After an initial degree in Biology, I started my professional career as a software developer. Following the completion of my software engineering degree at the CNAM, I joined the Institut Pasteur, where I initially worked in the “Software and Databases” group. I joined the Bioinformatics and Biostatistics Hub within the Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI) as a Research Engineer in 2017, where I lead the WINTER group.
Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This hands-on workshop will cover basic concepts and tools, including […]
ELIXIR bio.tools – Tools Interoperability and Service Registry
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 […]
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 […]
A personal database system for large scale quantitative results exploration (Cassandre, PTR 463)
Cassandre is a project of personal database system, integrating a “user-friendly” interface to manage and explore multiple sets of large-scale experimental results in biology. Large-scale experiments that generate quantitative data, such as changes in […]
BIGSdb-Pasteur is the genomic-based strain taxonomy and nomenclature platform of Institut Pasteur, powered by the BIGSdb software developed at Oxford University. This web platform hosts collections of curated, open or private databases of bacterial […]
JASS – Joint Analysis of (GWAS) Summary Statistics
JASS is a python package that handles the computation of the joint statistics over sets of selected GWAS results, and the interactive exploration of the results through a web interface. The generation of joint […]
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 […]
Flemmingsome- A Midbody Remnant Proteome database
Cytokinesis leads to the physical separation of daughter cells and concludes cell division. Final abscission occurs close to the midbody (or Flemming body), a prominent structure that matures at the center of the intercellular […]
HARIBOSS is a database of RNA-small molecules structures retrieved from the PDB database. HARIBOSS is regularly updated with all the structures resolved by X-ray, NMR, and cryo-EM, in which ligands with drug-like properties interact […]
Python-cwlgen is a python library for the generation of CWL programmatically. It supports the generation of CommandLineTool and DockerRequirement. The library works for both Python 2.7.12+ and 3.6.0.
We have recently developed tools to visualize the results of CRISPR screens and design novel guide RNA for use in bacteria. These tools are available at crispr.pasteur.fr .
This project aims at efficiently storing millions of unique molecular compounds along with some of their already calculated properties. The database named Chem-REST is able to deal with extensive sets of data: millions of […]
ToolDog – Tool Description Generator
ToolDog is a program that generates tool description from a tool entry from https://bio.tools.
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 […]
2022Methods Included, Communications of the ACM, 2022.
2022HARIBOSS: a curated database of RNA-small molecules structures to aid rational drug design, bioRxiv (2022) 10.1101/2022.05.17.492306.
2021ELIXIR and Toxicology: a community in development, F1000Research 2021, 10(ELIXIR):1129.
2021Multitrait GWAS to connect disease variants and biological mechanisms., PLoS Genet 2021 Aug; 17(8): e1009713.
2021Gene expression analysis in EBV-infected ataxia-telangiectasia cell lines by RNA-sequencing reveals protein synthesis defect and immune abnormalities., Orphanet J Rare Dis 2021 06; 16(1): 288.
2021Viral Host Range database, an online tool for recording, analyzing and disseminating virus-host interactions., Bioinformatics 2021 Feb; (): .
2021biotoolsSchema: a formalized schema for bioinformatics software description., Gigascience 2021 Jan; 10(1): .
2021The iPPI-DB initiative: A Community-centered database of Protein-Protein Interaction modulators., Bioinformatics 2021 Jan; (): .
2021Perspectives on automated composition of workflows in the life sciences., F1000Res 2021 ; 10(): 897.
2021Bioimage analysis workflows: community resources to navigate through a complex ecosystem., F1000Res 2021 ; 10(): 320.
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