{"id":"https://openalex.org/W2129740358","doi":"https://doi.org/10.2390/biecoll-jib-2010-113","title":"A New Approach for Modelling Gene Regulatory Networks Using Fuzzy Petri Nets","display_name":"A New Approach for Modelling Gene Regulatory Networks Using Fuzzy Petri Nets","publication_year":2009,"publication_date":"2009-01-01","ids":{"openalex":"https://openalex.org/W2129740358","doi":"https://doi.org/10.2390/biecoll-jib-2010-113","mag":"2129740358","pmid":"https://pubmed.ncbi.nlm.nih.gov/20134077"},"language":"en","primary_location":{"id":"pmid:20134077","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20134077","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 integrative bioinformatics","raw_type":null},"type":"article","indexed_in":["datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doaj.org/article/a6b799a14f574b3698a2726b094256f3","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102781949","display_name":"Raed I. Hamed","orcid":"https://orcid.org/0000-0003-0093-2142"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Hamed, Raed I.","raw_affiliation_strings":["Department of Computer Science, JMI University, New Delhi 110025, India. raed.inf@gmail.com"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, JMI University, New Delhi 110025, India. raed.inf@gmail.com","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053022380","display_name":"S.I. Ahson","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ahson, S. I.","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5024883122","display_name":"Rabea Parveen","orcid":"https://orcid.org/0000-0003-3687-5506"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Parveen, R.","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5102781949"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.9575,"has_fulltext":false,"cited_by_count":34,"citation_normalized_percentile":{"value":0.75075794,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"7","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9987000226974487,"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":0.9987000226974487,"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/T12029","display_name":"DNA and Biological Computing","score":0.991100013256073,"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/T11125","display_name":"Petri Nets in System Modeling","score":0.9889000058174133,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7234145998954773},{"id":"https://openalex.org/keywords/fuzzy-logic","display_name":"Fuzzy logic","score":0.6927664279937744},{"id":"https://openalex.org/keywords/petri-net","display_name":"Petri net","score":0.6356810331344604},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.5231843590736389},{"id":"https://openalex.org/keywords/construct","display_name":"Construct (python library)","score":0.5195203423500061},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.49672991037368774},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.4789736270904541},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.37800583243370056},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3031555116176605},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.19301781058311462},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.17056098580360413},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.13934192061424255},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.07705509662628174},{"id":"https://openalex.org/keywords/computer-network","display_name":"Computer network","score":0.06262817978858948}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7234145998954773},{"id":"https://openalex.org/C58166","wikidata":"https://www.wikidata.org/wiki/Q224821","display_name":"Fuzzy logic","level":2,"score":0.6927664279937744},{"id":"https://openalex.org/C38677869","wikidata":"https://www.wikidata.org/wiki/Q724168","display_name":"Petri net","level":2,"score":0.6356810331344604},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.5231843590736389},{"id":"https://openalex.org/C2780801425","wikidata":"https://www.wikidata.org/wiki/Q5164392","display_name":"Construct (python library)","level":2,"score":0.5195203423500061},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.49672991037368774},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.4789736270904541},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.37800583243370056},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3031555116176605},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.19301781058311462},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.17056098580360413},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.13934192061424255},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.07705509662628174},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.06262817978858948},{"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":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":"D017143","descriptor_name":"Fuzzy Logic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017143","descriptor_name":"Fuzzy Logic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017143","descriptor_name":"Fuzzy Logic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D046228","descriptor_name":"Microarray Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D046228","descriptor_name":"Microarray Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D046228","descriptor_name":"Microarray Analysis","qualifier_ui":null,"qualifier_name":null,"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":4,"locations":[{"id":"pmid:20134077","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20134077","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 integrative bioinformatics","raw_type":null},{"id":"pmh:oai:biecoll.ub.uni-bielefeld.de:2056","is_oa":false,"landing_page_url":"http://biecoll.ub.uni-bielefeld.de/volltexte/2010/2056/","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://journal.imbio.de/article.php?aid=113","raw_type":"Journal Article"},{"id":"pmh:oai:doaj.org/article:a6b799a14f574b3698a2726b094256f3","is_oa":true,"landing_page_url":"https://doaj.org/article/a6b799a14f574b3698a2726b094256f3","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":"Journal of Integrative Bioinformatics, Vol 7, Iss 1, Pp 1-16 (2010)","raw_type":"article"},{"id":"doi:10.2390/biecoll-jib-2010-113","is_oa":true,"landing_page_url":"https://doi.org/10.2390/biecoll-jib-2010-113","pdf_url":null,"source":{"id":"https://openalex.org/S4306401670","display_name":"PUB \u2013 Publications at Bielefeld University (Bielefeld University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I20121455","host_organization_name":"Bielefeld University","host_organization_lineage":["https://openalex.org/I20121455"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"pmh:oai:doaj.org/article:a6b799a14f574b3698a2726b094256f3","is_oa":true,"landing_page_url":"https://doaj.org/article/a6b799a14f574b3698a2726b094256f3","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":"Journal of Integrative Bioinformatics, Vol 7, Iss 1, Pp 1-16 (2010)","raw_type":"article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":30,"referenced_works":["https://openalex.org/W173042357","https://openalex.org/W1481919380","https://openalex.org/W1482095202","https://openalex.org/W1494233870","https://openalex.org/W1520434657","https://openalex.org/W1535437554","https://openalex.org/W1893505266","https://openalex.org/W1933713351","https://openalex.org/W1968347726","https://openalex.org/W1970321745","https://openalex.org/W1975954590","https://openalex.org/W1987270093","https://openalex.org/W1994188141","https://openalex.org/W1996109622","https://openalex.org/W2027888593","https://openalex.org/W2043120306","https://openalex.org/W2096473476","https://openalex.org/W2104644194","https://openalex.org/W2109480258","https://openalex.org/W2118640031","https://openalex.org/W2136722496","https://openalex.org/W2138042010","https://openalex.org/W2138352609","https://openalex.org/W2142460132","https://openalex.org/W2146764933","https://openalex.org/W2151098983","https://openalex.org/W2156742897","https://openalex.org/W2161464089","https://openalex.org/W2165671180","https://openalex.org/W2169990030"],"related_works":["https://openalex.org/W2991994798","https://openalex.org/W2161464089","https://openalex.org/W2159706884","https://openalex.org/W1893505266","https://openalex.org/W2058213704","https://openalex.org/W2032047675","https://openalex.org/W2163930132","https://openalex.org/W2172083806","https://openalex.org/W2138042010","https://openalex.org/W2128970094","https://openalex.org/W2109378014","https://openalex.org/W2912565176","https://openalex.org/W2058221907","https://openalex.org/W122736534","https://openalex.org/W2168161076","https://openalex.org/W1982762533","https://openalex.org/W2156742897","https://openalex.org/W1612376515","https://openalex.org/W2071174193","https://openalex.org/W1520853569"],"abstract_inverted_index":{"Gene":[0],"Regulatory":[1],"Networks":[2],"are":[3],"models":[4],"of":[5,16,73,79,110,140],"genes":[6],"and":[7,132],"gene":[8],"interactions":[9],"at":[10],"the":[11,29,35,61,68,80,94,127,141],"expression":[12,77,85,138],"level.":[13,86],"The":[14,65,123],"advent":[15],"microarray":[17,44],"technology":[18],"has":[19,39],"challenged":[20],"computer":[21],"scientists":[22],"to":[23,42,117,134],"develop":[24],"better":[25],"algorithms":[26],"for":[27,46,104],"modeling":[28],"underlying":[30],"regulatory":[31,48,69,106],"relationship":[32],"in":[33,76,137],"between":[34],"genes.":[36],"Fuzzy":[37,62],"system":[38],"an":[40,115],"ability":[41],"search":[43,102],"datasets":[45],"activator/repressor":[47],"relationship.":[49,107],"In":[50],"this":[51],"paper,":[52],"we":[53,113],"present":[54],"a":[55,100,119],"fuzzy":[56,96,111],"reasoning":[57,121],"model":[58,66,97],"based":[59,82],"on":[60,83],"Petri":[63],"Net.":[64],"considers":[67],"triplets":[70],"by":[71],"means":[72],"predicting":[74],"changes":[75,136],"level":[78,139],"target":[81,142],"input":[84],"This":[87],"method":[88],"eliminates":[89],"possible":[90],"false":[91],"predictions":[92],"from":[93],"classical":[95],"thereby":[98],"allowing":[99],"wider":[101],"space":[103],"inferring":[105],"Through":[108],"formalization":[109],"reasoning,":[112],"propose":[114],"approach":[116,129],"construct":[118],"rulebased":[120],"system.":[122],"experimental":[124],"results":[125],"show":[126],"proposed":[128],"is":[130],"feasible":[131],"acceptable":[133],"predict":[135],"gene.":[143]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":7},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":2}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}
