{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,2]],"date-time":"2026-04-02T18:00:00Z","timestamp":1775152800678,"version":"3.50.1"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: We developed a new algorithmic method, VirusSeq, for detecting known viruses and their integration sites in the human genome using next-generation sequencing data. We evaluated VirusSeq on whole-transcriptome sequencing (RNA-Seq) data of 256 human cancer samples from The Cancer Genome Atlas. Using these data, we showed that VirusSeq accurately detects the known viruses and their integration sites with high sensitivity and specificity. VirusSeq can also perform this function using whole-genome sequencing data of human tissue.<\/jats:p>\n               <jats:p>Availability: VirusSeq has been implemented in PERL and is available at http:\/\/odin.mdacc.tmc.edu\/\u223cxsu1\/VirusSeq.html.<\/jats:p>\n               <jats:p>Contact: \u00a0xsu1@mdanderson.org<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts665","type":"journal-article","created":{"date-parts":[[2012,11,18]],"date-time":"2012-11-18T02:50:02Z","timestamp":1353207002000},"page":"266-267","source":"Crossref","is-referenced-by-count":147,"title":["VirusSeq: software to identify viruses and their integration sites using next-generation sequencing of human cancer tissue"],"prefix":"10.1093","volume":"29","author":[{"given":"Yunxin","family":"Chen","sequence":"first","affiliation":[{"name":"1 Department of Genitourinary Medical Oncology, 2Department of Bioinformatics and Computational Biology and 3Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA"}]},{"given":"Hui","family":"Yao","sequence":"additional","affiliation":[{"name":"1 Department of Genitourinary Medical Oncology, 2Department of Bioinformatics and Computational Biology and 3Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA"}]},{"given":"Erika J.","family":"Thompson","sequence":"additional","affiliation":[{"name":"1 Department of Genitourinary Medical Oncology, 2Department of Bioinformatics and Computational Biology and 3Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA"}]},{"given":"Nizar M.","family":"Tannir","sequence":"additional","affiliation":[{"name":"1 Department of Genitourinary Medical Oncology, 2Department of Bioinformatics and Computational Biology and 3Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA"}]},{"given":"John N.","family":"Weinstein","sequence":"additional","affiliation":[{"name":"1 Department of Genitourinary Medical Oncology, 2Department of Bioinformatics and Computational Biology and 3Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA"}]},{"given":"Xiaoping","family":"Su","sequence":"additional","affiliation":[{"name":"1 Department of Genitourinary Medical Oncology, 2Department of Bioinformatics and Computational Biology and 3Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA"}]}],"member":"286","published-online":{"date-parts":[[2012,11,17]]},"reference":[{"key":"2023012810184278000_bts665-B1","doi-asserted-by":"crossref","first-page":"1096","DOI":"10.1126\/science.1152586","article-title":"Clonal integration of a polyomavirus in human Merkel cell carcinoma","volume":"319","author":"Feng","year":"2008","journal-title":"Science"},{"key":"2023012810184278000_bts665-B2","doi-asserted-by":"crossref","first-page":"3813","DOI":"10.1038\/sj.onc.1206528","article-title":"Integrations of the hepatitis B virus (HBV) and human papillomavirus (HPV) into the human telomerase reverse transcriptase (hTERT) gene in liver and cervical cancers","volume":"22","author":"Ferber","year":"2003","journal-title":"Oncogene"},{"key":"2023012810184278000_bts665-B3","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.virol.2009.06.001","article-title":"The search for infectious causes of human cancers: where and why","volume":"329","author":"Hausen","year":"2009","journal-title":"Virology"},{"key":"2023012810184278000_bts665-B4","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1038\/nmeth.1179","article-title":"Whole-genome sequencing and variant discovery in C. elegans","volume":"5","author":"Hiller","year":"2008","journal-title":"Nat. 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