{"id":"https://openalex.org/W2093072756","doi":"https://doi.org/10.1109/bibm.2013.6732484","title":"Inference of gene regulatory networks by integrating gene expressions and genetic perturbations","display_name":"Inference of gene regulatory networks by integrating gene expressions and genetic perturbations","publication_year":2013,"publication_date":"2013-12-01","ids":{"openalex":"https://openalex.org/W2093072756","doi":"https://doi.org/10.1109/bibm.2013.6732484","mag":"2093072756"},"language":"en","primary_location":{"id":"doi:10.1109/bibm.2013.6732484","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2013.6732484","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2013 IEEE International Conference on Bioinformatics and Biomedicine","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5080215015","display_name":"Dongchul Kim","orcid":"https://orcid.org/0000-0002-5659-1394"},"institutions":[{"id":"https://openalex.org/I189196454","display_name":"The University of Texas at Arlington","ror":"https://ror.org/019kgqr73","country_code":"US","type":"education","lineage":["https://openalex.org/I189196454"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dong-Chul Kim","raw_affiliation_strings":["Department of Computer Science and Engineering University of Texas at Arlington, Arlington, TX 76019, USA","[Department of Computer Science & Engineering, University of Texas at Arlington, Arlington, TX, USA]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering University of Texas at Arlington, Arlington, TX 76019, USA","institution_ids":["https://openalex.org/I189196454"]},{"raw_affiliation_string":"[Department of Computer Science & Engineering, University of Texas at Arlington, Arlington, TX, USA]","institution_ids":["https://openalex.org/I189196454"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100343306","display_name":"Chunyu Liu","orcid":"https://orcid.org/0000-0002-5986-4415"},"institutions":[{"id":"https://openalex.org/I39422238","display_name":"University of Illinois Chicago","ror":"https://ror.org/02mpq6x41","country_code":"US","type":"education","lineage":["https://openalex.org/I39422238"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chunyu Liu","raw_affiliation_strings":["Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 66012, USA","Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 66012, USA","institution_ids":["https://openalex.org/I39422238"]},{"raw_affiliation_string":"Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA;","institution_ids":["https://openalex.org/I39422238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073760358","display_name":"Xiaoyong Wu","orcid":"https://orcid.org/0000-0001-7190-2253"},"institutions":[{"id":"https://openalex.org/I15062923","display_name":"Tianjin Normal University","ror":"https://ror.org/05x2td559","country_code":"CN","type":"education","lineage":["https://openalex.org/I15062923"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaoyong Wu","raw_affiliation_strings":["College of Electronic and Communication Engineering, Tianjin Normal University, Tianjin, China 300387","College of Electron and Communication Engineering, Tianjin Normal University, Tianjin, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Electronic and Communication Engineering, Tianjin Normal University, Tianjin, China 300387","institution_ids":["https://openalex.org/I15062923"]},{"raw_affiliation_string":"College of Electron and Communication Engineering, Tianjin Normal University, Tianjin, China","institution_ids":["https://openalex.org/I15062923"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034763948","display_name":"Baoju Zhang","orcid":"https://orcid.org/0000-0002-1435-7401"},"institutions":[{"id":"https://openalex.org/I15062923","display_name":"Tianjin Normal University","ror":"https://ror.org/05x2td559","country_code":"CN","type":"education","lineage":["https://openalex.org/I15062923"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Baoju Zhang","raw_affiliation_strings":["College of Electronic and Communication Engineering, Tianjin Normal University, Tianjin, China 300387","College of Electron and Communication Engineering, Tianjin Normal University, Tianjin, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Electronic and Communication Engineering, Tianjin Normal University, Tianjin, China 300387","institution_ids":["https://openalex.org/I15062923"]},{"raw_affiliation_string":"College of Electron and Communication Engineering, Tianjin Normal University, Tianjin, China","institution_ids":["https://openalex.org/I15062923"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5015128288","display_name":"Jean Gao","orcid":"https://orcid.org/0000-0002-9077-7803"},"institutions":[{"id":"https://openalex.org/I189196454","display_name":"The University of Texas at Arlington","ror":"https://ror.org/019kgqr73","country_code":"US","type":"education","lineage":["https://openalex.org/I189196454"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jean Gao","raw_affiliation_strings":["Department of Computer Science and Engineering University of Texas at Arlington, Arlington, TX 76019, USA","[Department of Computer Science & Engineering, University of Texas at Arlington, Arlington, TX, USA]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering University of Texas at Arlington, Arlington, TX 76019, USA","institution_ids":["https://openalex.org/I189196454"]},{"raw_affiliation_string":"[Department of Computer Science & Engineering, University of Texas at Arlington, Arlington, TX, USA]","institution_ids":["https://openalex.org/I189196454"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.11528313,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":null,"issue":null,"first_page":"182","last_page":"187"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11468","display_name":"Genetic Mapping and Diversity in Plants and Animals","score":0.9987000226974487,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T11468","display_name":"Genetic Mapping and Diversity in Plants and Animals","score":0.9987000226974487,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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":0.9973000288009644,"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/T10594","display_name":"Genetic and phenotypic traits in livestock","score":0.9961000084877014,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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":0.710529088973999},{"id":"https://openalex.org/keywords/lasso","display_name":"Lasso (programming language)","score":0.6528058052062988},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.6150336265563965},{"id":"https://openalex.org/keywords/regression","display_name":"Regression","score":0.5506946444511414},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5429903864860535},{"id":"https://openalex.org/keywords/expression-quantitative-trait-loci","display_name":"Expression quantitative trait loci","score":0.5159435868263245},{"id":"https://openalex.org/keywords/elastic-net-regularization","display_name":"Elastic net regularization","score":0.49335137009620667},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.45938044786453247},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3942483365535736},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3373214304447174},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3339947760105133},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3208836317062378},{"id":"https://openalex.org/keywords/single-nucleotide-polymorphism","display_name":"Single-nucleotide polymorphism","score":0.31865182518959045},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.28700220584869385},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2647727131843567},{"id":"https://openalex.org/keywords/feature-selection","display_name":"Feature selection","score":0.2202184498310089},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.21859070658683777},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1925012469291687}],"concepts":[{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.710529088973999},{"id":"https://openalex.org/C37616216","wikidata":"https://www.wikidata.org/wiki/Q3218363","display_name":"Lasso (programming language)","level":2,"score":0.6528058052062988},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.6150336265563965},{"id":"https://openalex.org/C83546350","wikidata":"https://www.wikidata.org/wiki/Q1139051","display_name":"Regression","level":2,"score":0.5506946444511414},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5429903864860535},{"id":"https://openalex.org/C168393362","wikidata":"https://www.wikidata.org/wiki/Q5421706","display_name":"Expression quantitative trait loci","level":5,"score":0.5159435868263245},{"id":"https://openalex.org/C203868755","wikidata":"https://www.wikidata.org/wiki/Q5353562","display_name":"Elastic net regularization","level":3,"score":0.49335137009620667},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.45938044786453247},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3942483365535736},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3373214304447174},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3339947760105133},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3208836317062378},{"id":"https://openalex.org/C153209595","wikidata":"https://www.wikidata.org/wiki/Q501128","display_name":"Single-nucleotide polymorphism","level":4,"score":0.31865182518959045},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.28700220584869385},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2647727131843567},{"id":"https://openalex.org/C148483581","wikidata":"https://www.wikidata.org/wiki/Q446488","display_name":"Feature selection","level":2,"score":0.2202184498310089},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.21859070658683777},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1925012469291687},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.0},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm.2013.6732484","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2013.6732484","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2013 IEEE International Conference on Bioinformatics and Biomedicine","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":24,"referenced_works":["https://openalex.org/W1990514789","https://openalex.org/W2037069407","https://openalex.org/W2047028564","https://openalex.org/W2050559302","https://openalex.org/W2055234679","https://openalex.org/W2057536311","https://openalex.org/W2063928888","https://openalex.org/W2068497484","https://openalex.org/W2074693857","https://openalex.org/W2106287359","https://openalex.org/W2108069662","https://openalex.org/W2108120899","https://openalex.org/W2109384743","https://openalex.org/W2110556769","https://openalex.org/W2114382052","https://openalex.org/W2115078845","https://openalex.org/W2119862467","https://openalex.org/W2122796918","https://openalex.org/W2122825543","https://openalex.org/W2124999415","https://openalex.org/W2129651180","https://openalex.org/W2135046866","https://openalex.org/W2148460690","https://openalex.org/W4234698323"],"related_works":["https://openalex.org/W2468272465","https://openalex.org/W2429564919","https://openalex.org/W757986597","https://openalex.org/W4212910148","https://openalex.org/W4210804200","https://openalex.org/W4213314600","https://openalex.org/W4285814086","https://openalex.org/W3123944750","https://openalex.org/W2787225985","https://openalex.org/W3155171010"],"abstract_inverted_index":{"To":[0,168],"elucidate":[1],"the":[2,28,31,111,160,170,172,183,206,211,216,224,227,270],"overall":[3],"relationships":[4],"between":[5],"gene":[6,19,118,212],"expressions":[7],"and":[8,73,104,142,186,215],"genetic":[9],"perturbations,":[10],"many":[11,136],"approaches":[12],"for":[13,67],"SNPs":[14,74],"to":[15,63,129,159,176,193,258],"be":[16],"involved":[17],"in":[18,202,223],"regulatory":[20,213],"network":[21,59],"(GRNs)":[22],"inference":[23,214,264],"have":[24],"been":[25],"suggested.":[26],"In":[27,61,110],"most":[29],"of":[30,33,43,71,94,218,235],"inferences":[32],"networks":[34,185],"named":[35],"as":[36,135,140,244,246],"SNP-Gene":[37],"Regulatory":[38],"Networks":[39],"(SGRNs)":[40],"inference,":[41,112],"pairs":[42],"SNP-gene":[44],"are":[45,55,128,147,198],"still":[46],"separately":[47],"given":[48,69],"by":[49,149,255,277],"performing":[50],"eQTL":[51,77,219,266],"mappings":[52],"but":[53],"eQTLs":[54,275],"not":[56],"identified":[57,276],"during":[58],"constructions.":[60],"order":[62],"build":[64],"a":[65,68,81,87,120],"SGRN":[66],"set":[70],"genes":[72,222],"without":[75,265],"pre-defined":[76],"information,":[78],"we":[79],"propose":[80],"method":[82,92,173,189,208],"that":[83,116,154,178,220,231,262,272],"is":[84,114,165,174,179,190,253],"based":[85],"on":[86],"structural":[88],"equation":[89],"model.":[90],"The":[91,124,188],"consists":[93],"three":[95,199],"steps:":[96],"(i)":[97],"ridge":[98],"regression,":[99,103],"(ii)":[100],"elastic":[101],"net":[102],"(iii)":[105],"iterative":[106,150],"adaptive":[107,151],"lasso":[108,152],"regression.":[109],"it":[113,252,257],"assumed":[115],"each":[117],"has":[119],"single":[121],"unknown":[122],"eQTL.":[123],"first":[125],"two":[126],"steps":[127],"remove":[130],"false":[131,248],"positive":[132,138,249],"edges":[133,139,146,243],"keeping":[134],"true":[137,242],"possible,":[141],"then":[143],"lastly,":[144],"final":[145],"selected":[148],"regression":[153,237],"iteratively":[155],"gives":[156],"more":[157],"weight":[158],"edge":[161],"whose":[162],"coefficient":[163],"value":[164],"relatively":[166],"high.":[167],"evaluate":[169],"performance,":[171],"applied":[175,192],"data":[177,261],"randomly":[180],"generated":[181],"from":[182],"simulated":[184],"parameters.":[187],"also":[191],"psychiatric":[194,259],"disorder":[195,260],"data.":[196],"There":[197],"main":[200],"contributions":[201],"this":[203],"work.":[204,280],"First,":[205],"proposed":[207],"provides":[209],"both":[210],"identification":[217],"affect":[221],"network.":[225],"Second,":[226],"simulation":[228],"result":[229],"proves":[230],"an":[232],"integrative":[233],"approach":[234],"multiple":[236],"methods":[238],"can":[239,268],"effectively":[240],"detect":[241],"well":[245],"filter":[247],"edges.":[250],"Lastly,":[251],"demonstrated":[254],"applying":[256],"our":[263,278],"information":[267],"discover":[269],"SGRNs":[271],"partially":[273],"confirms":[274],"previous":[279]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
