Section: Partnerships and Cooperations

National Initiatives

ANR

MAPPI

Participants : 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 : 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.

COLIB'READ

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

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. Usually, a generic assembly (pre-treatment) is applied to the data, and then, in a second step, any information of interest is extracted. Our aim is to avoid this protocol that leads to a significant loss of information, or generates chimerical results because of the heuristics used in the assembly. Instead, the project will propose a set of innovative approaches for extracting information of biological interest from HTS data, with methods that bypass any costly and often inaccurate assembly phase, not requiring the availability of a reference genome. It is funded by ANR call BLANC and coordinated by P. Peterlongo from March 2013 to February 2016. https://colibread.inria.fr/

GATB

Participants : Dominique Lavenier, Erwan Drezen, Pierre Peterlongo, Claire Lemaitre, Guillaume Rizk.

GATB (Genome Assembly Tool Box) is a project that aims to provide algorithms and tools for genome assembly. The strength of these algorithms comes from the underlying structure that has a low memory footprint, which enables to assemble genomes on a simple desktop computer. The GATB project will provide several software components, such as low level libraries, binaries and pipelines providing a full spectrum of tools for genome assembly. It is a 2 years ANR project started in February 2013. http://gatb.inria.fr

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 and 2013, 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 2013.

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 Dec. 2013.

Structuring of NGS for diagnostic purpose in cancer

Participants : Dominique Lavenier, Claire Lemaitre, Pierre Peterlongo.

This 18 months project is funded by the national institute of cancer (INCa). Genscale is involved in the optimization of bioinformatics workflows to detect variants in glioblastoma cancer.

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.