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6th edition of the Workshop 

"Recent Computational Advances in Metagenomics (RCAM'19)"

September 30 - October 1, 2019

Amphi Duclaux, Institut Pasteur, Paris, France 

[Note: your ID will be asked to enter the campus; please arrive 15 minutes in avance]

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 session for PhD students/postdoctoral fellows 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 result presentations of bioanalysis studies.

PRELIMINARY PROGRAM (to be confirmed)

Monday 30th September [9h00 - 17h30]


09h30 - 10h00: welcome coffee and registration
10h00 - 11h00: Otso Ovaskainen (Research Centre for Ecological Change, University of Helsinki, Helsinki, Finland)
Hierarchical modelling of species communities accounting for environment, traits and phylogeny in space and time
11h00 - 11h30: Antoine Bichat (Entérome, Paris, France)
Impact of tree choice in metagenomics differential abundance studies [abstract]
11h30 - 12h00: Nils Giordano (LS2N, Nantes University, Nantes, France)
Co-activity networks reveal the structure of planktonic symbioses in the global ocean [abstract]

12h00 - 14h00: lunch

14h00 - 15h00: Mathieu Almeida (MetaGenoPolis, INRA, Jouy-en-Josas, France)
An overview of hybrid metagenomic methodologies for microbial species exploration
15h00 - 15h30: Benjamin Churcheward (LS2N, Nantes University, Nantes, France)
Assembly strategies for the recovery of Metagenome Assembled Genomes [abstract]
15h30 - 16h00: Gleb Goussarov (Microbiology Unit, Belgian Nuclear Research Centre (SCK-CEN), Belgium)
A Fast alignment-free whole-genome distance calculator with applications in post-assembly bin validation and annotation of Metagenomic samples [abstract]

16h00 - 16h30: coffee break

16h30 - 17h00: Camille Marchet (CRIStAL UMR 9189, CNRS / Université de Lille, Lille, France)
Read correction for non-uniform coverages [abstract]

17h00 - 17h30: Amine Ghozlane (Hub de Bioinformatique, Institut Pasteur, Paris, France)
Prediction of the intestinal resistome by a three-dimensional structure-based method [abstract]

Tuesday 1st October [9h30 - 12h30]

09h30 - 10h30: Johannes Soeding (MaxPlanck Institute for Biophysical Chemistry, Göttingen, Germany)
Bioinformatics tools for the age of metagenomics
10h30 - 11h00: Mohamed Mysara (Microbiology Unit, Belgian Nuclear Research Centre (SCK-CEN), Belgium)
OCToPUS: a comprehensive pipeline for 16S rRNA metagenetic data analysis [abstract]

11h00 - 11h30: coffee break

11h30 - 12h30: Béatrice Laroche (INRA - MaIAGE, Université Paris-Saclay, Jouy-en-Josas, France)
Modelling aggregated functional traits from metagenomics data: application to dietary fiber degradation



  • Johannes Soeding (Max Planck Institute): "Bioinformatics tools for the age of metagenomics"
  • Otso Ovaskainen (University of Helsinki): "Hierarchical modelling of species communities accounting for environment, traits and phylogeny in space and time"
  • Béatrice Laroche (INRA): "Modelling aggregated functional traits from metagenomics data: application to dietary fiber degradation"
  • Mathieu Almeida (INRA): "An overview of hybrid metagenomic methodologies for microbial species exploration


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.


There is no registration fee to attend the RCAM worskhop but for security reason and room capacity, the registration is mandatory. Registration is closed.

Submission Deadline : September 4, 2019
Notification: September 9, 2019
Workshop Date: September 30 - October 1, 2019. The worskop will start at 10:00am on Monday and will end at 1pm on Tuesday.

Valentin Loux, INRA/MaIAGE, Jouy-en-Josas, France
Mahendra Mariadassou, INRA/MaIAGE, Jouy-en-Josas, France
Pierre Peterlongo, Inria/IRISA, Rennes, France
Eduardo Rocha, Institut Pasteur, Paris, 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), by the "GdR Molecular Bioinformatics" (GdR BiM) and by the "Genomes and Genetics Department" from Institut Pasteur.



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