Projects & Collaborations

 

Current projects

This list sums up our current funded projects. See our activity reports for more details.

  • ANR Divalps – 2021-2025

studying local adaptation and speciation of an alpin butterfly. We develop methods to represent and compare genomes from close lineages and hybridation events. (PI: Laurence Desprès from the LECA in Grenoble).

ALPACA (ALgorithms for PAngenome Computational Analysis) is an EU funded Innovative Training Network for talented PhD Students. In view of ultra-large amounts of genome sequence data emerging from rapidly advancing genome sequencing devices the driving, urgent question is: How can we arrange and analyze these data masses in a formally rigorous, computationally efficient and biomedically rewarding manner?

  • ANR Supergene – 2020-2024

studying inversion polymorphsim in a mimetic butterfly (H. numata). We develop methods to discover and genotype inversions with linked-read sequencing data. (PI: Mathieu Joron from the CEFE in Montpellier).

We propose a new scaling breakthrough, allowing users to directly query large unassembled raw sequencing data on the fly in order to tap into the largest underexploited resource in life sciences.

 

Some past projects

  • ANR SpecRep – 2015-2019

studying speciation of amazonian mimetic butterflies. We participated in reference genome assembly with various sequencing data and population RAD-seq analyses with discoSnpRAD (PI: Marianne Elias from the MNHN).

Aims to design new methods for efficient detection of biological information from non assembled HTS data.

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.

  • Mastondons C3G – 2017
  • France-Génomique ALPAGA – 2016
  • ANR Ada-spodo – 2012-2015

studying adaptation of two strains of a major agricultural pest (Spodopera frugiperda). We participated in reference genome assembly and whole genome comparisons (PI: Emmanuelle d’Alençon from INRA Montpellier).

Collaborations

International

  • Los Alamos National Lab, USA
  • CWI, Amsterdam, Netherlands
  • Sofia University, Bulgaria
  • University Federal of Minas Gerais, Brazil

Industry

  • uPmem: Implementation of genomic algorithms on “Processor-in-Memory” architecture
  • Kalray: Implementation of bioinformatics software on the MPPA many-core processor
  • KorilLog: Transfer of the PLAST software

Permanent link to this article: https://team.inria.fr/genscale/projects-contracts/