{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,25]],"date-time":"2025-09-25T14:59:35Z","timestamp":1758812375624,"version":"3.37.3"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2017,10,23]],"date-time":"2017-10-23T00:00:00Z","timestamp":1508716800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/100000163","name":"ARC","doi-asserted-by":"publisher","award":["SFI20121205549"],"award-info":[{"award-number":["SFI20121205549"]}],"id":[{"id":"10.13039\/100000163","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100008530","name":"Fonds Europ\u00e9en de D\u00e9veloppement R\u00e9gional","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100008530","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002924","name":"FEDER","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002924","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>L1 Chimeric Transcripts (LCTs) are initiated by repeated LINE-1 element antisense promoters and include the L1 5\u2032UTR sequence in antisense orientation followed by the adjacent genomic region. LCTs have been characterized mainly using bioinformatics approaches to query dbEST. To take advantage of NGS data to unravel the transcriptome composition, we developed Chimeric LIne Finder (CLIFinder), a new bioinformatics tool. Using stranded paired-end RNA-seq data, we demonstrated that CLIFinder can identify genome-wide transcribed chimera sequences corresponding to potential LCTs. Moreover, CLIFinder can be adapted to study transcription from other repeat types.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The code is available at: https:\/\/github.com\/GReD-Clermont\/CLIFinder; and for Galaxy users, it is directly accessible in the tool shed at: https:\/\/toolshed.g2.bx.psu.edu\/view\/clifinder\/clifinder\/.<\/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\/btx671","type":"journal-article","created":{"date-parts":[[2017,10,19]],"date-time":"2017-10-19T11:09:19Z","timestamp":1508411359000},"page":"688-690","source":"Crossref","is-referenced-by-count":16,"title":["CLIFinder: identification of LINE-1 chimeric transcripts in RNA-seq data"],"prefix":"10.1093","volume":"34","author":[{"given":"Marie-Elisa","family":"Pinson","sequence":"first","affiliation":[{"name":"GReD, Universit\u00e9 Clermont Auvergne, CNRS, INSERM, Clermont-Ferrand, France"}]},{"given":"Romain","family":"Pogorelcnik","sequence":"additional","affiliation":[{"name":"GReD, Universit\u00e9 Clermont Auvergne, CNRS, INSERM, Clermont-Ferrand, France"}]},{"given":"Franck","family":"Court","sequence":"additional","affiliation":[{"name":"GReD, Universit\u00e9 Clermont Auvergne, CNRS, INSERM, Clermont-Ferrand, France"}]},{"given":"Philippe","family":"Arnaud","sequence":"additional","affiliation":[{"name":"GReD, Universit\u00e9 Clermont Auvergne, CNRS, INSERM, Clermont-Ferrand, France"}]},{"given":"Catherine","family":"Vaurs-Barri\u00e8re","sequence":"additional","affiliation":[{"name":"GReD, Universit\u00e9 Clermont Auvergne, CNRS, INSERM, Clermont-Ferrand, France"}]}],"member":"286","published-online":{"date-parts":[[2017,10,23]]},"reference":[{"key":"2023012712394006900_btx671-B1","doi-asserted-by":"crossref","first-page":"3025","DOI":"10.1158\/1078-0432.CCR-15-2657","article-title":"Neoadjuvant chemotherapy modulates the immune microenvironment in metastases of tubo-ovarian high-grade serous carcinoma","volume":"22","author":"B\u00f6hm","year":"2016","journal-title":"Clin. 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