{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,15]],"date-time":"2026-07-15T22:08:30Z","timestamp":1784153310088,"version":"3.55.0"},"reference-count":58,"publisher":"Oxford University Press (OUP)","issue":"22","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Most RNA-seq data analysis software packages are not designed to handle the complexities involved in properly apportioning short sequencing reads to highly repetitive regions of the genome. These regions are often occupied by transposable elements (TEs), which make up between 20 and 80% of eukaryotic genomes. They can contribute a substantial portion of transcriptomic and genomic sequence reads, but are typically ignored in most analyses.<\/jats:p>\n               <jats:p>Results: Here, we present a method and software package for including both gene- and TE-associated ambiguously mapped reads in differential expression analysis. Our method shows improved recovery of TE transcripts over other published expression analysis methods, in both synthetic data and qPCR\/NanoString-validated published datasets.<\/jats:p>\n               <jats:p>Availability and implementation: The source code, associated GTF files for TE annotation, and testing data are freely available at http:\/\/hammelllab.labsites.cshl.edu\/software.<\/jats:p>\n               <jats:p>Contact: \u00a0mhammell@cshl.edu.<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv422","type":"journal-article","created":{"date-parts":[[2015,7,24]],"date-time":"2015-07-24T00:53:42Z","timestamp":1437699222000},"page":"3593-3599","source":"Crossref","is-referenced-by-count":755,"title":["TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets"],"prefix":"10.1093","volume":"31","author":[{"given":"Ying","family":"Jin","sequence":"first","affiliation":[{"name":"Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Oliver H.","family":"Tam","sequence":"additional","affiliation":[{"name":"Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eric","family":"Paniagua","sequence":"additional","affiliation":[{"name":"Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Molly","family":"Hammell","sequence":"additional","affiliation":[{"name":"Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2015,7,23]]},"reference":[{"key":"2023020202405744800_btv422-B1","doi-asserted-by":"crossref","first-page":"R106","DOI":"10.1186\/gb-2010-11-10-r106","article-title":"Differential expression analysis for sequence count data","volume":"11","author":"Anders","year":"2010","journal-title":"Genome Biol."},{"key":"2023020202405744800_btv422-B2","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1093\/bioinformatics\/btu638","article-title":"Htseq\u2014a python framework to work with high-throughput sequencing data","volume":"31","author":"Anders","year":"2014","journal-title":"Bioinformatics"},{"key":"2023020202405744800_btv422-B3","doi-asserted-by":"crossref","first-page":"1159","DOI":"10.1016\/j.cell.2010.05.021","article-title":"LINE-1 retrotransposition activity in human genomes","volume":"141","author":"Beck","year":"2010","journal-title":"Cell"},{"key":"2023020202405744800_btv422-B4","doi-asserted-by":"crossref","first-page":"1875","DOI":"10.1101\/gr.081737.108","article-title":"Active alu retotransposons in the human genome","volume":"18","author":"Bennett","year":"2008","journal-title":"Genome Res."},{"key":"2023020202405744800_btv422-B5","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1038\/nature10532","article-title":"The evolution of gene expression levels in mammalian organs","volume":"478","author":"Brawand","year":"2011","journal-title":"Nature"},{"key":"2023020202405744800_btv422-B6","doi-asserted-by":"crossref","first-page":"306","DOI":"10.1016\/j.neuron.2013.10.053","article-title":"Increased L1 retrotransposition in the neuronal genome in schizophrenia","volume":"81","author":"Bundo","year":"2014","journal-title":"Neuron"},{"key":"2023020202405744800_btv422-B7","doi-asserted-by":"crossref","first-page":"e1002111","DOI":"10.1371\/journal.pcbi.1002111","article-title":"Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-Seq data","volume":"7","author":"Chung","year":"2011","journal-title":"PLoS Comput. 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