Metabolism & Systems Biology

From annotation and analysis of microbial genomes, Genome-Scale Metabolic Networks (GSMN) can be obtained and contain all of the known metabolic reactions in a given organism and the genes that encode each enzyme. Part of our research activities are focused on the curation of GSMN and the development of databases and methods to improve their reconstruction.

Two main bottlenecks limit the understanding of metabolic consequences encoded in a genome: the difficulty in associating correct functions to genes and the lack of experimental characterization of enzyme activities for which proteins are sometimes unknown, i.e. orphan enzymes. In the light of enzymatic screening and metabolomics experiments, we develop bioinformatics methods and perform bioanalysis for the discovery of new enzyme families and the exploration of their functional diversity. Methods are mainly based on sequence analysis, genomic and metabolic context exploration and structural bioinformatics.

ALADIN project: Active Learning to Accelerate biocatalyst Development for INdustrial biotechnology

The ALADIN project aims to build an integrated and distributed technological platform which will rely on the combination of combinatory genetics with artificial intelligence. It will enable the exploration of natural molecular diversity, its appropriation to build new purpose-based catalysts (enzymes and micro-organisms), and the rapid expansion of the knowledge ...
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MODAMDH project: In silico approach for amine dehydrogenase discovery

The current trend in Chemistry is to perform the energy transition successfully by considering cheaper and greener alternatives. This can be achieved by the substitution of some chemical steps by biocatalyzed ones or the design of new enzymatic routes, thus reducing waste and polluting organometallic catalysts. As useful building blocks ...
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Discovery of the complete catabolic pathway for red algal carrageenans in marine bacteria

Discovery of the complete catabolic pathway for red algal carrageenans in marine bacteria An international consortium coordinated by the Marine Glycobiology team (UMR8227 – CNRS/UPMC) has just published the discovery of the complete system for the utilization of carrageenans, sulfated polysaccharides which are a major component of the cell walls ...
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NetSyn – Exploring Syntenies Networks of Genes

We developed a method to classify proteins of a family based on their conserved genomic contexts. Each protein genomic context is compared against all others to determine syntenies. A graph is generated where nodes are input proteins connected by edges when a synteny is observed. Edges weight represent the mean ...
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Mining secondary metabolites in cyanobacterial genomes

Cyanobacteria are an ancient lineage of photosynthetic bacteria, which are prolific producers of secondary metabolites. Hundreds of bioactive compounds with diverse chemical structures , such as toxins and molecules of pharmaceutical interest, have been characterized from cyanobacteria ...
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