{"id":"https://openalex.org/W4377225074","doi":"https://doi.org/10.1093/bioinformatics/btad333","title":"MultiNEP: a multi-omics network enhancement framework for prioritizing disease genes and metabolites simultaneously","display_name":"MultiNEP: a multi-omics network enhancement framework for prioritizing disease genes and metabolites simultaneously","publication_year":2023,"publication_date":"2023-05-22","ids":{"openalex":"https://openalex.org/W4377225074","doi":"https://doi.org/10.1093/bioinformatics/btad333","pmid":"https://pubmed.ncbi.nlm.nih.gov/37216914"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad333","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad333","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad333/50418334/btad333.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad333/50418334/btad333.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5049387413","display_name":"Zhuoran Xu","orcid":"https://orcid.org/0000-0001-6733-541X"},"institutions":[{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]},{"id":"https://openalex.org/I4387153466","display_name":"Weill Cornell Medicine","ror":"https://ror.org/02r109517","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295","https://openalex.org/I4387153466"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhuoran Xu","raw_affiliation_strings":["Department of Pathology and Laboratory Medicine, Weill Cornell Medicine , New York, NY 10065, United States"],"affiliations":[{"raw_affiliation_string":"Department of Pathology and Laboratory Medicine, Weill Cornell Medicine , New York, NY 10065, United States","institution_ids":["https://openalex.org/I205783295","https://openalex.org/I4387153466"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079978893","display_name":"Luigi Marchionni","orcid":"https://orcid.org/0000-0002-7336-8071"},"institutions":[{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]},{"id":"https://openalex.org/I4387153466","display_name":"Weill Cornell Medicine","ror":"https://ror.org/02r109517","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295","https://openalex.org/I4387153466"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Luigi Marchionni","raw_affiliation_strings":["Department of Pathology and Laboratory Medicine, Weill Cornell Medicine , New York, NY 10065, United States"],"affiliations":[{"raw_affiliation_string":"Department of Pathology and Laboratory Medicine, Weill Cornell Medicine , New York, NY 10065, United States","institution_ids":["https://openalex.org/I205783295","https://openalex.org/I4387153466"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100375568","display_name":"Shuang Wang","orcid":"https://orcid.org/0000-0002-1693-6888"},"institutions":[{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Shuang Wang","raw_affiliation_strings":["Department of Biostatistics, Columbia University , New York, NY 10032, United States"],"affiliations":[{"raw_affiliation_string":"Department of Biostatistics, Columbia University , New York, NY 10032, United States","institution_ids":["https://openalex.org/I78577930"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5100375568"],"corresponding_institution_ids":["https://openalex.org/I78577930"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.3079,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.62802029,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":96},"biblio":{"volume":"39","issue":"6","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":0.9998999834060669,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9965999722480774,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.994700014591217,"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/metabolite","display_name":"Metabolite","score":0.6929435729980469},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.6583836078643799},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6516402363777161},{"id":"https://openalex.org/keywords/metabolome","display_name":"Metabolome","score":0.6125683784484863},{"id":"https://openalex.org/keywords/metabolomics","display_name":"Metabolomics","score":0.5835429430007935},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.531947910785675},{"id":"https://openalex.org/keywords/omics","display_name":"Omics","score":0.47902289032936096},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.47553181648254395},{"id":"https://openalex.org/keywords/metabolic-network","display_name":"Metabolic network","score":0.4733869135379791},{"id":"https://openalex.org/keywords/toxicogenomics","display_name":"Toxicogenomics","score":0.44639524817466736},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.43610838055610657},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.4298418462276459},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.35725846886634827},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3444540202617645},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.24265366792678833},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.22912681102752686},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.1297016739845276},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.05875155329704285}],"concepts":[{"id":"https://openalex.org/C2777477808","wikidata":"https://www.wikidata.org/wiki/Q407595","display_name":"Metabolite","level":2,"score":0.6929435729980469},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.6583836078643799},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6516402363777161},{"id":"https://openalex.org/C135870905","wikidata":"https://www.wikidata.org/wiki/Q903667","display_name":"Metabolome","level":3,"score":0.6125683784484863},{"id":"https://openalex.org/C21565614","wikidata":"https://www.wikidata.org/wiki/Q12149006","display_name":"Metabolomics","level":2,"score":0.5835429430007935},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.531947910785675},{"id":"https://openalex.org/C157585117","wikidata":"https://www.wikidata.org/wiki/Q158666","display_name":"Omics","level":2,"score":0.47902289032936096},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.47553181648254395},{"id":"https://openalex.org/C101810790","wikidata":"https://www.wikidata.org/wiki/Q2263094","display_name":"Metabolic network","level":2,"score":0.4733869135379791},{"id":"https://openalex.org/C93231420","wikidata":"https://www.wikidata.org/wiki/Q841450","display_name":"Toxicogenomics","level":4,"score":0.44639524817466736},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.43610838055610657},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.4298418462276459},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.35725846886634827},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3444540202617645},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.24265366792678833},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.22912681102752686},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.1297016739845276},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.05875155329704285}],"mesh":[{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","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":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055442","descriptor_name":"Metabolome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055442","descriptor_name":"Metabolome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055442","descriptor_name":"Metabolome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055442","descriptor_name":"Metabolome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btad333","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad333","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad333/50418334/btad333.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"pmid:37216914","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37216914","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10250081","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10250081","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10250081/pdf/btad333.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad333","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad333","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad333/50418334/btad333.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":[{"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals","score":0.4300000071525574}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4377225074.pdf"},"referenced_works_count":30,"referenced_works":["https://openalex.org/W1960974681","https://openalex.org/W2044055595","https://openalex.org/W2051436873","https://openalex.org/W2108723074","https://openalex.org/W2113613985","https://openalex.org/W2114090713","https://openalex.org/W2119220491","https://openalex.org/W2131347449","https://openalex.org/W2154654747","https://openalex.org/W2164298117","https://openalex.org/W2179544415","https://openalex.org/W2423570221","https://openalex.org/W2537679995","https://openalex.org/W2720897370","https://openalex.org/W2789128799","https://openalex.org/W2790295707","https://openalex.org/W2945582641","https://openalex.org/W2988201157","https://openalex.org/W2990251597","https://openalex.org/W3042999896","https://openalex.org/W3044988544","https://openalex.org/W3083885734","https://openalex.org/W3093449011","https://openalex.org/W3112212292","https://openalex.org/W3123070532","https://openalex.org/W3135743495","https://openalex.org/W3176109697","https://openalex.org/W3177488148","https://openalex.org/W4294326454","https://openalex.org/W4297894402"],"related_works":["https://openalex.org/W3181218443","https://openalex.org/W3128373529","https://openalex.org/W2133150343","https://openalex.org/W2130939068","https://openalex.org/W3163717165","https://openalex.org/W2114466827","https://openalex.org/W2129949791","https://openalex.org/W2791736663","https://openalex.org/W2806770614","https://openalex.org/W2350653470"],"abstract_inverted_index":{"The":[0],"developed":[1],"MultiNEP":[2],"framework":[3],"is":[4],"implemented":[5],"in":[6],"an":[7],"R":[8],"package":[9],"and":[10],"available":[11],"at:":[12],"https://github.com/Karenxzr/MultiNep.":[13]},"counts_by_year":[{"year":2024,"cited_by_count":2}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}