Projects & Collaborations

 

Current projects

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

  • ANR GenoPIM – 2022-2024

the GenoPIM project aims to make fast (>20-50x faster than currently available), energy-efficient (consuming >70% less energy than current platforms), and cost-efficient (>10-20x cheaper than standard servers) genome analysis using Processin-in-Memory technology.

  • 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?

The dnarXiv project aims to explore data storage on DNA molecules. The goal is to develop a large-scale multi-user DNA-based data storage system that is reliable, secure, efficient, affordable and with random access.

  • 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

  • CWI, Amsterdam, Netherlands
  • Sofia University, Bulgaria
  • Bielefeld University, Germany

Industry

  • uPmem: Implementation of genomic algorithms on “Processor-in-Memory” architecture

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