{"id":"https://openalex.org/W4320855961","doi":"https://doi.org/10.1093/bioinformatics/btad072","title":"wpLogicNet: logic gate and structure inference in gene regulatory networks","display_name":"wpLogicNet: logic gate and structure inference in gene regulatory networks","publication_year":2023,"publication_date":"2023-02-01","ids":{"openalex":"https://openalex.org/W4320855961","doi":"https://doi.org/10.1093/bioinformatics/btad072","pmid":"https://pubmed.ncbi.nlm.nih.gov/36790055"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad072","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad072","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/2/btad072/49243644/btad072.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":"gold","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/39/2/btad072/49243644/btad072.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5056440187","display_name":"Seyed Amir Malekpour","orcid":"https://orcid.org/0000-0002-3525-3548"},"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"]}],"countries":["IR"],"is_corresponding":true,"raw_author_name":"Seyed Amir Malekpour","raw_affiliation_strings":["School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM) , Tehran 19395-5746, Iran"],"raw_orcid":"https://orcid.org/0000-0002-3525-3548","affiliations":[{"raw_affiliation_string":"School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM) , Tehran 19395-5746, Iran","institution_ids":["https://openalex.org/I4210146419"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068203709","display_name":"Maryam Shahdoust","orcid":"https://orcid.org/0000-0003-1176-6784"},"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"]}],"countries":["IR"],"is_corresponding":false,"raw_author_name":"Maryam Shahdoust","raw_affiliation_strings":["School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM) , Tehran 19395-5746, Iran"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM) , Tehran 19395-5746, Iran","institution_ids":["https://openalex.org/I4210146419"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018832888","display_name":"Rosa Aghdam","orcid":"https://orcid.org/0000-0001-9045-9592"},"institutions":[{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]},{"id":"https://openalex.org/I2802999273","display_name":"Wisconsin Institutes for Discovery","ror":"https://ror.org/05gbven85","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2802999273"]},{"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"]}],"countries":["IR","US"],"is_corresponding":false,"raw_author_name":"Rosa Aghdam","raw_affiliation_strings":["School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM) , Tehran 19395-5746, Iran","Wisconsin Institute for Discovery, University of Wisconsin-Madison , Madison, WI 53715, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM) , Tehran 19395-5746, Iran","institution_ids":["https://openalex.org/I4210146419"]},{"raw_affiliation_string":"Wisconsin Institute for Discovery, University of Wisconsin-Madison , Madison, WI 53715, USA","institution_ids":["https://openalex.org/I135310074","https://openalex.org/I2802999273"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101481326","display_name":"Mehdi Sadeghi","orcid":"https://orcid.org/0000-0001-5900-8697"},"institutions":[{"id":"https://openalex.org/I4210137727","display_name":"National Institute of Genetic Engineering and Biotechnology","ror":"https://ror.org/03ckh6215","country_code":"IR","type":"facility","lineage":["https://openalex.org/I4210137727"]}],"countries":["IR"],"is_corresponding":false,"raw_author_name":"Mehdi Sadeghi","raw_affiliation_strings":["Department of Medical Genetics, National Institute for Genetic Engineering and Biotechnology , Tehran 1497716316, Iran"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medical Genetics, National Institute for Genetic Engineering and Biotechnology , Tehran 1497716316, Iran","institution_ids":["https://openalex.org/I4210137727"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5056440187"],"corresponding_institution_ids":["https://openalex.org/I4210146419"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.6703,"has_fulltext":true,"cited_by_count":18,"citation_normalized_percentile":{"value":0.8366257,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"39","issue":"2","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":0.9779000282287598,"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":0.9779000282287598,"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":0.010099999606609344,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.00430000014603138,"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/inference","display_name":"Inference","score":0.788836658000946},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.675661563873291},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5404518246650696},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.48743370175361633},{"id":"https://openalex.org/keywords/and-gate","display_name":"AND gate","score":0.4124346971511841},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.36601972579956055},{"id":"https://openalex.org/keywords/logic-gate","display_name":"Logic gate","score":0.34972745180130005},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3335638642311096},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2930224537849426},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2675670087337494},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.21589189767837524},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.16553595662117004},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.11005938053131104}],"concepts":[{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.788836658000946},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.675661563873291},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5404518246650696},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.48743370175361633},{"id":"https://openalex.org/C10418432","wikidata":"https://www.wikidata.org/wiki/Q560370","display_name":"AND gate","level":3,"score":0.4124346971511841},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.36601972579956055},{"id":"https://openalex.org/C131017901","wikidata":"https://www.wikidata.org/wiki/Q170451","display_name":"Logic gate","level":2,"score":0.34972745180130005},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3335638642311096},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2930224537849426},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2675670087337494},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.21589189767837524},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.16553595662117004},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.11005938053131104}],"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":"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":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":3,"locations":[{"id":"doi:10.1093/bioinformatics/btad072","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad072","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/2/btad072/49243644/btad072.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36790055","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36790055","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:pubmedcentral.nih.gov:9936836","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9936836","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC9936836/pdf/btad072.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad072","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad072","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/2/btad072/49243644/btad072.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Partnerships for the goals","score":0.550000011920929,"id":"https://metadata.un.org/sdg/17"}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4320855961.pdf","grobid_xml":"https://content.openalex.org/works/W4320855961.grobid-xml"},"referenced_works_count":31,"referenced_works":["https://openalex.org/W1644997609","https://openalex.org/W1979073566","https://openalex.org/W1994892791","https://openalex.org/W1996264210","https://openalex.org/W2010507548","https://openalex.org/W2017218687","https://openalex.org/W2048070895","https://openalex.org/W2057306408","https://openalex.org/W2069545688","https://openalex.org/W2069728939","https://openalex.org/W2075941967","https://openalex.org/W2076372398","https://openalex.org/W2076513103","https://openalex.org/W2110699703","https://openalex.org/W2122342005","https://openalex.org/W2132935366","https://openalex.org/W2136453810","https://openalex.org/W2143076232","https://openalex.org/W2157581457","https://openalex.org/W2161922735","https://openalex.org/W2524911207","https://openalex.org/W2586478664","https://openalex.org/W2621589069","https://openalex.org/W2757026735","https://openalex.org/W2901318940","https://openalex.org/W3008895300","https://openalex.org/W3043066708","https://openalex.org/W3117326807","https://openalex.org/W3142178348","https://openalex.org/W3184607208","https://openalex.org/W4290787198"],"related_works":["https://openalex.org/W2560421304","https://openalex.org/W2950199998","https://openalex.org/W2951387065","https://openalex.org/W2134575910","https://openalex.org/W4385727351","https://openalex.org/W4306798985","https://openalex.org/W4385417763","https://openalex.org/W2909211499","https://openalex.org/W3119688974","https://openalex.org/W2060067973"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,162,193,218],"gene":[2,13,31,79,134],"regulatory":[3,32],"process":[4],"resembles":[5],"a":[6,11,17,30,48,84,97,123,142],"logic":[7,18,62,89,140,151,164],"system":[8],"in":[9,145,153,206,227],"which":[10],"target":[12,73,133],"is":[14,184,203],"regulated":[15],"by":[16],"gate":[19,114,141],"among":[20,64,91,213],"its":[21],"regulators.":[22],"While":[23],"various":[24],"computational":[25],"techniques":[26],"are":[27,109,166,225,236],"developed":[28],"for":[29],"network":[33,209],"(GRN)":[34],"reconstruction,":[35],"the":[36,57,88,104,113,129,132,139,150,179,182,208,228],"study":[37],"of":[38,94,131,171,223],"logical":[39,211],"relationships":[40,212],"has":[41],"received":[42],"little":[43],"attention.":[44],"Here,":[45],"we":[46],"propose":[47],"novel":[49],"tool":[50],"called":[51],"wpLogicNet":[52,82,102,148,202,224],"that":[53,70,108,196],"simultaneously":[54],"infers":[55],"both":[56],"directed":[58],"GRN":[59],"structures":[60],"and":[61,136,190,210,220],"gates":[63,90,152,165],"genes":[65,117],"or":[66,118,155],"transcription":[67],"factors":[68],"(TFs)":[69],"regulate":[71],"their":[72],"genes,":[74],"based":[75],"on":[76,168,186],"continuous":[77],"steady-state":[78],"expressions.":[80],"RESULTS:":[81],"proposes":[83],"framework":[85],"to":[86,111,127,137,198],"infer":[87,138],"any":[92],"number":[93],"regulators,":[95],"with":[96,159],"low":[98],"time-complexity.":[99],"This":[100],"distinguishes":[101],"from":[103,175,188],"existing":[105],"logic-based":[106],"models":[107],"limited":[110],"inferring":[112],"between":[115],"two":[116],"TFs.":[119],"Our":[120],"method":[121,183],"applies":[122],"Bayesian":[124],"mixture":[125],"model":[126],"estimate":[128],"likelihood":[130],"profile":[135],"posteriori.":[143],"Furthermore,":[144],"structure-aware":[146],"mode,":[147],"reconstructs":[149],"TF-gene":[154,172],"gene-gene":[156],"interaction":[157,173],"networks":[158,174],"known":[160],"structures.":[161],"predicted":[163],"validated":[167,185],"simulated":[169],"datasets":[170,187,219],"Escherichia":[176],"coli.":[177],"For":[178],"directed-edge":[180],"inference,":[181],"E.coli":[189],"DREAM":[191],"project.":[192],"results":[194],"show":[195],"compared":[197],"other":[199],"well-known":[200],"methods,":[201],"more":[204],"precise":[205],"reconstructing":[207],"genes.":[214],"AVAILABILITY":[215],"AND":[216],"IMPLEMENTATION:":[217],"R":[221],"package":[222],"available":[226,237],"github":[229],"repository,":[230],"https://github.com/CompBioIPM/wpLogicNet.":[231],"SUPPLEMENTARY":[232],"INFORMATION:":[233],"Supplementary":[234],"data":[235],"at":[238],"Bioinformatics":[239],"online.":[240]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":1}],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2025-10-10T00:00:00"}
