{"id":"https://openalex.org/W2738925829","doi":"https://doi.org/10.1186/s13015-017-0110-3","title":"Identification of bifurcation transitions in biological regulatory networks using Answer-Set Programming","display_name":"Identification of bifurcation transitions in biological regulatory networks using Answer-Set Programming","publication_year":2017,"publication_date":"2017-07-20","ids":{"openalex":"https://openalex.org/W2738925829","doi":"https://doi.org/10.1186/s13015-017-0110-3","mag":"2738925829","pmid":"https://pubmed.ncbi.nlm.nih.gov/28736575"},"language":"en","primary_location":{"id":"doi:10.1186/s13015-017-0110-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-017-0110-3","pdf_url":"https://almob.biomedcentral.com/track/pdf/10.1186/s13015-017-0110-3","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://almob.biomedcentral.com/track/pdf/10.1186/s13015-017-0110-3","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5041147420","display_name":"Louis Fippo Fitime","orcid":null},"institutions":[{"id":"https://openalex.org/I100445878","display_name":"\u00c9cole Centrale de Nantes","ror":"https://ror.org/03nh7d505","country_code":"FR","type":"education","lineage":["https://openalex.org/I100445878","https://openalex.org/I97188460"]},{"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/I4210091279","display_name":"Universit\u00e9 Sorbonne Paris Nord","ror":"https://ror.org/0199hds37","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210091279"]},{"id":"https://openalex.org/I4210117005","display_name":"Laboratoire des Sciences du Num\u00e9rique de Nantes","ror":"https://ror.org/02snf8m58","country_code":"FR","type":"facility","lineage":["https://openalex.org/I100445878","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I205703379","https://openalex.org/I4210117005","https://openalex.org/I4210124215","https://openalex.org/I4210127572","https://openalex.org/I4210139971","https://openalex.org/I97188460","https://openalex.org/I97188460"]},{"id":"https://openalex.org/I4210156583","display_name":"Laboratoire d'Informatique de Paris-Nord","ror":"https://ror.org/05g1zjw44","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I4210091279","https://openalex.org/I4210156583","https://openalex.org/I4210159245"]},{"id":"https://openalex.org/I4210159731","display_name":"LIP6","ror":"https://ror.org/05krcen59","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I39804081","https://openalex.org/I4210159245","https://openalex.org/I4210159731"]},{"id":"https://openalex.org/I97188460","display_name":"Nantes Universit\u00e9","ror":"https://ror.org/03gnr7b55","country_code":"FR","type":"education","lineage":["https://openalex.org/I97188460"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Louis Fippo Fitime","raw_affiliation_strings":["LS2N, UMR CNRS 6004, Ecole Centrale de Nantes, Nantes, France","Laboratoire d'Informatique de Paris Nord (LIPN), UMR 7030, Universit\u00e9 Paris 13, 99 avenue Jean-Baptiste Cl\u00e9ment, 93430 Villetaneuse, France","LIPN - Laboratoire d'Informatique de Paris-Nord (Institut Galil\u00e9e, Universit\u00e9 Paris 13, 99 avenue Jean-Baptiste Cl\u00e9ment, F-93430, Villetaneuse - France)","LS2N - \u00e9quipe M\u00e9ForBio - M\u00e9thodes Formelles pour la Bioinformatique (France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"LS2N, UMR CNRS 6004, Ecole Centrale de Nantes, Nantes, France","institution_ids":["https://openalex.org/I97188460","https://openalex.org/I100445878","https://openalex.org/I4210117005","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"Laboratoire d'Informatique de Paris Nord (LIPN), UMR 7030, Universit\u00e9 Paris 13, 99 avenue Jean-Baptiste Cl\u00e9ment, 93430 Villetaneuse, France","institution_ids":["https://openalex.org/I4210159731","https://openalex.org/I4210156583","https://openalex.org/I4210091279"]},{"raw_affiliation_string":"LIPN - Laboratoire d'Informatique de Paris-Nord (Institut Galil\u00e9e, Universit\u00e9 Paris 13, 99 avenue Jean-Baptiste Cl\u00e9ment, F-93430, Villetaneuse - France)","institution_ids":["https://openalex.org/I4210091279","https://openalex.org/I4210156583"]},{"raw_affiliation_string":"LS2N - \u00e9quipe M\u00e9ForBio - M\u00e9thodes Formelles pour la Bioinformatique (France)","institution_ids":["https://openalex.org/I97188460","https://openalex.org/I4210117005"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008022222","display_name":"Olivier Roux","orcid":"https://orcid.org/0000-0003-1563-7066"},"institutions":[{"id":"https://openalex.org/I100445878","display_name":"\u00c9cole Centrale de Nantes","ror":"https://ror.org/03nh7d505","country_code":"FR","type":"education","lineage":["https://openalex.org/I100445878","https://openalex.org/I97188460"]},{"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/I4210117005","display_name":"Laboratoire des Sciences du Num\u00e9rique de Nantes","ror":"https://ror.org/02snf8m58","country_code":"FR","type":"facility","lineage":["https://openalex.org/I100445878","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I205703379","https://openalex.org/I4210117005","https://openalex.org/I4210124215","https://openalex.org/I4210127572","https://openalex.org/I4210139971","https://openalex.org/I97188460","https://openalex.org/I97188460"]},{"id":"https://openalex.org/I97188460","display_name":"Nantes Universit\u00e9","ror":"https://ror.org/03gnr7b55","country_code":"FR","type":"education","lineage":["https://openalex.org/I97188460"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Olivier Roux","raw_affiliation_strings":["LS2N, UMR CNRS 6004, Ecole Centrale de Nantes, Nantes, France","LS2N - \u00e9quipe M\u00e9ForBio - M\u00e9thodes Formelles pour la Bioinformatique (France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"LS2N, UMR CNRS 6004, Ecole Centrale de Nantes, Nantes, France","institution_ids":["https://openalex.org/I97188460","https://openalex.org/I100445878","https://openalex.org/I4210117005","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"LS2N - \u00e9quipe M\u00e9ForBio - M\u00e9thodes Formelles pour la Bioinformatique (France)","institution_ids":["https://openalex.org/I97188460","https://openalex.org/I4210117005"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067131511","display_name":"Carito Guzio\u0142owski","orcid":"https://orcid.org/0000-0001-5192-0745"},"institutions":[{"id":"https://openalex.org/I100445878","display_name":"\u00c9cole Centrale de Nantes","ror":"https://ror.org/03nh7d505","country_code":"FR","type":"education","lineage":["https://openalex.org/I100445878","https://openalex.org/I97188460"]},{"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/I4210117005","display_name":"Laboratoire des Sciences du Num\u00e9rique de Nantes","ror":"https://ror.org/02snf8m58","country_code":"FR","type":"facility","lineage":["https://openalex.org/I100445878","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I205703379","https://openalex.org/I4210117005","https://openalex.org/I4210124215","https://openalex.org/I4210127572","https://openalex.org/I4210139971","https://openalex.org/I97188460","https://openalex.org/I97188460"]},{"id":"https://openalex.org/I97188460","display_name":"Nantes Universit\u00e9","ror":"https://ror.org/03gnr7b55","country_code":"FR","type":"education","lineage":["https://openalex.org/I97188460"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Carito Guziolowski","raw_affiliation_strings":["LS2N, UMR CNRS 6004, Ecole Centrale de Nantes, Nantes, France","LS2N - \u00e9quipe M\u00e9ForBio - M\u00e9thodes Formelles pour la Bioinformatique (France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"LS2N, UMR CNRS 6004, Ecole Centrale de Nantes, Nantes, France","institution_ids":["https://openalex.org/I97188460","https://openalex.org/I100445878","https://openalex.org/I4210117005","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"LS2N - \u00e9quipe M\u00e9ForBio - M\u00e9thodes Formelles pour la Bioinformatique (France)","institution_ids":["https://openalex.org/I97188460","https://openalex.org/I4210117005"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5067946028","display_name":"Lo\u00efc Paulev\u00e9","orcid":"https://orcid.org/0000-0002-7219-2027"},"institutions":[{"id":"https://openalex.org/I102197404","display_name":"Universit\u00e9 Paris-Sud","ror":"https://ror.org/028rypz17","country_code":"FR","type":"education","lineage":["https://openalex.org/I102197404"]},{"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/I277688954","display_name":"Universit\u00e9 Paris-Saclay","ror":"https://ror.org/03xjwb503","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954"]},{"id":"https://openalex.org/I4210144804","display_name":"Laboratoire de Recherche en Informatique","ror":"https://ror.org/04e3ktk27","country_code":"FR","type":"facility","lineage":["https://openalex.org/I102197404","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I4210144804","https://openalex.org/I4210159245"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Lo\u00efc Paulev\u00e9","raw_affiliation_strings":["LRI UMR 8623, Univ. Paris-Sud-CNRS, Universit\u00e9 Paris-Saclay, 91405 Orsay, France","BioInfo - LRI - Bioinformatique (LRI) (Universit\u00e9 Paris Sud\r\nB\u00e2t. 650 Lovelace\r\n91405 Orsay Cedex - France)"],"raw_orcid":"https://orcid.org/0000-0002-7219-2027","affiliations":[{"raw_affiliation_string":"LRI UMR 8623, Univ. Paris-Sud-CNRS, Universit\u00e9 Paris-Saclay, 91405 Orsay, France","institution_ids":["https://openalex.org/I277688954","https://openalex.org/I102197404","https://openalex.org/I1294671590","https://openalex.org/I4210144804"]},{"raw_affiliation_string":"BioInfo - LRI - Bioinformatique (LRI) (Universit\u00e9 Paris Sud\r\nB\u00e2t. 650 Lovelace\r\n91405 Orsay Cedex - France)","institution_ids":["https://openalex.org/I102197404","https://openalex.org/I4210144804"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1490,"currency":"GBP","value_usd":1827},"apc_paid":{"value":1490,"currency":"GBP","value_usd":1827},"fwci":0.673,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":{"value":0.69114885,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"12","issue":"1","first_page":"19","last_page":"19"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9248999953269958,"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":0.9248999953269958,"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/T10142","display_name":"Formal Methods in Verification","score":0.018300000578165054,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T13362","display_name":"Slime Mold and Myxomycetes Research","score":0.014999999664723873,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/reachability","display_name":"Reachability","score":0.8234479427337646},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7541294097900391},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.7035619616508484},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.6388645172119141},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.61544269323349},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5524786114692688},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.5520473122596741},{"id":"https://openalex.org/keywords/attractor","display_name":"Attractor","score":0.542270839214325},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.520058810710907},{"id":"https://openalex.org/keywords/asynchronous-communication","display_name":"Asynchronous communication","score":0.5149322152137756},{"id":"https://openalex.org/keywords/cellular-automaton","display_name":"Cellular automaton","score":0.4732430875301361},{"id":"https://openalex.org/keywords/automaton","display_name":"Automaton","score":0.4423052668571472},{"id":"https://openalex.org/keywords/state","display_name":"State (computer science)","score":0.41523459553718567},{"id":"https://openalex.org/keywords/answer-set-programming","display_name":"Answer set programming","score":0.41462987661361694},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.20925292372703552},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.16949567198753357},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.16739043593406677},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.09129416942596436}],"concepts":[{"id":"https://openalex.org/C136643341","wikidata":"https://www.wikidata.org/wiki/Q1361526","display_name":"Reachability","level":2,"score":0.8234479427337646},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7541294097900391},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.7035619616508484},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.6388645172119141},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.61544269323349},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5524786114692688},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.5520473122596741},{"id":"https://openalex.org/C164380108","wikidata":"https://www.wikidata.org/wiki/Q507187","display_name":"Attractor","level":2,"score":0.542270839214325},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.520058810710907},{"id":"https://openalex.org/C151319957","wikidata":"https://www.wikidata.org/wiki/Q752739","display_name":"Asynchronous communication","level":2,"score":0.5149322152137756},{"id":"https://openalex.org/C35527583","wikidata":"https://www.wikidata.org/wiki/Q189156","display_name":"Cellular automaton","level":2,"score":0.4732430875301361},{"id":"https://openalex.org/C112505250","wikidata":"https://www.wikidata.org/wiki/Q787116","display_name":"Automaton","level":2,"score":0.4423052668571472},{"id":"https://openalex.org/C48103436","wikidata":"https://www.wikidata.org/wiki/Q599031","display_name":"State (computer science)","level":2,"score":0.41523459553718567},{"id":"https://openalex.org/C182620335","wikidata":"https://www.wikidata.org/wiki/Q2852531","display_name":"Answer set programming","level":3,"score":0.41462987661361694},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.20925292372703552},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.16949567198753357},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.16739043593406677},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.09129416942596436},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1186/s13015-017-0110-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-017-0110-3","pdf_url":"https://almob.biomedcentral.com/track/pdf/10.1186/s13015-017-0110-3","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},{"id":"pmid:28736575","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28736575","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":"Algorithms for molecular biology : AMB","raw_type":null},{"id":"pmh:oai:HAL:hal-01566380v1","is_oa":false,"landing_page_url":"https://hal.science/hal-01566380","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Algorithms for Molecular Biology, 2017, 12 (1), pp.19. &#x27E8;10.1186/s13015-017-0110-3&#x27E9;","raw_type":"Journal articles"},{"id":"pmh:oai:doaj.org/article:c8166175daa440a9a3e30c8e97f22dac","is_oa":true,"landing_page_url":"https://doaj.org/article/c8166175daa440a9a3e30c8e97f22dac","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Algorithms for Molecular Biology, Vol 12, Iss 1, Pp 1-14 (2017)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:4362896","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5520421","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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13015-017-0110-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-017-0110-3","pdf_url":"https://almob.biomedcentral.com/track/pdf/10.1186/s13015-017-0110-3","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Life in Land","score":0.6399999856948853,"id":"https://metadata.un.org/sdg/15"}],"awards":[{"id":"https://openalex.org/G2204419101","display_name":null,"funder_award_id":"ANR-16-CE12-0034","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G7428494302","display_name":null,"funder_award_id":"ANR-16-CE12","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"}],"funders":[{"id":"https://openalex.org/F4320320883","display_name":"Agence Nationale de la Recherche","ror":"https://ror.org/00rbzpz17"},{"id":"https://openalex.org/F4320322892","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2738925829.pdf","grobid_xml":"https://content.openalex.org/works/W2738925829.grobid-xml"},"referenced_works_count":38,"referenced_works":["https://openalex.org/W123856239","https://openalex.org/W1489391022","https://openalex.org/W1493657719","https://openalex.org/W1525816981","https://openalex.org/W1568909857","https://openalex.org/W1603626552","https://openalex.org/W1606891084","https://openalex.org/W1672891595","https://openalex.org/W1767513498","https://openalex.org/W1823120935","https://openalex.org/W1922300461","https://openalex.org/W1973482879","https://openalex.org/W1989431662","https://openalex.org/W1996760951","https://openalex.org/W2004414305","https://openalex.org/W2015377888","https://openalex.org/W2025028416","https://openalex.org/W2027510758","https://openalex.org/W2042459594","https://openalex.org/W2046538693","https://openalex.org/W2075846943","https://openalex.org/W2079928950","https://openalex.org/W2094097101","https://openalex.org/W2111676921","https://openalex.org/W2117189826","https://openalex.org/W2120938811","https://openalex.org/W2127808973","https://openalex.org/W2129325583","https://openalex.org/W2145093247","https://openalex.org/W2147013823","https://openalex.org/W2157947216","https://openalex.org/W2160264790","https://openalex.org/W2160533336","https://openalex.org/W2167180332","https://openalex.org/W2269418830","https://openalex.org/W2462966030","https://openalex.org/W3100049063","https://openalex.org/W4211177236"],"related_works":["https://openalex.org/W2127267268","https://openalex.org/W2136512912","https://openalex.org/W2067910792","https://openalex.org/W2156446763","https://openalex.org/W2150194458","https://openalex.org/W2143461633","https://openalex.org/W2889071233","https://openalex.org/W4321471459","https://openalex.org/W4221156924","https://openalex.org/W2380814829"],"abstract_inverted_index":{"BACKGROUND:":[0],"Numerous":[1],"cellular":[2],"differentiation":[3],"processes":[4],"can":[5,201],"be":[6,202],"captured":[7],"using":[8],"discrete":[9,133],"qualitative":[10],"models":[11,17,138],"of":[12,22,25,47,60,68,77,101,117,124,139,151,167,173,185,193,221],"biological":[13,140,168],"regulatory":[14,163],"networks.":[15],"These":[16],"describe":[18],"the":[19,23,26,35,44,58,66,99,102,126,149,171,191,222],"temporal":[20],"evolution":[21],"state":[24],"network":[27,164],"subject":[28],"to":[29,37,120,195,204],"different":[30,38],"competing":[31],"transitions,":[32],"potentially":[33],"leading":[34],"system":[36],"attractors.":[39],"This":[40],"paper":[41],"focusses":[42],"on":[43,136,161],"formal":[45,181],"identification":[46,76,184],"states":[48],"and":[49,182,212],"transitions":[50,81,92,146,186],"that":[51],"are":[52,93,188],"crucial":[53],"for":[54,97,142,190],"preserving":[55],"or":[56],"pre-empting":[57],"reachability":[59,118,150],"a":[61,74,84,162,180,197],"given":[62,85,152,198],"behaviour.":[63,154],"METHODS:":[64],"In":[65,155],"context":[67],"non-deterministic":[69],"automata":[70,207],"networks,":[71,208],"we":[72,144,157],"propose":[73],"static":[75,115],"so-called":[78],"bifurcations,":[79],"i.e.,":[80],"after":[82],"which":[83,143,147,187,209],"goal":[86],"is":[87,217],"no":[88],"longer":[89],"reachable.":[90],"Such":[91],"naturally":[94],"good":[95],"candidates":[96],"controlling":[98],"occurrence":[100],"goal,":[103],"notably":[104],"by":[105],"modulating":[106],"their":[107],"propensity.":[108],"Our":[109,177],"method":[110,178],"combines":[111],"Answer-Set":[112],"Programming":[113],"with":[114],"analysis":[116,135],"properties":[119],"provide":[121],"an":[122],"under-approximation":[123],"all":[125],"existing":[127],"bifurcations.":[128],"RESULTS:":[129],"We":[130],"illustrate":[131],"our":[132,159,174],"bifurcation":[134],"several":[137],"systems,":[141],"identify":[145],"impact":[148],"long-term":[153],"particular,":[156],"apply":[158],"implementation":[160,216],"among":[165],"hundreds":[166],"species,":[169],"supporting":[170],"scalability":[172],"approach.":[175],"CONCLUSIONS:":[176],"allows":[179],"scalable":[183],"responsible":[189],"lost":[192],"capability":[194],"reach":[196],"state.":[199],"It":[200],"applied":[203],"any":[205],"asynchronous":[206],"encompass":[210],"Boolean":[211],"multi-valued":[213],"models.":[214],"An":[215],"provided":[218],"as":[219],"part":[220],"Pint":[223],"software,":[224],"available":[225],"at":[226],"http://loicpauleve.name/pint.":[227]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":2}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
