{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,11]],"date-time":"2026-03-11T23:52:32Z","timestamp":1773273152110,"version":"3.50.1"},"reference-count":31,"publisher":"Oxford University Press (OUP)","issue":"13","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1613,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: High-throughput sequencing enables expression analysis at the level of individual transcripts. The analysis of transcriptome expression levels and differential expression (DE) estimation requires a probabilistic approach to properly account for ambiguity caused by shared exons and finite read sampling as well as the intrinsic biological variance of transcript expression.<\/jats:p>\n               <jats:p>Results: We present Bayesian inference of transcripts from sequencing data (BitSeq), a Bayesian approach for estimation of transcript expression level from RNA-seq experiments. Inferred relative expression is represented by Markov chain Monte Carlo samples from the posterior probability distribution of a generative model of the read data. We propose a novel method for DE analysis across replicates which propagates uncertainty from the sample-level model while modelling biological variance using an expression-level-dependent prior. We demonstrate the advantages of our method using simulated data as well as an RNA-seq dataset with technical and biological replication for both studied conditions.<\/jats:p>\n               <jats:p>Availability: The implementation of the transcriptome expression estimation and differential expression analysis, BitSeq, has been written in C++ and Python. The software is available online from http:\/\/code.google.com\/p\/bitseq\/, version 0.4 was used for generating results presented in this article.<\/jats:p>\n               <jats:p>Contact: \u00a0glaus@cs.man.ac.uk, antti.honkela@hiit.fi or m.rattray@sheffield.ac.uk<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts260","type":"journal-article","created":{"date-parts":[[2012,5,5]],"date-time":"2012-05-05T09:09:30Z","timestamp":1336208970000},"page":"1721-1728","source":"Crossref","is-referenced-by-count":172,"title":["Identifying differentially expressed transcripts from RNA-seq data with biological variation"],"prefix":"10.1093","volume":"28","author":[{"given":"Peter","family":"Glaus","sequence":"first","affiliation":[{"name":"1 School of Computer Science, University of Manchester, Oxford Road, Manchester M13 9PL, UK, 2Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, P.O. Box 68, FI-00014 University of Helsinki, Finland and 3Department of Computer Science and Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield S10 2HQ, UK"}]},{"given":"Antti","family":"Honkela","sequence":"additional","affiliation":[{"name":"1 School of Computer Science, University of Manchester, Oxford Road, Manchester M13 9PL, UK, 2Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, P.O. Box 68, FI-00014 University of Helsinki, Finland and 3Department of Computer Science and Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield S10 2HQ, UK"}]},{"given":"Magnus","family":"Rattray","sequence":"additional","affiliation":[{"name":"1 School of Computer Science, University of Manchester, Oxford Road, Manchester M13 9PL, UK, 2Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, P.O. Box 68, FI-00014 University of Helsinki, Finland and 3Department of Computer Science and Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield S10 2HQ, UK"}]}],"member":"286","published-online":{"date-parts":[[2012,5,3]]},"reference":[{"key":"2023012512381760800_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":"2023012512381760800_B2","doi-asserted-by":"crossref","first-page":"54","DOI":"10.2307\/2683591","article-title":"LOWESS: a program for smoothing scatterplots by robust locally weighted regression","volume":"35","author":"Cleveland","year":"1981","journal-title":"Am. 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