{"id":"https://openalex.org/W2161503024","doi":"https://doi.org/10.1093/bioinformatics/btv653","title":"Evaluation of hierarchical models for integrative genomic analyses","display_name":"Evaluation of hierarchical models for integrative genomic analyses","publication_year":2015,"publication_date":"2015-11-05","ids":{"openalex":"https://openalex.org/W2161503024","doi":"https://doi.org/10.1093/bioinformatics/btv653","mag":"2161503024","pmid":"https://pubmed.ncbi.nlm.nih.gov/26545823"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btv653","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv653","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/5/738/25894147/btv653.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/32/5/738/25894147/btv653.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5026116157","display_name":"Marie Denis","orcid":"https://orcid.org/0000-0002-1693-9894"},"institutions":[{"id":"https://openalex.org/I131077856","display_name":"Centre de Coop\u00e9ration Internationale en Recherche Agronomique pour le D\u00e9veloppement","ror":"https://ror.org/05kpkpg04","country_code":"FR","type":"facility","lineage":["https://openalex.org/I131077856"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I4210120904","display_name":"Am\u00e9lioration G\u00e9n\u00e9tique et Adaptation des Plantes m\u00e9diterran\u00e9ennes et tropicales","ror":"https://ror.org/02w4exq36","country_code":"FR","type":"facility","lineage":["https://openalex.org/I131077856","https://openalex.org/I19894307","https://openalex.org/I24906876","https://openalex.org/I4210088668","https://openalex.org/I4210117091","https://openalex.org/I4210120904","https://openalex.org/I4399657933"]}],"countries":["FR","US"],"is_corresponding":true,"raw_author_name":"Marie Denis","raw_affiliation_strings":["1 UMR AGAP, CIRAD, Montpellier, France,","2 Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA and"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 UMR AGAP, CIRAD, Montpellier, France,","institution_ids":["https://openalex.org/I131077856","https://openalex.org/I4210120904"]},{"raw_affiliation_string":"2 Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA and","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5086793581","display_name":"Mahlet G. Tadesse","orcid":"https://orcid.org/0000-0003-2671-1663"},"institutions":[{"id":"https://openalex.org/I184565670","display_name":"Georgetown University","ror":"https://ror.org/05vzafd60","country_code":"US","type":"education","lineage":["https://openalex.org/I184565670"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Mahlet G. Tadesse","raw_affiliation_strings":["3 Department of Mathematics and Statistics, Georgetown University, Washington, DC, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"3 Department of Mathematics and Statistics, Georgetown University, Washington, DC, USA","institution_ids":["https://openalex.org/I184565670"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5026116157","https://openalex.org/A5086793581"],"corresponding_institution_ids":["https://openalex.org/I131077856","https://openalex.org/I136199984","https://openalex.org/I184565670","https://openalex.org/I4210120904"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.1378,"has_fulltext":true,"cited_by_count":24,"citation_normalized_percentile":{"value":0.54070803,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"32","issue":"5","first_page":"738","last_page":"746"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.33320000767707825,"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":0.33320000767707825,"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":0.11020000278949738,"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":0.08209999650716782,"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/computer-science","display_name":"Computer science","score":0.7065211534500122},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5294278264045715},{"id":"https://openalex.org/keywords/biological-data","display_name":"Biological data","score":0.48022136092185974},{"id":"https://openalex.org/keywords/data-type","display_name":"Data type","score":0.46537017822265625},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3513675928115845},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3378371000289917},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.2937173843383789},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.20195627212524414}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7065211534500122},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5294278264045715},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.48022136092185974},{"id":"https://openalex.org/C138958017","wikidata":"https://www.wikidata.org/wiki/Q190087","display_name":"Data type","level":2,"score":0.46537017822265625},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3513675928115845},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3378371000289917},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2937173843383789},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20195627212524414},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"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":"D005909","descriptor_name":"Glioblastoma","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005909","descriptor_name":"Glioblastoma","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005909","descriptor_name":"Glioblastoma","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":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btv653","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv653","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/5/738/25894147/btv653.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26545823","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26545823","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:agritrop.cirad.fr:580168","is_oa":false,"landing_page_url":"http://agritrop.cirad.fr/580168/","pdf_url":null,"source":{"id":"https://openalex.org/S4306402311","display_name":"Agritrop (Cirad)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I131077856","host_organization_name":"Centre de Coop\u00e9ration Internationale en Recherche Agronomique pour le D\u00e9veloppement","host_organization_lineage":["https://openalex.org/I131077856"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:europepmc.org:5030535","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5939889","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:32/5/738","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/32/5/738","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btv653","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv653","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/5/738/25894147/btv653.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals","score":0.4099999964237213}],"awards":[{"id":"https://openalex.org/G2455011602","display_name":null,"funder_award_id":"R01-HD-059827","funder_id":"https://openalex.org/F4320337611","funder_display_name":"Eunice Kennedy Shriver National Institute of Child Health and Human Development"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337611","display_name":"Eunice Kennedy Shriver National Institute of Child Health and Human Development","ror":"https://ror.org/04byxyr05"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2161503024.pdf","grobid_xml":"https://content.openalex.org/works/W2161503024.grobid-xml"},"referenced_works_count":32,"referenced_works":["https://openalex.org/W80720732","https://openalex.org/W1978034558","https://openalex.org/W2006810478","https://openalex.org/W2014606320","https://openalex.org/W2031821463","https://openalex.org/W2034461204","https://openalex.org/W2040569146","https://openalex.org/W2060110090","https://openalex.org/W2067245109","https://openalex.org/W2097360283","https://openalex.org/W2105245626","https://openalex.org/W2105717378","https://openalex.org/W2113847025","https://openalex.org/W2122825543","https://openalex.org/W2123162799","https://openalex.org/W2123696077","https://openalex.org/W2126017970","https://openalex.org/W2135046866","https://openalex.org/W2138848739","https://openalex.org/W2144268162","https://openalex.org/W2154361640","https://openalex.org/W2161056048","https://openalex.org/W2171304795","https://openalex.org/W2529222270","https://openalex.org/W3175417087","https://openalex.org/W4252676770","https://openalex.org/W4294541781","https://openalex.org/W6644927703","https://openalex.org/W6676078265","https://openalex.org/W6676883664","https://openalex.org/W6684935140","https://openalex.org/W6728147186"],"related_works":["https://openalex.org/W2380602769","https://openalex.org/W2348097614","https://openalex.org/W2164324468","https://openalex.org/W4233387348","https://openalex.org/W1549950088","https://openalex.org/W2167239434","https://openalex.org/W2923940588","https://openalex.org/W2950373261","https://openalex.org/W2161503024","https://openalex.org/W4247267178"],"abstract_inverted_index":{"MOTIVATION:":[0],"Advances":[1],"in":[2,112],"high-throughput":[3],"technologies":[4],"have":[5,46],"led":[6,47],"to":[7,48,105,128,173],"the":[8,17,32,90,113,142,154,171],"acquisition":[9],"of":[10,13,35,43,54,62,65,141],"various":[11,85],"types":[12,111],"-omic":[14],"data":[15,22,194],"on":[16,72,97],"same":[18],"biological":[19,33,56,86,143],"samples.":[20],"Each":[21],"type":[23],"gives":[24],"independent":[25,41],"and":[26,76,82,94,120,132,166],"complementary":[27],"information":[28],"that":[29],"can":[30],"explain":[31],"mechanisms":[34,57,144],"interest.":[36],"While":[37],"several":[38],"studies":[39],"performing":[40],"analyses":[42],"each":[44],"dataset":[45],"significant":[49],"results,":[50],"a":[51,98,138],"better":[52,139],"understanding":[53,140],"complex":[55],"requires":[58],"an":[59],"integrative":[60,125,155],"analysis":[61,181],"different":[63,91],"sources":[64],"data.":[66,175],"RESULTS:":[67],"Flexible":[68],"modeling":[69],"approaches,":[70],"based":[71],"penalized":[73],"likelihood":[74],"methods":[75],"expectation-maximization":[77],"(EM)":[78],"algorithms,":[79],"are":[80,103,182,195],"studied":[81],"tested":[83],"under":[84],"relationship":[87],"scenarios":[88],"between":[89],"molecular":[92],"features":[93],"their":[95],"effects":[96],"clinical":[99],"outcome.":[100],"The":[101,124,176],"models":[102,126,156,172],"applied":[104],"genomic":[106],"datasets":[107,165,178],"from":[108],"two":[109],"cancer":[110],"Cancer":[114],"Genome":[115],"Atlas":[116],"project:":[117],"glioblastoma":[118],"multiforme":[119],"ovarian":[121],"serous":[122],"cystadenocarcinoma.":[123],"lead":[127],"improved":[129],"model":[130],"fit":[131],"predictive":[133],"performance.":[134],"They":[135],"also":[136],"provide":[137],"underlying":[145],"patients'":[146],"survival.":[147],"AVAILABILITY":[148],"AND":[149],"IMPLEMENTATION:":[150],"Source":[151],"code":[152],"implementing":[153],"is":[157],"freely":[158],"available":[159,184,196],"at":[160,185,197],"https://github.com/mgt000/IntegrativeAnalysis":[161],"along":[162],"with":[163],"example":[164],"sample":[167],"R":[168],"script":[169],"applying":[170],"these":[174],"TCGA":[177],"used":[179],"for":[180],"publicly":[183],"https://tcga-data.nci.nih.gov/tcga/tcgaDownload.jsp":[186],"CONTACT:":[187],"marie.denis@cirad.fr":[188],"or":[189],"mgt26@georgetown.edu":[190],"SUPPLEMENTARY":[191],"INFORMATION:":[192],"Supplementary":[193],"Bioinformatics":[198],"online.":[199]},"counts_by_year":[{"year":2025,"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":17},{"year":2019,"cited_by_count":2},{"year":2016,"cited_by_count":1}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}
