Estimating the Expression of Transcript Isoforms from mRNA-Seq via Nonnegative Least Squares

mRNA-Seq is an emerging massive parallel sequencing based technology for identification and quantification of gene transcripts. Although gene level expression can easily be estimated from mRNA-Seq data, estimating the isoform level expression poses serious problems, and appropriate methods are required. In this paper, we introduce a mathematical method to estimate transcript isoform concentrations, i.e. transcript isoform expression estimation via nonnegative least squares (TIEE/NLS).