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JOBIM Scientific Agenda

Programme Scientifique de la Conférence JOBIM 2015 : Lundi 6 Juillet 12h00 - Jeudi 9 Juillet 12h00

© JOBIM2015
Scientific Agenda of the JOBIM 2015 Conference : Monday, July 6th at noon - Thursday, July 9th at noon
Programme at a glance

Programme at a glance

Dimanche 5 Juillet 2015

  • 14h00 – 16h00 : Salles Commission 12-13 / Niveau 2 - SéminaireJeBiF

16h00 - 16h30 - Hall de Commission / Niveau 2 - Pause-café petits fours sucrés

  • 16h30 – 18h00 : Salles Commission 12-13 / Niveau 2 - SéminaireJeBiF

Lundi 6 Juillet 2015 - Monday, July 6th 2015

  • 09h00 - 10h00 : Salles Commission 12-13 / Niveau 2 - SéminaireJeBiF

10h00 - 10h30 - Hall de Commission / Niveau 2 - Pause-café viennoiseries

  • 10h30 – 12h00 : Salles Commission 12-13 / Niveau 2 - Séminaire JeBiF

12h00 - 13h30 - Espace "Entre 2 villes" - Déjeuner Séminaire JeBiF


12h30 - 14h00 : Hall d'Accueil, Rez-de-Chaussée -

Accueil JOBIM 2015  --  Pause-café petits fours sucrés / Coffee Break


  • 14h00 - 14h30 : Amphithéâtre - Ouverture de la Conférence JOBIM 2015- JOBIM 2015 Opening
    • Présidence Université d’Auvergne - Philippe DULBECCO
      • représenté par Alain Eschalier Vice Président Recherche - Université d'Auvergne
    • Présidence Université Blaise Pascal - Mathias BERNARD
      • représenté par Khalil DRISSI Vice Président Valorisation - Université Blaise Pascal
    • Présidence Centre INRA Auvergne-Rhône-Alpes - Jean-Baptiste COULON
      • représenté par Thierry LANGIN Directeur de l'Unité de Recherche UMR INRA/UBP 1095 GDEC
    • Invitée d’Honneur - Marie-France SAGOT


Plenary Session I - Amphithéâtre/Amphitheater

Biochimie, Biologie Structurale & Bioinformatique Structurale - Biochemistry, Structural Biology & Structural Bioinformatics

Chair: Jean-François GIBRAT (Institut Français de Bioinformatique - IFB, France)

  • 14h30 - 15h10 Keynote-01 - Christine ORENGO - University College London (UCL), UK
    • A Structural Perspective on the Evolution of Protein Functions
  • 15h10 - 15h30 Proc-01 - Yasaman Karami - Iran University of Science and Technology, Iran
    • Accelerating Protein Structure Prediction using Particle Swarm  Optimization on GPU
  • 15h30 - 15h50 Proc-02 - Isaure Chauvot de Beauchene - Technical University Munich, Germany
    • Modelling ssRNA-protein complexes at atomic resolution
  • 15h50 - 16h10 Proc-03 - Seyed Ziaeddin Alborzi - Université de Lorraine - LORIA, France
    • EC-PSI: Associating Enzyme Commission Numbers with Pfam Domains
  • 16h10 - 16h30 High-01 - Marco Pasi - CNRS UMR5086/Université Lyon I, France
    • Sequence determines the structure and microsecond-scale dynamics of B-DNA and its bound cations

16h30 - 17h00 - Pause-café petits fours sucrés (installation Affiches) / Coffee Break (Posters installation)

Plenary Session II - Amphithéâtre/Amphitheater

Évolution, Phylogénie & Paléogénomique - Evolution, Phylogeny & Paleogenomics

Chair: Guy PERRIERE (CNRS, LBBE, France)

  • 17h00 - 17h40 Keynote-02 -Ziheng YANG - University College London (UCL), UK
    • Estimation of species divergence times incorporating fossil and molecular information.
  • 17h40 - 18h00 Proc-04 - Elodie Cassan - UMR5506 CNRS, Université de Montpellier, France
    • Evolutionary analyses support that ASP (Anti Sense Protein) overlapping ORF is the 10th gene of HIV-1 M pandemic group
  • 18h00 - 18h20 High-02 - Blerina Sinaimeri - INRIA Grenoble Rhône-Alpes, France
    • Cophylogeny Reconstruction via an Approximate Bayesian Computation
  • 18h20 - 18h40 High-03 - Gabriel Markov - Max Planck Institute for Developmental Biology, Germany
    • The same or not the same: Lineage-specific gene expansions and homology relationships in multigene families in nematodes
  • 18h40 - 19h00 - Announcement (2 x 10 min)
    • Christoph GRUNAU - Réseaux thématiques pluridisciplinaires 3E «Epigénétique en Ecologie et Evolution »
    • Dominique JOLY - Groupement De Recherche en Génomique Environnementale (GDR GE)

Soirée Libre / Free Evening

Mardi 7 Juillet 2015 - Tuesday, July 7th 2015

Plenary Session III - Amphithéâtre/Amphitheater

Organisation & Expression des Génomes - Organization & Genome Expression

Chair: Gisèle BRONNER (LMGE, Université Blaise Pascal, France)

  • 09h00 - 09h40 Keynote-03 - Stéphane ROMBAUTS - VIB, Gand, Belgique
    • The next challenge: sequencing, assembling and annotation of complex genomes with NGS
  • 09h40 - 10h00 Proc-05 - Jérémy Tournayre - INRA, UMR1213 Herbivores, France
    • Fat&MuscleDB: A database to understand tissue growth processes contributing to body or muscle composition
  • 10h00 - 10h20 High-04 - Alexandre Cormier - CNRS-UPMC UMR8227 LBI2M, Station Biologique de Roscoff, France
    • Sexual dimorphism and the evolution of sex-biased gene expression in the brown alga Ectocarpus
  • 10h20 - 10h40 High-05 - Frédéric Choulet - INRA/UBP UMR1095 GDEC, France
    • A Reference Sequence of the Bread Wheat Chromosome 3B

10h40 - 11h10 - Pause-Café viennoiseries / Coffee Break

Plenary Session IVa - Amphithéâtre/Amphitheater

Spéciale Conférence Invitées - Special "Invited Speakers"

  • 11h10 - 11h50 keynote-04 - Imagerie & Traitement de l’Image - Imaging & Image Processing
    • Chair: Valérie POLONAIS (IUT Aurillac, Université d'Auvergne, France)
    • Thomas WALTER - Institut Curie, France
      • Bioimage Informatics for Phenomics
  • 11h50 - 12h30 keynote-05 - Réseaux, Régulation & Modélisation - Network, Regulation & Modeling
    • Chair: Franck GIACOMONI (INRA, France)
    • Daniel SEGRÈ - Boston University, USA
      • Spatio-temporal models of metabolism in microbial communities
  • 12h30 - 13h00 - Announcement
    • Jean-François GIBRAT - IFB-core

13h00 - 14h30 - Déjeuner - Ticket Bleu / Lunch - Blue Ticket

Parallel Sessions - Démos/Demos

Session A

Session B

Session C

Espace Restauration Niveau 2

Amphithéâtre / Amphitheater

Salles Commission 11-12-13 - Niveau 2


Gabriel MARKOV

Benoit BELY


Réseaux, Régulation & Modélisation

Méta-omiques & Génomique Environnementale

Méthodologies pour l'analyse des séquences et des données omiques

14h30 - 14h50

Demo-A1 - Jacques van Helden

Demo-B1 - Géraldine Pascal

Demo-C1 - Nicolas Kaspric

Services, Ressources & Infrastructures pour la Bioinformatique

14h50 - 15h10

Demo-A2 - Laurent Bulteau

Demo-B2 - Bryan Brancotte

Demo-C2 - Isabelle Guigon

  • Demo-A1 : Regulatory Sequence Analysis Tools (RSAT)
  • Demo-A2 : DINGHY: Dynamic Interactive Navigator for General Hypergraphs in Biology
  • Demo-B1 : FROGS: Find Rapidly OTU with Galaxy Solution
  • Demo-B2 : Interrogation de bases de données biologiques publiques par reformulation de requêtes et classement des résultats avec ConQuR-Bio
  • Demo-C1 : Proteome data mining using ProteINSIDE online tool
  • Demo-C2 : Finding and analysing microRNAs in plant genomes with miRkwood

15h10 - 16h10 - Session Affiches / Posters (even poster numbers / posters nombres pairs)

16h10 - 16h40 - Pause-Café petits fours sucrés / Coffee Break

Plenary Session V - Amphithéâtre/Amphitheater

Méthodologies pour l’Analyse des Séquences et des Données Omiques - Methodologies for Sequence Analysis & Omics Data

Chair: Pierre PETERLONGO (INRIA, France)

  • 16h40 - 17h20 Keynote-06 - Anthony COX - Illumina Cambridge Ltd, UK
    • The power of populations: methods that scale to thousands of human genomes
  • 17h20 - 17h40 Proc-06 - Aymeric Antoine-Lorquin - IRISA UMR 6074, Inria et Université de Rennes1, France
    • Comparison of the targets obtained by a scoring matrix and by a regular expression. Application to the search for LXR binding sites
  • 17h40 - 18h00 Proc-07 - Mathilde Le Boudic-Jamin - IRISA UMR 6074 et Université de Rennes 1, France
    • De novo detection of structure repeats in Proteins
  • 18h00 - 18h20 High-06 - Morgane Thomas-Chollier - Institut de Biologie de l'Ecole Normale Supérieure de Paris, France
    • ExoProfiler : a motif-based approach to analyse ChIP-exo signal
  • 18h20 - 18h40 High-07 - Nicolas Terrapon - UMR 7257 CNRS Aix-Marseille Université, France
    • How does the human gut microbiota breakdown complex polysaccharides
  • 18h40 - 19h10 : Announcement (2 x 15 min)
    • Valérie POLONAIS - IUT Aurillac
    • Gisèle BRONNER - Master Bioinformatique Université Blaise-Pascal

19h30 - 22h00 - Cocktail - Polydome - Espace "Entre 2 Villes"

Espace Entre 2 Villes - Polydome

Espace Entre 2 Villes - Polydome

Mercredi 8 Juillet 2015 - Wednesday, July 8th 2015

Plenary Session VI - Amphithéâtre/Amphitheater

Méta-omiques & Génomique Environnementale - Meta-omics & Environnemental Genomics

Chair:Eric PELLETIER (CEA / Genoscope, France)

  • 08h10 - 08h50 Keynote-07 - Rob FINN - European Bioinformatics Institute (EMBL-EBI), UK
    • Towards understanding the functional and taxonomic repertoire of a metagenome 
  • 08h50 - 09h10 Proc-08 - Guy Perrière - UMR CNRS 5558, Université Claude Bernard - Lyon 1, France
    • RecStat: a set of R utilities for coding DNA sequences prediction in metagenomes
  • 09h10 - 09h30 Proc-09 - Faouzi Jaziri - Université d’Auvergne EA 4678 CIDAM, France
    • Propositional Logic for Efficient Microbial Community Assessment by DNA Microarray Data Analysis

Plenary Session VII - Amphitéâtre/Amphitheater

Biologie Translationnelle & Pharmacogénomique - Translational Biology & Pharmacogenomics

Chair: Nathalie RIVIERE ( Biogemma, France)

  • 09h30 - 10h10 Keynote-08Ana CONESA - Centro de Investigaciones Príncipe Felipe, Spain
    • Lessons and results of integrative multi-omics data analysis
  • 10h10 - 10h30 High-08Jacques Colinge - IRCM Inserm U1194, University of Montpellier, France
    • Computational Analysis of Promiscuous Drug Protein Target Spectra

10h30 - 11h00 - Pause-Café viennoiseries / Coffee Break

Plenary Session IVb - Amphithéâtre/Amphitheater

Spéciale Conférence Invitées - Special "Invited Speakers"

  • 11h00 - 11h40 keynote-09 - Génétique & Génétique des Populations - Genetics & Population Genetics
    • Chair: Dominique JOLY (CNRS, France) 
    • Laurence MOREAU - INRA, France
      • New prospects and challenges raised by the implementation of Genome-wide association mapping and Genomic Selection in plants. Illustrations in maize

Parallel Sessions - Démos/Demos

Session D

Session E

Session F

Salles Commission 11-12-13 - Niveau 2

Espace Restauration Niveau 2

Amphithéâtre / Amphitheater




Valentin LOUX

Méthodologies pour l'analyse des séquences et des données omiques

Méthodologies pour l'analyse des séquences et des données omiques

Services, Ressources & Infrastructures pour la Bioinformatique

11h40 - 12h00

Demo-D1 - Magali Berland

Demo-E1 - Marie-Laure Franchinard

Demo-F1 - Laurent Jourdren

Génétique & Génétique des Populations

12h00 - 12h20

Demo-D2 - Bérénice Batut

Demo-E2 - Lydia Ait Braham

Demo-F2 - Stéphane Télétchéa

Services, Ressources & Infrastructures pour la Bioinformatique

12h20 - 12h40

Demo-D3 - Alexandra Louis

Demo-E3  - Benoit Bely

Demo-F3 - Delphine Steinbach

  • Demo-D1 : Demo of metagenomic data analysis: from reads to biomarkers with METEOR and MetaOMineR
  • Demo-D2 : ASAIM: an intuitive and adjustable pipeline to process metatranscriptomic data from intestinal microbiota
  • Demo-D3 : Genomicus: fast and intuitive comparative genomics in eukaryotes
  • Demo-E1 : View and synchronize several genotypes using IGV
  • Demo-E2 : BioMercator : A complete framework to integrate QTL, meta-QTL, genome annotation and genome-wide association studies
  • Demo-E3 : How UniProtKB/TrEMBL Tackles High Redundant Proteomes
  • Demo-F1 : Eoulsan 2: Facilitating expansion to new NGS tools and execution platforms
  • Demo-F2 : DockNmine, a web portal to compare virtual and experimental interaction data
  • Demo-F3 : GnpIS-Asso : a new generic tool for managing and exploiting genetic association studies results using high throughput genotyping and phenotyping data

12h40 - 13h30 - Déjeuner - Ticket Vert / Lunch - Green Ticket

13h30 - 14h30 - Session Affiches (Affiches nombres impairs / odd poster numbers)

14h30 - 15h30 - Assemblée Générale de la Société Française de Bioinformatique - SFBI

Société Française de Bioinformatique

Société Française de Bioinformatique

15h30 - 16h00 - Pause-Café petits fours sucrés / Coffee Break

Plenary Session VIII - Amphithéâtre/Amphitheater

Epigénétique & Epigénomique - Epigenetics & Epigenomics

Chair: Emilie BRASSET (GReD, Université d'Auvergne, France)

  • 16h00 - 16h40 Keynote-10- Christoph GRUNAU - IHPE, Université de Perpignan, France
    • Environmental and evolutionary epigenomics of non-model organisms : challenges and solutions.
  • 16h40 - 17h00 High-09 - Daniel Jost - Université Joseph Fourier, UMR5525 CNRS, France
    • Interactions between chromatin states shape the epigenome nuclear organization
  • 17h00 - 17h30 Announcement
    • Nathalie RIVIERES - Biogemma
    • Jean-Pierre MARTINANT - Limagrain

17H30 - Rassemblement pour la Photo de Groupe / Group photo

18h30 - Départ en Bus / Bus departure to Vulcania

19h00 - Soirée de Gala à Vulcania / Gala Dinner at Vulcania -

Soirée Gala Vulcania

Soirée Gala Vulcania

24h00 (minuit) - Retour aux Hôtels / Back to Hotels

Jeudi 9 Juillet 2015 - Thursday, July 9th 2015

Plenary Session IX - Amphithéâtre/Amphitheater

Services, Ressources &  Infrastructures pour la bioinformatique - Services, Resources & Infrastructures for Bioinformatics

Chair: Christophe BLANCHET (IFB, France)

  • 09h00 - 09h40 Keynote-11 - Katharina HUBER - Computational Biology Laboratory at the University of East Anglia, UK
    • Dealing with big evolutionary data
  • 09h40 - 10h10 Proc-10 - Imene Boudellioua - King Abdullah University of Science and Technology, Kingdom of Saudi Arabia
    • Association Rule Mining for Metabolic Pathway Prediction
  • 10h10 - 10h30 Proc-11 - Nicolas Daccord - UMR8071 CNRS, Université Evry-Val d’Essonne IBGBI, France
    • TopoIBase: a comprehensive database dedicated to type IA DNA-topoisomerases

10h30 - 11h00 - Pause-Café viennoiseries / Coffee Break

  • 11h00 - 11h20 High-10 - Vincent Henry - STATSARRAY / CISMeF, TIBS, LITIS EA 4108, CHU et Université de Rouen, France
    • OMICtools: A workflow for multi-omic data analysis
  • 11h20 - 11h40 High-11 - Mélanie Pétéra - PFEM, UMR1019 INRA, France
    • Workflow4Metabolomics: A collaborative research infrastructure for computational metabolomics
  • 11h40 - 12h30
    • Remise des Récompenses par S. Schbath & M.F. Sagot
      • Meilleure présentation Orale / Best oral talk
      • Deux meilleures Affiches / Two best poster presentations
    • Annonce JOBIM2016 - F. Picard
    • Clôture JOBIM2015 - P. Peyret

12h30 : Distribution des Lunch-Box - Ticket Rouge (à réserver le jour de l'accueil) / Lunch box distribution - Red Ticket (to be reserved at the frontdesk the first day)

See also

Liste Keynote lectures

Liste Proceedings - Article Originale

Liste Highlights - Résumé Étendu

Démos - Résumé Court

Affiches/Posters - Résumé Court - premier appel (Comité de lecture)

Affiches/Posters - Résumé Court - deuxième appel (sans Comité de lecture)