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Workshop "Recent Computational Advances in Metagenomics (RCAM)" 2015


2nd edition of the Workshop

"Recent Computational Advances in Metagenomics (RCAM'15)"

6th October, 2015
Insitut Pasteur, 28 rue du Dr Roux, Paris, France

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 will  illustrate  how  these  methods  produce  insightful biological knowledge.

The program of this workshop will consist mainly of presentations of refereed papers (30 minutes) and  invited talks (50 minutes). 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,
* data reduction,
* comparative metaomics,
* models for community assembly,
* challenges for tackling the complexity of metaomics datasets.

PROGRAM [Leaflet]

9h00-9h25  Welcome coffee
9h25-9h30  Opening Remarks
9h30-10h30 Keynote : Martin S. Lindner.  Robert Koch Institute (Berlin) and 4-Antibody (Basel)
"Augmenting taxonomic profiling with coverage information to improve sensitivity and specificity" (abstract)
10h30-11h00  Vitor C. Piro, Martin S. Lindner, Bernhard Y. Renard. Research Group Bioinformatics (NG4), Robert Koch Institut, Berlin, Germany
DUDes: a top-down taxonomic profiler for metagenomics samples(abstract)
11h00-11h30 Ari Ugarte, Juliana Bernardes, Alessandra Carbone. Laboratory of Computational and Quantitative Biology (LCQB) UMR 7238 CNRS - Université Pierre et Marie Curie, Paris, France.
"META-CLADE : a new tool to identify domains and functionally annotate metagenomic and metatranscriptomic sequences." (abstract)
11h30-12h30 KeynoteChristopher Quince, University of Glasgow, UK.
"Inferring microbial species and strains directly from metagenom data" (abstract)
12h30-14h15 Lunch break 
14h15-15h15 KeynoteAlex L. Mitchell, EBI.
"The EBI Metagenomics Portal - a free to use analysis platform for metagenomic data" (abstract)
15h15-15h45 Frédéric Escudié, Lucas Auer, Maria Bernard, Laurent Cauquil, Katia Vidal, Sarah Maman, Mahendra Mariadassou, Guillermina Hernandez-raquet, Géraldine Pascal. INRA, UMR1313, SIGENAE, F-78352 Jouy-en-Josas, France.
"FROGS: Find Rapidly OTU with Galaxy Solution". (abstract)
15h45-16h15 Daniel H. Huson, Benjamin Buchfink and Hans-Joachim Ruscheweyh. Center for Bioinformatics, Universität Tübingen, Germany. Life Sciences Institute, National University of Singapore.
"An Efficient Pipeline for Microbiome Analysis". (abstract)
16h15-16h45 Coffee break
16h45-17h15 Mohamed Mysara, Natalie Leys Jeroen Raes and Pieter Monsieurs. Unit of Microbiology, Belgian Nuclear Research Centre (SCK-CEN), Mol, Belgium. Department of Bioscience Engineering, Vrije Universiteit Brussel, Brussels, Belgium. VIB Center for the Biology of Disease, VIB, Leuven, Belgium.
"From Reads to OTUs. Improved Algorithms for Preprocessing Amplicon Sequencing data." (abstract)
17h15-17h45 Gaëtan Benoit, Pierre Peterlongo, Dominique Lavenier and Claire Lemaitre. Inria Rennes Bretagne Atlantique, UMR 6074 Irisa, Genscale, Rennes, France.
"Simka : Fast kmer-based method for estimating the similarity between numerous metagenomic datasets." (abstract)
17h45-18h15 Karel Brinda, Maciej Sykulski and Gregory Kucherov. Laboratoire d’Informatique Gaspard-Monge, Universit ́e Paris-Est & CNRS, France.
"Improved computational techniques for k-mer-based metagenomic classification." (abstract)

The worskhop is free of registration fees but registration is still mandatory through this registration form (registration is closed for security reason). Moreover, for security reasons, the organizers would have to provide the name of all the participants to Institut Pasteur some days before ; participants need then to register before October 1st.

Insitut Pasteur, 25 rue du Dr Roux, Paris, France
Badges will be given at the reception desk, 25 rue du Dr Roux.

Institut Pasteur is 5 minutes walk from the metro "Pasteur"
(See map: https://www.google.fr/maps/dir/Pasteur,+France/48.8406117,2.311018/@48.8416918,2.309531,17z/data=!3m1!4b1!4m8!4m7!1m5!1m1!1s0x47e670312105e921:0xb6976ffe50d65112!2m2!1d2.312681!2d48.842843!1m0)

Further information on access to Institut Pasteur: http://www.pasteur.fr/en/adress-and-access.

Further information on public transit in Paris, please see: http://www.ratp.fr/en/ratp/c_21879/visiting-paris/.

Anne-Laure Abraham, INRA/MICALIS, Jouy-en-Josas, France
Valentin Loux, INRA/MaIAGE, Jouy-en-Josas, France
Mahendra Mariadassou, INRA/MaIAGE, Jouy-en-Josas, France
Eduardo Rocha, Institut Pasteur, Paris, France
Sophie Schbath, INRA/MaIAGE, Jouy-en-Josas, France

The workshop is supported by the metaprogramme "Metaomics of Microbial Ecosystems (M2E)" from the French National Institute for Agricultural Research (INRA) and the Institut Pasteur.

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