{"id":"https://openalex.org/W2969663251","doi":"https://doi.org/10.1093/bioinformatics/btz655","title":"MEXCOwalk: mutual exclusion and coverage based random walk to identify cancer modules","display_name":"MEXCOwalk: mutual exclusion and coverage based random walk to identify cancer modules","publication_year":2019,"publication_date":"2019-08-19","ids":{"openalex":"https://openalex.org/W2969663251","doi":"https://doi.org/10.1093/bioinformatics/btz655","mag":"2969663251","pmid":"https://pubmed.ncbi.nlm.nih.gov/31432076"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz655","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz655","pdf_url":null,"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":"green","oa_url":"http://hdl.handle.net/20.500.12566/190","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5070809274","display_name":"Rafsan Ahmed","orcid":"https://orcid.org/0000-0003-0321-420X"},"institutions":[{"id":"https://openalex.org/I4210100577","display_name":"Antalya Bilim University","ror":"https://ror.org/013sqra93","country_code":"TR","type":"education","lineage":["https://openalex.org/I4210100577"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Rafsan Ahmed","raw_affiliation_strings":["Electrical and Computer Engineering Graduate Program, Department of Computer Engineering, Antalya Bilim University , Antalya 07190, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Electrical and Computer Engineering Graduate Program, Department of Computer Engineering, Antalya Bilim University , Antalya 07190, Turkey","institution_ids":["https://openalex.org/I4210100577"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040663044","display_name":"Ilyes Baali","orcid":"https://orcid.org/0000-0002-8655-1721"},"institutions":[{"id":"https://openalex.org/I4210100577","display_name":"Antalya Bilim University","ror":"https://ror.org/013sqra93","country_code":"TR","type":"education","lineage":["https://openalex.org/I4210100577"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Ilyes Baali","raw_affiliation_strings":["Electrical and Computer Engineering Graduate Program, Department of Computer Engineering, Antalya Bilim University , Antalya 07190, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Electrical and Computer Engineering Graduate Program, Department of Computer Engineering, Antalya Bilim University , Antalya 07190, Turkey","institution_ids":["https://openalex.org/I4210100577"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066274617","display_name":"Cesim Erten","orcid":"https://orcid.org/0000-0002-8149-7113"},"institutions":[{"id":"https://openalex.org/I4210100577","display_name":"Antalya Bilim University","ror":"https://ror.org/013sqra93","country_code":"TR","type":"education","lineage":["https://openalex.org/I4210100577"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Cesim Erten","raw_affiliation_strings":["Department of Computer Engineering, Antalya Bilim University , Antalya 07190, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Antalya Bilim University , Antalya 07190, Turkey","institution_ids":["https://openalex.org/I4210100577"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082891004","display_name":"Evis Hoxha","orcid":null},"institutions":[{"id":"https://openalex.org/I4210100577","display_name":"Antalya Bilim University","ror":"https://ror.org/013sqra93","country_code":"TR","type":"education","lineage":["https://openalex.org/I4210100577"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Evis Hoxha","raw_affiliation_strings":["Department of Computer Engineering, Antalya Bilim University , Antalya 07190, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Antalya Bilim University , Antalya 07190, Turkey","institution_ids":["https://openalex.org/I4210100577"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5074332682","display_name":"Hilal Kazan","orcid":"https://orcid.org/0000-0003-2461-4579"},"institutions":[{"id":"https://openalex.org/I4210100577","display_name":"Antalya Bilim University","ror":"https://ror.org/013sqra93","country_code":"TR","type":"education","lineage":["https://openalex.org/I4210100577"]}],"countries":["TR"],"is_corresponding":true,"raw_author_name":"Hilal Kazan","raw_affiliation_strings":["Department of Computer Engineering, Antalya Bilim University , Antalya 07190, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Antalya Bilim University , Antalya 07190, Turkey","institution_ids":["https://openalex.org/I4210100577"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5074332682"],"corresponding_institution_ids":["https://openalex.org/I4210100577"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.8806,"has_fulltext":false,"cited_by_count":36,"citation_normalized_percentile":{"value":0.86330748,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":99},"biblio":{"volume":"36","issue":"3","first_page":"872","last_page":"879"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.7735000252723694,"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":0.7735000252723694,"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":0.09030000120401382,"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/T10261","display_name":"Genetic Associations and Epidemiology","score":0.04320000112056732,"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/identification","display_name":"Identification (biology)","score":0.6552774310112},{"id":"https://openalex.org/keywords/cancer","display_name":"Cancer","score":0.5987523794174194},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5477092862129211},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5429683327674866},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.494368314743042},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4671420753002167},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.43609970808029175},{"id":"https://openalex.org/keywords/scripting-language","display_name":"Scripting language","score":0.43079710006713867},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3346327543258667},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.30305761098861694}],"concepts":[{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.6552774310112},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.5987523794174194},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5477092862129211},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5429683327674866},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.494368314743042},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4671420753002167},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.43609970808029175},{"id":"https://openalex.org/C61423126","wikidata":"https://www.wikidata.org/wiki/Q187432","display_name":"Scripting language","level":2,"score":0.43079710006713867},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3346327543258667},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.30305761098861694},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","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":"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":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btz655","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz655","pdf_url":null,"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:31432076","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31432076","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:http://acikerisim.antalya.edu.tr:20.500.12566/190","is_oa":true,"landing_page_url":"http://hdl.handle.net/20.500.12566/190","pdf_url":null,"source":{"id":"https://openalex.org/S7407055351","display_name":"Antalya Bilim University Institutional Repository","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"pmh:oai:http://acikerisim.antalya.edu.tr:20.500.12566/190","is_oa":true,"landing_page_url":"http://hdl.handle.net/20.500.12566/190","pdf_url":null,"source":{"id":"https://openalex.org/S7407055351","display_name":"Antalya Bilim University Institutional Repository","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"},"sustainable_development_goals":[{"score":0.8100000023841858,"display_name":"Reduced inequalities","id":"https://metadata.un.org/sdg/10"}],"awards":[{"id":"https://openalex.org/G3346257279","display_name":"Kanser Gen \u00d6ncelle\u015ftirimi ve Mod\u00fcl \u00c7\u0131kar\u0131m\u0131na Y\u00f6nelik \u00d6zg\u00fcn Yakla\u015f\u0131mlar","funder_award_id":"117E879","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":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":42,"referenced_works":["https://openalex.org/W1966331733","https://openalex.org/W1971843650","https://openalex.org/W2000771269","https://openalex.org/W2009019945","https://openalex.org/W2009720434","https://openalex.org/W2017283085","https://openalex.org/W2038122249","https://openalex.org/W2042851051","https://openalex.org/W2043764521","https://openalex.org/W2046024621","https://openalex.org/W2047647439","https://openalex.org/W2073482997","https://openalex.org/W2074549773","https://openalex.org/W2088891952","https://openalex.org/W2095319945","https://openalex.org/W2110065044","https://openalex.org/W2126172213","https://openalex.org/W2140883620","https://openalex.org/W2141545130","https://openalex.org/W2141811925","https://openalex.org/W2143897427","https://openalex.org/W2144940507","https://openalex.org/W2145135780","https://openalex.org/W2158485828","https://openalex.org/W2168395849","https://openalex.org/W2256708280","https://openalex.org/W2340547575","https://openalex.org/W2531532678","https://openalex.org/W2532527181","https://openalex.org/W2558715006","https://openalex.org/W2560866543","https://openalex.org/W2611492308","https://openalex.org/W2737623232","https://openalex.org/W2753100140","https://openalex.org/W2761386711","https://openalex.org/W2762514397","https://openalex.org/W2768685411","https://openalex.org/W2890112540","https://openalex.org/W2950568721","https://openalex.org/W2950753203","https://openalex.org/W2964156730","https://openalex.org/W4230962320"],"related_works":["https://openalex.org/W2046765700","https://openalex.org/W2780629932","https://openalex.org/W4384345686","https://openalex.org/W2357937784","https://openalex.org/W2547618384","https://openalex.org/W4394391052","https://openalex.org/W2145834781","https://openalex.org/W2577782152","https://openalex.org/W262455470","https://openalex.org/W4242899858"],"abstract_inverted_index":{"MOTIVATION:":[0],"Genomic":[1],"analyses":[2],"from":[3],"large":[4],"cancer":[5,64,75,104,122,143,163,171,175],"cohorts":[6],"have":[7],"revealed":[8],"the":[9,15,34,60,71,92,146,182,187],"mutational":[10],"heterogeneity":[11],"problem":[12,30],"which":[13],"hinders":[14],"identification":[16],"of":[17,57,63,73,94,119,129],"driver":[18,76,105],"genes":[19,37,58,172,176],"based":[20],"only":[21],"on":[22,113],"mutation":[23,55],"profiles.":[24],"One":[25],"way":[26],"to":[27,32,69,102],"tackle":[28],"this":[29],"is":[31],"incorporate":[33],"fact":[35],"that":[36,87,126,136,177],"act":[38],"together":[39,53],"in":[40,47,91,117,141,161,181],"functional":[41],"modules.":[42,77,106],"The":[43,185],"connectivity":[44,89],"knowledge":[45],"present":[46,80],"existing":[48],"protein-protein":[49,95],"interaction":[50],"(PPI)":[51],"networks":[52],"with":[54,150],"frequencies":[56],"and":[59,100,132,135,158,173,190],"mutual":[61,98],"exclusivity":[62,99],"mutations":[65,140],"can":[66,153],"be":[67],"utilized":[68],"increase":[70],"accuracy":[72],"identifying":[74],"RESULTS:":[78],"We":[79],"a":[81],"novel":[82],"edge-weighted":[83],"random":[84],"walk-based":[85],"approach":[86],"incorporates":[88],"information":[90],"form":[93],"interactions":[96],"(PPIs),":[97],"coverage":[101],"identify":[103],"MEXCOwalk":[107,165],"outperforms":[108],"several":[109],"state-of-the-art":[110],"computational":[111],"methods":[112],"TCGA":[114],"pan-cancer":[115,183],"data":[116,200],"terms":[118],"recovering":[120],"known":[121],"genes,":[123],"providing":[124],"modules":[125,152,167],"are":[127,137,178,193,201],"capable":[128],"classifying":[130],"normal":[131],"tumor":[133],"samples":[134],"enriched":[138],"for":[139],"specific":[142],"types.":[144,164],"Furthermore,":[145],"risk":[147],"scores":[148],"determined":[149],"output":[151],"stratify":[154],"patients":[155],"into":[156],"low-risk":[157],"high-risk":[159],"groups":[160],"multiple":[162],"identifies":[166],"containing":[168],"both":[169],"well-known":[170],"putative":[174],"rarely":[179],"mutated":[180],"data.":[184],"data,":[186],"source":[188],"code":[189],"useful":[191],"scripts":[192],"available":[194,202],"at:":[195],"https://github.com/abu-compbio/MEXCOwalk.":[196],"SUPPLEMENTARY":[197],"INFORMATION:":[198],"Supplementary":[199],"at":[203],"Bioinformatics":[204],"online.":[205]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":8},{"year":2021,"cited_by_count":10},{"year":2020,"cited_by_count":4}],"updated_date":"2026-06-22T08:00:12.763002","created_date":"2025-10-10T00:00:00"}
