{"id":"https://openalex.org/W2161084419","doi":"https://doi.org/10.1145/1839764.1839773","title":"Action-based analysis of discrete regulatory networks with short-term stimuli","display_name":"Action-based analysis of discrete regulatory networks with short-term stimuli","publication_year":2010,"publication_date":"2010-09-29","ids":{"openalex":"https://openalex.org/W2161084419","doi":"https://doi.org/10.1145/1839764.1839773","mag":"2161084419"},"language":"en","primary_location":{"id":"doi:10.1145/1839764.1839773","is_oa":false,"landing_page_url":"https://doi.org/10.1145/1839764.1839773","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 8th International Conference on Computational Methods in Systems Biology","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5108110824","display_name":"Christian Krause","orcid":"https://orcid.org/0000-0002-3071-3605"},"institutions":[{"id":"https://openalex.org/I2800006345","display_name":"Leiden University Medical Center","ror":"https://ror.org/05xvt9f17","country_code":"NL","type":"funder","lineage":["https://openalex.org/I2800006345"]},{"id":"https://openalex.org/I1341640284","display_name":"Centrum Wiskunde & Informatica","ror":"https://ror.org/00x7ekv49","country_code":"NL","type":"facility","lineage":["https://openalex.org/I1341640284","https://openalex.org/I2800991832"]}],"countries":["NL"],"is_corresponding":true,"raw_author_name":"Christian Krause","raw_affiliation_strings":["Leiden University Medical Center","Software Engineering, CWI Amsterdam"],"affiliations":[{"raw_affiliation_string":"Leiden University Medical Center","institution_ids":["https://openalex.org/I2800006345"]},{"raw_affiliation_string":"Software Engineering, CWI Amsterdam","institution_ids":["https://openalex.org/I1341640284"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061638625","display_name":"Carola Krause","orcid":null},"institutions":[{"id":"https://openalex.org/I2800006345","display_name":"Leiden University Medical Center","ror":"https://ror.org/05xvt9f17","country_code":"NL","type":"funder","lineage":["https://openalex.org/I2800006345"]},{"id":"https://openalex.org/I1341640284","display_name":"Centrum Wiskunde & Informatica","ror":"https://ror.org/00x7ekv49","country_code":"NL","type":"facility","lineage":["https://openalex.org/I1341640284","https://openalex.org/I2800991832"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Carola Krause","raw_affiliation_strings":["Leiden University Medical Center","Software Engineering, CWI Amsterdam"],"affiliations":[{"raw_affiliation_string":"Leiden University Medical Center","institution_ids":["https://openalex.org/I2800006345"]},{"raw_affiliation_string":"Software Engineering, CWI Amsterdam","institution_ids":["https://openalex.org/I1341640284"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5018760156","display_name":"E.P. de Vink","orcid":"https://orcid.org/0000-0001-9514-2260"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Erik P. de Vink","raw_affiliation_strings":["Formal Methods, TU Eindhoven"],"affiliations":[{"raw_affiliation_string":"Formal Methods, TU Eindhoven","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5108110824"],"corresponding_institution_ids":["https://openalex.org/I1341640284","https://openalex.org/I2800006345"],"apc_list":null,"apc_paid":null,"fwci":0.1352,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.55240162,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"57","issue":null,"first_page":"66","last_page":"75"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998000264167786,"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":0.9998000264167786,"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/T11178","display_name":"Receptor Mechanisms and Signaling","score":0.9805999994277954,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9769999980926514,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/term","display_name":"Term (time)","score":0.6298739910125732},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.5895832180976868},{"id":"https://openalex.org/keywords/observable","display_name":"Observable","score":0.5778859853744507},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5299937129020691},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5103892683982849},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5017666816711426},{"id":"https://openalex.org/keywords/control-theory","display_name":"Control theory (sociology)","score":0.48438674211502075},{"id":"https://openalex.org/keywords/stability","display_name":"Stability (learning theory)","score":0.44630900025367737},{"id":"https://openalex.org/keywords/extension","display_name":"Extension (predicate logic)","score":0.4298902451992035},{"id":"https://openalex.org/keywords/action","display_name":"Action (physics)","score":0.4141315817832947},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.40286165475845337},{"id":"https://openalex.org/keywords/topology","display_name":"Topology (electrical circuits)","score":0.36520129442214966},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.3468620777130127},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.32712459564208984},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.24858903884887695},{"id":"https://openalex.org/keywords/control","display_name":"Control (management)","score":0.16684502363204956},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.12919935584068298},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.128709077835083},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.11937123537063599}],"concepts":[{"id":"https://openalex.org/C61797465","wikidata":"https://www.wikidata.org/wiki/Q1188986","display_name":"Term (time)","level":2,"score":0.6298739910125732},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.5895832180976868},{"id":"https://openalex.org/C32848918","wikidata":"https://www.wikidata.org/wiki/Q845789","display_name":"Observable","level":2,"score":0.5778859853744507},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5299937129020691},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5103892683982849},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5017666816711426},{"id":"https://openalex.org/C47446073","wikidata":"https://www.wikidata.org/wiki/Q5165890","display_name":"Control theory (sociology)","level":3,"score":0.48438674211502075},{"id":"https://openalex.org/C112972136","wikidata":"https://www.wikidata.org/wiki/Q7595718","display_name":"Stability (learning theory)","level":2,"score":0.44630900025367737},{"id":"https://openalex.org/C2778029271","wikidata":"https://www.wikidata.org/wiki/Q5421931","display_name":"Extension (predicate logic)","level":2,"score":0.4298902451992035},{"id":"https://openalex.org/C2780791683","wikidata":"https://www.wikidata.org/wiki/Q846785","display_name":"Action (physics)","level":2,"score":0.4141315817832947},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.40286165475845337},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.36520129442214966},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3468620777130127},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.32712459564208984},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.24858903884887695},{"id":"https://openalex.org/C2775924081","wikidata":"https://www.wikidata.org/wiki/Q55608371","display_name":"Control (management)","level":2,"score":0.16684502363204956},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.12919935584068298},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.128709077835083},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.11937123537063599},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","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/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"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/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"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/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1145/1839764.1839773","is_oa":false,"landing_page_url":"https://doi.org/10.1145/1839764.1839773","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 8th International Conference on Computational Methods in Systems Biology","raw_type":"proceedings-article"},{"id":"pmh:oai:pure.tue.nl:publications/6512f810-6372-4202-a886-d778c3f077b4","is_oa":false,"landing_page_url":"https://research.tue.nl/en/publications/6512f810-6372-4202-a886-d778c3f077b4","pdf_url":null,"source":{"id":"https://openalex.org/S4406922641","display_name":"TU/e Research Portal","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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Krause, C & Vink, de, E P 2010, Action-based analysis of discrete regulatory networks with short-term stimuli. in P Quaglia (ed.), Proceedings of the 8th Conference on Computational Methods in Systems Biology (CMSB 2010, Trento, Italy, September 29-October 1, 2010). Association for Computing Machinery, Inc., New York NY, pp. 65-75, conference; The 8th Conference on Computational Methods in Systems Biology (CMSB 2010); 2010-09-29; 2010-10-01, 29/09/10. https://doi.org/10.1145/1839764.1839773","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:cwi:oai:cwi.nl:16910","is_oa":false,"landing_page_url":"https://ir.cwi.nl/pub/16910","pdf_url":null,"source":{"id":"https://openalex.org/S4306401843","display_name":"Data Archiving and Networked Services (DANS)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1322597698","host_organization_name":"Royal Netherlands Academy of Arts and Sciences","host_organization_lineage":["https://openalex.org/I1322597698"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/conferencepaper"},{"id":"pmh:tue:oai:pure.tue.nl:publications/6512f810-6372-4202-a886-d778c3f077b4","is_oa":false,"landing_page_url":"https://research.tue.nl/nl/publications/6512f810-6372-4202-a886-d778c3f077b4","pdf_url":null,"source":{"id":"https://openalex.org/S4306401843","display_name":"Data Archiving and Networked Services (DANS)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1322597698","host_organization_name":"Royal Netherlands Academy of Arts and Sciences","host_organization_lineage":["https://openalex.org/I1322597698"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Proceedings of the 8th Conference on Computational Methods in Systems Biology (CMSB 2010, Trento, Italy, September 29-October 1, 2010), 65 - 75","raw_type":"info:eu-repo/semantics/conferencepaper"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Peace, Justice and strong institutions","score":0.5,"id":"https://metadata.un.org/sdg/16"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":45,"referenced_works":["https://openalex.org/W258022877","https://openalex.org/W1503973138","https://openalex.org/W1543126301","https://openalex.org/W1559033975","https://openalex.org/W1572391577","https://openalex.org/W1581408534","https://openalex.org/W1585692887","https://openalex.org/W1971135164","https://openalex.org/W1971224531","https://openalex.org/W1980325398","https://openalex.org/W1983350265","https://openalex.org/W1989431662","https://openalex.org/W2002999999","https://openalex.org/W2022624450","https://openalex.org/W2044987829","https://openalex.org/W2045679108","https://openalex.org/W2046538693","https://openalex.org/W2066322491","https://openalex.org/W2072890688","https://openalex.org/W2083227084","https://openalex.org/W2091117137","https://openalex.org/W2108654339","https://openalex.org/W2118039525","https://openalex.org/W2120878557","https://openalex.org/W2121149194","https://openalex.org/W2122808924","https://openalex.org/W2124082948","https://openalex.org/W2128804846","https://openalex.org/W2129780949","https://openalex.org/W2133569473","https://openalex.org/W2144501202","https://openalex.org/W2148357359","https://openalex.org/W2148895036","https://openalex.org/W2161186807","https://openalex.org/W2168167613","https://openalex.org/W2169062290","https://openalex.org/W2169804422","https://openalex.org/W2744090537","https://openalex.org/W4205156278","https://openalex.org/W4237523908","https://openalex.org/W4299438414","https://openalex.org/W6630104300","https://openalex.org/W6630473272","https://openalex.org/W6635014150","https://openalex.org/W6685124837"],"related_works":["https://openalex.org/W1994680671","https://openalex.org/W2000283393","https://openalex.org/W2002320543","https://openalex.org/W2061947244","https://openalex.org/W2150232912","https://openalex.org/W2054940838","https://openalex.org/W3106170641","https://openalex.org/W4321855183","https://openalex.org/W2952513607","https://openalex.org/W3102440103"],"abstract_inverted_index":{"To":[0],"incorporate":[1],"instant":[2],"effects":[3],"and":[4,93,101],"different":[5],"timescales":[6],"within":[7],"a":[8,25,33,42,66,86,102],"single":[9],"biological":[10],"system,":[11],"an":[12],"extension":[13],"of":[14,27,62,85,98],"discrete":[15],"regulatory":[16],"networks":[17],"with":[18],"short-term":[19],"stimuli":[20],"is":[21,81],"proposed.":[22],"By":[23],"maintaining":[24],"vector":[26],"recent":[28],"changes,":[29],"activities":[30],"initiated":[31],"by":[32,83],"steep":[34],"increase":[35],"or":[36],"decrease":[37],"can":[38],"be":[39],"captured":[40],"in":[41],"qualitative":[43],"setting.":[44],"In":[45],"order":[46],"to":[47,53,88,107],"compensate":[48],"for":[49,75,95],"the":[50,72,89,96],"blow-up":[51],"due":[52],"enhanced":[54],"states,":[55],"we":[56],"focus":[57],"on":[58],"observable":[59],"behavior.":[60],"Identification":[61],"bisimilar":[63],"states":[64],"yields":[65],"compact":[67],"system":[68],"representation":[69],"truthfully":[70],"expressing":[71],"information":[73],"relevant":[74],"deciding":[76],"logical":[77],"properties.":[78],"The":[79],"approach":[80],"implemented":[82],"means":[84],"front-end":[87],"mCRL2":[90],"tool":[91],"set":[92],"illustrated":[94],"switching":[97],"bacteriophage":[99],"lambda":[100],"bio-medical":[103],"case":[104],"study":[105],"related":[106],"TGF\u03b2":[108],"driven":[109],"fibrotic":[110],"conditions.":[111]},"counts_by_year":[],"updated_date":"2026-03-24T08:02:53.985720","created_date":"2016-06-24T00:00:00"}