{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,2]],"date-time":"2026-06-02T12:00:21Z","timestamp":1780401621679,"version":"3.54.1"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2022,12,15]],"date-time":"2022-12-15T00:00:00Z","timestamp":1671062400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100014440","name":"Ministerio de Ciencia, Innovaci\u00f3n y Universidades","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100014440","id-type":"DOI","asserted-by":"publisher"}]},{"name":"ERDF-EU"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Transposable elements (TE) have played a major role in configuring the structures of mammalian genomes through evolution. In normal conditions, the expression of these elements is repressed by different epigenetic regulation mechanisms such as DNA methylation, histone modification and regulation by small RNAs. TE re-activation is associated with stemness potential acquisition, regulation of innate immunity and disease, such as cancer. However, the vast majority of current knowledge in the field is based on bulk expression studies, and very little is known on cell-type- or state-specific expression of TE-derived transcripts. Therefore, cost-efficient single-cell-resolution TE expression analytical approaches are needed.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We have implemented an analytical approach based on pseudoalignment to consensus sequences to incorporate TE expression information to scRNAseq data.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>All the data and code implemented are available as Supplementary data and in: https:\/\/github.com\/jmzvillarreal\/kallisto_TE_scRNAseq.<\/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\/btac737","type":"journal-article","created":{"date-parts":[[2022,12,14]],"date-time":"2022-12-14T23:38:49Z","timestamp":1671061129000},"source":"Crossref","is-referenced-by-count":3,"title":["Pseudoalignment tools as an efficient alternative to detect repeated transposable elements in scRNAseq data"],"prefix":"10.1093","volume":"39","author":[{"given":"Jaime Mart\u00ednez","family":"de Villarreal","sequence":"first","affiliation":[{"name":"Epithelial Carcinogenesis Group, Spanish National Cancer Research Centre-CNIO , Madrid, Spain"},{"name":"CIBERONC , Madrid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark","family":"Kalisz","sequence":"additional","affiliation":[{"name":"Epithelial Carcinogenesis Group, Spanish National Cancer Research Centre-CNIO , Madrid, Spain"},{"name":"CIBERONC , Madrid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8701-1084","authenticated-orcid":false,"given":"Gabriel","family":"Piedrafita","sequence":"additional","affiliation":[{"name":"Epithelial Carcinogenesis Group, Spanish National Cancer Research Centre-CNIO , Madrid, Spain"},{"name":"Departamento de Bioqu\u00edmica y Biolog\u00eda Molecular, Facultad de CC Qu\u00edmicas, Universidad Complutense de Madrid , Madrid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Osvaldo","family":"Gra\u00f1a-Castro","sequence":"additional","affiliation":[{"name":"Bioinformatic Unit, Spanish National Cancer Research Centre-CNIO , Madrid, Spain"},{"name":"Department of Basic Medical Sciences, Institute of Applied Molecular Medicine (IMMA-Nemesio D\u00edez), School of Medicine, San Pablo-CEU University, CEU Universities, Boadilla del Monte , Madrid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dafni","family":"Chondronasiou","sequence":"additional","affiliation":[{"name":"Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST) , Barcelona, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manuel","family":"Serrano","sequence":"additional","affiliation":[{"name":"Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST) , Barcelona, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9501-498X","authenticated-orcid":false,"given":"Francisco X","family":"Real","sequence":"additional","affiliation":[{"name":"Epithelial Carcinogenesis Group, Spanish National Cancer Research Centre-CNIO , Madrid, Spain"},{"name":"CIBERONC , Madrid, Spain"},{"name":"Department of Medicine and Life Sciences, Universitat Pompeu Fabra , Barcelona, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,12,15]]},"reference":[{"key":"2023010805370605500_btac737-B1","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":"Mob. 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