Workshop "Recent Computational Advances in Metagenomics (RCAM)" 2016

3rd edition of the Workshop

"Recent Computational Advances in Metagenomics (RCAM'16)"

4th September, 2016
ECCB'16, The Hague, Netherlands.

OBJECTIVES
---------------
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.

SCOPE
--------
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,
• inference of co-occurrence patterns,
• challenges for tackling the complexity of metaomics datasets.

KEYNOTES
---------

• Karoline Faust (VIB, KU Leuven, Belgium): "Network inference meets metagenomics: challenges, tools and applications"
• Alexander Schönhuth (CWI, Amsterdam, The Netherlands): "Advanced stratregies for strain aware assembly" 
• Pierre Peterlongo (IRISA, France): "De novo comparison of (large number of) metagenomic samples. What are the technical challenges and what can we expect from this?"

IMPORTANT DATES
----------------
Submission Deadline (abstract): May 20, 2016
Notification: May 27, 2016
Registration deadline : August 19, 2016
Workshop Date: September 4, 2016

SELECTED PRESENTATIONS
-----------------------

• Latent Block Model for Metagenomics data by Julie Aubert
• Integrating metagenome analysis tools to improve taxonomic profiling and organism identification by Victor Piro
• Integrating Tara Oceans data sets using multiple kernels by Jérôme Mariette
• Taxonomic assignment of protist metatranscriptomes by Daniela Beisser
• Detection of mutated primers and impact on targeted metagenomics results by Antoine-Lorquin
• Minimum Curvilinear Embedding unveils nonlinear patterns in 16S metagenomic data by Carlo Vittorio Cannistraci

PROGRAM
----------------

9h: Opening
9h-10h: keynote : Karoline Faust (VIB, KU Leuven, Belgium)
Network inference meets metagenomics: challenges, tools and applications [slides]

10h-10h30: Antoine Lorquin (IRISA, INRIA, France)
Detection of mutated primers and impact on targeted metagenomics results [abstract] [slides]

10h30 - 11h: Coffee break

11h-11h30: Julie Aubert (INRA/AgroParisTech, France)
Latent Block Model for Metagenomics data [abstract] [slides]

11h30-12h: Jérôme Mariette (INRA, France)
Integrating Tara Oceans data sets using multiple kernels [abstract] [slides]

12h-12h30: Carlo Vittorio Cannistraci (BIOTEC, TU Dresden, Germany)
Minimum Curvilinear Embedding unveils nonlinear patterns in 16S metagenomic data [abstract] [slides]

12h30-14h00: Lunch

14h00-14h30: Daniela Beisser (Institute of Human Genetics, University of Duisburg-Essen, Germany)
Taxonomic assignment of protist metatranscriptomes [abstract] For slides, contact daniela.beisser@uni-due.de

14h30 - 15h: Vitor Piro (NG4 Bioinformatics, Robert Koch Institute, Germany)
Integrating metagenome analysis tools to improve taxonomic profiling and organism identification [abstract] For slides, contact PiroV@rki.de

15h - 15h30: Coffee break

15h30 - 16h30: Keynote Pierre Peterlongo (IRISA, France)
De novo comparison of (large number of) metagenomic samples. What are the technical challenges and what can we expect from this? [slides]

16h30: Closing remarks

REGISTRATION

----------------
The worskhop is a satellite workshop of ECCB'16 and registration should proceed through ECCB registration website:
http://www.eccb2016.org/registration/
Registration will close on August 19 (July 29 for early birds)

ORGANIZERS
------------
Valentin Loux, INRA/MaIAGE, Jouy-en-Josas, France
Mahendra Mariadassou, INRA/MaIAGE, Jouy-en-Josas, France
Sophie Schbath, INRA/MaIAGE, Jouy-en-Josas, France

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