{"id":"https://openalex.org/W2799474655","doi":"https://doi.org/10.1109/tcbb.2018.2834529","title":"Inferring Gene Network Rewiring by Combining Gene Expression and Gene Mutation Data","display_name":"Inferring Gene Network Rewiring by Combining Gene Expression and Gene Mutation Data","publication_year":2018,"publication_date":"2018-05-09","ids":{"openalex":"https://openalex.org/W2799474655","doi":"https://doi.org/10.1109/tcbb.2018.2834529","mag":"2799474655","pmid":"https://pubmed.ncbi.nlm.nih.gov/29993891"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2018.2834529","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2018.2834529","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","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/A5059809364","display_name":"Jia-Juan Tu","orcid":"https://orcid.org/0000-0002-7912-6030"},"institutions":[{"id":"https://openalex.org/I40963666","display_name":"Central China Normal University","ror":"https://ror.org/03x1jna21","country_code":"CN","type":"education","lineage":["https://openalex.org/I40963666"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jia-Juan Tu","raw_affiliation_strings":["Central China Normal University, Wuhan, China","School of Mathematics and Statistics, Central China Normal University, Wuhan, China"],"raw_orcid":"https://orcid.org/0000-0002-7912-6030","affiliations":[{"raw_affiliation_string":"Central China Normal University, Wuhan, China","institution_ids":["https://openalex.org/I40963666"]},{"raw_affiliation_string":"School of Mathematics and Statistics, Central China Normal University, Wuhan, China","institution_ids":["https://openalex.org/I40963666"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030129372","display_name":"Le Ou-Yang","orcid":"https://orcid.org/0000-0003-4007-4568"},"institutions":[{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Le Ou-Yang","raw_affiliation_strings":["Shenzhen University, Shenzhen, China","College of Information Engineering, Shenzhen University, Shenzhen, China"],"raw_orcid":"https://orcid.org/0000-0003-4007-4568","affiliations":[{"raw_affiliation_string":"Shenzhen University, Shenzhen, China","institution_ids":["https://openalex.org/I180726961"]},{"raw_affiliation_string":"College of Information Engineering, Shenzhen University, Shenzhen, China","institution_ids":["https://openalex.org/I180726961"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101569679","display_name":"Xiaohua Hu","orcid":"https://orcid.org/0000-0002-4777-3022"},"institutions":[{"id":"https://openalex.org/I40963666","display_name":"Central China Normal University","ror":"https://ror.org/03x1jna21","country_code":"CN","type":"education","lineage":["https://openalex.org/I40963666"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaohua Hu","raw_affiliation_strings":["Central China Normal University, Wuhan, China","School of Computer, Central China Normal University, Wuhan, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Central China Normal University, Wuhan, China","institution_ids":["https://openalex.org/I40963666"]},{"raw_affiliation_string":"School of Computer, Central China Normal University, Wuhan, China","institution_ids":["https://openalex.org/I40963666"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100447043","display_name":"Xiao-Fei Zhang","orcid":"https://orcid.org/0000-0002-5052-9725"},"institutions":[{"id":"https://openalex.org/I40963666","display_name":"Central China Normal University","ror":"https://ror.org/03x1jna21","country_code":"CN","type":"education","lineage":["https://openalex.org/I40963666"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiao-Fei Zhang","raw_affiliation_strings":["Central China Normal University, Wuhan, China","School of Mathematics and Statistics, Central China Normal University, Wuhan, China"],"raw_orcid":"https://orcid.org/0000-0002-5052-9725","affiliations":[{"raw_affiliation_string":"Central China Normal University, Wuhan, China","institution_ids":["https://openalex.org/I40963666"]},{"raw_affiliation_string":"School of Mathematics and Statistics, Central China Normal University, Wuhan, China","institution_ids":["https://openalex.org/I40963666"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.3299,"has_fulltext":false,"cited_by_count":9,"citation_normalized_percentile":{"value":0.55064765,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"16","issue":"3","first_page":"1042","last_page":"1048"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9993000030517578,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9993000030517578,"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":0.9944999814033508,"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/T10261","display_name":"Genetic Associations and Epidemiology","score":0.9882000088691711,"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/gene-regulatory-network","display_name":"Gene regulatory network","score":0.5979440212249756},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5446426868438721},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5439552664756775},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5157516002655029},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.47755345702171326},{"id":"https://openalex.org/keywords/data-type","display_name":"Data type","score":0.46816346049308777},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.41670069098472595},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.39315178990364075},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.33585864305496216},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.30485817790031433},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.14019456505775452}],"concepts":[{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.5979440212249756},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5446426868438721},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5439552664756775},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5157516002655029},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.47755345702171326},{"id":"https://openalex.org/C138958017","wikidata":"https://www.wikidata.org/wiki/Q190087","display_name":"Data type","level":2,"score":0.46816346049308777},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.41670069098472595},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.39315178990364075},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.33585864305496216},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.30485817790031433},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.14019456505775452},{"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":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":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D010051","descriptor_name":"Ovarian Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010051","descriptor_name":"Ovarian Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010051","descriptor_name":"Ovarian Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"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":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2018.2834529","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2018.2834529","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:29993891","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29993891","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":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.7400000095367432,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"awards":[{"id":"https://openalex.org/G4434048650","display_name":null,"funder_award_id":"61602309","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7534660035","display_name":null,"funder_award_id":"61402190","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8543904368","display_name":null,"funder_award_id":"61532008","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":73,"referenced_works":["https://openalex.org/W4952878","https://openalex.org/W1491541693","https://openalex.org/W1492765740","https://openalex.org/W1495663238","https://openalex.org/W1733915400","https://openalex.org/W1822971372","https://openalex.org/W1837170756","https://openalex.org/W1965055200","https://openalex.org/W1974105260","https://openalex.org/W1996344455","https://openalex.org/W2021556180","https://openalex.org/W2030391580","https://openalex.org/W2042101240","https://openalex.org/W2047031939","https://openalex.org/W2054596996","https://openalex.org/W2062533676","https://openalex.org/W2065799563","https://openalex.org/W2081746825","https://openalex.org/W2086443735","https://openalex.org/W2108156593","https://openalex.org/W2111900617","https://openalex.org/W2113328646","https://openalex.org/W2118089467","https://openalex.org/W2120340025","https://openalex.org/W2123696077","https://openalex.org/W2125631472","https://openalex.org/W2128208871","https://openalex.org/W2132555912","https://openalex.org/W2136526350","https://openalex.org/W2145657329","https://openalex.org/W2151199601","https://openalex.org/W2152482800","https://openalex.org/W2158485828","https://openalex.org/W2163487866","https://openalex.org/W2163702333","https://openalex.org/W2163707651","https://openalex.org/W2165009258","https://openalex.org/W2166794017","https://openalex.org/W2245213139","https://openalex.org/W2267413798","https://openalex.org/W2268996423","https://openalex.org/W2288659799","https://openalex.org/W2289922904","https://openalex.org/W2347110697","https://openalex.org/W2465098683","https://openalex.org/W2524076512","https://openalex.org/W2553094489","https://openalex.org/W2604161816","https://openalex.org/W2604751662","https://openalex.org/W2607356028","https://openalex.org/W2621059596","https://openalex.org/W2624945631","https://openalex.org/W2777527666","https://openalex.org/W2913535645","https://openalex.org/W2950225911","https://openalex.org/W2963001078","https://openalex.org/W2963269830","https://openalex.org/W3098888484","https://openalex.org/W3105034597","https://openalex.org/W3106319742","https://openalex.org/W4244393449","https://openalex.org/W4293052541","https://openalex.org/W4293471949","https://openalex.org/W4301588852","https://openalex.org/W4388323202","https://openalex.org/W6676664377","https://openalex.org/W6684098844","https://openalex.org/W6684415991","https://openalex.org/W6693509263","https://openalex.org/W6717352481","https://openalex.org/W6747488457","https://openalex.org/W6786596762","https://openalex.org/W6844212664"],"related_works":["https://openalex.org/W2055243143","https://openalex.org/W4321636575","https://openalex.org/W1986418932","https://openalex.org/W2357796999","https://openalex.org/W2950199998","https://openalex.org/W2560421304","https://openalex.org/W2951387065","https://openalex.org/W2134575910","https://openalex.org/W4385727351","https://openalex.org/W4306798985"],"abstract_inverted_index":{"Gene":[0],"dependency":[1],"networks":[2,15,106,209],"often":[3],"undergo":[4],"changes":[5],"with":[6,174],"respect":[7],"to":[8,36,98,168,191,200],"different":[9,19,69,78,109,140],"disease":[10,20],"states.":[11],"Understanding":[12],"how":[13],"these":[14],"rewire":[16],"between":[17,104,139],"two":[18],"states":[21],"is":[22],"an":[23],"important":[24,215],"task":[25,39],"in":[26,206,217],"genomic":[27],"research.":[28],"Although":[29],"many":[30],"computational":[31],"methods":[32,95],"have":[33,153],"been":[34],"proposed":[35],"undertake":[37],"this":[38,113],"via":[40,145],"differential":[41,105,119,188,197,208],"network":[42,120,126,171],"analysis,":[43],"most":[44],"of":[45,57,91],"them":[46],"are":[47,96,143,186],"designed":[48],"for":[49],"a":[50,117,146],"predefined":[51],"data":[52,79,92,110,141,193,202],"type.":[53,93],"With":[54],"the":[55,58,100,160,207],"development":[56],"high":[59],"throughput":[60],"technologies,":[61],"gene":[62,125,130,133,170],"activity":[63],"measurements":[64],"can":[65],"be":[66],"collected":[67],"from":[68,108,179],"aspects":[70],"(e.g.,":[71],"mRNA":[72],"expression":[73,131],"and":[74,86,102,132,137,195],"DNA":[75],"mutation).":[76],"These":[77],"types":[80,142,194],"might":[81],"share":[82],"some":[83,196],"common":[84,190],"characteristics":[85],"include":[87],"certain":[88,187],"unique":[89,199],"properties":[90],"New":[94],"needed":[97],"explore":[99],"similarity":[101],"difference":[103],"estimated":[107],"types.":[111,203],"In":[112],"study,":[114],"we":[115],"develop":[116],"new":[118],"inference":[121],"model":[122],"which":[123],"identifies":[124],"rewiring":[127,172],"by":[128,211],"combining":[129],"mutation":[134],"data.":[135,184],"Similarities":[136],"differences":[138],"learned":[144],"group":[147],"bridge":[148],"penalty":[149],"function.":[150],"Simulation":[151],"studies":[152],"demonstrated":[154],"that":[155],"our":[156,166,212],"method":[157,167,213],"consistently":[158],"outperforms":[159],"competing":[161],"methods.":[162],"We":[163],"also":[164],"apply":[165],"identify":[169],"associated":[173],"ovarian":[175,218],"cancer":[176,219],"platinum":[177],"resistance":[178],"The":[180],"Cancer":[181],"Genome":[182],"Atlas":[183],"There":[185],"edges":[189,198],"both":[192],"individual":[201],"Hub":[204],"genes":[205],"inferred":[210],"play":[214],"roles":[216],"drug":[220],"resistance.":[221]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2}],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2025-10-10T00:00:00"}
