{"id":"https://openalex.org/W4282825414","doi":"https://doi.org/10.1371/journal.pcbi.1010175","title":"Discrete modeling for integration and analysis of large-scale signaling networks","display_name":"Discrete modeling for integration and analysis of large-scale signaling networks","publication_year":2022,"publication_date":"2022-06-13","ids":{"openalex":"https://openalex.org/W4282825414","doi":"https://doi.org/10.1371/journal.pcbi.1010175","pmid":"https://pubmed.ncbi.nlm.nih.gov/35696426"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1010175","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010175","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010175&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.1010175&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5040911977","display_name":"Pierre Vignet","orcid":null},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I165283593","display_name":"\u00c9cole des Hautes \u00c9tudes en Sant\u00e9 Publique","ror":"https://ror.org/01sc83v92","country_code":"FR","type":"education","lineage":["https://openalex.org/I165283593"]},{"id":"https://openalex.org/I2802519937","display_name":"Institut de Recherche en Informatique et Syst\u00e8mes Al\u00e9atoires","ror":"https://ror.org/00myn0z94","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I205703379","https://openalex.org/I2802204017","https://openalex.org/I2802519937","https://openalex.org/I28221208","https://openalex.org/I4210127572","https://openalex.org/I4210159245","https://openalex.org/I56067802"]},{"id":"https://openalex.org/I4210108239","display_name":"Institut de Recherche en Sant\u00e9, Environnement et Travail","ror":"https://ror.org/01p178v10","country_code":"FR","type":"facility","lineage":["https://openalex.org/I154526488","https://openalex.org/I165283593","https://openalex.org/I4210108239","https://openalex.org/I49451733","https://openalex.org/I56067802"]},{"id":"https://openalex.org/I56067802","display_name":"Universit\u00e9 de Rennes","ror":"https://ror.org/015m7wh34","country_code":"FR","type":"education","lineage":["https://openalex.org/I56067802"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Pierre Vignet","raw_affiliation_strings":["Univ Rennes, Inria, CNRS, IRISA, UMR 6074, Rennes, France","Univ Rennes, Inserm, EHESP, Irset, UMR S1085, Rennes, France","Irset - Institut de recherche en sant\u00e9, environnement et travail (263 avenue G\u00e9n\u00e9ral Leclerc 35042 Rennes Cedex - France)","Dyliss - Dynamics, Logics and Inference for biological Systems and Sequences (Campus de Beaulieu 35042 Rennes cedex - France)"],"affiliations":[{"raw_affiliation_string":"Univ Rennes, Inria, CNRS, IRISA, UMR 6074, Rennes, France","institution_ids":["https://openalex.org/I2802519937","https://openalex.org/I56067802","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"Univ Rennes, Inserm, EHESP, Irset, UMR S1085, Rennes, France","institution_ids":["https://openalex.org/I165283593","https://openalex.org/I154526488","https://openalex.org/I56067802","https://openalex.org/I4210108239"]},{"raw_affiliation_string":"Irset - Institut de recherche en sant\u00e9, environnement et travail (263 avenue G\u00e9n\u00e9ral Leclerc 35042 Rennes Cedex - France)","institution_ids":["https://openalex.org/I4210108239"]},{"raw_affiliation_string":"Dyliss - Dynamics, Logics and Inference for biological Systems and Sequences (Campus de Beaulieu 35042 Rennes cedex - France)","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031115761","display_name":"Jean Coquet","orcid":"https://orcid.org/0000-0002-7008-6925"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I2802519937","display_name":"Institut de Recherche en Informatique et Syst\u00e8mes Al\u00e9atoires","ror":"https://ror.org/00myn0z94","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I205703379","https://openalex.org/I2802204017","https://openalex.org/I2802519937","https://openalex.org/I28221208","https://openalex.org/I4210127572","https://openalex.org/I4210159245","https://openalex.org/I56067802"]},{"id":"https://openalex.org/I56067802","display_name":"Universit\u00e9 de Rennes","ror":"https://ror.org/015m7wh34","country_code":"FR","type":"education","lineage":["https://openalex.org/I56067802"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Jean Coquet","raw_affiliation_strings":["Univ Rennes, Inria, CNRS, IRISA, UMR 6074, Rennes, France","Dyliss - Dynamics, Logics and Inference for biological Systems and Sequences (Campus de Beaulieu 35042 Rennes cedex - France)"],"affiliations":[{"raw_affiliation_string":"Univ Rennes, Inria, CNRS, IRISA, UMR 6074, Rennes, France","institution_ids":["https://openalex.org/I2802519937","https://openalex.org/I56067802","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"Dyliss - Dynamics, Logics and Inference for biological Systems and Sequences (Campus de Beaulieu 35042 Rennes cedex - France)","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086137694","display_name":"S\u00e9bastien Auber","orcid":null},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I165283593","display_name":"\u00c9cole des Hautes \u00c9tudes en Sant\u00e9 Publique","ror":"https://ror.org/01sc83v92","country_code":"FR","type":"education","lineage":["https://openalex.org/I165283593"]},{"id":"https://openalex.org/I2802519937","display_name":"Institut de Recherche en Informatique et Syst\u00e8mes Al\u00e9atoires","ror":"https://ror.org/00myn0z94","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I205703379","https://openalex.org/I2802204017","https://openalex.org/I2802519937","https://openalex.org/I28221208","https://openalex.org/I4210127572","https://openalex.org/I4210159245","https://openalex.org/I56067802"]},{"id":"https://openalex.org/I4210108239","display_name":"Institut de Recherche en Sant\u00e9, Environnement et Travail","ror":"https://ror.org/01p178v10","country_code":"FR","type":"facility","lineage":["https://openalex.org/I154526488","https://openalex.org/I165283593","https://openalex.org/I4210108239","https://openalex.org/I49451733","https://openalex.org/I56067802"]},{"id":"https://openalex.org/I56067802","display_name":"Universit\u00e9 de Rennes","ror":"https://ror.org/015m7wh34","country_code":"FR","type":"education","lineage":["https://openalex.org/I56067802"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"S\u00e9bastien Auber","raw_affiliation_strings":["Univ Rennes, Inria, CNRS, IRISA, UMR 6074, Rennes, France","Univ Rennes, Inserm, EHESP, Irset, UMR S1085, Rennes, France","Irset - Institut de recherche en sant\u00e9, environnement et travail (263 avenue G\u00e9n\u00e9ral Leclerc 35042 Rennes Cedex - France)","Dyliss - Dynamics, Logics and Inference for biological Systems and Sequences (Campus de Beaulieu 35042 Rennes cedex - France)"],"affiliations":[{"raw_affiliation_string":"Univ Rennes, Inria, CNRS, IRISA, UMR 6074, Rennes, France","institution_ids":["https://openalex.org/I2802519937","https://openalex.org/I56067802","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"Univ Rennes, Inserm, EHESP, Irset, UMR S1085, Rennes, France","institution_ids":["https://openalex.org/I165283593","https://openalex.org/I154526488","https://openalex.org/I56067802","https://openalex.org/I4210108239"]},{"raw_affiliation_string":"Irset - Institut de recherche en sant\u00e9, environnement et travail (263 avenue G\u00e9n\u00e9ral Leclerc 35042 Rennes Cedex - France)","institution_ids":["https://openalex.org/I4210108239"]},{"raw_affiliation_string":"Dyliss - Dynamics, Logics and Inference for biological Systems and Sequences (Campus de Beaulieu 35042 Rennes cedex - France)","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057933882","display_name":"Mat\u00e9o Boudet","orcid":"https://orcid.org/0000-0002-7028-7620"},"institutions":[{"id":"https://openalex.org/I2800285241","display_name":"Institut Agro Rennes-Angers","ror":"https://ror.org/01s3fs709","country_code":"FR","type":"education","lineage":["https://openalex.org/I2800285241","https://openalex.org/I4210117091","https://openalex.org/I4399657933"]},{"id":"https://openalex.org/I4210088668","display_name":"Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement","ror":"https://ror.org/003vg9w96","country_code":"FR","type":"government","lineage":["https://openalex.org/I4210088668"]},{"id":"https://openalex.org/I4210141755","display_name":"Institut de G\u00e9n\u00e9tique, Environnement et Protection des Plantes","ror":"https://ror.org/038kxsm48","country_code":"FR","type":"facility","lineage":["https://openalex.org/I2800285241","https://openalex.org/I4210088668","https://openalex.org/I4210117091","https://openalex.org/I4210141755","https://openalex.org/I4399657933","https://openalex.org/I56067802"]},{"id":"https://openalex.org/I56067802","display_name":"Universit\u00e9 de Rennes","ror":"https://ror.org/015m7wh34","country_code":"FR","type":"education","lineage":["https://openalex.org/I56067802"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Mat\u00e9o Boudet","raw_affiliation_strings":["IGEPP, Agrocampus Ouest, INRAE, Universit\u00e9 de Rennes 1, Le Rheu, France","IGEPP - Institut de G\u00e9n\u00e9tique, Environnement et Protection des Plantes (Domaine de la Motte au Vicomte BP 35327\r\n35653 Le Rheu - France)"],"affiliations":[{"raw_affiliation_string":"IGEPP, Agrocampus Ouest, INRAE, Universit\u00e9 de Rennes 1, Le Rheu, France","institution_ids":["https://openalex.org/I2800285241","https://openalex.org/I4210141755","https://openalex.org/I56067802","https://openalex.org/I4210088668"]},{"raw_affiliation_string":"IGEPP - Institut de G\u00e9n\u00e9tique, Environnement et Protection des Plantes (Domaine de la Motte au Vicomte BP 35327\r\n35653 Le Rheu - France)","institution_ids":["https://openalex.org/I4210141755"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063755415","display_name":"Anne Siegel","orcid":"https://orcid.org/0000-0001-6542-1568"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I2802519937","display_name":"Institut de Recherche en Informatique et Syst\u00e8mes Al\u00e9atoires","ror":"https://ror.org/00myn0z94","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I205703379","https://openalex.org/I2802204017","https://openalex.org/I2802519937","https://openalex.org/I28221208","https://openalex.org/I4210127572","https://openalex.org/I4210159245","https://openalex.org/I56067802"]},{"id":"https://openalex.org/I56067802","display_name":"Universit\u00e9 de Rennes","ror":"https://ror.org/015m7wh34","country_code":"FR","type":"education","lineage":["https://openalex.org/I56067802"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Anne Siegel","raw_affiliation_strings":["Univ Rennes, Inria, CNRS, IRISA, UMR 6074, Rennes, France","Dyliss - Dynamics, Logics and Inference for biological Systems and Sequences (Campus de Beaulieu 35042 Rennes cedex - France)"],"affiliations":[{"raw_affiliation_string":"Univ Rennes, Inria, CNRS, IRISA, UMR 6074, Rennes, France","institution_ids":["https://openalex.org/I2802519937","https://openalex.org/I56067802","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"Dyliss - Dynamics, Logics and Inference for biological Systems and Sequences (Campus de Beaulieu 35042 Rennes cedex - France)","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5046388663","display_name":"Nathalie Th\u00e9ret","orcid":"https://orcid.org/0000-0002-5857-7828"},"institutions":[{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I165283593","display_name":"\u00c9cole des Hautes \u00c9tudes en Sant\u00e9 Publique","ror":"https://ror.org/01sc83v92","country_code":"FR","type":"education","lineage":["https://openalex.org/I165283593"]},{"id":"https://openalex.org/I4210108239","display_name":"Institut de Recherche en Sant\u00e9, Environnement et Travail","ror":"https://ror.org/01p178v10","country_code":"FR","type":"facility","lineage":["https://openalex.org/I154526488","https://openalex.org/I165283593","https://openalex.org/I4210108239","https://openalex.org/I49451733","https://openalex.org/I56067802"]},{"id":"https://openalex.org/I56067802","display_name":"Universit\u00e9 de Rennes","ror":"https://ror.org/015m7wh34","country_code":"FR","type":"education","lineage":["https://openalex.org/I56067802"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Nathalie Th\u00e9ret","raw_affiliation_strings":["Univ Rennes, Inserm, EHESP, Irset, UMR S1085, Rennes, France","Dyliss - Dynamics, Logics and Inference for biological Systems and Sequences (Campus de Beaulieu 35042 Rennes cedex - France)","Irset - Institut de recherche en sant\u00e9, environnement et travail (263 avenue G\u00e9n\u00e9ral Leclerc 35042 Rennes Cedex - France)"],"affiliations":[{"raw_affiliation_string":"Univ Rennes, Inserm, EHESP, Irset, UMR S1085, Rennes, France","institution_ids":["https://openalex.org/I165283593","https://openalex.org/I154526488","https://openalex.org/I56067802","https://openalex.org/I4210108239"]},{"raw_affiliation_string":"Dyliss - Dynamics, Logics and Inference for biological Systems and Sequences (Campus de Beaulieu 35042 Rennes cedex - France)","institution_ids":[]},{"raw_affiliation_string":"Irset - Institut de recherche en sant\u00e9, environnement et travail (263 avenue G\u00e9n\u00e9ral Leclerc 35042 Rennes Cedex - France)","institution_ids":["https://openalex.org/I4210108239"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5046388663","https://openalex.org/A5063755415"],"corresponding_institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I154526488","https://openalex.org/I165283593","https://openalex.org/I2802519937","https://openalex.org/I4210108239","https://openalex.org/I56067802"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2417,"currency":"EUR","value_usd":2606},"fwci":0.0867,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.41648669,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"18","issue":"6","first_page":"e1010175","last_page":"e1010175"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9987999796867371,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9941999912261963,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6964187622070312},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.6634013056755066},{"id":"https://openalex.org/keywords/complementarity","display_name":"Complementarity (molecular biology)","score":0.46506789326667786},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.45352089405059814},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.346922367811203},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.33829206228256226},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3340819776058197},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1784515678882599}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6964187622070312},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.6634013056755066},{"id":"https://openalex.org/C202269582","wikidata":"https://www.wikidata.org/wiki/Q2644277","display_name":"Complementarity (molecular biology)","level":2,"score":0.46506789326667786},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.45352089405059814},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.346922367811203},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.33829206228256226},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3340819776058197},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1784515678882599},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001686","descriptor_name":"Biological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001686","descriptor_name":"Biological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001686","descriptor_name":"Biological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1010175","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010175","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010175&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:35696426","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35696426","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:HAL:hal-03693653v1","is_oa":true,"landing_page_url":"https://inria.hal.science/hal-03693653","pdf_url":null,"source":{"id":"https://openalex.org/S4406922466","display_name":"SPIRE - Sciences Po Institutional REpository","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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, 2022, 18 (6), pp.e1010175. ⟨10.1371/journal.pcbi.1010175⟩","raw_type":"Journal articles"},{"id":"pmh:oai:doaj.org/article:52918137ace746518787c7d819c32802","is_oa":true,"landing_page_url":"https://doaj.org/article/52918137ace746518787c7d819c32802","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 18, Iss 6, p e1010175 (2022)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:9232147","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9232147","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"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.1010175","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010175","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010175&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":[{"score":0.6100000143051147,"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320320893","display_name":"Institut National de la Sant\u00e9 et de la Recherche M\u00e9dicale","ror":"https://ror.org/02vjkv261"},{"id":"https://openalex.org/F4320324509","display_name":"Universit\u00e9 de Rennes 1","ror":"https://ror.org/015m7wh34"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4282825414.pdf","grobid_xml":"https://content.openalex.org/works/W4282825414.grobid-xml"},"referenced_works_count":56,"referenced_works":["https://openalex.org/W893557411","https://openalex.org/W1534987406","https://openalex.org/W1599839677","https://openalex.org/W1969709265","https://openalex.org/W1972587504","https://openalex.org/W1982380661","https://openalex.org/W1996937427","https://openalex.org/W2003003919","https://openalex.org/W2014938226","https://openalex.org/W2016550161","https://openalex.org/W2020102380","https://openalex.org/W2030151880","https://openalex.org/W2031218556","https://openalex.org/W2049345643","https://openalex.org/W2057156693","https://openalex.org/W2068701781","https://openalex.org/W2073903631","https://openalex.org/W2083447892","https://openalex.org/W2085736551","https://openalex.org/W2096766502","https://openalex.org/W2111842613","https://openalex.org/W2119876770","https://openalex.org/W2123297155","https://openalex.org/W2124082948","https://openalex.org/W2128230435","https://openalex.org/W2129325583","https://openalex.org/W2146384526","https://openalex.org/W2150908245","https://openalex.org/W2151322467","https://openalex.org/W2155363874","https://openalex.org/W2156934474","https://openalex.org/W2159937805","https://openalex.org/W2164298117","https://openalex.org/W2213867049","https://openalex.org/W2430015611","https://openalex.org/W2436063217","https://openalex.org/W2546451980","https://openalex.org/W2557833574","https://openalex.org/W2588297910","https://openalex.org/W2611696724","https://openalex.org/W2770430263","https://openalex.org/W2809309048","https://openalex.org/W2884626935","https://openalex.org/W2901905047","https://openalex.org/W2943005115","https://openalex.org/W3010327973","https://openalex.org/W3093194543","https://openalex.org/W3096828292","https://openalex.org/W3166269910","https://openalex.org/W3168953667","https://openalex.org/W3211402536","https://openalex.org/W4211233744","https://openalex.org/W4213007074","https://openalex.org/W4213127256","https://openalex.org/W4226331025","https://openalex.org/W6682816326"],"related_works":["https://openalex.org/W2158714033","https://openalex.org/W78967844","https://openalex.org/W3213185671","https://openalex.org/W4210989272","https://openalex.org/W4206945140","https://openalex.org/W4386628104","https://openalex.org/W2509687359","https://openalex.org/W4212865750","https://openalex.org/W2362023034","https://openalex.org/W2947028852"],"abstract_inverted_index":{"Most":[0],"biological":[1,55,105,202,223,264],"processes":[2],"are":[3,10,19,279],"orchestrated":[4],"by":[5,129],"large-scale":[6,13,78,88],"molecular":[7],"networks":[8,90],"which":[9,124,156],"described":[11],"in":[12,77,95,137,205,220,252],"model":[14,150],"repositories":[15],"and":[16,100,134,183,217,225,275,284],"whose":[17,36],"dynamics":[18,128],"extremely":[20],"complex.":[21],"An":[22],"observed":[23],"phenotype":[24,76],"is":[25,38,49],"a":[26,75,109,120,126,153,193,260,263,286],"state":[27],"of":[28,104,139,173,178,187,201,222,229,231,238,249,254,256,271],"this":[29],"system":[30,127],"that":[31,73,107,240,258,278],"results":[32,210,267],"from":[33,91,161],"control":[34,74,108],"mechanisms":[35],"identification":[37],"key":[39],"to":[40,52,58,86,97,101,146,152,169,184,198],"its":[41],"understanding.":[42],"The":[43,111,141,164],"Biological":[44],"Pathway":[45,180],"Exchange":[46],"(BioPAX)":[47],"format":[48],"widely":[50],"used":[51,197],"standardize":[53],"the":[54,71,116,170,179,185,206,212,215,227,232,236,246,250,269,282],"information":[56],"relative":[57],"regulatory":[59],"processes.":[60],"However,":[61],"few":[62],"modeling":[63,122],"approaches":[64],"developed":[65,82],"so":[66],"far":[67],"enable":[68],"for":[69,273,289],"computing":[70],"events":[72,136],"networks.":[79],"Here":[80],"we":[81],"an":[83],"integrated":[84],"approach":[85,113,123],"build":[87],"dynamic":[89],"BioPAX":[92,148,162,171,233],"knowledge":[93],"databases":[94,251],"order":[96],"analyse":[98],"trajectories":[99],"identify":[102,285],"sets":[103,200],"entities":[106,203],"phenotype.":[110,261],"Cadbiom":[112,159,165],"relies":[114],"on":[115],"guarded":[117],"transitions":[118],"formalism,":[119],"discrete":[121],"models":[125,160,239],"taking":[130],"into":[131],"account":[132],"competition":[133],"cooperation":[135],"chains":[138],"reactions.":[140],"method":[142],"can":[143],"be":[144],"applied":[145,168],"every":[147],"(large-scale)":[149],"thanks":[151],"specific":[154],"package":[155],"automatically":[157],"generates":[158],"files.":[163],"framework":[166],"was":[167,196],"version":[172],"two":[174],"resources":[175,219],"(PID,":[176],"KEGG)":[177],"Commons":[181],"database":[182],"Atlas":[186],"Cancer":[188],"Signalling":[189],"Network":[190],"(ACSN).":[191],"As":[192],"case-study,":[194],"it":[195],"characterize":[199],"implicated":[204],"epithelial-mesenchymal":[207],"transition.":[208],"Our":[209],"highlight":[211],"similarities":[213],"between":[214],"PID":[216],"ACSN":[218],"terms":[221,253],"content,":[224],"underline":[226],"heterogeneity":[228],"usage":[230],"semantics":[234],"limiting":[235],"fusion":[237],"require":[241],"curation.":[242],"Causality":[243],"analyses":[244],"demonstrate":[245],"smart":[247],"complementarity":[248],"combinatorics":[255],"controllers":[257,272],"explain":[259],"From":[262],"perspective,":[265],"our":[266],"show":[268],"specificity":[270],"epithelial":[274],"mesenchymal":[276],"phenotypes":[277],"consistent":[280],"with":[281],"literature":[283],"novel":[287],"signature":[288],"intermediate":[290],"states.":[291]},"counts_by_year":[{"year":2024,"cited_by_count":1}],"updated_date":"2026-03-27T14:29:43.386196","created_date":"2025-10-10T00:00:00"}