{"id":"https://openalex.org/W4400430468","doi":"https://doi.org/10.3389/fbinf.2024.1365200","title":"Network analysis of driver genes in human cancers","display_name":"Network analysis of driver genes in human cancers","publication_year":2024,"publication_date":"2024-07-08","ids":{"openalex":"https://openalex.org/W4400430468","doi":"https://doi.org/10.3389/fbinf.2024.1365200","pmid":"https://pubmed.ncbi.nlm.nih.gov/39040139","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/11260686"},"language":"en","primary_location":{"id":"doi:10.3389/fbinf.2024.1365200","doi":"https://doi.org/10.3389/fbinf.2024.1365200","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2024.1365200","pdf_url":null,"source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","jufo-1","ki-jl-1","norway-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.3389/fbinf.2024.1365200","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5035488577","display_name":"Shruti Sunil Patil","orcid":"https://orcid.org/0009-0008-2036-8220","observed_orcids":["https://orcid.org/0009-0008-2036-8220"]},"institutions":[{"id":"https://openalex.org/I72951846","display_name":"Washington State University","ror":"https://ror.org/05dk0ce17","country_code":"US","type":"education","lineage":["https://openalex.org/I72951846"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shruti S. Patil","raw_affiliation_strings":["School of Electrical Engineering and Computer Science, Washington State University, Pullman, WA, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Electrical Engineering and Computer Science, Washington State University, Pullman, WA, United States","institution_ids":["https://openalex.org/I72951846"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045510214","display_name":"Steven A. Roberts","orcid":"https://orcid.org/0000-0002-3628-5808","observed_orcids":["https://orcid.org/0000-0002-3628-5808"]},"institutions":[{"id":"https://openalex.org/I111236770","display_name":"University of Vermont","ror":"https://ror.org/0155zta11","country_code":"US","type":"education","lineage":["https://openalex.org/I111236770"]},{"id":"https://openalex.org/I2801980284","display_name":"University of Vermont Medical Center","ror":"https://ror.org/04cewr321","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2801980284"]},{"id":"https://openalex.org/I72951846","display_name":"Washington State University","ror":"https://ror.org/05dk0ce17","country_code":"US","type":"education","lineage":["https://openalex.org/I72951846"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Steven A. Roberts","raw_affiliation_strings":["Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT, United States","School of Molecular Biosciences, Washington State University, Pullman, WA, United States","UVM's Larner College of Medicine, University of Vermont Cancer Center, Burlington, VT, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT, United States","institution_ids":["https://openalex.org/I111236770"]},{"raw_affiliation_string":"School of Molecular Biosciences, Washington State University, Pullman, WA, United States","institution_ids":["https://openalex.org/I72951846"]},{"raw_affiliation_string":"UVM's Larner College of Medicine, University of Vermont Cancer Center, Burlington, VT, United States","institution_ids":["https://openalex.org/I111236770","https://openalex.org/I2801980284"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5049685547","display_name":"Assefaw Hadish Gebremedhin","orcid":"https://orcid.org/0000-0001-5383-8032","observed_orcids":["https://orcid.org/0000-0001-5383-8032"]},"institutions":[{"id":"https://openalex.org/I72951846","display_name":"Washington State University","ror":"https://ror.org/05dk0ce17","country_code":"US","type":"education","lineage":["https://openalex.org/I72951846"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Assefaw H. Gebremedhin","raw_affiliation_strings":["School of Electrical Engineering and Computer Science, Washington State University, Pullman, WA, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Electrical Engineering and Computer Science, Washington State University, Pullman, WA, United States","institution_ids":["https://openalex.org/I72951846"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5049685547"],"corresponding_institution_ids":["https://openalex.org/I72951846"],"apc_list":{"value":2125,"currency":"USD","value_usd":2125},"apc_paid":{"value":2125,"currency":"USD","value_usd":2125},"fwci":0.7981,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.6891481,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"4","issue":null,"first_page":"1365200","last_page":"1365200"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.8095999956130981,"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"}},"topics":[{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.8095999956130981,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.18250000476837158,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.0008999999845400453,"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/driver-mutations","display_name":"driver mutations","score":0.8679999709129333},{"id":"https://openalex.org/keywords/driver-genes","display_name":"driver genes","score":0.8190000057220459},{"id":"https://openalex.org/keywords/cancer-genomics","display_name":"cancer genomics","score":0.8299999833106995},{"id":"https://openalex.org/keywords/sequence-similarity-networks","display_name":"sequence similarity networks","score":0.7440000176429749},{"id":"https://openalex.org/keywords/bipartite-graphs","display_name":"bipartite graphs","score":0.8679999709129333},{"id":"https://openalex.org/keywords/gene-co-occurrence","display_name":"gene co-occurrence","score":0.8880000114440918},{"id":"https://openalex.org/keywords/data-reduction","display_name":"data reduction","score":0.7459999918937683},{"id":"https://openalex.org/keywords/therapeutic-vulnerabilities","display_name":"therapeutic vulnerabilities","score":0.3610000014305115}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5824441909790039},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5779099464416504},{"id":"https://openalex.org/C197657726","wikidata":"https://www.wikidata.org/wiki/Q174733","display_name":"Bipartite graph","level":3,"score":0.5235804319381714},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.49647098779678345},{"id":"https://openalex.org/C32946077","wikidata":"https://www.wikidata.org/wiki/Q618079","display_name":"Network analysis","level":2,"score":0.4720476567745209},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.4426390826702118},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.43953800201416016},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.4293574094772339},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3672722578048706},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.36149266362190247},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32198983430862427},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.177801251411438},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.16800153255462646},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.09071102738380432},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.3389/fbinf.2024.1365200","doi":"https://doi.org/10.3389/fbinf.2024.1365200","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2024.1365200","pdf_url":null,"source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","jufo-1","ki-jl-1","norway-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:11260686","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11260686","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11260686/pdf/fbinf-04-1365200.pdf","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,"listed_in":[],"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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Front Bioinform","raw_type":"Text"},{"id":"pmid:39040139","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39040139","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,"listed_in":[],"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":"Frontiers in bioinformatics","raw_type":"Journal Article"},{"id":"pmh:oai:doaj.org/article:f60a5687c15440969c56990d58ce9887","doi":null,"is_oa":false,"landing_page_url":"https://doaj.org/article/f60a5687c15440969c56990d58ce9887","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,"listed_in":[],"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":"Frontiers in Bioinformatics, Vol 4 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.3389/fbinf.2024.1365200","doi":"https://doi.org/10.3389/fbinf.2024.1365200","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2024.1365200","pdf_url":null,"source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","jufo-1","ki-jl-1","norway-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.6240000128746033,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"study_designs":[],"awards":[{"id":"https://openalex.org/G9000897853","display_name":"Regulation of APOBEC3 cytidine deaminase-induced mutation during cancerdevelopment","funder_award_id":"R01CA269784","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":51,"referenced_works":["https://openalex.org/W229097380","https://openalex.org/W1880949099","https://openalex.org/W1920250001","https://openalex.org/W2011941471","https://openalex.org/W2017283085","https://openalex.org/W2044433401","https://openalex.org/W2062533676","https://openalex.org/W2083045667","https://openalex.org/W2086744970","https://openalex.org/W2088891952","https://openalex.org/W2116753551","https://openalex.org/W2121906867","https://openalex.org/W2129769331","https://openalex.org/W2158485828","https://openalex.org/W2396849069","https://openalex.org/W2490926353","https://openalex.org/W2558715006","https://openalex.org/W2765099905","https://openalex.org/W2770548163","https://openalex.org/W2796153844","https://openalex.org/W2796408191","https://openalex.org/W2808263699","https://openalex.org/W2894573839","https://openalex.org/W2898789672","https://openalex.org/W2904847915","https://openalex.org/W2924107965","https://openalex.org/W2932370125","https://openalex.org/W2940518587","https://openalex.org/W2944141861","https://openalex.org/W2945138188","https://openalex.org/W2945891661","https://openalex.org/W2947209894","https://openalex.org/W2958066336","https://openalex.org/W2974344506","https://openalex.org/W3004859565","https://openalex.org/W3004866745","https://openalex.org/W3004883393","https://openalex.org/W3006500278","https://openalex.org/W3014963373","https://openalex.org/W3047825284","https://openalex.org/W3093780683","https://openalex.org/W3106172960","https://openalex.org/W3119089136","https://openalex.org/W3156796720","https://openalex.org/W3202162462","https://openalex.org/W3207791129","https://openalex.org/W3210864383","https://openalex.org/W4289530026","https://openalex.org/W4385635696","https://openalex.org/W4388682045","https://openalex.org/W4388849343"],"related_works":["https://openalex.org/W2471330250","https://openalex.org/W7212231037","https://openalex.org/W4405489970","https://openalex.org/W2092180333","https://openalex.org/W7097983560","https://openalex.org/W4402630664","https://openalex.org/W7110680895","https://openalex.org/W3135457246","https://openalex.org/W4285087096","https://openalex.org/W6999327861"],"abstract_inverted_index":{"Cancer":[0],"is":[1,37,97,135],"a":[2,98,131,178,212,242,254,293],"heterogeneous":[3,207],"disease":[4,36],"that":[5,18,229,267,300],"results":[6],"from":[7],"genetic":[8],"alteration":[9],"of":[10,100,151,163,169,249,256,258,296],"cell":[11],"cycle":[12],"and":[13,25,47,58,104,166,208,224,237,282,286,305],"proliferation":[14],"controls.":[15],"Identifying":[16],"mutations":[17,29,238,287],"drive":[19],"cancer,":[20],"understanding":[21,295],"cancer":[22,44,191,235,276,290],"type":[23],"specificities,":[24],"delineating":[26],"how":[27],"driver":[28,75,140,259,284,298],"interact":[30],"with":[31,148],"each":[32,201],"other":[33,202],"to":[34,73,118,175,200,211,240,302],"establish":[35],"vital":[38],"for":[39,124,137,288],"identifying":[40],"therapeutic":[41],"vulnerabilities.":[42],"Such":[43],"specific":[45,289],"patterns":[46,77],"gene":[48,76,141,222,247],"co-occurrences":[49],"can":[50,270],"be":[51,271],"identified":[52,227],"by":[53],"studying":[54],"tumor":[55,79,303],"genome":[56],"sequences,":[57],"networks":[59,172,252],"have":[60],"proven":[61],"effective":[62,273],"in":[63,193,233,261,275],"uncovering":[64],"relationships":[65],"between":[66],"sequences.":[67],"We":[68,226],"present":[69],"two":[70],"network-based":[71,268],"approaches":[72,269],"identify":[74,190],"among":[78],"samples.":[80],"The":[81,185,215,278],"first":[82],"approach":[83,107],"relies":[84],"on":[85],"analysis":[86,218,279],"using":[87],"the":[88,105,120,125,139,149,152,158,171,250,297],"Directed":[89],"Weighted":[90],"All":[91],"Nearest":[92],"Neighbors":[93],"(DiWANN)":[94],"model,":[95,155],"which":[96,194],"variant":[99],"sequence":[101,126,134],"similarity":[102,127],"network,":[103],"second":[106],"uses":[108],"bipartite":[109,216,251],"network":[110,128,154,187,217],"analysis.":[111],"A":[112],"data":[113,144],"reduction":[114,145],"framework":[115],"was":[116],"implemented":[117],"extract":[119],"minimal":[121],"relevant":[122],"information":[123],"analysis,":[129],"where":[130],"transformed":[132],"reference":[133],"generated":[136],"constructing":[138],"network.":[142],"This":[143],"process":[146],"combined":[147],"efficiency":[150],"DiWANN":[153,186],"greatly":[156],"lowered":[157],"computational":[159],"cost":[160],"(in":[161],"terms":[162],"execution":[164],"time":[165],"memory":[167],"usage)":[168],"generating":[170],"enabling":[173],"us":[174,189],"work":[176],"at":[177],"much":[179],"larger":[180],"scale":[181],"than":[182],"previously":[183],"possible.":[184],"helped":[188],"types":[192,236],"samples":[195],"were":[196,230],"more":[197],"closely":[198],"connected":[199],"suggesting":[203],"they":[204],"are":[205],"less":[206],"potentially":[209],"susceptible":[210],"common":[213],"drug.":[214],"provided":[219],"insight":[220],"into":[221],"associations":[223],"co-occurrences.":[225],"genes":[228,260,285,299],"broadly":[231],"mutated":[232],"multiple":[234],"exclusive":[239,283],"only":[241],"few.":[243],"Additionally,":[244],"weighted":[245],"one-mode":[246],"projections":[248],"revealed":[253],"pattern":[255],"occurrence":[257],"different":[262],"cancers.":[263],"Our":[264],"study":[265],"demonstrates":[266],"an":[272],"tool":[274],"genomics.":[277],"identifies":[280],"co-occurring":[281],"types,":[291],"providing":[292],"better":[294],"lead":[301],"initiation":[304],"evolution.":[306]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":2}],"updated_date":"2026-10-30T12:39:25.321706","created_date":"2024-07-09T00:00:00"}
