{"id":"https://openalex.org/W2150153992","doi":"https://doi.org/10.1093/bioinformatics/btm560","title":"Petri net-based method for the analysis of the dynamics of signal propagation in signaling pathways","display_name":"Petri net-based method for the analysis of the dynamics of signal propagation in signaling pathways","publication_year":2007,"publication_date":"2007-11-22","ids":{"openalex":"https://openalex.org/W2150153992","doi":"https://doi.org/10.1093/bioinformatics/btm560","mag":"2150153992","pmid":"https://pubmed.ncbi.nlm.nih.gov/18033796"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btm560","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm560","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/2/209/49044417/bioinformatics_24_2_209.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":null,"license_id":null,"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":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/24/2/209/49044417/bioinformatics_24_2_209.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5019500401","display_name":"Simon Hardy","orcid":"https://orcid.org/0000-0003-4014-2014"},"institutions":[{"id":"https://openalex.org/I45683168","display_name":"Polytechnique Montr\u00e9al","ror":"https://ror.org/05f8d4e86","country_code":"CA","type":"education","lineage":["https://openalex.org/I45683168"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Simon Hardy","raw_affiliation_strings":["Department of Computer Engineering, \u00c9cole Polytechnique de Montr\u00e9al, P.O. Box 6079, Station Centre-Ville, Montr\u00e9al, H3C 3A7, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, \u00c9cole Polytechnique de Montr\u00e9al, P.O. Box 6079, Station Centre-Ville, Montr\u00e9al, H3C 3A7, Canada","institution_ids":["https://openalex.org/I45683168"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5108652072","display_name":"Pierre N. Robillard","orcid":null},"institutions":[{"id":"https://openalex.org/I45683168","display_name":"Polytechnique Montr\u00e9al","ror":"https://ror.org/05f8d4e86","country_code":"CA","type":"education","lineage":["https://openalex.org/I45683168"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Pierre N. Robillard","raw_affiliation_strings":["Department of Computer Engineering, \u00c9cole Polytechnique de Montr\u00e9al, P.O. Box 6079, Station Centre-Ville, Montr\u00e9al, H3C 3A7, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, \u00c9cole Polytechnique de Montr\u00e9al, P.O. Box 6079, Station Centre-Ville, Montr\u00e9al, H3C 3A7, Canada","institution_ids":["https://openalex.org/I45683168"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5019500401"],"corresponding_institution_ids":["https://openalex.org/I45683168"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.4737,"has_fulltext":true,"cited_by_count":45,"citation_normalized_percentile":{"value":0.8151298,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"24","issue":"2","first_page":"209","last_page":"217"},"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9927999973297119,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9731000065803528,"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/petri-net","display_name":"Petri net","score":0.8755544424057007},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7213839292526245},{"id":"https://openalex.org/keywords/signal","display_name":"SIGNAL (programming language)","score":0.5754349231719971},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.5573926568031311},{"id":"https://openalex.org/keywords/signal-flow-graph","display_name":"Signal-flow graph","score":0.5105258226394653},{"id":"https://openalex.org/keywords/dynamics","display_name":"Dynamics (music)","score":0.4804401099681854},{"id":"https://openalex.org/keywords/network-dynamics","display_name":"Network dynamics","score":0.4560132622718811},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.4444171190261841},{"id":"https://openalex.org/keywords/signal-transduction","display_name":"Signal transduction","score":0.43645384907722473},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.4247039258480072},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.37563556432724},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3327043056488037},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.24998241662979126},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1823107898235321},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.1724717617034912},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.12265613675117493},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.10874336957931519}],"concepts":[{"id":"https://openalex.org/C38677869","wikidata":"https://www.wikidata.org/wiki/Q724168","display_name":"Petri net","level":2,"score":0.8755544424057007},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7213839292526245},{"id":"https://openalex.org/C2779843651","wikidata":"https://www.wikidata.org/wiki/Q7390335","display_name":"SIGNAL (programming language)","level":2,"score":0.5754349231719971},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.5573926568031311},{"id":"https://openalex.org/C166501922","wikidata":"https://www.wikidata.org/wiki/Q1786523","display_name":"Signal-flow graph","level":2,"score":0.5105258226394653},{"id":"https://openalex.org/C145912823","wikidata":"https://www.wikidata.org/wiki/Q113558","display_name":"Dynamics (music)","level":2,"score":0.4804401099681854},{"id":"https://openalex.org/C123757187","wikidata":"https://www.wikidata.org/wiki/Q9195957","display_name":"Network dynamics","level":2,"score":0.4560132622718811},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.4444171190261841},{"id":"https://openalex.org/C62478195","wikidata":"https://www.wikidata.org/wiki/Q828130","display_name":"Signal transduction","level":2,"score":0.43645384907722473},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.4247039258480072},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.37563556432724},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3327043056488037},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.24998241662979126},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1823107898235321},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.1724717617034912},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.12265613675117493},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.10874336957931519},{"id":"https://openalex.org/C118615104","wikidata":"https://www.wikidata.org/wiki/Q121416","display_name":"Discrete mathematics","level":1,"score":0.0},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","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/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"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/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btm560","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm560","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/2/209/49044417/bioinformatics_24_2_209.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:18033796","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18033796","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:publications.polymtl.ca:20696","is_oa":false,"landing_page_url":"https://publications.polymtl.ca/20696/","pdf_url":null,"source":{"id":"https://openalex.org/S4306401013","display_name":"PolyPublie (\u00c9cole Polytechnique de Montr\u00e9al)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I45683168","host_organization_name":"Polytechnique Montr\u00e9al","host_organization_lineage":["https://openalex.org/I45683168"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article de revue"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btm560","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm560","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/2/209/49044417/bioinformatics_24_2_209.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G63464629","display_name":null,"funder_award_id":"A-0141","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"}],"funders":[{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2150153992.pdf","grobid_xml":"https://content.openalex.org/works/W2150153992.grobid-xml"},"referenced_works_count":18,"referenced_works":["https://openalex.org/W1544455702","https://openalex.org/W1561267729","https://openalex.org/W1592257313","https://openalex.org/W1968347726","https://openalex.org/W1989262356","https://openalex.org/W1991650117","https://openalex.org/W2030134162","https://openalex.org/W2088062845","https://openalex.org/W2104855667","https://openalex.org/W2112332161","https://openalex.org/W2133667940","https://openalex.org/W2140960985","https://openalex.org/W2146367686","https://openalex.org/W2148357359","https://openalex.org/W2158691076","https://openalex.org/W2162505680","https://openalex.org/W6635380619","https://openalex.org/W6681405575"],"related_works":["https://openalex.org/W1551257573","https://openalex.org/W4230983483","https://openalex.org/W1980200158","https://openalex.org/W2132799268","https://openalex.org/W2154794415","https://openalex.org/W1538101305","https://openalex.org/W791317142","https://openalex.org/W2285033125","https://openalex.org/W2774972313","https://openalex.org/W1653056629"],"abstract_inverted_index":{"This":[0],"article":[1],"introduces":[2],"a":[3,44,58],"new":[4],"method":[5,21],"for":[6],"analyzing":[7],"the":[8,25,42,49,53],"dynamics":[9,56],"of":[10,48,52,60],"signal":[11,39,54],"propagation":[12,40,55],"in":[13,41],"signaling":[14,62],"pathways":[15],"using":[16],"Petri":[17],"net":[18],"theory.":[19],"The":[20,33],"is":[22],"demonstrated":[23],"with":[24],"Ca(2+)/calmodulin-dependent":[26],"protein":[27],"kinase":[28],"II":[29],"(CaMKII)":[30],"regulation":[31,65],"network.":[32],"results":[34],"constitute":[35],"temporal":[36],"information":[37],"about":[38],"network,":[43],"simplified":[45],"graphical":[46],"representation":[47],"network":[50],"and":[51,57],"characterization":[59],"some":[61],"routes":[63],"as":[64],"motifs.":[66]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":5},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":3}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
