Accéder directement au contenu Accéder directement à la navigation
Article dans une revue

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, *
* Auteur correspondant
3 Statistique en grande dimension pour la génomique
PEGASE - Département PEGASE [LBBE]
4 LEAR - Learning and recognition in vision
Grenoble INP [2007-2019] - Institut polytechnique de Grenoble - Grenoble Institute of Technology [2007-2019], LJK [2007-2015] - Laboratoire Jean Kuntzmann [2007-2015], Inria Grenoble - Rhône-Alpes
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
Liste complète des métadonnées

Littérature citée [2 références]  Voir  Masquer  Télécharger
Contributeur : Elsa Bernard <>
Soumis le : jeudi 21 août 2014 - 11:13:44
Dernière modification le : mardi 22 septembre 2020 - 03:55:54
Archivage à long terme le : : mardi 11 avril 2017 - 20:08:26



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⟩



Consultations de la notice


Téléchargements de fichiers