I work as Research Software Engineer in the Bioinformatics and Biostatistics HUB of Institut Pasteur. My main mission is to help researchers to create the most efficient, scalable, and sustainable research codes possible in order to enable new scientific advances.
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 […]
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 […]
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 […]
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 […]
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 […]
Counter RNAseq Window (CRAW)
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 […]
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 […]
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 […]
MacSyFinder & MacSyView
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 […]
TXSSdb, a database of protein secretion systems
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 […]
TXSScan – models and profiles for protein secretion systems
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 […]
Secreton – Non-Flagellar Type III Secretion Systems in sequenced genomes
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 […]
ConjDB – a database of conjugative & mobilization systems and T4SS
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, […]
- Help scientists to develop new tools (architecture, design, implementation).
- animate the Python Working Group at pasteur .
- O|B|F (http://www.open-bio.org/) member.
- Strong programming experience in Python.
- Software architecture and design.
- NoSQL DataBase (MongoDB, CouchDB)
- continuous integration (github/travis-CI/readthedocs, gitlab/gitlab-CI)
- containers (Docker, Singularity)
- linux (Gentoo, Xubuntu)
Main projects on the campus
- MacsyFinder (ongoing project)
- IntegronFinder (ongoing project)
- correlationplus(ongoing projetct)
- CRAW (former project)
- Mobyle (former project)
- Mobyle: a new full web bioinformatics framework
- access to my projects on github
- 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)
2018CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins, Nucleic Acids Res. 2018 Jul;46(W1):W246-W251.
2018Antisense transcriptional interference mediates condition-specific gene repression in budding yeast, Nucleic Acids Res. 2018 May;.
2017Abundance and co-occurrence of extracellular capsules increase environmental breadth: Implications for the emergence of pathogens, PLoS Pathog. 2017 Jul;13(7):e1006525.
2016Identification and analysis of integrons and cassette arrays in bacterial genomes., Nucleic Acids Res. 2016 Apr 29. pii: gkw319..
2016Identification of protein secretion systems in bacterial genomes, Scientific Reports 6, 23080 (2016).
2014MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems, PLoS ONE 2014;9(10):e110726.
2014Key components of the eight classes of type IV secretion systems involved in bacterial conjugation or protein secretion, Nucleic Acids Res. 2014 May;42(9):5715-27.
2012Bioinformatics Applications Discovery and Composition with the Mobyle Suite and MobyleNet, Bioinformatics applications discovery and composition with the mobyle suite and mobylenet." Resource Discovery. Springer Berlin Heidelberg, 2012. 11-22..
2009Mobyle: a new full web bioinformatics framework, Bioinformatics 2009 Nov;25(22):3005-11.
2002Activated MAPK/ERK kinase (MEK-1) induces transdifferentiation of pigmented epithelium into neural retina, Dev. Biol. 2002 Aug;248(2):251-64.
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