Simon Roux

Postdoctoral Researcher

The Ohio State University, Department of Microbiology

Riffe Building
496 W 12th Ave
Columbus, OH 43210
Lab: Rm932

Lab Telephone: (614) 247-1617
Email: roux.8@osu.edu

· Curriculum Vitae (pdf)
· Google Scholar Page

Simon joined the Sullivan Lab in November 2013 from the Université Blaise Pascal (Clermont-Ferrand, France), where his PhD work focused on the bioinformatics anlaysis of viral metagenomes, from the development of tools dedicated to these datasets, to the analysis and meta-analysis of viromes toward a better understanding of the ecology and evolution of viruses. At the Sullivan lab, his main projects again involve both the development of new tools to process viral genomes and metagenomes, and the analysis of viral signal in large-scale genomics and metagenomics datasets. Overall, these different projects all work toward a better understanding of the “viral dark matter”: the incredibly vast and still largely unexplored set of environmental viruses infecting microbes, with special interest in deciphering the extent of viral diversity in nature, the mechanisms shaping the long-term evolutionary history of viral genomes, and the ecological drivers of these communities in aquatic biomes.

Education

• 2010-2013: Ph.D. (Bioinformatics, Metagenomics, Ecology) Université Blaise Pascal, Clermont-Ferrand, France
• 2008-2010: M.S. (Genetic and Physiology) Université Blaise Pascal, Clermont-Ferrand, France
• 2005-2008: B.S. (Biology) Université Blaise Pascal, Clermont-Ferrand, France

Publications

An updated publication list is also available via Google Scholar.

• Brum JR*, Ignacio-Espinoza J-C*, Kim EH*, Trubl G, Jones RM, Roux S, VerBerkmoes NC, Rich VI, Sullivan MB.(2016) Illuminating structural proteins in viral metagenomic ‘dark matter’. PNAS 113(9): 2436-2441. [*co-first authors, listed alphabetically]
• Guidi L*, Chaffron S*, Bittner L*, Eveillard D*, Larhlimi L, Roux S,…, Sullivan MB, Raes J, Karsenti E, Bowler C, Gorsky G. (2016) Plankton networks driving carbon export in the oligotrophic ocean. Nature. In press  [*co-first authors]
• Roux S, Enault F, Ravet V, Colombet J, Bettarel Y, Auguet JC, Bouvier T, Soizick L, Vellet A, Prangishvili D, Forterre P, Debroas D, Sime-Ngando T. (2016) Analysis of metagenomic data reveals common features of halophilic viral communities across continents. Environmental Microbiology 18 (3):889-903.
• Roux S, Hallam SJ, Woyke T, Sullivan MB. (2015) Viral dark matter and virus–host interactions resolved from publicly available microbial genomes. eLife 4, e08490.
• Brum J*, Ignacio-Espinoza J-C*, Roux S*…, and Sullivan MB. (2015) Patterns and ecological drivers of ocean viral communities. Science. [*co-first authors, listed alphabetically]
• Lima-Mendez G*, Faust K*, Henry N*, … Roux S, … Sullivan MB, Bowler C, Karsenti E, de Vargas C, and Raes J. (2015) Top-down determinants of community structure in the global plankton interactome. Science. [*co-first authors, listed alphabetically]
• Villar E, Audic S, … Roux S, …, Sullivan MB, Sunagawa S, Wincker P, Zingone A, Karsenti E, Not F, Hingamp P and Iudicone D. (2015) Environmental characteristics of Agulhas rings affect inter-ocean plankton transport. Science.
• Roux S, Enault F, Hurwitz BL, and Sullivan MB. VirSorter: mining viral signal from microbial genomic data. PeerJ (in press)
• Quaiser A, Dufresne A, Ballaud F, Roux S, Zivanovic Y, Colombet J, Sime-Ngando T, and Francez A-J. (2015) Diversity and comparative genomics of Microviridae in Sphagnum-dominated peatlands. Frontiers in Microbiology. 6: 37.
• Wood-Charlson EM, Weynberg KD, Suttle CA, Roux S, and Van Oppen MJH. (2015) Metagenomic characterization of viral communities in corals: mining biological signal from methodological noise. Environmental Microbiology.
• Roux S, Enault F, Ravet V, Pereira O, and Sullivan MB. (2015) Genomic characteristics and environmental distributions of the uncultivated Far-T4 phages. Frontiers in Microbiology. 6.
• Pascault N, Roux S, Artigas J, Pesce S, Leloup J, Tadonleke RD, Debroas D, Bouchez A, and Humbert J-F. (2015) A high-throughput sequencing ecotoxicology study of freshwater bacterial communities and their responses to tebuconazole. FEMS Microbiology Ecology. 90 (3).
• Roux S, Hawley AK, Torres Beltran M, Scofield M, … Woyke T, Hallam S, Sullivan MB. (2014) Cultivation-independent exploration of SUP05 virus-host interactions in a model Oxygen Minimum Zone. eLife. 3: e03125.
• Hopkins M, Kailasan S, Cohen A, Roux S, Tucker KP, Shevenell A, … Breitbart M. (2014) Diversity of environmental single-stranded DNA phages revealed by PCR amplification of the partial major capsid protein. ISME Journal. 8: 2093–2103.
• Roux S., Tournayre J., Mahul A., Debroas D. and Enault F. (2013) Metavir 2: Comparison of viral metagenomes and analysis of assembled datasets. Submitted to BMC Bioinformatics.
• Roux S., Krupovic M., Debroas D., Forterre P. and Enault F. (2013) Uncontaminated viromes reveal the abundance and diversity of metabolism genes in environmental viruses. Open Biology.
• Roux S., Enault F., Bronner G., Vaulot D., Forterre P. and Krupovic M. (2013) Chimeric viruses blur the border between the major groups of eukaryotic single-stranded DNA viruses. Nature Communications.
• Roux S., Enault F., Debroas D. (2013) Application des approches métagénomiques à l’étude de la diversité virale environnementale. Virologie. (Article in french)
• Roux S., Krupovic M, Poulet A, Debroas D, Enault F (2012) Evolution and Diversity of the Microviridae Viral Family through a Collection of 81 New Complete Genomes Assembled from Virome Reads. PLoS ONE. 7(7): e40418. doi:10.1371/journal.pone.0040418
• Roux S., Enault F, Robin A, Ravet V, Personnic S, Theil S, Colombet J, Sime-Ngando T, Debroas D. (2012) Assessing the Diversity and Specificity of Two Freshwater Viral Communities through Metagenomics. PLoS ONE. 7(3): e33641. doi:10.1371/journal.pone.0033641
• Roux S., Faubladier M, Mahul A, Paulhe N, Bernard A, Debroas D, Enault F. (2011) Metavir: a web server dedicated to virome analysis. Bioinformatics. 27(21):3074-5.
• Roux S., Enault F., Bronner G., Debroas D. (2011) Comparison of 16S rRNA and protein-coding genes as molecular markers for assessing microbial diversity (Bacteria and Archaea) in ecosystems. FEMS Microbiol Ecol. 78(3):617-28. doi: 10.1111/j.1574-6941.2011.01190.x.