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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
Projets
Logiciel
Outils
CV
Activities
- Pasteur Galaxy Server Maintenance
- Web development and software development
Skills
- Programming Languages : Python, XML
- Versionning : Git
- Web development : Django, Javascript, HTML 5, Bootstrap, GraphQL, Django Rest Framework
- 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
- InDeep Web
- A web interface for InDeep software https://gitlab.pasteur.fr/InDeep/InDeep
- Galaxy
- https://galaxy.pasteur.fr
- To ask for a new tool, contact galaxy@pasteur.fr
- iPPI-DB
- https://ippidb.pasteur.fr
- Rachel Torchet, Karen Druart, Luis Checa Ruano, Alexandra Moine-Franel, Hélène Borges, Olivia Doppelt-Azeroual, Bryan Brancotte, Fabien Mareuil, Michael Nilges, Hervé Ménager, Olivier Sperandio, The iPPI-DB initiative: a community-centered database of protein–protein interaction modulators, Bioinformatics, Volume 37, Issue 1, 1 January 2021, Pages 89–96, https://doi.org/10.1093/bioinformatics/btaa1091
- https://ippidb.pasteur.fr
- ARIAweb
- https://ariaweb.pasteur.fr a web interface for ARIA
- Wolfgang Rieping, Michael Habeck, Benjamin Bardiaux, Aymeric Bernard, Thérèse E. Malliavin, Michael Nilges, ARIA2: Automated NOE assignment and data integration in NMR structure calculation, Bioinformatics, Volume 23, Issue 3, 1 February 2007, Pages 381–382, https://doi.org/10.1093/bioinformatics/btl589
- Fabrice Allain, Fabien Mareuil, Hervé Ménager, Michael Nilges, Benjamin Bardiaux, ARIAweb: a server for automated NMR structure calculation, Nucleic Acids Research, Volume 48, Issue W1, 02 July 2020, Pages W41–W47, https://doi.org/10.1093/nar/gkaa362
- https://ariaweb.pasteur.fr a web interface for ARIA
- ReGaTe
- https://github.com/C3BI-pasteur-fr/ReGaTE
- http://regate.readthedocs.org/en/latest/
- Olivia Doppelt-Azeroual, Fabien Mareuil, Eric Deveaud, Matúš Kalaš, Nicola Soranzo, Marius van den Beek, Björn Grüning, Jon Ison, Hervé Ménager, ReGaTE: Registration of Galaxy Tools in Elixir, GigaScience, Volume 6, Issue 6, June 2017, gix022, https://doi.org/10.1093/gigascience/gix022
Teaching
- Pasteur Teaching : Galaxy Initiation
- External Teaching : Galaxy4Bioinformatics
Education
- 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.
Publications
Télécharger-
2024A comprehensive dataset of protein-protein interactions and ligand binding pockets for advancing drug discovery, Scientific Data , 2024, 11 (1), pp.402. ⟨10.1038/s41597-024-03233-z⟩.
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2021The iPPI-DB initiative: a community-centered database of protein-protein interaction modulators., Bioinformatics 2021 Apr; 37(1): 89-96.
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2020ARIAweb: a server for automated NMR structure calculation., Nucleic Acids Res. 2020 May; (): .
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2019NGPhylogeny.fr: new generation phylogenetic services for non-specialists, Nucleic Acids Res. 2019 Jul;47(W1):W260-W265.
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2018Community-Driven Data Analysis Training for Biology, Cell Syst 2018 Jun;6(6):752-758.e1.
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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) .
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2017ReGaTE: Registration of Galaxy Tools in Elixir, Gigascience 2017 Jun;6(6):1-4.
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2017Scientific workflows for computational reproducibility in the life sciences: Status, challenges and opportunities, Future Generation Computer Systems.
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2015Tools and data services registry: a community effort to document bioinformatics resources, Nucleic Acids Res. 2015 Nov;.
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2015Improved reliability, accuracy and quality in automated NMR structure calculation with ARIA, J. Biomol. NMR 2015 Aug;62(4):425-38.
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