Section: Other Grants and Activities

National initiatives and cooperations

National initiatives

We participate in the following national projects:

• ANR BRASERO (2007-2009). The project aims at providing relevant and efficient tools for the RNA comparison problem. The project is coordinated by A. Denise (now in Amib INRIA team). Other leading partners are Sequoia , the bioinformatics group of LaBRI, Bordeaux (with P. Ferraro), and the Bamboo project of INRIA Rhône-Alpes (with M.-F. Sagot). The project also involves researchers from Institut de Génétique et Microbiologie (Orsay), Centre de Génétique Moléculaire (Gif-sur-Yvette) and Maturation des ARN et Enzymologie Moléculaire (Nancy).

• ANR CoCoGen (2008-2011). The goal of this project is to study new methods for comparison of complete genomes. The project is coordinated by E. Rivals (LIRMM, Montpellier). Others participants are MIG and UBLO teams of INRA (Jouy-en-Josas), INA-PG (Paris). The budget of this project is managed by the Montpellier partner. It covers travel fees to attend meetings.

• NCRNA, RNG-Renabi, national network for bioinformatics (2007-2009). The objective is to develop an open-source annotation platform for noncoding RNA genes (see RNAspace in Section 3.3 ). This project involves the bioinformatics platforms of Génopole Toulouse-Midi-Pyrénées and Sequoia , and is supervised by C. Gaspin (Toulouse-Midi-Pyrénées). New support is planned for 2010.

• working groups Sequence analysis and Structural bioinformatics of the multidisciplinary GDR Molecular bioinformatics (http://www.gdr-bim.u-psud.fr ).

• working group Combinatoire des mots, algorithmique du texte et du génome of the GDR Informatique Mathématique (http://www.gdr-im.fr/ ).

National cooperations

• Work on mapping SOLiD reads: Group of E. Barillot (Institut Curie, Paris)

• The following scientists were invited in the past year to give a talk at the team seminar: David Hot (Institut Pasteur de Lille), Guillaume Rizk (INRIA Rennes), Mikaël Salson (Université de Rouen), Peter Steffen (Universität Bielefeld), Martin Figeac (INSERM, Université Lille 2), Sylvain Sené (Université Grenoble 1), Christophe Pinchon (Institut Pasteur), Pavlos Antoniou (King's College London), Aïda Ouangraoua (Simon Fraser University), Samuel Blanquart (LIRMM), Géraldine Jean (LaBRI), Mathieu Raffinot (LIAFA)

• We collaborate for several years with the INRIA team Symbiose (Rennes), with D. Lavenier and P. Peterlongo, on indexation and seed-based heuristics.