{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T18:26:12Z","timestamp":1786991172989,"version":"build-2736575974"},"reference-count":40,"publisher":"Elsevier BV","issue":"1","license":[{"start":{"date-parts":[[2023,1,1]],"date-time":"2023-01-01T00:00:00Z","timestamp":1672531200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2023,1,1]],"date-time":"2023-01-01T00:00:00Z","timestamp":1672531200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2022,12,15]],"date-time":"2022-12-15T00:00:00Z","timestamp":1671062400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["iScience"],"published-print":{"date-parts":[[2023,1]]},"DOI":"10.1016\/j.isci.2022.105826","type":"journal-article","created":{"date-parts":[[2022,12,17]],"date-time":"2022-12-17T02:04:52Z","timestamp":1671242692000},"page":"105826","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":3,"title":["From pseudo to real-time dynamics of T\u00a0cell thymic differentiation"],"prefix":"10.1016","volume":"26","author":[{"given":"Avishai","family":"Gavish","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benny","family":"Chain","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tomer M.","family":"Salame","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yaron E.","family":"Antebi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shir","family":"Nevo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shlomit","family":"Reich-Zeliger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nir","family":"Friedman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.isci.2022.105826_bib1","doi-asserted-by":"crossref","first-page":"547","DOI":"10.1038\/s41587-019-0071-9","article-title":"A comparison of single-cell trajectory inference methods","volume":"37","author":"Saelens","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.isci.2022.105826_bib2","doi-asserted-by":"crossref","first-page":"2496","DOI":"10.1002\/eji.201646347","article-title":"Computational methods for trajectory inference from single-cell transcriptomics","volume":"46","author":"Cannoodt","year":"2016","journal-title":"Eur. J. Immunol."},{"key":"10.1016\/j.isci.2022.105826_bib3","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1038\/s41467-017-00039-z","article-title":"Reconstructing cell cycle pseudo time-series via single-cell transcriptome data","volume":"8","author":"Liu","year":"2017","journal-title":"Nat. Commun."},{"key":"10.1016\/j.isci.2022.105826_bib4","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13059-019-1663-x","article-title":"PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells","volume":"20","author":"Wolf","year":"2019","journal-title":"Genome Biol."},{"key":"10.1016\/j.isci.2022.105826_bib5","doi-asserted-by":"crossref","first-page":"637","DOI":"10.1038\/nbt.3569","article-title":"Wishbone identifies bifurcating developmental trajectories from single-cell data","volume":"34","author":"Setty","year":"2016","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.isci.2022.105826_bib6","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1146\/annurev-cellbio-092910-154008","article-title":"Mechanisms of T\u00a0cell development and transformation","volume":"27","author":"Koch","year":"2011","journal-title":"Annu. Rev. Cell Dev. Biol."},{"key":"10.1016\/j.isci.2022.105826_bib7","doi-asserted-by":"crossref","first-page":"529","DOI":"10.1038\/nri3702","article-title":"Developmental gene networks: a triathlon on the course to T\u00a0cell identity","volume":"14","author":"Yui","year":"2014","journal-title":"Nat. Rev. Immunol."},{"key":"10.1016\/j.isci.2022.105826_bib8","doi-asserted-by":"crossref","first-page":"14","DOI":"10.3389\/fimmu.2014.00019","article-title":"From pre-DP, post-DP, SP4, and SP8 thymocyte cell counts to a dynamical model of cortical and medullary selection","volume":"5","author":"Sawicka","year":"2014","journal-title":"Front. Immunol."},{"key":"10.1016\/j.isci.2022.105826_bib9","doi-asserted-by":"crossref","first-page":"E2467","DOI":"10.1073\/pnas.1714723115","article-title":"Fundamental limits on dynamic inference from single-cell snapshots","volume":"115","author":"Weinreb","year":"2018","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.isci.2022.105826_bib10","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1038\/s41587-019-0088-0","article-title":"Inferring population dynamics from single-cell RNA-sequencing time series data","volume":"37","author":"Fischer","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.isci.2022.105826_bib11","doi-asserted-by":"crossref","first-page":"e43882","DOI":"10.7554\/eLife.43882","article-title":"Single-cell expression profiling reveals dynamic flux of cardiac stromal, vascular and immune cells in health and injury","volume":"8","author":"Farbehi","year":"2019","journal-title":"Elife"},{"key":"10.1016\/j.isci.2022.105826_bib12","doi-asserted-by":"crossref","first-page":"3619","DOI":"10.1038\/s41598-020-60400-z","article-title":"Reconstructing temporal and spatial dynamics from single-cell pseudotime using prior knowledge of real scale cell densities","volume":"10","author":"Kuritz","year":"2020","journal-title":"Sci. Rep."},{"key":"10.1016\/j.isci.2022.105826_bib13","doi-asserted-by":"crossref","first-page":"531","DOI":"10.1002\/eji.201545821","article-title":"Transcriptional regulation of early T-cell development in the thymus","volume":"46","author":"Seo","year":"2016","journal-title":"Eur. J. Immunol."},{"key":"10.1016\/j.isci.2022.105826_bib14","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1038\/nri798","article-title":"t-cell development and the CD4-CD8 lineage decision","volume":"2","author":"Germain","year":"2002","journal-title":"Nat. Rev. Immunol."},{"key":"10.1016\/j.isci.2022.105826_bib15","doi-asserted-by":"crossref","first-page":"4017","DOI":"10.4049\/jimmunol.1302259","article-title":"An overview of the intrathymic intricacies of T\u00a0cell development","volume":"192","author":"Shah","year":"2014","journal-title":"J.\u00a0Immunol."},{"key":"10.1016\/j.isci.2022.105826_bib16","doi-asserted-by":"crossref","first-page":"1662","DOI":"10.1002\/eji.201142338","article-title":"Thymocyte death by neglect: contribution of engulfing macrophages","volume":"42","author":"Szondy","year":"2012","journal-title":"Eur. J. Immunol."},{"key":"10.1016\/j.isci.2022.105826_bib17","doi-asserted-by":"crossref","first-page":"1139","DOI":"10.1093\/intimm\/5.9.1139","article-title":"CD69 cell surface expression identifies developing thymocytes which audition for T\u00a0cell antigen receptor-mediated positive selection","volume":"5","author":"Yamashita","year":"1993","journal-title":"Int. Immunol."},{"key":"10.1016\/j.isci.2022.105826_bib18","doi-asserted-by":"crossref","first-page":"E2550","DOI":"10.1073\/pnas.1408482111","article-title":"Distinct phases in the positive selection of CD8+ T\u00a0cells distinguished by intrathymic migration and T-cell receptor signaling patterns","volume":"111","author":"Ross","year":"2014","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.isci.2022.105826_bib19","doi-asserted-by":"crossref","first-page":"114","DOI":"10.1111\/imr.12398","article-title":"T-cell selection in the thymus: a spatial and temporal perspective","volume":"271","author":"Kurd","year":"2016","journal-title":"Immunol. Rev."},{"key":"10.1016\/j.isci.2022.105826_bib20","doi-asserted-by":"crossref","first-page":"437","DOI":"10.3390\/e23040437","article-title":"Modeling the dynamics of t-cell development in the thymus","volume":"23","author":"Robert","year":"2021","journal-title":"Entropy"},{"key":"10.1016\/j.isci.2022.105826_bib21","doi-asserted-by":"crossref","first-page":"ra92","DOI":"10.1126\/scisignal.2004400","article-title":"Distinct temporal patterns of T\u00a0cell receptor signaling during positive versus negative selection in\u00a0situ","volume":"6","author":"Melichar","year":"2013","journal-title":"Sci. Signal."},{"key":"10.1016\/j.isci.2022.105826_bib22","doi-asserted-by":"crossref","first-page":"865","DOI":"10.1016\/j.ceb.2010.08.003","article-title":"Life and death in the thymus-cell death signaling during T\u00a0cell development","volume":"22","author":"Hernandez","year":"2010","journal-title":"Curr. Opin. Cell Biol."},{"key":"10.1016\/j.isci.2022.105826_bib23","doi-asserted-by":"crossref","first-page":"3226","DOI":"10.4049\/jimmunol.1900191","article-title":"Measuring thymic clonal deletion at the population level","volume":"202","author":"Breed","year":"2019","journal-title":"J.\u00a0Immunol."},{"key":"10.1016\/j.isci.2022.105826_bib24","doi-asserted-by":"crossref","first-page":"13","DOI":"10.3389\/fimmu.2014.00013","article-title":"Theories and quantification of thymic selection","volume":"5","author":"Yates","year":"2014","journal-title":"Front. Immunol."},{"key":"10.1016\/j.isci.2022.105826_bib25","doi-asserted-by":"crossref","first-page":"1664","DOI":"10.4049\/jimmunol.168.4.1664","article-title":"Quantitative and qualitative adjustment of thymic T\u00a0cell production by clonal expansion of premigrant thymocytes","volume":"168","author":"le Campion","year":"2002","journal-title":"J.\u00a0Immunol."},{"key":"10.1016\/j.isci.2022.105826_bib26","doi-asserted-by":"crossref","first-page":"1105","DOI":"10.1016\/j.immuni.2020.05.010","article-title":"Single-cell RNA-seq mapping of human thymopoiesis reveals lineage specification trajectories and a commitment spectrum in T\u00a0cell development","volume":"52","author":"Le","year":"2020","journal-title":"Immunity"},{"key":"10.1016\/j.isci.2022.105826_bib27","doi-asserted-by":"crossref","first-page":"1182","DOI":"10.1016\/j.immuni.2020.10.024","article-title":"An integrated epigenomic and transcriptomic map of mouse and human \u03b1\u03b2 T\u00a0cell development","volume":"53","author":"Chopp","year":"2020","journal-title":"Immunity"},{"key":"10.1016\/j.isci.2022.105826_bib28","doi-asserted-by":"crossref","first-page":"465","DOI":"10.1097\/TP.0b013e3181e7e54f","article-title":"The role of the thymus in tolerance","volume":"90","author":"Griesemer","year":"2010","journal-title":"Transplantation"},{"key":"10.1016\/j.isci.2022.105826_bib29","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1038\/nri1707","article-title":"Central tolerance: learning self-control in the thymus","volume":"5","author":"Hogquist","year":"2005","journal-title":"Nat. Rev. Immunol."},{"key":"10.1016\/j.isci.2022.105826_bib30","doi-asserted-by":"crossref","first-page":"590","DOI":"10.1038\/nature03724","article-title":"Cellular and genetic mechanisms of self tolerance and autoimmunity","volume":"435","author":"Goodnow","year":"2005","journal-title":"Nature"},{"key":"10.1016\/j.isci.2022.105826_bib31","doi-asserted-by":"crossref","first-page":"552","DOI":"10.1002\/cyto.a.22075","article-title":"Single-cell mass cytometry adapted to measurements of the cell cycle","volume":"81","author":"Behbehani","year":"2012","journal-title":"Cytometry A."},{"key":"10.1016\/j.isci.2022.105826_bib32","doi-asserted-by":"crossref","first-page":"480","DOI":"10.1038\/nature11897","article-title":"Dynamics extracted from fixed cells reveal feedback linking cell growth to cell cycle","volume":"494","author":"Kafri","year":"2013","journal-title":"Nature"},{"key":"10.1016\/j.isci.2022.105826_bib33","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1093\/embo-reports\/kvd050","article-title":"Rapid caspase-3 activation during apoptosis revealed using fluorescence-resonance energy transfer","volume":"1","author":"Tyas","year":"2000","journal-title":"EMBO Rep."},{"key":"10.1016\/j.isci.2022.105826_bib34","doi-asserted-by":"crossref","first-page":"4679","DOI":"10.1073\/pnas.1217532110","article-title":"Murine thymic selection quantified using a unique method to capture deleted T\u00a0cells","volume":"110","author":"Stritesky","year":"2013","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.isci.2022.105826_bib36","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1080\/01926230701320337","article-title":"Apoptosis: a Review of programmed cell death","volume":"35","author":"Elmore","year":"2007","journal-title":"Toxicol. Pathol."},{"key":"10.1016\/j.isci.2022.105826_bib35","doi-asserted-by":"crossref","first-page":"1069","DOI":"10.1093\/intimm\/dxh108","article-title":"New insights into the proliferation and differentiation of early mouse thymocytes","volume":"16","author":"Laurent","year":"2004","journal-title":"Int. Immunol."},{"key":"10.1016\/j.isci.2022.105826_bib37","doi-asserted-by":"crossref","first-page":"108967","DOI":"10.1016\/j.celrep.2021.108967","article-title":"Self-renewal of double-negative 3 early thymocytes enables thymus autonomy but compromises the \u03b2-selection checkpoint","volume":"35","author":"Paiva","year":"2021","journal-title":"Cell Rep."},{"key":"10.1016\/j.isci.2022.105826_bib38","doi-asserted-by":"crossref","first-page":"463","DOI":"10.1146\/annurev.cellbio.23.090506.123547","article-title":"The thymus as an inductive site for T lymphopoiesis","volume":"23","author":"Ciofani","year":"2007","journal-title":"Annu. Rev. Cell Dev. Biol."},{"key":"10.1016\/j.isci.2022.105826_bib39","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1186\/s13073-021-00861-7","article-title":"Development of double-positive thymocytes at single-cell resolution","volume":"13","author":"Li","year":"2021","journal-title":"Genome Med."},{"key":"10.1016\/j.isci.2022.105826_bib40","doi-asserted-by":"crossref","first-page":"1201","DOI":"10.1038\/s41467-020-14766-3","article-title":"Trajectory-based differential expression analysis for single-cell sequencing data","volume":"11","author":"van den Berge","year":"2020","journal-title":"Nat. Commun."}],"container-title":["iScience"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2589004222020995?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2589004222020995?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,11,11]],"date-time":"2025-11-11T17:14:58Z","timestamp":1762881298000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2589004222020995"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,1]]},"references-count":40,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2023,1]]}},"alternative-id":["S2589004222020995"],"URL":"https:\/\/doi.org\/10.1016\/j.isci.2022.105826","relation":{},"ISSN":["2589-0042"],"issn-type":[{"value":"2589-0042","type":"print"}],"subject":[],"published":{"date-parts":[[2023,1]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"From pseudo to real-time dynamics of T\u00a0cell thymic differentiation","name":"articletitle","label":"Article Title"},{"value":"iScience","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.isci.2022.105826","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2022 The Author(s).","name":"copyright","label":"Copyright"}],"article-number":"105826"}}