{"id":"https://openalex.org/W3094378225","doi":"https://doi.org/10.1093/bioinformatics/btaa902","title":"GNET2: an R package for constructing gene regulatory networks from transcriptomic data","display_name":"GNET2: an R package for constructing gene regulatory networks from transcriptomic data","publication_year":2020,"publication_date":"2020-10-08","ids":{"openalex":"https://openalex.org/W3094378225","doi":"https://doi.org/10.1093/bioinformatics/btaa902","mag":"3094378225","pmid":"https://pubmed.ncbi.nlm.nih.gov/33270838"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa902","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa902","pdf_url":null,"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":"green","oa_url":"https://www.osti.gov/biblio/1984728","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100418423","display_name":"Chen Chen","orcid":"https://orcid.org/0000-0002-2973-461X"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chen Chen","raw_affiliation_strings":["Electrical Engineering and Computer Science Department, University of Missouri , Columbia, MO 65211, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Electrical Engineering and Computer Science Department, University of Missouri , Columbia, MO 65211, USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022495891","display_name":"Jie Hou","orcid":"https://orcid.org/0000-0002-8584-5154"},"institutions":[{"id":"https://openalex.org/I47838141","display_name":"Saint Louis University","ror":"https://ror.org/01p7jjy08","country_code":"US","type":"education","lineage":["https://openalex.org/I47838141"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jie Hou","raw_affiliation_strings":["Department of Computer Science, Saint Louis University , St. Louis, MO 63103, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Saint Louis University , St. Louis, MO 63103, USA","institution_ids":["https://openalex.org/I47838141"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064189829","display_name":"Xiaowen Shi","orcid":"https://orcid.org/0000-0001-6532-4522"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiaowen Shi","raw_affiliation_strings":["Division of Biological Sciences, University of Missouri , Columbia, MO 65211, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Biological Sciences, University of Missouri , Columbia, MO 65211, USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015256862","display_name":"Hua Yang","orcid":"https://orcid.org/0000-0002-9796-5663"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hua Yang","raw_affiliation_strings":["Division of Biological Sciences, University of Missouri , Columbia, MO 65211, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Biological Sciences, University of Missouri , Columbia, MO 65211, USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039076657","display_name":"James A. Birchler","orcid":"https://orcid.org/0000-0003-3643-2756"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James A Birchler","raw_affiliation_strings":["Division of Biological Sciences, University of Missouri , Columbia, MO 65211, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Biological Sciences, University of Missouri , Columbia, MO 65211, USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5044354277","display_name":"Jianlin Cheng","orcid":"https://orcid.org/0000-0003-0305-2853"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jianlin Cheng","raw_affiliation_strings":["Electrical Engineering and Computer Science Department, University of Missouri , Columbia, MO 65211, USA"],"raw_orcid":"https://orcid.org/0000-0003-0305-2853","affiliations":[{"raw_affiliation_string":"Electrical Engineering and Computer Science Department, University of Missouri , Columbia, MO 65211, USA","institution_ids":["https://openalex.org/I76835614"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5044354277"],"corresponding_institution_ids":["https://openalex.org/I76835614"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":0.1498,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.461365,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"37","issue":"14","first_page":"2068","last_page":"2069"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9994999766349792,"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":0.9994999766349792,"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":0.9948999881744385,"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/T10878","display_name":"CRISPR and Genetic Engineering","score":0.9919000267982483,"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/computer-science","display_name":"Computer science","score":0.7732813954353333},{"id":"https://openalex.org/keywords/preprocessor","display_name":"Preprocessor","score":0.639335036277771},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.6065458059310913},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5259171724319458},{"id":"https://openalex.org/keywords/initialization","display_name":"Initialization","score":0.5177494883537292},{"id":"https://openalex.org/keywords/flexibility","display_name":"Flexibility (engineering)","score":0.48750922083854675},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4762316346168518},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.4657346308231354},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.42704036831855774},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4263855218887329},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.20596885681152344},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.19477176666259766},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.13708645105361938},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.09120851755142212}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7732813954353333},{"id":"https://openalex.org/C34736171","wikidata":"https://www.wikidata.org/wiki/Q918333","display_name":"Preprocessor","level":2,"score":0.639335036277771},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.6065458059310913},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5259171724319458},{"id":"https://openalex.org/C114466953","wikidata":"https://www.wikidata.org/wiki/Q6034165","display_name":"Initialization","level":2,"score":0.5177494883537292},{"id":"https://openalex.org/C2780598303","wikidata":"https://www.wikidata.org/wiki/Q65921492","display_name":"Flexibility (engineering)","level":2,"score":0.48750922083854675},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4762316346168518},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.4657346308231354},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.42704036831855774},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4263855218887329},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.20596885681152344},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.19477176666259766},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.13708645105361938},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.09120851755142212},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","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},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btaa902","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa902","pdf_url":null,"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:33270838","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33270838","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":"Journal Article"},{"id":"pmh:oai:osti.gov:1984728","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1984728","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:osti.gov:2278969","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/2278969","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:osti.gov:2318535","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/2318535","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"pmh:oai:osti.gov:1984728","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1984728","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure","score":0.5099999904632568}],"awards":[{"id":"https://openalex.org/G7437309148","display_name":"RESEARCH-PGR: Genomic Balance Analysis in Maize","funder_award_id":"1545780","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8702456827","display_name":"DEEP GREEN: STRUCTURAL AND FUNCTIONAL GENOMIC CHARACTERIZATION OF CONSERVED UNANNOTATED GREEN LINEAGE PROTEINS","funder_award_id":"DESC0020400","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":6,"referenced_works":["https://openalex.org/W1671207526","https://openalex.org/W2062029454","https://openalex.org/W2111064102","https://openalex.org/W2136409528","https://openalex.org/W2167190345","https://openalex.org/W2900569176"],"related_works":["https://openalex.org/W3204184292","https://openalex.org/W3176564347","https://openalex.org/W1985458517","https://openalex.org/W2355833770","https://openalex.org/W2950199998","https://openalex.org/W4249277012","https://openalex.org/W2560421304","https://openalex.org/W2951387065","https://openalex.org/W4385727351","https://openalex.org/W4306798985"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,25,90,128],"Gene":[2],"Network":[3],"Estimation":[4],"Tool":[5],"(GNET)":[6],"is":[7,96,133],"designed":[8],"to":[9,49],"build":[10],"gene":[11,17],"regulatory":[12,76,108],"networks":[13],"(GRNs)":[14],"from":[15,111],"transcriptomic":[16,112],"expression":[18],"data":[19,26,91,140],"with":[20],"a":[21,116],"probabilistic":[22],"graphical":[23],"model.":[24],"preprocessing,":[27],"model":[28],"construction":[29,78],"and":[30,51,75],"visualization":[31],"modules":[32],"of":[33,61,86,94,131],"the":[34,81,87,104],"original":[35,88],"GNET":[36,62],"software":[37],"were":[38,45],"developed":[39],"on":[40,80,122],"different":[41],"programming":[42],"platforms,":[43],"which":[44],"inconvenient":[46],"for":[47,72,107,119],"users":[48],"deploy":[50],"use.":[52],"RESULTS:":[53],"Here,":[54],"we":[55],"present":[56],"GNET2,":[57],"an":[58,64,99],"improved":[59],"implementation":[60],"as":[63],"integrated":[65],"R":[66,100],"package.":[67],"GNET2":[68,95,114,132],"provides":[69],"more":[70],"flexibility":[71],"parameter":[73],"initialization":[74],"module":[77],"based":[79],"core":[82],"iterative":[83],"modeling":[84],"process":[85],"algorithm.":[89],"exchange":[92],"interface":[93],"handled":[97],"within":[98],"session":[101],"automatically.":[102],"Given":[103],"growing":[105],"demand":[106],"network":[109],"reconstruction":[110],"data,":[113],"offers":[115],"convenient":[117],"option":[118],"GRN":[120],"inference":[121],"large":[123],"datasets.":[124],"AVAILABILITY":[125],"AND":[126],"IMPLEMENTATION:":[127],"source":[129],"code":[130],"available":[134,142],"at":[135,143],"https://github.com/jianlin-cheng/GNET2.":[136],"SUPPLEMENTARY":[137],"INFORMATION:":[138],"Supplementary":[139],"are":[141],"Bioinformatics":[144],"online.":[145]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2020-10-29T00:00:00"}
