{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:00Z","timestamp":1772138040849,"version":"3.50.1"},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2020,10,14]],"date-time":"2020-10-14T00:00:00Z","timestamp":1602633600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100021082","name":"Birkbeck","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100021082","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Wellcome Trust Institutional Strategic Support Fund"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,6,16]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>We present flexible Modeling of Alternative PolyAdenylation (flexiMAP), a new beta-regression-based method implemented in R, for discovering differential alternative polyadenylation events in standard RNA-seq data.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We show, using both simulated and real data, that flexiMAP exhibits a good balance between specificity and sensitivity and compares favourably to existing methods, especially at low fold changes. In addition, the tests on simulated data reveal some hitherto unrecognized caveats of existing methods. Importantly, flexiMAP allows modeling of multiple known covariates that often confound the results of RNA-seq data analysis.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The flexiMAP R package is available at: https:\/\/github.com\/kszkop\/flexiMAP. Scripts and data to reproduce the analysis in this paper are available at: https:\/\/doi.org\/10.5281\/zenodo.3689788.<\/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\/btaa854","type":"journal-article","created":{"date-parts":[[2020,9,30]],"date-time":"2020-09-30T08:38:19Z","timestamp":1601455099000},"page":"1461-1464","source":"Crossref","is-referenced-by-count":2,"title":["flexiMAP: a regression-based method for discovering differential alternative polyadenylation events in standard RNA-seq data"],"prefix":"10.1093","volume":"37","author":[{"given":"Krzysztof J","family":"Szkop","sequence":"first","affiliation":[{"name":"Institute of Structural and Molecular Biology Department of Biological Sciences, , Birkbeck, University of London, London WC1E 7HX, UK"},{"name":"Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet , Solna, Sweden"}]},{"given":"David S","family":"Moss","sequence":"additional","affiliation":[{"name":"Institute of Structural and Molecular Biology Department of Biological Sciences, , Birkbeck, University of London, London WC1E 7HX, UK"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8616-170X","authenticated-orcid":false,"given":"Irene","family":"Nobeli","sequence":"additional","affiliation":[{"name":"Institute of Structural and Molecular Biology Department of Biological Sciences, , Birkbeck, University of London, London WC1E 7HX, UK"}]}],"member":"286","published-online":{"date-parts":[[2020,11,25]]},"reference":[{"key":"2023051709340816300_btaa854-B1","doi-asserted-by":"crossref","first-page":"2008","DOI":"10.1101\/gr.133744.111","article-title":"Detecting differential usage of exons from RNA-seq data","volume":"22","author":"Anders","year":"2012","journal-title":"Genome Res"},{"key":"2023051709340816300_btaa854-B2","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1186\/s13059-018-1418-0","article-title":"Full-length mRNA sequencing uncovers a widespread coupling between transcription initiation and mRNA processing","volume":"19","author":"Anvar","year":"2018","journal-title":"Genome Biol"},{"key":"2023051709340816300_btaa854-B3","first-page":"2521","article-title":"TAPAS: tool for alternative polyadenylation site analysis","volume":"34","author":"Arefeen","year":"2018","journal-title":"Bioinformatics (Oxford, England)"},{"key":"2023051709340816300_btaa854-B4","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1186\/1471-2105-11-94","article-title":"Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments","volume":"11","author":"Bullard","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2023051709340816300_btaa854-B5","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18637\/jss.v034.i02","article-title":"Beta regression in R","volume":"34","author":"Cribari-Neto","year":"2010","journal-title":"J. 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