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5th edition of the Workshop 

"Recent Computational Advances in Metagenomics (RCAM'18)"

September 9, 2018

Stavros Niarchos Foundation Cultural Center, Athens, Greece

This workshop aims at promoting discussions and collaborations between biologists (modelers),  computer scientists and applied-mathematicians involved in metagenomics and/or metatranscriptomics studies, either in the bioinformatics or statistical aspects of such analysis.
Metagenomics  studies  refer   to  analyses  based  on high-throughput sequencing  of environmental samples  and microbial ecosystems. Both marker-gene (16S, 18S, ITS,  ...)  and whole-genome strategies will be adressed to  cover a wide  array of question ranging  from quantifying the  microbial  diversity in  order  to  find  structuring factors to assessing the functional role of microbial communities.
The workshop will provide  an overview of the state-of-the-art methods currently used in metaomics including comparative metagenomics and metatranscriptomics.  At the  other end  of the  spectrum, case-studies with a strong methodological component will illustrate how and when these methods are useful and how they produce new biological knowledge. This includes studies that investigate the shortcomings of mature or novel methods (e.g. for clustering, inference of co-occurrence networks, detection of certain types of interaction between taxa, etc) in real life settings. 

The program of this workshop will consist mainly of presentations of refereed papers (30 minutes) and  invited talks (50 minutes). A poster session will be also organized. Contributions are welcomed on all aspects  about bioinformatics and statistical analyses of metaomics datasets, including, but not limited to:

  • new methods, tools or pipelines involved in the characterisation of microbial diversity,
  • original methods for taxonomical assignment,
  • Metagenomics/metatranscriptomics assembly,
  • data reduction,
  • comparative metaomics,
  • models for community assembly,
  • inference of co-occurrence/abundance patterns,
  • challenges for tackling the complexity of metaomics datasets.

Note that this workshop focuses mainly on methodological aspects of metagenomics and is not dedicated to bioanalyse result presentations.


9h00-10h00 Keynote : Frédéric Mahé (LSTM, Montpellier, France)
10h00-10h30  Anne-Laure Abraham (MaIAGE, Inra, Jouy-en-Josas,France)
10h30-11h00 Coffee break 
11h00-11h30 Alba Crespi-Boixader (University of Edinburgh, UK)
"A metagenomic toolbox to improve taxonomic sequence profiling" (abstract).
11h30-12h00 Riccardo Vicedomini (LBCQ, Sorbonne Université, UPMC, CNRS, IBPS, Paris, France)
12h00-13h00 Lunch break 
13h00-14h00 Keynote : Mahendra Mariadassou (MaIAGE, Inra, Jouy-en-Josas,France)
14h00-14h30 Mohammed-Amin Madoui (Genoscope, Evry, France)
 "Reference-free approach for population genomic analysis using metagenomics" (abstract).
14h30-15h00 Coffee break
15h00-15h30 Gregory Butler (Concordia University, Montréal, Québec, Canada)
"Predicting transport proteins for microbiomes: Challenges" (abstract).
15h30-16h30 Keynote : Anton Korobeynikov (CBT, St Petersburg State University, Russia)
"Challenges of metagenome assemblies: how to deal with them and how to live with them?"

Please send the abstract to rcam@jouy.inra.fr

All submitted abstracts will be peer-reviewed by the program committee. Submitted abstracts should not exceed 2 pages including bibliography. Abstracts must be written and presented in English. They may describe work that has already been published or that is simultaneously submitted to a journal, conference, or workshop with reefreed proceedings.

The RCAM worskhop is a satellite workshop of ECCB'18 and registrations fees are those corresponding to ECCB workshops: see here for more information.

Submission Deadline : July 09 at noon
Notification: July 13, 2018
Workshop Date: September 9, 2018. The worskop will start at 9:00am.

Valentin Loux, INRA/MaIAGE, Jouy-en-Josas, France
Mahendra Mariadassou, INRA/MaIAGE, Jouy-en-Josas, France
Pierre Peterlongo, Inria/IRISA, Rennes, France
Sophie Schbath, INRA/MaIAGE, Jouy-en-Josas, France

The workshop is supported by the metaprogramme "Microbial Ecosystems and Metaomics (MEM)" from the French National Institute for Agricultural Research (INRA).

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