{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,3]],"date-time":"2026-06-03T20:25:00Z","timestamp":1780518300129,"version":"3.54.1"},"reference-count":38,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2021,11,8]],"date-time":"2021-11-08T00:00:00Z","timestamp":1636329600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003725","name":"National Research Foundation of Korea","doi-asserted-by":"publisher","award":["2018R1A5A2025079"],"award-info":[{"award-number":["2018R1A5A2025079"]}],"id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003725","name":"National Research Foundation of Korea","doi-asserted-by":"publisher","award":["2018M3C9A5064709"],"award-info":[{"award-number":["2018M3C9A5064709"]}],"id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003725","name":"National Research Foundation of Korea","doi-asserted-by":"publisher","award":["2019M3A9B6065192"],"award-info":[{"award-number":["2019M3A9B6065192"]}],"id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Brain Korea 21"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,7]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Network medicine has proven useful for dissecting genetic organization of complex human diseases. We have previously published HumanNet, an integrated network of human genes for disease studies. Since the release of the last version of HumanNet, many large-scale protein\u2013protein interaction datasets have accumulated in public depositories. Additionally, the numbers of research papers and functional annotations for gene\u2013phenotype associations have increased significantly. Therefore, updating HumanNet is a timely task for further improvement of network-based research into diseases. Here, we present HumanNet v3 (https:\/\/www.inetbio.org\/humannet\/, covering 99.8% of human protein coding genes) constructed by means of the expanded data with improved network inference algorithms. HumanNet v3 supports a three-tier model: HumanNet-PI (a protein\u2013protein physical interaction network), HumanNet-FN (a functional gene network), and HumanNet-XC (a functional network extended by co-citation). Users can select a suitable tier of HumanNet for their study purpose. We showed that on disease gene predictions, HumanNet v3 outperforms both the previous HumanNet version and other integrated human gene networks. Furthermore, we demonstrated that HumanNet provides a feasible approach for selecting host genes likely to be associated with COVID-19.<\/jats:p>","DOI":"10.1093\/nar\/gkab1048","type":"journal-article","created":{"date-parts":[[2021,10,19]],"date-time":"2021-10-19T11:34:56Z","timestamp":1634643296000},"page":"D632-D639","source":"Crossref","is-referenced-by-count":131,"title":["HumanNet v3: an improved database of human gene networks for disease research"],"prefix":"10.1093","volume":"50","author":[{"given":"Chan Yeong","family":"Kim","sequence":"first","affiliation":[{"name":"Department of Biotechnology, College of Life Sciences and Biotechnology, Yonsei University, Seoul 03722, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Seungbyn","family":"Baek","sequence":"additional","affiliation":[{"name":"Department of Biotechnology, College of Life Sciences and Biotechnology, Yonsei University, Seoul 03722, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junha","family":"Cha","sequence":"additional","affiliation":[{"name":"Department of Biotechnology, College of Life Sciences and Biotechnology, Yonsei University, Seoul 03722, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sunmo","family":"Yang","sequence":"additional","affiliation":[{"name":"Department of Biotechnology, College of Life Sciences and Biotechnology, Yonsei University, Seoul 03722, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eiru","family":"Kim","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Edward\u00a0M","family":"Marcotte","sequence":"additional","affiliation":[{"name":"Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA"},{"name":"Department of Molecular Biosciences, University of Texas at Austin, TX 78712, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1880-3341","authenticated-orcid":false,"given":"Traver","family":"Hart","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3146-6180","authenticated-orcid":false,"given":"Insuk","family":"Lee","sequence":"additional","affiliation":[{"name":"Department of Biotechnology, College of Life Sciences and Biotechnology, Yonsei University, Seoul 03722, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,11,8]]},"reference":[{"key":"2022010507342029600_B1","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1038\/47048","article-title":"A combined algorithm for genome-wide prediction of protein function","volume":"402","author":"Marcotte","year":"1999","journal-title":"Nature"},{"key":"2022010507342029600_B2","doi-asserted-by":"crossref","first-page":"D605","DOI":"10.1093\/nar\/gkaa1074","article-title":"The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene\/measurement sets","volume":"49","author":"Szklarczyk","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2022010507342029600_B3","doi-asserted-by":"crossref","first-page":"166835","DOI":"10.1016\/j.jmb.2021.166835","article-title":"FunCoup 5: functional association networks in all domains of life, supporting directed links and tissue-specificity","volume":"433","author":"Persson","year":"2021","journal-title":"J. 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