{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,1]],"date-time":"2026-04-01T19:03:09Z","timestamp":1775070189271,"version":"3.50.1"},"reference-count":28,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2019,10,4]],"date-time":"2019-10-04T00:00:00Z","timestamp":1570147200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"National Institutres of Health National Institute on Aging","award":["P01AG051449"],"award-info":[{"award-number":["P01AG051449"]}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>LINE-1 elements are retrotransposons that are capable of copying their sequence to new genomic loci. LINE-1 derepression is associated with a number of disease states, and has the potential to cause significant cellular damage. Because LINE-1 elements are repetitive, it is difficult to quantify LINE-1 RNA at specific loci and to separate transcripts with protein coding capability from other sources of LINE-1 RNA.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We provide a tool, L1EM that uses the expectation maximization algorithm to quantify LINE-1 RNA at each genomic locus, separating transcripts that are capable of generating retrotransposition from those that are not. We show the accuracy of L1EM on simulated data and against long read sequencing from HEK cells.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>L1EM is written in python. The source code along with the necessary annotations are available at https:\/\/github.com\/FenyoLab\/L1EM and distributed under GPLv3.<\/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\/btz724","type":"journal-article","created":{"date-parts":[[2019,9,26]],"date-time":"2019-09-26T07:28:48Z","timestamp":1569482928000},"page":"1167-1173","source":"Crossref","is-referenced-by-count":44,"title":["L1EM: a tool for accurate locus specific LINE-1 RNA quantification"],"prefix":"10.1093","volume":"36","author":[{"given":"Wilson","family":"McKerrow","sequence":"first","affiliation":[{"name":"Institute for Systems Genetics , USA"},{"name":"Department for Biochemistry and Molecular Pharmacology, NYU School of Medicine , New York, NY, USA"}]},{"given":"David","family":"Feny\u00f6","sequence":"additional","affiliation":[{"name":"Institute for Systems Genetics , USA"},{"name":"Department for Biochemistry and Molecular Pharmacology, NYU School of Medicine , New York, NY, USA"}]}],"member":"286","published-online":{"date-parts":[[2019,10,4]]},"reference":[{"key":"2023013110162173200_btz724-B1","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1038\/nature21715","article-title":"DHX9 suppresses RNA processing defects originating from the Alu invasion of the human genome","volume":"544","author":"Akta\u015f","year":"2017","journal-title":"Nature"},{"key":"2023013110162173200_btz724-B2","doi-asserted-by":"crossref","first-page":"11.","DOI":"10.1186\/s13100-015-0041-9","article-title":"Repbase update, a database of repetitive elements in eukaryotic genomes","volume":"6","author":"Bao","year":"2015","journal-title":"Mobile DNA"},{"key":"2023013110162173200_btz724-B4","doi-asserted-by":"crossref","first-page":"1127","DOI":"10.1038\/nature08248","article-title":"L1 retrotransposition in human neural progenitor cells","volume":"460","author":"Coufal","year":"2009","journal-title":"Nature"},{"key":"2023013110162173200_btz724-B6","doi-asserted-by":"crossref","first-page":"73.","DOI":"10.1038\/s41586-018-0784-9","article-title":"L1 drives IFN in senescent cells and promotes age-associated inflammation","volume":"566","author":"De Cecco","year":"2019","journal-title":"Nature"},{"key":"2023013110162173200_btz724-B7","doi-asserted-by":"crossref","first-page":"e31.","DOI":"10.1093\/nar\/gkw1067","article-title":"A comprehensive approach to expression of L1 loci","volume":"45","author":"Deininger","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2023013110162173200_btz724-B8","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1111\/j.2517-6161.1977.tb01600.x","article-title":"Maximum likelihood from incomplete data via the EM algorithm","volume":"39","author":"Dempster","year":"1977","journal-title":"J. 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