{"id":"https://openalex.org/W1501606775","doi":"https://doi.org/10.1371/journal.pcbi.1004324","title":"A Minimal Regulatory Network of Extrinsic and Intrinsic Factors Recovers Observed Patterns of CD4+ T Cell Differentiation and Plasticity","display_name":"A Minimal Regulatory Network of Extrinsic and Intrinsic Factors Recovers Observed Patterns of CD4+ T Cell Differentiation and Plasticity","publication_year":2015,"publication_date":"2015-06-19","ids":{"openalex":"https://openalex.org/W1501606775","doi":"https://doi.org/10.1371/journal.pcbi.1004324","mag":"1501606775","pmid":"https://pubmed.ncbi.nlm.nih.gov/26090929"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1004324","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004324","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004324&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004324&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5011141054","display_name":"Mariana Esther Mart\u00ednez-S\u00e1nchez","orcid":"https://orcid.org/0000-0002-6115-1449"},"institutions":[{"id":"https://openalex.org/I8961855","display_name":"Universidad Nacional Aut\u00f3noma de M\u00e9xico","ror":"https://ror.org/01tmp8f25","country_code":"MX","type":"education","lineage":["https://openalex.org/I8961855"]},{"id":"https://openalex.org/I4210154133","display_name":"Instituto de Ecolog\u00eda","ror":"https://ror.org/03yvabt26","country_code":"MX","type":"facility","lineage":["https://openalex.org/I4210154133"]}],"countries":["MX"],"is_corresponding":false,"raw_author_name":"Mariana Esther Martinez-Sanchez","raw_affiliation_strings":["Departamento de Ecolog\u00eda Funcional, Instituto de Ecolog\u00eda, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Coyoac\u00e1n, M\u00e9xico Distrito Federal, M\u00e9xico; Centro de Ciencias de la Complejidad, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Coyoac\u00e1n, M\u00e9xico Distrito Federal, M\u00e9xico","Centro de Ciencias de la Complejidad, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Coyoac\u00e1n, M\u00e9xico Distrito Federal, M\u00e9xico","Departamento de Ecolog\u00eda Funcional, Instituto de Ecolog\u00eda, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Coyoac\u00e1n, M\u00e9xico Distrito Federal, M\u00e9xico"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departamento de Ecolog\u00eda Funcional, Instituto de Ecolog\u00eda, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Coyoac\u00e1n, M\u00e9xico Distrito Federal, M\u00e9xico; Centro de Ciencias de la Complejidad, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Coyoac\u00e1n, M\u00e9xico Distrito Federal, M\u00e9xico","institution_ids":[]},{"raw_affiliation_string":"Centro de Ciencias de la Complejidad, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Coyoac\u00e1n, M\u00e9xico Distrito Federal, M\u00e9xico","institution_ids":["https://openalex.org/I8961855"]},{"raw_affiliation_string":"Departamento de Ecolog\u00eda Funcional, Instituto de Ecolog\u00eda, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Coyoac\u00e1n, M\u00e9xico Distrito Federal, M\u00e9xico","institution_ids":["https://openalex.org/I8961855","https://openalex.org/I4210154133"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072755654","display_name":"Luis Mendoza","orcid":"https://orcid.org/0000-0002-3321-3083"},"institutions":[{"id":"https://openalex.org/I8961855","display_name":"Universidad Nacional Aut\u00f3noma de M\u00e9xico","ror":"https://ror.org/01tmp8f25","country_code":"MX","type":"education","lineage":["https://openalex.org/I8961855"]}],"countries":["MX"],"is_corresponding":false,"raw_author_name":"Luis Mendoza","raw_affiliation_strings":["Departamento de Biolog\u00eda Molecular y Biotecnolog\u00eda, Instituto de Investigaciones Biom\u00e9dicas, Universidad Nacional Aut\u00f3noma de M\u00e9xico, M\u00e9xico Distrito Federal, M\u00e9xico"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departamento de Biolog\u00eda Molecular y Biotecnolog\u00eda, Instituto de Investigaciones Biom\u00e9dicas, Universidad Nacional Aut\u00f3noma de M\u00e9xico, M\u00e9xico Distrito Federal, M\u00e9xico","institution_ids":["https://openalex.org/I8961855"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008755301","display_name":"Carlos Villarreal","orcid":"https://orcid.org/0000-0003-3569-2820"},"institutions":[{"id":"https://openalex.org/I8961855","display_name":"Universidad Nacional Aut\u00f3noma de M\u00e9xico","ror":"https://ror.org/01tmp8f25","country_code":"MX","type":"education","lineage":["https://openalex.org/I8961855"]}],"countries":["MX"],"is_corresponding":false,"raw_author_name":"Carlos Villarreal","raw_affiliation_strings":["Centro de Ciencias de la Complejidad, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Coyoac\u00e1n, M\u00e9xico Distrito Federal, M\u00e9xico; Departamento de F\u00edsica Te\u00f3rica, Instituto de F\u00edsica, Universidad Nacional Aut\u00f3noma de M\u00e9xico, M\u00e9xico Distrito Federal, M\u00e9xico","Centro de Ciencias de la Complejidad, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Coyoac\u00e1n, M\u00e9xico Distrito Federal, M\u00e9xico","Departamento de F\u00edsica Te\u00f3rica, Instituto de F\u00edsica, Universidad Nacional Aut\u00f3noma de M\u00e9xico, M\u00e9xico Distrito Federal, M\u00e9xico"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centro de Ciencias de la Complejidad, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Coyoac\u00e1n, M\u00e9xico Distrito Federal, M\u00e9xico; Departamento de F\u00edsica Te\u00f3rica, Instituto de F\u00edsica, Universidad Nacional Aut\u00f3noma de M\u00e9xico, M\u00e9xico Distrito Federal, M\u00e9xico","institution_ids":[]},{"raw_affiliation_string":"Centro de Ciencias de la Complejidad, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Coyoac\u00e1n, M\u00e9xico Distrito Federal, M\u00e9xico","institution_ids":["https://openalex.org/I8961855"]},{"raw_affiliation_string":"Departamento de F\u00edsica Te\u00f3rica, Instituto de F\u00edsica, Universidad Nacional Aut\u00f3noma de M\u00e9xico, M\u00e9xico Distrito Federal, M\u00e9xico","institution_ids":["https://openalex.org/I8961855"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5022055568","display_name":"Elena \u00c1lvarez\u2010Buylla","orcid":"https://orcid.org/0000-0002-7938-6473"},"institutions":[{"id":"https://openalex.org/I8961855","display_name":"Universidad Nacional Aut\u00f3noma de M\u00e9xico","ror":"https://ror.org/01tmp8f25","country_code":"MX","type":"education","lineage":["https://openalex.org/I8961855"]},{"id":"https://openalex.org/I4210154133","display_name":"Instituto de Ecolog\u00eda","ror":"https://ror.org/03yvabt26","country_code":"MX","type":"facility","lineage":["https://openalex.org/I4210154133"]}],"countries":["MX"],"is_corresponding":true,"raw_author_name":"Elena R. Alvarez-Buylla","raw_affiliation_strings":["Departamento de Ecolog\u00eda Funcional, Instituto de Ecolog\u00eda, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Coyoac\u00e1n, M\u00e9xico Distrito Federal, M\u00e9xico; Centro de Ciencias de la Complejidad, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Coyoac\u00e1n, M\u00e9xico Distrito Federal, M\u00e9xico","Departamento de Ecolog\u00eda Funcional, Instituto de Ecolog\u00eda, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Coyoac\u00e1n, M\u00e9xico Distrito Federal, M\u00e9xico","Centro de Ciencias de la Complejidad, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Coyoac\u00e1n, M\u00e9xico Distrito Federal, M\u00e9xico"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departamento de Ecolog\u00eda Funcional, Instituto de Ecolog\u00eda, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Coyoac\u00e1n, M\u00e9xico Distrito Federal, M\u00e9xico; Centro de Ciencias de la Complejidad, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Coyoac\u00e1n, M\u00e9xico Distrito Federal, M\u00e9xico","institution_ids":[]},{"raw_affiliation_string":"Departamento de Ecolog\u00eda Funcional, Instituto de Ecolog\u00eda, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Coyoac\u00e1n, M\u00e9xico Distrito Federal, M\u00e9xico","institution_ids":["https://openalex.org/I8961855","https://openalex.org/I4210154133"]},{"raw_affiliation_string":"Centro de Ciencias de la Complejidad, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Coyoac\u00e1n, M\u00e9xico Distrito Federal, M\u00e9xico","institution_ids":["https://openalex.org/I8961855"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5022055568"],"corresponding_institution_ids":["https://openalex.org/I4210154133","https://openalex.org/I8961855"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":3.8884,"has_fulltext":true,"cited_by_count":87,"citation_normalized_percentile":{"value":0.93966083,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"11","issue":"6","first_page":"e1004324","last_page":"e1004324"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10031","display_name":"T-cell and B-cell Immunology","score":0.9986000061035156,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10031","display_name":"T-cell and B-cell Immunology","score":0.9986000061035156,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11020","display_name":"Immune Cell Function and Interaction","score":0.984000027179718,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10580","display_name":"Immunotherapy and Immune Responses","score":0.9603000283241272,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.621040940284729},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5814149379730225},{"id":"https://openalex.org/keywords/cell-fate-determination","display_name":"Cell fate determination","score":0.5768492817878723},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.5202204585075378},{"id":"https://openalex.org/keywords/foxp3","display_name":"FOXP3","score":0.5182454586029053},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.513386607170105},{"id":"https://openalex.org/keywords/t-cell","display_name":"T cell","score":0.48951852321624756},{"id":"https://openalex.org/keywords/transcriptional-regulation","display_name":"Transcriptional regulation","score":0.41953834891319275},{"id":"https://openalex.org/keywords/cellular-differentiation","display_name":"Cellular differentiation","score":0.4194149971008301},{"id":"https://openalex.org/keywords/phenotype","display_name":"Phenotype","score":0.4153791069984436},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3660057783126831},{"id":"https://openalex.org/keywords/immune-system","display_name":"Immune system","score":0.31567418575286865},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.30179816484451294},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.19212988018989563},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.1434941291809082}],"concepts":[{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.621040940284729},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5814149379730225},{"id":"https://openalex.org/C163952510","wikidata":"https://www.wikidata.org/wiki/Q5058196","display_name":"Cell fate determination","level":4,"score":0.5768492817878723},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.5202204585075378},{"id":"https://openalex.org/C2779727006","wikidata":"https://www.wikidata.org/wiki/Q426188","display_name":"FOXP3","level":3,"score":0.5182454586029053},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.513386607170105},{"id":"https://openalex.org/C2776090121","wikidata":"https://www.wikidata.org/wiki/Q193529","display_name":"T cell","level":3,"score":0.48951852321624756},{"id":"https://openalex.org/C27153228","wikidata":"https://www.wikidata.org/wiki/Q3787274","display_name":"Transcriptional regulation","level":4,"score":0.41953834891319275},{"id":"https://openalex.org/C148738053","wikidata":"https://www.wikidata.org/wiki/Q210861","display_name":"Cellular differentiation","level":3,"score":0.4194149971008301},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.4153791069984436},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3660057783126831},{"id":"https://openalex.org/C8891405","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune system","level":2,"score":0.31567418575286865},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.30179816484451294},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.19212988018989563},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.1434941291809082}],"mesh":[{"descriptor_ui":"D000066670","descriptor_name":"Cell Plasticity","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000066670","descriptor_name":"Cell Plasticity","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000066670","descriptor_name":"Cell Plasticity","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000066670","descriptor_name":"Cell Plasticity","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D002454","descriptor_name":"Cell Differentiation","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D002454","descriptor_name":"Cell Differentiation","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D002454","descriptor_name":"Cell Differentiation","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D002454","descriptor_name":"Cell Differentiation","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D015496","descriptor_name":"CD4-Positive T-Lymphocytes","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D015496","descriptor_name":"CD4-Positive T-Lymphocytes","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D015496","descriptor_name":"CD4-Positive T-Lymphocytes","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D015496","descriptor_name":"CD4-Positive T-Lymphocytes","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D016207","descriptor_name":"Cytokines","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016207","descriptor_name":"Cytokines","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016207","descriptor_name":"Cytokines","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016207","descriptor_name":"Cytokines","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D018448","descriptor_name":"Models, Immunological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018448","descriptor_name":"Models, Immunological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018448","descriptor_name":"Models, Immunological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018448","descriptor_name":"Models, Immunological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060833","descriptor_name":"Cellular Microenvironment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060833","descriptor_name":"Cellular Microenvironment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060833","descriptor_name":"Cellular Microenvironment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060833","descriptor_name":"Cellular Microenvironment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1004324","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004324","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004324&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:26090929","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26090929","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:doaj.org/article:3aa339f6407c4854814151a5c9f02635","is_oa":true,"landing_page_url":"https://doaj.org/article/3aa339f6407c4854814151a5c9f02635","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 11, Iss 6, p e1004324 (2015)","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/1455773","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/_A_Minimal_Regulatory_Network_of_Extrinsic_and_Intrinsic_Factors_Recovers_Observed_Patterns_of_CD4_T_Cell_Differentiation_and_Plasticity_/1455773","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Dataset"},{"id":"pmh:oai:pubmedcentral.nih.gov:4475012","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4475012","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1004324","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004324","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004324&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being","score":0.5099999904632568}],"awards":[{"id":"https://openalex.org/G6078673949","display_name":null,"funder_award_id":"180380","funder_id":"https://openalex.org/F4320321739","funder_display_name":"Consejo Nacional de Ciencia y Tecnolog\u00eda"},{"id":"https://openalex.org/G8942296229","display_name":null,"funder_award_id":"180098","funder_id":"https://openalex.org/F4320321739","funder_display_name":"Consejo Nacional de Ciencia y Tecnolog\u00eda"}],"funders":[{"id":"https://openalex.org/F4320321739","display_name":"Consejo Nacional de Ciencia y Tecnolog\u00eda","ror":"https://ror.org/059ex5q34"},{"id":"https://openalex.org/F4320323401","display_name":"Universidad Nacional Aut\u00f3noma de M\u00e9xico","ror":"https://ror.org/01tmp8f25"},{"id":"https://openalex.org/F4320323662","display_name":"ERAB: The European Foundation for Alcohol Research","ror":"https://ror.org/04g6qfd94"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1501606775.pdf","grobid_xml":"https://content.openalex.org/works/W1501606775.grobid-xml"},"referenced_works_count":69,"referenced_works":["https://openalex.org/W175676769","https://openalex.org/W1509258310","https://openalex.org/W1523376838","https://openalex.org/W1567420244","https://openalex.org/W1599839677","https://openalex.org/W1690266756","https://openalex.org/W1763873242","https://openalex.org/W1942668068","https://openalex.org/W1968758858","https://openalex.org/W1971849554","https://openalex.org/W1977912132","https://openalex.org/W1982926364","https://openalex.org/W1984471114","https://openalex.org/W1987076250","https://openalex.org/W1987735044","https://openalex.org/W1992851412","https://openalex.org/W1997989189","https://openalex.org/W2013495037","https://openalex.org/W2017893786","https://openalex.org/W2020304403","https://openalex.org/W2021340905","https://openalex.org/W2030459888","https://openalex.org/W2031466112","https://openalex.org/W2035145195","https://openalex.org/W2040580015","https://openalex.org/W2041924570","https://openalex.org/W2043776488","https://openalex.org/W2043872798","https://openalex.org/W2046388159","https://openalex.org/W2052998574","https://openalex.org/W2057609434","https://openalex.org/W2058139816","https://openalex.org/W2059012075","https://openalex.org/W2059189469","https://openalex.org/W2059498834","https://openalex.org/W2065546165","https://openalex.org/W2066740231","https://openalex.org/W2066906123","https://openalex.org/W2070685885","https://openalex.org/W2070769098","https://openalex.org/W2070791475","https://openalex.org/W2071019594","https://openalex.org/W2080721009","https://openalex.org/W2082450021","https://openalex.org/W2082602434","https://openalex.org/W2082871926","https://openalex.org/W2085347930","https://openalex.org/W2088963966","https://openalex.org/W2089715072","https://openalex.org/W2092975931","https://openalex.org/W2095649879","https://openalex.org/W2103600875","https://openalex.org/W2105254505","https://openalex.org/W2112120433","https://openalex.org/W2117201337","https://openalex.org/W2136645272","https://openalex.org/W2139565733","https://openalex.org/W2142877732","https://openalex.org/W2143417567","https://openalex.org/W2143609829","https://openalex.org/W2152014155","https://openalex.org/W2161636210","https://openalex.org/W2162742070","https://openalex.org/W2163998704","https://openalex.org/W2167437179","https://openalex.org/W2314143613","https://openalex.org/W4210457135","https://openalex.org/W4313324526","https://openalex.org/W6665352542"],"related_works":["https://openalex.org/W4387096194","https://openalex.org/W4387096200","https://openalex.org/W4387095958","https://openalex.org/W4366722611","https://openalex.org/W1995507342","https://openalex.org/W4390011121","https://openalex.org/W1985607197","https://openalex.org/W4281759407","https://openalex.org/W1590000685","https://openalex.org/W2508191807"],"abstract_inverted_index":{"CD4+":[0,27,41,83,99,189,212,257,266],"T":[1,28,42,84,100,158,188,213,258,267],"cells":[2,65],"orchestrate":[3],"the":[4,21,34,54,60,77,134,145,182,200,226,264,274,277,284,288],"adaptive":[5],"immune":[6],"response":[7],"in":[8,26,82,194],"vertebrates.":[9],"While":[10],"both":[11],"experimental":[12,123],"and":[13,31,53,56,115,133,156,167,205,246,269,283,298],"modeling":[14],"work":[15],"has":[16],"been":[17,173],"conducted":[18],"to":[19,96,241,254],"understand":[20],"molecular":[22],"genetic":[23],"mechanisms":[24],"involved":[25,81],"cell":[29,147,190,214,259],"responses":[30,62],"fate":[32],"attainment,":[33],"dynamic":[35,57],"role":[36],"of":[37,59,63,142,144,181,202,248,291],"intrinsic":[38,278],"(produced":[39,46],"by":[40,47,222],"lymphocytes)":[43],"versus":[44],"extrinsic":[45],"other":[48,295],"cells)":[49],"components":[50],"remains":[51,66],"unclear,":[52],"mechanistic":[55],"understanding":[58],"plastic":[61,260,296],"these":[64],"incomplete.":[67],"In":[68,262],"this":[69,91,177,292],"work,":[70],"we":[71,234],"studied":[72],"a":[73,105,113,195,236],"regulatory":[74,108,159,163,281],"network":[75,109,118,127,137,164],"for":[76,186,294],"core":[78,92,282],"transcription":[79],"factors":[80],"cell-fate":[85,196,218],"attainment.":[86],"We":[87,102,198,286],"first":[88],"show":[89],"that":[90,119,171,243],"is":[93,120,165],"not":[94],"sufficient":[95],"recover":[97],"common":[98],"phenotypes.":[101],"thus":[103],"postulate":[104],"minimal":[106,126],"Boolean":[107],"model":[110,138,178],"derived":[111],"from":[112,273],"larger":[114],"more":[116],"comprehensive":[117],"based":[121],"on":[122,208],"data.":[124],"The":[125],"integrates":[128],"transcriptional":[129],"regulation,":[130],"signaling":[131,250],"pathways":[132],"micro-environment.":[135,285],"This":[136,161],"recovers":[139,168,179],"reported":[140,174],"configurations":[141,170],"most":[143,217],"characterized":[146],"types":[148],"(Th0,":[149],"Th1,":[150],"Th2,":[151],"Th17,":[152],"Tfh,":[153],"Th9,":[154],"iTreg,":[155],"Foxp3-independent":[157],"cells).":[160],"transcriptional-signaling":[162],"robust":[166],"mutant":[169],"have":[172],"experimentally.":[175],"Additionally,":[176],"many":[180],"plasticity":[183],"patterns":[184,271],"documented":[185],"different":[187],"types,":[191],"as":[192],"summarized":[193],"map.":[197],"tested":[199],"effects":[201],"various":[203],"micro-environments":[204],"transient":[206,223,231],"perturbations":[207],"such":[209],"transitions":[210,219],"among":[211],"types.":[215],"Interestingly,":[216],"were":[220],"induced":[221],"activations,":[224],"with":[225,230],"opposite":[227],"behavior":[228],"associated":[229],"inhibitions.":[232],"Finally,":[233],"used":[235,240],"novel":[237],"methodology":[238],"was":[239],"establish":[242],"T-bet,":[244],"TGF-\u03b2":[245],"suppressors":[247],"cytokine":[249],"proteins":[251],"are":[252],"keys":[253],"recovering":[255],"observed":[256,265],"responses.":[261],"conclusion,":[263],"cell-types":[268],"transition":[270],"emerge":[272],"feedback":[275],"between":[276],"or":[279],"intracellular":[280],"discuss":[287],"broader":[289],"use":[290],"approach":[293],"systems":[297],"possible":[299],"therapeutic":[300],"interventions.":[301]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":17},{"year":2023,"cited_by_count":8},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":8},{"year":2018,"cited_by_count":13},{"year":2017,"cited_by_count":10},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":1}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}
