{"id":"https://openalex.org/W1991650117","doi":"https://doi.org/10.1142/s021972000600234x","title":"STRUCTURAL MODELING AND ANALYSIS OF SIGNALING PATHWAYS BASED ON PETRI NETS","display_name":"STRUCTURAL MODELING AND ANALYSIS OF SIGNALING PATHWAYS BASED ON PETRI NETS","publication_year":2006,"publication_date":"2006-10-01","ids":{"openalex":"https://openalex.org/W1991650117","doi":"https://doi.org/10.1142/s021972000600234x","mag":"1991650117","pmid":"https://pubmed.ncbi.nlm.nih.gov/17099944"},"language":"en","primary_location":{"id":"doi:10.1142/s021972000600234x","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s021972000600234x","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5100369855","display_name":"Chen Li","orcid":"https://orcid.org/0000-0002-6367-0998"},"institutions":[{"id":"https://openalex.org/I173915773","display_name":"Yamaguchi University","ror":"https://ror.org/03cxys317","country_code":"JP","type":"education","lineage":["https://openalex.org/I173915773"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"CHEN LI","raw_affiliation_strings":["Graduate School of Science and Engineering, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8511, Japan"],"affiliations":[{"raw_affiliation_string":"Graduate School of Science and Engineering, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8511, Japan","institution_ids":["https://openalex.org/I173915773"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068171515","display_name":"Shunichi Suzuki","orcid":"https://orcid.org/0000-0001-8441-5999"},"institutions":[{"id":"https://openalex.org/I21620634","display_name":"Toyo Engineering (Japan)","ror":"https://ror.org/05bjr0894","country_code":"JP","type":"company","lineage":["https://openalex.org/I21620634"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"SHUNICHI SUZUKI","raw_affiliation_strings":["Tokyo Head Office, TIS System Service Inc., Toyo Center Bldg., 29-15, Toyo-cho 5-chome, Koto-ku, Tokyo 135-0016, Japan"],"affiliations":[{"raw_affiliation_string":"Tokyo Head Office, TIS System Service Inc., Toyo Center Bldg., 29-15, Toyo-cho 5-chome, Koto-ku, Tokyo 135-0016, Japan","institution_ids":["https://openalex.org/I21620634"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108826586","display_name":"Qi\u2010Wei Ge","orcid":null},"institutions":[{"id":"https://openalex.org/I173915773","display_name":"Yamaguchi University","ror":"https://ror.org/03cxys317","country_code":"JP","type":"education","lineage":["https://openalex.org/I173915773"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"QI-WEI GE","raw_affiliation_strings":["Faculty of Education, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8511, Japan"],"affiliations":[{"raw_affiliation_string":"Faculty of Education, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8511, Japan","institution_ids":["https://openalex.org/I173915773"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101292050","display_name":"Mitsuru Nakata","orcid":null},"institutions":[{"id":"https://openalex.org/I173915773","display_name":"Yamaguchi University","ror":"https://ror.org/03cxys317","country_code":"JP","type":"education","lineage":["https://openalex.org/I173915773"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"MITSURU NAKATA","raw_affiliation_strings":["Faculty of Education, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8511, Japan"],"affiliations":[{"raw_affiliation_string":"Faculty of Education, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8511, Japan","institution_ids":["https://openalex.org/I173915773"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113762836","display_name":"Hiroshi Matsuno","orcid":null},"institutions":[{"id":"https://openalex.org/I173915773","display_name":"Yamaguchi University","ror":"https://ror.org/03cxys317","country_code":"JP","type":"education","lineage":["https://openalex.org/I173915773"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"HIROSHI MATSUNO","raw_affiliation_strings":["Graduate School of Science and Engineering, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8512, Japan"],"affiliations":[{"raw_affiliation_string":"Graduate School of Science and Engineering, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8512, Japan","institution_ids":["https://openalex.org/I173915773"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5088167618","display_name":"Satoru Miyano","orcid":"https://orcid.org/0000-0002-1753-6616"},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]},{"id":"https://openalex.org/I161296585","display_name":"Tokyo University of Science","ror":"https://ror.org/05sj3n476","country_code":"JP","type":"education","lineage":["https://openalex.org/I161296585"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"SATORU MIYANO","raw_affiliation_strings":["Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokane-dai, Minato-ku, Tokyo 108-8639, Japan"],"affiliations":[{"raw_affiliation_string":"Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokane-dai, Minato-ku, Tokyo 108-8639, Japan","institution_ids":["https://openalex.org/I74801974","https://openalex.org/I161296585"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5100369855"],"corresponding_institution_ids":["https://openalex.org/I173915773"],"apc_list":null,"apc_paid":null,"fwci":2.0431,"has_fulltext":false,"cited_by_count":40,"citation_normalized_percentile":{"value":0.85234696,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"04","issue":"05","first_page":"1119","last_page":"1140"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9908000230789185,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9908000230789185,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9854999780654907,"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":0.9487000107765198,"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":0.9540754556655884},{"id":"https://openalex.org/keywords/petri-dish","display_name":"Petri dish","score":0.6262226104736328},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6125052571296692},{"id":"https://openalex.org/keywords/invariant","display_name":"Invariant (physics)","score":0.4807281792163849},{"id":"https://openalex.org/keywords/process-architecture","display_name":"Process architecture","score":0.47420433163642883},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3912171721458435},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3620825409889221},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.25744590163230896},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2541351318359375},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2195190191268921},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.07478269934654236}],"concepts":[{"id":"https://openalex.org/C38677869","wikidata":"https://www.wikidata.org/wiki/Q724168","display_name":"Petri net","level":2,"score":0.9540754556655884},{"id":"https://openalex.org/C146763376","wikidata":"https://www.wikidata.org/wiki/Q81714","display_name":"Petri dish","level":2,"score":0.6262226104736328},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6125052571296692},{"id":"https://openalex.org/C190470478","wikidata":"https://www.wikidata.org/wiki/Q2370229","display_name":"Invariant (physics)","level":2,"score":0.4807281792163849},{"id":"https://openalex.org/C136155141","wikidata":"https://www.wikidata.org/wiki/Q7247260","display_name":"Process architecture","level":3,"score":0.47420433163642883},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3912171721458435},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3620825409889221},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.25744590163230896},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2541351318359375},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2195190191268921},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.07478269934654236},{"id":"https://openalex.org/C37914503","wikidata":"https://www.wikidata.org/wiki/Q156495","display_name":"Mathematical physics","level":1,"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":"D002468","descriptor_name":"Cell Physiological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002468","descriptor_name":"Cell Physiological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002468","descriptor_name":"Cell Physiological Phenomena","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":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009716","descriptor_name":"Numerical Analysis, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009716","descriptor_name":"Numerical Analysis, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009716","descriptor_name":"Numerical Analysis, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"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}],"locations_count":3,"locations":[{"id":"doi:10.1142/s021972000600234x","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s021972000600234x","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},{"id":"pmid:17099944","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17099944","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":"Journal of bioinformatics and computational biology","raw_type":null},{"id":"pmh:oai:irdb.nii.ac.jp:00828:0000991442","is_oa":false,"landing_page_url":"https://petit.lib.yamaguchi-u.ac.jp/17256","pdf_url":null,"source":{"id":"https://openalex.org/S7407056385","display_name":"Institutional Repositories DataBase (IRDB)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I184597095","host_organization_name":"National Institute of Informatics","host_organization_lineage":["https://openalex.org/I184597095"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of bioinformatics and computational biology","raw_type":"journal article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":27,"referenced_works":["https://openalex.org/W12256183","https://openalex.org/W190590157","https://openalex.org/W219883683","https://openalex.org/W1535437554","https://openalex.org/W1563476066","https://openalex.org/W1591890109","https://openalex.org/W1592257313","https://openalex.org/W1605229095","https://openalex.org/W1758395617","https://openalex.org/W1810769493","https://openalex.org/W1981471739","https://openalex.org/W1983281982","https://openalex.org/W1983509844","https://openalex.org/W1994188141","https://openalex.org/W2019840092","https://openalex.org/W2089372815","https://openalex.org/W2099039198","https://openalex.org/W2100486049","https://openalex.org/W2109952945","https://openalex.org/W2128276963","https://openalex.org/W2146367686","https://openalex.org/W2169804422","https://openalex.org/W2169810918","https://openalex.org/W2325341754","https://openalex.org/W2412839122","https://openalex.org/W4234356172","https://openalex.org/W4302167780"],"related_works":["https://openalex.org/W1938017683","https://openalex.org/W2158814988","https://openalex.org/W1543378523","https://openalex.org/W2355954834","https://openalex.org/W2285444239","https://openalex.org/W2257573499","https://openalex.org/W2901841247","https://openalex.org/W2091260341","https://openalex.org/W597347111","https://openalex.org/W2064254377"],"abstract_inverted_index":{"The":[0],"purpose":[1],"of":[2,55,90],"this":[3],"paper":[4],"is":[5,104],"to":[6,9,32,49,64,79],"discuss":[7],"how":[8,101],"model":[10],"and":[11,36,60,109],"analyze":[12],"signaling":[13,58,111],"pathways":[14,59],"by":[15,29,86,114],"using":[16],"Petri":[17,27,71,95],"net.":[18],"Firstly,":[19],"we":[20,39,75,99],"propose":[21],"a":[22,41,65,88],"modeling":[23,108],"method":[24,103],"based":[25],"on":[26],"net":[28,72,96],"paying":[30],"attention":[31],"the":[33,70,94],"molecular":[34],"interactions":[35],"mechanisms.":[37],"Then,":[38],"introduce":[40],"new":[42],"notion":[43],"\"activation":[44],"transduction":[45],"component\"":[46],"in":[47,57,69,93,107],"order":[48],"describe":[50],"an":[51,77,117],"enzymic":[52,83],"activation":[53,84],"process":[54],"reactions":[56],"shows":[61],"its":[62],"correspondence":[63],"so-called":[66],"elementary":[67,91],"T-invariant":[68],"models.":[73,97],"Further,":[74],"design":[76],"algorithm":[78],"effectively":[80],"find":[81],"basic":[82],"processes":[85],"obtaining":[87],"series":[89],"T-invariants":[92],"Finally,":[98],"demonstrate":[100],"our":[102],"practically":[105],"used":[106],"analyzing":[110],"pathway":[112],"mediated":[113],"thrombopoietin":[115],"as":[116],"example.":[118]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":4},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":3},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":3}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
