IUEM Banner,

  lm2E





Previous workshops





5th EBAME Workshop on Computational

Microbial Ecogenomics

October 19 - November 2 , 2019 in Brest - France


2019 EBAME 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.


•  Jesse Shapiro. Associate Professor of Biology at the Université de Montréal, his group tracks evolving microbial populations in real time, using whole-genome and whole-community DNA sequencing to understand their evolution and predict how they adapt to changing environments

•  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.

•  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.

•Sheri Simmons is a Bioinformatics Researcher, Johnson&Johnson, Cambridge, U.S.A. Sheri works on medical applications of the  human microbiome.

•  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

•  Rob James is a postdoctoral researcher in the department of Life Sciences at University of Warwick. His research interests include the anthropogenic drivers of selection in farmland ecosystems and the subsequent spread of pathogens, such as Mycobacterium bovis, through the environment.

Sebastien Raguideau  is a postdoctoral researcher at the University of Warwick. He is developing novel bioinformatics and statistics tools to resolve the genomic context of AMR genes from short read shotgun metagenomics data

Christophe Blanchet is working at the french bioinformatics institute and is providing support with virtual machine design for the EBAME course.


2019 Teaching Assistants

Özcan C. Esen - U Chicago Sowftware Guru

Clarisse Lemonnier - Postdoc U Brest

Johanne Aubé - Research Engineer, IFREMER

Florian Trigodet - Postdoc, U Chicago


Blandine Trouche - UBO PhD student




2019 organizing committee


Loïs Maignien - Assistant Professor UBO / CNRS

Julie Reveillaud - INRA researcher

Clarisse Lemonnier - Postdoc U Brest

Blandine Trouche - UBO PhD student

Florian Trigodet -
Postdoc, U Chicago

Ashley Grosche - Postdoc U Brest

Scott Klasek - Postdoc MBL

Anaëlle Le Roux - Continuing education U Brest


Stéphanie Renard - Admin. assistant
U Brest



logo UBO, logo CNRS
logo ifremer, isblue