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  • Visiting Scientist
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  • Director of Center
  • Director of Department
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Scientific Fields
Diseases
Organisms
Applications
Technique

Courses

09:30
06
Mar 2017
Course

Scientific Programming in Python

The ever growing usage of high throughput technologies in Biology is revolutionizing the life sciences and profoundly changing its practices. Scripting languages are used on a daily basis in life science labs in order […]
2017-03-06 09:30:00 2017-03-18 17:00:00 Europe/Paris Scientific Programming in Python The ever growing usage of high throughput technologies in Biology is revolutionizing the life sciences and profoundly changing its practices. Scripting languages are used on a daily basis in life science labs in order […] 25 Rue du Dr Roux, 75015 Paris, France
09:30
04
Jun 2018
Course

Introduction to Python Programming

Python is often used to learn programming as it is very readable and easy to write. Python is a very popular language in bioinformatics where many programs and libraries are written in python. This […]
2018-06-04 09:30:00 2018-06-08 17:00:00 Europe/Paris Introduction to Python Programming Python is often used to learn programming as it is very readable and easy to write. Python is a very popular language in bioinformatics where many programs and libraries are written in python. This […] 25 Rue du Dr Roux, 75015 Paris, France
09:00
16
Jan 2017
Course

Introduction to data analysis

This five weeks graduate level course will give participants basic skills and hands-on training in biostatistics. It will cover all the steps of an analysis workflow : design, collection, curation, hypothesis testing and data […]
2017-01-16 09:00:00 2017-02-17 13:00:00 Europe/Paris Introduction to data analysis This five weeks graduate level course will give participants basic skills and hands-on training in biostatistics. It will cover all the steps of an analysis workflow : design, collection, curation, hypothesis testing and data […] 28 Rue du Docteur Roux, Paris, France

Projects

project
Ongoing
16 Members

Bioconvert

Thomas Cokelaer (PI)

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another. Life science uses many different formats. They may be old, or with complex syntax and converting […]
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
Completed
2 Members

Mobyle

Bertrand Néron (PI)

For the biologist, running bioinformatics analyses involves a time-consuming management of data and tools. Users need support to organize their work, retrieve parameters and reproduce their analyses. They also need to be able to […]

Software

software
Ongoing
2 Members

Counter RNAseq Window (CRAW)

Bertrand Néron (PI)

CRAW is a package which aim to compute and visualize the coverage of RNA seq experiments. The main feature of this tools is the coverage is computed on the both strands, and is centred […]
software
Ongoing
3 Members

IntegronFinder

Eduardo Rocha (PI)

IntegronFinder is a program that detects integrons in DNA sequences. The program is available on a webserver (Galaxy), or by command line (IntegronFinder on github). Integrons are major genetic element, notorious for their major […]
software
Ongoing
5 Members

CONJscan-T4SSscan

Eduardo Rocha (PI)

Scans a set of protein sequences for type IV secretion systems and relaxases using HMM profiles. See Guglielmini et al. (2011) for our criteria to class loci on the basis of this output. Except […]
software
Ongoing
4 Members

MacSyFinder & MacSyView

Eduardo Rocha (PI)

Macromolecular System Finder (MacSyFinder) provides a flexible framework to model the properties of molecular systems (cellular machinery or pathway) including their components, evolutionary associations with other systems and genetic architecture. Modelled features also include […]

Tools

tool
Ongoing
3 Members

TXSSdb, a database of protein secretion systems

Eduardo Rocha (PI)

The database TXSSdb includes all results from our works on the detection of protein secretion systems in 1,528 complete genomes of bacteria with diderm-LPS cellular enveloppes. It is by far the most complete database […]
tool
Ongoing
6 Members

TXSScan – models and profiles for protein secretion systems

Eduardo Rocha (PI)

Protein secretion systems are key virulence factors of all major bacterial pathogens with an LPS-containing outer membrane: Shigella, Escherichia coli, Yersinia pestis, Salmonella, Pseudomonas aeruginosa, Helicobacter pylori, Vibrio cholerae, etc. Protein secretion systems are […]
tool
Ongoing
2 Members

Secreton – Non-Flagellar Type III Secretion Systems in sequenced genomes

Eduardo Rocha (PI)

Non-Flagellar Type III Secretion Systems (NF-T3SS, or injectisomes) are bacterial machineries partially homologous to the bacterial flagellum, which allow direct injection of bacterial effectors from bacterial cytoplasm to eukaryotic cells via a molecular needle […]
tool
Completed
3 Members

ConjDB – a database of conjugative & mobilization systems and T4SS

Eduardo Rocha (PI)

This website allows to query a dataset of 947 conjugative systems, 646 non-conjugative T4SS and 1,180 mobilization systems retrieved from 2,269 complete genome sequences. These systems were detected with protein profiles of T4SS components, […]

CV

Activities

Skills

  • Strong programming experience in Python.
  • Software architecture and design.
  • NoSQL DataBase (MongoDB, CouchDB)
  • XML/YAML
  • continuous integration (github/travis-CI/readthedocs, gitlab/gitlab-CI)
  • containers (Docker, Singularity)
  • linux (Gentoo, Xubuntu)
  • IFB developer

Main projects on the campus

Teaching

Education

  • 2002 Phd in Molecular and cellular biology.
    • “Rôle de deux protéines QN1 et PATF impliquées dans l’arrêt de prolifération des cellules de la neurorétine aviaire au cours du developpement”.
  • 2001 “Informatique En Biologie” course (Pasteur)

Publications

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