{"id":"https://openalex.org/W3164908261","doi":"https://doi.org/10.1186/s12859-021-04203-7","title":"driveR: a novel method for prioritizing cancer driver genes using somatic genomics data","display_name":"driveR: a novel method for prioritizing cancer driver genes using somatic genomics data","publication_year":2021,"publication_date":"2021-05-24","ids":{"openalex":"https://openalex.org/W3164908261","doi":"https://doi.org/10.1186/s12859-021-04203-7","mag":"3164908261","pmid":"https://pubmed.ncbi.nlm.nih.gov/34030627"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-021-04203-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04203-7","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-04203-7","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-04203-7","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5003760055","display_name":"Ege \u00dclgen","orcid":"https://orcid.org/0000-0003-2090-3621"},"institutions":[{"id":"https://openalex.org/I4210143914","display_name":"Kent Hastanesi","ror":"https://ror.org/0599zba67","country_code":"TR","type":"healthcare","lineage":["https://openalex.org/I4210143914"]},{"id":"https://openalex.org/I4210163811","display_name":"Ac\u0131badem Adana Hospital","ror":"https://ror.org/05g2amy04","country_code":"TR","type":"healthcare","lineage":["https://openalex.org/I4210163811"]}],"countries":["TR"],"is_corresponding":true,"raw_author_name":"Ege \u00dclgen","raw_affiliation_strings":["Department of Biostatistics and Medical Informatics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey. egeulgen@gmail.com","Department of Biostatistics and Medical Informatics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey"],"raw_orcid":"https://orcid.org/0000-0003-2090-3621","affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Medical Informatics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey. egeulgen@gmail.com","institution_ids":["https://openalex.org/I4210143914"]},{"raw_affiliation_string":"Department of Biostatistics and Medical Informatics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey","institution_ids":["https://openalex.org/I4210143914","https://openalex.org/I4210163811"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5039717404","display_name":"Osman U\u011fur Sezerman","orcid":"https://orcid.org/0000-0003-0905-6783"},"institutions":[{"id":"https://openalex.org/I4210143914","display_name":"Kent Hastanesi","ror":"https://ror.org/0599zba67","country_code":"TR","type":"healthcare","lineage":["https://openalex.org/I4210143914"]},{"id":"https://openalex.org/I4210163811","display_name":"Ac\u0131badem Adana Hospital","ror":"https://ror.org/05g2amy04","country_code":"TR","type":"healthcare","lineage":["https://openalex.org/I4210163811"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"O. U\u011fur Sezerman","raw_affiliation_strings":["Department of Biostatistics and Medical Informatics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Medical Informatics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey","institution_ids":["https://openalex.org/I4210143914","https://openalex.org/I4210163811"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5003760055"],"corresponding_institution_ids":["https://openalex.org/I4210143914","https://openalex.org/I4210163811"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":0.6653,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.65638699,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":97},"biblio":{"volume":"22","issue":"1","first_page":"263","last_page":"263"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.34209999442100525,"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":0.34209999442100525,"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.2628999948501587,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T11297","display_name":"Ferroptosis and cancer prognosis","score":0.10130000114440918,"subfield":{"id":"https://openalex.org/subfields/2740","display_name":"Pulmonary and Respiratory Medicine"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.6457462310791016},{"id":"https://openalex.org/keywords/prioritization","display_name":"Prioritization","score":0.5842433571815491},{"id":"https://openalex.org/keywords/personalized-medicine","display_name":"Personalized medicine","score":0.5392633080482483},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5092319250106812},{"id":"https://openalex.org/keywords/wilcoxon-signed-rank-test","display_name":"Wilcoxon signed-rank test","score":0.46710124611854553},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.43723607063293457},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.40374064445495605},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.33414435386657715},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.29373258352279663},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.27813923358917236},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1833096444606781},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.14996230602264404},{"id":"https://openalex.org/keywords/internal-medicine","display_name":"Internal medicine","score":0.10733139514923096},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.08942833542823792},{"id":"https://openalex.org/keywords/mann\u2013whitney-u-test","display_name":"Mann\u2013Whitney U test","score":0.0841209888458252}],"concepts":[{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.6457462310791016},{"id":"https://openalex.org/C2777615720","wikidata":"https://www.wikidata.org/wiki/Q11888847","display_name":"Prioritization","level":2,"score":0.5842433571815491},{"id":"https://openalex.org/C32220436","wikidata":"https://www.wikidata.org/wiki/Q2072214","display_name":"Personalized medicine","level":2,"score":0.5392633080482483},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5092319250106812},{"id":"https://openalex.org/C206041023","wikidata":"https://www.wikidata.org/wiki/Q1751970","display_name":"Wilcoxon signed-rank test","level":3,"score":0.46710124611854553},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.43723607063293457},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.40374064445495605},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.33414435386657715},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.29373258352279663},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.27813923358917236},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1833096444606781},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.14996230602264404},{"id":"https://openalex.org/C126322002","wikidata":"https://www.wikidata.org/wiki/Q11180","display_name":"Internal medicine","level":1,"score":0.10733139514923096},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.08942833542823792},{"id":"https://openalex.org/C12868164","wikidata":"https://www.wikidata.org/wiki/Q1424533","display_name":"Mann\u2013Whitney U test","level":2,"score":0.0841209888458252},{"id":"https://openalex.org/C539667460","wikidata":"https://www.wikidata.org/wiki/Q2414942","display_name":"Management science","level":1,"score":0.0}],"mesh":[{"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":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","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":"D009857","descriptor_name":"Oncogenes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009857","descriptor_name":"Oncogenes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009857","descriptor_name":"Oncogenes","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":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","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":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-021-04203-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04203-7","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-04203-7","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34030627","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34030627","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:8142487","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8142487","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:c67ed18962014c568dbc1348bd00006c","is_oa":true,"landing_page_url":"https://doaj.org/article/c67ed18962014c568dbc1348bd00006c","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 22, Iss 1, Pp 1-17 (2021)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-021-04203-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04203-7","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-04203-7","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G23707222","display_name":null,"funder_award_id":"118C039","funder_id":"https://openalex.org/F4320322626","funder_display_name":"T\u00fcrkiye Bilimsel ve Teknolojik Ara\u015ft\u0131rma Kurumu"}],"funders":[{"id":"https://openalex.org/F4320322626","display_name":"T\u00fcrkiye Bilimsel ve Teknolojik Ara\u015ft\u0131rma Kurumu","ror":"https://ror.org/04w9kkr77"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3164908261.pdf","grobid_xml":"https://content.openalex.org/works/W3164908261.grobid-xml"},"referenced_works_count":63,"referenced_works":["https://openalex.org/W954754213","https://openalex.org/W1880949099","https://openalex.org/W1970413157","https://openalex.org/W1977859620","https://openalex.org/W1982993862","https://openalex.org/W1984068087","https://openalex.org/W1990347487","https://openalex.org/W2009720434","https://openalex.org/W2010559811","https://openalex.org/W2011582941","https://openalex.org/W2023568503","https://openalex.org/W2038473742","https://openalex.org/W2042210471","https://openalex.org/W2044433401","https://openalex.org/W2052565988","https://openalex.org/W2059145105","https://openalex.org/W2059300459","https://openalex.org/W2072810564","https://openalex.org/W2076865561","https://openalex.org/W2094122486","https://openalex.org/W2096460732","https://openalex.org/W2100867326","https://openalex.org/W2101412130","https://openalex.org/W2111326065","https://openalex.org/W2114029728","https://openalex.org/W2118527670","https://openalex.org/W2132623845","https://openalex.org/W2139227366","https://openalex.org/W2143238378","https://openalex.org/W2144940507","https://openalex.org/W2145187337","https://openalex.org/W2149082178","https://openalex.org/W2149441684","https://openalex.org/W2152176732","https://openalex.org/W2155845523","https://openalex.org/W2159482845","https://openalex.org/W2161162779","https://openalex.org/W2163485494","https://openalex.org/W2167852161","https://openalex.org/W2375577403","https://openalex.org/W2436745791","https://openalex.org/W2557187647","https://openalex.org/W2565848986","https://openalex.org/W2606778219","https://openalex.org/W2784142616","https://openalex.org/W2796408191","https://openalex.org/W2890112540","https://openalex.org/W2893021323","https://openalex.org/W2894573839","https://openalex.org/W2898789672","https://openalex.org/W2900569176","https://openalex.org/W2905452503","https://openalex.org/W2917858269","https://openalex.org/W2940627982","https://openalex.org/W2949124738","https://openalex.org/W2976852018","https://openalex.org/W2983296017","https://openalex.org/W2985613549","https://openalex.org/W3004318979","https://openalex.org/W3004392981","https://openalex.org/W3047825284","https://openalex.org/W3098804002","https://openalex.org/W4294216483"],"related_works":["https://openalex.org/W2506292322","https://openalex.org/W4283209547","https://openalex.org/W3085397617","https://openalex.org/W2100132513","https://openalex.org/W2137444486","https://openalex.org/W4367627632","https://openalex.org/W2434800423","https://openalex.org/W4299900939","https://openalex.org/W2061799646","https://openalex.org/W2011965958"],"abstract_inverted_index":{"BACKGROUND:":[0],"Cancer":[1],"develops":[2],"due":[3],"to":[4],"\"driver\"":[5],"alterations.":[6],"Numerous":[7],"approaches":[8],"exist":[9],"for":[10,20,38,182],"predicting":[11],"cancer":[12,59,187],"drivers":[13],"from":[14],"cohort-scale":[15],"genomics":[16,44,50],"data.":[17],"However,":[18],"methods":[19],"personalized":[21,105,165,190],"analysis":[22,36,91,106,145,166],"of":[23,83,98,122],"driver":[24,39,60,184],"genes":[25,61,185],"are":[26],"underdeveloped.":[27],"In":[28],"this":[29,72],"study,":[30],"we":[31],"developed":[32],"a":[33,63,80,95,115,149],"novel":[34],"personalized/batch":[35],"approach":[37,181],"gene":[40],"prioritization":[41],"utilizing":[42],"somatic":[43],"data,":[45],"called":[46],"driveR.":[47],"RESULTS:":[48],"Combining":[49],"information":[51],"and":[52,94,138,148,159,179],"prior":[53],"biological":[54],"knowledge,":[55],"driveR":[56,76,194],"accurately":[57],"prioritizes":[58],"via":[62],"multi-task":[64],"learning":[65],"model.":[66],"Testing":[67],"on":[68,87,102,143,164,197],"28":[69,89],"different":[70],"datasets,":[71,93,147],"study":[73,170],"demonstrates":[74,171],"that":[75,172],"performs":[77],"adequately,":[78],"achieving":[79,114],"median":[81,96,118,152],"AUC":[82,97,119,153],"0.684":[84],"(range":[85,100],"0.651-0.861)":[86],"the":[88,103,173],"batch":[90,144,192],"test":[92,107,126,146],"0.773":[99],"0-1)":[101],"5157":[104],"samples.":[108],"Moreover,":[109],"it":[110],"outperforms":[111],"existing":[112],"approaches,":[113],"significantly":[116,150],"higher":[117,151],"than":[120,154],"all":[121],"MutSigCV":[123],"(Wilcoxon":[124],"rank-sum":[125],"p":[127],"<":[128,132,136,141,157,162],"0.001),":[129,133],"DriverNet":[130],"(p":[131,135,140,156,161],"OncodriveFML":[134],"0.001)":[137,142,158,163],"MutPanning":[139],"DawnRank":[155],"PRODIGY":[160],"datasets.":[167],"CONCLUSIONS:":[168],"This":[169],"proposed":[174],"method":[175],"is":[176,195],"an":[177],"accurate":[178],"easy-to-utilize":[180],"prioritizing":[183],"in":[186,189],"genomes":[188],"or":[191],"analyses.":[193],"available":[196],"CRAN:":[198],"https://cran.r-project.org/package=driveR":[199],".":[200]},"counts_by_year":[{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":3}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2025-10-10T00:00:00"}
