{"id":"https://openalex.org/W2156091616","doi":"https://doi.org/10.1093/bioinformatics/btp214","title":"Modeling stochasticity and robustness in gene regulatory networks","display_name":"Modeling stochasticity and robustness in gene regulatory networks","publication_year":2009,"publication_date":"2009-05-27","ids":{"openalex":"https://openalex.org/W2156091616","doi":"https://doi.org/10.1093/bioinformatics/btp214","mag":"2156091616","pmid":"https://pubmed.ncbi.nlm.nih.gov/19477975"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btp214","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp214","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/12/i101/470287/btp214.pdf","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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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://academic.oup.com/bioinformatics/article-pdf/25/12/i101/470287/btp214.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5103535490","display_name":"Abhishek Garg","orcid":null},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I4210113211","display_name":"Merck Serono S.A. (Switzerland)","ror":"https://ror.org/01vp49361","country_code":"CH","type":"company","lineage":["https://openalex.org/I164928964","https://openalex.org/I4210113211"]},{"id":"https://openalex.org/I5124864","display_name":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","ror":"https://ror.org/02s376052","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I5124864"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Abhishek Garg","raw_affiliation_strings":["1 Ecole Polytechnique Federale de Lausanne, Station 14, 1015 Lausanne, Switzerland, 2Rice University, Houston, TX 77005, USA, 3Merck Serono, 1202 Geneva and 4Swiss Institute of Bioinformatics, Vital-IT Group, 1015 Lausanne, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Ecole Polytechnique Federale de Lausanne, Station 14, 1015 Lausanne, Switzerland, 2Rice University, Houston, TX 77005, USA, 3Merck Serono, 1202 Geneva and 4Swiss Institute of Bioinformatics, Vital-IT Group, 1015 Lausanne, Switzerland","institution_ids":["https://openalex.org/I12708293","https://openalex.org/I4210113211","https://openalex.org/I5124864"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021693439","display_name":"Kartik Mohanram","orcid":null},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I4210113211","display_name":"Merck Serono S.A. (Switzerland)","ror":"https://ror.org/01vp49361","country_code":"CH","type":"company","lineage":["https://openalex.org/I164928964","https://openalex.org/I4210113211"]},{"id":"https://openalex.org/I5124864","display_name":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","ror":"https://ror.org/02s376052","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I5124864"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Kartik Mohanram","raw_affiliation_strings":["1 Ecole Polytechnique Federale de Lausanne, Station 14, 1015 Lausanne, Switzerland, 2Rice University, Houston, TX 77005, USA, 3Merck Serono, 1202 Geneva and 4Swiss Institute of Bioinformatics, Vital-IT Group, 1015 Lausanne, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Ecole Polytechnique Federale de Lausanne, Station 14, 1015 Lausanne, Switzerland, 2Rice University, Houston, TX 77005, USA, 3Merck Serono, 1202 Geneva and 4Swiss Institute of Bioinformatics, Vital-IT Group, 1015 Lausanne, Switzerland","institution_ids":["https://openalex.org/I12708293","https://openalex.org/I4210113211","https://openalex.org/I5124864"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111936576","display_name":"Alessandro Di Cara","orcid":null},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I4210113211","display_name":"Merck Serono S.A. (Switzerland)","ror":"https://ror.org/01vp49361","country_code":"CH","type":"company","lineage":["https://openalex.org/I164928964","https://openalex.org/I4210113211"]},{"id":"https://openalex.org/I5124864","display_name":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","ror":"https://ror.org/02s376052","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I5124864"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Alessandro Di Cara","raw_affiliation_strings":["1 Ecole Polytechnique Federale de Lausanne, Station 14, 1015 Lausanne, Switzerland, 2Rice University, Houston, TX 77005, USA, 3Merck Serono, 1202 Geneva and 4Swiss Institute of Bioinformatics, Vital-IT Group, 1015 Lausanne, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Ecole Polytechnique Federale de Lausanne, Station 14, 1015 Lausanne, Switzerland, 2Rice University, Houston, TX 77005, USA, 3Merck Serono, 1202 Geneva and 4Swiss Institute of Bioinformatics, Vital-IT Group, 1015 Lausanne, Switzerland","institution_ids":["https://openalex.org/I12708293","https://openalex.org/I4210113211","https://openalex.org/I5124864"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072927296","display_name":"Giovanni De Micheli","orcid":"https://orcid.org/0000-0002-7827-3215"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I4210113211","display_name":"Merck Serono S.A. (Switzerland)","ror":"https://ror.org/01vp49361","country_code":"CH","type":"company","lineage":["https://openalex.org/I164928964","https://openalex.org/I4210113211"]},{"id":"https://openalex.org/I5124864","display_name":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","ror":"https://ror.org/02s376052","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I5124864"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Giovanni De Micheli","raw_affiliation_strings":["1 Ecole Polytechnique Federale de Lausanne, Station 14, 1015 Lausanne, Switzerland, 2Rice University, Houston, TX 77005, USA, 3Merck Serono, 1202 Geneva and 4Swiss Institute of Bioinformatics, Vital-IT Group, 1015 Lausanne, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Ecole Polytechnique Federale de Lausanne, Station 14, 1015 Lausanne, Switzerland, 2Rice University, Houston, TX 77005, USA, 3Merck Serono, 1202 Geneva and 4Swiss Institute of Bioinformatics, Vital-IT Group, 1015 Lausanne, Switzerland","institution_ids":["https://openalex.org/I12708293","https://openalex.org/I4210113211","https://openalex.org/I5124864"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5065825020","display_name":"Ioannis X\u00e9narios","orcid":"https://orcid.org/0000-0002-3413-6841"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I4210113211","display_name":"Merck Serono S.A. (Switzerland)","ror":"https://ror.org/01vp49361","country_code":"CH","type":"company","lineage":["https://openalex.org/I164928964","https://openalex.org/I4210113211"]},{"id":"https://openalex.org/I5124864","display_name":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","ror":"https://ror.org/02s376052","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I5124864"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Ioannis Xenarios","raw_affiliation_strings":["1 Ecole Polytechnique Federale de Lausanne, Station 14, 1015 Lausanne, Switzerland, 2Rice University, Houston, TX 77005, USA, 3Merck Serono, 1202 Geneva and 4Swiss Institute of Bioinformatics, Vital-IT Group, 1015 Lausanne, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Ecole Polytechnique Federale de Lausanne, Station 14, 1015 Lausanne, Switzerland, 2Rice University, Houston, TX 77005, USA, 3Merck Serono, 1202 Geneva and 4Swiss Institute of Bioinformatics, Vital-IT Group, 1015 Lausanne, Switzerland","institution_ids":["https://openalex.org/I12708293","https://openalex.org/I4210113211","https://openalex.org/I5124864"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5065825020"],"corresponding_institution_ids":["https://openalex.org/I12708293","https://openalex.org/I4210113211","https://openalex.org/I5124864"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.6367,"has_fulltext":true,"cited_by_count":52,"citation_normalized_percentile":{"value":0.83310912,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"25","issue":"12","first_page":"i101","last_page":"i109"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9991999864578247,"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":0.9991999864578247,"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":9.999999747378752e-05,"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/T10217","display_name":"Cardiac electrophysiology and arrhythmias","score":0.0,"subfield":{"id":"https://openalex.org/subfields/2705","display_name":"Cardiology and Cardiovascular Medicine"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.7747679948806763},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.7620559334754944},{"id":"https://openalex.org/keywords/toolbox","display_name":"Toolbox","score":0.7306747436523438},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6846800446510315},{"id":"https://openalex.org/keywords/boolean-network","display_name":"Boolean network","score":0.676201343536377},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.6536262631416321},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.4957922399044037},{"id":"https://openalex.org/keywords/boolean-function","display_name":"Boolean function","score":0.4618057608604431},{"id":"https://openalex.org/keywords/stochastic-modelling","display_name":"Stochastic modelling","score":0.4569982886314392},{"id":"https://openalex.org/keywords/boolean-model","display_name":"Boolean model","score":0.4463299810886383},{"id":"https://openalex.org/keywords/modelling-biological-systems","display_name":"Modelling biological systems","score":0.44530150294303894},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.4330423176288605},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.4244942367076874},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3145498037338257},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.27971822023391724},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.25230252742767334},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2184426486492157},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.16058829426765442},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.13783949613571167},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.08444550633430481}],"concepts":[{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.7747679948806763},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.7620559334754944},{"id":"https://openalex.org/C2777655017","wikidata":"https://www.wikidata.org/wiki/Q1501161","display_name":"Toolbox","level":2,"score":0.7306747436523438},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6846800446510315},{"id":"https://openalex.org/C134444547","wikidata":"https://www.wikidata.org/wiki/Q585230","display_name":"Boolean network","level":3,"score":0.676201343536377},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.6536262631416321},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.4957922399044037},{"id":"https://openalex.org/C187455244","wikidata":"https://www.wikidata.org/wiki/Q942353","display_name":"Boolean function","level":2,"score":0.4618057608604431},{"id":"https://openalex.org/C127491075","wikidata":"https://www.wikidata.org/wiki/Q7617825","display_name":"Stochastic modelling","level":2,"score":0.4569982886314392},{"id":"https://openalex.org/C67499762","wikidata":"https://www.wikidata.org/wiki/Q4943358","display_name":"Boolean model","level":2,"score":0.4463299810886383},{"id":"https://openalex.org/C137866125","wikidata":"https://www.wikidata.org/wiki/Q4299308","display_name":"Modelling biological systems","level":3,"score":0.44530150294303894},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.4330423176288605},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4244942367076874},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3145498037338257},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.27971822023391724},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.25230252742767334},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2184426486492157},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.16058829426765442},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.13783949613571167},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.08444550633430481},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":7,"locations":[{"id":"doi:10.1093/bioinformatics/btp214","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp214","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/12/i101/470287/btp214.pdf","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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:19477975","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19477975","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:iris.unil.ch:iris/105375","is_oa":true,"landing_page_url":"https://iris.unil.ch/handle/iris/105375","pdf_url":"https://iris.unil.ch/bitstreams/ae9cb0e1-aa67-49e3-97d8-e8cfd1161a74/download","source":{"id":"https://openalex.org/S7407055444","display_name":"IRIS","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"journal article"},{"id":"pmh:oai:doc.rero.ch:301438","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306400148","display_name":"reroDoc Digital Library","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":null},{"id":"pmh:oai:europepmc.org:1855996","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2687968","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:infoscience.epfl.ch:159777","is_oa":true,"landing_page_url":"http://infoscience.epfl.ch/record/159777","pdf_url":null,"source":{"id":"https://openalex.org/S4306400487","display_name":"Infoscience (Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:serval.unil.ch:BIB_3C1AE80B8836","is_oa":true,"landing_page_url":"https://serval.unil.ch/notice/serval:BIB_3C1AE80B8836","pdf_url":null,"source":{"id":"https://openalex.org/S4306401797","display_name":"SERVAL (Universit\u00e9 de Lausanne)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210093590","host_organization_name":"Swiss School of Archaeology in Greece","host_organization_lineage":["https://openalex.org/I4210093590"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, vol. 25, no. 12, pp. i101-i109","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btp214","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp214","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/12/i101/470287/btp214.pdf","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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17","score":0.41999998688697815}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W2156091616.pdf"},"referenced_works_count":41,"referenced_works":["https://openalex.org/W569716420","https://openalex.org/W1493523706","https://openalex.org/W1530386720","https://openalex.org/W1590222219","https://openalex.org/W1807981783","https://openalex.org/W1886819223","https://openalex.org/W1968856189","https://openalex.org/W1971224531","https://openalex.org/W1978329448","https://openalex.org/W1988791304","https://openalex.org/W1989284002","https://openalex.org/W2003702678","https://openalex.org/W2026452170","https://openalex.org/W2032811716","https://openalex.org/W2033539827","https://openalex.org/W2042321087","https://openalex.org/W2046881634","https://openalex.org/W2062029454","https://openalex.org/W2077720193","https://openalex.org/W2091198609","https://openalex.org/W2098739408","https://openalex.org/W2107342968","https://openalex.org/W2111123076","https://openalex.org/W2114518254","https://openalex.org/W2121149194","https://openalex.org/W2122902176","https://openalex.org/W2132935366","https://openalex.org/W2132980978","https://openalex.org/W2136559804","https://openalex.org/W2139504329","https://openalex.org/W2141545875","https://openalex.org/W2142895432","https://openalex.org/W2150750144","https://openalex.org/W2152563826","https://openalex.org/W2155418451","https://openalex.org/W2156335342","https://openalex.org/W2160533336","https://openalex.org/W2171280873","https://openalex.org/W2886978647","https://openalex.org/W2912435306","https://openalex.org/W6865662717"],"related_works":["https://openalex.org/W2155261113","https://openalex.org/W4363647300","https://openalex.org/W2128085946","https://openalex.org/W2063978705","https://openalex.org/W2038409079","https://openalex.org/W2085116222","https://openalex.org/W1926696424","https://openalex.org/W2004073264","https://openalex.org/W2156091616","https://openalex.org/W198703374"],"abstract_inverted_index":{"MOTIVATION:":[0],"Understanding":[1],"gene":[2,40,72],"regulation":[3],"in":[4,35,71,76,86,106,116,132,139,183],"biological":[5,122,146],"processes":[6],"and":[7,118,155,161],"modeling":[8,37,58,193],"the":[9,63,87,92,130,149,152,159,168,177],"robustness":[10],"of":[11,65,79,94,114,142,151,181],"underlying":[12],"regulatory":[13,41,73],"networks":[14,42],"is":[15,20,51,69],"an":[16],"important":[17],"problem":[18],"that":[19,68,167],"currently":[21],"being":[22],"addressed":[23,83],"by":[24,90],"computational":[25],"systems":[26],"biologists.":[27],"Lately,":[28],"there":[29],"has":[30,81],"been":[31,82],"a":[32,101],"renewed":[33],"interest":[34],"Boolean":[36,77,140,192],"techniques":[38],"for":[39,136],"(GRNs).":[43],"However,":[44],"due":[45],"to":[46,54,62,111,158],"their":[47],"deterministic":[48],"nature,":[49],"it":[50,157],"often":[52],"difficult":[53],"identify":[55],"whether":[56],"these":[57],"approaches":[59],"are":[60,187],"robust":[61,174],"addition":[64],"stochastic":[66],"noise":[67,115],"widespread":[70],"processes.":[74],"Stochasticity":[75],"models":[78,141],"GRNs":[80,117],"relatively":[84],"sparingly":[85],"past,":[88],"mainly":[89],"flipping":[91],"expression":[93,98],"genes":[95],"between":[96],"different":[97],"levels":[99],"with":[100,121],"predefined":[102],"probability.":[103],"This":[104],"stochasticity":[105,131,138,182],"nodes":[107],"(SIN)":[108],"model":[109,135,154,170,180],"leads":[110],"over":[112],"representation":[113],"hence":[119],"non-correspondence":[120],"observations.":[123],"RESULTS:":[124],"In":[125],"this":[126],"article,":[127],"we":[128,165],"introduce":[129],"functions":[133],"(SIF)":[134],"simulating":[137],"GRNs.":[143,184],"By":[144],"providing":[145],"motivation":[147],"behind":[148],"use":[150],"SIF":[153,169],"applying":[156],"T-helper":[160],"T-cell":[162],"activation":[163],"networks,":[164],"show":[166],"provides":[171],"more":[172],"biologically":[173],"results":[175],"than":[176],"existing":[178],"SIN":[179],"AVAILABILITY:":[185],"Algorithms":[186],"made":[188],"available":[189],"under":[190],"our":[191],"toolbox,":[194],"GenYsis.":[195],"The":[196],"software":[197],"binaries":[198],"can":[199],"be":[200],"downloaded":[201],"from":[202],"http://si2.epfl.ch/":[203],"approximately":[204],"garg/genysis.html.":[205]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":8},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":9},{"year":2012,"cited_by_count":7}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
