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Efficient RNA Isoform Identification and Quantification from RNA-Seq Data with Network Flows

Elsa Bernard 1, 2 Laurent Jacob 3 Julien Mairal 4 Jean-Philippe Vert 1, 2, *
* Corresponding author
3 Statistique en grande dimension pour la génomique
PEGASE - Département PEGASE [LBBE]
4 LEAR - Learning and recognition in vision
Inria Grenoble - Rhône-Alpes, LJK - Laboratoire Jean Kuntzmann, Grenoble INP - Institut polytechnique de Grenoble - Grenoble Institute of Technology
Abstract : Several state-of-the-art methods for isoform identification and quantification are based on l1- regularized regression, such as the Lasso. However, explicitly listing the--possibly exponentially-- large set of candidate transcripts is intractable for genes with many exons. For this reason, existing approaches using the l1-penalty are either restricted to genes with few exons, or only run the regression algorithm on a small set of pre-selected isoforms. We introduce a new technique called FlipFlop which can efficiently tackle the sparse estimation problem on the full set of candidate isoforms by using network flow optimization. Our technique removes the need of a preselection step, leading to better isoform identification while keeping a low computational cost. Experiments with synthetic and real RNA-Seq data confirm that our approach is more accurate than alternative methods and one of the fastest available. Source code is freely available as an R package from the Bioconductor web site ( and more information is available at
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Submitted on : Thursday, August 21, 2014 - 11:13:44 AM
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Elsa Bernard, Laurent Jacob, Julien Mairal, Jean-Philippe Vert. Efficient RNA Isoform Identification and Quantification from RNA-Seq Data with Network Flows. Bioinformatics, Oxford University Press (OUP), 2014, 30 (17), pp.2447-2455. ⟨10.1093/bioinformatics/btu317⟩. ⟨hal-00803134v3⟩



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