{"id":"https://openalex.org/W4362457921","doi":"https://doi.org/10.1093/bib/bbad112","title":"Cooperative driver pathways discovery by multiplex network embedding","display_name":"Cooperative driver pathways discovery by multiplex network embedding","publication_year":2023,"publication_date":"2023-03-30","ids":{"openalex":"https://openalex.org/W4362457921","doi":"https://doi.org/10.1093/bib/bbad112","pmid":"https://pubmed.ncbi.nlm.nih.gov/37000166"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbad112","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad112","pdf_url":"https://academic.oup.com/bib/article-pdf/doi/10.1093/bib/bbad112/50410501/bbad112.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in 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/bib/article-pdf/doi/10.1093/bib/bbad112/50410501/bbad112.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100384767","display_name":"Jun Wang","orcid":"https://orcid.org/0000-0002-5890-0365"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]},{"id":"https://openalex.org/I4210100255","display_name":"Beijing Academy of Artificial Intelligence","ror":"https://ror.org/016a74861","country_code":"CN","type":"other","lineage":["https://openalex.org/I4210100255"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jun Wang","raw_affiliation_strings":["SDU-NTU Centre for Artificial Intelligence Research (C-FAIR), Shandong University , China"],"affiliations":[{"raw_affiliation_string":"SDU-NTU Centre for Artificial Intelligence Research (C-FAIR), Shandong University , China","institution_ids":["https://openalex.org/I4210100255","https://openalex.org/I154099455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100329932","display_name":"Xi Chen","orcid":"https://orcid.org/0000-0002-3160-614X"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xi Chen","raw_affiliation_strings":["School of Software, Shandong University , China"],"affiliations":[{"raw_affiliation_string":"School of Software, Shandong University , China","institution_ids":["https://openalex.org/I154099455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067236756","display_name":"Zhengtian Wu","orcid":null},"institutions":[{"id":"https://openalex.org/I308837","display_name":"Suzhou University of Science and Technology","ror":"https://ror.org/04en8wb91","country_code":"CN","type":"education","lineage":["https://openalex.org/I308837"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhengtian Wu","raw_affiliation_strings":["School of Electronic and Information Engineering, Suzhou University of Science and Technology , China"],"affiliations":[{"raw_affiliation_string":"School of Electronic and Information Engineering, Suzhou University of Science and Technology , China","institution_ids":["https://openalex.org/I308837"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079800756","display_name":"Maozu Guo","orcid":"https://orcid.org/0000-0001-6228-6276"},"institutions":[{"id":"https://openalex.org/I62853816","display_name":"Beijing University of Civil Engineering and Architecture","ror":"https://ror.org/02yj0p855","country_code":"CN","type":"education","lineage":["https://openalex.org/I62853816"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Maozu Guo","raw_affiliation_strings":["College of Electrical and Information Engineering, Beijing University of Civil Engineering and Architecture , China"],"affiliations":[{"raw_affiliation_string":"College of Electrical and Information Engineering, Beijing University of Civil Engineering and Architecture , China","institution_ids":["https://openalex.org/I62853816"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5027082940","display_name":"Guoxian Yu","orcid":"https://orcid.org/0000-0002-1667-6705"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Guoxian Yu","raw_affiliation_strings":["School of Software, Shandong University , China"],"affiliations":[{"raw_affiliation_string":"School of Software, Shandong University , China","institution_ids":["https://openalex.org/I154099455"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5027082940"],"corresponding_institution_ids":["https://openalex.org/I154099455"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":0.4568,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.6600524,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"24","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":1.0,"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":1.0,"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":0.9995999932289124,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9918000102043152,"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/computational-biology","display_name":"Computational biology","score":0.5505337119102478},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.544605553150177},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.4500822424888611},{"id":"https://openalex.org/keywords/decipher","display_name":"DECIPHER","score":0.44911515712738037},{"id":"https://openalex.org/keywords/multiplex","display_name":"Multiplex","score":0.4251108169555664},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3057556450366974},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.29367682337760925},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.25073933601379395},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.24977093935012817},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.13694798946380615}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5505337119102478},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.544605553150177},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.4500822424888611},{"id":"https://openalex.org/C164614171","wikidata":"https://www.wikidata.org/wiki/Q5204775","display_name":"DECIPHER","level":2,"score":0.44911515712738037},{"id":"https://openalex.org/C2781188995","wikidata":"https://www.wikidata.org/wiki/Q6934982","display_name":"Multiplex","level":2,"score":0.4251108169555664},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3057556450366974},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.29367682337760925},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.25073933601379395},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.24977093935012817},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13694798946380615}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","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":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D063646","descriptor_name":"Carcinogenesis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D063646","descriptor_name":"Carcinogenesis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D063646","descriptor_name":"Carcinogenesis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbad112","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad112","pdf_url":"https://academic.oup.com/bib/article-pdf/doi/10.1093/bib/bbad112/50410501/bbad112.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37000166","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37000166","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":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bib/bbad112","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad112","pdf_url":"https://academic.oup.com/bib/article-pdf/doi/10.1093/bib/bbad112/50410501/bbad112.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2087396116","display_name":null,"funder_award_id":"China","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3317480652","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5994120800","display_name":null,"funder_award_id":"Natural","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G631735505","display_name":null,"funder_award_id":"62272276","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8056994637","display_name":null,"funder_award_id":"62072380","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320311026","display_name":"Shandong University","ror":"https://ror.org/0207yh398"},{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4362457921.pdf","grobid_xml":"https://content.openalex.org/works/W4362457921.grobid-xml"},"referenced_works_count":74,"referenced_works":["https://openalex.org/W1555100311","https://openalex.org/W1663251599","https://openalex.org/W1964427001","https://openalex.org/W1973690102","https://openalex.org/W1986932232","https://openalex.org/W1998767819","https://openalex.org/W2003332201","https://openalex.org/W2010269182","https://openalex.org/W2011912935","https://openalex.org/W2023568503","https://openalex.org/W2029452593","https://openalex.org/W2039156817","https://openalex.org/W2042851051","https://openalex.org/W2044433401","https://openalex.org/W2045156863","https://openalex.org/W2047766188","https://openalex.org/W2049621625","https://openalex.org/W2053485292","https://openalex.org/W2068816193","https://openalex.org/W2071324577","https://openalex.org/W2072174486","https://openalex.org/W2073455500","https://openalex.org/W2076183717","https://openalex.org/W2079645368","https://openalex.org/W2080232352","https://openalex.org/W2082463968","https://openalex.org/W2083960841","https://openalex.org/W2086541375","https://openalex.org/W2087906138","https://openalex.org/W2092289533","https://openalex.org/W2095081508","https://openalex.org/W2096173332","https://openalex.org/W2101306957","https://openalex.org/W2103017472","https://openalex.org/W2105956673","https://openalex.org/W2112426819","https://openalex.org/W2116798163","https://openalex.org/W2120763806","https://openalex.org/W2121443461","https://openalex.org/W2121906867","https://openalex.org/W2122778851","https://openalex.org/W2123696077","https://openalex.org/W2132083787","https://openalex.org/W2151821775","https://openalex.org/W2156120082","https://openalex.org/W2163798887","https://openalex.org/W2170567505","https://openalex.org/W2197807472","https://openalex.org/W2288437288","https://openalex.org/W2609603613","https://openalex.org/W2745712403","https://openalex.org/W2765480939","https://openalex.org/W2796153225","https://openalex.org/W2796408191","https://openalex.org/W2884728705","https://openalex.org/W2895679848","https://openalex.org/W2910111050","https://openalex.org/W2912879817","https://openalex.org/W2950568721","https://openalex.org/W2964156730","https://openalex.org/W2977712660","https://openalex.org/W2983872259","https://openalex.org/W2985532194","https://openalex.org/W3007629644","https://openalex.org/W3037117187","https://openalex.org/W3112600195","https://openalex.org/W4233182706","https://openalex.org/W4246271082","https://openalex.org/W4255109328","https://openalex.org/W4256361765","https://openalex.org/W6696707883","https://openalex.org/W6742181258","https://openalex.org/W6773939556","https://openalex.org/W6791034896"],"related_works":["https://openalex.org/W2115350162","https://openalex.org/W2330145053","https://openalex.org/W4249875204","https://openalex.org/W4242620632","https://openalex.org/W3205440178","https://openalex.org/W4256069380","https://openalex.org/W2416520078","https://openalex.org/W2113606293","https://openalex.org/W2409656713","https://openalex.org/W2053972265"],"abstract_inverted_index":{"Cooperative":[0],"driver":[1,50,141,148,171],"pathways":[2,51,144],"discovery":[3,14],"helps":[4],"researchers":[5],"to":[6,47,73,115,138,145,168],"study":[7,185],"the":[8,23,37,70,75,84,108,125,132,140],"pathogenesis":[9],"of":[10,64,77,98,193],"cancer.":[11],"However,":[12],"most":[13],"methods":[15],"mainly":[16],"focus":[17],"on":[18,152],"genomics":[19],"data,":[20],"and":[21,27,61,82,88,105,123,135,156,178],"neglect":[22],"known":[24],"pathway":[25,71,126],"information":[26,63,119],"other":[28],"related":[29],"multi-omics":[30,166,197],"data;":[31],"thus":[32],"they":[33],"cannot":[34],"faithfully":[35],"decipher":[36],"carcinogenic":[38],"process.":[39],"We":[40],"propose":[41],"CDPMiner":[42,67,130,162,187],"(Cooperative":[43],"Driver":[44],"Pathways":[45],"Miner)":[46],"discover":[48,146,169],"cooperative":[49,147],"by":[52,195],"multiplex":[53,95],"network":[54,96,109,134],"embedding,":[55],"which":[56,173],"can":[57,163],"jointly":[58],"model":[59],"relational":[60],"attribute":[62],"multi-type":[65],"molecules.":[66],"first":[68],"uses":[69],"topology":[72],"quantify":[74],"weight":[76,142],"genes":[78,87,104],"in":[79],"different":[80],"pathways,":[81,106,172],"optimizes":[83],"relations":[85],"between":[86,143],"pathways.":[89,149],"Then":[90],"it":[91],"constructs":[92],"an":[93],"attributed":[94],"consisting":[97],"micro":[99],"RNAs,":[100,103],"long":[101],"noncoding":[102],"embeds":[107],"through":[110],"deep":[111],"joint":[112],"matrix":[113],"factorization":[114],"mine":[116],"more":[117,170,190],"essential":[118],"for":[120,181,188],"pathway-level":[121],"analysis":[122,192],"reconstructs":[124],"interaction":[127],"network.":[128],"Finally,":[129],"leverages":[131],"reconstructed":[133],"mutation":[136],"data":[137,167],"define":[139],"Experimental":[150],"results":[151],"Breast":[153],"invasive":[154],"carcinoma":[155],"Stomach":[157],"adenocarcinoma":[158],"datasets":[159],"show":[160],"that":[161],"effectively":[164],"fuse":[165],"indeed":[174],"cooperatively":[175],"trigger":[176],"cancers":[177],"are":[179],"valuable":[180],"carcinogenesis":[182],"analysis.":[183],"Ablation":[184],"justifies":[186],"a":[189],"comprehensive":[191],"cancer":[194],"fusing":[196],"data.":[198]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
