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UMR 6197

Microbiology of  Extreme Environments

Previous workshops

EBAME Workshop on Computational

Microbial Ecogenomics

September 29 -October 6, 2018 in Brest - France

Confirmed 2018 Faculty

•  A. Murat Eren (Meren). Assistant Professor at the Department of Medicine, University of Chicago (USA). Meren studies the ecology of microbes using genome-resolved metagenomics and comparative genomics.

•  Antonio Fernández-Guerra is a postdoc at the Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology in Bremen (Germany). Antonio is interested in the ecological implications of the uncharacterized functional fraction of microbial genomes and metagenomes.

•  Chirstopher Quince. Principal Research Fellow at Warwick Medical School, University of Warwick (UK). Chris develops novel algorithms and statistics for resolving microbial species and strains from metagenomics data.

•   Damien Eveillard. Associate Professor at the Department of Computer Science, Université de Nantes (France). His research topic concerns systems biology and development of new computational approaches for biological modeling. His recent interests focus on metabolic modeling of genome-scale microbial ecosystems.

•   Julie Reveillaud is a research scientist at the Institut National de Recherche Agronomique (Montpellier France). Julie applies microbial ecogenomics to insect microbiome research in the context of emerging tropical diseases.

•  Martial Marbouty is a CNRS researcher in the Lab « Spatial Regulation of Genomes », Institut Pasteur (Paris, France). Martial is working on human microbiome and is mainly interested in studying phages-bacteria relationships. He has actively participated in the development of techniques aiming at improving genome annotations, assembly and metagenomic analysis using DNA collisions frequencies as a marker of cellular compartment.

•  Samuel Chaffron is CNRS researcher at the Laboratoire des Sciences du Numérique de Nantes, France (LS2N - UMR6004). His main research interest lies in understanding natural microbial communities and their structures at different levels of organization (genes, species, networks) in various habitats (including the human intestinal tract and the world’s oceans) using comparative (meta-)genomics and systems ecology

•  Nick Loman  Nick works as Professor of Microbial Genomics and Bioinformatics in the Institute for Microbiology and Infection at the University of Birmingham. His research explores the use of cutting-edge genomics and metagenomics approaches to the diagnosis, treatment and surveillance of infectious disease.

•  Marie-Agnès Petit: Marie-Agnès is leading the Phage team in the  Micalis institut at the National Institute for Agronomy Research. She  aims at understanding the behavior of temperate phages in the gut using both global and reconstruction approaches, to understand how phages evolve and acquire new genes, and to develop new bio-informatic tools to facilitate phage genome annotations.

•  Tom O. Delmont is a postdoc at the Genoscope, CEA (France). Tom studies the evolutionary history, functioning and niche partitioning of archaeal, bacterial and eukaryotic plankton at large-scale using genome-resolved metagenomics, single cell genomics and cultivation.

2018 Teaching Assistants

Damien Courtine - UBO PhD student

Özcan C. Esen - U Chicago Sowftware Guru

Clarisse Lemonnier - UBO PhD student

Florian Trigodet - Institut Corrosion / UBO PhD student

Blandine Trouche - UBO PhD student

Sam Nicholls - Postdoc at Loman Lab

2018 organizing committee

Loïs Maignien - Assistant Professor UBO / CNRS

Julie Reveillaud - INRA-Cirad Researcher

Clarisse Lemonnier - UBO PhD student

Blandine Trouche - UBO PhD student

Florian Trigodet - Institut Corrosion / UBO PhD student

Damien Courtine - UBO PhD student

Stéphanie Renard - UBO Admin. assistant

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