Analysis and Annotation of DNA Repeats and Dark Matter in Eukaryotic Genomes

Convenors :

• Dr. Peter Arensburger , LE STUDIUM® RESEARCH FELLOW
  on leave from California State Polytechnic University, Pomona, California - USA,
  in residence UMR INRA-CNRS 7247 Physiologie de la Reproduction et des Comportements - Centre INRA Val de Loire Nouzilly - France.
• Dr. Yves Bigot,
  CNRS Research Director UMR INRA-CNRS 7247 Physiologie de la Reproduction et des Comportements - Centre INRA Val de Loire Nouzilly - France

Confirmed Speakers:

• Dr. Peter Arensburger
  Biological Sciences Department, California State Polytechnic University, Pomona, CA 91768, USA
• Dr. Yves Bigot
  UMR INRA-CNRS 7247, Centre INRA Val de Loire, France
• Dr. Philippe Collas
  University Oslo Institute of Basic Medical Sciences, Department of Biochemistry, Oslo, Norway
• Dr. David Gabellini
  San Raffaele Scientific Institute Division of Regenerative Medicine, Milano, Italy
• Dr. Sébastien Guizard
  CNRS, UMR 7247, Centre INRA Val de Loire, France
• Dr. Jiri Macas
  Institute of Plant Molecular Biology, xxx, Czec Republic
• Dr. Klaus May
  Genomatix Software GmbH, Munich, Germany
• Dr. Florian Maumus
  Unité de Recherches en Génomique-Info, UR INRA 1164, INRA, Centre de recherche de Versailles, France
• Dr. Attila Nemeth
  University of Regensburg, Biochemistry Center Regensburg, Germany
• Dr. David Pollocq
  University Colorado Denver, Department of Biochemistry & Molecular Genetics, USA
• Dr. Hadi Quesneville
  Unité de Recherches en Génomique-Info, UR INRA 1164, INRA, Centre de recherche de Versailles, France
• Dr. Sébastien Tempel
  Université Aix-Marseilles, Laboratoire de Chimie Bactérienne, UMR 7283, Marseille, France
• Pr. Jean-Nicolas Volf
  Ecole Normale Supérieure de Lyon, Institut de Génomique Fonctionnelle de Lyon, Equipe Génomique des Poissons, Lyon, France

Programme:

Download in pdf

8 July 2015

14h00 - Official opening of the Conference 
LE STUDIUM representative
Yves Bigot (CNRS - INRA Nouzilly) & Peter Arensburger (California State University, Pomona, USA)
 

SESSION ONE 

14h20 - Introduction talks - Chairman: Yves Bigot

• Yves Bigot: Introduction to the complexity of eukaryotic genomes - Scientific challenges of the meeting 

SESSION TWO

14H30 - Analysis and annotation of the repeats in assembled eukaryotic genomes - methodological approaches - Chairman: David Pollocq
David Pollocq: Identification of repeat structures in large genomes using repeat probability clouds

15h30 - Coffee break

16h30 - Florian Maumus: REPET, Repeatscout and Repeatmodeler : principes and efficiencies.

16h30 - Hadi Quesneville: De novo annotation with REPET and P-clouds : beyond default parameters

17h15 - Conclusion of the session 2 by the Chairman

18.30 - LE STUDIUM® LECTURE

Dr Peter Arensburger: Éléments transposables, la partie cachée des génomes

9 July 2015

SESSION THREE
Analysis and annotation of the repeats in eukaryotic genome - Chairman: Jiri Macas

09H00 - Assembled genomes

• Sébastien Guizard: Diving in the deep annotation the genome of the red jungle fowl genome
• Jean Nicolas Volff: Did alive animal fossils contain DNA fossils in their genomes ?

10h30 - Coffee break

11h00 - Unassembled genomes

• Jiri Macas: Repeat Explorer : beyond default parameters
• Yves Bigot: Analyzing repeats in breeds of chickens with RE and complementary approaches

Conclusion of the session 3 by the Chairman

12h30 - Lunch

SESSION FOUR

14h00 - Repetitive elements involved in chromatin activity - Chairman: Davide Gebellini

• Davide Gabellini: A repetitive elements perspective in Polycomb epigenetics
• Bruno Pitard: New concepts to factory antibody library for OMICS
• Yves Bigot: Silencer and mariner transposable elements 

16h00 - Coffee break

16h30 - Repetitive elements involved in nuclear organisation - Chairman: Nicolas Mermod

• Jan Øivind Moskaug : Diversity, dynamics and annotations of Lamina Associated Domains in eukaryotic genomes
• Attila Nemeth: Diversity, dynamics and annotations of Nucleolus Associated Domains in eukaryotic genomes

Conclusion of the session 4 by the Chairman

19H30 - Conference Gala Dinner
    (by shuttle, meeting Place Jean Jaurès at 19h00)
    Bistrot de la Bulle à Charentilly

10 July 2015 

SESSION FIVE

09H00 - Can we annotate without to classify ? - Chairman : Hadi Quesneville

• Jiri Macas: How can we model a “repeat species” for annotation ?
• Sébastien Tempel: “repeat species” for annotation : using model-based identification tools

10h00 - Coffee break

10H30 - Can we annotate without to classify ? 

• Peter Arensburger: A survey of transposable element classification systems – a call for a fundamental update to meet the challenge of their diversity and complexity

Conclusion of the session 5 by the Chairman

11h30 - Conclusions

• Yves Bigot: Future lanes that could be continued from the Ins and outs of this meeting

12h00 - Boxed lunch

Topics:

• eukaryotic genomes
• genomic dark matter
• non-genic sequence features
• genetic repeats
• repeat classification