Programme scientifique

Session 1 – Protein Structure

Conférence invitée * Sarah TEICHMANN – Evolution and Assembly of Protein Complexes

PEP-FOLD: Biased Approach for the de novo Prediction of Peptide and Miniprotein Structure –  Y. Shen, J. Maupetit, P. Derreumaux and P. Tufféry
Protein Complex Co-Evolution from a Structural Perspective –  G. Faure, J. Andreani and R. Guérois
Protein-protein Docking based on Shape Complementarity and Voronoi Fingerprints – T. Bourquard, J. Azé, A. Poupon and D. Ritchie

Session 2 – Evolution

Conférence invitée * Patrick FORTERRE – The Role of Viruses (Virocell) in the Origin and Diversification of Biological Information

Sessions parallèles

3A. Protein Structure

Analysis of Co-evolution at Protein Complex Interfaces –  J. Andreani, G. Faure and R. Guérois
New Developments and Applications for Protein Peeling Algorithm –  J.-C. Gelly and A. De Brevern
How significant is a Threading Score? –  A. Fayyaz Movaghar, G. Launay, S. Schbath, J.F. Gibrat and F. Rodolphe

3B. Regulation and Pathways

Identification of Cis-Regulatory Elements Involved in Zygotic Genome Activation During Early Drosophila melanogaster Embryogenesis –  E. Darbo, T. Lecuit, D. Thieffry and J. Van Helden
[ Présentation industrielle ] An Integrative Signaling Pathway Analysis for Determining Master Regulators and Dysregulated Pathways in Her2 Over-Expressed Human Breast Cancer – P. Vera-Licona, A. Zinovyev, I. Kuperstein, O. Kel, A. Kel, T. Dubois, G. Tucker and E. Barillot 
Identifi”cation of Shortened 3'Untranslated Regions and Impact on MicroRNA Regulation – L. Martignetti, K. Laud-Duval, F. Tirode, E. Barillot, O. Delattre and A. Zinovyev

3C. Gene and Genome Function

Interaction Networks and Intrinsic Disorder: Another Way to Investigate Extracellular Matrix Functions –  F. Peysselon, R. Salza, M. Fatoux-Ardore, E. Chautard, N. Thierry-Mieg and S. Ricard-Blum
Candidate Gene Prioritization in Prokaryotes Based on Multiple Genomes Data –  R. Barriot, Y. Quentin and G. Fichant
Skew N-domains and Replication U-domains: Gradients of Replication Fork Polarity in the Human Genome –  C.-L. Chen, L. Duquenne, Y. D'Aubenton-Carafa, C. Thermes, A. Goldar, G. Guilbaud, A. Rappailles, O. Hyrien, A. Baker, B. Audit and A. Arneodo

3D. Algorithmic Development

NeMo: Fast Count of Network Motifs –  M. Koskas, G. Grasseau, E. Birmelé, S. Schbath and S. Robin
Waffect: a Method to Simulate Case-Control Samples in Genome-Wide Association Studies –  V. Perduca, R. Mourad, C. Sinoquet and G. Nuel
A Sequential Monte Carlo Method for Estimating Transcriptional Landscape at Base-pair Level from RNA-Seq Data –  B. Mirauta, P. Nicolas and  H. Richard

Session 4 – The Challenges of NGS

Conférence invitée * Michael BRUDNO – Discovering and Visualizing Structural Variation from High Throughput Sequencing Data

An Exact Algorithm for the Segmentation of NGS Profiles Using Compression – G. Rigaill
Distributed High Throughput Sequencing Data Analysis on Cloud Computing – L. Jourdren, M. Bernard, M.-A. Dillies and S. Le Crom
Complex Plant Genome Sequencing Using Combined Sequencing Technologies and de novo Assemblers – M. Zouine, C. Rousseau, P. Frasse, C. Klopp  and  M. Bouzayen
Identification of Regulatory Elements from Gene Expression Data without Clustering – M. Lajoie, O. Gascuel  and  L. Brehelin
Mapping Genetic Interactions in Various Contexts Provides Complementary Information – M. Michaut  and  G. Bader

Session 5 – Systems Biology

Conférence invitée * Edda KLIPP – Mathematical Modeling of Yeast Stress Response

Sessions parallèles

6A. Phylogeny and Evolution

PhyleasProg: a User-Oriented Web Server for Wide Evolutionary Analyses – J. Busset, C. Cabau, C. Meslin  and  G. Pascal
Investment in Growth Determines the Evolutionary Rates of Proteins – S. Vieira-Silva  and  E. Rocha
Horizontal Gene Transfer of a Chloroplast Protein to Thaumarchaeota: The Unique Case of a Ferredoxine and a J-domain Fusion – C. Petitjean, C. Brochier-Armanet, P. López-Garcia  and  D. Moreira
Tpms: a Tree Pattern-Matching Utility for Querying Gene Trees Collections – T. Bigot, V. Daubin  and  G. Perrière

6B. Annotation

NGS: Neglected Genome Sequencing. Assembly and Annotation Challenges in a Highly Divergent Protozoan Genome – S. Moreira, M. Turcotte  and  G. Burger 
Integrated Gene Prediction for Prokaryotic Genomes Using EuGene – E. Sallet, J. Gouzy, B. Roux, D. Capela, L. Sauviac, C. Bruand, P. Gamas  and  T. Schiex
URGI Genome Annotation System: an Integrated System for Structural and Functional Genome Annotation – J. Amselem, M. Alaux, N. Choisne, N. Lapalu, B. Brault, A. Keliet, E. Kimmel, F. Alfama-Depauw, S. Arnoux, M. Bras, L. Brigitte, O. Inizan, V. Jamilloux, J. Kreplak, F. Legeai, I. Luyten, C. Pommier, S. Reboux, S. Sidibe-Bocs, M.-H. Lebrun, D. Steinbach  and  H. Quesneville

6C. Software Tools

ecoQuery: a Semantic Module to Query Biodiversity Data on the Web – J. Chabalier, O. Coullet, A. Sahl  and  O. Rovellotti
[ Présentation industrielle ] Integrated Bioinformatics Solutions for Microbial Genome, Proteome and Metabolome Comparative Analysis – A. Iltis, P.-E. Ciron  and  F. Rechenmann
SynTView: a Dynamic Genome Browser for Microbial Synteny and Polymorphism Information – P. Lechat, E. Souche  and  I. Moszer
[ Présentation industrielle ] Mining Databanks to Analyse Functional and Taxonomic Diversity of Sequences – A. Meil, G. Kerbellec  and  P. Durand

Session 7 – Algorithms and Evolution

Conférence invitée * Marie France SAGOT – Towards an Algorithmic and Mathematical Exploration of Symbiosis

Influence Function for Robust Phylogenetic Reconstruction –  M. Mariadassou  and  A. Bar-Hen
Character Trimming Algorithms to Build a Compositionally Homogeneous Character Subset from a Multiple Sequence Alignment –  A. Criscuolo
A Comparison of Regression Models for Testing QTL/eQTL co-Location –  X. Wang, J.-M. Elsen , O. Filangi   and  P. Le Roy

Session 8 – Genome Analysis

Conférence invitée * Mathieu BLANCHETTE – Ancestral Mammalian Genome Reconstruction and its Uses toward Annotating the Human Genome

Rearrangements Occur Mostly Neutrally in Eukaryotic Genomes –  C. Berthelot, M. Muffato  and  H. Roest Crollius
Exploration of the Genetic Diversity of the Lachancea kluyveri Yeast Species –  A. Friedrich, C. Reisser, P. Jung  and J. Schacherer
An Evolutionary Analysis of the Type III Secretion System –  S. Abby  and  E. Rocha
Identification of Putative Parasitism Genes in Plant-Parasitic Nematodes –  A. Campan-Fournier, L. Perfus-Barbeoch, M.-N. Rosso, M.-J. Arguel, C. Da Silva, C. Vens, N. Marteu, K. Labadie, F. Artiguenave, P. Abad  and  E. Danchin

Session 9 – RNA and Transcription

Conférence invitée * Peter STADLER – The RNA Zoo: Diversity and Complexity of Transcriptomes

Five Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding –  D. Schmidt, M. Wilson, B. Ballester, P. Schwalie, G. Brown, A. Marshall, C. Kutter, S. Watt, C. Martinez-Jimenez, S. Mackay, I. Talianidis, P. Flicek  and  D. Odom

Session 10 – Protein Sequence Analysis

AuPosSOM: New Approach for the Identification of Active Compounds in the Set of Docked Molecules –  A. Mantsyzov, G. Bouvier, N. Evrard-Todeschi  and G. Bertho
Ancestral HMMs and their Use to Detect Distant Homologs –  J.-B. Domelevo Entfellner  and O. Gascuel
Fitting Hidden Markov Models of Protein Domains to a Target Species –  N. Terrapon, O. Gascuel  and L. Brehelin