The seminars take place on Tuesdays at 2 pm in the CGFB conference room (unless otherwise specified)


Next Seminar :

8 Décember 2020 - Jean Delmotte, University of Montpellier (IHPE, UMR 5244), France

Abstract :

Phylogeography, genetic diversity and connectivity of Ostreid herpesvirus-1 population in France

Recurrent mortalities have been affecting juvenile Pacific oysters (Crassostrea gigas) for more than 30 years. Among the pathogens involved, the preponderant role of the Ostreid herpesvirus 1 (OsHV-1) virus in the mortality syndrome called “Pacific Oyster Mortality Syndrome” (POMS) has recently been demonstrated. The OsHV-1 epidemics in oyster farming areas have made this virus a major threat to the oyster industry. However, genomic epidemiology in certain regions at risk, in particular in France, remains limited. We report 21 OsHV-1 genomes generated using high-throughput sequencing during mass mortality episodes in 3 regions of the French coast. Using new bioinformatics methodology and adopting a three-set genomic variation analysis strategy, we reveal the connectivity of OsHV-1 viral population in France. The main source is probably the Marenne d'Oléron area, the viruses are then introduced into other shellfish-growing areas, probably following the transfer of oyster spat. The spatial heterogeneity of the transmission of OsHV-1 calls into question the surveillance of malacoherpesviruses and disease control measures.


Upcoming seminars

February 9, 2021 - Samuel Chaffron (University of Nantes)


Past seminars

24 November 2020 - Tiffany Delhomme (IRB Barcelona, Spain)

Abstract :

Drawing the landscape of genetic mutations from “hard” data analysis with needlestack and hyperstack.

Modern genomics has a great potential in applied cancer sciences, and currently is honouring his promises notably through the development of Next Generation Sequencing (NGS). This technique enables the identification of DNA sequences for hundreds or even thousands of individuals with reasonable costs and experiment times, and is applied recently to the identification of single-cell genomes. However, it is prone to errors of two types: from sequencing, and from amplification in the case of single-cell sequencing. In a first part, I will present needlestack, a new bioinformatics tools that can efficiently detect somatic mutations from NGS data, and I will present some of its applications in early cancer detection. In a second part, I will introduce hyperstack, an adaptation of needlestack for the reconstruction of mutational profiles from single-cell data. Hyperstack integrates a step of machine learning in order to estimate the amplification errors, in addition to sequencing errors detected by needlestack. I will finally present an application of hyperstack in a case of lowcoverage single-cell DNA data.

11 Février 2020 - Anais Baudot (Marseille Medical Genetics Institute, Aix-Marseille Université )

Mining networks to study rare and common diseases

Abstract :

Networks are scaling-up the analysis of gene and protein functions, thereby offering new avenues to study the diseases in which these macromolecules are involved. I will discuss the exploration of -omics networks containing thousands of physical and functional interactions between genes and proteins. In particular, we now focus on multiplex networks, i.e., networks composed of layers containing the same nodes but different interaction categories, such as protein-protein interactions, molecular complexes or correlations of expression.

We develop algorithms (e.g., community detections, random walks) to explore these large and complex biological networks, integrate information (e.g., expression), and mine the functional knowledge they contain. I will show how we use these tools to study rare and common genetic diseases, in particular premature aging diseases and diseases-disease comorbidity relationships.

Associated publications

  • The DREAM Module Identification Challenge Consortium, Choobdar S, Ahsen ME, Crawford J, Tomasoni M, Fang T, et al. Assessment of network module identification across complex diseases. Nature Methods. 2019 Sep;16(9):843–52.
  • Valdeolivas A, Tichit L, Navarro C, Perrin S, Odelin G, Levy N, et al. Random Walk with Restart on Multiplex and Heterogeneous Biological Networks. Bioinformatics. 2018 Jul 18;
  • Ibáñez K, Boullosa C, Tabarés-Seisdedos R, Baudot A, Valencia A. Molecular Evidence for the Inverse Comorbidity between Central Nervous System Disorders and Cancers Detected by Transcriptomic Meta-analyses. Horwitz MS, editor. PLoS Genetics. 2014 Feb 20;10(2):e1004173.


4 Février 2020 - Alexandra Calteau (LABGeM bioinformatics team of the UMR 8030 Genomics Metabolics, research structure of Genoscope )

MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis
Abstract :
Large-scale genome sequencing and the increasingly massive use of high-throughput approaches produce a vast amount of new information that completely transforms our understanding of thousands of microbial species. However, despite the development of powerful bioinformatics approaches, full interpretation of the content of these genomes remains a difficult task. Launched in 2005, the MicroScope platform ( has been under continuous development and provides analysis for prokaryotic genome projects together with metabolic network reconstruction and post-genomic experiments allowing users to improve the understanding of gene functions. Recently new tools and pipeline have been developed to perform comparative analyses on hundreds of genomes based on pangenome graphs. 
To date, MicroScope contains data for >12 300 microbial genomes, part of which are manually curated and maintained by microbiologists (>4700 personal accounts in January 2020). The platform enables collaborative work in a rich comparative genomic context and improves community-based curation efforts.


22 Octobre 2019  - Guillaume Bernard (Sorbonne university, MNHN, Paris)

Next-generation phylogenomics: alignment-free approaches, sequence similarity networks and more.


8 Octobre 2019 - Laurent Brehelin (LIRMM, Montpellier)

Probing transcriptional regulation with statistical models


21 Mai 2019 - Eduardo Rocha (Institut Pasteur)

Horizontal gene transfer: from acquisition to functional innovation


7 Mai 2019 - Florian Thibord (UPMC Université Paris 6)

Alignement des données miRseq


26 Mars 2019 - Julien Chiquet (AgroParisTech)

A collection of Poisson lognormal models for multivariate analysis of count data


19 Février 2019 - Magali Champion (Université Paris Descartes)

AMARETTO: Multi-omics data fusion for cancer data


8 Janvier 2019 - Warren Francis (University of Southern Denmark)

Comparative genomics and the nature of placozoan species


29 Novembre 2018 - Antonio Marco (University of Essex, UK), TBA

On sex, mothers and microRNA


11 Novembre 2018 - Clovis Galliez (Université de Grenoble)

Making sense of the metagenomics mixture: identifying bacterial hosts from phage sequences and binning billions of contigs