Timeline

Rachel Legendre

Research Engineer

29 Nov 2022

course

2ème Ecole de Bioinformatique AVIESAN – IFB – INSERM Niveau 2

29 Nov 2022

course

11ème école de bioinformatique AVIESAN-INSERM-IFB

27 Aug 2022

publication

IRF8 regulates efficacy of therapeutic anti-CD20 monoclonal antibodies.

15 Jul 2022

publication

Y RNAs are conserved endogenous RIG-I ligands across RNA virus infection and are targeted by HIV-1.

10 Jun 2022

software

ePeak

01 Jun 2022

publication

ePeak: from replicated chromatin profiling data to epigenomic dynamics.

06 May 2022

news

New publication – PDGFRα-induced stromal maturation is required to restrain postnatal intestinal epithelial stemness and promote defense mechanisms

05 May 2022

publication

PDGFRα-induced stromal maturation is required to restrain postnatal intestinal epithelial stemness and promote defense mechanisms.

15 Apr 2022

news

A recent study by the team of Laurent Debarbieux has been highlighted in the BIP (15/04/2022)

13 Apr 2022

publication

The gut environment regulates bacterial gene expression which modulates susceptibility to bacteriophage infection.

16 Mar 2022

publication

Experimental evolution links post-transcriptional regulation to Leishmania fitness gain.

25 Feb 2022

publication

Trained ILC3 responses promote intestinal defense.

03 Feb 2022

course

Multiple roles of RNAs

31 Jan 2022

course

1ere école EBAII Assemblage & Annotation

22 Dec 2021

publication

sgDI-tector: defective interfering viral genome bioinformatics for detection of coronavirus subgenomic RNAs.

14 Dec 2021

project

Towards understanding of immunostimulatory properties of SARS-CoV-2 RNAs

14 Dec 2021

publication

Mosquito-bacteria interactions during larval development trigger metabolic changes with carry-over effects on adult fitness.

13 Dec 2021

publication

Early Transcriptional Changes in Rabies Virus-Infected Neurons and Their Impact on Neuronal Functions.

01 Dec 2021

publication

The oxidative stress response of pathogenic Leptospira is controlled by two peroxide stress regulators which putatively cooperate in controlling virulence.

17 Oct 2021

publication

Role of the major determinant of polar flagellation FlhG in the endoflagella-containing spirochete Leptospira.

01 Sep 2021

publication

The CovR regulatory network drives the evolution of Group B Streptococcus virulence.

27 Jul 2021

publication

HP1γ binding pre-mRNA intronic repeats modulates RNA splicing decisions.

10 Jun 2021

publication

Transcriptional adaptation of Mycobacterium ulcerans in an original mouse model: New insights into the regulation of mycolacton

18 May 2021

publication

Functional Genomic and Biochemical Analysis Reveals Pleiotropic Effect of Congo Red on Aspergillus fumigatus.

16 Apr 2021

course

1ème Ecole de Bioinformatique AVIESAN – IFB – INSERM Niveau 2

09 Mar 2021

publication

Queuine Is a Nutritional Regulator of Entamoeba histolytica Response to Oxidative Stress and a Virulence Attenuator.

24 Feb 2021

publication

SIV-induced terminally differentiated adaptive NK cells in lymph nodes associated with enhanced MHC-E restricted activity.

18 Feb 2021

publication

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

12 Jan 2021

project

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

06 Jan 2021

publication

Aspergillus fumigatus, One Uninucleate Species with Disparate Offspring.

04 Jan 2021

publication

Systemic viral spreading and defective host responses are associated with fatal Lassa fever in macaques.

01 Jan 2021

publication

CD32+CD4+ T Cells Sharing B Cell Properties Increase With Simian Immunodeficiency Virus Replication in Lymphoid Tissues.

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.

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

01 Aug 2020

publication

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

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

13 Apr 2020

publication

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

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

15 May 2019

publication

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

19 Jul 2018

project

Bioconvert

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

16 May 2018

course

7ème école de bioinformatique AVIESAN-IFB

28 Mar 2018

team

Expertise group: GORE – Genome Organization Regulation and Expression

19 Jan 2018

publication

Sequanix: A Dynamic Graphical Interface for Snakemake Workflows

16 Nov 2017

publication

A missense variant in the coil1A domain of the keratin 25 gene is associated with the dominant curly hair coat trait (Crd) in horse

14 Nov 2017

publication

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

31 Oct 2017

course

Hands-on course on High Throughput Sequencing data analysis: Genomics, Transcriptomics, Epigenomics

19 Apr 2017

course

6ème école de bioinformatique AVIESAN-IFB

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

24 Jan 2017

event

Journée ChIP-seq WP2.6 France Génomique

29 Nov 2016

course

5ème école de bioinformatique AVIESAN-IFB

22 Nov 2016

software

Sequana: a set of flexible NGS pipelines

12 Oct 2016

event

5th school of bioinformatics AVIESAN-IFB

22 Sep 2016

course

Workshop: Bacterial RNAseq

15 Jun 2016

publication

GH16 and GH81 family β-(1,3)-glucanases in Aspergillus fumigatus are essential for conidial cell wall morphogenesis

18 May 2016

project

Gene expression profiling in germinal center B cells

26 Apr 2016

event

Training: analysis of the transcriptome by RNAseq

20 Apr 2016

course

Training: analysis of the transcriptome by RNAseq

02 Jan 2016

publication

Translation Analysis at the Genome Scale by Ribosome Profiling

01 Jan 2016

publication

Global translational impacts of the loss of the tRNA modification t6A in yeast

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.

07 Sep 2015

publication

VING: a software for visualization of deep sequencing signals

26 Jun 2015

team

Bioinformatics and Biostatistics HUB

18 Mar 2015

team

Biomics

15 Mar 2015

publication

RiboTools: a Galaxy toolbox for qualitative ribosome profiling analysis

31 Jan 2015

project

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

17 Sep 2014

publication

Next-generation sequencing identifies equine cartilage and subchondral bone miRNAs and suggests their involvement in osteochondrosis physiopathology

24 Jul 2014

publication

Genome-wide translational changes induced by the prion [PSI+]

20 Mar 2014

publication

Involvement of mitochondrial dysfunction and ER-stress in the physiopathology of equine osteochondritis dissecans (OCD)

05 Oct 2012

publication

Hyperstructure interactions influence the virulence of the type 3 secretion system in yersiniae and other bacteria

19 Mar 2012

publication

A little guide for advanced search:

2ème Ecole de Bioinformatique AVIESAN – IFB – INSERM Niveau 2

11ème école de bioinformatique AVIESAN-INSERM-IFB

IRF8 regulates efficacy of therapeutic anti-CD20 monoclonal antibodies.

Y RNAs are conserved endogenous RIG-I ligands across RNA virus infection and are targeted by HIV-1.

ePeak

ePeak: from replicated chromatin profiling data to epigenomic dynamics.

New publication – PDGFRα-induced stromal maturation is required to restrain postnatal intestinal epithelial stemness and promote defense mechanisms

PDGFRα-induced stromal maturation is required to restrain postnatal intestinal epithelial stemness and promote defense mechanisms.

A recent study by the team of Laurent Debarbieux has been highlighted in the BIP (15/04/2022)

The gut environment regulates bacterial gene expression which modulates susceptibility to bacteriophage infection.

Experimental evolution links post-transcriptional regulation to Leishmania fitness gain.

Trained ILC3 responses promote intestinal defense.

Multiple roles of RNAs

1ere école EBAII Assemblage & Annotation

sgDI-tector: defective interfering viral genome bioinformatics for detection of coronavirus subgenomic RNAs.

Towards understanding of immunostimulatory properties of SARS-CoV-2 RNAs

Mosquito-bacteria interactions during larval development trigger metabolic changes with carry-over effects on adult fitness.

Early Transcriptional Changes in Rabies Virus-Infected Neurons and Their Impact on Neuronal Functions.

The oxidative stress response of pathogenic Leptospira is controlled by two peroxide stress regulators which putatively cooperate in controlling virulence.

Role of the major determinant of polar flagellation FlhG in the endoflagella-containing spirochete Leptospira.

The CovR regulatory network drives the evolution of Group B Streptococcus virulence.

HP1γ binding pre-mRNA intronic repeats modulates RNA splicing decisions.

Transcriptional adaptation of Mycobacterium ulcerans in an original mouse model: New insights into the regulation of mycolacton

Functional Genomic and Biochemical Analysis Reveals Pleiotropic Effect of Congo Red on Aspergillus fumigatus.

1ème Ecole de Bioinformatique AVIESAN – IFB – INSERM Niveau 2

Queuine Is a Nutritional Regulator of Entamoeba histolytica Response to Oxidative Stress and a Virulence Attenuator.

SIV-induced terminally differentiated adaptive NK cells in lymph nodes associated with enhanced MHC-E restricted activity.

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

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

Aspergillus fumigatus, One Uninucleate Species with Disparate Offspring.

Systemic viral spreading and defective host responses are associated with fatal Lassa fever in macaques.

CD32+CD4+ T Cells Sharing B Cell Properties Increase With Simian Immunodeficiency Virus Replication in Lymphoid Tissues.

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.

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

Bioinformatics program for PhD students 2020-2021

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

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

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

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

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

Bioconvert

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

7ème école de bioinformatique AVIESAN-IFB

Expertise group: GORE – Genome Organization Regulation and Expression

Sequanix: A Dynamic Graphical Interface for Snakemake Workflows

A missense variant in the coil1A domain of the keratin 25 gene is associated with the dominant curly hair coat trait (Crd) in horse

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

Hands-on course on High Throughput Sequencing data analysis: Genomics, Transcriptomics, Epigenomics

6ème école de bioinformatique AVIESAN-IFB

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

Journée ChIP-seq WP2.6 France Génomique

5ème école de bioinformatique AVIESAN-IFB

Sequana: a set of flexible NGS pipelines

5th school of bioinformatics AVIESAN-IFB

Workshop: Bacterial RNAseq

GH16 and GH81 family β-(1,3)-glucanases in Aspergillus fumigatus are essential for conidial cell wall morphogenesis

Gene expression profiling in germinal center B cells

Training: analysis of the transcriptome by RNAseq

Training: analysis of the transcriptome by RNAseq

Translation Analysis at the Genome Scale by Ribosome Profiling

Global translational impacts of the loss of the tRNA modification t6A in yeast

HIV signature on RIG-I-like receptors

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

VING: a software for visualization of deep sequencing signals

Bioinformatics and Biostatistics HUB

Biomics

RiboTools: a Galaxy toolbox for qualitative ribosome profiling analysis

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

Next-generation sequencing identifies equine cartilage and subchondral bone miRNAs and suggests their involvement in osteochondrosis physiopathology

Genome-wide translational changes induced by the prion [PSI+]

Involvement of mitochondrial dysfunction and ER-stress in the physiopathology of equine osteochondritis dissecans (OCD)