IsoLasso: A LASSO Regression Approach to RNA-Seq Based Transcriptome Assembly

摘要

Abstract The new second generation sequencing technology revolutionizes many biology-related research fields and poses various computational biology challenges. One of them is transcriptome assembly based on RNA-Seq data, which aims at reconstructing all full-length mRNA transcripts simultaneously from millions of short reads. In this article, we consider three objectives in transcriptome assembly: the maximization of prediction accuracy, minimization of interpretation, and maximization of completeness. The first objective, the maximization of prediction accuracy, requires that the estimated expression levels based on assembled transcripts should be as close as possible to the observed ones for every expressed region of the genome. The minimization of interpretation follows the parsimony principle to seek as few transcripts in the prediction as possible. The third objective, the maximization of completeness, requires that the maximum number of mapped reads (or “expressed segments” in gene models) be expla..." /> rel="meta" type="application/atom+xml" href="http://dx.doi.org/10.1089%2Fcmb.2011.0171" /> rel="meta" type="application/rdf+json" href="http://dx.doi.org/10.1089%2Fcmb.2011.0171" /> rel="meta" type="application/unixref+xml" href="http://dx.doi.org/10.1089%2Fcmb.2011.0171" /> 展开▼