Projects

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

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

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.

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.

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 : 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.

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. Alban Gaignard and Marie-Dominique Desvignes represent ELIXIR-FR in this group. Alban works on Bioschemas  project which aims to improve the Findability on the Web of life sciences resouces such as datasets, software, and training materials.

One of the major current problems in biology is to homogenise data formats and structures so that they can be analysed together, rather than in silos.
The objective of the MoDaL project is to bridge the gap between actors and resources in genomics, in-vivo and in-vitro imaging in order to consider the algorithmic (semantic and statistical) exploitation of heterogeneous data.

Sofia is involved in facilitating this issue on the scale of the Grand Ouest network, i.e. enabling the various actors in the field to be in contact with each other and to communicate on current projects.