{"id":"https://openalex.org/W2981478121","doi":"https://doi.org/10.1109/tcbb.2019.2949039","title":"Time-Varying Differential Network Analysis for Revealing Network Rewiring over Cancer Progression","display_name":"Time-Varying Differential Network Analysis for Revealing Network Rewiring over Cancer Progression","publication_year":2019,"publication_date":"2019-10-23","ids":{"openalex":"https://openalex.org/W2981478121","doi":"https://doi.org/10.1109/tcbb.2019.2949039","mag":"2981478121","pmid":"https://pubmed.ncbi.nlm.nih.gov/31647444"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2019.2949039","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2019.2949039","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/A5103178673","display_name":"Ting Xu","orcid":"https://orcid.org/0000-0002-6843-5663"},"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":"Ting Xu","raw_affiliation_strings":["School of Mathematics and Statistics, Central China Normal University, Wuhan, China"],"raw_orcid":null,"affiliations":[{"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":["Guangdong Key Laboratory of Intelligent Information Processing and Shenzhen Key Laboratory of Media Security, Shenzhen University, Shenzhen, China"],"raw_orcid":"https://orcid.org/0000-0003-4007-4568","affiliations":[{"raw_affiliation_string":"Guangdong Key Laboratory of Intelligent Information Processing and Shenzhen Key Laboratory of Media Security, Shenzhen University, Shenzhen, China","institution_ids":["https://openalex.org/I180726961"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100644375","display_name":"Hong Yan","orcid":"https://orcid.org/0000-0001-9661-3095"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Hong Yan","raw_affiliation_strings":["Department of Electrical Engineering, City University of Hong Kong, Hong Kong, China"],"raw_orcid":"https://orcid.org/0000-0001-9661-3095","affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering, City University of Hong Kong, Hong Kong, China","institution_ids":["https://openalex.org/I168719708"]}]},{"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, Central China Normal University, Wuhan, China"],"raw_orcid":"https://orcid.org/0000-0002-5052-9725","affiliations":[{"raw_affiliation_string":"School of Mathematics and Statistics, 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":0.4554,"has_fulltext":false,"cited_by_count":10,"citation_normalized_percentile":{"value":0.60960727,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"18","issue":"4","first_page":"1632","last_page":"1642"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9988999962806702,"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":0.9984999895095825,"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":0.586554765701294},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.5595709085464478},{"id":"https://openalex.org/keywords/differential","display_name":"Differential (mechanical device)","score":0.5423922538757324},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3206559419631958},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.28107866644859314},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2791300415992737},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.14888814091682434},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.0941067636013031}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.586554765701294},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.5595709085464478},{"id":"https://openalex.org/C93226319","wikidata":"https://www.wikidata.org/wiki/Q193137","display_name":"Differential (mechanical device)","level":2,"score":0.5423922538757324},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3206559419631958},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.28107866644859314},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2791300415992737},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.14888814091682434},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0941067636013031},{"id":"https://openalex.org/C146978453","wikidata":"https://www.wikidata.org/wiki/Q3798668","display_name":"Aerospace engineering","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","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":"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":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":true},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016011","descriptor_name":"Normal Distribution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016011","descriptor_name":"Normal Distribution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016011","descriptor_name":"Normal Distribution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018450","descriptor_name":"Disease Progression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018450","descriptor_name":"Disease Progression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018450","descriptor_name":"Disease Progression","qualifier_ui":null,"qualifier_name":null,"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":"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.2019.2949039","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2019.2949039","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:31647444","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31647444","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":[{"id":"https://metadata.un.org/sdg/3","score":0.6299999952316284,"display_name":"Good health and well-being"}],"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/G500467270","display_name":null,"funder_award_id":"CCNU18TS026","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G549144630","display_name":null,"funder_award_id":"2019A1515011384","funder_id":"https://openalex.org/F4320337111","funder_display_name":"Basic and Applied Basic Research Foundation of Guangdong Province"},{"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},{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null},{"id":"https://openalex.org/F4320337111","display_name":"Basic and Applied Basic Research Foundation of Guangdong Province","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":51,"referenced_works":["https://openalex.org/W3219084","https://openalex.org/W765497804","https://openalex.org/W1497745584","https://openalex.org/W1987939948","https://openalex.org/W2010824638","https://openalex.org/W2014571900","https://openalex.org/W2019306466","https://openalex.org/W2030391580","https://openalex.org/W2033322043","https://openalex.org/W2047031939","https://openalex.org/W2062533676","https://openalex.org/W2074605890","https://openalex.org/W2081746825","https://openalex.org/W2096283457","https://openalex.org/W2108156593","https://openalex.org/W2109907994","https://openalex.org/W2134602357","https://openalex.org/W2136426251","https://openalex.org/W2138178479","https://openalex.org/W2152482800","https://openalex.org/W2155205047","https://openalex.org/W2159482845","https://openalex.org/W2163702333","https://openalex.org/W2165009258","https://openalex.org/W2347110697","https://openalex.org/W2465098683","https://openalex.org/W2524076512","https://openalex.org/W2553094489","https://openalex.org/W2604751662","https://openalex.org/W2607356028","https://openalex.org/W2621059596","https://openalex.org/W2777527666","https://openalex.org/W2793711594","https://openalex.org/W2862690536","https://openalex.org/W2899400513","https://openalex.org/W2913535645","https://openalex.org/W2913868028","https://openalex.org/W2950225911","https://openalex.org/W2963269830","https://openalex.org/W3098834468","https://openalex.org/W3103144163","https://openalex.org/W4244393449","https://openalex.org/W4294216483","https://openalex.org/W4301588852","https://openalex.org/W6600126799","https://openalex.org/W6629935912","https://openalex.org/W6676181923","https://openalex.org/W6679981094","https://openalex.org/W6679988015","https://openalex.org/W6684098844","https://openalex.org/W6684415991"],"related_works":["https://openalex.org/W2348097614","https://openalex.org/W2347219288","https://openalex.org/W2354822586","https://openalex.org/W2366221835","https://openalex.org/W3149424243","https://openalex.org/W2358841807","https://openalex.org/W2969723784","https://openalex.org/W3003389177","https://openalex.org/W1985899955","https://openalex.org/W2777527666"],"abstract_inverted_index":{"To":[0],"reveal":[1],"how":[2],"gene":[3,58,170],"regulatory":[4],"networks":[5,13,56,97,132,184],"change":[6],"over":[7,102,173],"cancer":[8,16,103,176],"development,":[9],"multiple":[10,94],"time-varying":[11,95],"differential":[12,45,55,70,78,96,113,131,141,183],"between":[14,76],"adjacent":[15],"stages":[17],"should":[18],"be":[19,27,38],"estimated":[20,182],"simultaneously.":[21],"Since":[22],"the":[23,30,74,112,124,134,181,191],"network":[24,100,171],"rewiring":[25,101,172],"may":[26,37],"driven":[28],"by":[29,43,129],"perturbation":[31],"of":[32,62,195],"certain":[33],"individual":[34,140],"genes,":[35],"there":[36],"some":[39],"hub":[40,126,136],"nodes":[41,127,137,179],"shared":[42,128],"these":[44],"networks.":[46,79,114,142],"Although":[47],"several":[48],"methods":[49],"have":[50],"been":[51],"developed":[52],"to":[53,91,110,122,139,162,168],"estimate":[54,93],"from":[57],"expression":[59],"data,":[60],"most":[61,155],"them":[63],"are":[64],"designed":[65,121],"for":[66,98],"estimating":[67],"a":[68,85],"single":[69],"network,":[71],"which":[72],"neglect":[73],"similarities":[75],"different":[77,130,174],"In":[80],"this":[81],"article,":[82],"we":[83],"propose":[84],"new":[86],"Gaussian":[87],"graphical":[88],"model-based":[89],"method":[90,149,161],"jointly":[92],"identifying":[99],"development.":[104],"A":[105,115],"D-trace":[106],"loss":[107],"is":[108,120],"used":[109],"determine":[111],"tree-structured":[116],"group":[117],"Lasso":[118],"penalty":[119],"identify":[123],"common":[125],"and":[133,193],"specific":[135],"unique":[138],"Simulation":[143],"experiment":[144],"results":[145],"demonstrate":[146],"that":[147],"our":[148,160],"outperforms":[150],"other":[151],"state-of-the-art":[152],"techniques":[153],"in":[154,180],"cases.":[156],"We":[157],"also":[158],"apply":[159],"The":[163],"Cancer":[164],"Genome":[165],"Atlas":[166],"data":[167],"explore":[169],"breast":[175,196],"stages.":[177],"Hub":[178],"rediscover":[185],"well":[186],"known":[187],"genes":[188],"associated":[189],"with":[190],"development":[192],"progression":[194],"cancer.":[197]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"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"}
