{"id":"https://openalex.org/W2916122295","doi":"https://doi.org/10.1109/tcbb.2019.2901473","title":"Identifying Gene Network Rewiring Using Robust Differential Graphical Model with Multivariate t -Distribution","display_name":"Identifying Gene Network Rewiring Using Robust Differential Graphical Model with Multivariate t -Distribution","publication_year":2019,"publication_date":"2019-02-25","ids":{"openalex":"https://openalex.org/W2916122295","doi":"https://doi.org/10.1109/tcbb.2019.2901473","mag":"2916122295","pmid":"https://pubmed.ncbi.nlm.nih.gov/30802872"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2019.2901473","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2019.2901473","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/A5101849945","display_name":"Rui Yuan","orcid":"https://orcid.org/0000-0002-7869-3156"},"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":"Rui Yuan","raw_affiliation_strings":["School of Mathematics and Statistics & Hubei Key Laboratory of Mathematical Sciences, Central China Normal University, Wuhan, China"],"raw_orcid":"https://orcid.org/0000-0002-7869-3156","affiliations":[{"raw_affiliation_string":"School of Mathematics and Statistics & Hubei Key Laboratory of Mathematical Sciences, 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":["College of Information Engineering & Shenzhen Key Laboratory of Media Security, Shenzhen University, Shenzhen, China"],"raw_orcid":"https://orcid.org/0000-0003-4007-4568","affiliations":[{"raw_affiliation_string":"College of Information Engineering & Shenzhen Key Laboratory of Media Security, 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/I72816309","display_name":"Drexel University","ror":"https://ror.org/04bdffz58","country_code":"US","type":"education","lineage":["https://openalex.org/I72816309"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiaohua Hu","raw_affiliation_strings":["College of Computing & Informatics, Drexel University, Philadelphia, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computing & Informatics, Drexel University, Philadelphia, USA","institution_ids":["https://openalex.org/I72816309"]}]},{"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":["School of Mathematics and Statistics & Hubei Key Laboratory of Mathematical Sciences, Central China Normal University, Wuhan, China"],"raw_orcid":"https://orcid.org/0000-0002-5052-9725","affiliations":[{"raw_affiliation_string":"School of Mathematics and Statistics & Hubei Key Laboratory of Mathematical Sciences, Central China Normal University, Wuhan, China","institution_ids":["https://openalex.org/I40963666"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.3795,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.56491876,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"17","issue":"2","first_page":"712","last_page":"718"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","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/T10885","display_name":"Gene expression and cancer classification","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/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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9941999912261963,"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/multivariate-statistics","display_name":"Multivariate statistics","score":0.7560099363327026},{"id":"https://openalex.org/keywords/graphical-model","display_name":"Graphical model","score":0.6776013374328613},{"id":"https://openalex.org/keywords/differential","display_name":"Differential (mechanical device)","score":0.5537409782409668},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4448014497756958},{"id":"https://openalex.org/keywords/multivariate-analysis","display_name":"Multivariate analysis","score":0.410695344209671},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.37294647097587585},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.3485676050186157},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.34637224674224854},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.32385754585266113},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.26367124915122986},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.10981163382530212}],"concepts":[{"id":"https://openalex.org/C161584116","wikidata":"https://www.wikidata.org/wiki/Q1952580","display_name":"Multivariate statistics","level":2,"score":0.7560099363327026},{"id":"https://openalex.org/C155846161","wikidata":"https://www.wikidata.org/wiki/Q1143367","display_name":"Graphical model","level":2,"score":0.6776013374328613},{"id":"https://openalex.org/C93226319","wikidata":"https://www.wikidata.org/wiki/Q193137","display_name":"Differential (mechanical device)","level":2,"score":0.5537409782409668},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4448014497756958},{"id":"https://openalex.org/C38180746","wikidata":"https://www.wikidata.org/wiki/Q1952580","display_name":"Multivariate analysis","level":2,"score":0.410695344209671},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.37294647097587585},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.3485676050186157},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.34637224674224854},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32385754585266113},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.26367124915122986},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.10981163382530212},{"id":"https://openalex.org/C146978453","wikidata":"https://www.wikidata.org/wiki/Q3798668","display_name":"Aerospace engineering","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":"D001932","descriptor_name":"Brain Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001932","descriptor_name":"Brain Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001932","descriptor_name":"Brain Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D005909","descriptor_name":"Glioblastoma","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005909","descriptor_name":"Glioblastoma","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005909","descriptor_name":"Glioblastoma","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D015999","descriptor_name":"Multivariate Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015999","descriptor_name":"Multivariate Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015999","descriptor_name":"Multivariate Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2019.2901473","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2019.2901473","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:30802872","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30802872","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":[],"awards":[{"id":"https://openalex.org/G2101438006","display_name":null,"funder_award_id":"JCYJ20170817095210760","funder_id":"https://openalex.org/F4320329801","funder_display_name":"Shenzhen Research and Development Program"},{"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/G6771178980","display_name":null,"funder_award_id":"2018CFB521","funder_id":"https://openalex.org/F4320322186","funder_display_name":"Natural Science Foundation of Hubei Province"},{"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"},{"id":"https://openalex.org/G8657404496","display_name":"\u57fa\u4e8e\u7a00\u758f\u6982\u7387\u56fe\u6a21\u578b\u7684\u591a\u764c\u75c7\u591a\u7ec4\u5b66\u751f\u7269\u7f51\u7edc\u6784\u5efa\u65b9\u6cd5\u7814\u7a76","funder_award_id":"11871026","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"},{"id":"https://openalex.org/F4320322186","display_name":"Natural Science Foundation of Hubei Province","ror":null},{"id":"https://openalex.org/F4320329801","display_name":"Shenzhen Research and Development Program","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":66,"referenced_works":["https://openalex.org/W229097380","https://openalex.org/W1511986666","https://openalex.org/W1965055200","https://openalex.org/W1967186439","https://openalex.org/W1972382100","https://openalex.org/W1981409633","https://openalex.org/W1988263223","https://openalex.org/W2015696818","https://openalex.org/W2030391580","https://openalex.org/W2031947549","https://openalex.org/W2035278339","https://openalex.org/W2040847667","https://openalex.org/W2047031939","https://openalex.org/W2049633694","https://openalex.org/W2081746825","https://openalex.org/W2096283457","https://openalex.org/W2106465830","https://openalex.org/W2108156593","https://openalex.org/W2118089467","https://openalex.org/W2124005900","https://openalex.org/W2132555912","https://openalex.org/W2136422121","https://openalex.org/W2137892504","https://openalex.org/W2137971377","https://openalex.org/W2138156760","https://openalex.org/W2143970376","https://openalex.org/W2155205047","https://openalex.org/W2158602565","https://openalex.org/W2159482845","https://openalex.org/W2161289668","https://openalex.org/W2161884651","https://openalex.org/W2163516107","https://openalex.org/W2163702333","https://openalex.org/W2165009258","https://openalex.org/W2166794017","https://openalex.org/W2169583213","https://openalex.org/W2204770850","https://openalex.org/W2303176828","https://openalex.org/W2326655300","https://openalex.org/W2347110697","https://openalex.org/W2465098683","https://openalex.org/W2494631976","https://openalex.org/W2524076512","https://openalex.org/W2553094489","https://openalex.org/W2562162676","https://openalex.org/W2604751662","https://openalex.org/W2607356028","https://openalex.org/W2621059596","https://openalex.org/W2777527666","https://openalex.org/W2793711594","https://openalex.org/W2799474655","https://openalex.org/W2862690536","https://openalex.org/W2950225911","https://openalex.org/W2963269830","https://openalex.org/W3103354362","https://openalex.org/W4247458062","https://openalex.org/W4301260464","https://openalex.org/W4301588852","https://openalex.org/W4399549420","https://openalex.org/W6608852248","https://openalex.org/W6680464913","https://openalex.org/W6680564993","https://openalex.org/W6684098844","https://openalex.org/W6684415991","https://openalex.org/W6701664435","https://openalex.org/W6727689234"],"related_works":["https://openalex.org/W2406638334","https://openalex.org/W40745829","https://openalex.org/W4318262572","https://openalex.org/W1978357124","https://openalex.org/W1578824628","https://openalex.org/W2032728545","https://openalex.org/W1570805059","https://openalex.org/W4250754046","https://openalex.org/W4243682621","https://openalex.org/W2036849593"],"abstract_inverted_index":{"Identifying":[0],"gene":[1,34,68,149,162,178],"network":[2,35,69,150,163,179],"rewiring":[3,70,151,164,180],"under":[4],"different":[5],"biological":[6],"conditions":[7,73,113],"is":[8,82,107,144],"important":[9],"for":[10],"understanding":[11],"the":[12,22,25,38,46,76,88,101,116,126,139,166],"mechanisms":[13],"underlying":[14],"complex":[15],"diseases.":[16],"Gaussian":[17],"graphical":[18,64],"models,":[19],"which":[20,176],"assume":[21,40],"data":[23,47,133],"follow":[24],"multivariate":[26,77,80],"normal":[27,89],"distribution,":[28],"are":[29,48,181],"widely":[30],"used":[31,108],"to":[32,66,85,109,114,124,147],"identify":[33,67,148],"rewiring.":[36],"However,":[37],"normality":[39],"often":[41],"fails":[42],"in":[43,53],"reality":[44],"since":[45,91],"contaminated":[49],"by":[50],"extreme":[51],"outliers":[52,86],"general.":[54],"In":[55],"this":[56],"study,":[57],"we":[58],"propose":[59],"a":[60],"new":[61],"robust":[62,84],"differential":[63],"model":[65],"between":[71,152,165],"two":[72],"based":[74],"on":[75,131],"t-distribution.":[78],"The":[79],"t-distribution":[81],"more":[83],"than":[87],"distribution":[90],"it":[92],"has":[93],"heavy":[94],"tails":[95],"and":[96,155,161,168],"allows":[97],"values":[98],"far":[99],"from":[100],"mean.":[102],"A":[103,154],"fused":[104],"lasso":[105],"penalty":[106],"borrow":[110],"information":[111],"across":[112],"improve":[115],"results.":[117],"We":[118],"develop":[119],"an":[120],"expectation":[121],"maximization":[122],"algorithm":[123],"solve":[125],"optimization":[127],"model.":[128],"Experiment":[129],"results":[130],"simulated":[132],"show":[134],"that":[135],"our":[136],"method":[137,143],"outperforms":[138],"state-of-the-art":[140],"methods.":[141],"Our":[142],"also":[145],"applied":[146],"luminal":[153],"basal-like":[156],"subtypes":[157,170],"of":[158,171],"breast":[159],"cancer,":[160],"proneural":[167],"mesenchymal":[169],"glioblastoma.":[172],"Several":[173],"key":[174],"genes":[175],"drive":[177],"discovered.":[182]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":1}],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2025-10-10T00:00:00"}