Hugo Varet

This project is a part of the international Infect-Era program, AMOEBAC: Entamoeba histolytica-bacterium interaction and the role of this interaction in intestinal pathogenesis (http://www.infect-era.eu/2nd-call-2014) The aim of this investigation is to understand the induced […]

Entamoeba histolytica is a protozoan parasite and an amitochondriate pathogenic amoeba, which may cause dysentery and liver abscess in humans (i.e. amoebiasis). Differential pathogenicity is observed among E. histolytica strains: strain HM1:IMSS is virulent […]

In collaboration with the Institute of Vertebrate Biology in Brno, Czech Republic (Dr. Natalia Martinkova and Markéta Harazim), the aim of this project is to study the mechanisms of lyssavirus infection in bats based […]

Mycobacterium abscessus (M. abs) is an emerging pathogen causing lung infections in cystic fibrosis patients. Although the environmental reservoir of M. abs is currently unknown, M. abs possesses a gene pool dedicated to a […]

Vertebrate adult neural stem cells (NSCs) are generally quiescent, and the frequency of their cell cycle re-entry (“activation”) conditions their lifespan. Little is known of the molecular pathways controlling the NSC quiescence/activation balance. We […]

“The thymus is a specialized organ that provides a unique environment for T cell development and differentiation. The study the thymus-settling progenitors (TSPs) and how they differentiate is important for the characterization of the […]

Germinal centers (GC) are essential for an effective humoral immune response. The GC provides an environment that stimulates B cells to proliferate in response to antigens and accumulate somatic mutations in immunoglobulin (Ig) genes, […]

The pathogenesis of HIV infection, and in particular the development of immunodeficiency, remains incompletely understood. During HIV infection both innate and adaptive immune responses are raised, but they appear to be insufficient or too […]

The three HP1 (Heterochromatin Protein 1), HP1a, HP1b, and HP1g proteins are epigenetic markers of heterochromatin, the condensed, repressed form of chromatin. They are typically known to associate to the di-/tri-methylated lysine 9 of […]

Dengue is the most rapidly expanding, globally dominant arthropod-borne (arbo) viral disease. It affects close to 400 million people each year in more than 125 countries. Recent reports of autochtonous cases in Southern France […]

Il est aujourd’hui connu que les protéines ribosomiques ont des fonctions extra-ribosomiques, et qu’en particulier, certaines d’entre elles contrôlent la transcription. Nous avons montré que, chez la drosophile, RPL12 interagit avec le facteur épigénétique […]

We present ePeak, a Snakemake-based pipeline for the identification and quantification of reproducible peaks from raw ChIP-seq, CUT&RUN and CUT&Tag epigenomic profiling techniques. It also includes a statistical module to perform tailored differential marking […]

SHADE is a Shiny application for providing support to research teams in refining their experiments designs. In particular, SHADE was designed to help biologist with nested designs, raising awareness on common statistical biases. It […]

SARTools is a R package dedicated to the differential analysis of RNA-seq data. It provides tools to generate descriptive and diagnostic graphs, to run the differential analysis with one of the well known DESeq2 […]

EXOTICS (EXplOre sysTems omICS) is a shiny app to perform functional enrichment analysis of bulk transcriptomic data at the gene-set level to complement gene-level analyses. The classical transcriptomics analysis consists of differential expression analysis, […]

checkMyIndex is an application whose goal is to help in finding a set of compatible indexes for a sequencing experiment. It has been developped using the R/Shiny environment and is freely available at https://checkmyindex.pasteur.fr/. […]