{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,24]],"date-time":"2026-02-24T18:03:29Z","timestamp":1771956209939,"version":"3.50.1"},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2021,11,10]],"date-time":"2021-11-10T00:00:00Z","timestamp":1636502400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R35GM138184"],"award-info":[{"award-number":["R35GM138184"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100012615","name":"University of Texas Health Science Center at Houston","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100012615","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>A knowledgebase of the systematic functional annotation of fusion genes is critical for understanding genomic breakage context and developing therapeutic strategies. FusionGDB is a unique functional annotation database of human fusion genes and has been widely used for studies with diverse aims. In this study, we report fusion gene annotation updates aided by deep learning (FusionGDB 2.0) available at https:\/\/compbio.uth.edu\/FusionGDB2\/. FusionGDB 2.0 has substantial updates of contents such as up-to-date human fusion genes, fusion gene breakage tendency score with FusionAI deep learning model based on 20\u00a0kb DNA sequence around BP, investigation of overlapping between fusion breakpoints with 44 human genomic features across five cellular role's categories, transcribed chimeric sequence and following open reading frame analysis with coding potential based on deep learning approach with Ribo-seq read features, and rigorous investigation of the protein feature retention of individual fusion partner genes in the protein level. Among \u223c102k fusion genes, about 15k kept their ORF as In-frames, which is two times compared to the previous version, FusionGDB. FusionGDB 2.0 will be used as the reference knowledgebase of fusion gene annotations. FusionGDB 2.0 provides eight categories of annotations and it will be helpful for diverse human genomic studies.<\/jats:p>","DOI":"10.1093\/nar\/gkab1056","type":"journal-article","created":{"date-parts":[[2021,11,5]],"date-time":"2021-11-05T12:23:26Z","timestamp":1636115006000},"page":"D1221-D1230","source":"Crossref","is-referenced-by-count":49,"title":["FusionGDB 2.0: fusion gene annotation updates aided by deep learning"],"prefix":"10.1093","volume":"50","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8321-6864","authenticated-orcid":false,"given":"Pora","family":"Kim","sequence":"first","affiliation":[{"name":"School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4090-113X","authenticated-orcid":false,"given":"Hua","family":"Tan","sequence":"additional","affiliation":[{"name":"School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA"}]},{"given":"Jiajia","family":"Liu","sequence":"additional","affiliation":[{"name":"School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA"}]},{"given":"Haeseung","family":"Lee","sequence":"additional","affiliation":[{"name":"Intellectual Information Team, Future Medicine Division, Korea Institute of Oriental Medicine, Daejeon, South Korea"}]},{"given":"Hyesoo","family":"Jung","sequence":"additional","affiliation":[{"name":"Department of Neurology, Asan Medical Center, Seoul, Korea"}]},{"given":"Himanshu","family":"Kumar","sequence":"additional","affiliation":[{"name":"School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7191-6495","authenticated-orcid":false,"given":"Xiaobo","family":"Zhou","sequence":"additional","affiliation":[{"name":"School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA"},{"name":"McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA"},{"name":"School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA"}]}],"member":"286","published-online":{"date-parts":[[2021,11,10]]},"reference":[{"key":"2022010507375007500_B1","doi-asserted-by":"crossref","first-page":"D994","DOI":"10.1093\/nar\/gky1067","article-title":"FusionGDB: fusion gene annotation DataBase","volume":"47","author":"Kim","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2022010507375007500_B2","doi-asserted-by":"crossref","first-page":"103164","DOI":"10.1016\/j.isci.2021.103164","article-title":"FusionAI: predicting fusion breakpoint from DNA sequence with deep 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