{"id":"https://openalex.org/W4410772492","doi":"https://doi.org/10.1186/s13040-025-00452-x","title":"Network-based analyses of multiomics data in biomedicine","display_name":"Network-based analyses of multiomics data in biomedicine","publication_year":2025,"publication_date":"2025-05-27","ids":{"openalex":"https://openalex.org/W4410772492","doi":"https://doi.org/10.1186/s13040-025-00452-x","pmid":"https://pubmed.ncbi.nlm.nih.gov/40426270"},"language":"en","primary_location":{"id":"doi:10.1186/s13040-025-00452-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-025-00452-x","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/s13040-025-00452-x","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":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/s13040-025-00452-x","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5055137078","display_name":"Rachit Kumar","orcid":"https://orcid.org/0000-0002-7736-3307"},"institutions":[{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rachit Kumar","raw_affiliation_strings":["Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA","Medical Scientist Training Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA","institution_ids":["https://openalex.org/I79576946"]},{"raw_affiliation_string":"Medical Scientist Training Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA","institution_ids":["https://openalex.org/I79576946"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078589723","display_name":"Joseph D. Romano","orcid":"https://orcid.org/0000-0002-7999-4399"},"institutions":[{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joseph D. Romano","raw_affiliation_strings":["Division of Informatics, Department of Biostatistics, Epidemiology & Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA","Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Informatics, Department of Biostatistics, Epidemiology & Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA","institution_ids":["https://openalex.org/I79576946"]},{"raw_affiliation_string":"Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA","institution_ids":["https://openalex.org/I79576946"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5081769614","display_name":"Marylyn D. Ritchie","orcid":"https://orcid.org/0000-0002-1208-1720"},"institutions":[{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Marylyn D. Ritchie","raw_affiliation_strings":["Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. marylyn@pennmedicine.upenn.edu","Division of Informatics, Department of Biostatistics, Epidemiology & Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. marylyn@pennmedicine.upenn.edu","Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. marylyn@pennmedicine.upenn.edu"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. marylyn@pennmedicine.upenn.edu","institution_ids":["https://openalex.org/I79576946"]},{"raw_affiliation_string":"Division of Informatics, Department of Biostatistics, Epidemiology & Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. marylyn@pennmedicine.upenn.edu","institution_ids":["https://openalex.org/I79576946"]},{"raw_affiliation_string":"Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. marylyn@pennmedicine.upenn.edu","institution_ids":["https://openalex.org/I79576946"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5081769614"],"corresponding_institution_ids":["https://openalex.org/I79576946"],"apc_list":{"value":2490,"currency":"USD","value_usd":2490},"apc_paid":{"value":2490,"currency":"USD","value_usd":2490},"fwci":4.36,"has_fulltext":true,"cited_by_count":11,"citation_normalized_percentile":{"value":0.95053482,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"18","issue":"1","first_page":"37","last_page":"37"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998999834060669,"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":0.9998999834060669,"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":0.996999979019165,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9876999855041504,"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/biomedicine","display_name":"Biomedicine","score":0.7965348958969116},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.6141897439956665},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4923149347305298},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.19136294722557068},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1797599494457245}],"concepts":[{"id":"https://openalex.org/C66782513","wikidata":"https://www.wikidata.org/wiki/Q864601","display_name":"Biomedicine","level":2,"score":0.7965348958969116},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.6141897439956665},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4923149347305298},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.19136294722557068},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1797599494457245}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13040-025-00452-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-025-00452-x","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/s13040-025-00452-x","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:40426270","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40426270","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:d9c639bee7374ef6979a8f6dc3a2e08a","is_oa":true,"landing_page_url":"https://doaj.org/article/d9c639bee7374ef6979a8f6dc3a2e08a","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":"BioData Mining, Vol 18, Iss 1, Pp 1-22 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12117783","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12117783","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":"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/s13040-025-00452-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-025-00452-x","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/s13040-025-00452-x","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":[{"id":"https://openalex.org/G1026427696","display_name":null,"funder_award_id":"R00-LM013646","funder_id":"https://openalex.org/F4320337372","funder_display_name":"U.S. National Library of Medicine"},{"id":"https://openalex.org/G1301277494","display_name":"Training Program in Computational Genomics","funder_award_id":"5t32hg000046-25","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G1579370318","display_name":null,"funder_award_id":"P30AG073105","funder_id":"https://openalex.org/F4320309370","funder_display_name":"University of Pennsylvania"},{"id":"https://openalex.org/G232507684","display_name":"Pharmacogenomics of HIV Therapy","funder_award_id":"2r01ai077505-12","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2446501125","display_name":"Artificial Intelligence Strategies for Alzheimer's Disease Research","funder_award_id":"3u01ag066833-04s1","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2858356746","display_name":null,"funder_award_id":"T32GM007170","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G3296670579","display_name":"Institutional Clinical and Translational Science Award","funder_award_id":"3ul1tr001878-06s1","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3443090233","display_name":"Enhancing biomedical research training program evaluation capacity","funder_award_id":"3t32gm007170-46s1","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G386151491","display_name":null,"funder_award_id":"P30AG073105","funder_id":"https://openalex.org/F4320337337","funder_display_name":"National Institute on Aging"},{"id":"https://openalex.org/G634671584","display_name":null,"funder_award_id":"U01 AG066833","funder_id":"https://openalex.org/F4320337337","funder_display_name":"National Institute on Aging"},{"id":"https://openalex.org/G813767937","display_name":null,"funder_award_id":"P30ES013508","funder_id":"https://openalex.org/F4320337361","funder_display_name":"National Institute of Environmental Health Sciences"},{"id":"https://openalex.org/G8499075012","display_name":"Discovering clinical endpoints of toxicity via graph machine learning and semantic data analysis","funder_award_id":"5r00lm013646-04","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320309370","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337337","display_name":"National Institute on Aging","ror":"https://ror.org/049v75w11"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337361","display_name":"National Institute of Environmental Health Sciences","ror":"https://ror.org/00j4k1h63"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4410772492.pdf","grobid_xml":"https://content.openalex.org/works/W4410772492.grobid-xml"},"referenced_works_count":80,"referenced_works":["https://openalex.org/W1990312420","https://openalex.org/W2062533676","https://openalex.org/W2100714130","https://openalex.org/W2108191052","https://openalex.org/W2134469465","https://openalex.org/W2164727176","https://openalex.org/W2276765849","https://openalex.org/W2329659234","https://openalex.org/W2460110786","https://openalex.org/W2559588208","https://openalex.org/W2579879861","https://openalex.org/W2611138580","https://openalex.org/W2769478615","https://openalex.org/W2790295707","https://openalex.org/W2912006845","https://openalex.org/W2912411326","https://openalex.org/W2922073769","https://openalex.org/W2950434449","https://openalex.org/W2954515343","https://openalex.org/W2956963717","https://openalex.org/W2970119293","https://openalex.org/W2995215286","https://openalex.org/W3003192283","https://openalex.org/W3006721466","https://openalex.org/W3025739297","https://openalex.org/W3033896008","https://openalex.org/W3039127696","https://openalex.org/W3085380432","https://openalex.org/W3093800747","https://openalex.org/W3112212292","https://openalex.org/W3116286104","https://openalex.org/W3124569282","https://openalex.org/W3129102067","https://openalex.org/W3134939446","https://openalex.org/W3139601120","https://openalex.org/W3165208819","https://openalex.org/W3170986249","https://openalex.org/W3173875945","https://openalex.org/W3194730353","https://openalex.org/W3213224786","https://openalex.org/W4200509736","https://openalex.org/W4205529838","https://openalex.org/W4206564180","https://openalex.org/W4206956476","https://openalex.org/W4210311596","https://openalex.org/W4210546025","https://openalex.org/W4220684263","https://openalex.org/W4225278475","https://openalex.org/W4283519547","https://openalex.org/W4294613167","https://openalex.org/W4297733535","https://openalex.org/W4300935520","https://openalex.org/W4307228554","https://openalex.org/W4307717106","https://openalex.org/W4309010659","https://openalex.org/W4312106615","https://openalex.org/W4319759388","https://openalex.org/W4323036511","https://openalex.org/W4327569165","https://openalex.org/W4327675690","https://openalex.org/W4362508795","https://openalex.org/W4366974966","https://openalex.org/W4366986862","https://openalex.org/W4376872641","https://openalex.org/W4379521442","https://openalex.org/W4380203269","https://openalex.org/W4385576721","https://openalex.org/W4386159972","https://openalex.org/W4389224344","https://openalex.org/W4390502662","https://openalex.org/W4391107757","https://openalex.org/W4392975641","https://openalex.org/W4399892951","https://openalex.org/W4400702846","https://openalex.org/W4401798479","https://openalex.org/W4402094108","https://openalex.org/W4402574423","https://openalex.org/W4402590079","https://openalex.org/W4403419477","https://openalex.org/W6786048916"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2017899917","https://openalex.org/W2080571363","https://openalex.org/W2481322495","https://openalex.org/W2898682754","https://openalex.org/W2889841093","https://openalex.org/W2151082141","https://openalex.org/W2365236913"],"abstract_inverted_index":{"Network":[0],"representations":[1,101],"of":[2,13,68,104,111,129],"data":[3,26,57,75,105],"are":[4],"designed":[5],"to":[6,124],"encode":[7],"relationships":[8,70],"between":[9,15,44],"concepts":[10],"as":[11,132,134],"sets":[12],"edges":[14],"nodes.":[16],"Human":[17],"biology":[18],"is":[19,23,37],"inherently":[20],"complex":[21],"and":[22,43,51,88,102,114,121,127],"represented":[24],"by":[25],"that":[27,40],"often":[28],"exists":[29,41],"in":[30,58,98,106,108],"a":[31,59],"hierarchical":[32],"nature.":[33],"One":[34],"canonical":[35],"example":[36],"the":[38,65,109,135,140],"relationship":[39],"within":[42],"various":[45,72,95,130],"-omics":[46],"datasets,":[47],"including":[48,77],"genomics,":[49],"transcriptomics,":[50],"proteomics,":[52],"among":[53],"others.":[54],"Encoding":[55],"such":[56,69],"network-based":[60],"or":[61],"graph-based":[62],"representation":[63],"allows":[64],"explicit":[66],"incorporation":[67],"into":[71,119],"biomedical":[73],"big":[74],"tasks,":[76],"(but":[78],"not":[79],"limited":[80],"to)":[81],"disease":[82],"subtyping,":[83],"interaction":[84],"prediction,":[85],"biomarker":[86],"identification,":[87],"patient":[89],"classification.":[90],"This":[91],"review":[92],"will":[93],"present":[94],"existing":[96],"approaches":[97,131],"using":[99],"network":[100],"analysis":[103],"multiomics":[107],"framework":[110],"deep":[112],"learning":[113,116],"machine":[115],"approaches,":[117,123],"subdivided":[118],"supervised":[120],"unsupervised":[122],"identify":[125],"benefits":[126],"drawbacks":[128],"well":[133],"possible":[136],"next":[137],"steps":[138],"for":[139],"field.":[141]},"counts_by_year":[{"year":2026,"cited_by_count":8},{"year":2025,"cited_by_count":3}],"updated_date":"2026-08-08T07:41:36.138363","created_date":"2025-10-10T00:00:00"}
