Hugo Varet is a biostatistician engineer from the Ensai (Ecole Nationale de la Statistique et de l’Analyse de l’Information) and has been recruited by the hub of the C3BI (Center of Bioinformatics, Biostatistics and Integrative Biology) to work at the Transcriptome & Epigenome Platform. He is in charge of the statistical analyses of the RNA-Seq data produced by the platform and develops R pipelines that help in this task. One of them is named SARTools and is available on GitHub: https://github.com/PF2-pasteur-fr/SARTools.
6ème école de bioinformatique AVIESAN-IFB
Objectifs La formation s’adresse à des chercheurs et ingénieurs directement impliqués dans des projets “Next Generation Sequencing” (NGS). Cette édition de l’école s’adresse aux nouveaux enjeux technologiques: elle inclura notamment une ouverture aux technologies […]
5ème école de bioinformatique AVIESAN-IFB
Initiation au traitement des données de génomique obtenues par séquençage à haut débit Objectifs Les domaines des sciences du vivant liés à l’analyse du génome ont vu au cours des dernières années une accumulation […]
Training: analysis of the transcriptome by RNAseq
The Transcriptome and Epigenome platform of the Biomics pole is organizing a one week (October 10, 2016 – October 14, 2016) training session dedicated to the analysis of the transcriptome by RNAseq. It is […]
Deciphering the virulence factors of Mycobacterium abscessus activated in the presence of environmental amoebae
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 […]
Régulation transcriptionnelle par l’Enhancer de Trithorax et Polycomb Corto et la Protéine Ribosomique L12.
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 […]
Transcriptome of different quiescence sub-states of neural stem cells in adult zebrafish
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 role of lncRNA H19 in Thymopoiesis
“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 […]
Interactions between HP1 proteins and RNA
The three HP1 proteins (Heterochromatin Protein 1 alpha, -beta, -gamma) 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 histone […]
Gene expression profiling in germinal center B cells
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, […]
HIV signature on RIG-I-like receptors
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 […]
Functional characterization of mosquito genes involved in dengue virus transmission identified by RNA-seq at the individual midgut level
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 […]
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 […]
SHAMAN: SHiny Application for Metagenomic ANalysis
SHAMAN is a SHiny Application for Metagenomic ANalysis including the normalization, the differential analysis and mutiple visualization. SHAMAN is based on DESeq2 R package [Anders and Huber 2010] for the analysis of metagenomic data, […]
- 2013-Present: Institut Pasteur – Transcriptome & Epigenome Platform and Bioinformatics & Biostatistics Hub, Paris (75), France
- 2012-2013: Necker Hospital and Paris Descartes University – Biostatistics & Medical Informatics Service, Paris (75), France
- 2011-2012: Henri Mondor Hospital – Clinical Research Unit, Créteil (94), France
- 2008-2011: National School For Statistics and Information Analysis, Rennes (35), France
- 2006-2008: Intensive general program for Top Schools in Mathematics & Physics, Le Mans (72), France
2017Comparison of biofilm formation and motility processes in arsenic-resistant Thiomonas spp. strains revealed divergent response to arsenite, Microb Biotechnol. 2017 Feb 7. doi: 10.1111/1751-7915.12556.
2017Promyelocytic Leukemia Protein (PML) Controls Listeria monocytogenes Infection, mBio 8:e02179-16..
2016Extensive transcriptome analysis correlates the plasticity of Entamoeba histolytica pathogenesis to rapid phenotype changes depending on the environment, Sci Rep. 2016 Oct 21;6:35852. doi: 10.1038/srep35852..
2016SARTools: A DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data, PLoS One. 2016 Jun 9;11(6):e0157022. doi: 10.1371/journal.pone.0157022. eCollection 2016.
2016Gender as a Modifying Factor Influencing Myotonic Dystrophy Type 1 Phenotype Severity and Mortality: A Nationwide Multiple Databases Cross-Sectional Observational Study, PLoS One. 2016 Feb 5;11(2):e0148264.
2015Deficiency of multidrug resistance 2 contributes to cell transformation through oxidative stress, Carcinogenesis 2016 Jan;37(1):39-48.
2015Normal and Cystic Fibrosis Human Bronchial Epithelial Cells Infected with Pseudomonas aeruginosa Exhibit Distinct Gene Activation Patterns, PLoS ONE 2015;10(10):e0140979.
2014Ventilator-associated pneumonia during weaning from mechanical ventilation: role of fluid management, Chest 2014 Jul;146(1):58-65.
2012Revisiting the classification of clinical phenotypes of anti-neutrophil cytoplasmic antibody-associated vasculitis: a cluster analysis, Ann. Rheum. Dis. 2013 Jun;72(6):1003-10.