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  • PhD Student
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About

After a Master degree in Genome Analysis and Molecular Modeling at Denis Diderot University, I did a PhD in NMR / bioinformatics at Denis Diderot University, where I worked on the development and use of a software named DaDiModO which uses SAXS data and RDC/NMR data to calculate models of structural proteins.

After a postdoc aiming to adapt ARIA software to allow execution on computing grid in the Structural Bioinformatic Team at Institut Pasteur in collaboration with IBCP, I joined CIB/DSI Team where I was responsible for the development of bioinformatics projects and the deployment, maintenance and evolution of the Pasteur Galaxy server.

I joined the Hub team in 2017 as research engineer where I’m involved in several projects such as structural bioinformatics, softwares and web development. I am also in charge of the maintenance of the Galaxy Pasteur instance.

Courses

09:00
06
Jun 2016
Course

Workshop: Bacterial RNAseq

We propose a skills training for PhD students on Bacterial RNAseq experiments Using total RNAs, we will i) enrich the mRNAs by depleting the rRNAs ; ii) prepare and sequence cDNA library and iii) analyse […]
Pathogenesis of Bacterial Anaerobes
Biomics
Microbiology
Marc Monot
Isabelle Martin-Verstraete
Bruno Dupuy
Odile Sismeiro
Rachel Legendre
Fabien Mareuil
Olivia Doppelt-Azeroual
2016-06-06 09:00:00 2016-06-10 17:00:00 Europe/Paris Workshop: Bacterial RNAseq We propose a skills training for PhD students on Bacterial RNAseq experiments Using total RNAs, we will i) enrich the mRNAs by depleting the rRNAs ; ii) prepare and sequence cDNA library and iii) analyse […] 28 Rue du Docteur Roux, Paris, France
09:00
10
Oct 2016
Course

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 […]
Biomics
Genomes and Genetics
Odile Sismeiro
Jean-Yves Coppee
Marie-Agnès Dillies
Hugo Varet
Rachel Legendre
Olivia Doppelt-Azeroual
Fabien Mareuil
Natalia Pietrosemoli
2016-10-10 09:00:00 2016-10-14 17:00:00 Europe/Paris 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 […] 28 Rue du Docteur Roux, Paris, France

Projects

Project
Ongoing
4 Members

ELIXIR bio.tools – Tools Interoperability and Service Registry

Hervé Menager (PI)

The cornerstone of the ELIXIR Tools platform is the bio.tools ELIXIR Tools and Data Services Registry, a discovery portal for a wide range of key bioinformatics resources, which is developed through ELIXIR-EXCELERATE Work Package […]
Project
Completed
7 Members

NGPhylogeny.fr

Frédéric Lemoine (PI)

New Generation Phylogeny.fr: Refactoring Phylogeny.fr for innovative phylogenetic services Phylogeny.fr is one of the main server available today able to run phylogenetic analysis pipelines. In the context of scientific workflows, none of the workflow […]
Project
Ongoing
8 Members

Bioweb

Hervé Menager (PI)

Bioweb is a web portal to search and access the bioinformatics resources available at the Institut Pasteur. It provides an overview of the resources available in the central infrastructure, as well as features to identify […]
Project
Ongoing
3 Members

ARIA for hybrid structure determination on the cloud

Benjamin Bardiaux (PI)

Protein structure determination is crucial for understanding protein function, as it paves the way to the discovery of new drugs and of new approaches to control pathological biological processes. The recent advances in structural […]
Project
Ongoing
5 Members

ReGaTE

Hervé Menager (PI)

ReGaTE is a software component enabling the automated publication of Galaxy tools and workflows into the ELIXIR Tools and Data Services Registry. This registry is a web portal for the exploration of bioinformatics resources, […]

Software

Software
Ongoing
4 Members

SatelliteFinder

Eduardo Rocha (PI)

Bacteriophage–bacteria interactions are affected by phage satellites, elements that exploit phages for transfer between bacteria. Satellites can encode defense systems, antibiotic resistance genes, and virulence factors, but their number and diversity are unknown. We […]
Software
Ongoing
4 Members

NGPhylogeny.fr

Frédéric Lemoine (PI)

NGPhylogeny.fr is a Free, simple to use web service dedicated to reconstructing and analyzing phylogenetic relationships between molecular sequences.
Software
Ongoing
8 Members

SHAMAN: SHiny Application for Metagenomic ANalysis

Amine Ghozlane (PI)

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, […]

Tools

Tool
Ongoing
3 Members

ARIAweb: a server for automated NMR structure calculation

Benjamin Bardiaux (PI)

The ARIAweb server provides access to the main ARIA software functionalities (NMR data conversion and structure calculation). In addition, structure calculation results can be easily visualised, with a dedicated molecular viewer and graphical displays […]
Tool
Ongoing
12 Members

iPPI-DB Initiative

Olivier Sperandio (PI)

In order to boost the identification of low-molecular-weight drugs on protein-protein interactions (PPI), it is essential to properly collect and annotate experimental data about successful examples. This provides the scientific community with the necessary […]
Tool
Ongoing
6 Members

Pasteur Galaxy Platform

Fabien Mareuil (PI)

Galaxy is an open source, web-based platform for data intensive biomedical research. It is developed by the Galaxy Team, which is based at the part of the Center for Comparative Genomics and Bioinformatics at […]

CV

Activities

  • Pasteur Galaxy Server Maintenance
  • Web development and software development

Skills

  • Programming Languages : Python, XML
  • Versionning : Git
  • Web development : Django, Javascript, HTML 5, Bootstrap, GraphQL, Django Rest Framework
  • Galaxy : XML development, API/Bioblend expertise
  • Background in Structural Biology : Molecular Modeling, Nuclear Magnetic Resonance, Small Angle Xray Scattering, Homology Modelling

Main projects on the campus

Teaching

Education

Publications

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