Section: Partnerships and Cooperations

National Initiatives

ANR

Project HydroGen: Metagenomic applied to ocean life study

Participants : Dominique Lavenier, Pierre Peterlongo, Claire Lemaitre, Guillaume Rizk, Gaetan 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, Jeremy Gauthier, Fabrice Legeai, Claire Lemaitre, Pierre Peterlongo.

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)

Duration:7.5 year (2012-2019)

Partners: 5 companies, 9 academic research labs.

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. (http://www.rapsodyn.fr)

Institut Français de Bioinformatique: Plant node

Participant : Fabrice Legeai.

Coordinator: Hadi Quesneville (INRA, Versailles)

The aim of the Institut Francais de Bioinformatique (IFB) offers resources for a large community of French biologist. With INRA and CIRAD, we were part of the plant node of IFB, and focused on delivering efficient tools for sharing agronomical data, such as Askomics.

Programs from research institutions

Inria ADT DiagCancer

Participants : Dominique Lavenier, Patrick Durand.

Since October 1st, 2016, Genscale 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.

CNRS Mastodons program: C3G

Participants : Dominique Lavenier, Pierre Peterlongo, Claire Lemaitre, Camille Marchet, Lolita Lecompte.

High-throughput sequencing applications now cover all life sciences: from medicine to agronomy. The 3rd generation sequencing produces very long reads, but the reads are extremely noisy, which has a strong impact on the quality of bioinformatics analyses. The challenge of the C3G project is to bring this type of data to a high level of quality through the development of new correction strategies.

Inria Project Lab: Neuromarkers

Participants : Dominique Lavenier, Pierre Peterlongo, Claire Lemaitre.

The IPL Neuromarkers aims to design imaging biomarkers of neurodegenerative diseases for clinical trials and study of their genetic associations. In this project, GenScale bring its expertise in the genomic field.