{"id":"https://openalex.org/W2951856423","doi":"https://doi.org/10.1093/bioinformatics/bty766","title":"PhysiBoSS: a multi-scale agent-based modelling framework integrating physical dimension and cell signalling","display_name":"PhysiBoSS: a multi-scale agent-based modelling framework integrating physical dimension and cell signalling","publication_year":2018,"publication_date":"2018-08-30","ids":{"openalex":"https://openalex.org/W2951856423","doi":"https://doi.org/10.1093/bioinformatics/bty766","mag":"2951856423","pmid":"https://pubmed.ncbi.nlm.nih.gov/30169736"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty766","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty766","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.1093/bioinformatics/bty766","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5017317489","display_name":"Ga\u00eblle Letort","orcid":"https://orcid.org/0000-0002-5866-0322"},"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/I190752583","display_name":"ParisTech","ror":"https://ror.org/05c2qg481","country_code":"FR","type":"education","lineage":["https://openalex.org/I190752583"]},{"id":"https://openalex.org/I2746051580","display_name":"Universit\u00e9 Paris Sciences et Lettres","ror":"https://ror.org/013cjyk83","country_code":"FR","type":"education","lineage":["https://openalex.org/I2746051580"]},{"id":"https://openalex.org/I80043","display_name":"Institut Curie","ror":"https://ror.org/04t0gwh46","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I80043"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Gaelle Letort","raw_affiliation_strings":["CBIO-Centre for Computational Biology, MINES ParisTech, PSL Research University, Paris, France","INSERM, U900, Paris, France","Institut Curie, PSL Research University, Paris, France"],"raw_orcid":"https://orcid.org/0000-0002-5866-0322","affiliations":[{"raw_affiliation_string":"CBIO-Centre for Computational Biology, MINES ParisTech, PSL Research University, Paris, France","institution_ids":["https://openalex.org/I2746051580","https://openalex.org/I190752583"]},{"raw_affiliation_string":"INSERM, U900, Paris, France","institution_ids":["https://openalex.org/I154526488"]},{"raw_affiliation_string":"Institut Curie, PSL Research University, Paris, France","institution_ids":["https://openalex.org/I2746051580","https://openalex.org/I80043"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051818233","display_name":"Arnau Montagud","orcid":"https://orcid.org/0000-0002-7696-1241"},"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/I190752583","display_name":"ParisTech","ror":"https://ror.org/05c2qg481","country_code":"FR","type":"education","lineage":["https://openalex.org/I190752583"]},{"id":"https://openalex.org/I2746051580","display_name":"Universit\u00e9 Paris Sciences et Lettres","ror":"https://ror.org/013cjyk83","country_code":"FR","type":"education","lineage":["https://openalex.org/I2746051580"]},{"id":"https://openalex.org/I80043","display_name":"Institut Curie","ror":"https://ror.org/04t0gwh46","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I80043"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Arnau Montagud","raw_affiliation_strings":["CBIO-Centre for Computational Biology, MINES ParisTech, PSL Research University, Paris, France","INSERM, U900, Paris, France","Institut Curie, PSL Research University, Paris, France"],"raw_orcid":"https://orcid.org/0000-0002-7696-1241","affiliations":[{"raw_affiliation_string":"CBIO-Centre for Computational Biology, MINES ParisTech, PSL Research University, Paris, France","institution_ids":["https://openalex.org/I2746051580","https://openalex.org/I190752583"]},{"raw_affiliation_string":"INSERM, U900, Paris, France","institution_ids":["https://openalex.org/I154526488"]},{"raw_affiliation_string":"Institut Curie, PSL Research University, Paris, France","institution_ids":["https://openalex.org/I2746051580","https://openalex.org/I80043"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063687089","display_name":"Gautier Stoll","orcid":"https://orcid.org/0000-0002-0862-4139"},"institutions":[{"id":"https://openalex.org/I110736937","display_name":"D\u00e9l\u00e9gation Paris 5","ror":"https://ror.org/02e0y6e06","country_code":"FR","type":"government","lineage":["https://openalex.org/I110736937","https://openalex.org/I154526488"]},{"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/I204730241","display_name":"Universit\u00e9 Paris Cit\u00e9","ror":"https://ror.org/05f82e368","country_code":"FR","type":"education","lineage":["https://openalex.org/I204730241"]},{"id":"https://openalex.org/I2801843802","display_name":"Institut Gustave Roussy","ror":"https://ror.org/0321g0743","country_code":"FR","type":"facility","lineage":["https://openalex.org/I2801843802"]},{"id":"https://openalex.org/I4210091437","display_name":"Sorbonne Paris Cit\u00e9","ror":"https://ror.org/001z21q04","country_code":"FR","type":"other","lineage":["https://openalex.org/I4210091437"]},{"id":"https://openalex.org/I4210092322","display_name":"Centre de Recherche des Cordeliers","ror":"https://ror.org/00dmms154","country_code":"FR","type":"facility","lineage":["https://openalex.org/I154526488","https://openalex.org/I204730241","https://openalex.org/I39804081","https://openalex.org/I4210092322"]},{"id":"https://openalex.org/I4210095243","display_name":"La Ligue Contre le Cancer","ror":"https://ror.org/00rkrv905","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I4210095243"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Gautier Stoll","raw_affiliation_strings":["Equipe 11 Labellis\u00e9e par la Ligue Nationale Contre le Cancer, Centre de Recherche des Cordeliers, Paris, France","Gustave Roussy Cancer Campus, Villejuif, France","INSERM, U1138, Paris, France","Universit\u00e9 Paris Descartes/Paris V, Sorbonne Paris Cit\u00e9, Paris, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Equipe 11 Labellis\u00e9e par la Ligue Nationale Contre le Cancer, Centre de Recherche des Cordeliers, Paris, France","institution_ids":["https://openalex.org/I4210092322","https://openalex.org/I4210095243"]},{"raw_affiliation_string":"Gustave Roussy Cancer Campus, Villejuif, France","institution_ids":["https://openalex.org/I2801843802"]},{"raw_affiliation_string":"INSERM, U1138, Paris, France","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I4210092322"]},{"raw_affiliation_string":"Universit\u00e9 Paris Descartes/Paris V, Sorbonne Paris Cit\u00e9, Paris, France","institution_ids":["https://openalex.org/I110736937","https://openalex.org/I4210091437","https://openalex.org/I204730241"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058904152","display_name":"Randy Heiland","orcid":"https://orcid.org/0000-0002-7440-2905"},"institutions":[{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Randy Heiland","raw_affiliation_strings":["Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA","institution_ids":["https://openalex.org/I4210119109"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062067186","display_name":"Emmanuel Barillot","orcid":"https://orcid.org/0000-0003-2724-2002"},"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/I190752583","display_name":"ParisTech","ror":"https://ror.org/05c2qg481","country_code":"FR","type":"education","lineage":["https://openalex.org/I190752583"]},{"id":"https://openalex.org/I2746051580","display_name":"Universit\u00e9 Paris Sciences et Lettres","ror":"https://ror.org/013cjyk83","country_code":"FR","type":"education","lineage":["https://openalex.org/I2746051580"]},{"id":"https://openalex.org/I80043","display_name":"Institut Curie","ror":"https://ror.org/04t0gwh46","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I80043"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Emmanuel Barillot","raw_affiliation_strings":["CBIO-Centre for Computational Biology, MINES ParisTech, PSL Research University, Paris, France","INSERM, U900, Paris, France","Institut Curie, PSL Research University, Paris, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CBIO-Centre for Computational Biology, MINES ParisTech, PSL Research University, Paris, France","institution_ids":["https://openalex.org/I2746051580","https://openalex.org/I190752583"]},{"raw_affiliation_string":"INSERM, U900, Paris, France","institution_ids":["https://openalex.org/I154526488"]},{"raw_affiliation_string":"Institut Curie, PSL Research University, Paris, France","institution_ids":["https://openalex.org/I2746051580","https://openalex.org/I80043"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052380564","display_name":"Paul Macklin","orcid":"https://orcid.org/0000-0002-9925-0151"},"institutions":[{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Paul Macklin","raw_affiliation_strings":["Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA","institution_ids":["https://openalex.org/I4210119109"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077253721","display_name":"Andre\u00ef Zinovyev","orcid":"https://orcid.org/0000-0002-9517-7284"},"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/I190752583","display_name":"ParisTech","ror":"https://ror.org/05c2qg481","country_code":"FR","type":"education","lineage":["https://openalex.org/I190752583"]},{"id":"https://openalex.org/I2746051580","display_name":"Universit\u00e9 Paris Sciences et Lettres","ror":"https://ror.org/013cjyk83","country_code":"FR","type":"education","lineage":["https://openalex.org/I2746051580"]},{"id":"https://openalex.org/I80043","display_name":"Institut Curie","ror":"https://ror.org/04t0gwh46","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I80043"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Andrei Zinovyev","raw_affiliation_strings":["CBIO-Centre for Computational Biology, MINES ParisTech, PSL Research University, Paris, France","INSERM, U900, Paris, France","Institut Curie, PSL Research University, Paris, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CBIO-Centre for Computational Biology, MINES ParisTech, PSL Research University, Paris, France","institution_ids":["https://openalex.org/I2746051580","https://openalex.org/I190752583"]},{"raw_affiliation_string":"INSERM, U900, Paris, France","institution_ids":["https://openalex.org/I154526488"]},{"raw_affiliation_string":"Institut Curie, PSL Research University, Paris, France","institution_ids":["https://openalex.org/I2746051580","https://openalex.org/I80043"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5061154457","display_name":"Laurence Calzone","orcid":"https://orcid.org/0000-0002-7835-1148"},"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/I190752583","display_name":"ParisTech","ror":"https://ror.org/05c2qg481","country_code":"FR","type":"education","lineage":["https://openalex.org/I190752583"]},{"id":"https://openalex.org/I2746051580","display_name":"Universit\u00e9 Paris Sciences et Lettres","ror":"https://ror.org/013cjyk83","country_code":"FR","type":"education","lineage":["https://openalex.org/I2746051580"]},{"id":"https://openalex.org/I80043","display_name":"Institut Curie","ror":"https://ror.org/04t0gwh46","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I80043"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Laurence Calzone","raw_affiliation_strings":["CBIO-Centre for Computational Biology, MINES ParisTech, PSL Research University, Paris, France","INSERM, U900, Paris, France","Institut Curie, PSL Research University, Paris, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CBIO-Centre for Computational Biology, MINES ParisTech, PSL Research University, Paris, France","institution_ids":["https://openalex.org/I2746051580","https://openalex.org/I190752583"]},{"raw_affiliation_string":"INSERM, U900, Paris, France","institution_ids":["https://openalex.org/I154526488"]},{"raw_affiliation_string":"Institut Curie, PSL Research University, Paris, France","institution_ids":["https://openalex.org/I2746051580","https://openalex.org/I80043"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5017317489","https://openalex.org/A5061154457"],"corresponding_institution_ids":["https://openalex.org/I154526488","https://openalex.org/I190752583","https://openalex.org/I2746051580","https://openalex.org/I80043"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":5.9426,"has_fulltext":false,"cited_by_count":126,"citation_normalized_percentile":{"value":0.96931877,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"35","issue":"7","first_page":"1188","last_page":"1196"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11829","display_name":"Mathematical Biology Tumor Growth","score":0.728600025177002,"subfield":{"id":"https://openalex.org/subfields/2611","display_name":"Modeling and Simulation"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11829","display_name":"Mathematical Biology Tumor Growth","score":0.728600025177002,"subfield":{"id":"https://openalex.org/subfields/2611","display_name":"Modeling and Simulation"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.1607999950647354,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.014299999922513962,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/multicellular-organism","display_name":"Multicellular organism","score":0.7939634323120117},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.6338173747062683},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6137896180152893},{"id":"https://openalex.org/keywords/signalling","display_name":"Signalling","score":0.57819002866745},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.3426559567451477},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3415389657020569},{"id":"https://openalex.org/keywords/cell","display_name":"Cell","score":0.3114994764328003},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.30790990591049194},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.13184243440628052},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.09604021906852722}],"concepts":[{"id":"https://openalex.org/C74318829","wikidata":"https://www.wikidata.org/wiki/Q36458","display_name":"Multicellular organism","level":3,"score":0.7939634323120117},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.6338173747062683},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6137896180152893},{"id":"https://openalex.org/C39743133","wikidata":"https://www.wikidata.org/wiki/Q3262595","display_name":"Signalling","level":2,"score":0.57819002866745},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.3426559567451477},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3415389657020569},{"id":"https://openalex.org/C1491633281","wikidata":"https://www.wikidata.org/wiki/Q7868","display_name":"Cell","level":2,"score":0.3114994764328003},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.30790990591049194},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13184243440628052},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.09604021906852722},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0},{"id":"https://openalex.org/C149923435","wikidata":"https://www.wikidata.org/wiki/Q37732","display_name":"Demography","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013597","descriptor_name":"Systems Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013597","descriptor_name":"Systems Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013597","descriptor_name":"Systems Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":6,"locations":[{"id":"doi:10.1093/bioinformatics/bty766","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty766","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30169736","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30169736","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:HAL:hal-05263687v1","is_oa":true,"landing_page_url":"https://hal.science/hal-05263687","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"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":"Bioinformatics, 2019, 35 (7), pp.1188-1196. ⟨10.1093/bioinformatics/bty766⟩","raw_type":"Journal articles"},{"id":"pmh:oai:europepmc.org:5438750","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC6449758","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":"Text"},{"id":"pmh:oai:iu.tind.io:2448","is_oa":false,"landing_page_url":"http://iu.tind.io/record/2448","pdf_url":null,"source":{"id":"https://openalex.org/S4306402656","display_name":"IUScholarWorks Open (Indiana University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I592451","host_organization_name":"Indiana University","host_organization_lineage":["https://openalex.org/I592451"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://iu.tind.io/record/2448","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:6449758","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6449758","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty766","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty766","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.41999998688697815,"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320306260","display_name":"Breast Cancer Research Foundation","ror":"https://ror.org/0348ff195"},{"id":"https://openalex.org/F4320316625","display_name":"Jayne Koskinas Ted Giovanis Foundation for Health and Policy","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":84,"referenced_works":["https://openalex.org/W1636269875","https://openalex.org/W1966176927","https://openalex.org/W1976821656","https://openalex.org/W1977973890","https://openalex.org/W1986482900","https://openalex.org/W1989103896","https://openalex.org/W1990251632","https://openalex.org/W1994395641","https://openalex.org/W1996187477","https://openalex.org/W1996198135","https://openalex.org/W1996269383","https://openalex.org/W1998352455","https://openalex.org/W2003003919","https://openalex.org/W2006067863","https://openalex.org/W2008783268","https://openalex.org/W2011420188","https://openalex.org/W2013541867","https://openalex.org/W2021766626","https://openalex.org/W2024857915","https://openalex.org/W2025238477","https://openalex.org/W2026256462","https://openalex.org/W2034684613","https://openalex.org/W2036395023","https://openalex.org/W2041585886","https://openalex.org/W2042332837","https://openalex.org/W2047377602","https://openalex.org/W2056180229","https://openalex.org/W2065191902","https://openalex.org/W2072966096","https://openalex.org/W2083337908","https://openalex.org/W2088925327","https://openalex.org/W2090790734","https://openalex.org/W2092578710","https://openalex.org/W2095242749","https://openalex.org/W2095433609","https://openalex.org/W2098800695","https://openalex.org/W2104162805","https://openalex.org/W2105054044","https://openalex.org/W2107197409","https://openalex.org/W2124688359","https://openalex.org/W2127225632","https://openalex.org/W2133054656","https://openalex.org/W2136445803","https://openalex.org/W2142171814","https://openalex.org/W2146335969","https://openalex.org/W2154289334","https://openalex.org/W2154599522","https://openalex.org/W2154718031","https://openalex.org/W2157154485","https://openalex.org/W2157947216","https://openalex.org/W2175622107","https://openalex.org/W2256248976","https://openalex.org/W2272546316","https://openalex.org/W2273569416","https://openalex.org/W2281946615","https://openalex.org/W2289399824","https://openalex.org/W2403795281","https://openalex.org/W2411288489","https://openalex.org/W2414848736","https://openalex.org/W2508839463","https://openalex.org/W2514145607","https://openalex.org/W2559413716","https://openalex.org/W2566910492","https://openalex.org/W2582477723","https://openalex.org/W2588279759","https://openalex.org/W2593809500","https://openalex.org/W2605880863","https://openalex.org/W2759285908","https://openalex.org/W2767281692","https://openalex.org/W2769842713","https://openalex.org/W2772348961","https://openalex.org/W2774281968","https://openalex.org/W2884605652","https://openalex.org/W2949797623","https://openalex.org/W2951378914","https://openalex.org/W2953317739","https://openalex.org/W3192580736","https://openalex.org/W4237376056","https://openalex.org/W4251104453","https://openalex.org/W6636125642","https://openalex.org/W6673870799","https://openalex.org/W6682651408","https://openalex.org/W6744732721","https://openalex.org/W6746232878"],"related_works":["https://openalex.org/W1963836821","https://openalex.org/W2522472446","https://openalex.org/W2145740829","https://openalex.org/W4281994149","https://openalex.org/W2166797439","https://openalex.org/W2805325890","https://openalex.org/W4247350725","https://openalex.org/W2132267912","https://openalex.org/W4387161370","https://openalex.org/W2476390134"],"abstract_inverted_index":{"MOTIVATION:":[0],"Due":[1],"to":[2,60,83,100,128],"the":[3,23,62,73,77,133,139,147,153,158,188],"complexity":[4],"and":[5,22,44,56,66,86,138],"heterogeneity":[6],"of":[7,64,69,106,118,135,141,149,160],"multicellular":[8,45,88],"biological":[9],"systems,":[10],"mathematical":[11],"models":[12],"that":[13],"take":[14],"into":[15],"account":[16],"cell":[17,19,123],"signalling,":[18],"population":[20,74,98,154],"behaviour":[21,46,140],"extracellular":[24],"environment":[25],"are":[26,196],"particularly":[27],"helpful.":[28],"We":[29,131,145],"present":[30],"PhysiBoSS,":[31,119],"an":[32],"open":[33,185],"source":[34,186],"software":[35],"which":[36],"combines":[37],"intracellular":[38],"signalling":[39],"using":[40,47],"Boolean":[41],"modelling":[42,49],"(MaBoSS)":[43],"agent-based":[48],"(PhysiCell).":[50],"RESULTS:":[51],"PhysiBoSS":[52,90,169],"provides":[53],"a":[54,115,177],"flexible":[55],"computationally":[57],"efficient":[58],"framework":[59],"explore":[61],"effect":[63,134,159],"environmental":[65],"genetic":[67],"alterations":[68],"individual":[70],"cells":[71],"at":[72,198],"level,":[75],"bridging":[76],"critical":[78],"gap":[79],"from":[80],"single-cell":[81,84],"genotype":[82],"phenotype":[85],"emergent":[87],"behaviour.":[89],"thus":[91],"becomes":[92],"very":[93],"useful":[94],"when":[95],"studying":[96],"heterogeneous":[97,122],"response":[99,127],"treatment,":[101],"mutation":[102],"effects,":[103],"different":[104,136],"modes":[105],"invasion":[107],"or":[108],"isomorphic":[109],"morphogenesis":[110],"events.":[111],"To":[112],"concretely":[113],"illustrate":[114],"potential":[116],"use":[117],"we":[120],"studied":[121],"fate":[124],"decisions":[125],"in":[126],"TNF":[129],"treatment.":[130],"explored":[132],"treatments":[137],"several":[142],"resistant":[143],"mutants.":[144],"highlighted":[146],"importance":[148],"spatial":[150],"information":[151],"on":[152,173],"dynamics":[155],"by":[156],"considering":[157],"competition":[161],"for":[162],"resources":[163],"like":[164],"oxygen.":[165],"AVAILABILITY":[166],"AND":[167],"IMPLEMENTATION:":[168],"is":[170,182],"freely":[171],"available":[172,197],"GitHub":[174],"(https://github.com/sysbio-curie/PhysiBoSS),":[175],"with":[176],"Docker":[178],"image":[179],"(https://hub.docker.com/r/gletort/physiboss/).":[180],"It":[181],"distributed":[183],"as":[184],"under":[187],"BSD":[189],"3-clause":[190],"license.":[191],"SUPPLEMENTARY":[192],"INFORMATION:":[193],"Supplementary":[194],"data":[195],"Bioinformatics":[199],"online.":[200]},"counts_by_year":[{"year":2026,"cited_by_count":6},{"year":2025,"cited_by_count":14},{"year":2024,"cited_by_count":20},{"year":2023,"cited_by_count":16},{"year":2022,"cited_by_count":25},{"year":2021,"cited_by_count":18},{"year":2020,"cited_by_count":14},{"year":2019,"cited_by_count":12},{"year":2012,"cited_by_count":1}],"updated_date":"2026-05-30T09:04:40.226872","created_date":"2025-10-10T00:00:00"}