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.
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Timeline
https://orcid.org/0000-0002-0220-0482Courses
Analyse de données reproductible
La production de données de plus en plus massives, le développement de méthodes d’analyse de plus en plus complexes, et le nombre en constante augmentation d’outils disponibles amènent les scientifiques à développer des chaines de traitement (workflows) de plus […]
2021-06-21 09:00:00
2021-06-29 17:00:00
Europe/Paris
Analyse de données reproductible
La production de données de plus en plus massives, le développement de méthodes d’analyse de plus en plus complexes, et le nombre en constante augmentation d’outils disponibles amènent les scientifiques à développer des chaines de traitement (workflows) de plus […]
28 Rue du Dr Roux, Paris, France
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
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
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
Software
Tools
CV
Activities
- Help scientists to develop new tools (architecture, design, implementation).
- O|B|F (http://www.open-bio.org/) member.
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, Apptainer/Singularity)
- linux (Gentoo, Xubuntu)
Main projects on the campus
- MacsyFinder (ongoing project)
- IntegronFinder (ongoing project)
- correlationplus (former project)
- bioconvert (former project)
- CRAW (former project)
- Mobyle (former project)
- http://Mobyle.pasteur.fr
- Mobyle: a new full web bioinformatics framework
access to my projects on github
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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2022IntegronFinder 2.0: Identification and Analysis of Integrons across Bacteria, with a Focus on Antibiotic Resistance in Klebsiella., Microorganisms 2022 Mar; 10(4): .
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2021Extracting Dynamical Correlations and Identifying Key Residues for Allosteric Communication in Proteins by correlationplus., J Chem Inf Model 2021 Oct; 61(10): 4832-4838.
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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.
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2018Antisense transcriptional interference mediates condition-specific gene repression in budding yeast, Nucleic Acids Res. 2018 May;.
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2017Abundance and co-occurrence of extracellular capsules increase environmental breadth: Implications for the emergence of pathogens, PLoS Pathog. 2017 Jul;13(7):e1006525.
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2016Identification and analysis of integrons and cassette arrays in bacterial genomes., Nucleic Acids Res. 2016 Apr 29. pii: gkw319..
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2016Identification of protein secretion systems in bacterial genomes, Scientific Reports 6, 23080 (2016).
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2014MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems, PLoS ONE 2014;9(10):e110726.
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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.
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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..
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