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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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