Section: Partnerships and Cooperations

National Initiatives

ANR

BIOWIC

Participants : Rumen Andonov, Dominique Lavenier, François Moreews.

The BioWIC project aims to speed up both the design and the execution of bioinformatics workflows. It is funded by ANR call ARPEGE and coordinated by D. Lavenier from Jan. 2009 to June 2012. http://biowic.inria.fr/

MAPPI

Participants : Rayan Chikhi, Dominique Lavenier, Claire Lemaitre, Nicolas Maillet, Pierre Peterlongo.

The MAPPI project aims to develop new algorithms and Bioinformatics methods for processing high trougthput genomic data. It is funded by ANR call COSINUS and coordinated by M. Raffinot (LIAFA, Paris VII) from Oct 2010 to Dec. 2013.

FATINTEGER

Participants : Dominique Lavenier, François Moreews.

The FatInteger project aims to identify some of the transcriptional key players of animal lipid metabolism plasticity, combining high throughput data with statistical approaches, bioinformatics and phylogenetic. It is funded by ANR call BLANC and coordinated by F. Gondret from 2012 to 2015.

SPECIAPHID

Participants : Thomas Derrien, Anaïs Gouin, Fabrice Legeai, Claire Lemaitre.

The SPECIAPHID project aims to understand the adaptation and speciation of pea aphids by re-sequencing and comparing the genomes of numerous aphid individuals. Genscale's task, as associate partner, is to apply and develop new methods to detect variation between re-sequenced genomes, and in particular complex variants such as structural ones. It is funded by ANR call BLANC and coordinated by J-C Simon (Inra, Rennes) from January 2012 to Dec. 2014.

ADA-SPODO

Participants : Rumen Andonov, Dominique Lavenier, Fabrice Legeai, Claire Lemaitre, François Moreews, Pierre Peterlongo.

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 post-genomic and regulatory data. It is funded by ANR call BLANC and coordinated by E. d'Alençon (Inra, Montpellier) from October 2012 to Dec. 2015.

RAPSODYN

Participants : Dominique Lavenier, Claire Lemaitre, Pierre Peterlongo, Erwann Scaon.

RAPSODYN is a long term project funded by the IA French program (Investissement d’Avenir) for 7.5 years (07/2012-12/2019). The objective is the optimisation of the rapeseed oil content and yield under low nitrogen input. GenScale is involved in the bioinformatics workpackage to elaborate advanced tools dedicated to polymorphism.

LEPIDOLF

Participants : Dominique Lavenier, Fabrice Legeai.

The LEPIDOLF project aims at better understanding olfactory mechanisms in insects. The goal is to establish the antennal transcriptome of the cotton leafworm Spodoptera littoralis, a noctuid representative of crop pest insects. It is funded by ANR call Blanc and coordinated by E. Jacquin-Joly from UMR PISC (INRA) from 2009 to 2012. As part of this project, a post-doctoral student, Aurore Gallot, visited Genscale for 5 months.

Programs from research institutions

Mapsembler

Participants : Alexan Andrieux, Dominique Lavenier, Claire Lemaitre, Pierre Peterlongo.

The Mapsembler project aims at finalizing and to distributing the Mapsembler tool. It is funded by Inria ADT call (2012) and coordinated by P. Peterlongo from oct. 2012 to sept. 2014. http://alcovna.genouest.org/mapsembler/

Mastodons

Participants : Dominique Lavenier, Claire Lemaitre, Pierre Peterlongo.

This project, funded by the CNRS Big Data program in 2012, aims do investigate the challenge brought by the processing of high throughput sequencing genomic data. It is coordinated by D. Lavenier from june 2012 to december 2012.

BioManyCores

Participants : Guillaume Chapuis, Charles Deltel, Dominique Lavenier.

The BioManyCores project aims to develop a library of bioinformatics softwares implemented on manycore structures such as GPU. It is funded by Inria ADT call and supervised by J.S. Varré in Sequoia Team in Lille. http://www.biomanycores.org/

ParaQtlMap

Participants : Guillaume Chapuis, Charles Deltel, Dominique Lavenier.

The ParaQtlMap project is a join initiative from Genscale team and Genetique Animale. to design high performance software for detecting quantitative trait locus. It is funded by Inria/INRA call and coordinated by D. Lavenier (Genscale) and P. Leroy (GA INRA) from oct. 2010 to sept. 2012. https://qgp.jouy.inra.fr/index.php?option=com_content&task=view&id=17&Itemid=28

Barcoding de nouvelle génération

Participants : Dominique Lavenier, Claire Lemaitre, Pierre Peterlongo.

This project is a join initiative between Genscale and LECA (Laboratoire d'Ecologie Alpine in Grenoble). It aims at developping new algorithmic approaches for the species identification from low coverage NGS data. It is funded by a PEPS program at CNRS/Inria and coordinated by C. Lemaitre from sept. 2012 to december. 2013.

Poly-BNF

Participants : Dominique Lavenier, Claire Lemaitre, Pierre Peterlongo, Erwann Scaon.

This projects aims to develop bioinformatics strategies for studying polyploid genomes. It is a one year project (09/2012 – 09/2013) funded by the University of Rennes 1. It is a joined project with CNRS/EcoBio lab and INRA/IGEPP lab.

Cooperations

Inria Bamboo Team

Participants : Claire Lemaitre, Pierre Peterlongo.

We maintain a long term collaboration with Inria Bamboo Team on the problems of finding biological information, such as variants, in NGS raw data.

LIGM, Paris

Participant : Pierre Peterlongo.

P. Peterlongo collaborates with the LIGM lab in Paris (UMR 8049), on problems of large NGS raw data indexation.

LIX

Participant : Antonio Mucherino.

A. Mucherino collaborates since 5 years with LIX, Ecole Polytechnique, in Palaiseau on the distance geometry problem. We reformulated the problem as a combinatorial optimization problem and we conceived an ad-hoc algorithm for the solution of this class of problems.