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
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.
February 9, 2021 - Samuel Chaffron (University of Nantes)
24 November 2020 - Tiffany Delhomme (IRB Barcelona, Spain)
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
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.
- 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
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