Section: Partnerships and Cooperations

National Initiatives


Project ADA-SPODO: Genetic variation of Spodoptera Frugiperda

Participants : Claire Lemaitre, Fabrice Legeai, Anaïs Gouin, Dominique Lavenier, Pierre Peterlongo.

Coordinator: E. D’Alençon (Inra, Montpellier)

Duration: 45 months (Oct. 2012 – May 2016)

Partners: DGIMI Inra Montpellier, CBGP Inra Montpellier, URGI Inra Versailles, Genscale Inria/IRISA Rennes.

The ADA-SPODO project aims at identifying all sources of genetic variation between two strains of an insect pest: Lepidoptera Spodoptera Frugiperda in order to correlate them with host-plant adaptation and speciation. GenScale’s task is to develop new efficient methods to compare complete genomes along with their postgenomic and regulatory data.

Project COLIB'READ: Advanced algorithms for NGS data

Participants : Pierre Peterlongo, Antoine Limasset, Camille Marchet, Claire Lemaitre, Dominique Lavenier, Fabrice Legeai, Guillaume Rizk, Chloé Riou.

Coordinator: P. Peterlongo (Inria, GenScale, Rennes)

Duration: 45 months (Mar. 2013 – Dec. 2016)

Partners: LIRMM Montpellier, Erable Inria Lyon, Genscale Inria/IRISA Rennes.

The main goal of the Colib’Read project is to design new algorithms dedicated to the extraction of biological knowledge from raw data produced by High Throughput Sequencers (HTS). The project proposes an original way of extracting information from such data. The goal is to avoid the assembly step that often leads to a significant loss of information, or generates chimerical results due to complex heuristics. Instead, the strategy proposes a set of innovative approaches that bypass the assembly phase, and that do not require the availability of a reference genome. https://colibread.inria.fr/

Project HydroGen: Metagenomic applied to ocean life study

Participants : Dominique Lavenier, Pierre Peterlongo, Claire Lemaitre, Guillaume Rizk, Gaëtan Benoit.

Coordinator: P. Peterlongo (Inria/Irisa, GenScale, Rennes)

Duration: 42 months (Nov. 2014 – Apr. 2018)

Partners: CEA (GenosScope, Evry), INRA (AgroParisTech, Paris – MIG, Jouy-en-Jossas).

The HydroGen project aims to design new statistical and computational tools to measure and analyze biodiversity through comparative metagenomic approaches. The support application is the study of ocean biodiversity based on the analysis of seawater samples available from the Tara Oceans expedition.

Project SpeCrep: speciation processes in butterflies

Participants : Dominique Lavenier, Pierre Peterlongo, Claire Lemaitre, Fabrice Legeai.

Coordinator: M. Elias (Museum National d'Histoire Naturelle, Institut de Systematique et d'Evolution de la Biodiversite, Paris)

Duration: 48 months (Jan. 2015 – Dec. 2018)

Partners: MNHN (Paris), INRA (Versailles-Grignon), Genscale Inria/IRISA Rennes.

The SpeCrep project aims at better understanding the speciation processes, in particular by comparing natural replicates from several butterfly species in a suture zone system. GenScale’s task is to develop new efficient methods for the assembly of reference genomes and the evaluation of the genetic diversity in several butterfly populations.

PIA: Programme Investissement d’Avenir

RAPSODYN: Optimization of the rapeseed oil content under low nitrogen

Participants : Dominique Lavenier, Claire Lemaitre, Sebastien Letort, Pierre Peterlongo.

Coordinator: N. Nesi (Inra, IGEPP, Rennes)

The objective of the Rapsodyn project is the optimization of the rapeseed oil content and yield under low nitrogen input. GenScale is involved in the bioinformatics work package to elaborate advanced tools dedicated to polymorphism and application to the rapeseed plant.

France Génomique: Bio-informatics and Genomic Analysis

Participants : Laurent Bouri, Dominique Lavenier.

Coordinator: J. Weissenbach (Genoscope, Evry)

France Génomique gathers resources from the main French platforms in genomic and bio-informatics. It offers to the scientific community an access to these resources, a high level of expertise and the possibilities to participate in ambitious national and international projects. The GenScale team is involved in the work package “assembly” to provide expertise and to design new assembly tools for the 3rd generation sequencing.

Programs from research institutions

Inria ADT DiagCancer

Participants : Dominique Lavenier, Patrick Durand.

Since October 1st, 2016, Genscale has started a one-year Inria ADT called DiagCancer. It aims at: (1) including the DiscoSnp++ tool within the current data production pipeline at Pontchaillou Hospital (Rennes), (2) providing a new prediction tool applied to the calling of cancer related mutations from DNA sequencing data and (3) creating new analysis tools to facilitate the interpretation of results by end-users (biologists, doctors). The project is done in close collaboration with Haematology Service, CHU Pontchaillou, Rennes.