LIX Bioinformatics Colloquium 2010

Ecole Polytechnique

November 8-10, 2010


A PDF version of the talks/poster abstracts is now available.

The conference is hosted by the École Polytechnique (See our direction page) in the Amphithéatre Becquerel.
A mouse click on the talk titles will expand the abstract.

Monday, November 8: High Throughput and Omics
Registration & Opening address
  • 9h45-10h15: Registration & Coffee Break
  • 10h15-10h30: Welcome address
Session 1: High Throughput and Omics 1 - Chair: Gregory Kucherov
  • 10h30-11h30: [Keynote] - Éric Rivals - CNRS, LIRMM, Montpellier, France
    An integrated approach to read analysis
  • 11h30-12h00: Andrei Zinovyev Computational Systems Biology of Cancer, Institut Curie, France
    High-throughput sequencing for better understanding cancer
  • 12h00-12h30: Ivan V. Kulakovskiy NIIGenetika, Moscow, Russian Federation  [Slides]
    Deep and wide digging for binding motifs in ChIP-Seq data
  • 12h30-14h30: Lunch+Poster session
Session 2: High Throughput and Omics
  • 14h30-15h00: Stéphane Vialette IGM-Labinfo, Université Paris-Est, Marne-la-Vallée, France
    A polynomial-time algorithm for finding minimal conflicting sets
  • 15h00-15h30: Vincent Picaud CEA Saclay, France  [Slides]
    DNA Sequencing by MALDI-TOF MS using alkali cleavage of RNA / DNA Chimera
  • 15h30-16h00: David James Sherman CNRS LaBRI/INRIA MAGNOME, Université Bordeaux I
    Methods for understanding function and history in small eukaryote genomes
  • 16h00-16h15: Coffee break
  • 16h15-16h45: Matthias Zytnicki URGI, INRA Versailles, France  [Slides]
    S-MART: What will you do with all this RNA-Seq data?
  • 16h45-17h15: Stéphane Robin AgroParisTech/INRA, France
    Bayesian Model Averaging for Estimating Species Abundance. Application to Metagenomics
  • 17h15-18h15: [Keynote] - Antoine Danchin - AMAbiotics, Evry, France
Tuesday, November 9: In silico RNA
Session 3: In silico RNA 1 - Chair: Alain Denise
  • 10h00-11h00: [Keynote] - Rolf Backofen - University of Freiburg, Germany
    Non-Coding RNAs: Exploring the Cell's Dark Matter
  • 11h00-11h30: Daniel Gautheret IGM, Université Paris Sud, Orsay, France  [Slides]
    Phylogenetic signatures of RNA-RNA contacts in bacteria
  • 11h30-11h45: Coffee break
  • 11h45-12h15: Mathieu Giraud LIFL, Université Lille 1/INRIA Lille, France  [Slides]
    CUDA and OpenCL Parallelization of Algebraic Dynamic Programming (ADP)
  • 12h15-12h45: Hervé Isambert Institut Curie, Paris, France  [Slides]
    RNA switches and nanostructures.
  • 12h45-15h00: Lunch+Poster session
Session 4: In silico RNA 2 - Chair: Alessandra Carbone
  • 15h00-15h30: Christine Gaspin BIA, INRA Toulouse, France  [Slides]
    Prediction and annotation of non coding RNA: arguments for the integration of complementary approaches
  • 15h30-16h00: Alain Laederach Developmental Genetics and Bioinformatics, Wadsworth, Albany, USA  [Slides]
    Disease-Associated Mutations that alter the RNA structural ensemble: Identifying new RiboSNitches
  • 16h00-16h15: Coffee break
  • 16h15-16h45: Stefan Janssen Faculty of Technology, Bielefeld University, Germany  [Slides]
    Prediction of RNA secondary structure including kissing hairpin motifs
  • 16h45-17h45: [Keynote] - Zasha Weinberg - Howard Hughes Medical Institute, Yale University, USA  [Slides (Private)]
    From context-free grammars to sophisticated RNAs
  • 20h00-???: Conference dinner in Paris
    Restaurant: Au Moulin Vert - 34bis, rue des Plantes, 75014 Paris.
    Tel. +33 (0) 1 45 39 31 31
Wednesday, November 10: CSB and integrative biology
Session 5: Computational Structural Biology
  • 9h30-10h30: [Keynote] - Ora Schueler-Furman - The Hebrew University of Jerusalem, Israel  [Slides (Private)]
    Structure-based characterization and manipulation of peptide-mediated protein interactions
  • 10h30-11h00: Joel Janin Université Paris-Sud, Orsay, France  [Slides]
    Assessing predictions of protein-protein interaction: nine years of the CAPRI experiment
  • 11h00-11h15: Coffee break
  • 11h10-11h45: Alexandre Bonvin Bijvoet Center for Biomolecular Research, Utrecht, Netherlands  [Slides]
    Building macromolecular assemblies by information-driven docking. Challenges and perspectives
  • 11h45-12h15: Dave Ritchie LORIA, Nancy, France  [Slides]
    Using Graphics Processors to Accelerate Protein Docking Calculations
  • 13h15-14h15: Lunch+Poster session
  • 13h45-14h15: Alessandra Carbone Laboratoire de Génomique des Microorganismes, Paris, France
    Combinatorial methods to extract networks of co-evolved residues in proteins
  • 14h15-14h45: Nicolas Ferey LIMSI, Orsay, France
    An augmented elastic network approach for interactive and multi-scale molecular simulations
Session 6: Integrative Biology
  • 14h45-15h45: [Keynote] - Eric Reiter - BIOS, INRA Tours, France
    Systems biology approaches to unravel the complexity and dynamics of G protein-coupled receptor signalling networks.
  • 15h45-16h15: Sylvie Hamel Université de Montréal, Canada  [Slides]
    Medians of permutations and gene orders
  • 16h15-16h30: Coffee break
  • 16h30-17h00: Aicha Demidem INRA, Theix, France  [Slides]
    Metabolomic analysis of Human Hepatocellular Carcinoma by proton NMR spectroscopy
  • 17h00-17h30: William Vainchenker Institut Gustave Roussy, Villejuif, France  [Slides]
    Will it be possible to model the pathogenesis and treatment of Myloproliferative disorders?
Concluding remarks
  • 17h30-17h45: Concluding remarks
X GDR Bioinformatique Moléculaire CNRS INRIA