{"id":"https://openalex.org/W2936460186","doi":"https://doi.org/10.1142/s0219720019500185","title":"TIGRNCRN: Trustful inference of gene regulatory network using clustering and refining the network","display_name":"TIGRNCRN: Trustful inference of gene regulatory network using clustering and refining the network","publication_year":2019,"publication_date":"2019-04-10","ids":{"openalex":"https://openalex.org/W2936460186","doi":"https://doi.org/10.1142/s0219720019500185","mag":"2936460186","pmid":"https://pubmed.ncbi.nlm.nih.gov/31288638"},"language":"en","primary_location":{"id":"doi:10.1142/s0219720019500185","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720019500185","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/A5036749459","display_name":"Jamshid Pirgazi","orcid":"https://orcid.org/0000-0002-2461-1143"},"institutions":[{"id":"https://openalex.org/I99861883","display_name":"University of Zanjan","ror":"https://ror.org/05e34ej29","country_code":"IR","type":"education","lineage":["https://openalex.org/I99861883"]}],"countries":["IR"],"is_corresponding":false,"raw_author_name":"Jamshid Pirgazi","raw_affiliation_strings":["Department of Computer Engineering, Engineering Faculty, University of Zanjan, Zanjan, Iran"],"affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Engineering Faculty, University of Zanjan, Zanjan, Iran","institution_ids":["https://openalex.org/I99861883"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041675442","display_name":"Alireza Khanteymoori","orcid":"https://orcid.org/0000-0001-6811-9196"},"institutions":[{"id":"https://openalex.org/I4210146419","display_name":"Institute for Research in Fundamental Sciences","ror":"https://ror.org/04xreqs31","country_code":"IR","type":"facility","lineage":["https://openalex.org/I4210146419"]},{"id":"https://openalex.org/I99861883","display_name":"University of Zanjan","ror":"https://ror.org/05e34ej29","country_code":"IR","type":"education","lineage":["https://openalex.org/I99861883"]}],"countries":["IR"],"is_corresponding":true,"raw_author_name":"Ali Reza Khanteymoori","raw_affiliation_strings":["Department of Computer Engineering, Engineering Faculty, University of Zanjan, Zanjan, Iran","School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran"],"affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Engineering Faculty, University of Zanjan, Zanjan, Iran","institution_ids":["https://openalex.org/I99861883"]},{"raw_affiliation_string":"School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran","institution_ids":["https://openalex.org/I4210146419"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5050313491","display_name":"Maryam Jalilkhani","orcid":null},"institutions":[{"id":"https://openalex.org/I99861883","display_name":"University of Zanjan","ror":"https://ror.org/05e34ej29","country_code":"IR","type":"education","lineage":["https://openalex.org/I99861883"]}],"countries":["IR"],"is_corresponding":false,"raw_author_name":"Maryam Jalilkhani","raw_affiliation_strings":["Department of Computer Engineering, Engineering Faculty, University of Zanjan, Zanjan, Iran"],"affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Engineering Faculty, University of Zanjan, Zanjan, Iran","institution_ids":["https://openalex.org/I99861883"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5041675442"],"corresponding_institution_ids":["https://openalex.org/I4210146419","https://openalex.org/I99861883"],"apc_list":null,"apc_paid":null,"fwci":0.5114,"has_fulltext":false,"cited_by_count":9,"citation_normalized_percentile":{"value":0.6353729,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"17","issue":"03","first_page":"1950018","last_page":"1950018"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9988999962806702,"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":0.9980000257492065,"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/cluster-analysis","display_name":"Cluster analysis","score":0.7650827765464783},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.7068279385566711},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.6821191310882568},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.6195501685142517},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.604577898979187},{"id":"https://openalex.org/keywords/bayesian-network","display_name":"Bayesian network","score":0.5815629959106445},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5211865305900574},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5048766732215881},{"id":"https://openalex.org/keywords/dynamic-bayesian-network","display_name":"Dynamic Bayesian network","score":0.4407753050327301},{"id":"https://openalex.org/keywords/bayes-theorem","display_name":"Bayes' theorem","score":0.42075252532958984},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.41375356912612915},{"id":"https://openalex.org/keywords/enhanced-data-rates-for-gsm-evolution","display_name":"Enhanced Data Rates for GSM Evolution","score":0.41115012764930725},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.3703583776950836},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.26451510190963745},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.17773935198783875},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1375458538532257},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.10334032773971558}],"concepts":[{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.7650827765464783},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.7068279385566711},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.6821191310882568},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.6195501685142517},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.604577898979187},{"id":"https://openalex.org/C33724603","wikidata":"https://www.wikidata.org/wiki/Q812540","display_name":"Bayesian network","level":2,"score":0.5815629959106445},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5211865305900574},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5048766732215881},{"id":"https://openalex.org/C82142266","wikidata":"https://www.wikidata.org/wiki/Q3456604","display_name":"Dynamic Bayesian network","level":3,"score":0.4407753050327301},{"id":"https://openalex.org/C207201462","wikidata":"https://www.wikidata.org/wiki/Q182505","display_name":"Bayes' theorem","level":3,"score":0.42075252532958984},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.41375356912612915},{"id":"https://openalex.org/C162307627","wikidata":"https://www.wikidata.org/wiki/Q204833","display_name":"Enhanced Data Rates for GSM Evolution","level":2,"score":0.41115012764930725},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.3703583776950836},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.26451510190963745},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.17773935198783875},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1375458538532257},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.10334032773971558},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012372","descriptor_name":"ROC Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012372","descriptor_name":"ROC Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012372","descriptor_name":"ROC Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"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":"D019295","descriptor_name":"Computational Biology","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":"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":2,"locations":[{"id":"doi:10.1142/s0219720019500185","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720019500185","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:31288638","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31288638","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}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320323645","display_name":"Institute for Research in Fundamental Sciences","ror":"https://ror.org/04xreqs31"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":50,"referenced_works":["https://openalex.org/W1599969036","https://openalex.org/W1973260612","https://openalex.org/W1984183317","https://openalex.org/W1995008770","https://openalex.org/W1998544165","https://openalex.org/W2011863452","https://openalex.org/W2015271344","https://openalex.org/W2021164824","https://openalex.org/W2023348596","https://openalex.org/W2025803032","https://openalex.org/W2036058623","https://openalex.org/W2044525257","https://openalex.org/W2076513103","https://openalex.org/W2094191210","https://openalex.org/W2094587261","https://openalex.org/W2094595302","https://openalex.org/W2103224920","https://openalex.org/W2105129830","https://openalex.org/W2108579152","https://openalex.org/W2109384743","https://openalex.org/W2112656672","https://openalex.org/W2125904845","https://openalex.org/W2126345910","https://openalex.org/W2129672766","https://openalex.org/W2131398297","https://openalex.org/W2133254377","https://openalex.org/W2134179844","https://openalex.org/W2138019504","https://openalex.org/W2140217512","https://openalex.org/W2151098983","https://openalex.org/W2156247618","https://openalex.org/W2157581457","https://openalex.org/W2158418996","https://openalex.org/W2160533336","https://openalex.org/W2161922735","https://openalex.org/W2163296115","https://openalex.org/W2164398451","https://openalex.org/W2165700458","https://openalex.org/W2165925645","https://openalex.org/W2169950095","https://openalex.org/W2199776355","https://openalex.org/W2550255991","https://openalex.org/W2586478664","https://openalex.org/W2587170806","https://openalex.org/W2741425937","https://openalex.org/W2803928488","https://openalex.org/W2850647469","https://openalex.org/W3099289621","https://openalex.org/W4242577767","https://openalex.org/W4244006029"],"related_works":["https://openalex.org/W2544242547","https://openalex.org/W1604786655","https://openalex.org/W2530648058","https://openalex.org/W2104172901","https://openalex.org/W2533075990","https://openalex.org/W2176372122","https://openalex.org/W2137203368","https://openalex.org/W2587170806","https://openalex.org/W2116290764","https://openalex.org/W3200936403"],"abstract_inverted_index":{"In":[0,175],"this":[1,192,242],"study,":[2],"in":[3,12,92,117,123,133,146,191,211,225,241],"order":[4,176],"to":[5,25,31,51,100,103,177,217,232],"deal":[6],"with":[7,128,187,238],"the":[8,23,42,45,56,64,69,73,124,139,144,147,153,163,179,181,201,205,226],"noise":[9],"and":[10,47,107,138,166,196,229],"uncertainty":[11],"gene":[13,33,95,234],"expression":[14],"data,":[15],"learning":[16,49],"networks,":[17,20],"especially":[18],"Bayesian":[19,154,212],"that":[21,40,80,204],"have":[22,41,59,82],"ability":[24],"use":[26],"prior":[27],"knowledge,":[28],"were":[29,131,173],"used":[30,61],"infer":[32],"regulatory":[34,96,168,209,235],"network.":[35],"Learning":[36],"networks":[37,97,236],"are":[38,98,114],"methods":[39,57,91,113,190,240],"structure":[43],"of":[44,55,94,119,141,200,219],"network":[46,155],"a":[48],"process":[50,214],"obtain":[52],"relationships.":[53],"One":[54],"which":[58,222],"been":[60,185],"for":[62],"measuring":[63],"relationship":[65],"between":[66,143],"genes":[67,76,127,145],"is":[68,223,230],"correlation":[70,130,172],"metrics,":[71],"but":[72],"high":[74,129],"correlated":[75],"not":[77],"necessarily":[78],"mean":[79],"they":[81],"causal":[83],"effect":[84],"on":[85,89,158],"each":[86],"other.":[87],"Studies":[88],"common":[90,189],"inference":[93],"yet":[99],"pay":[101],"attention":[102],"their":[104],"biological":[105,120,171,220],"importance":[106],"as":[108],"such,":[109],"predictions":[110],"by":[111],"these":[112],"less":[115],"accurate":[116],"terms":[118],"significance.":[121],"Hence,":[122],"proposed":[125,182,206],"method,":[126],"identified":[132],"one":[134],"cluster":[135,148],"using":[136,170,218],"clustering,":[137,162],"existence":[140],"edge":[142],"was":[149],"prevented.":[150],"Finally,":[151],"after":[152],"modeling,":[156],"based":[157],"knowledge":[159,221],"gained":[160],"from":[161],"refining":[164],"phase":[165],"improving":[167],"interactions":[169],"done.":[174],"show":[178],"efficiency,":[180],"method":[183,207],"has":[184],"compared":[186],"several":[188],"area":[193],"including":[194],"GENIE3":[195],"BMALR.":[197],"The":[198],"results":[199],"evaluation":[202],"indicate":[203],"recognized":[208],"relations":[210],"modeling":[213],"well,":[215],"due":[216],"hidden":[224],"data":[227],"collection,":[228],"able":[231],"recognize":[233],"align":[237],"important":[239],"field.":[243]},"counts_by_year":[{"year":2024,"cited_by_count":3},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}