title: Efficient RNA isoform identification and quantification from RNA-Seq data with network flows.
abstract: BACKGROUND
  Several state-of-the-art methods for isoform identification and quantification are based on [Formula: see text]-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 [Formula: see text]-penalty are either restricted to genes with few exons or only run the regression algorithm on a small set of preselected isoforms.
  
  
  RESULTS
  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.
  
  
  METHODS
  Source code is freely available as an R package from the Bioconductor Web site (http://www.bioconductor.org/), and more information is available at http://cbio.ensmp.fr/flipflop.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Mines ParisTech, Centre for Computational Biology, 77300 Fontainebleau, Institut Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, INSERM U900, Paris F-75248, France, Laboratoire Biométrie et Biologie Evolutive, Université de Lyon, Université Lyon 1, CNRS, INRA, UMR5558, Villeurbanne, France and LEAR Project-Team, INRIA Grenoble Rhône Alpes, 38330 Montbonnot, France Mines ParisTech, Centre for Computational Biology, 77300 Fontainebleau, Institut Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, INSERM U900, Paris F-75248, France, Laboratoire Biométrie et Biologie Evolutive, Université de Lyon, Université Lyon 1, CNRS, INRA, UMR5558, Villeurbanne, France and LEAR Project-Team, INRIA Grenoble Rhône Alpes, 38330 Montbonnot, France Mines ParisTech, Centre for Computational Biology, 77300 Fontainebleau, Institut Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, INSERM U900, Paris F-75248, France, Laboratoire Biométrie et Biologie Evolutive, Université de Lyon, Université Lyon 1, CNRS, INRA, UMR5558, Villeurbanne, France and LEAR Project-Team, INRIA Grenoble Rhône Alpes, 38330 Montbonnot, France.
authors.forename: Elsa
authors.initials: E
authors.lastname: Bernard
authors.affiliation: Mines ParisTech, Centre for Computational Biology, 77300 Fontainebleau, Institut Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, INSERM U900, Paris F-75248, France, Laboratoire Biométrie et Biologie Evolutive, Université de Lyon, Université Lyon 1, CNRS, INRA, UMR5558, Villeurbanne, France and LEAR Project-Team, INRIA Grenoble Rhône Alpes, 38330 Montbonnot, France.
authors.forename: Laurent
authors.initials: L
authors.lastname: Jacob
authors.affiliation: Mines ParisTech, Centre for Computational Biology, 77300 Fontainebleau, Institut Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, INSERM U900, Paris F-75248, France, Laboratoire Biométrie et Biologie Evolutive, Université de Lyon, Université Lyon 1, CNRS, INRA, UMR5558, Villeurbanne, France and LEAR Project-Team, INRIA Grenoble Rhône Alpes, 38330 Montbonnot, France.
authors.forename: Julien
authors.initials: J
authors.lastname: Mairal
authors.affiliation: Mines ParisTech, Centre for Computational Biology, 77300 Fontainebleau, Institut Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, INSERM U900, Paris F-75248, France, Laboratoire Biométrie et Biologie Evolutive, Université de Lyon, Université Lyon 1, CNRS, INRA, UMR5558, Villeurbanne, France and LEAR Project-Team, INRIA Grenoble Rhône Alpes, 38330 Montbonnot, France Mines ParisTech, Centre for Computational Biology, 77300 Fontainebleau, Institut Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, INSERM U900, Paris F-75248, France, Laboratoire Biométrie et Biologie Evolutive, Université de Lyon, Université Lyon 1, CNRS, INRA, UMR5558, Villeurbanne, France and LEAR Project-Team, INRIA Grenoble Rhône Alpes, 38330 Montbonnot, France Mines ParisTech, Centre for Computational Biology, 77300 Fontainebleau, Institut Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, INSERM U900, Paris F-75248, France, Laboratoire Biométrie et Biologie Evolutive, Université de Lyon, Université Lyon 1, CNRS, INRA, UMR5558, Villeurbanne, France and LEAR Project-Team, INRIA Grenoble Rhône Alpes, 38330 Montbonnot, France.
authors.forename: Jean-Philippe
authors.initials: JP
authors.lastname: Vert
mesh_terms: D000465:Algorithms; D005091:Exons; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D015233:Models, Statistical; D059368:RNA Isoforms / Q000737:chemistry* / Q000378:metabolism; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
chemical_list: D059368:RNA Isoforms