Timeline

Hugo Varet

Research Engineer

18 Feb 2021

publication

Tissue damage induces a conserved stress response that initiates quiescent muscle stem cell activation.

18 Jan 2021

team

Metabolomics Core Facility

12 Jan 2021

project

Insights into amebiasis using a human 3D-intestinal model (ANR-14-IFEC-0001-02)

08 Jan 2021

project

Understanding the Pathogenicity of Entamoeba Using Comparative Transcriptomics and Phylogenomics – GENAMIBE. Project-ANR-10-GENM-0011

06 Jan 2021

publication

Aspergillus fumigatus, One Uninucleate Species with Disparate Offspring.

05 Jan 2021

publication

Characterization of a Four-Component Regulatory System Controlling Bacteriocin Production in Streptococcus gallolyticus

02 Dec 2020

publication

4-Methylcytosine DNA modification is critical for global epigenetic regulation and virulence in the human pathogen Leptospira interrogans.

01 Nov 2020

publication

Functionally distinct resident macrophage subsets differentially shape responses to infection in the bladder.

09 Oct 2020

publication

Effect of arsenite and growth in biofilm conditions on the evolution of Thiomonas sp. CB2.

06 Oct 2020

publication

The transcriptional response of pathogenic Leptospira to peroxide reveals new defenses against infection-related oxidative stress.

24 Sep 2020

course

Bioinformatics program for PhD students 2020-2021

25 Aug 2020

publication

Cellular and molecular profiling of T-cell subsets at the onset of human acute GVHD.

01 Aug 2020

publication

Insights into amebiasis using a human 3D-intestinal model.

09 Jun 2020

publication

Leishmania amazonensis Subverts the Transcription Factor Landscape in Dendritic Cells to Avoid Inflammasome Activation and Stall Maturation

02 Jun 2020

publication

Human Immune Response Triggered by Entamoeba histolytica in a 3D-Intestinal Model

14 May 2020

publication

BAHD1 haploinsufficiency results in anxiety-like phenotypes in male mice

04 May 2020

publication

Intracellular Staphylococcus aureus persisters upon antibiotic exposure

29 Apr 2020

publication

Macromolecular crowding links ribosomal protein gene dosage to growth rate in Vibrio cholerae

13 Apr 2020

publication

Transcytosis subversion by M cell-to-enterocyte spread promotes Shigella flexneri and Listeria monocytogenes intracellular bacterial dissemination

20 Mar 2020

project

Deciphering the mechanisms of infection of lyssaviruses at the cellular level in bats

11 Feb 2020

publication

Targeting Macrophage Histone H3 Modification as a Leishmania Strategy to Dampen the NF-κB/NLRP3-Mediated Inflammatory Response.

11 Feb 2020

publication

Tudor-SN Promotes Early Replication of Dengue Virus in the Aedes aegypti Midgut

03 Feb 2020

publication

Bread feeding is a robust and more physiological enteropathogen administration method compared to oral gavage

08 Nov 2019

publication

Mycobacterium abscessus virulence traits unraveled by transcriptomic profiling in amoeba and macrophages

21 Oct 2019

publication

Non-specific interference of cobalt with siderophore-dependent iron uptake pathways

02 Aug 2019

team

Biomics – Dry-Lab

01 Jul 2019

publication

Cryptococcus neoformans resists to drastic conditions by switching to viable but non-culturable cell phenotype.

15 May 2019

publication

Transcriptional profiling of a laboratory and clinical Mycobacterium tuberculosis strain suggests respiratory poisoning upon exposure to delamanid

10 Jan 2019

publication

Immune parameters and outcomes during Ebola virus disease

25 Aug 2018

publication

checkMyIndex: a web-based R/Shiny interface for choosing compatible sequencing indexes

19 Jul 2018

course

Introduction to data analysis

19 Jul 2018

course

Morning session – Introduction to NGS data analysis

19 Jul 2018

course

Morning session – Data analysis using R

19 Jul 2018

course

Introduction to Data Analysis

19 Jul 2018

course

Introduction to Data Analysis

19 Jul 2018

course

Introduction to Data Analysis

06 Jul 2018

publication

Enzymatic synthesis of random sequences of RNA and RNA analogues by DNA polymerase theta mutants for the generation of aptamer libraries

13 Jun 2018

publication

Enteric bacteria boost defences against oxidative stress in Entamoeba histolytica

21 May 2018

publication

Expansion of the SOS regulon of Vibrio cholerae through extensive transcriptome analysis and experimental validation

16 May 2018

course

7ème école de bioinformatique AVIESAN-IFB

15 May 2018

publication

A CRISPRi screen in E. coli reveals sequence-specific toxicity of dCas9

28 Mar 2018

team

Expertise group : Stats

28 Mar 2018

team

Expertise group: GORE – Genome Organization Regulation and Expression

27 Dec 2017

news

Hot off the press: DENV host factors identified by innovative transcriptomics approach

19 Dec 2017

publication

Individual co-variation between viral RNA load and gene expression reveals novel host factors during early dengue virus infection of the Aedes aegypti midgut

14 Nov 2017

publication

In Situ Fixation Redefines Quiescence and Early Activation of Skeletal Muscle Stem Cells

19 Apr 2017

course

6ème école de bioinformatique AVIESAN-IFB

07 Feb 2017

publication

Comparison of biofilm formation and motility processes in arsenic-resistant Thiomonas spp. strains revealed divergent response to arsenite

02 Feb 2017

project

Deciphering the virulence factors of Mycobacterium abscessus activated in the presence of environmental amoebae

31 Jan 2017

project

Transcriptome of different quiescence sub-states of neural stem cells in adult zebrafish

31 Jan 2017

project

The role of lncRNA H19 in Thymopoiesis

27 Jan 2017

news

checkMyIndex: a new tool to choose sequencing indexes

26 Jan 2017

tool

checkMyIndex

10 Jan 2017

publication

Promyelocytic Leukemia Protein (PML) Controls Listeria monocytogenes Infection

29 Nov 2016

course

5ème école de bioinformatique AVIESAN-IFB

21 Oct 2016

publication

Extensive transcriptome analysis correlates the plasticity of Entamoeba histolytica pathogenesis to rapid phenotype changes depending on the environment

12 Oct 2016

event

5th school of bioinformatics AVIESAN-IFB

09 Jun 2016

publication

SARTools: A DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data

18 May 2016

project

Gene expression profiling in germinal center B cells

18 May 2016

software

SARTools

26 Apr 2016

event

Training: analysis of the transcriptome by RNAseq

20 Apr 2016

course

Training: analysis of the transcriptome by RNAseq

05 Feb 2016

publication

Gender as a Modifying Factor Influencing Myotonic Dystrophy Type 1 Phenotype Severity and Mortality: A Nationwide Multiple Databases Cross-Sectional Observational Study

05 Nov 2015

publication

Deficiency of multidrug resistance 2 contributes to cell transformation through oxidative stress

20 Oct 2015

publication

Normal and Cystic Fibrosis Human Bronchial Epithelial Cells Infected with Pseudomonas aeruginosa Exhibit Distinct Gene Activation Patterns

30 Sep 2015

news

4th Bioinformatics school AVIESAN, Hugo Varet course

14 Sep 2015

project

HIV signature on RIG-I-like receptors

08 Sep 2015

project

Dynamic regulation of chromatin and transcription by HP1 Heterochromatin Proteins in relationship with RNA.

06 Sep 2015

project

Functional characterization of mosquito genes involved in dengue virus transmission identified by RNA-seq at the individual midgut level

26 Jun 2015

team

Bioinformatics and Biostatistics HUB

18 Mar 2015

team

Biomics

31 Jan 2015

project

Régulation transcriptionnelle par l’Enhancer de Trithorax et Polycomb Corto et la Protéine Ribosomique L12.

01 Jul 2014

publication

Ventilator-associated pneumonia during weaning from mechanical ventilation: role of fluid management

08 Sep 2012

publication

A little guide for advanced search:

Tissue damage induces a conserved stress response that initiates quiescent muscle stem cell activation.

Metabolomics Core Facility

Insights into amebiasis using a human 3D-intestinal model (ANR-14-IFEC-0001-02)

Understanding the Pathogenicity of Entamoeba Using Comparative Transcriptomics and Phylogenomics – GENAMIBE. Project-ANR-10-GENM-0011

Aspergillus fumigatus, One Uninucleate Species with Disparate Offspring.

Characterization of a Four-Component Regulatory System Controlling Bacteriocin Production in Streptococcus gallolyticus

4-Methylcytosine DNA modification is critical for global epigenetic regulation and virulence in the human pathogen Leptospira interrogans.

Functionally distinct resident macrophage subsets differentially shape responses to infection in the bladder.

Effect of arsenite and growth in biofilm conditions on the evolution of Thiomonas sp. CB2.

The transcriptional response of pathogenic Leptospira to peroxide reveals new defenses against infection-related oxidative stress.

Bioinformatics program for PhD students 2020-2021

Cellular and molecular profiling of T-cell subsets at the onset of human acute GVHD.

Insights into amebiasis using a human 3D-intestinal model.

Leishmania amazonensis Subverts the Transcription Factor Landscape in Dendritic Cells to Avoid Inflammasome Activation and Stall Maturation

Human Immune Response Triggered by Entamoeba histolytica in a 3D-Intestinal Model

BAHD1 haploinsufficiency results in anxiety-like phenotypes in male mice

Intracellular Staphylococcus aureus persisters upon antibiotic exposure

Macromolecular crowding links ribosomal protein gene dosage to growth rate in Vibrio cholerae

Transcytosis subversion by M cell-to-enterocyte spread promotes Shigella flexneri and Listeria monocytogenes intracellular bacterial dissemination

Deciphering the mechanisms of infection of lyssaviruses at the cellular level in bats

Targeting Macrophage Histone H3 Modification as a Leishmania Strategy to Dampen the NF-κB/NLRP3-Mediated Inflammatory Response.

Tudor-SN Promotes Early Replication of Dengue Virus in the Aedes aegypti Midgut

Bread feeding is a robust and more physiological enteropathogen administration method compared to oral gavage

Mycobacterium abscessus virulence traits unraveled by transcriptomic profiling in amoeba and macrophages

Non-specific interference of cobalt with siderophore-dependent iron uptake pathways

Biomics – Dry-Lab

Cryptococcus neoformans resists to drastic conditions by switching to viable but non-culturable cell phenotype.

Transcriptional profiling of a laboratory and clinical Mycobacterium tuberculosis strain suggests respiratory poisoning upon exposure to delamanid

Immune parameters and outcomes during Ebola virus disease

checkMyIndex: a web-based R/Shiny interface for choosing compatible sequencing indexes

Introduction to data analysis

Morning session – Introduction to NGS data analysis

Morning session – Data analysis using R

Introduction to Data Analysis

Introduction to Data Analysis

Introduction to Data Analysis

Enzymatic synthesis of random sequences of RNA and RNA analogues by DNA polymerase theta mutants for the generation of aptamer libraries

Enteric bacteria boost defences against oxidative stress in Entamoeba histolytica

Expansion of the SOS regulon of Vibrio cholerae through extensive transcriptome analysis and experimental validation

7ème école de bioinformatique AVIESAN-IFB

A CRISPRi screen in E. coli reveals sequence-specific toxicity of dCas9

Expertise group : Stats

Expertise group: GORE – Genome Organization Regulation and Expression

Hot off the press: DENV host factors identified by innovative transcriptomics approach

Individual co-variation between viral RNA load and gene expression reveals novel host factors during early dengue virus infection of the Aedes aegypti midgut

In Situ Fixation Redefines Quiescence and Early Activation of Skeletal Muscle Stem Cells

6ème école de bioinformatique AVIESAN-IFB

Comparison of biofilm formation and motility processes in arsenic-resistant Thiomonas spp. strains revealed divergent response to arsenite

Deciphering the virulence factors of Mycobacterium abscessus activated in the presence of environmental amoebae

Transcriptome of different quiescence sub-states of neural stem cells in adult zebrafish

The role of lncRNA H19 in Thymopoiesis

checkMyIndex: a new tool to choose sequencing indexes

checkMyIndex

Promyelocytic Leukemia Protein (PML) Controls Listeria monocytogenes Infection

5ème école de bioinformatique AVIESAN-IFB

Extensive transcriptome analysis correlates the plasticity of Entamoeba histolytica pathogenesis to rapid phenotype changes depending on the environment

5th school of bioinformatics AVIESAN-IFB

SARTools: A DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data

Gene expression profiling in germinal center B cells

SARTools

Training: analysis of the transcriptome by RNAseq

Training: analysis of the transcriptome by RNAseq

Gender as a Modifying Factor Influencing Myotonic Dystrophy Type 1 Phenotype Severity and Mortality: A Nationwide Multiple Databases Cross-Sectional Observational Study

Deficiency of multidrug resistance 2 contributes to cell transformation through oxidative stress

Normal and Cystic Fibrosis Human Bronchial Epithelial Cells Infected with Pseudomonas aeruginosa Exhibit Distinct Gene Activation Patterns

4th Bioinformatics school AVIESAN, Hugo Varet course

HIV signature on RIG-I-like receptors

Dynamic regulation of chromatin and transcription by HP1 Heterochromatin Proteins in relationship with RNA.

Functional characterization of mosquito genes involved in dengue virus transmission identified by RNA-seq at the individual midgut level

Bioinformatics and Biostatistics HUB

Biomics

Régulation transcriptionnelle par l’Enhancer de Trithorax et Polycomb Corto et la Protéine Ribosomique L12.

Ventilator-associated pneumonia during weaning from mechanical ventilation: role of fluid management

Revisiting the classification of clinical phenotypes of anti-neutrophil cytoplasmic antibody-associated vasculitis: a cluster analysis