{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,4]],"date-time":"2026-03-04T23:09:36Z","timestamp":1772665776735,"version":"3.50.1"},"reference-count":37,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2021,10,19]],"date-time":"2021-10-19T00:00:00Z","timestamp":1634601600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100007316","name":"Klaus Tschira Stiftung","doi-asserted-by":"publisher","award":["03.136.2018"],"award-info":[{"award-number":["03.136.2018"]}],"id":[{"id":"10.13039\/501100007316","id-type":"DOI","asserted-by":"publisher"}]},{"name":"German Federal Ministry of Education and Research","award":["031L0106D"],"award-info":[{"award-number":["031L0106D"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,17]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Transposable elements (TEs) have been associated with many, frequently detrimental, biological roles. Consequently, the regulations of TEs, e.g. via DNA-methylation and histone modifications, are considered critical for maintaining genomic integrity and other functions. Still, the high-throughput study of TEs is usually limited to the family or consensus-sequence level because of alignment problems prompted by high-sequence similarities and short read lengths. To entirely comprehend the effects and reasons of TE expression, however, it is necessary to assess the TE expression at the level of individual instances. Our simulation study demonstrates that sequence similarities and short read lengths do not rule out the accurate assessment of (differential) expression of TEs at the instance-level. With only slight modifications to existing methods, TE expression analysis works surprisingly well for conventional paired-end sequencing data. We find that SalmonTE and Telescope can accurately tally a considerable amount of TE instances, allowing for differential expression recovery in model and non-model organisms.<\/jats:p>","DOI":"10.1093\/bib\/bbab417","type":"journal-article","created":{"date-parts":[[2021,9,14]],"date-time":"2021-09-14T11:11:44Z","timestamp":1631617904000},"source":"Crossref","is-referenced-by-count":26,"title":["Locus-specific expression analysis of transposable elements"],"prefix":"10.1093","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0654-0943","authenticated-orcid":false,"given":"Robert","family":"Schwarz","sequence":"first","affiliation":[{"name":"Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11, 07745 Jena, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2825-7943","authenticated-orcid":false,"given":"Philipp","family":"Koch","sequence":"additional","affiliation":[{"name":"CF Life Science Computing, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11, 07745 Jena, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0363-3837","authenticated-orcid":false,"given":"Jeanne","family":"Wilbrandt","sequence":"additional","affiliation":[{"name":"CF Life Science Computing, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11, 07745 Jena, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5239-7201","authenticated-orcid":false,"given":"Steve","family":"Hoffmann","sequence":"additional","affiliation":[{"name":"Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11, 07745 Jena, Germany"}]}],"member":"286","published-online":{"date-parts":[[2021,10,19]]},"reference":[{"issue":"307","key":"2022011921221276000_ref1","doi-asserted-by":"crossref","first-page":"307ra153","DOI":"10.1126\/scitranslmed.aac8201","article-title":"Human endogenous retrovirus-K contributes to motor neuron 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