Post-doc position: metabolic networks and enzyme families

The LABGeM team (CEA/Genoscope, CNRS UMR 8030, France, Dir. Claudine Médigue) is developing integrated approaches which combines bioinformatics methods and databases for the discovery of new enzymatic activities in the light of metabolic pathway evolution:

–       The CanOE method, developed in collaboration with INRIA, combines genomic and metabolic contexts for the discovery of candidate genes for orphan enzymes (Smith et al., 2012).

–       A new representation of metabolism extends the notion of metabolic context to detect conserved reaction modules using networks of chemical transformations (Sorokina et al., 2015, see ISMB/ECCB NetBio presentation).

–       From a structural point of view, the ASMC method finds and compares catalytic pockets for the classification of enzymes within a family and detect key amino acids responsible for the substrate specificity (de Melo-Minardi and Bastard et al., 2010).

These methods were successfully applied in the study of protein families of unknown function to reveal their diversity of enzymatic functions (Bastard et al., 2014). An exhaustive analysis of orphan enzymes was also recently conducted (Sorokina et al., 2014). This work is supported by genomic and metabolic network data from MicroScope, an integrated platform dedicated to microbial genome analyses (Vallenet et al., 2013).

Within this framework, we are hiring a post-doctoral fellow for the development of innovative bioinformatics methods to explore metabolic networks and enzyme families. These methods will be based on protein family analysis and graph approaches combining genomic and metabolic contexts. Applications will be conducted through the discovery of novel enzymes for the valorization of algal biomass (Blue Enzymes project).

–       PhD degree in bioinformatics or computational biology
–       Previous experience in network or protein family analysis
–       Programming skills (C/C++, Python, Java) and in common biostatistical analyses
–       Team player, innovative and creative thinking, good oral and written communication skills

24 months, Post Doctoral position
Start: from December 2015
Place: CEA, Genoscope UMR8030, LABGeM (Laboratory of Bioinformatics Analyses for Genomics and Metabolism), Evry, France
Contact: David Vallenet,
Remuneration per month: from 2,850 €

Interested candidates should send their CV, statement of research interests, and contact information of at least 2 references to David Vallenet (


Post-doc position: metabolic networks and enzyme families