Participant 3 | CNRS

The French National sequencing center Genoscope is a part of the François Jacob Institute located at the CEA/Paris-Saclay site of Evry, at ~30km south of Paris. Historically, Genoscope represent the pillar of the French scientific contribution to the human genome project, notably due to their release of the DNA sequence and analysis of human chromosome 14. Currently Genoscope participates at major sequencing projects focused on environmental genomics, but also to the exploitation of sequence data, extended by the experimental identification of biological functions. Specifically, Genoscope host the mixed research unit (UMR) 8030 “Metabolomics Genomics”, composed by research teams issued from the “Centre National de la recherche Scientifique” (CNRS), the local University of Evry, as well as the Atomic Energy center (CEA).

Dr. Marco Antonio Mendoza-Parra is at the head of the team SysFate (Systems Biology of Cell Fate decisions) within the UMR-8030 at Genoscope. His current research activities are focused to the study of cell fate decisions from a systems biology perspective, i.e. by aiming to understand their transitions from the reorganization of complex regulatory wires defining their biological state. To address this question, his team uses cell differentiation assays characterized by the use of modern functional genomics readouts, but in addition compiles the important number of sequence datasets retrieved in the public domain into reconstructed gene regulatory networks per cell/tissue systems studied by the scientific community. For this, his team developed over years several computational solutions providing means to (i) evaluate the quality of public sequence datasets; (ii) detect and compare enriched patterns within profiled protein-DNA interaction maps; (iii) integrate (temporal) transcriptome readouts with protein-DNA interaction readouts to reconstruct gene regulatory wires.

At term the aim is to provide a comprehensive view of the gene regulatory wires defining each of the cell/tissue types in an organism, thus representing a landmark catalog for the future therapeutic developments in regenerative medicine.

Within T-FITNESS, the team SysFate (CNRS) will provide the bioinformatics expertise for revealing major deregulated transcription factors during T cell exhaustion from both publicly available datasets and those generated by other members of the consortium.

Marco Antonio Mendoza
Head of SysFate (Systems Biology of Cell Fate decisions) at Genoscope
Ariel Galindo
Bioinformatics and molecular biology Researcher
Maximilien Duvina
Bioinformatics engineer