{"id":"https://openalex.org/W4309243977","doi":"https://doi.org/10.1093/bioinformatics/btac735","title":"Gene set proximity analysis: expanding gene set enrichment analysis through learned geometric embeddings, with drug-repurposing applications in COVID-19","display_name":"Gene set proximity analysis: expanding gene set enrichment analysis through learned geometric embeddings, with drug-repurposing applications in COVID-19","publication_year":2022,"publication_date":"2022-11-17","ids":{"openalex":"https://openalex.org/W4309243977","doi":"https://doi.org/10.1093/bioinformatics/btac735","pmid":"https://pubmed.ncbi.nlm.nih.gov/36394254"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac735","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac735","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac735/48448718/btac735.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac735/48448718/btac735.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5067002378","display_name":"Henry C. Cousins","orcid":"https://orcid.org/0000-0002-8694-0604"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Henry Cousins","raw_affiliation_strings":["Department of Biomedical Data Science, Stanford University School of Medicine , Stanford, CA 94305, USA"],"raw_orcid":"https://orcid.org/0000-0002-8694-0604","affiliations":[{"raw_affiliation_string":"Department of Biomedical Data Science, Stanford University School of Medicine , Stanford, CA 94305, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041309921","display_name":"Taryn O. Hall","orcid":"https://orcid.org/0000-0001-6018-8613"},"institutions":[{"id":"https://openalex.org/I4210124242","display_name":"Optum (United States)","ror":"https://ror.org/0370sjj75","country_code":"US","type":"company","lineage":["https://openalex.org/I4210124242"]},{"id":"https://openalex.org/I4210133485","display_name":"UnitedHealth Group (United States)","ror":"https://ror.org/04a8rt780","country_code":"US","type":"company","lineage":["https://openalex.org/I4210133485"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Taryn Hall","raw_affiliation_strings":["Optum Labs at UnitedHealth Group , Minneapolis, MN 55343, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Optum Labs at UnitedHealth Group , Minneapolis, MN 55343, USA","institution_ids":["https://openalex.org/I4210124242","https://openalex.org/I4210133485"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103228987","display_name":"Yinglong Guo","orcid":"https://orcid.org/0000-0003-3456-4077"},"institutions":[{"id":"https://openalex.org/I4210124242","display_name":"Optum (United States)","ror":"https://ror.org/0370sjj75","country_code":"US","type":"company","lineage":["https://openalex.org/I4210124242"]},{"id":"https://openalex.org/I4210133485","display_name":"UnitedHealth Group (United States)","ror":"https://ror.org/04a8rt780","country_code":"US","type":"company","lineage":["https://openalex.org/I4210133485"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yinglong Guo","raw_affiliation_strings":["Optum Labs at UnitedHealth Group , Minneapolis, MN 55343, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Optum Labs at UnitedHealth Group , Minneapolis, MN 55343, USA","institution_ids":["https://openalex.org/I4210124242","https://openalex.org/I4210133485"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067484677","display_name":"Luke Tso","orcid":null},"institutions":[{"id":"https://openalex.org/I4210124242","display_name":"Optum (United States)","ror":"https://ror.org/0370sjj75","country_code":"US","type":"company","lineage":["https://openalex.org/I4210124242"]},{"id":"https://openalex.org/I4210133485","display_name":"UnitedHealth Group (United States)","ror":"https://ror.org/04a8rt780","country_code":"US","type":"company","lineage":["https://openalex.org/I4210133485"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Luke Tso","raw_affiliation_strings":["Optum Labs at UnitedHealth Group , Minneapolis, MN 55343, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Optum Labs at UnitedHealth Group , Minneapolis, MN 55343, USA","institution_ids":["https://openalex.org/I4210124242","https://openalex.org/I4210133485"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058079833","display_name":"Kathy Tzeng","orcid":null},"institutions":[{"id":"https://openalex.org/I4210124242","display_name":"Optum (United States)","ror":"https://ror.org/0370sjj75","country_code":"US","type":"company","lineage":["https://openalex.org/I4210124242"]},{"id":"https://openalex.org/I4210133485","display_name":"UnitedHealth Group (United States)","ror":"https://ror.org/04a8rt780","country_code":"US","type":"company","lineage":["https://openalex.org/I4210133485"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kathy T H Tzeng","raw_affiliation_strings":["Optum Labs at UnitedHealth Group , Minneapolis, MN 55343, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Optum Labs at UnitedHealth Group , Minneapolis, MN 55343, USA","institution_ids":["https://openalex.org/I4210124242","https://openalex.org/I4210133485"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080765172","display_name":"Le Cong","orcid":"https://orcid.org/0000-0003-4725-8714"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Le Cong","raw_affiliation_strings":["Department of Genetics, Stanford University School of Medicine , Stanford, CA 94305, USA","Department of Pathology, Stanford University School of Medicine , Stanford, CA 94305, USA"],"raw_orcid":"https://orcid.org/0000-0003-4725-8714","affiliations":[{"raw_affiliation_string":"Department of Genetics, Stanford University School of Medicine , Stanford, CA 94305, USA","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Department of Pathology, Stanford University School of Medicine , Stanford, CA 94305, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5084043782","display_name":"Russ B. Altman","orcid":"https://orcid.org/0000-0003-3859-2905"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Russ B Altman","raw_affiliation_strings":["Department of Bioengineering, Stanford University , Stanford, CA 94305, USA","Department of Biomedical Data Science, Stanford University School of Medicine , Stanford, CA 94305, USA","Department of Genetics, Stanford University School of Medicine , Stanford, CA 94305, USA","Department of Medicine, Stanford University School of Medicine , Stanford, CA 94305, USA"],"raw_orcid":"https://orcid.org/0000-0003-3859-2905","affiliations":[{"raw_affiliation_string":"Department of Bioengineering, Stanford University , Stanford, CA 94305, USA","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Department of Biomedical Data Science, Stanford University School of Medicine , Stanford, CA 94305, USA","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Department of Genetics, Stanford University School of Medicine , Stanford, CA 94305, USA","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Department of Medicine, Stanford University School of Medicine , Stanford, CA 94305, USA","institution_ids":["https://openalex.org/I97018004"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5067002378","https://openalex.org/A5084043782"],"corresponding_institution_ids":["https://openalex.org/I97018004"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.7047,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.66432986,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":98},"biblio":{"volume":"39","issue":"1","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":0.9028000235557556,"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":0.9028000235557556,"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":0.022199999541044235,"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/T10261","display_name":"Genetic Associations and Epidemiology","score":0.014999999664723873,"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/repurposing","display_name":"Repurposing","score":0.8936758041381836},{"id":"https://openalex.org/keywords/drug-repositioning","display_name":"Drug repositioning","score":0.8206344842910767},{"id":"https://openalex.org/keywords/coronavirus-disease-2019","display_name":"Coronavirus disease 2019 (COVID-19)","score":0.7005882263183594},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.6452893018722534},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5944374799728394},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5618278980255127},{"id":"https://openalex.org/keywords/severe-acute-respiratory-syndrome-coronavirus-2","display_name":"Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)","score":0.4767407178878784},{"id":"https://openalex.org/keywords/2019-20-coronavirus-outbreak","display_name":"2019-20 coronavirus outbreak","score":0.44562119245529175},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4319131672382355},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.39674270153045654},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3200072944164276},{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.3155617117881775},{"id":"https://openalex.org/keywords/virology","display_name":"Virology","score":0.3068162202835083},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.16544675827026367},{"id":"https://openalex.org/keywords/pharmacology","display_name":"Pharmacology","score":0.13506922125816345},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.07366722822189331}],"concepts":[{"id":"https://openalex.org/C519536355","wikidata":"https://www.wikidata.org/wiki/Q21021151","display_name":"Repurposing","level":2,"score":0.8936758041381836},{"id":"https://openalex.org/C103637391","wikidata":"https://www.wikidata.org/wiki/Q5308921","display_name":"Drug repositioning","level":3,"score":0.8206344842910767},{"id":"https://openalex.org/C3008058167","wikidata":"https://www.wikidata.org/wiki/Q84263196","display_name":"Coronavirus disease 2019 (COVID-19)","level":4,"score":0.7005882263183594},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.6452893018722534},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5944374799728394},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5618278980255127},{"id":"https://openalex.org/C3007834351","wikidata":"https://www.wikidata.org/wiki/Q82069695","display_name":"Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)","level":5,"score":0.4767407178878784},{"id":"https://openalex.org/C3006700255","wikidata":"https://www.wikidata.org/wiki/Q81068910","display_name":"2019-20 coronavirus outbreak","level":3,"score":0.44562119245529175},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4319131672382355},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.39674270153045654},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3200072944164276},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.3155617117881775},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.3068162202835083},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.16544675827026367},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.13506922125816345},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.07366722822189331},{"id":"https://openalex.org/C116675565","wikidata":"https://www.wikidata.org/wiki/Q3241045","display_name":"Outbreak","level":2,"score":0.0},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.0},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.0},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.0},{"id":"https://openalex.org/C524204448","wikidata":"https://www.wikidata.org/wiki/Q788926","display_name":"Infectious disease (medical specialty)","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","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":"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":"D012189","descriptor_name":"Retrospective Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012189","descriptor_name":"Retrospective Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012189","descriptor_name":"Retrospective Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012189","descriptor_name":"Retrospective Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012189","descriptor_name":"Retrospective Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012189","descriptor_name":"Retrospective Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058492","descriptor_name":"Drug Repositioning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058492","descriptor_name":"Drug Repositioning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058492","descriptor_name":"Drug Repositioning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058492","descriptor_name":"Drug Repositioning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058492","descriptor_name":"Drug Repositioning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058492","descriptor_name":"Drug Repositioning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btac735","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac735","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac735/48448718/btac735.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:9805577","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9805577","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmid:36394254","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36394254","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}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btac735","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac735","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac735/48448718/btac735.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.5299999713897705}],"awards":[{"id":"https://openalex.org/G1185824193","display_name":"Combining systems biology and structural biology to find new therapeutics","funder_award_id":"5r01gm102365-08","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G1743763002","display_name":null,"funder_award_id":"R01GM102365","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G4195985275","display_name":"Medical Scientist Training Program","funder_award_id":"5t32gm007365-43","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5463676585","display_name":null,"funder_award_id":"T32-GM007365","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320318127","display_name":"UnitedHealth Group","ror":"https://ror.org/04a8rt780"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4309243977.pdf","grobid_xml":"https://content.openalex.org/works/W4309243977.grobid-xml"},"referenced_works_count":49,"referenced_works":["https://openalex.org/W2004670370","https://openalex.org/W2009274826","https://openalex.org/W2070050178","https://openalex.org/W2084533385","https://openalex.org/W2097948046","https://openalex.org/W2103017472","https://openalex.org/W2110687686","https://openalex.org/W2112220625","https://openalex.org/W2123106337","https://openalex.org/W2129099812","https://openalex.org/W2130410032","https://openalex.org/W2134736660","https://openalex.org/W2142879323","https://openalex.org/W2155330008","https://openalex.org/W2158217645","https://openalex.org/W2166574880","https://openalex.org/W2277498598","https://openalex.org/W2341504574","https://openalex.org/W2433454023","https://openalex.org/W2511125937","https://openalex.org/W2537623931","https://openalex.org/W2559588208","https://openalex.org/W2767490506","https://openalex.org/W2776525882","https://openalex.org/W2803116354","https://openalex.org/W2904964912","https://openalex.org/W2962756421","https://openalex.org/W2996005515","https://openalex.org/W3004747635","https://openalex.org/W3027187955","https://openalex.org/W3035387075","https://openalex.org/W3039150496","https://openalex.org/W3093900830","https://openalex.org/W3094597057","https://openalex.org/W3110976643","https://openalex.org/W3111023021","https://openalex.org/W3112600195","https://openalex.org/W3119033482","https://openalex.org/W3128897426","https://openalex.org/W3130155181","https://openalex.org/W3165113039","https://openalex.org/W3183460801","https://openalex.org/W3196127692","https://openalex.org/W3196971188","https://openalex.org/W3204079698","https://openalex.org/W3213672354","https://openalex.org/W4297571622","https://openalex.org/W6707620307","https://openalex.org/W6762654376"],"related_works":["https://openalex.org/W2899096130","https://openalex.org/W3190782215","https://openalex.org/W2902729297","https://openalex.org/W3110500039","https://openalex.org/W4255531208","https://openalex.org/W4396858017","https://openalex.org/W4400165188","https://openalex.org/W4206422705","https://openalex.org/W4320009247","https://openalex.org/W3186872001"],"abstract_inverted_index":{"MOTIVATION:":[0],"Gene":[1],"set":[2,18,53,67,109],"analysis":[3,55,69,111,140],"methods":[4],"rely":[5],"on":[6],"knowledge-based":[7],"representations":[8,27],"of":[9,15,28,43,51,91,106,141],"genetic":[10,29],"interactions":[11,30],"in":[12,83],"the":[13,40],"form":[14],"both":[16],"gene":[17,52,66,85,96,108],"collections":[19],"and":[20,157],"protein-protein":[21],"interaction":[22],"(PPI)":[23],"networks.":[24],"However,":[25],"explicit":[26],"often":[31],"fail":[32],"to":[33,56,79,103,121],"capture":[34],"complex":[35],"interdependencies":[36],"among":[37],"genes,":[38],"limiting":[39],"analytic":[41],"power":[42],"such":[44],"methods.":[45],"RESULTS:":[46],"We":[47,117],"propose":[48],"an":[49],"extension":[50],"enrichment":[54,92,110],"a":[57,104,113,149,154,160,175],"latent":[58],"embedding":[59],"space":[60],"reflecting":[61],"PPI":[62],"network":[63],"topology,":[64],"called":[65],"proximity":[68],"(GSPA).":[70],"Compared":[71],"with":[72,126],"existing":[73],"methods,":[74],"GSPA":[75,98,169],"provides":[76],"improved":[77],"ability":[78],"identify":[80,122],"disease-associated":[81],"pathways":[82],"disease-matched":[84],"expression":[86],"datasets,":[87],"while":[88],"improving":[89],"reproducibility":[90],"statistics":[93],"for":[94,151,163,172],"similar":[95],"sets.":[97],"is":[99,170],"statistically":[100],"straightforward,":[101],"reducing":[102],"version":[105],"traditional":[107],"through":[112,137],"single":[114],"user-defined":[115],"parameter.":[116],"apply":[118],"our":[119,133],"method":[120],"novel":[123],"drug":[124,134],"associations":[125],"SARS-CoV-2":[127],"viral":[128],"entry.":[129],"Finally,":[130],"we":[131],"validate":[132],"association":[135],"predictions":[136],"retrospective":[138],"clinical":[139],"claims":[142],"data":[143,184],"from":[144],"8":[145],"million":[146],"patients,":[147],"supporting":[148],"role":[150],"gabapentin":[152],"as":[153,159,174],"risk":[155],"factor":[156,162],"metformin":[158],"protective":[161],"severe":[164],"COVID-19.":[165],"AVAILABILITY":[166],"AND":[167],"IMPLEMENTATION:":[168],"available":[171,186],"download":[173],"command-line":[176],"Python":[177],"package":[178],"at":[179,187],"https://github.com/henrycousins/gspa.":[180],"SUPPLEMENTARY":[181],"INFORMATION:":[182],"Supplementary":[183],"are":[185],"Bioinformatics":[188],"online.":[189]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":5}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2025-10-10T00:00:00"}
