Post Doc

h-index: 5

Grégory Farrant

Development of RoskoBaz, a database of genetic markers for studying time and spacial variations of microbial communities in the Channel

SCIENTIFIC INTEREST

Ecology and diversity of microorganisms in marine and sub-glacial environments. Bio-analysis of genomic and metagenomic data through computational biology. Genome and marker assembly, recruitment of diversity and functional markers. Work on marine picocyanobacteria in the TARA Oceans dataset. Work on the biodiversity in the subglacial volcanic lake Skaftárkatlar, Iceland.

 

background

I studied laboratory practice and technologies before a Civil Engineer degree in Agronomy, with specialisation in Microbiology. During which I started working in computational biology as part of internships at the Ecole Normale Supérieure and later more specifically on cyanobacteria at the Pasteur Institute in Paris. I later started my Ph.D. at the Station Biologique in Roscoff, to study marine picocyanobacteria (projects METASYN, SAMOSA, TARA Oceans). After my defense, I decided to apply my computational biology knowledge to a different field of biology by moving to Iceland at the Matís ohf. research company. There I got fund from the Marie Skłodowska-Curie Actions, for the project AstroLakes. This project aimed at studying biodiversity in the pristine subglacial volcanic lake Skaftárkatlar and various other hotspring, soil, microbiome or marine samples. There I also took an active role in the development of a cluster grid for computational biology and biological data repository. I also took part in the design of the website for the ISCaR collection of strains, cultures and samples. And recently, I moved back to the Station Biologique to embrace a more engineering path, by developing the RoskoBaz database of genetic markers for marine microbial species.

 

Publications

Farrant G.K., Vannier P., Klonowski A., Gaidos E., Þorsteinsson Þ. and Marteinsson V. Þ. Metagenomic analyses of microbial communities from the subglacial volcanic Lake East Skaftárkatlar, Vatnajökull, Iceland. (under review)

Grébert T., Doré H., Partensky F., Farrant G.K., Boss E.S., Picheral M., Guidi L., Pesant S., Scanlan D.J., Wincker P., Acinas S.G., Kehoe D.M. and Garczarek L. Light color acclimation: a key process in the global ocean distribution of Synechococcus cyanobacteria. PNAS 2018, https://doi.org/10.1073/pnas.1717069115.

Farrant G.K., Doré H., Cornejo-Castillo F.M., Partensky F., Ratin M., Ostrowski M., Pitt F.D., Wincker P., Scanlan D.J., Iudicone D., Acinas S.G. and Garczarek L. Delineating ecologically significant taxonomic units from global patterns of marine picocyanobacterial. PNAS 2016, cgi/doi/10.1073/pnas.1524865113.

Farrant G.K., Hoebeke M., Partensky F., Andres G., Corre E. and Garczarek L. WiseScaffolder: an algorithm for the semi-automatic scaffolding of Next Generation Sequencing data. BMC Bioinformatics 2015, 10.1186/s12859-015-0705-y.

E. Villar, G. K. Farrant, M. Follows, L. Garczarek, S. Speich, S. Audic, L. Bittner, B. Blanke, J. R. Brum, C. Brunet, R. Casotti, A. Chase, J. R. Dolan, F. d'Ortenzio, J.P. Gattuso, N. Grima, L. Guidi, C. N. Hill, O. Jahn, J. L. Jamet, H. Le Goff, C. Lepoivre, S. Malviya, E. Pelletier, J. B. Romagnan, S. Roux, S. Santini, E. Scalco, S.M. Schwenck, A. Tanaka, P. Testor, T. Vannier, F. Vincent, A. Zingone, C. Dimier, S. Kandels-Lewis, M. Picheral, S. Searson, Tara Oceans coordinators, S. G. Acinas, P. Bork, E. Boss, C. de Vargas, G. Gorsky, H. Ogata, S. Pesant, M. B. Sullivan, S. Sunagawa, P. Wincker, E. Karsenti, C. Bowler, F. Not, P. Hingamp and D. Iudicone. Dispersal and remodeling of plankton communities by Agulhas rings. Science 2015, 348(6237):1261447.