{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,2]],"date-time":"2026-05-02T06:33:40Z","timestamp":1777703620466,"version":"3.51.4"},"reference-count":30,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2007,1,26]],"date-time":"2007-01-26T00:00:00Z","timestamp":1169769600000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.0030013","type":"journal-article","created":{"date-parts":[[2007,1,24]],"date-time":"2007-01-24T01:12:11Z","timestamp":1169601131000},"page":"e13","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":58,"title":["Emergent Dynamics of Thymocyte Development and Lineage Determination"],"prefix":"10.1371","volume":"3","author":[{"given":"Sol","family":"Efroni","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David","family":"Harel","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Irun R","family":"Cohen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2007,1,26]]},"reference":[{"key":"pcbi-0030013-b001","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1038\/35095500","article-title":"Lymphostromal interactions in thymic development and function.","volume":"1","year":"2001","journal-title":"Nat Rev Immunol"},{"key":"pcbi-0030013-b002","doi-asserted-by":"crossref","first-page":"859","DOI":"10.1038\/nri1223","article-title":"Cell migration and the control of post-natal T-cell lymphopoiesis in the thymus.","volume":"3","year":"2003","journal-title":"Nat Rev Immunol"},{"key":"pcbi-0030013-b003","unstructured":"JanewayC\n\t\t\t\t\t2001\n\t\t\t\t\tImmunobiology: The immune system in health and disease\n\t\t\t\t\tNew York\n\t\t\t\t\tGarland Science\n\t\t\t\t\t600"},{"key":"pcbi-0030013-b004","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","year":"2006","journal-title":"Nat Rev Immunol"},{"key":"pcbi-0030013-b005","doi-asserted-by":"crossref","first-page":"2485","DOI":"10.1101\/gr.1215303","article-title":"Toward rigorous comprehension of biological complexity: Modeling, execution, and visualization of thymic T-cell maturation.","volume":"13","year":"2003","journal-title":"Genome Res"},{"key":"pcbi-0030013-b006","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1109\/MC.2005.31","article-title":"Reactive animation: Realistic modeling of complex dynamic systems.","volume":"38","year":"2005","journal-title":"Computer"},{"key":"pcbi-0030013-b007","doi-asserted-by":"crossref","first-page":"136","DOI":"10.1007\/978-3-540-39656-7_5","article-title":"Reactive animation.","volume":"2852","year":"2003","journal-title":"Lect Notes Comput Sci"},{"key":"pcbi-0030013-b008","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1016\/0167-6423(87)90035-9","article-title":"Statecharts: A visual formalism for complex systems.","volume":"8","year":"1987","journal-title":"Sci Comput Programming"},{"key":"pcbi-0030013-b009","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1016\/0025-5564(96)00022-3","article-title":"Equilibrium binding of multivalent ligands to cells: Effects of cell and receptor density.","volume":"135","year":"1996","journal-title":"Math Biosci"},{"key":"pcbi-0030013-b010","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1006\/jtbi.1994.1160","article-title":"T cell repertoires and competitive exclusion.","volume":"169","year":"1994","journal-title":"J Theor Biol"},{"key":"pcbi-0030013-b011","doi-asserted-by":"crossref","first-page":"862","DOI":"10.1016\/S0264-410X(00)00225-5","article-title":"A systematic approach to vaccine complexity using an automaton model of the cellular and humoral immune system. I. Viral characteristics and polarized responses.","volume":"19","year":"2000","journal-title":"Vaccine"},{"key":"pcbi-0030013-b012","doi-asserted-by":"crossref","first-page":"791","DOI":"10.1038\/ni1095","article-title":"CD4 enhances T cell sensitivity to antigen by coordinating Lck accumulation at the immunological synapse.","volume":"5","year":"2004","journal-title":"Nat Immunol"},{"key":"pcbi-0030013-b013","first-page":"PE10","article-title":"How and why does the immunological synapse form? Physical chemistry meets cell biology.","volume":"2002","year":"2002","journal-title":"Sci STKE"},{"key":"pcbi-0030013-b014","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1016\/j.smim.2004.08.004","article-title":"Antigen receptor genes and the evolution of a recombinase.","volume":"16","year":"2004","journal-title":"Semin Immunol"},{"key":"pcbi-0030013-b015","unstructured":"Meier-SchellersheimM\n\t\t\t\t\t1999\n\t\t\t\t\tSIMMUNE, a tool for simulating and analyzing immune system behavior\n\t\t\t\t\tHamburg\n\t\t\t\t\tDeutsches Elektronen-Synchrotron (DESY)"},{"issue":"(7)","key":"pcbi-0030013-b016","article-title":"Key role of local regulation in chemosensing revealed by a new molecular interaction\u2013based modeling method.","volume":"2","year":"2006","journal-title":"PLoS Comput Biol"},{"key":"pcbi-0030013-b017","doi-asserted-by":"crossref","first-page":"601","DOI":"10.1146\/annurev.immunol.23.021704.115737","article-title":"Molecular genetics of T cell development.","volume":"23","year":"2005","journal-title":"Annu Rev Immunol"},{"key":"pcbi-0030013-b018","doi-asserted-by":"crossref","first-page":"262","DOI":"10.1002\/1521-4141(200001)30:1<262::AID-IMMU262>3.0.CO;2-0","article-title":"The chemokine TECK is expressed by thymic and intestinal epithelial cells and attracts double- and single-positive thymocytes expressing the TECK receptor CCR9.","volume":"30","year":"2000","journal-title":"Eur J Immunol"},{"key":"pcbi-0030013-b019","doi-asserted-by":"crossref","first-page":"4521","DOI":"10.4049\/jimmunol.171.9.4521","article-title":"Critical role for CXCR4 signaling in progenitor localization and T cell differentiation in the postnatal thymus.","volume":"171","year":"2003","journal-title":"J Immunol"},{"key":"pcbi-0030013-b020","doi-asserted-by":"crossref","first-page":"2811","DOI":"10.4049\/jimmunol.168.6.2811","article-title":"A role for CCR9 in T lymphocyte development and migration.","volume":"168","year":"2002","journal-title":"J Immunol"},{"key":"pcbi-0030013-b021","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1146\/annurev.immunol.18.1.309","article-title":"Glucocorticoids in T cell development and function*.","volume":"18","year":"2000","journal-title":"Annu Rev Immunol"},{"key":"pcbi-0030013-b022","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1016\/S1074-7613(00)80171-5","article-title":"Thymocyte resistance to glucocorticoids leads to antigen-specific unresponsiveness due to \u201choles\u201d in the T cell repertoire.","volume":"12","year":"2000","journal-title":"Immunity"},{"key":"pcbi-0030013-b023","doi-asserted-by":"crossref","first-page":"1639","DOI":"10.1126\/science.1071551","article-title":"Control of T cell function by positive and negative regulators.","volume":"296","year":"2002","journal-title":"Science"},{"key":"pcbi-0030013-b024","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1006\/smim.2000.0234","article-title":"Discrimination and dialogue in the immune system.","volume":"12","year":"2000","journal-title":"Semin Immunol"},{"key":"pcbi-0030013-b025","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1038\/nri798","article-title":"T-cell development and the CD4\u2013CD8 lineage decision.","volume":"2","year":"2002","journal-title":"Nat Rev Immunol"},{"key":"pcbi-0030013-b026","doi-asserted-by":"crossref","first-page":"826","DOI":"10.1038\/nature03338","article-title":"The zinc finger transcription factor Th-POK regulates CD4 versus CD8 T-cell lineage commitment.","volume":"433","year":"2005","journal-title":"Nature"},{"key":"pcbi-0030013-b027","doi-asserted-by":"crossref","first-page":"1709","DOI":"10.1084\/jem.20030170","article-title":"Unraveling a revealing paradox: Why major histocompatibility complex I-signaled thymocytes \u201cparadoxically\u201d appear as CD4+8lo transitional cells during positive selection of CD8+ T cells.","volume":"197","year":"2003","journal-title":"J Exp Med"},{"key":"pcbi-0030013-b028","unstructured":"CohenIR\n\t\t\t\t\t2000\n\t\t\t\t\tTending Adam's garden: Evolving the cognitive immune self\n\t\t\t\t\tSan Diego (California)\n\t\t\t\t\tAcademic Press\n\t\t\t\t\t266"},{"key":"pcbi-0030013-b029","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1038\/nbt0405-495","article-title":"A Turing-like test for biological modeling.","volume":"23","year":"2005","journal-title":"Nat Biotechnol"},{"key":"pcbi-0030013-b030","first-page":"3","article-title":"The late stage of T cell development within mouse thymus.","volume":"1","year":"2004","journal-title":"Cell Mol Immunol"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.0030013","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,6]],"date-time":"2020-05-06T21:54:07Z","timestamp":1588802047000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.0030013"}},"subtitle":[],"editor":[{"given":"Howard","family":"Petrie","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2007,1,26]]},"references-count":30,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2007,1,26]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.0030013","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2007,1,26]]}}}