{"id":"https://openalex.org/W4408957790","doi":"https://doi.org/10.1186/s13040-025-00442-z","title":"Network-based multi-omics integrative analysis methods in drug discovery: a systematic review","display_name":"Network-based multi-omics integrative analysis methods in drug discovery: a systematic review","publication_year":2025,"publication_date":"2025-03-28","ids":{"openalex":"https://openalex.org/W4408957790","doi":"https://doi.org/10.1186/s13040-025-00442-z","pmid":"https://pubmed.ncbi.nlm.nih.gov/40155979"},"language":"en","primary_location":{"id":"doi:10.1186/s13040-025-00442-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-025-00442-z","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/s13040-025-00442-z","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioData Mining","raw_type":"journal-article"},"type":"review","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/s13040-025-00442-z","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101542494","display_name":"Wei Jiang","orcid":"https://orcid.org/0000-0002-0068-8664"},"institutions":[{"id":"https://openalex.org/I75900474","display_name":"Hubei University","ror":"https://ror.org/03a60m280","country_code":"CN","type":"education","lineage":["https://openalex.org/I75900474"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wei Jiang","raw_affiliation_strings":["School of Life Sciences, Hubei University, Wuhan, China"],"affiliations":[{"raw_affiliation_string":"School of Life Sciences, Hubei University, Wuhan, China","institution_ids":["https://openalex.org/I75900474"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011295525","display_name":"Weicai Ye","orcid":"https://orcid.org/0000-0001-6215-1347"},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Weicai Ye","raw_affiliation_strings":["School of Computer Science and Engineering, Guangdong Province Key Laboratory of Computational Science, National Engineering Laboratory for Big Data Analysis and Application, Sun Yat-sen University, Guangzhou, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Guangdong Province Key Laboratory of Computational Science, National Engineering Laboratory for Big Data Analysis and Application, Sun Yat-sen University, Guangzhou, China","institution_ids":["https://openalex.org/I157773358"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051320768","display_name":"Xiaoming Tan","orcid":"https://orcid.org/0000-0002-1258-247X"},"institutions":[{"id":"https://openalex.org/I75900474","display_name":"Hubei University","ror":"https://ror.org/03a60m280","country_code":"CN","type":"education","lineage":["https://openalex.org/I75900474"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaoming Tan","raw_affiliation_strings":["School of Life Sciences, Hubei University, Wuhan, China"],"affiliations":[{"raw_affiliation_string":"School of Life Sciences, Hubei University, Wuhan, China","institution_ids":["https://openalex.org/I75900474"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5048170064","display_name":"Yun\u2010Juan Bao","orcid":"https://orcid.org/0000-0002-2654-2321"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Yun-Juan Bao","raw_affiliation_strings":[", No.368 Youyi Avenue, Wuhan, 430062, China. yjbao@hubu.edu.cn","School of Life Sciences, Hubei University, Wuhan, China. yjbao@hubu.edu.cn","No.368 Youyi Avenue, Wuhan, 430062, China"],"affiliations":[{"raw_affiliation_string":", No.368 Youyi Avenue, Wuhan, 430062, China. yjbao@hubu.edu.cn","institution_ids":[]},{"raw_affiliation_string":"School of Life Sciences, Hubei University, Wuhan, China. yjbao@hubu.edu.cn","institution_ids":[]},{"raw_affiliation_string":"No.368 Youyi Avenue, Wuhan, 430062, China","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5048170064"],"corresponding_institution_ids":[],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":39.9083,"has_fulltext":false,"cited_by_count":51,"citation_normalized_percentile":{"value":0.99919003,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"18","issue":"1","first_page":"27","last_page":"27"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9994999766349792,"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":0.9994999766349792,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9829999804496765,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9775999784469604,"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/computer-science","display_name":"Computer science","score":0.6349189877510071},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.5441159009933472},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.49405577778816223},{"id":"https://openalex.org/keywords/omics","display_name":"Omics","score":0.4740431308746338},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3663528561592102},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3618343472480774},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.2148011028766632},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1226506233215332}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6349189877510071},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.5441159009933472},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.49405577778816223},{"id":"https://openalex.org/C157585117","wikidata":"https://www.wikidata.org/wiki/Q158666","display_name":"Omics","level":2,"score":0.4740431308746338},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3663528561592102},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3618343472480774},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2148011028766632},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1226506233215332}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13040-025-00442-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-025-00442-z","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/s13040-025-00442-z","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioData Mining","raw_type":"journal-article"},{"id":"pmid:40155979","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40155979","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":"BioData mining","raw_type":null},{"id":"pmh:oai:doaj.org/article:b5bac95096e949f6a7a1bac92bc25114","is_oa":true,"landing_page_url":"https://doaj.org/article/b5bac95096e949f6a7a1bac92bc25114","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BioData Mining, Vol 18, Iss 1, Pp 1-29 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:11954193","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11954193","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BioData Min","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13040-025-00442-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-025-00442-z","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/s13040-025-00442-z","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioData Mining","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4408957790.pdf"},"referenced_works_count":132,"referenced_works":["https://openalex.org/W953912505","https://openalex.org/W1963522244","https://openalex.org/W1979946545","https://openalex.org/W1987219048","https://openalex.org/W2002582122","https://openalex.org/W2009313526","https://openalex.org/W2009742334","https://openalex.org/W2018838463","https://openalex.org/W2036614090","https://openalex.org/W2088891952","https://openalex.org/W2096283457","https://openalex.org/W2096822173","https://openalex.org/W2108068107","https://openalex.org/W2114759909","https://openalex.org/W2119412782","https://openalex.org/W2132992030","https://openalex.org/W2134469465","https://openalex.org/W2148851475","https://openalex.org/W2158485828","https://openalex.org/W2180749449","https://openalex.org/W2264481086","https://openalex.org/W2329674354","https://openalex.org/W2344976140","https://openalex.org/W2401761997","https://openalex.org/W2402270313","https://openalex.org/W2411666094","https://openalex.org/W2537679995","https://openalex.org/W2557833574","https://openalex.org/W2583911935","https://openalex.org/W2596629674","https://openalex.org/W2599403676","https://openalex.org/W2601520864","https://openalex.org/W2624021832","https://openalex.org/W2624850887","https://openalex.org/W2733047156","https://openalex.org/W2764110565","https://openalex.org/W2767281692","https://openalex.org/W2768921712","https://openalex.org/W2769383666","https://openalex.org/W2776619248","https://openalex.org/W2786016794","https://openalex.org/W2794479004","https://openalex.org/W2810986024","https://openalex.org/W2826750344","https://openalex.org/W2883248903","https://openalex.org/W2884639138","https://openalex.org/W2901601040","https://openalex.org/W2901775822","https://openalex.org/W2912041567","https://openalex.org/W2917087462","https://openalex.org/W2920670758","https://openalex.org/W2920961981","https://openalex.org/W2921853542","https://openalex.org/W2938156108","https://openalex.org/W2938634307","https://openalex.org/W2944727022","https://openalex.org/W2954515343","https://openalex.org/W2978726586","https://openalex.org/W2999771243","https://openalex.org/W3000043291","https://openalex.org/W3003038853","https://openalex.org/W3003192283","https://openalex.org/W3005769002","https://openalex.org/W3007701192","https://openalex.org/W3008895300","https://openalex.org/W3021373494","https://openalex.org/W3034111501","https://openalex.org/W3034288498","https://openalex.org/W3085362629","https://openalex.org/W3087138092","https://openalex.org/W3096828292","https://openalex.org/W3097145107","https://openalex.org/W3100788068","https://openalex.org/W3102745472","https://openalex.org/W3102943483","https://openalex.org/W3103118351","https://openalex.org/W3118955581","https://openalex.org/W3125046749","https://openalex.org/W3130891725","https://openalex.org/W3133594175","https://openalex.org/W3134580323","https://openalex.org/W3137962378","https://openalex.org/W3147787140","https://openalex.org/W3150675149","https://openalex.org/W3152893301","https://openalex.org/W3156270925","https://openalex.org/W3159101980","https://openalex.org/W3160534044","https://openalex.org/W3192677404","https://openalex.org/W3193170798","https://openalex.org/W3195317458","https://openalex.org/W3201067114","https://openalex.org/W3204024051","https://openalex.org/W4200581587","https://openalex.org/W4206010710","https://openalex.org/W4206718607","https://openalex.org/W4225305704","https://openalex.org/W4280603130","https://openalex.org/W4282939468","https://openalex.org/W4283784350","https://openalex.org/W4292723103","https://openalex.org/W4295128409","https://openalex.org/W4295885518","https://openalex.org/W4296480486","https://openalex.org/W4306353209","https://openalex.org/W4306644994","https://openalex.org/W4307571978","https://openalex.org/W4308834893","https://openalex.org/W4309848592","https://openalex.org/W4310701303","https://openalex.org/W4311666191","https://openalex.org/W4319813194","https://openalex.org/W4321248593","https://openalex.org/W4321452549","https://openalex.org/W4321611238","https://openalex.org/W4365455465","https://openalex.org/W4385841574","https://openalex.org/W4386471322","https://openalex.org/W4386758612","https://openalex.org/W4387111992","https://openalex.org/W4388455891","https://openalex.org/W4390116356","https://openalex.org/W4391107757","https://openalex.org/W4391168615","https://openalex.org/W4391338580","https://openalex.org/W4392346236","https://openalex.org/W4395660270","https://openalex.org/W4398226202","https://openalex.org/W4399889929","https://openalex.org/W4401567681","https://openalex.org/W4402574423","https://openalex.org/W4406050423"],"related_works":["https://openalex.org/W177137871","https://openalex.org/W4292302930","https://openalex.org/W4386960635","https://openalex.org/W2594649246","https://openalex.org/W2924366642","https://openalex.org/W2013003323","https://openalex.org/W1981076832","https://openalex.org/W2024773645","https://openalex.org/W2001717001","https://openalex.org/W2043147644"],"abstract_inverted_index":{"The":[0],"integration":[1,42,61,128],"of":[2,28,55,89,95,113],"multi-omics":[3,22,41,60,127],"data":[4,140],"from":[5],"diverse":[6],"high-throughput":[7],"technologies":[8],"has":[9,129],"revolutionized":[10],"drug":[11,48,64,96,99,102,106,133],"discovery.":[12,49],"While":[13,125],"various":[14],"network-based":[15,38,59,126],"methods":[16,30,62,68,91,115],"have":[17],"been":[18],"developed":[19],"to":[20,36],"integrate":[21],"data,":[23],"systematic":[24],"evaluation":[25,161],"and":[26,43,66,80,105,108,120,142,152,158],"comparison":[27],"these":[29],"remain":[31,136],"challenging.":[32],"This":[33],"review":[34,54],"aims":[35],"analyze":[37],"approaches":[39],"for":[40],"evaluate":[44],"their":[45,118],"applications":[46,88],"in":[47,63,92,122,132,137],"We":[50,84],"conducted":[51],"a":[52],"comprehensive":[53],"literature":[56],"(2015-2024)":[57],"on":[58,149],"discovery,":[65,97,134],"categorized":[67],"into":[69],"four":[70],"primary":[71],"types:":[72],"network":[73,81],"propagation/diffusion,":[74],"similarity-based":[75],"approaches,":[76],"graph":[77],"neural":[78],"networks,":[79],"inference":[82],"models.":[83],"also":[85],"discussed":[86],"the":[87,90,111,114],"three":[93],"scenario":[94],"including":[98],"target":[100],"identification,":[101],"response":[103],"prediction,":[104],"repurposing,":[107],"finally":[109],"evaluated":[110],"performance":[112],"by":[116],"highlighting":[117],"advantages":[119],"limitations":[121],"specific":[123],"applications.":[124],"shown":[130],"promise":[131],"challenges":[135],"computational":[138],"scalability,":[139],"integration,":[141],"biological":[143],"interpretation.":[144],"Future":[145],"developments":[146],"should":[147],"focus":[148],"incorporating":[150],"temporal":[151],"spatial":[153],"dynamics,":[154],"improving":[155],"model":[156],"interpretability,":[157],"establishing":[159],"standardized":[160],"frameworks.":[162]},"counts_by_year":[{"year":2026,"cited_by_count":21},{"year":2025,"cited_by_count":30}],"updated_date":"2026-04-04T08:04:53.788161","created_date":"2025-10-10T00:00:00"}
