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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 […]
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
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 […]
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
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 […]
Olivier Gascuel (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 […]
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 […]
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 […]
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, […]
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 […]
- Pasteur Galaxy Server Maintenance
- Web development and software development
- Programming Languages : Python, XML
- Versionning : Git, SVN
- 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
- Future directory of bioinformatics resources at the Institut Pasteur
- Pasteur Teaching : Galaxy Initiation
- External Teaching : Galaxy4Bioinformatics
- 2011 : PhD Analyse des Génomes et Modélisation Moléculaire, University of Paris VII, Paris. DaDiModO, a genetic algorithm for modular proteins study with NMR and SAXS data. Application to the S1 ribosomal protein of Escherichia coli.
2018Community-Driven Data Analysis Training for Biology, Cell Syst 2018 Jun;6(6):752-758.e1.
2017Galaxy@pasteur, Mareuil F, Doppelt-Azeroual O and Ménager H. A public Galaxy platform at Pasteur used as an execution engine for web services [version 1; not peer reviewed]. F1000Research 2017, 6:1030 (poster) (doi: 10.7490/f1000research.1114334.1) .
2017ReGaTE: Registration of Galaxy Tools in Elixir, Gigascience 2017 Jun;6(6):1-4.
2017Scientific workflows for computational reproducibility in the life sciences: Status, challenges and opportunities, Future Generation Computer Systems.
2015Tools and data services registry: a community effort to document bioinformatics resources, Nucleic Acids Res. 2015 Nov;.
2015Improved reliability, accuracy and quality in automated NMR structure calculation with ARIA, J. Biomol. NMR 2015 Aug;62(4):425-38.
2011Grid computing for improving conformational sampling in NMR structure calculation, Bioinformatics 2011 Jun;27(12):1713-4.
2008S1 ribosomal protein functions in translation initiation and ribonuclease RegB activation are mediated by similar RNA-protein interactions: an NMR and SAXS analysis, J. Biol. Chem. 2008 May;283(19):13289-301.
2007A simple genetic algorithm for the optimization of multidomain protein homology models driven by NMR residual dipolar coupling and small angle X-ray scattering data, Eur. Biophys. J. 2007 Dec;37(1):95-104.