SYSMICS

SysMics is an integrated genomics research cluster labelled by the I-SITE NExT, which is based on the GenoBiRD infrastructure. SysMics aims to federate the NExT community with a shared objective: to anticipate the emergence of systemic medicine by co-developing 3 large-scale genomic screening approaches: genome sequencing of patient populations, genomic profiling on single cells and metagenomics applied to microbiota(s). The first mission of SysMics is to build on site all the resources necessary to implement or consolidate these 3 approaches. The second step will be to combine these approaches in the context of pilot projects in immunology, oncology and pathophysiology of cardiovascular, metabolic, respiratory and neuro-digestive diseases

Collaborations

BiRD is collaborating on several research projects with the associated teams of l'institut du thorax and LS2N, and also with IFB projects.

RegioCard

Adrien Foucal is is in charge of epigenetic data analysis for the Regiocard project led by Julien Barc (genetic team of l’institut du thorax). This team develops strategies based on whole genome for cardiac arrhythmia disorders and sudden death. Furthermore they particularly interested in investigating the role of variants in the non-coding region of the genome, seat of the gene regulation. They developed research programs on cardiac epigenetics to functionally annotate the gene regulatory regions of the genome.

INEX-MED

Alban Gaignard leads INEX-MED project : INtegration and EXploration of heterogeneous bio-MEDical data. The objective of this pilot project supported by the IFB is to develop a sustainable infrastructure for integration, exploitation and modelling (semantic/statistical) on heterogeneous data sources and multi-site computing infrastructures in the biomedical area.

Mibiogate

Philippe Bordron and Erwan Delage are involved in the Mibiogate project.
Philippe works more specifically in the analysis and interpretation of transcriptomic data from host organs in the context of stress studies on barriers.
Erwan works on the implementation of tools for the analysis and integration of metagenomic, biological and clinical data for the study of chronic pathologies and more particularly on the development of a complete metagenomic analysis pipeline (from raw sequences to the construction of gene catalogues, the reconstruction of genomes and the generation of tables of abundance at the taxonomic and functional level).

Mibiogate is a project to study biological barriers and their microbiota in the development of chronic diseases, supported by the Pays de la Loire Region. The consortium created aims to structure a research network specialized in the study of the dysfunctions of the biological barriers of the different organs in chronic pathologies of interest.

CEPH Recherche

CEPH Recherche : Pilot project for the secure storage of massive research data using CEPH technology on a principle of sharing equipment and staff of partner members : CCIPL, BiRD, LS2N, CEISAM, DSIN.

IFB Biosphere

IFB Biosphère : French Institute of Bioinformatics (IFB) provides life scientists with a federation of clouds, Biosphere, and bioinformatics cloud services to analyze life science data. Biosphere is used for scientific production in the life sciences, developments, and to support events like cloud and scientific training sessions, hackathons or workshops.

ELIXIR Interoperabillity Platform

The goal of the Interoperability Platform is to help people and machines to discover, access, integrate and analyse biological data. It encourages the life science community to adopt standardised file formats, metadata, vocabularies and identifiers and works internationally to achieve its goals.

ANR ImPeKAB

Camille Trottier took part with Damien Eveillard in the ANR ImPeKAB project, led by Fabrice NOT, at the Roscoff Biological Station. The project consists in studying the effects of abiotic forcings on plankton, focusing more specifically on photosymbiotic species and the bleaching phenomenon. The bioinformatics analyses carried out in Nantes aim to apply eco-systemic approaches to evaluate the response of photosymbiotic eukaryotes to different abiotic stresses.

ANR SAMOSA et CINNAMON

Julie Haguait took part with Damien Eveillard in the ANR SAMOSA and CINNAMON project, led by Laurence Garczarek, from the Roscoff biological station. The two projects aim to study the adaptation and acclimatization phenomena of cyanobacteria. The bioinformatics analyses carried out in Nantes focus on genomic and transcriptomic data of autotrophic bacteria, in order to understand biological behaviours both at the scale of genes and at the scale of populations in the global ocean.

ProBioSTIC

Erwan Delage was involved in the AtlanSTIC 2020 ProBioSTIC project, led by Damien Eveillard (Combi team, LS2N). The project consists of studying the metabolic behaviour of microbial communities. Once this behaviour has been modelled by constraints, ProBioSTIC aims to search for probiotic strains to incorporate into the ecosystem in order to modify its overall behaviour. This approach aims to propose new probiotic strategies via IT decision support.