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GdrBIMUniversité de Rennes 1



Centre de recherche commun Inria Microsoft Research

JOBIM 2012

Journées Ouvertes en Biologie, Informatique et Mathématiques

3 - 6 juillet 2012


programme détaillé JOBIM 2012

Mardi 3 juillet

8h30 - 9h45 Accueil des participants
9h45 - 10h00

Ouverture conférence

10h00 - 12h30

Session1 - Molecules and Sequences

Conférence invitée : David B. Searls - Molecules, Languages, and Automata.

Expressive Pattern Matching with Logol. Application to the Modelling of -1 Ribosomal Frameshift events.
Catherine Belleannée, Olivier Sallou and Jacques Nicolas
SA-Mot: a new web server for the extraction of motifs of interest from protein loops.
Leslie Regad, Juliette Martin, Colette Geneix and Anne-Claude Camproux
The sequence space of G-protein-coupled receptors: Implications for molecular modeling.
Jean-Michel Becu, Julien Pele, Hervé Abdi and Marie Chabbert
12h30 - 14h15
14h15 - 15h30

Session 2 - Regulation

Conférence invitée : Martin Vingron - Computational Regulatory Genomics.

Institut Français de Bioinformatique
Jean-François Gibrat
15h30 - 17h15

Session posters 1 / pause-café

17h15 - 18h30

Sessions parallèles


Session 3-A : RNA

Development of a pipeline for Scyliorhinus canicula miRNA identification from NGS data.
Wilfrid Carré, Pierre Pericard, Christophe Caron, Erwan Corre and Sylvie Mazan
BoostSVM: A miRNA classifier with high accuracy using boosting SVM.
Van Du Tran, Benjamin Zerath, Sebastien Tempel, Farida Zehraoui and Fariza Tahi
miRNAFold: A fast ab-initio method for searching for miRNA precursors in whole genomes.
Sébastien Tempel and Fariza Tahi

Session 3-B : Protein structure

A Modular Network Analysis (MONETA) of Protein Structures for Exploring and Predicting Allosteric Communication.
Elodie Laine, Christian Auclair and Luba Tchertanov
Impact of the D802V Mutation on the Structure and Dynamics of the CSF-1R Tyrosine Kinase Receptor.
Priscila Da Silva Figueiredo Celestino, Elodie Laine, Pedro Geraldo Pascutti and Luba Tchertanov
Structural determinants of Raltegravir specific recognition by the HIV-1 Integrase.
Rohit Arora and Luba Tchertanov

Session 3-C : Genes

Importance of family size and function in the fate of duplicated genes in the protein-protein interactome of Arabidopsis thaliana.
Justin Whalley, Etienne Birmelé and Carène Rizzon
GO2PUB PubMed Query Tool Based on Semantic Expansion of Gene Ontology Terms, a Lipid Metabolism Case Study.
Charles Bettembourg, Christian Diot, Anita Burgun and Olivier Dameron
Retrospective Analysis of a Gene by Mining Texts: The Hepcidin Gene Use-Case.
Fouzia Moussouni, Bertrand Ameline De Cadeville, Ulf Leser and Olivier Loréal

Session 3-D : High througput sequencing

Rapid Prioritization and Annotation of Variants from Human Re-sequencing Studies.
Elodie Dubus, D Richards, R Flannery, A Kramer, J Lerman et A Kutchma (Ingenuity Systems)
Extracting relevant information from UHTS data.
Patricia Otten-Hernandez, L Baerlocher , J Prados , N González , W Baroni , M Osteras et L Farinelli (Fasteris)
KLAST: high-performance sequence similarity search tool.
Erwan Drezen, Alain Meil, Dominique Lavenier et Patrick Durand (Korilog & Inria/IRISA GenScale team)
19h00 - 20h00 Réception à la maire de Rennes
20h00 Dîner libre

Mercredi 4 juillet

9h00 - 11h00

Session 4 - Non-protein world

Conférence invitée : Ivo Hofacker - RNA Structures, Interactions, and Folding Kinetics

Computational detection and expression profiling of conserved long non-coding RNAs in the domestic dog.
Thomas Derrien, Amaury Vaysse, Benoit Hennuy, Wouter Coppieters, Benoit Hedan, Catherine Andre and Christophe Hitte
NRPS toolbox for the discovery of new nonribosomal peptides and synthetases.
Maude Pupin, Malika Smaïl-Tabbone, Philippe Jacques, Marie-Dominique Devignes and Valerie Leclère
11h00 - 11h45

Session Posters 2 / Pause-café

11h45 - 12h30


12h30 - 14h15 Déjeuner
14h15 - 16h30

Session 5 - Proteins and interactions

Conférence invitée : Pierre Baldi -Machine Learning Approaches in Proteomics

Protein-protein interaction network inference with semi-supervised Output Kernel Regression.
Celine Brouard, Marie Szafranski and Florence D'Alché-Buc
Improving gene signatures by the identification of differentially expressed modules in molecular networks : a local-score approach.
Marine Jeanmougin, Christophe Ambroise, Matthieu Bouaziz and Mickaël Guedj
Présentation Yoann Mouscaz
16h30 Départ pour St-Malo
18h00 - 19h15 Temps libre à St-Malo
19h15 - 00h00 Dîner de gala au Palais du Grand Large


Jeudi 5 juillet

9h00 - 10h30

Session 6 - Evolution

Conférence invitée : Hugues Roest Crollius - The 4th dimension of Biology. A historical perspective of biological processes.

Non-adaptive expansion of gene families.
Param-Priya Singh, Severine Affeldt and Herve Isambert
10h30 - 11h00 Pause café
11h00 - 12h30

Session 7 - Systems biology

Logical modelling of cellular decision processes with GINsim.
Claudine Chaouiya, Aurélien Naldi, Lionel Spinelli, Pedro T. Monteiro, Duncan Berenguier, Luca Grieco, Abibatou Mbodj, Samuel Collombet, Anna Niarakis, Laurent Tichit, Elisabeth Remy and Denis Thieffry
Using large scale knowledge databases about reactions and regulations to find key regulators of sets of genes.
Pierre Blavy, Florence Gondret, Sandrine Lagarrigue, Jaap van Milgen and Anne Siegel
Using Mutual Information and Answer Set Programming to refine PWM based transcription regulation network.
Andres Aravena, Carito Guziolowski, Anne Siegel and Alejandro Maass
12h30 - 14h15 Déjeuner
14h15 - 16h15

Session 8 - Algorithms for genomics

Conférence invitée : Bertil Schmidt - Scalable Algorithms and Tools for Biological Sequence Analysis.

Mapping Reads on a Genomic Sequence: a Practical Comparative Analysis.
Sophie Schbath, Véronique Martin, Matthias Zytnicki, Julien Fayolle, Valentin Loux and Jean-François Gibrat
SortMeRNA: a new software to filter total RNA for metatranscriptomic or RNA analysis.
Evguenia Kopylova, Laurent Noé and Hélène Touzet
Présentation Jebif
16h15 - 17h30

Session posters 3 / pause-café

17h30 - 19h00

Sessions parallèles


Session 9-A : Protein and genome structure

CSA: Comparaison compréhensive d'alignement de paires de structures de protéines.
Inken Wohlers, Noël Malod-Dognin, Rumen Andonov and Gunnar Klau
A Novel Approach of Spatial Motif Extraction to Classify Protein Structures.
Rabie Saidi, Wajdi Dhifli, Mondher Maddouri and Engelbert Mephu Nguifo
On the Complexity of two Problems on Orientations of Mixed Graphs.
Hafedh Mohamed Babou, Guillaume Fertin and Irena Rusu

Session 9-B : Sequence analysis

Fast Homology Search Using Domain-Architecture Alignment.
Nicolas Terrapon, Sonja Grath, January Weiner, Andrew D. Moore and Erich Bornberg-Bauer
Fast estimation of posterior probabilities in change-point models through a constrained hidden Markov model.
The Minh Luong, Yves Rozenholc and Gregory Nuel
Detecting Outliers in HMM modeling through Relative Entropy with Applications to Change-Point Detection.
Vittorio Perduca and Gregory Nuel

Session 9-C : Distributed data and computation

Towards a Distributed Infrastructure for Bioinformatics: French GRISBI Perspective.
Christophe Blanchet, Clément Gauthey, Christophe Caron, Olivier Collin, Stéphane Delmotte, Tiphaine Martin, Simon Penel, Aurélien Roult, Franck Samson and Bruno Spataro
Parallel Storage: Addressing the Big Data Challenge.
Sven Neirynck (Panasas)
Plus de simulations pour des résultats encore plus rapide avec les GPU NVIDIA.
Jean-Christophe Baratault (NVIDIA - Tesla Sales EMEA)
20h00 Dîner libre

Vendredi 6 juillet

9h00 - 10h30

Session 10 - Evolution

Conférence invitée : Toni Gabaldón - Phylogenomics in the light of ever-growing sequencing data.

Evolution of conjugation and type IV secretion systems.
Julien Guglielmini, Fernando de La Cruz and Eduardo P.C. Rocha
Présentation DE^CODAGE
Philippe Leroy
10h30 - 11h00 Pause-café
11h00 - 12h30

Session 10 - Evolution (suite)

EvoluCode: an original view of Human Systems Evolution.
Benjamin Linard, Olivier Poch and Julie Thompson
Haplotype-based method for detecting regions under selection in the domestic dog.
Hillel Jean-Baptiste-Adolphe, Mathieu Emily, Amaury Vaysse, Catherine André and Christophe Hitte
GECA: Gene Evolution/Conservation Analysis tool for Eukaryotic gene families.
Nizar Fawal, Bruno Savelli, Christophe Dunand and Catherine Mathé
12h30 - 13h00

Prix + Jobim 2013

13h00 - 14h30 Déjeuner Galettes-saucisses