{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,25]],"date-time":"2026-03-25T07:32:05Z","timestamp":1774423925116,"version":"3.50.1"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"19","license":[{"start":{"date-parts":[[2019,2,21]],"date-time":"2019-02-21T00:00:00Z","timestamp":1550707200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Natural Sciences and Engineering Council of Canada"},{"name":"Natural Sciences and Engineering Council of Canada Alexander Graham Bell Graduate Scholarship"},{"name":"Roman Babicki Fellowship in Medical Research"},{"DOI":"10.13039\/501100005247","name":"University of British Columbia","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100005247","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Transposable elements (TEs) influence the evolution of novel transcriptional networks yet the specific and meaningful interpretation of how TE-derived transcriptional initiation contributes to the transcriptome has been marred by computational and methodological deficiencies. We developed LIONS for the analysis of RNA-seq data to specifically detect and quantify TE-initiated transcripts.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Source code, container, test data and instruction manual are freely available at www.github.com\/ababaian\/LIONS.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz130","type":"journal-article","created":{"date-parts":[[2019,2,19]],"date-time":"2019-02-19T15:13:31Z","timestamp":1550589211000},"page":"3839-3841","source":"Crossref","is-referenced-by-count":28,"title":["LIONS: analysis suite for detecting and quantifying transposable element initiated transcription from RNA-seq"],"prefix":"10.1093","volume":"35","author":[{"given":"Artem","family":"Babaian","sequence":"first","affiliation":[{"name":"Terry Fox Laboratory, BC Cancer , Vancouver, BC, Canada"},{"name":"University of British Columbia , Vancouver, BC, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"I Richard","family":"Thompson","sequence":"additional","affiliation":[{"name":"Qatar Biomedical Research Institute, Hamad Bin Khalifa University , Doha, Qatar"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jake","family":"Lever","sequence":"additional","affiliation":[{"name":"University of British Columbia , Vancouver, BC, Canada"},{"name":"Michael Smith Genome Sciences Centre, BC Cancer , Vancouver, BC, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Liane","family":"Gagnier","sequence":"additional","affiliation":[{"name":"Terry Fox Laboratory, BC Cancer , Vancouver, BC, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mohammad M","family":"Karimi","sequence":"additional","affiliation":[{"name":"MRC London Institute of Medical Sciences, Imperial Colleg e, London, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5955-2550","authenticated-orcid":false,"given":"Dixie L","family":"Mager","sequence":"additional","affiliation":[{"name":"Terry Fox Laboratory, BC Cancer , Vancouver, BC, Canada"},{"name":"University of British Columbia , Vancouver, BC, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,2,21]]},"reference":[{"key":"2023013108194427900_btz130-B1","doi-asserted-by":"crossref","first-page":"24.","DOI":"10.1186\/s13100-016-0080-x","article-title":"Endogenous retroviral promoter exaptation in human cancer","volume":"7","author":"Babaian","year":"2016","journal-title":"Mob. 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