{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T01:06:26Z","timestamp":1773277586992,"version":"3.50.1"},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2016,10,5]],"date-time":"2016-10-05T00:00:00Z","timestamp":1475625600000},"content-version":"vor","delay-in-days":2088,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Retroviral integration has been implicated in several biomedical applications, including identification of cancer-associated genes and malignant transformation in gene therapy clinical trials. We introduce an efficient and scalable method for fast identification of viral vector integration sites from long read high-throughput sequencing. Individual sequence reads are masked to remove non-genomic sequence, aligned to the host genome and assembled into contiguous fragments used to pinpoint the position of integration.<\/jats:p>\n               <jats:p>Availability and Implementation: The method is implemented in a publicly accessible web server platform, SeqMap 2.0, containing analysis tools and both private and shared lab workspaces that facilitate collaboration among researchers. Available at http:\/\/seqmap.compbio.iupui.edu\/.<\/jats:p>\n               <jats:p>Contact: \u00a0troyhawk@iupui.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq722","type":"journal-article","created":{"date-parts":[[2011,1,19]],"date-time":"2011-01-19T01:29:49Z","timestamp":1295400589000},"page":"720-722","source":"Crossref","is-referenced-by-count":32,"title":["Identifying viral integration sites using SeqMap 2.0"],"prefix":"10.1093","volume":"27","author":[{"given":"Troy B.","family":"Hawkins","sequence":"first","affiliation":[{"name":"1 Department of Medical and Molecular Genetics, 2Center for Computational Biology and Bioinformatics, 3Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, 4Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405 and 5The Buck Institute for Age Research, Novato, CA 94945, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jessica","family":"Dantzer","sequence":"additional","affiliation":[{"name":"1 Department of Medical and Molecular Genetics, 2Center for Computational Biology and Bioinformatics, 3Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, 4Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405 and 5The Buck Institute for Age Research, Novato, CA 94945, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Brandon","family":"Peters","sequence":"additional","affiliation":[{"name":"1 Department of Medical and Molecular Genetics, 2Center for Computational Biology and Bioinformatics, 3Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, 4Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405 and 5The Buck Institute for Age Research, Novato, CA 94945, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mary","family":"Dinauer","sequence":"additional","affiliation":[{"name":"1 Department of Medical and Molecular Genetics, 2Center for Computational Biology and Bioinformatics, 3Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, 4Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405 and 5The Buck Institute for Age Research, Novato, CA 94945, USA"},{"name":"1 Department of Medical and Molecular Genetics, 2Center for Computational Biology and Bioinformatics, 3Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, 4Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405 and 5The Buck Institute for Age Research, Novato, CA 94945, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Keithanne","family":"Mockaitis","sequence":"additional","affiliation":[{"name":"1 Department of Medical and Molecular Genetics, 2Center for Computational Biology and Bioinformatics, 3Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, 4Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405 and 5The Buck Institute for Age Research, Novato, CA 94945, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sean","family":"Mooney","sequence":"additional","affiliation":[{"name":"1 Department of Medical and Molecular Genetics, 2Center for Computational Biology and Bioinformatics, 3Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, 4Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405 and 5The Buck Institute for Age Research, Novato, CA 94945, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kenneth","family":"Cornetta","sequence":"additional","affiliation":[{"name":"1 Department of Medical and Molecular Genetics, 2Center for Computational Biology and Bioinformatics, 3Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, 4Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405 and 5The Buck Institute for Age Research, Novato, CA 94945, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2011,1,17]]},"reference":[{"key":"2023012511571445000_B1","doi-asserted-by":"crossref","first-page":"D523","DOI":"10.1093\/nar\/gkh013","article-title":"RTCGD: retroviral tagged cancer gene database","volume":"32","author":"Akagi","year":"2004","journal-title":"Nucleic 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