Seminars & Events

Argonne National Laboratory
"Extending FBA to Metagenome Analyses"

DATE: November 28, 2007
TIME: 11:30 am
SPEAKER: Benjamin Candelon, Institut National de la Recherche Agronomique
LOCATION: Building 221 Conference Room A216, Argonne National Laboratory
HOST: Jen Zinner

Description:
Bacterial virulence and more generally organism interactions are complex. During my early career as a microbiologist, I got insights of these phenomena at the molecular level. In
2006, I widened my field of investigation to BioInformatics to address these questions with a more global approach.

During my post doctoral period at the INRA, I have been involved in the integration of metabolic data in the iMoMi database which holds all the NCBI available bacterial genomes. I devised a dedicated tool for this integration with strong specifications to guarantee data consistency. The developed tool is available as a Win32 binary file and allows integration of metabolic data for a bacterial genome within few minutes.

Disposing of metabolic data in the iMoMi database allowed me to contribute to other investigations. Notably, I set up a workflow to assess the potential co-expression of genes that
are related in the metabolism. I also devised and implemented a methodology to design pangenomic oligoarrays dedicated to the typing of starter strains that are used in yogurt and cheese fabrication.

Nowadays, I would be interested in building tools simulating and predicting cell communities behaviors. As a first step, proposing a method to combine of metagenomic data with
the Flux Balance Analysis (FBA) method (Varma A et al., 1994) could be of great help. A so-called metagenomic FBA tool would give opportunity to better understand bacterial communities behaviors and bacteria host interactions. Applications of the potential results could range from
health to cell factory designs.

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