to share information across tissue samples and data modalities. Using this model, we identify cellular and molecular gradients along the adult colonic tract and across the main crypt axis and multicellular programs associated with aging in the large intestine. Our multimodal framework for the investigation of cell and tissue organization can aid in the understanding of cellular roles in tissue-level pathology.", "doi": "10.1038/s41587-025-02830-6", "pmid": "41125832", "labels": {"Sanja Vickovic": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "10.1038/s41587-025-02830-6"}], "notes": [], "created": "2025-10-30T14:08:07.365Z", "modified": "2025-12-04T16:47:00.987Z"}, {"entity": "publication", "iuid": "837a6cde941b4d4e9486efa8a156a7b5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/837a6cde941b4d4e9486efa8a156a7b5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/837a6cde941b4d4e9486efa8a156a7b5"}}, "title": "Spatial host-microbiome sequencing reveals niches in the mouse gut.", "authors": [{"family": "L\u00f6tstedt", "given": "Britta", "initials": "B"}, {"family": "Stra\u017ear", "given": "Martin", "initials": "M", "orcid": "0000-0003-3064-1055", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ee6e09d221f246f6acaf95f4b6814036.json"}}, {"family": "Xavier", "given": "Ramnik", "initials": "R"}, {"family": "Regev", "given": "Aviv", "initials": "A", "orcid": "0000-0003-3293-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca26c12602774846b5d8156baf52dfb6.json"}}, {"family": "Vickovic", "given": "Sanja", "initials": "S", "orcid": "0000-0003-0985-9885", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2d4188f01ed74ba499ef845e0ad9fe97.json"}}], "type": "journal article", "published": "2023-11-20", "journal": {"title": "Nat. Biotechnol.", "issn": "1546-1696", "issn-l": "1087-0156"}, "abstract": "Mucosal and barrier tissues, such as the gut, lung or skin, are composed of a complex network of cells and microbes forming a tight niche that prevents pathogen colonization and supports host-microbiome symbiosis. Characterizing these networks at high molecular and cellular resolution is crucial for understanding homeostasis and disease. Here we present spatial host-microbiome sequencing (SHM-seq), an all-sequencing-based approach that captures tissue histology, polyadenylated RNAs and bacterial 16S sequences directly from a tissue by modifying spatially barcoded glass surfaces to enable simultaneous capture of host transcripts and hypervariable regions of the 16S bacterial ribosomal RNA. We applied our approach to the mouse gut as a model system, used a deep learning approach for data mapping and detected spatial niches defined by cellular composition and microbial geography. We show that subpopulations of gut cells express specific gene programs in different microenvironments characteristic of regional commensal bacteria and impact host-bacteria interactions. SHM-seq should enhance the study of native host-microbe interactions in health and disease.", "doi": "10.1038/s41587-023-01988-1", "pmid": "37985876", "labels": {"Sanja Vickovic": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "10.1038/s41587-023-01988-1"}], "notes": [], "created": "2023-12-03T15:48:49.796Z", "modified": "2023-12-03T15:48:49.841Z"}, {"entity": "publication", "iuid": "9ab88ab53119448d933cf0ad7207726a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9ab88ab53119448d933cf0ad7207726a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9ab88ab53119448d933cf0ad7207726a"}}, "title": "In silico tissue generation and power analysis for spatial omics.", "authors": [{"family": "Baker", "given": "Ethan A G", "initials": "EAG", "orcid": "0000-0003-1833-8053", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c7dccb07230f43c895ec6931f82d6b90.json"}}, {"family": "Schapiro", "given": "Denis", "initials": "D", "orcid": "0000-0002-9391-5722", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f4b55f07bfc0474dbdad813fa2d11e7e.json"}}, {"family": "Dumitrascu", "given": "Bianca", "initials": "B", "orcid": "0000-0001-8328-2354", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/30b0ab95a3cd4138abbae61c6b98819f.json"}}, {"family": "Vickovic", "given": "Sanja", "initials": "S", "orcid": "0000-0003-0985-9885", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2d4188f01ed74ba499ef845e0ad9fe97.json"}}, {"family": "Regev", "given": "Aviv", "initials": "A", "orcid": "0000-0003-3293-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca26c12602774846b5d8156baf52dfb6.json"}}], "type": "journal article", "published": "2023-03-00", "journal": {"title": "Nat. Methods", "issn": "1548-7105", "volume": "20", "issue": "3", "pages": "424-431", "issn-l": "1548-7091"}, "abstract": "As spatially resolved multiplex profiling of RNA and proteins becomes more prominent, it is increasingly important to understand the statistical power available to test specific hypotheses when designing and interpreting such experiments. Ideally, it would be possible to create an oracle that predicts sampling requirements for generalized spatial experiments. However, the unknown number of relevant spatial features and the complexity of spatial data analysis make this challenging. Here, we enumerate multiple parameters of interest that should be considered in the design of a properly powered spatial omics study. We introduce a method for tunable in silico tissue (IST) generation and use it with spatial profiling data sets to construct an exploratory computational framework for spatial power analysis. Finally, we demonstrate that our framework can be applied across diverse spatial data modalities and tissues of interest. While we demonstrate ISTs in the context of spatial power analysis, these simulated tissues have other potential use cases, including spatial method benchmarking and optimization.", "doi": "10.1038/s41592-023-01766-6", "pmid": "36864197", "labels": {"Sanja Vickovic": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC9998272"}, {"db": "pii", "key": "10.1038/s41592-023-01766-6"}], "notes": [], "created": "2023-12-03T15:45:45.399Z", "modified": "2023-12-03T15:45:45.539Z"}, {"entity": "publication", "iuid": "e267160a56c248bb89f587879aefbc77", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e267160a56c248bb89f587879aefbc77.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e267160a56c248bb89f587879aefbc77"}}, "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-affiliated.scilifelab.se/researcher/2d4188f01ed74ba499ef845e0ad9fe97.json"}}, {"family": "Schapiro", "given": "Denis", "initials": "D", "orcid": "0000-0002-9391-5722", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f4b55f07bfc0474dbdad813fa2d11e7e.json"}}, {"family": "Carlberg", "given": "Konstantin", "initials": "K", "orcid": "0000-0002-1774-6058", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5a1be27e2c624fb292bd1516a91a5161.json"}}, {"family": "L\u00f6tstedt", "given": "Britta", "initials": "B"}, {"family": "Larsson", "given": "Ludvig", "initials": "L", "orcid": "0000-0003-4209-2911", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/36ad34c94b64432ab74d61fbc6d16905.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-affiliated.scilifelab.se/researcher/833b610a34424918827421ae3c8dc8c3.json"}}, {"family": "Malmstr\u00f6m", "given": "Vivianne", "initials": "V", "orcid": "0000-0001-9251-8082", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/206e1bc761464dd3bc906afdee8c49c2.json"}}, {"family": "Regev", "given": "Aviv", "initials": "A", "orcid": "0000-0003-3293-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca26c12602774846b5d8156baf52dfb6.json"}}, {"family": "St\u00e5hl", "given": "Patrik L", "initials": "PL", "orcid": "0000-0002-2207-7370", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/132000c8241249d9b2c4cfeb4a058862.json"}}], "type": "journal article", "published": "2022-02-11", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "5", "issue": "1", "pages": "129", "issn-l": "2399-3642"}, "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": {"Sanja Vickovic": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC8837632"}, {"db": "pii", "key": "10.1038/s42003-022-03050-3"}], "notes": [], "created": "2023-12-03T15:46:02.170Z", "modified": "2023-12-03T15:46:02.394Z"}, {"entity": "publication", "iuid": "ab667d31fb0e4bbeb87d2e9af420d3ab", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ab667d31fb0e4bbeb87d2e9af420d3ab.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ab667d31fb0e4bbeb87d2e9af420d3ab"}}, "title": "SM-Omics is an automated platform for high-throughput spatial multi-omics.", "authors": [{"family": "Vickovic", "given": "S", "initials": "S", "orcid": "0000-0003-0985-9885", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2d4188f01ed74ba499ef845e0ad9fe97.json"}}, {"family": "L\u00f6tstedt", "given": "B", "initials": "B", "orcid": "0000-0003-3545-5489", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5865e21892fd48e09972aca7b3d11d9b.json"}}, {"family": "Klughammer", "given": "J", "initials": "J", "orcid": "0000-0002-3628-9278", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8e55a4df3bef48e1a3980d9186dbe987.json"}}, {"family": "Mages", "given": "S", "initials": "S"}, {"family": "Segerstolpe", "given": "\u00c5", "initials": "\u00c5"}, {"family": "Rozenblatt-Rosen", "given": "O", "initials": "O", "orcid": "0000-0001-6313-3570", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8d219a623b5d4e46af7841b1f32036c3.json"}}, {"family": "Regev", "given": "A", "initials": "A", "orcid": "0000-0003-3293-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca26c12602774846b5d8156baf52dfb6.json"}}], "type": "journal article", "published": "2022-02-10", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "13", "issue": "1", "pages": "795", "issn-l": "2041-1723"}, "abstract": "The spatial organization of cells and molecules plays a key role in tissue function in homeostasis and disease. Spatial transcriptomics has recently emerged as a key technique to capture and positionally barcode RNAs directly in tissues. Here, we advance the application of spatial transcriptomics at scale, by presenting Spatial Multi-Omics (SM-Omics) as a fully automated, high-throughput all-sequencing based platform for combined and spatially resolved transcriptomics and antibody-based protein measurements. SM-Omics uses DNA-barcoded antibodies, immunofluorescence or a combination thereof, to scale and combine spatial transcriptomics and spatial antibody-based multiplex protein detection. SM-Omics allows processing of up to 64 in situ spatial reactions or up to 96 sequencing-ready libraries, of high complexity, in a ~2 days process. We demonstrate SM-Omics in the mouse brain, spleen and colorectal cancer model, showing its broad utility as a high-throughput platform for spatial multi-omics.", "doi": "10.1038/s41467-022-28445-y", "pmid": "35145087", "labels": {"Sanja Vickovic": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC8831571"}, {"db": "pii", "key": "10.1038/s41467-022-28445-y"}], "notes": [], "created": "2023-12-03T15:46:04.963Z", "modified": "2023-12-03T15:46:05.108Z"}, {"entity": "publication", "iuid": "c8759874a4b74e2a9f869b5d19f34aef", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c8759874a4b74e2a9f869b5d19f34aef.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c8759874a4b74e2a9f869b5d19f34aef"}}, "title": "Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram.", "authors": [{"family": "Biancalani", "given": "Tommaso", "initials": "T", "orcid": "0000-0001-9104-9755", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c0db684c8c3b41f583d3eac14796b940.json"}}, {"family": "Scalia", "given": "Gabriele", "initials": "G", "orcid": "0000-0003-3305-9220", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2e4f9c5c3fc14b19ac3d5a9fcaabcf8b.json"}}, {"family": "Buffoni", "given": "Lorenzo", "initials": "L", "orcid": "0000-0002-8191-3375", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a9cef96f946b49ca90a0fe209b6e63af.json"}}, {"family": "Avasthi", "given": "Raghav", "initials": "R"}, {"family": "Lu", "given": "Ziqing", "initials": "Z"}, {"family": "Sanger", "given": "Aman", "initials": "A"}, {"family": "Tokcan", "given": "Neriman", "initials": "N"}, {"family": "Vanderburg", "given": "Charles R", "initials": "CR", "orcid": "0000-0001-8979-5054", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6eca16a567a143efb31a1d0fd21af6e7.json"}}, {"family": "Segerstolpe", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Zhang", "given": "Meng", "initials": "M", "orcid": "0000-0002-9753-0635", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/16800f4a30db4dc4bc6a042714a346df.json"}}, {"family": "Avraham-Davidi", "given": "Inbal", "initials": "I"}, {"family": "Vickovic", "given": "Sanja", "initials": "S", "orcid": "0000-0003-0985-9885", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2d4188f01ed74ba499ef845e0ad9fe97.json"}}, {"family": "Nitzan", "given": "Mor", "initials": "M"}, {"family": "Ma", "given": "Sai", "initials": "S", "orcid": "0000-0002-9785-7929", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/176a5249c3a84883962824fdd8f6f260.json"}}, {"family": "Subramanian", "given": "Ayshwarya", "initials": "A"}, {"family": "Lipinski", "given": "Michal", "initials": "M", "orcid": "0000-0001-8200-5056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1b30db3ed19043e6876dddc2fab1a7f3.json"}}, {"family": "Buenrostro", "given": "Jason", "initials": "J"}, {"family": "Brown", "given": "Nik Bear", "initials": "NB"}, {"family": "Fanelli", "given": "Duccio", "initials": "D", "orcid": "0000-0001-8545-9424", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a2e28fc1550341db90fdfd83c6ed6d7e.json"}}, {"family": "Zhuang", "given": "Xiaowei", "initials": "X", "orcid": "0000-0002-6034-7853", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d2d9fb3b5f054061b4787f1679db825d.json"}}, {"family": "Macosko", "given": "Evan Z", "initials": "EZ", "orcid": "0000-0002-2794-5165", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dd1d8f8392774c4dadeeeac00af7155a.json"}}, {"family": "Regev", "given": "Aviv", "initials": "A", "orcid": "0000-0003-3293-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca26c12602774846b5d8156baf52dfb6.json"}}], "type": "journal article", "published": "2021-11-00", "journal": {"title": "Nat. Methods", "issn": "1548-7105", "volume": "18", "issue": "11", "pages": "1352-1362", "issn-l": "1548-7091"}, "abstract": "Charting an organs' biological atlas requires us to spatially resolve the entire single-cell transcriptome, and to relate such cellular features to the anatomical scale. Single-cell and single-nucleus RNA-seq (sc/snRNA-seq) can profile cells comprehensively, but lose spatial information. Spatial transcriptomics allows for spatial measurements, but at lower resolution and with limited sensitivity. Targeted in situ technologies solve both issues, but are limited in gene throughput. To overcome these limitations we present Tangram, a method that aligns sc/snRNA-seq data to various forms of spatial data collected from the same region, including MERFISH, STARmap, smFISH, Spatial Transcriptomics (Visium) and histological images. Tangram can map any type of sc/snRNA-seq data, including multimodal data such as those from SHARE-seq, which we used to reveal spatial patterns of chromatin accessibility. We demonstrate Tangram on healthy mouse brain tissue, by reconstructing a genome-wide anatomically integrated spatial map at single-cell resolution of the visual and somatomotor areas.", "doi": "10.1038/s41592-021-01264-7", "pmid": "34711971", "labels": {"Sanja Vickovic": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "mid", "key": "NIHMS1732416"}, {"db": "pmc", "key": "PMC8566243"}, {"db": "pii", "key": "10.1038/s41592-021-01264-7"}], "notes": [], "created": "2023-12-03T15:47:17.533Z", "modified": "2023-12-03T15:47:17.972Z"}, {"entity": "publication", "iuid": "bd3b85ed215b4f949c6b84362c0ed2bf", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/bd3b85ed215b4f949c6b84362c0ed2bf.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/bd3b85ed215b4f949c6b84362c0ed2bf"}}, "title": "The Human Cell Atlas.", "authors": [{"family": "Regev", "given": "Aviv", "initials": "A", "orcid": "0000-0003-3293-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca26c12602774846b5d8156baf52dfb6.json"}}, {"family": "Teichmann", "given": "Sarah A", "initials": "SA"}, {"family": "Lander", "given": "Eric S", "initials": "ES"}, {"family": "Amit", "given": "Ido", "initials": "I"}, {"family": "Benoist", "given": "Christophe", "initials": "C"}, {"family": "Birney", "given": "Ewan", "initials": "E"}, {"family": "Bodenmiller", "given": "Bernd", "initials": "B"}, {"family": "Campbell", "given": "Peter", "initials": "P"}, {"family": "Carninci", "given": "Piero", "initials": "P", "orcid": "0000-0001-7202-7243", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c9101681a8aa41dab4a9345dfd03add4.json"}}, {"family": "Clatworthy", "given": "Menna", "initials": "M"}, {"family": "Clevers", "given": "Hans", "initials": "H"}, {"family": "Deplancke", "given": "Bart", "initials": "B", "orcid": "0000-0001-9935-843X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/beaa96c0c3ea4fbe8f1508f96cbe7b9d.json"}}, {"family": "Dunham", "given": "Ian", "initials": "I"}, {"family": "Eberwine", "given": "James", "initials": "J"}, {"family": "Eils", "given": "Roland", "initials": "R"}, {"family": "Enard", "given": "Wolfgang", "initials": "W", "orcid": "0000-0002-4056-0550", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/717045b716ef4626b55dd5f0578c61e6.json"}}, {"family": "Farmer", "given": "Andrew", "initials": "A"}, {"family": "Fugger", "given": "Lars", "initials": "L"}, {"family": "G\u00f6ttgens", "given": "Berthold", "initials": "B", "orcid": "0000-0001-6302-5705", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8beeb19de2a446edaef1d0502d33acae.json"}}, {"family": "Hacohen", "given": "Nir", "initials": "N"}, {"family": "Haniffa", "given": "Muzlifah", "initials": "M", "orcid": "0000-0002-3927-2084", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0702147e80fd42358ad19a66451e2442.json"}}, {"family": "Hemberg", "given": "Martin", "initials": "M"}, {"family": "Kim", "given": "Seung", "initials": "S"}, {"family": "Klenerman", "given": "Paul", "initials": "P"}, {"family": "Kriegstein", "given": "Arnold", "initials": "A"}, {"family": "Lein", "given": "Ed", "initials": "E", "orcid": "0000-0001-9012-6552", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/667d53a701f24f339b9d8eec3eaaef1d.json"}}, {"family": "Linnarsson", "given": "Sten", "initials": "S"}, {"family": "Lundberg", "given": "Emma", "initials": "E"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J"}, {"family": "Majumder", "given": "Partha", "initials": "P"}, {"family": "Marioni", "given": "John C", "initials": "JC"}, {"family": "Merad", "given": "Miriam", "initials": "M"}, {"family": "Mhlanga", "given": "Musa", "initials": "M"}, {"family": "Nawijn", "given": "Martijn", "initials": "M"}, {"family": "Netea", "given": "Mihai", "initials": "M"}, {"family": "Nolan", "given": "Garry", "initials": "G"}, {"family": "Pe'er", "given": "Dana", "initials": "D"}, {"family": "Phillipakis", "given": "Anthony", "initials": "A"}, {"family": "Ponting", "given": "Chris P", "initials": "CP", "orcid": "0000-0003-0202-7816", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f3576ad4015245819becfb1296fc6e74.json"}}, {"family": "Quake", "given": "Stephen", "initials": "S"}, {"family": "Reik", "given": "Wolf", "initials": "W"}, {"family": "Rozenblatt-Rosen", "given": "Orit", "initials": "O"}, {"family": "Sanes", "given": "Joshua", "initials": "J", "orcid": "0000-0001-8926-8836", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e69f10f8f7849168bea8aa89ccfb2b3.json"}}, {"family": "Satija", "given": "Rahul", "initials": "R", "orcid": "0000-0001-9448-8833", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8805ad737eca413bbccd997370c912ee.json"}}, {"family": "Schumacher", "given": "Ton N", "initials": "TN"}, {"family": "Shalek", "given": "Alex", "initials": "A"}, {"family": "Shapiro", "given": "Ehud", "initials": "E"}, {"family": "Sharma", "given": "Padmanee", "initials": "P"}, {"family": "Shin", "given": "Jay W", "initials": "JW"}, {"family": "Stegle", "given": "Oliver", "initials": "O"}, {"family": "Stratton", "given": "Michael", "initials": "M"}, {"family": "Stubbington", "given": "Michael J T", "initials": "MJT"}, {"family": "Theis", "given": "Fabian J", "initials": "FJ"}, {"family": "Uhlen", "given": "Matthias", "initials": "M"}, {"family": "van Oudenaarden", "given": "Alexander", "initials": "A"}, {"family": "Wagner", "given": "Allon", "initials": "A"}, {"family": "Watt", "given": "Fiona", "initials": "F", "orcid": "0000-0001-9151-5154", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/aa3563c602e24683a6a16778d03442b5.json"}}, {"family": "Weissman", "given": "Jonathan", "initials": "J", "orcid": "0000-0003-2445-670X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/167955ef29a6467da39978796a45b39d.json"}}, {"family": "Wold", "given": "Barbara", "initials": "B"}, {"family": "Xavier", "given": "Ramnik", "initials": "R"}, {"family": "Yosef", "given": "Nir", "initials": "N", "orcid": "0000-0001-9004-1225", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b325de62489b41a0b7c8754d6f54d42b.json"}}, {"family": "Human Cell Atlas Meeting Participants", "given": "", "initials": ""}], "type": "journal article", "published": "2017-12-05", "journal": {"title": "Elife", "issn": "2050-084X", "volume": "6", "issue": null, "issn-l": "2050-084X"}, "abstract": "The recent advent of methods for high-throughput single-cell molecular profiling has catalyzed a growing sense in the scientific community that the time is ripe to complete the 150-year-old effort to identify all cell types in the human body. The Human Cell Atlas Project is an international collaborative effort that aims to define all human cell types in terms of distinctive molecular profiles (such as gene expression profiles) and to connect this information with classical cellular descriptions (such as location and morphology). An open comprehensive reference map of the molecular state of cells in healthy human tissues would propel the systematic study of physiological states, developmental trajectories, regulatory circuitry and interactions of cells, and also provide a framework for understanding cellular dysregulation in human disease. Here we describe the idea, its potential utility, early proofs-of-concept, and some design considerations for the Human Cell Atlas, including a commitment to open data, code, and community.", "doi": "10.7554/eLife.27041", "pmid": "29206104", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pmc", "key": "PMC5762154"}, {"db": "pii", "key": "e27041"}], "notes": [], "created": "2018-12-05T09:23:48.756Z", "modified": "2023-06-19T14:05:56.005Z"}]}