{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,29]],"date-time":"2026-08-29T15:54:39Z","timestamp":1788018879730,"version":"build-2784847793"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"3","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: A significant proportion of eukaryote genomes consist of transposable element (TE)-derived sequence. These elements are known to have the capacity to modulate gene function and genome evolution. We have developed RetroSeq for detecting non-reference TE insertions from Illumina paired-end whole-genome sequencing data. We evaluate RetroSeq on a human trio from the 1000 Genomes Project, showing that it produces highly accurate TE calls.<\/jats:p>\n               <jats:p>Availabilty: RetroSeq is open-source and available from https:\/\/github.com\/tk2\/RetroSeq.<\/jats:p>\n               <jats:p>Contact: \u00a0tk2@sanger.ac.uk<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts697","type":"journal-article","created":{"date-parts":[[2012,12,12]],"date-time":"2012-12-12T03:06:16Z","timestamp":1355281576000},"page":"389-390","source":"Crossref","is-referenced-by-count":196,"title":["RetroSeq: transposable element discovery from next-generation sequencing data"],"prefix":"10.1093","volume":"29","author":[{"given":"Thomas M.","family":"Keane","sequence":"first","affiliation":[{"name":"Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kim","family":"Wong","sequence":"additional","affiliation":[{"name":"Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David J.","family":"Adams","sequence":"additional","affiliation":[{"name":"Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2012,12,10]]},"reference":[{"key":"2023012810185390500_bts697-B1","doi-asserted-by":"crossref","first-page":"869","DOI":"10.1101\/gr.075770.107","article-title":"Extensive variation between inbred mouse strains due to endogenous L1 retrotransposition","volume":"18","author":"Akagi","year":"2008","journal-title":"Genome Res."},{"key":"2023012810185390500_bts697-B2","doi-asserted-by":"crossref","first-page":"985","DOI":"10.1101\/gr.114777.110","article-title":"Whole-genome resequencing allows detection of many rare LINE-1 insertion alleles in humans","volume":"21","author":"Ewing","year":"2011","journal-title":"Genome Res."},{"key":"2023012810185390500_bts697-B3","doi-asserted-by":"crossref","first-page":"3727","DOI":"10.1007\/s00018-009-0107-2","article-title":"Retroelements and their impact on genome evolution and functioning","volume":"66","author":"Gogvadze","year":"2009","journal-title":"Cell Mol. 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