{"id":"https://openalex.org/W2121600919","doi":"https://doi.org/10.1109/cibcb.2009.4925734","title":"Modeling oncology gene pathways network with multiple genotypes and phenotypes via a copula method","display_name":"Modeling oncology gene pathways network with multiple genotypes and phenotypes via a copula method","publication_year":2009,"publication_date":"2009-03-01","ids":{"openalex":"https://openalex.org/W2121600919","doi":"https://doi.org/10.1109/cibcb.2009.4925734","mag":"2121600919"},"language":"en","primary_location":{"id":"doi:10.1109/cibcb.2009.4925734","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cibcb.2009.4925734","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2009 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology","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/A5010808240","display_name":"Le Bao","orcid":"https://orcid.org/0000-0003-0191-5918"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Le Bao","raw_affiliation_strings":["Department of statistics, University of Washington, Seattle, WA, USA","Department of Statistics University of Washington Seattle WA 98195 USA"],"affiliations":[{"raw_affiliation_string":"Department of statistics, University of Washington, Seattle, WA, USA","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Department of Statistics University of Washington Seattle WA 98195 USA","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077097017","display_name":"Zhou Zhu","orcid":"https://orcid.org/0000-0002-0642-8919"},"institutions":[{"id":"https://openalex.org/I180857899","display_name":"Pfizer (United States)","ror":"https://ror.org/01xdqrp08","country_code":"US","type":"company","lineage":["https://openalex.org/I180857899"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhou Zhu","raw_affiliation_strings":["Structural and computational biology, Pfizer Global Research and Development, Pfizer, Inc., San Diego, CA, USA","Structural and computational biology, Pfizer Global Research and Development, Pfizer Inc., San Diego, CA 92121 USA"],"affiliations":[{"raw_affiliation_string":"Structural and computational biology, Pfizer Global Research and Development, Pfizer, Inc., San Diego, CA, USA","institution_ids":["https://openalex.org/I180857899"]},{"raw_affiliation_string":"Structural and computational biology, Pfizer Global Research and Development, Pfizer Inc., San Diego, CA 92121 USA","institution_ids":["https://openalex.org/I180857899"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101676263","display_name":"Jingjing Ye","orcid":"https://orcid.org/0009-0000-8906-4454"},"institutions":[{"id":"https://openalex.org/I180857899","display_name":"Pfizer (United States)","ror":"https://ror.org/01xdqrp08","country_code":"US","type":"company","lineage":["https://openalex.org/I180857899"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jingjing Ye","raw_affiliation_strings":["Global Non-clinical Statistics, Pfizer Global Research and Development, Pfizer, Inc., San Diego, CA, USA","Global Non-clinical Statistics, Pfizer Global Research and Development, Pfizer Inc., 10777 Science Center Drive, San Diego, CA 92121 USA"],"affiliations":[{"raw_affiliation_string":"Global Non-clinical Statistics, Pfizer Global Research and Development, Pfizer, Inc., San Diego, CA, USA","institution_ids":["https://openalex.org/I180857899"]},{"raw_affiliation_string":"Global Non-clinical Statistics, Pfizer Global Research and Development, Pfizer Inc., 10777 Science Center Drive, San Diego, CA 92121 USA","institution_ids":["https://openalex.org/I180857899"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5010808240"],"corresponding_institution_ids":["https://openalex.org/I201448701"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.14760612,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"24","issue":null,"first_page":"237","last_page":"246"},"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/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/T10885","display_name":"Gene expression and cancer classification","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"}}],"keywords":[{"id":"https://openalex.org/keywords/phenotype","display_name":"Phenotype","score":0.6449463367462158},{"id":"https://openalex.org/keywords/copula","display_name":"Copula (linguistics)","score":0.637722909450531},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6353618502616882},{"id":"https://openalex.org/keywords/bivariate-analysis","display_name":"Bivariate analysis","score":0.5417450666427612},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5268572568893433},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.4706615209579468},{"id":"https://openalex.org/keywords/correlation","display_name":"Correlation","score":0.43513625860214233},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.4148298501968384},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4047454595565796},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.36945194005966187},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3224989175796509},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.22580784559249878},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.20547270774841309},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.18439358472824097},{"id":"https://openalex.org/keywords/econometrics","display_name":"Econometrics","score":0.17901292443275452},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.14981892704963684}],"concepts":[{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.6449463367462158},{"id":"https://openalex.org/C17618745","wikidata":"https://www.wikidata.org/wiki/Q207509","display_name":"Copula (linguistics)","level":2,"score":0.637722909450531},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6353618502616882},{"id":"https://openalex.org/C64341305","wikidata":"https://www.wikidata.org/wiki/Q4919225","display_name":"Bivariate analysis","level":2,"score":0.5417450666427612},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5268572568893433},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.4706615209579468},{"id":"https://openalex.org/C117220453","wikidata":"https://www.wikidata.org/wiki/Q5172842","display_name":"Correlation","level":2,"score":0.43513625860214233},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.4148298501968384},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4047454595565796},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.36945194005966187},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3224989175796509},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.22580784559249878},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.20547270774841309},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.18439358472824097},{"id":"https://openalex.org/C149782125","wikidata":"https://www.wikidata.org/wiki/Q160039","display_name":"Econometrics","level":1,"score":0.17901292443275452},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.14981892704963684},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/cibcb.2009.4925734","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cibcb.2009.4925734","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2009 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Good health and well-being","score":0.7799999713897705,"id":"https://metadata.un.org/sdg/3"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":47,"referenced_works":["https://openalex.org/W105785986","https://openalex.org/W129960861","https://openalex.org/W1542184596","https://openalex.org/W1588879036","https://openalex.org/W1590120741","https://openalex.org/W1673730923","https://openalex.org/W1969248194","https://openalex.org/W1969512609","https://openalex.org/W1980669461","https://openalex.org/W1989076816","https://openalex.org/W1990860515","https://openalex.org/W1991718539","https://openalex.org/W1992535794","https://openalex.org/W2028425429","https://openalex.org/W2033472199","https://openalex.org/W2042557026","https://openalex.org/W2049910743","https://openalex.org/W2052721939","https://openalex.org/W2058451329","https://openalex.org/W2070612147","https://openalex.org/W2078483536","https://openalex.org/W2082543204","https://openalex.org/W2088358109","https://openalex.org/W2093223772","https://openalex.org/W2111476798","https://openalex.org/W2113979998","https://openalex.org/W2114936864","https://openalex.org/W2116063398","https://openalex.org/W2117492258","https://openalex.org/W2119436275","https://openalex.org/W2123106337","https://openalex.org/W2130410032","https://openalex.org/W2134586291","https://openalex.org/W2145402497","https://openalex.org/W2148534890","https://openalex.org/W2151967815","https://openalex.org/W2163188200","https://openalex.org/W2167119716","https://openalex.org/W2168322240","https://openalex.org/W2170414736","https://openalex.org/W4241861175","https://openalex.org/W4249731213","https://openalex.org/W4302412750","https://openalex.org/W4389331059","https://openalex.org/W6637131211","https://openalex.org/W6845473283","https://openalex.org/W6858935255"],"related_works":["https://openalex.org/W2990837948","https://openalex.org/W3127236696","https://openalex.org/W2202466617","https://openalex.org/W2080551413","https://openalex.org/W2756923888","https://openalex.org/W2767176313","https://openalex.org/W4287838929","https://openalex.org/W2359012312","https://openalex.org/W2800558361","https://openalex.org/W3177005804"],"abstract_inverted_index":{"Identification":[0],"of":[1,22,39,69,98,127,136],"interactions":[2,60],"between":[3],"molecular":[4,51,128],"features":[5,129],"(e.g.":[6],"mutation,":[7],"gene":[8],"expression":[9],"change)":[10],"and":[11,16,66,87,111],"gross":[12],"phenotypes":[13,88],"in":[14,26],"diseases":[15],"other":[17],"biological":[18],"processes":[19],"is":[20,46,54,80,101,109,142],"one":[21],"the":[23,70,99,107,114,134],"important":[24],"challenges":[25],"genomic":[27],"research.":[28],"Popular":[29],"approaches":[30],"such":[31],"as":[32,133],"GSEA":[33],"are":[34],"limited":[35],"to":[36,82,89,144,156],"hypothesis":[37],"tests":[38],"bivariate":[40],"association.":[41],"However,":[42],"a":[43,63,76,146],"specific":[44],"phenotype":[45],"often":[47],"dependent":[48],"upon":[49],"multiple":[50],"features.":[52],"It":[53],"thus":[55],"worth":[56],"considering":[57],"all":[58],"possible":[59],"jointly":[61,83,131],"for":[62,96,113],"more":[64],"precise":[65],"realistic":[67],"representation":[68],"cellular":[71],"network.":[72],"In":[73],"this":[74,91],"article,":[75],"semiparametric":[77],"copula":[78,140],"model":[79,84,141],"developed":[81],"genotypes,":[85],"pathways":[86],"accomplish":[90],"object.":[92],"A":[93],"two-step":[94],"procedure":[95],"reconstruction":[97],"network":[100,115],"described.":[102],"Simulation":[103],"studies":[104],"indicate":[105],"that":[106,130],"method":[108],"effective":[110],"accurate":[112],"reconstruction.":[116],"Application":[117],"using":[118],"NCI60":[119],"cancer":[120,154],"cell":[121],"line":[122],"data":[123],"identifies":[124],"several":[125],"subsets":[126],"perform":[132],"predictors":[135],"clinical":[137],"phenotypes.":[138],"The":[139],"expected":[143],"have":[145],"broad":[147],"impact":[148],"on":[149],"biomedical":[150],"research,":[151],"ranging":[152],"from":[153],"treatment":[155],"disease":[157],"prevention.":[158]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2018,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
