{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,28]],"date-time":"2026-07-28T11:00:29Z","timestamp":1785236429789,"version":"3.55.0"},"reference-count":73,"publisher":"Elsevier BV","issue":"12","license":[{"start":{"date-parts":[[2024,12,1]],"date-time":"2024-12-01T00:00:00Z","timestamp":1733011200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2024,12,1]],"date-time":"2024-12-01T00:00:00Z","timestamp":1733011200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2024,11,6]],"date-time":"2024-11-06T00:00:00Z","timestamp":1730851200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/100028897","name":"Wellcome Leap","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100028897","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100017008","name":"Allen Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100017008","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000700","name":"Royal Commission for the Exhibition Of 1851","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000700","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000245","name":"Michael Smith Foundation for Health Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000245","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004410","name":"European Molecular Biology Organization","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100004410","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Cell Systems"],"published-print":{"date-parts":[[2024,12]]},"DOI":"10.1016\/j.cels.2024.11.001","type":"journal-article","created":{"date-parts":[[2024,11,29]],"date-time":"2024-11-29T15:31:32Z","timestamp":1732894292000},"page":"1245-1263.e10","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":12,"title":["Tracking the gene expression programs and clonal relationships that underlie mast, myeloid, and T lineage specification from stem cells"],"prefix":"10.1016","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6857-5922","authenticated-orcid":false,"given":"Yale S.","family":"Michaels","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew C.","family":"Major","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Becca","family":"Bonham-Carter","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jingqi","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tiam","family":"Heydari","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John M.","family":"Edgar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mona M.","family":"Siu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laura","family":"Greenstreet","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roser","family":"Vilarrasa-Blasi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Seungjoon","family":"Kim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elizabeth L.","family":"Castle","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aden","family":"Forrow","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M. Iliana","family":"Ibanez-Rios","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carla","family":"Zimmerman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yvonne","family":"Chung","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tara","family":"Stach","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nico","family":"Werschler","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David J.H.F.","family":"Knapp","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roser","family":"Vento-Tormo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Geoffrey","family":"Schiebinger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9568-733X","authenticated-orcid":false,"given":"Peter W.","family":"Zandstra","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.cels.2024.11.001_bib1","doi-asserted-by":"crossref","first-page":"1361","DOI":"10.1126\/science.aar6711","article-title":"CAR T\u00a0cell immunotherapy for human cancer","volume":"359","author":"June","year":"2018","journal-title":"Science"},{"key":"10.1016\/j.cels.2024.11.001_bib2","doi-asserted-by":"crossref","first-page":"430","DOI":"10.1038\/s41586-019-1546-z","article-title":"Targeting cardiac fibrosis with engineered T\u00a0cells","volume":"573","author":"Aghajanian","year":"2019","journal-title":"Nature"},{"key":"10.1016\/j.cels.2024.11.001_bib3","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1038\/s42255-022-00537-5","article-title":"CAR-based therapies: opportunities for immuno-medicine beyond cancer","volume":"4","author":"Aghajanian","year":"2022","journal-title":"Nat. Metab."},{"key":"10.1016\/j.cels.2024.11.001_bib4","doi-asserted-by":"crossref","first-page":"1460","DOI":"10.3389\/fimmu.2017.01460","article-title":"Engineered Tolerance: Tailoring Development, Function, and Antigen-Specificity of Regulatory T Cells","volume":"8","author":"Dawson","year":"2017","journal-title":"Front. Immunol."},{"key":"10.1016\/j.cels.2024.11.001_bib5","doi-asserted-by":"crossref","first-page":"106","DOI":"10.1089\/genbio.2023.0008","article-title":"Engineering T Cell Development for the Next Generation of Stem Cell-Derived Immunotherapies","volume":"2","author":"Michaels","year":"2023","journal-title":"GEN Biotechnol."},{"key":"10.1016\/j.cels.2024.11.001_bib6","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1038\/ni1560","article-title":"Of lineage and legacy: the development of mammalian hematopoietic stem cells","volume":"9","author":"Dzierzak","year":"2008","journal-title":"Nat. Immunol."},{"key":"10.1016\/j.cels.2024.11.001_bib7","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1038\/nri1781","article-title":"Journey through the thymus: stromal guides for T-cell development and selection","volume":"6","author":"Takahama","year":"2006","journal-title":"Nat. Rev. Immunol."},{"key":"10.1016\/j.cels.2024.11.001_bib8","doi-asserted-by":"crossref","first-page":"162","DOI":"10.1038\/s41577-020-00426-6","article-title":"How transcription factors drive choice of the T\u00a0cell fate","volume":"21","author":"Hosokawa","year":"2021","journal-title":"Nat. Rev. Immunol."},{"key":"10.1016\/j.cels.2024.11.001_bib9","doi-asserted-by":"crossref","first-page":"1088","DOI":"10.1016\/j.immuni.2020.03.019","article-title":"Integrated scRNA-Seq Identifies Human Postnatal Thymus Seeding Progenitors and Regulatory Dynamics of Differentiating Immature Thymocytes","volume":"52","author":"Lavaert","year":"2020","journal-title":"Immunity"},{"key":"10.1016\/j.cels.2024.11.001_bib10","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.cels.2024.11.001_bib11","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1016\/j.coi.2007.02.011","article-title":"T-cell potential and development in\u00a0vitro: the OP9-DL1 approach","volume":"19","author":"de Pooter","year":"2007","journal-title":"Curr. Opin. Immunol."},{"key":"10.1016\/j.cels.2024.11.001_bib12","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 Cell Development","volume":"52","author":"Le","year":"2020","journal-title":"Immunity"},{"key":"10.1016\/j.cels.2024.11.001_bib13","doi-asserted-by":"crossref","first-page":"930","DOI":"10.1016\/j.immuni.2019.09.008","article-title":"Single-Cell RNA Sequencing Resolves Spatiotemporal Development of Pre-thymic Lymphoid Progenitors and Thymus Organogenesis in Human Embryos","volume":"51","author":"Zeng","year":"2019","journal-title":"Immunity"},{"key":"10.1016\/j.cels.2024.11.001_bib14","doi-asserted-by":"crossref","DOI":"10.4155\/fsoa-2016-0095","article-title":"The development of T\u00a0cells from stem cells in mice and humans","volume":"3","author":"Famili","year":"2017","journal-title":"Future Sci. OA"},{"key":"10.1016\/j.cels.2024.11.001_bib15","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.exphem.2020.12.005","article-title":"Single-cell insights into the hematopoietic generation of T-lymphocyte precursors in mouse and human","volume":"95","author":"Rothenberg","year":"2021","journal-title":"Exp. Hematol."},{"key":"10.1016\/j.cels.2024.11.001_bib16","doi-asserted-by":"crossref","DOI":"10.1126\/science.aaw3381","article-title":"Lineage tracing on transcriptional landscapes links state to fate during differentiation","volume":"367","author":"Weinreb","year":"2020","journal-title":"Science"},{"key":"10.1016\/j.cels.2024.11.001_bib17","doi-asserted-by":"crossref","first-page":"585","DOI":"10.1038\/s41586-020-2503-6","article-title":"Single-cell lineage tracing unveils a role for TCF15 in haematopoiesis","volume":"583","author":"Rodriguez-Fraticelli","year":"2020","journal-title":"Nature"},{"key":"10.1016\/j.cels.2024.11.001_bib18","doi-asserted-by":"crossref","DOI":"10.1126\/science.aab2116","article-title":"Distinct routes of lineage development reshape the human blood hierarchy across ontogeny","volume":"351","author":"Notta","year":"2016","journal-title":"Science"},{"key":"10.1016\/j.cels.2024.11.001_bib19","doi-asserted-by":"crossref","first-page":"927","DOI":"10.1182\/blood-2018-10-878025","article-title":"A topological view of human CD34+ cell state trajectories from integrated single-cell output and proteomic data","volume":"133","author":"Knapp","year":"2019","journal-title":"Blood"},{"key":"10.1016\/j.cels.2024.11.001_bib20","doi-asserted-by":"crossref","first-page":"666","DOI":"10.1038\/ni.3412","article-title":"Distinct myeloid progenitor-differentiation pathways identified through single-cell RNA sequencing","volume":"17","author":"Drissen","year":"2016","journal-title":"Nat. Immunol."},{"key":"10.1016\/j.cels.2024.11.001_bib21","doi-asserted-by":"crossref","DOI":"10.1126\/sciadv.abn5522","article-title":"DLL4 and VCAM1 enhance the emergence of T\u00a0cell-competent hematopoietic progenitors from human pluripotent stem cells","volume":"8","author":"Michaels","year":"2022","journal-title":"Sci. Adv."},{"key":"10.1016\/j.cels.2024.11.001_bib22","doi-asserted-by":"crossref","first-page":"554","DOI":"10.1038\/nbt.2915","article-title":"Wnt signaling controls the specification of definitive and primitive hematopoiesis from human pluripotent stem cells","volume":"32","author":"Sturgeon","year":"2014","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.cels.2024.11.001_bib23","doi-asserted-by":"crossref","first-page":"580","DOI":"10.1038\/ncb3161","article-title":"Human definitive haemogenic endothelium and arterial vascular endothelium represent distinct lineages","volume":"17","author":"Ditadi","year":"2015","journal-title":"Nat. Cell Biol."},{"key":"10.1016\/j.cels.2024.11.001_bib24","doi-asserted-by":"crossref","first-page":"224","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.cels.2024.11.001_bib25","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.cels.2024.11.001_bib26","doi-asserted-by":"crossref","first-page":"534","DOI":"10.1038\/s41586-022-04571-x","article-title":"Mapping human haematopoietic stem cells from haemogenic endothelium to birth","volume":"604","author":"Calvanese","year":"2022","journal-title":"Nature"},{"key":"10.1016\/j.cels.2024.11.001_bib27","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/j.exphem.2018.11.007","article-title":"Arterial identity of hemogenic endothelium: a key to unlock definitive hematopoietic commitment in human pluripotent stem cell cultures","volume":"71","author":"Slukvin","year":"2019","journal-title":"Exp. Hematol."},{"key":"10.1016\/j.cels.2024.11.001_bib28","doi-asserted-by":"crossref","first-page":"4439","DOI":"10.1182\/bloodadvances.2022006969","article-title":"Single-cell transcriptomics reveals the identity and regulators of human mast cell progenitors","volume":"6","author":"Wu","year":"2022","journal-title":"Blood Adv."},{"key":"10.1016\/j.cels.2024.11.001_bib29","doi-asserted-by":"crossref","first-page":"1083","DOI":"10.1038\/nmeth.4463","article-title":"SCENIC: single-cell regulatory network inference and clustering","volume":"14","author":"Aibar","year":"2017","journal-title":"Nat. Methods"},{"key":"10.1016\/j.cels.2024.11.001_bib30","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1182\/blood-2011-04-285981","article-title":"Transcription factor networks in erythroid cell and megakaryocyte development","volume":"118","author":"Dor\u00e9","year":"2011","journal-title":"Blood"},{"key":"10.1016\/j.cels.2024.11.001_bib31","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1038\/s41586-019-1652-y","article-title":"Decoding human fetal liver haematopoiesis","volume":"574","author":"Popescu","year":"2019","journal-title":"Nature"},{"key":"10.1016\/j.cels.2024.11.001_bib32","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1038\/nri2024","article-title":"Transcription factors in myeloid development: balancing differentiation with transformation","volume":"7","author":"Rosenbauer","year":"2007","journal-title":"Nat. Rev. Immunol."},{"key":"10.1016\/j.cels.2024.11.001_bib33","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.cels.2024.11.001_bib34","doi-asserted-by":"crossref","first-page":"1168","DOI":"10.1038\/nbt.3702","article-title":"Differentiation of human embryonic stem cells to HOXA+ hemogenic vasculature that resembles the aorta-gonad-mesonephros","volume":"34","author":"Ng","year":"2016","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.cels.2024.11.001_bib35","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2021.109698","article-title":"Transitions in lineage specification and gene regulatory networks in hematopoietic stem\/progenitor cells over human development","volume":"36","author":"Roy","year":"2021","journal-title":"Cell Rep."},{"key":"10.1016\/j.cels.2024.11.001_bib36","doi-asserted-by":"crossref","first-page":"1888","DOI":"10.1016\/j.cell.2019.05.031","article-title":"Comprehensive Integration of Single-Cell Data","volume":"177","author":"Stuart","year":"2019","journal-title":"Cell"},{"key":"10.1016\/j.cels.2024.11.001_bib37","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1093\/bioinformatics\/btz592","article-title":"ACTINN: automated identification of cell types in single cell RNA sequencing","volume":"36","author":"Ma","year":"2020","journal-title":"Bioinformatics"},{"key":"10.1016\/j.cels.2024.11.001_bib38","doi-asserted-by":"crossref","first-page":"150","DOI":"10.1111\/j.1600-065X.2010.00964.x","article-title":"Multilayered specification of the T-cell lineage fate","volume":"238","author":"Rothenberg","year":"2010","journal-title":"Immunol. Rev."},{"key":"10.1016\/j.cels.2024.11.001_bib39","doi-asserted-by":"crossref","DOI":"10.1126\/science.abo0510","article-title":"Mapping the developing human immune system across organs","volume":"376","author":"Suo","year":"2022","journal-title":"Science"},{"key":"10.1016\/j.cels.2024.11.001_bib40","doi-asserted-by":"crossref","DOI":"10.1126\/science.abl5197","article-title":"Cross-tissue immune cell analysis reveals tissue-specific features in humans","volume":"376","author":"Dom\u00ednguez Conde","year":"2022","journal-title":"Science"},{"key":"10.1016\/j.cels.2024.11.001_bib41","doi-asserted-by":"crossref","first-page":"1445","DOI":"10.1084\/jem.181.4.1445","article-title":"Early human T\u00a0cell development: analysis of the human thymus at the time of initial entry of hematopoietic stem cells into the fetal thymic microenvironment","volume":"181","author":"Haynes","year":"1995","journal-title":"J.\u00a0Exp. Med."},{"key":"10.1016\/j.cels.2024.11.001_bib42","doi-asserted-by":"crossref","first-page":"328","DOI":"10.1186\/1471-2105-13-328","article-title":"Comparison of co-expression measures: mutual information, correlation, and model based indices","volume":"13","author":"Song","year":"2012","journal-title":"BMC Bioinformatics"},{"key":"10.1016\/j.cels.2024.11.001_bib43","doi-asserted-by":"crossref","first-page":"D325","DOI":"10.1093\/nar\/gkaa1113","article-title":"The Gene Ontology resource: enriching a GOld mine","volume":"49","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.cels.2024.11.001_bib44","doi-asserted-by":"crossref","first-page":"317","DOI":"10.1146\/annurev-cellbio-100814-125300","article-title":"Studying lineage decision-making in\u00a0vitro: emerging concepts and novel tools","volume":"31","author":"Semrau","year":"2015","journal-title":"Annu. Rev. Cell Dev. Biol."},{"key":"10.1016\/j.cels.2024.11.001_bib45","doi-asserted-by":"crossref","first-page":"16434","DOI":"10.1073\/pnas.1207852109","article-title":"Predictive computation of genomic logic processing functions in embryonic development","volume":"109","author":"Peter","year":"2012","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.cels.2024.11.001_bib46","article-title":"IQCELL: A platform for predicting the effect of gene perturbations on developmental trajectories using single-cell RNA-seq data","volume":"18","author":"Heydari","year":"2022","journal-title":"PLoS\u00a0Comput. Biol."},{"key":"10.1016\/j.cels.2024.11.001_bib47","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.cels.2024.11.001_bib48","doi-asserted-by":"crossref","DOI":"10.1038\/ncomms11171","article-title":"GATA3 induces human T-cell commitment by restraining Notch activity and repressing NK-cell fate","volume":"7","author":"Van de Walle","year":"2016","journal-title":"Nat. Commun."},{"key":"10.1016\/j.cels.2024.11.001_bib49","doi-asserted-by":"crossref","first-page":"1534","DOI":"10.1182\/blood-2012-08-449447","article-title":"E2A transcription factors limit expression of Gata3 to facilitate T lymphocyte lineage commitment","volume":"121","author":"Xu","year":"2013","journal-title":"Blood"},{"key":"10.1016\/j.cels.2024.11.001_bib50","doi-asserted-by":"crossref","first-page":"733","DOI":"10.1084\/jem.194.6.733","article-title":"Early thymocyte development is regulated by modulation of E2A protein activity","volume":"194","author":"Engel","year":"2001","journal-title":"J.\u00a0Exp. Med."},{"key":"10.1016\/j.cels.2024.11.001_bib51","doi-asserted-by":"crossref","first-page":"1719","DOI":"10.1158\/0008-5472.CAN-16-2159","article-title":"Systematic In\u00a0Vivo Inactivation of Chromatin-Regulating Enzymes Identifies Setd2 as a Potent Tumor Suppressor in Lung Adenocarcinoma","volume":"77","author":"Walter","year":"2017","journal-title":"Cancer Res."},{"key":"10.1016\/j.cels.2024.11.001_bib52","doi-asserted-by":"crossref","first-page":"547","DOI":"10.1016\/S1074-7613(00)80054-0","article-title":"Deficient T\u00a0cell fate specification in mice with an induced inactivation of Notch1","volume":"10","author":"Radtke","year":"1999","journal-title":"Immunity"},{"key":"10.1016\/j.cels.2024.11.001_bib53","doi-asserted-by":"crossref","first-page":"394","DOI":"10.1038\/3877","article-title":"Defective IL7R expression in T(-)B(+)NK(+) severe combined immunodeficiency","volume":"20","author":"Puel","year":"1998","journal-title":"Nat. Genet."},{"key":"10.1016\/j.cels.2024.11.001_bib54","doi-asserted-by":"crossref","first-page":"818","DOI":"10.1016\/j.immuni.2017.04.022","article-title":"The E-Id Protein Axis Specifies Adaptive Lymphoid Cell Identity and Suppresses Thymic Innate Lymphoid Cell Development","volume":"46","author":"Miyazaki","year":"2017","journal-title":"Immunity"},{"key":"10.1016\/j.cels.2024.11.001_bib55","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1038\/s41556-019-0445-8","article-title":"Multipotent RAG1+ progenitors emerge directly from haemogenic endothelium in human pluripotent stem cell-derived haematopoietic organoids","volume":"22","author":"Motazedian","year":"2020","journal-title":"Nat. Cell Biol."},{"key":"10.1016\/j.cels.2024.11.001_bib56","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1111\/imr.13191","article-title":"Mast cell ontogeny: from fetal development to life-long health and disease","volume":"315","author":"Chia","year":"2023","journal-title":"Immunol. Rev."},{"key":"10.1016\/j.cels.2024.11.001_bib57","doi-asserted-by":"crossref","first-page":"1160","DOI":"10.1016\/j.immuni.2018.04.025","article-title":"Hemogenic Endothelial Fate Mapping Reveals Dual Developmental Origin of Mast Cells","volume":"48","author":"Gentek","year":"2018","journal-title":"Immunity"},{"key":"10.1016\/j.cels.2024.11.001_bib58","doi-asserted-by":"crossref","first-page":"150","DOI":"10.1016\/j.ebiom.2019.03.089","article-title":"Single-cell analysis reveals the KIT D816V mutation in haematopoietic stem and progenitor cells in systemic mastocytosis","volume":"43","author":"Grootens","year":"2019","journal-title":"EBiomedicine"},{"key":"10.1016\/j.cels.2024.11.001_bib59","doi-asserted-by":"crossref","first-page":"640","DOI":"10.1016\/j.immuni.2018.09.023","article-title":"Adult Connective Tissue-Resident Mast Cells Originate from Late Erythro-Myeloid Progenitors","volume":"49","author":"Li","year":"2018","journal-title":"Immunity"},{"key":"10.1016\/j.cels.2024.11.001_bib60","doi-asserted-by":"crossref","first-page":"845","DOI":"10.1038\/ni1486","article-title":"Mast cell lineage diversion of T lineage precursors by the essential T\u00a0cell transcription factor GATA-3","volume":"8","author":"Taghon","year":"2007","journal-title":"Nat. Immunol."},{"key":"10.1016\/j.cels.2024.11.001_bib61","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0063718","article-title":"Lysophosphatidic acid mediates myeloid differentiation within the human bone marrow microenvironment","volume":"8","author":"Evseenko","year":"2013","journal-title":"PLoS One"},{"key":"10.1016\/j.cels.2024.11.001_bib62","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-021-25133-1","article-title":"LineageOT is a unified framework for lineage tracing and trajectory inference","volume":"12","author":"Forrow","year":"2021","journal-title":"Nat. Commun."},{"key":"10.1016\/j.cels.2024.11.001_bib63","doi-asserted-by":"crossref","first-page":"1066","DOI":"10.1038\/s41587-022-01209-1","article-title":"CoSpar identifies early cell fate biases from single-cell transcriptomic and lineage information","volume":"40","author":"Wang","year":"2022","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.cels.2024.11.001_bib64","doi-asserted-by":"crossref","first-page":"928","DOI":"10.1016\/j.cell.2019.01.006","article-title":"Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming","volume":"176","author":"Schiebinger","year":"2019","journal-title":"Cell"},{"key":"10.1016\/j.cels.2024.11.001_bib65","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/btae483","article-title":"Cellular proliferation biases clonal lineage tracing and trajectory inference","volume":"40","author":"Bonham-Carter","year":"2024","journal-title":"Bioinformatics"},{"key":"10.1016\/j.cels.2024.11.001_bib66","doi-asserted-by":"crossref","DOI":"10.1126\/sciimmunol.abm1920","article-title":"Single-cell deletion analyses show control of pro-T cell developmental speed and pathways by Tcf7, Spi1, Gata3, Bcl11a, Erg, and Bcl11b","volume":"7","author":"Zhou","year":"2022","journal-title":"Sci. Immunol."},{"key":"10.1016\/j.cels.2024.11.001_bib67","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1038\/s41586-023-05869-0","article-title":"Spatial multiomics map of trophoblast development in early pregnancy","volume":"616","author":"Arutyunyan","year":"2023","journal-title":"Nature"},{"key":"10.1016\/j.cels.2024.11.001_bib68","doi-asserted-by":"crossref","first-page":"5876","DOI":"10.1016\/j.cell.2023.11.026","article-title":"Automatic cell-type harmonization and integration across Human Cell Atlas datasets","volume":"186","author":"Xu","year":"2023","journal-title":"Cell"},{"key":"10.1016\/j.cels.2024.11.001_bib69","doi-asserted-by":"crossref","first-page":"477","DOI":"10.1186\/s12864-018-4772-0","article-title":"Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics","volume":"19","author":"Street","year":"2018","journal-title":"BMC Genomics"},{"key":"10.1016\/j.cels.2024.11.001_bib70","doi-asserted-by":"crossref","first-page":"251","DOI":"10.1007\/7651_2022_465","article-title":"Inferring Gene Regulatory Networks and Predicting the Effect of Gene Perturbations via IQCELL","volume":"2767","author":"Heydari","year":"2024","journal-title":"Methods Mol. Biol."},{"key":"10.1016\/j.cels.2024.11.001_bib71","series-title":"Z3: An Efficient SMT Solver","first-page":"337","author":"de Moura","year":"2008"},{"key":"10.1016\/j.cels.2024.11.001_bib72","doi-asserted-by":"crossref","DOI":"10.15252\/msb.20177952","article-title":"Modeling signaling-dependent pluripotency with Boolean logic to predict cell fate transitions","volume":"14","author":"Yachie-Kinoshita","year":"2018","journal-title":"Mol. Syst. Biol."},{"key":"10.1016\/j.cels.2024.11.001_bib73","doi-asserted-by":"crossref","first-page":"1202","DOI":"10.1016\/j.cell.2015.05.002","article-title":"Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets","volume":"161","author":"Macosko","year":"2015","journal-title":"Cell"}],"container-title":["Cell Systems"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2405471224003107?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2405471224003107?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2024,12,18]],"date-time":"2024-12-18T15:57:11Z","timestamp":1734537431000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2405471224003107"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,12]]},"references-count":73,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2024,12]]}},"alternative-id":["S2405471224003107"],"URL":"https:\/\/doi.org\/10.1016\/j.cels.2024.11.001","relation":{},"ISSN":["2405-4712"],"issn-type":[{"value":"2405-4712","type":"print"}],"subject":[],"published":{"date-parts":[[2024,12]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Tracking the gene expression programs and clonal relationships that underlie mast, myeloid, and T lineage specification from stem cells","name":"articletitle","label":"Article Title"},{"value":"Cell Systems","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.cels.2024.11.001","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"}]}}