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6th EBAME Workshop on Computational

Microbial Ecogenomics

October 25 - November 5 , 2021 in Brest - France
Faculty and teaching assistants

Confirmed speakers for EBAME6... List under construction and will be updated regularly.

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 Fernandez-Guerra is an assistant professor at the Globe institute in Copenhaguen. 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, Universite 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.

Tom Delmont explores the genomic diversity of plankton to better understand the ecology and evolution of co-occurring bacterial, eukaryotic and viral lineages abundant in the surface of the oceans. Tom takes advantage of deeply sequenced metagenomes and metatranscriptomes generated by the Tara Oceans consortium, transforming raw reads into manually curated metagenome-assembled genomes and determining their biogeography, functional potential and evolution.

Jessika Fuessel is a marine biogeochemist studying microbial metabolism and its role in global elemental cycles and microbial ecology using a combination of wet and dry lab approaches. 

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.

Rayan Chikhi is head of the sequence bioinformatics junior group at Pasteur institute

Riccardo Vicedomini
is a  postdoctoral researcher in the "Sequence Bioinformatics" group at Institut Pasteur (Paris, France)He worked on methods for genome assembly, protein domain annotation, and high-throughput-sequencing data analysis.Riccardo is currently focused on developing novel methods for metagenome assembly and, more specifically,resolving individual strain genomes.

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

Iva Veseli is a PhD Student in the Meren lab at the University of Chicago. She is broadly interested in the ecology and evolution of microbial communities, and is currently working on software for predicting microbial metabolism from genomes and metagenomes.

Rob James is a post-doctoral researcher at the Quadram Institute of Bioscience. His main research focus is elucidating the evolution and selective drivers of antibiotic resistance in complex ecosystems by using a range of molecular techniques such as qPCR and long-read sequencing

Sebastien Raguideau is a Post doctoral researcher at the Earlham Institute and part of Chris Quince group. My main interest is devising ad hoc bioinformatic pipeline and tools related to exploration of meta-omics datasets. I have been working on various subjects such as AMR, fiber degradation and syntrophy. My most recent projects are linked to coverage estimation from unique kmer and eukaryotic MAGs identification.

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

Eric Pelletier is senior researcher at CEA / Genoscope. He uses environmental genomics approaches to study genes, organisms and communities structures and functions and their relatioships with environment. He works on Tara Oceans project, focusing mainly on microbial eukaryote plankton

2021 Teaching Assistants

Blandine Trouche - Ifremer Research Assistant

Jolann Pommellec -  UBO PhD student

Scott Klasek - MBL / UWyoming postdoc

Clarisse Lemonnier - Postdoc U Brest

Florian Trigodet - UChicago Postdoc

Matt Schechter
- UChicago PhD student

Matt Klein - Uchicago Programmer

Iva Veseli - UChicago PhD student

2021 organizing committee

Lois Maignien - Assistant Professor UBO / CNRS

Julie Reveillaud - INRA researcher

Clarisse Lemonnier - Postdoc U Brest

Blandine Trouche - UBO PhD student

Emile Faure - UBO Postdoc

Stephanie Renard - Admin. assistant
U Brest

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