{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,29]],"date-time":"2026-10-29T01:52:08Z","timestamp":1793238728214,"version":"4.5.0"},"reference-count":148,"publisher":"Elsevier BV","issue":"2","license":[{"start":{"date-parts":[[2024,2,1]],"date-time":"2024-02-01T00:00:00Z","timestamp":1706745600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2024,2,1]],"date-time":"2024-02-01T00:00:00Z","timestamp":1706745600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2024,1,22]],"date-time":"2024-01-22T00:00:00Z","timestamp":1705881600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["SPP1937"],"award-info":[{"award-number":["SPP1937"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["HA5354\/10-1"],"award-info":[{"award-number":["HA5354\/10-1"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["HA5354\/13-1"],"award-info":[{"award-number":["HA5354\/13-1"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["KU1315\/14-1"],"award-info":[{"award-number":["KU1315\/14-1"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["HA5354\/12-1"],"award-info":[{"award-number":["HA5354\/12-1"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["HA5354\/8-2"],"award-info":[{"award-number":["HA5354\/8-2"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003329","name":"Ministerio de Econom\u00eda y Competitividad","doi-asserted-by":"publisher","award":["CB16\/12\/00334"],"award-info":[{"award-number":["CB16\/12\/00334"]}],"id":[{"id":"10.13039\/501100003329","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003329","name":"Ministerio de Econom\u00eda y Competitividad","doi-asserted-by":"publisher","award":["CB16\/12\/00225"],"award-info":[{"award-number":["CB16\/12\/00225"]}],"id":[{"id":"10.13039\/501100003329","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004837","name":"Ministerio de Ciencia e Innovaci\u00f3n","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004837","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100014139","name":"CIBERONC","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100014139","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012295","name":"NIHR Newcastle Biomedical Research Centre","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100012295","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002704","name":"Fundaci\u00f3n Cient\u00edfica Asociaci\u00f3n Espa\u00f1ola Contra el C\u00e1ncer","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002704","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100013114","name":"Broad Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100013114","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["223092\/Z\/21\/Z"],"award-info":[{"award-number":["223092\/Z\/21\/Z"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["220540\/Z\/20\/A"],"award-info":[{"award-number":["220540\/Z\/20\/A"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004361","name":"Krebsliga Schweiz","doi-asserted-by":"publisher","award":["BIL KLS-5130-08-2020"],"award-info":[{"award-number":["BIL KLS-5130-08-2020"]}],"id":[{"id":"10.13039\/501100004361","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000780","name":"European Union","doi-asserted-by":"publisher","award":["810287"],"award-info":[{"award-number":["810287"]}],"id":[{"id":"10.13039\/501100000780","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000289","name":"Cancer Research UK","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000289","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003741","name":"Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003741","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002924","name":"Federaci\u00f3n Espa\u00f1ola de Enfermedades Raras","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002924","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100013060","name":"European Molecular Biology Laboratory","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100013060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000781","name":"European Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000781","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100008530","name":"European Regional Development Fund","doi-asserted-by":"publisher","award":["PI19\/01772"],"award-info":[{"award-number":["PI19\/01772"]}],"id":[{"id":"10.13039\/501100008530","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005010","name":"Associazione Italiana per la Ricerca sul Cancro","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100005010","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100007601","name":"Horizon 2020","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100007601","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100014440","name":"Espa\u00f1a Ministerio de Ciencia e Innovaci\u00f3n","doi-asserted-by":"publisher","award":["PID2020-115439GB-I00"],"award-info":[{"award-number":["PID2020-115439GB-I00"]}],"id":[{"id":"10.13039\/100014440","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100014440","name":"Espa\u00f1a Ministerio de Ciencia e Innovaci\u00f3n","doi-asserted-by":"publisher","award":["RTI2018-094274-B-I00"],"award-info":[{"award-number":["RTI2018-094274-B-I00"]}],"id":[{"id":"10.13039\/100014440","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100014440","name":"Espa\u00f1a Ministerio de Ciencia e Innovaci\u00f3n","doi-asserted-by":"publisher","award":["PID2020-118167RB-I00"],"award-info":[{"award-number":["PID2020-118167RB-I00"]}],"id":[{"id":"10.13039\/100014440","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004587","name":"Instituto de Salud Carlos III","doi-asserted-by":"publisher","award":["PI19\/01772"],"award-info":[{"award-number":["PI19\/01772"]}],"id":[{"id":"10.13039\/501100004587","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002809","name":"Generalidad de Catalu\u00f1a","doi-asserted-by":"publisher","award":["2021-SGR-1343"],"award-info":[{"award-number":["2021-SGR-1343"]}],"id":[{"id":"10.13039\/501100002809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002809","name":"Generalidad de Catalu\u00f1a","doi-asserted-by":"publisher","award":["2021-SGR-1172"],"award-info":[{"award-number":["2021-SGR-1172"]}],"id":[{"id":"10.13039\/501100002809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010661","name":"Horizon 2020 Framework Programme","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100010661","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100016149","name":"New York Genome Center","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100016149","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100009691","name":"Fondation pour la Recherche Nuovo-Soldati","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100009691","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Immunity"],"published-print":{"date-parts":[[2024,2]]},"DOI":"10.1016\/j.immuni.2024.01.006","type":"journal-article","created":{"date-parts":[[2024,1,31]],"date-time":"2024-01-31T10:33:48Z","timestamp":1706697228000},"page":"379-399.e18","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":186,"title":["An atlas of cells in the human tonsil"],"prefix":"10.1016","volume":"57","author":[{"given":"Ramon","family":"Massoni-Badosa","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sergio","family":"Aguilar-Fern\u00e1ndez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juan C.","family":"Nieto","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paula","family":"Soler-Vila","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marc","family":"Elosua-Bayes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Domenica","family":"Marchese","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marta","family":"Kulis","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amaia","family":"Vilas-Zornoza","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marco Matteo","family":"B\u00fchler","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sonal","family":"Rashmi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Clara","family":"Alsinet","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ginevra","family":"Carat\u00f9","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Catia","family":"Moutinho","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sara","family":"Ruiz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Patricia","family":"Lorden","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Giulia","family":"Lunazzi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dolors","family":"Colomer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gerard","family":"Frigola","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Will","family":"Blevins","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lucia","family":"Romero-Rivero","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"V\u00edctor","family":"Jim\u00e9nez-Mart\u00ednez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna","family":"Vidal","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Judith","family":"Mateos-Jaimez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alba","family":"Maiques-Diaz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sara","family":"Ovejero","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J\u00e9r\u00f4me","family":"Moreaux","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sara","family":"Palomino","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Gomez-Cabrero","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xabier","family":"Agirre","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marc A.","family":"Weniger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hamish W.","family":"King","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lucy C.","family":"Garner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Federico","family":"Marini","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Francisco Javier","family":"Cervera-Paz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter M.","family":"Baptista","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Isabel","family":"Vilaseca","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cecilia","family":"Rosales","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Silvia","family":"Ruiz-Gasp\u00e0","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benjamin","family":"Talks","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Keval","family":"Sidhpura","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna","family":"Pascual-Reguant","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anja E.","family":"Hauser","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Muzlifah","family":"Haniffa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Felipe","family":"Prosper","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ralf","family":"K\u00fcppers","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ivo Glynne","family":"Gut","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elias","family":"Campo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jos\u00e9 Ignacio","family":"Martin-Subero","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3276-1889","authenticated-orcid":false,"given":"Holger","family":"Heyn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.immuni.2024.01.006_bib1","doi-asserted-by":"crossref","first-page":"2205","DOI":"10.4049\/jimmunol.0804324","article-title":"Secondary Lymphoid Organs: Responding to Genetic and Environmental Cues in Ontogeny and the Immune Response","volume":"183","author":"Ruddle","year":"2009","journal-title":"J.\u00a0Immunol."},{"key":"10.1016\/j.immuni.2024.01.006_bib2","doi-asserted-by":"crossref","first-page":"367","DOI":"10.1007\/s004290100210","article-title":"Morphology and immunology of the human palatine tonsil","volume":"204","author":"Nave","year":"2001","journal-title":"Anat. Embryol. (Berl.)"},{"key":"10.1016\/j.immuni.2024.01.006_bib3","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1038\/nri3804","article-title":"Dynamics of B cells in germinal centres","volume":"15","author":"De Silva","year":"2015","journal-title":"Nat. Rev. Immunol."},{"key":"10.1016\/j.immuni.2024.01.006_bib4","doi-asserted-by":"crossref","DOI":"10.1126\/science.aay3224","article-title":"A cell atlas of human thymic development defines T\u00a0cell repertoire formation","volume":"367","author":"Park","year":"2020","journal-title":"Science"},{"key":"10.1016\/j.immuni.2024.01.006_bib5","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1038\/s41556-019-0439-6","article-title":"Combined single-cell and spatial transcriptomics reveal the molecular, cellular and spatial bone marrow niche organization","volume":"22","author":"Baccin","year":"2020","journal-title":"Nat. Cell Biol."},{"key":"10.1016\/j.immuni.2024.01.006_bib6","doi-asserted-by":"crossref","first-page":"1577","DOI":"10.1038\/s41590-021-01059-0","article-title":"Single-cell proteo-genomic reference maps of the hematopoietic system enable the purification and massive profiling of precisely defined cell states","volume":"22","author":"Triana","year":"2021","journal-title":"Nat. Immunol."},{"key":"10.1016\/j.immuni.2024.01.006_bib7","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.27041","article-title":"The Human Cell Atlas","volume":"6","author":"Regev","year":"2017","journal-title":"eLife"},{"key":"10.1016\/j.immuni.2024.01.006_bib8","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1038\/s41587-021-01001-7","article-title":"Mapping single-cell data to reference atlases by transfer learning","volume":"40","author":"Lotfollahi","year":"2022","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.immuni.2024.01.006_bib9","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-021-25957-x","article-title":"Efficient and precise single-cell reference atlas mapping with Symphony","volume":"12","author":"Kang","year":"2021","journal-title":"Nat. Commun."},{"key":"10.1016\/j.immuni.2024.01.006_bib10","doi-asserted-by":"crossref","first-page":"1129","DOI":"10.1038\/s41556-021-00787-7","article-title":"Cell type ontologies of the Human Cell Atlas","volume":"23","author":"Osumi-Sutherland","year":"2021","journal-title":"Nat. Cell Biol."},{"key":"10.1016\/j.immuni.2024.01.006_bib11","doi-asserted-by":"crossref","first-page":"1145","DOI":"10.1038\/nbt.3711","article-title":"Revealing the vectors of cellular identity with single-cell genomics","volume":"34","author":"Wagner","year":"2016","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.immuni.2024.01.006_bib12","doi-asserted-by":"crossref","DOI":"10.1126\/sciimmunol.abe6291","article-title":"Single-cell analysis of human B cell maturation predicts how antibody class switching shapes selection dynamics","volume":"6","author":"King","year":"2021","journal-title":"Sci. Immunol."},{"key":"10.1016\/j.immuni.2024.01.006_bib13","doi-asserted-by":"crossref","DOI":"10.1126\/sciimmunol.abh3768","article-title":"Integrated single-cell transcriptomics and epigenomics reveals strong germinal center\u2013associated etiology of autoimmune risk loci","volume":"6","author":"King","year":"2021","journal-title":"Sci. Immunol."},{"key":"10.1016\/j.immuni.2024.01.006_bib14","doi-asserted-by":"crossref","first-page":"451","DOI":"10.1038\/ni.3368","article-title":"The heterogeneity of human CD127(+) innate lymphoid cells revealed by single-cell RNA sequencing","volume":"17","author":"Bj\u00f6rklund","year":"2016","journal-title":"Nat. Immunol."},{"key":"10.1016\/j.immuni.2024.01.006_bib15","doi-asserted-by":"crossref","first-page":"48","DOI":"10.1182\/blood-2014-05-521898","article-title":"Mantle cell lymphoma: evolving management strategies","volume":"125","author":"Campo","year":"2015","journal-title":"Blood"},{"key":"10.1016\/j.immuni.2024.01.006_bib16","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1016\/j.humpath.2021.10.001","article-title":"Mantle cell lymphoma involving tonsils: a clinicopathologic study of 83 cases","volume":"118","author":"Tashakori","year":"2021","journal-title":"Hum. Pathol."},{"key":"10.1016\/j.immuni.2024.01.006_bib17","doi-asserted-by":"crossref","first-page":"865","DOI":"10.1038\/nmeth.4380","article-title":"Simultaneous epitope and transcriptome measurement in single cells","volume":"14","author":"Stoeckius","year":"2017","journal-title":"Nat. Methods"},{"key":"10.1016\/j.immuni.2024.01.006_bib18","doi-asserted-by":"crossref","first-page":"3573","DOI":"10.1016\/j.cell.2021.04.048","article-title":"Integrated analysis of multimodal single-cell data","volume":"184","author":"Hao","year":"2021","journal-title":"Cell"},{"key":"10.1016\/j.immuni.2024.01.006_bib19","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-020-20849-y","article-title":"Dynamics of genome architecture and chromatin function during human B cell differentiation and neoplastic transformation","volume":"12","author":"Vilarrasa-Blasi","year":"2021","journal-title":"Nat. Commun."},{"key":"10.1016\/j.immuni.2024.01.006_bib20","doi-asserted-by":"crossref","first-page":"852","DOI":"10.1038\/s41590-019-0420-3","article-title":"Plasmacytoid dendritic cells develop from Ly6D+ lymphoid progenitors distinct from the myeloid lineage","volume":"20","author":"Dress","year":"2019","journal-title":"Nat. Immunol."},{"key":"10.1016\/j.immuni.2024.01.006_bib21","doi-asserted-by":"crossref","first-page":"1403","DOI":"10.1172\/JCI46125","article-title":"Evidence for a stepwise program of extrathymic T\u00a0cell development within the human tonsil","volume":"122","author":"McClory","year":"2012","journal-title":"J.\u00a0Clin. Invest."},{"key":"10.1016\/j.immuni.2024.01.006_bib22","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1177\/106689690301100105","article-title":"Lymphoid Progenitor Cells in Human Tonsils","volume":"11","author":"Strauchen","year":"2003","journal-title":"Int. J. Surg. Pathol."},{"key":"10.1016\/j.immuni.2024.01.006_bib23","doi-asserted-by":"crossref","first-page":"336","DOI":"10.1016\/j.it.2021.02.002","article-title":"Bcl6-Mediated Transcriptional Regulation of Follicular Helper T\u00a0cells (TFH)","volume":"42","author":"Choi","year":"2021","journal-title":"Trends Immunol."},{"key":"10.1016\/j.immuni.2024.01.006_bib24","doi-asserted-by":"crossref","first-page":"2247","DOI":"10.1038\/s41596-020-0336-2","article-title":"A scalable SCENIC workflow for single-cell gene regulatory network analysis","volume":"15","author":"Van de Sande","year":"2020","journal-title":"Nat. Protoc."},{"key":"10.1016\/j.immuni.2024.01.006_bib25","doi-asserted-by":"crossref","first-page":"1355","DOI":"10.1038\/s41592-023-01938-4","article-title":"SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks","volume":"20","author":"Bravo Gonz\u00e1lez-Blas","year":"2023","journal-title":"Nat. Methods"},{"key":"10.1016\/j.immuni.2024.01.006_bib26","doi-asserted-by":"crossref","first-page":"1132","DOI":"10.1016\/j.immuni.2019.04.011","article-title":"T Follicular Helper Cell Biology: A Decade of Discovery and Diseases","volume":"50","author":"Crotty","year":"2019","journal-title":"Immunity"},{"key":"10.1016\/j.immuni.2024.01.006_bib27","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1146\/annurev-immunol-041015-055605","article-title":"Follicular Helper T Cells","volume":"34","author":"Vinuesa","year":"2016","journal-title":"Annu. Rev. Immunol."},{"key":"10.1016\/j.immuni.2024.01.006_bib28","doi-asserted-by":"crossref","DOI":"10.3389\/fimmu.2021.670637","article-title":"The OX40\/OX40L Axis Regulates T Follicular Helper Cell Differentiation: Implications for Autoimmune Diseases","volume":"12","author":"Fu","year":"2021","journal-title":"Front. Immunol."},{"key":"10.1016\/j.immuni.2024.01.006_bib29","doi-asserted-by":"crossref","first-page":"529","DOI":"10.1016\/j.immuni.2014.10.004","article-title":"T Follicular Helper Cell Differentiation, Function, and Roles in Disease","volume":"41","author":"Crotty","year":"2014","journal-title":"Immunity"},{"key":"10.1016\/j.immuni.2024.01.006_bib30","doi-asserted-by":"crossref","first-page":"3719","DOI":"10.1182\/blood-2014-06-582700","article-title":"Global transcriptome analysis and enhancer landscape of human primary T follicular helper and T effector lymphocytes","volume":"124","author":"Weinstein","year":"2014","journal-title":"Blood"},{"key":"10.1016\/j.immuni.2024.01.006_bib31","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1016\/j.immuni.2016.08.012","article-title":"Multi-tiered Reorganization of the Genome during B Cell Affinity Maturation Anchored by a Germinal Center-Specific Locus Control Region","volume":"45","author":"Bunting","year":"2016","journal-title":"Immunity"},{"key":"10.1016\/j.immuni.2024.01.006_bib32","doi-asserted-by":"crossref","first-page":"2485","DOI":"10.1093\/bioinformatics\/btab003","article-title":"Nebulosa recovers single cell gene expression signals by kernel density estimation","volume":"37","author":"Alquicira-Hernandez","year":"2021","journal-title":"Bioinformatics"},{"key":"10.1016\/j.immuni.2024.01.006_bib33","doi-asserted-by":"crossref","first-page":"3931","DOI":"10.4049\/jimmunol.1701134","article-title":"Cutting Edge: c-Maf Is Required for Regulatory T Cells To Adopt ROR\u03b3t\u00a0+ and Follicular Phenotypes","volume":"199","author":"Wheaton","year":"2017","journal-title":"J.\u00a0Immunol."},{"key":"10.1016\/j.immuni.2024.01.006_bib34","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2111315118","article-title":"Profound Treg perturbations correlate with COVID-19 severity","volume":"118","author":"Galv\u00e1n-Pe\u00f1a","year":"2021","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.immuni.2024.01.006_bib35","doi-asserted-by":"crossref","first-page":"3629","DOI":"10.1016\/j.celrep.2019.05.061","article-title":"TCF1 and LEF1 Control Treg Competitive Survival and Tfr Development to Prevent Autoimmune Diseases","volume":"27","author":"Yang","year":"2019","journal-title":"Cell Rep."},{"key":"10.1016\/j.immuni.2024.01.006_bib36","doi-asserted-by":"crossref","first-page":"1292","DOI":"10.1016\/j.celrep.2019.12.099","article-title":"Human Fc Receptor-like 3 Inhibits Regulatory T Cell Function and Binds Secretory IgA","volume":"30","author":"Agarwal","year":"2020","journal-title":"Cell Rep."},{"key":"10.1016\/j.immuni.2024.01.006_bib37","doi-asserted-by":"crossref","first-page":"E6400","DOI":"10.1073\/pnas.1705551114","article-title":"A distinct subpopulation of CD25\u00a0\u2212 T-follicular regulatory cells localizes in the germinal centers","volume":"114","author":"Wing","year":"2017","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.immuni.2024.01.006_bib38","doi-asserted-by":"crossref","first-page":"1290","DOI":"10.1038\/nm.2446","article-title":"A human memory T\u00a0cell subset with stem cell\u2013like properties","volume":"17","author":"Gattinoni","year":"2011","journal-title":"Nat. Med."},{"key":"10.1016\/j.immuni.2024.01.006_bib39","doi-asserted-by":"crossref","first-page":"1270","DOI":"10.1016\/j.immuni.2016.10.018","article-title":"The Chemokine Receptor CX3CR1 Defines Three Antigen-Experienced CD8\u00a0T Cell Subsets with Distinct Roles in Immune Surveillance and Homeostasis","volume":"45","author":"Gerlach","year":"2016","journal-title":"Immunity"},{"key":"10.1016\/j.immuni.2024.01.006_bib40","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1038\/s41577-021-00590-3","article-title":"The precursors of CD8+ tissue resident memory T\u00a0cells: from lymphoid organs to infected tissues","volume":"22","author":"Kok","year":"2022","journal-title":"Nat. Rev. Immunol."},{"key":"10.1016\/j.immuni.2024.01.006_bib41","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1002\/eji.1830240112","article-title":"Professional presentation of antigen by activated human T\u00a0cells","volume":"24","author":"Barnaba","year":"1994","journal-title":"Eur. J. Immunol."},{"key":"10.1016\/j.immuni.2024.01.006_bib42","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-021-21994-8","article-title":"Multiplexed histology analyses for the phenotypic and spatial characterization of human innate lymphoid cells","volume":"12","author":"Pascual-Reguant","year":"2021","journal-title":"Nat. Commun."},{"key":"10.1016\/j.immuni.2024.01.006_bib43","article-title":"CXCR5+PD-1+ follicular helper CD8 T\u00a0cells control B cell tolerance","volume":"10","author":"Chen","year":"2019","journal-title":"Nat. Commun."},{"key":"10.1016\/j.immuni.2024.01.006_bib44","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1016\/j.immuni.2017.01.003","article-title":"CD8+ T Cells Orchestrate pDC-XCR1+ Dendritic Cell Spatial and Functional Cooperativity to Optimize Priming","volume":"46","author":"Brewitz","year":"2017","journal-title":"Immunity"},{"key":"10.1016\/j.immuni.2024.01.006_bib45","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0217393","article-title":"Interaction of CD99 and its ligand upregulates IL-6 and TNF-\u03b1 upon T\u00a0cell activation","volume":"14","author":"Takheaw","year":"2019","journal-title":"PLoS One"},{"key":"10.1016\/j.immuni.2024.01.006_bib46","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2020.107773","article-title":"High CD26 and Low CD94 Expression Identifies an IL-23 Responsive V\u03b42+ T Cell Subset with a MAIT Cell-like Transcriptional Profile","volume":"31","author":"Wragg","year":"2020","journal-title":"Cell Rep."},{"key":"10.1016\/j.immuni.2024.01.006_bib47","doi-asserted-by":"crossref","DOI":"10.3389\/fimmu.2018.00756","article-title":"Unique and Common Features of Innate-Like Human V\u03b42+ \u03b3\u03b4T Cells and Mucosal-Associated Invariant T Cells","volume":"9","author":"Provine","year":"2018","journal-title":"Front. Immunol."},{"key":"10.1016\/j.immuni.2024.01.006_bib48","doi-asserted-by":"crossref","first-page":"816005","DOI":"10.3389\/fimmu.2022.816005","article-title":"CD3+CD4-CD8- (Double-Negative) T Cells in Inflammation, Immune Disorders and Cancer","volume":"13","author":"Wu","year":"2022","journal-title":"Front. Immunol."},{"key":"10.1016\/j.immuni.2024.01.006_bib49","series-title":"A Temporal Transcriptional Map\u00a0of Human Natural Killer Cell Differentiation","author":"Pfefferle","year":"2019"},{"key":"10.1016\/j.immuni.2024.01.006_bib50","doi-asserted-by":"crossref","first-page":"1033","DOI":"10.1084\/jem.20052507","article-title":"Evidence for discrete stages of human natural killer cell differentiation in\u00a0vivo","volume":"203","author":"Freud","year":"2006","journal-title":"J.\u00a0Exp. Med."},{"key":"10.1016\/j.immuni.2024.01.006_bib51","doi-asserted-by":"crossref","first-page":"1104","DOI":"10.1016\/j.immuni.2018.05.013","article-title":"Innate Lymphoid Cells: Diversity, Plasticity, and Unique Functions in Immunity","volume":"48","author":"Colonna","year":"2018","journal-title":"Immunity"},{"key":"10.1016\/j.immuni.2024.01.006_bib52","doi-asserted-by":"crossref","first-page":"1054","DOI":"10.1016\/j.cell.2018.07.017","article-title":"Innate Lymphoid Cells: 10 Years On","volume":"174","author":"Vivier","year":"2018","journal-title":"Cell"},{"key":"10.1016\/j.immuni.2024.01.006_bib53","doi-asserted-by":"crossref","first-page":"1807","DOI":"10.1084\/jem.20072682","article-title":"Discriminating gene expression profiles of memory B cell subpopulations","volume":"205","author":"Ehrhardt","year":"2008","journal-title":"J.\u00a0Exp. Med."},{"key":"10.1016\/j.immuni.2024.01.006_bib54","doi-asserted-by":"crossref","first-page":"755","DOI":"10.1093\/intimm\/dxaa053","article-title":"Fc receptor-like 4 and 5 define human atypical memory B cells","volume":"32","author":"Li","year":"2020","journal-title":"Int. Immunol."},{"key":"10.1016\/j.immuni.2024.01.006_bib55","doi-asserted-by":"crossref","first-page":"2085","DOI":"10.1084\/jem.20132019","article-title":"IKK-induced NF-\u03baB1 p105 proteolysis is critical for B cell antibody responses to T\u00a0cell-dependent antigen","volume":"211","author":"Jacque","year":"2014","journal-title":"J.\u00a0Exp. Med."},{"key":"10.1016\/j.immuni.2024.01.006_bib56","doi-asserted-by":"crossref","first-page":"679","DOI":"10.1084\/jem.176.3.679","article-title":"In situ studies of the primary immune response to (4-hydroxy-3-nitrophenyl)acetyl. II. A common clonal origin for periarteriolar lymphoid sheath-associated foci and germinal centers","volume":"176","author":"Jacob","year":"1992","journal-title":"J.\u00a0Exp. Med."},{"key":"10.1016\/j.immuni.2024.01.006_bib57","doi-asserted-by":"crossref","first-page":"597","DOI":"10.1084\/jem.20111696","article-title":"A germinal center-independent pathway generates unswitched memory B cells early in the primary response","volume":"209","author":"Taylor","year":"2012","journal-title":"J.\u00a0Exp. Med."},{"key":"10.1016\/j.immuni.2024.01.006_bib58","doi-asserted-by":"crossref","first-page":"1142","DOI":"10.1016\/j.immuni.2017.11.022","article-title":"CCR6 Defines Memory B Cell Precursors in Mouse and Human Germinal Centers, Revealing Light-Zone Location and Predominant Low Antigen Affinity","volume":"47","author":"Suan","year":"2017","journal-title":"Immunity"},{"key":"10.1016\/j.immuni.2024.01.006_bib59","doi-asserted-by":"crossref","first-page":"3372","DOI":"10.1038\/s41467-018-05772-7","article-title":"Memory B cells are reactivated in subcapsular proliferative foci of lymph nodes","volume":"9","author":"Moran","year":"2018","journal-title":"Nat. Commun."},{"key":"10.1016\/j.immuni.2024.01.006_bib60","doi-asserted-by":"crossref","first-page":"536","DOI":"10.1038\/ni.2037","article-title":"The transcription factor BATF controls the global regulators of class-switch recombination in both B cells and T\u00a0cells","volume":"12","author":"Ise","year":"2011","journal-title":"Nat. Immunol."},{"key":"10.1016\/j.immuni.2024.01.006_bib61","doi-asserted-by":"crossref","first-page":"1083","DOI":"10.1038\/ni.2428","article-title":"The proto-oncogene MYC is required for selection in the germinal center and cyclic reentry","volume":"13","author":"Dominguez-Sola","year":"2012","journal-title":"Nat. Immunol."},{"key":"10.1016\/j.immuni.2024.01.006_bib62","doi-asserted-by":"crossref","first-page":"1227","DOI":"10.1084\/jem.20160832","article-title":"Plasma cell output from germinal centers is regulated by signals from Tfh and stromal cells","volume":"215","author":"Zhang","year":"2018","journal-title":"J.\u00a0Exp. Med."},{"key":"10.1016\/j.immuni.2024.01.006_bib63","doi-asserted-by":"crossref","first-page":"1259","DOI":"10.1084\/jem.20161533","article-title":"Differentiation of germinal center B cells into plasma cells is initiated by high-affinity antigen and completed by Tfh cells","volume":"214","author":"Kr\u00e4utler","year":"2017","journal-title":"J.\u00a0Exp. Med."},{"key":"10.1016\/j.immuni.2024.01.006_bib64","doi-asserted-by":"crossref","first-page":"1216","DOI":"10.1038\/ni.3519","article-title":"Plasma cell differentiation is coupled to division-dependent DNA hypomethylation and gene regulation","volume":"17","author":"Barwick","year":"2016","journal-title":"Nat. Immunol."},{"key":"10.1016\/j.immuni.2024.01.006_bib65","doi-asserted-by":"crossref","first-page":"1059","DOI":"10.1016\/j.celrep.2015.09.051","article-title":"Cell-Cycle-Dependent Reconfiguration of the DNA Methylome during Terminal Differentiation of Human B Cells into Plasma Cells","volume":"13","author":"Caron","year":"2015","journal-title":"Cell Rep."},{"key":"10.1016\/j.immuni.2024.01.006_bib66","doi-asserted-by":"crossref","first-page":"160","DOI":"10.1038\/nri3795","article-title":"The generation of antibody-secreting plasma cells","volume":"15","author":"Nutt","year":"2015","journal-title":"Nat. Rev. Immunol."},{"key":"10.1016\/j.immuni.2024.01.006_bib67","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1007\/s00418-020-01861-1","article-title":"Plasma cells, plasmablasts, and AID+\/CD30+ B lymphoblasts inside and outside germinal centres: details of the basal light zone and the outer zone in human palatine tonsils","volume":"154","author":"Steiniger","year":"2020","journal-title":"Histochem. Cell Biol."},{"key":"10.1016\/j.immuni.2024.01.006_bib68","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1084\/jem.20072049","article-title":"Oct2 enhances antibody-secreting cell differentiation through regulation of IL-5 receptor \u03b1 chain expression on activated B cells","volume":"205","author":"Emslie","year":"2008","journal-title":"J.\u00a0Exp. Med."},{"key":"10.1016\/j.immuni.2024.01.006_bib69","doi-asserted-by":"crossref","first-page":"7105","DOI":"10.1093\/emboj\/16.23.7105","article-title":"Using altered specificity Oct-1 and Oct-2 mutants to analyze the regulation of immunoglobulin gene transcription","volume":"16","author":"Shah","year":"1997","journal-title":"EMBO J."},{"key":"10.1016\/j.immuni.2024.01.006_bib70","doi-asserted-by":"crossref","DOI":"10.3389\/fimmu.2014.00108","article-title":"Oct2 and Obf1 as Facilitators of B:T Cell Collaboration during a Humoral Immune Response","volume":"5","author":"Corcoran","year":"2014","journal-title":"Front. Immunol."},{"key":"10.1016\/j.immuni.2024.01.006_bib71","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1186\/s13075-017-1231-2","article-title":"Circulating plasmablasts\/plasma cells: a potential biomarker for IgG4-related disease","volume":"19","author":"Lin","year":"2017","journal-title":"Arthritis Res. Ther."},{"key":"10.1016\/j.immuni.2024.01.006_bib72","doi-asserted-by":"crossref","first-page":"14338","DOI":"10.1038\/s41598-018-32705-7","article-title":"Site-1 protease function is essential for the generation of antibody secreting cells and reprogramming for secretory activity","volume":"8","author":"Al-Maskari","year":"2018","journal-title":"Sci. Rep."},{"key":"10.1016\/j.immuni.2024.01.006_bib73","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1038\/75500","article-title":"Heterozygous loss of Six5 in mice is sufficient to cause ocular cataracts","volume":"25","author":"Sarkar","year":"2000","journal-title":"Nat. Genet."},{"key":"10.1016\/j.immuni.2024.01.006_bib74","doi-asserted-by":"crossref","first-page":"1421","DOI":"10.1093\/hmg\/ddh161","article-title":"Six5 is required for spermatogenic cell survival and spermiogenesis","volume":"13","author":"Sarkar","year":"2004","journal-title":"Hum. Mol. Genet."},{"key":"10.1016\/j.immuni.2024.01.006_bib75","doi-asserted-by":"crossref","first-page":"821","DOI":"10.1038\/s41467-019-08679-z","article-title":"Long non-coding RNAs discriminate the stages and gene regulatory states of human humoral immune response","volume":"10","author":"Agirre","year":"2019","journal-title":"Nat. Commun."},{"key":"10.1016\/j.immuni.2024.01.006_bib76","doi-asserted-by":"crossref","first-page":"868","DOI":"10.1038\/s41591-018-0028-4","article-title":"The reference epigenome and regulatory chromatin landscape of chronic lymphocytic leukemia","volume":"24","author":"Beekman","year":"2018","journal-title":"Nat. Med."},{"key":"10.1016\/j.immuni.2024.01.006_bib77","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1016\/j.exphem.2018.09.004","article-title":"The Human Cell Atlas bone marrow single-cell interactive web portal","volume":"68","author":"Hay","year":"2018","journal-title":"Exp. Hematol."},{"key":"10.1016\/j.immuni.2024.01.006_bib78","doi-asserted-by":"crossref","first-page":"1451","DOI":"10.1038\/s41375-021-01234-0","article-title":"RNA-sequencing data-driven dissection of human plasma cell differentiation reveals new potential transcription regulators","volume":"35","author":"Kassambara","year":"2021","journal-title":"Leukemia"},{"key":"10.1016\/j.immuni.2024.01.006_bib79","doi-asserted-by":"crossref","first-page":"17046","DOI":"10.1038\/nrdp.2017.46","article-title":"Multiple myeloma","volume":"3","author":"Kumar","year":"2017","journal-title":"Nat. Rev. Dis. Primers"},{"key":"10.1016\/j.immuni.2024.01.006_bib80","doi-asserted-by":"crossref","first-page":"4090","DOI":"10.1016\/j.cell.2021.05.013","article-title":"Human oral mucosa cell atlas reveals a stromal-neutrophil axis regulating tissue immunity","volume":"184","author":"Williams","year":"2021","journal-title":"Cell"},{"key":"10.1016\/j.immuni.2024.01.006_bib81","doi-asserted-by":"crossref","first-page":"2381","DOI":"10.4049\/jimmunol.169.5.2381","article-title":"FDC-SP, a novel secreted protein expressed by follicular dendritic cells","volume":"169","author":"Marshall","year":"2002","journal-title":"J.\u00a0Immunol."},{"key":"10.1016\/j.immuni.2024.01.006_bib82","doi-asserted-by":"crossref","DOI":"10.1084\/jem.20210790","article-title":"Characterization of human FDCs reveals regulation of T\u00a0cells and antigen presentation to B cells","volume":"218","author":"Heesters","year":"2021","journal-title":"J.\u00a0Exp. Med."},{"key":"10.1016\/j.immuni.2024.01.006_bib83","doi-asserted-by":"crossref","first-page":"194","DOI":"10.1016\/j.cell.2012.05.032","article-title":"Follicular Dendritic Cells Emerge from Ubiquitous Perivascular Precursors","volume":"150","author":"Krautler","year":"2012","journal-title":"Cell"},{"key":"10.1016\/j.immuni.2024.01.006_bib84","doi-asserted-by":"crossref","first-page":"2862","DOI":"10.1158\/1078-0432.CCR-13-2367","article-title":"Pattern of CD14+ follicular dendritic cells and PD1+ T\u00a0cells independently predicts time to transformation in follicular lymphoma","volume":"20","author":"Smeltzer","year":"2014","journal-title":"Clin. Cancer Res."},{"key":"10.1016\/j.immuni.2024.01.006_bib85","doi-asserted-by":"crossref","DOI":"10.1126\/science.aah4573","article-title":"Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors","volume":"356","author":"Villani","year":"2017","journal-title":"Science"},{"key":"10.1016\/j.immuni.2024.01.006_bib86","doi-asserted-by":"crossref","first-page":"1902","DOI":"10.1016\/j.celrep.2018.07.033","article-title":"Large-Scale Human Dendritic Cell Differentiation Revealing Notch-Dependent Lineage Bifurcation and Heterogeneity","volume":"24","author":"Balan","year":"2018","journal-title":"Cell Rep."},{"key":"10.1016\/j.immuni.2024.01.006_bib87","doi-asserted-by":"crossref","first-page":"1062","DOI":"10.1016\/j.it.2020.10.002","article-title":"Decoding the Heterogeneity of Human Dendritic Cell Subsets","volume":"41","author":"Villar","year":"2020","journal-title":"Trends Immunol."},{"key":"10.1016\/j.immuni.2024.01.006_bib88","doi-asserted-by":"crossref","DOI":"10.1126\/sciimmunol.abl5053","article-title":"Single-cell multiomics defines tolerogenic extrathymic Aire-expressing populations with unique homology to thymic epithelium","volume":"6","author":"Wang","year":"2021","journal-title":"Sci. Immunol."},{"key":"10.1016\/j.immuni.2024.01.006_bib89","doi-asserted-by":"crossref","first-page":"560","DOI":"10.1016\/j.immuni.2013.08.005","article-title":"Extrathymic Aire-expressing cells are a distinct bone marrow-derived population that induce functional inactivation of CD4+ T\u00a0cells","volume":"39","author":"Gardner","year":"2013","journal-title":"Immunity"},{"key":"10.1016\/j.immuni.2024.01.006_bib90","doi-asserted-by":"crossref","first-page":"1104","DOI":"10.2353\/ajpath.2010.090956","article-title":"Human peripheral lymphoid tissues contain autoimmune regulator-expressing dendritic cells","volume":"176","author":"Poliani","year":"2010","journal-title":"Am. J. Pathol."},{"key":"10.1016\/j.immuni.2024.01.006_bib91","doi-asserted-by":"crossref","first-page":"9269","DOI":"10.1096\/fj.202000181R","article-title":"Deciphering the fate of slan+-monocytes in human tonsils by gene expression profiling","volume":"34","author":"Bianchetto-Aguilera","year":"2020","journal-title":"FASEB J."},{"key":"10.1016\/j.immuni.2024.01.006_bib92","doi-asserted-by":"crossref","DOI":"10.1038\/sdata.2016.18","article-title":"The FAIR Guiding Principles for scientific data management and stewardship","volume":"3","author":"Wilkinson","year":"2016","journal-title":"Sci. Data"},{"key":"10.1016\/j.immuni.2024.01.006_bib93","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1038\/s41592-019-0654-x","article-title":"Orchestrating single-cell analysis with Bioconductor","volume":"17","author":"Amezquita","year":"2020","journal-title":"Nat. Methods"},{"key":"10.1016\/j.immuni.2024.01.006_bib94","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1186\/s13059-017-1382-0","article-title":"SCANPY: large-scale single-cell gene expression data analysis","volume":"19","author":"Wolf","year":"2018","journal-title":"Genome Biol."},{"key":"10.1016\/j.immuni.2024.01.006_bib95","series-title":"zellkonverter: Conversion Between scRNA-seq Objects","author":"Zappia","year":"2023"},{"key":"10.1016\/j.immuni.2024.01.006_bib96","doi-asserted-by":"crossref","DOI":"10.12688\/f1000research.14966.1","article-title":"iSEE: Interactive SummarizedExperiment Explorer","volume":"7","author":"Rue-Albrecht","year":"2018","journal-title":"F1000Res"},{"key":"10.1016\/j.immuni.2024.01.006_bib97","doi-asserted-by":"crossref","first-page":"1563","DOI":"10.1038\/s41591-023-02327-2","article-title":"An integrated cell atlas of the lung in health and disease","volume":"29","author":"Sikkema","year":"2023","journal-title":"Nat. Med."},{"key":"10.1016\/j.immuni.2024.01.006_bib98","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-021-27150-6","article-title":"scCODA is a Bayesian model for compositional single-cell data analysis","volume":"12","author":"B\u00fcttner","year":"2021","journal-title":"Nat. Commun."},{"key":"10.1016\/j.immuni.2024.01.006_bib99","doi-asserted-by":"crossref","first-page":"624","DOI":"10.1038\/s41586-023-06234-x","article-title":"Y chromosome loss in cancer drives growth by evasion of adaptive immunity","volume":"619","author":"Abdel-Hafiz","year":"2023","journal-title":"Nature"},{"key":"10.1016\/j.immuni.2024.01.006_bib100","doi-asserted-by":"crossref","first-page":"949","DOI":"10.3324\/haematol.12656","article-title":"Recurrent loss of the Y chromosome and homozygous deletions within the pseudoautosomal region 1: association with male predominance in mantle cell lymphoma","volume":"93","author":"Niel\u00e4nder","year":"2008","journal-title":"Haematologica"},{"key":"10.1016\/j.immuni.2024.01.006_bib101","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1126\/science.aad0501","article-title":"Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq","volume":"352","author":"Tirosh","year":"2016","journal-title":"Science"},{"key":"10.1016\/j.immuni.2024.01.006_bib102","doi-asserted-by":"crossref","first-page":"1192","DOI":"10.1038\/s41588-022-01141-9","article-title":"Cancer cell states recur across tumor types and form specific interactions with the tumor microenvironment","volume":"54","author":"Barkley","year":"2022","journal-title":"Nat. Genet."},{"key":"10.1016\/j.immuni.2024.01.006_bib103","series-title":"Functional plasticity and recurrent cell states of malignant B cells in follicular lymphoma","author":"Attaf","year":"2022"},{"key":"10.1016\/j.immuni.2024.01.006_bib104","doi-asserted-by":"crossref","first-page":"1777","DOI":"10.1016\/j.cell.2022.04.003","article-title":"Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays","volume":"185","author":"Chen","year":"2022","journal-title":"Cell"},{"key":"10.1016\/j.immuni.2024.01.006_bib105","doi-asserted-by":"crossref","first-page":"3559","DOI":"10.1016\/j.cell.2021.05.010","article-title":"Microscopic examination of spatial transcriptome using Seq-Scope","volume":"184","author":"Cho","year":"2021","journal-title":"Cell"},{"key":"10.1016\/j.immuni.2024.01.006_bib106","doi-asserted-by":"crossref","first-page":"1333","DOI":"10.1038\/s41592-021-01282-5","article-title":"Single-cell chromatin state analysis with Signac","volume":"18","author":"Stuart","year":"2021","journal-title":"Nat. Methods"},{"key":"10.1016\/j.immuni.2024.01.006_bib107","doi-asserted-by":"crossref","first-page":"1289","DOI":"10.1038\/s41592-019-0619-0","article-title":"Fast, sensitive and accurate integration of single-cell data with Harmony","volume":"16","author":"Korsunsky","year":"2019","journal-title":"Nat. Methods"},{"key":"10.1016\/j.immuni.2024.01.006_bib108","article-title":"clusterProfiler 4.0: A universal enrichment tool for interpreting omics data","volume":"2","author":"Wu","year":"2021","journal-title":"Innovation (Camb)"},{"key":"10.1016\/j.immuni.2024.01.006_bib109","doi-asserted-by":"crossref","first-page":"3796","DOI":"10.1016\/j.csbj.2021.06.043","article-title":"UCell: Robust and scalable single-cell gene signature scoring","volume":"19","author":"Andreatta","year":"2021","journal-title":"Comput. Struct. Biotechnol. J."},{"key":"10.1016\/j.immuni.2024.01.006_bib110","doi-asserted-by":"crossref","DOI":"10.1186\/gb-2008-9-9-r137","article-title":"Model-based analysis of ChIP-Seq (MACS)","volume":"9","author":"Zhang","year":"2008","journal-title":"Genome Biol."},{"key":"10.1016\/j.immuni.2024.01.006_bib111","doi-asserted-by":"crossref","first-page":"975","DOI":"10.1038\/nmeth.4401","article-title":"chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data","volume":"14","author":"Schep","year":"2017","journal-title":"Nat. Methods"},{"key":"10.1016\/j.immuni.2024.01.006_bib112","doi-asserted-by":"crossref","first-page":"858","DOI":"10.1016\/j.molcel.2018.06.044","article-title":"Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data","volume":"71","author":"Pliner","year":"2018","journal-title":"Mol. Cell"},{"key":"10.1016\/j.immuni.2024.01.006_bib113","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1186\/s13059-019-1865-2","article-title":"Vireo: Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference","volume":"20","author":"Huang","year":"2019","journal-title":"Genome Biol."},{"key":"10.1016\/j.immuni.2024.01.006_bib114","doi-asserted-by":"crossref","first-page":"4569","DOI":"10.1093\/bioinformatics\/btab358","article-title":"Cellsnp-lite: an efficient tool for genotyping single cells","volume":"37","author":"Huang","year":"2021","journal-title":"Bioinformatics"},{"key":"10.1016\/j.immuni.2024.01.006_bib115","doi-asserted-by":"crossref","first-page":"4817","DOI":"10.1093\/bioinformatics\/btaa611","article-title":"Scirpy: a Scanpy extension for analyzing single-cell T-cell receptor-sequencing data","volume":"36","author":"Sturm","year":"2020","journal-title":"Bioinform. Oxf. Engl."},{"key":"10.1016\/j.immuni.2024.01.006_bib116","doi-asserted-by":"crossref","first-page":"e50","DOI":"10.1093\/nar\/gkab043","article-title":"SPOTlight: seeded NMF regression to deconvolute spatial transcriptomics spots with single-cell transcriptomes","volume":"49","author":"Elosua-Bayes","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.immuni.2024.01.006_bib117","doi-asserted-by":"crossref","first-page":"716","DOI":"10.1016\/j.cell.2018.05.061","article-title":"Recovering Gene Interactions from Single-Cell Data Using Data Diffusion","volume":"174","author":"van Dijk","year":"2018","journal-title":"Cell"},{"key":"10.1016\/j.immuni.2024.01.006_bib118","series-title":"Inferring Spatially Transient Gene Expression Pattern from Spatial Transcriptomic Studies","author":"Kueckelhaus","year":"2020"},{"key":"10.1016\/j.immuni.2024.01.006_bib119","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1016\/j.cels.2018.11.005","article-title":"Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data","volume":"8","author":"Wolock","year":"2019","journal-title":"Cell Syst."},{"key":"10.1016\/j.immuni.2024.01.006_bib120","doi-asserted-by":"crossref","DOI":"10.1002\/cpz1.585","article-title":"Exploring Epigenomic Datasets by ChIPseeker","volume":"2","author":"Wang","year":"2022","journal-title":"Curr. Protoc."},{"key":"10.1016\/j.immuni.2024.01.006_bib121","doi-asserted-by":"crossref","DOI":"10.1002\/imt2.43","article-title":"Complex heatmap visualization","volume":"1","author":"Gu","year":"2022","journal-title":"iMeta"},{"key":"10.1016\/j.immuni.2024.01.006_bib122","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gks543","article-title":"i-cisTarget: an integrative genomics method for the prediction of regulatory features and cis-regulatory modules","volume":"40","author":"Herrmann","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.immuni.2024.01.006_bib123","doi-asserted-by":"crossref","first-page":"W57","DOI":"10.1093\/nar\/gkv395","article-title":"i-cisTarget 2015 update: generalized cis-regulatory enrichment analysis in human, mouse and fly","volume":"43","author":"Imrichov\u00e1","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.immuni.2024.01.006_bib124","first-page":"D87","article-title":"JASPAR 2020: update of the open-access database of transcription factor binding profiles","volume":"48","author":"Fornes","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.immuni.2024.01.006_bib125","doi-asserted-by":"crossref","first-page":"1555","DOI":"10.1093\/bioinformatics\/btw024","article-title":"TFBSTools: an R\/bioconductor package for transcription factor binding site analysis","volume":"32","author":"Tan","year":"2016","journal-title":"Bioinform. Oxf. Engl."},{"key":"10.1016\/j.immuni.2024.01.006_bib126","doi-asserted-by":"crossref","DOI":"10.1186\/s13059-018-1603-1","article-title":"Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics","volume":"19","author":"Stoeckius","year":"2018","journal-title":"Genome Biol."},{"key":"10.1016\/j.immuni.2024.01.006_bib127","doi-asserted-by":"crossref","first-page":"676","DOI":"10.1038\/nmeth.2019","article-title":"Fiji: an open-source platform for biological-image analysis","volume":"9","author":"Schindelin","year":"2012","journal-title":"Nat. Methods"},{"key":"10.1016\/j.immuni.2024.01.006_bib128","doi-asserted-by":"crossref","DOI":"10.15252\/msb.20188746","article-title":"Current best practices in single-cell RNA-seq analysis: a tutorial","volume":"15","author":"Luecken","year":"2019","journal-title":"Mol. Syst. Biol."},{"key":"10.1016\/j.immuni.2024.01.006_bib129","doi-asserted-by":"crossref","first-page":"747","DOI":"10.1038\/s41587-020-0469-4","article-title":"Benchmarking single-cell RNA-sequencing protocols for cell atlas projects","volume":"38","author":"Mereu","year":"2020","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.immuni.2024.01.006_bib130","doi-asserted-by":"crossref","DOI":"10.1186\/s13059-019-1850-9","article-title":"A benchmark of batch-effect correction methods for single-cell RNA sequencing data","volume":"21","author":"Tran","year":"2020","journal-title":"Genome Biol."},{"key":"10.1016\/j.immuni.2024.01.006_bib131","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1016\/j.cels.2019.03.003","article-title":"DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors","volume":"8","author":"McGinnis","year":"2019","journal-title":"Cell Syst."},{"key":"10.1016\/j.immuni.2024.01.006_bib132","doi-asserted-by":"crossref","first-page":"999","DOI":"10.1016\/j.cell.2018.06.021","article-title":"Molecular Architecture of the Mouse Nervous System","volume":"174","author":"Zeisel","year":"2018","journal-title":"Cell"},{"key":"10.1016\/j.immuni.2024.01.006_bib133","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1038\/nprot.2008.211","article-title":"Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources","volume":"4","author":"Huang","year":"2009","journal-title":"Nat. Protoc."},{"key":"10.1016\/j.immuni.2024.01.006_bib134","doi-asserted-by":"crossref","first-page":"W216","DOI":"10.1093\/nar\/gkac194","article-title":"DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update). Nucleic Acids Res. gkac194","volume":"50","author":"Sherman","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.immuni.2024.01.006_bib135","doi-asserted-by":"crossref","first-page":"1217","DOI":"10.1101\/gr.265520.120","article-title":"Chromatin activation as a unifying principle underlying pathogenic mechanisms in multiple myeloma","volume":"30","author":"Ordo\u00f1ez","year":"2020","journal-title":"Genome Res."},{"key":"10.1016\/j.immuni.2024.01.006_bib136","doi-asserted-by":"crossref","first-page":"1179","DOI":"10.1093\/bioinformatics\/btw777","article-title":"Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R","volume":"33","author":"McCarthy","year":"2017","journal-title":"Bioinformatics"},{"key":"10.1016\/j.immuni.2024.01.006_bib137","doi-asserted-by":"crossref","first-page":"2159","DOI":"10.1093\/bioinformatics\/bty916","article-title":"GRNBoost2 and Arboreto: efficient and scalable inference of gene regulatory networks","volume":"35","author":"Moerman","year":"2019","journal-title":"Bioinform. Oxf. Engl."},{"key":"10.1016\/j.immuni.2024.01.006_bib138","doi-asserted-by":"crossref","first-page":"1436","DOI":"10.1016\/j.celrep.2018.10.045","article-title":"Revealing the Critical Regulators of Cell Identity in the Mouse Cell Atlas","volume":"25","author":"Suo","year":"2018","journal-title":"Cell Rep."},{"key":"10.1016\/j.immuni.2024.01.006_bib139","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1038\/s41592-021-01336-8","article-title":"Benchmarking atlas-level data integration in single-cell genomics","volume":"19","author":"Luecken","year":"2022","journal-title":"Nat. Methods"},{"key":"10.1016\/j.immuni.2024.01.006_bib140","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1038\/s41592-018-0303-9","article-title":"A discriminative learning approach to differential expression analysis for single-cell RNA-seq","volume":"16","author":"Ntranos","year":"2019","journal-title":"Nat. Methods"},{"key":"10.1016\/j.immuni.2024.01.006_bib141","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows\u2013Wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"10.1016\/j.immuni.2024.01.006_bib142","doi-asserted-by":"crossref","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve years of SAMtools and BCFtools","volume":"10","author":"Danecek","year":"2021","journal-title":"GigaScience"},{"key":"10.1016\/j.immuni.2024.01.006_bib143","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1038\/s41588-021-00790-6","article-title":"ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis","volume":"53","author":"Granja","year":"2021","journal-title":"Nat. Genet."},{"key":"10.1016\/j.immuni.2024.01.006_bib144","doi-asserted-by":"crossref","first-page":"422","DOI":"10.1093\/bioinformatics\/btaa692","article-title":"pyGenomeTracks: reproducible plots for multivariate genomic datasets","volume":"37","author":"Lopez-Delisle","year":"2021","journal-title":"Bioinformatics"},{"key":"10.1016\/j.immuni.2024.01.006_bib145","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1038\/nmeth.4636","article-title":"SpatialDE: identification of spatially variable genes","volume":"15","author":"Svensson","year":"2018","journal-title":"Nat. Methods"},{"key":"10.1016\/j.immuni.2024.01.006_bib146","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1038\/s41592-019-0701-7","article-title":"Statistical analysis of spatial expression patterns for spatially resolved transcriptomic studies","volume":"17","author":"Sun","year":"2020","journal-title":"Nat. Methods"},{"key":"10.1016\/j.immuni.2024.01.006_bib147","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1038\/s41576-023-00586-w","article-title":"Best practices for single-cell analysis across modalities","volume":"24","author":"Heumos","year":"2023","journal-title":"Nat. Rev. Genet."},{"key":"10.1016\/j.immuni.2024.01.006_bib148","doi-asserted-by":"crossref","DOI":"10.12688\/f1000research.73600.2","article-title":"Doublet Identification in Single-Cell Sequencing Data Using scDblFinder","volume":"10","author":"Germain","year":"2022","journal-title":"F1000Res."}],"container-title":["Immunity"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1074761324000311?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1074761324000311?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,5,1]],"date-time":"2026-05-01T04:00:07Z","timestamp":1777608007000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1074761324000311"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,2]]},"references-count":148,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2024,2]]}},"alternative-id":["S1074761324000311"],"URL":"https:\/\/doi.org\/10.1016\/j.immuni.2024.01.006","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2022.06.24.497299","asserted-by":"object"}]},"ISSN":["1074-7613"],"issn-type":[{"value":"1074-7613","type":"print"}],"subject":[],"published":{"date-parts":[[2024,2]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"An atlas of cells in the human tonsil","name":"articletitle","label":"Article Title"},{"value":"Immunity","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.immuni.2024.01.006","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2024 The Authors. Published by Elsevier Inc.","name":"copyright","label":"Copyright"}]}}