{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,30]],"date-time":"2026-01-30T09:43:55Z","timestamp":1769766235148,"version":"3.49.0"},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1359,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Insertional mutagenesis from virus infection is an important pathogenic risk for the development of cancer. Despite the advent of high-throughput sequencing, discovery of viral integration sites and expressed viral fusion events are still limited. Here, we present ViralFusionSeq (VFS), which combines soft-clipping information, read-pair analysis and targeted de novo assembly to discover and annotate viral\u2013human fusions. VFS was used in an RNA-Seq experiment, simulated DNA-Seq experiment and re-analysis of published DNA-Seq datasets. Our experiments demonstrated that VFS is both sensitive and highly accurate.<\/jats:p>\n               <jats:p>Availability: VFS is distributed under GPL version 3 at http:\/\/hkbic.cuhk.edu.hk\/software\/viralfusionseq<\/jats:p>\n               <jats:p>Contact: tf.chan@cuhk.edu.hk<\/jats:p>\n               <jats:p>Supplementary information: Supplementary data are available at Bioinformatics Online<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt011","type":"journal-article","created":{"date-parts":[[2013,1,13]],"date-time":"2013-01-13T01:41:16Z","timestamp":1358041276000},"page":"649-651","source":"Crossref","is-referenced-by-count":75,"title":["ViralFusionSeq: accurately discover viral integration events and reconstruct fusion transcripts at single-base resolution"],"prefix":"10.1093","volume":"29","author":[{"given":"Jing-Woei","family":"Li","sequence":"first","affiliation":[{"name":"1 School of Life Sciences, 2Hong Kong Bioinformatics Centre and 3Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong"},{"name":"1 School of Life Sciences, 2Hong Kong Bioinformatics Centre and 3Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong"},{"name":"1 School of Life Sciences, 2Hong Kong Bioinformatics Centre and 3Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Raymond","family":"Wan","sequence":"additional","affiliation":[{"name":"1 School of Life Sciences, 2Hong Kong Bioinformatics Centre and 3Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong"},{"name":"1 School of Life Sciences, 2Hong Kong Bioinformatics Centre and 3Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chi-Shing","family":"Yu","sequence":"additional","affiliation":[{"name":"1 School of Life Sciences, 2Hong Kong Bioinformatics Centre and 3Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong"},{"name":"1 School of Life Sciences, 2Hong Kong Bioinformatics Centre and 3Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ngai Na","family":"Co","sequence":"additional","affiliation":[{"name":"1 School of Life Sciences, 2Hong Kong Bioinformatics Centre and 3Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nathalie","family":"Wong","sequence":"additional","affiliation":[{"name":"1 School of Life Sciences, 2Hong Kong Bioinformatics Centre and 3Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ting-Fung","family":"Chan","sequence":"additional","affiliation":[{"name":"1 School of Life Sciences, 2Hong Kong Bioinformatics Centre and 3Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong"},{"name":"1 School of Life Sciences, 2Hong Kong Bioinformatics Centre and 3Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2013,1,12]]},"reference":[{"key":"2023051607331126800_btt011-B1","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1016\/j.canlet.2008.12.003","article-title":"Hepatitis B virus induced hepatocellular carcinoma","volume":"286","author":"Chemin","year":"2009","journal-title":"Cancer Lett."},{"key":"2023051607331126800_btt011-B2","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1093\/bioinformatics\/bts665","article-title":"VirusSeq: software to identify viruses and their integration sites using next-generation sequencing of human cancer tissue","volume":"29","author":"Chen","year":"2013","journal-title":"Bioinformatics"},{"key":"2023051607331126800_btt011-B3","doi-asserted-by":"crossref","first-page":"S75","DOI":"10.1016\/S1386-6532(05)80014-9","article-title":"HBV induced carcinogenesis","volume":"34","author":"Cougot","year":"2005","journal-title":"J. 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