After a PhD in bioinformatics at Inria/IRISA, Université de Rennes 1, Rennes (France), under the supervision of Dominique Lavenier and Pierre Peterlongo, I did a postdoc in bioinformatics at Laboratory of Ecology and Evolution of Plankton in Stazione Zoologica Anton Dohrn of Naples, Italy. Both my thesis and my postdoc were about the Tara Oceans projet and the development of new software to analyze huge quantities of raw reads coming from metagenomics sample. I am currently occupying a research engineer position at the Hub and focus on different computing problems including metagenomics, protein assembly and several short term developments.
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Timeline
Courses
Bioinformatics program for PhD students 2023 2024
This training program in statistics, bioinformatics and image analysis, financed by INCEPTION program, begins with a mandatory common core during which we will present all the tracks, and follow short courses on computer science, […]
Bioinformatics and Biostatistics HUB
Image Analysis Hub
INCEPTION – Institut Convergence for the study of Emergence of Pathology Through Individuals and Populations
Research and Resource Centre for Scientific Informatics
Emeline Perthame
Emmanuelle Permal
Marvin Albert
Jean-Yves Tinevez
Victoire Baillet
Thomas Bigot
Pascal Campagne
Elodie Chapeaublanc
Claudia Chica
Anđela Davidović
Stephan Fischer
Amine Ghozlane
Julien Guglielmini
Vincent Guillemot
Elise Jacquemet
Bernd Jagla
Hanna Julienne
Julia Kende
Vincent Laville
Frédéric Lemoine
Gaëlle Letort
Blaise Li
Yann Loe-Mie
Hélène Lopez-Maestre
Nicolas Maillet
Sébastien MELLA
Juliette Meyer
Olivier Mirabeau
Damien Mornico
Thomas Obadia
Adrien Pain
Minh-Son Phan
Natalia Pietrosemoli
Stéphane Rigaud
Violaine Saint-André
Rachel Torchet
Hugo Varet
Amaury Vaysse
Laura Xénard
2023-10-23 09:30:00
2024-06-28 17:00:00
Europe/Paris
Bioinformatics program for PhD students 2023 2024
This training program in statistics, bioinformatics and image analysis, financed by INCEPTION program, begins with a mandatory common core during which we will present all the tracks, and follow short courses on computer science, […]
25-28 Rue du Docteur Roux, Paris, France
Bioinformatics program for PhD students 2022-2023
This training program in statistics, bioinformatics and image analysis begins with a mandatory common core during which we will present all the tracks, and follow short courses on computer science, reproducible research, experimental design […]
Bioinformatics and Biostatistics HUB
Image Analysis Hub
Expertise group : SysBio – System Bioinformatics
INCEPTION – Institut Convergence for the study of Emergence of Pathology Through Individuals and Populations
Research and Resource Centre for Scientific Informatics
Emmanuelle Permal
Emeline Perthame
Jean-Yves Tinevez
Blaise Li
Sébastien MELLA
Anđela Davidović
Pascal Campagne
Thomas Obadia
Elise Jacquemet
Violaine Saint-André
Hanna Julienne
Thomas Bigot
Frédéric Lemoine
Nicolas Maillet
Claudia Chica
Julien Guglielmini
Vincent Guillemot
Bernd Jagla
Vincent Laville
Benoît Lelandais
Gaëlle Letort
Yann Loe-Mie
Hélène Lopez-Maestre
Marion Louveaux
Olivier Mirabeau
Damien Mornico
Adrien Pain
Natalia Pietrosemoli
Stéphane Rigaud
Hugo Varet
Amaury Vaysse
Minh-Son Phan
Marvin Albert
2022-10-21 09:30:00
2023-06-30 18:00:00
Europe/Paris
Bioinformatics program for PhD students 2022-2023
This training program in statistics, bioinformatics and image analysis begins with a mandatory common core during which we will present all the tracks, and follow short courses on computer science, reproducible research, experimental design […]
25-28 Rue du Docteur Roux, Paris, France
Bioinformatics program for PhD students 2020-2021
This mandatory training program, required for all Institut Pasteur PhD students, begins with a group of common core courses including a knowledge base in reproducible research, R Programming and Statistics. Each student then can […]
Image Analysis Hub
Bioinformatics and Biostatistics HUB
INCEPTION – Institut Convergence for the study of Emergence of Pathology Through Individuals and Populations
Computational Biology
Center for Technological Resources and Research
Vincent Guillemot
Christophe Malabat
Jean-Yves Tinevez
Marie-Agnès Dillies
Frédéric Lemoine
Nicolas Maillet
Blaise Li
Stevenn Volant
Pascal Campagne
Hugo Varet
Hanna Julienne
Violaine Saint-André
Julien Guglielmini
Thomas Bigot
Quentin Giai Gianetto
Claudia Chica
Rachel Legendre
Adrien Pain
Natalia Pietrosemoli
Emeline Perthame
Stéphane Rigaud
Benoît Lelandais
Dmitry Ershov
Sébastien MELLA
Anđela Davidović
Thomas Obadia
Véronique Hourdel
Amine Ghozlane
Alexis Criscuolo
Amaury Vaysse
2020-10-15 09:30:00
2021-06-03 17:00:00
Europe/Paris
Bioinformatics program for PhD students 2020-2021
This mandatory training program, required for all Institut Pasteur PhD students, begins with a group of common core courses including a knowledge base in reproducible research, R Programming and Statistics. Each student then can […]
25-28 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
Morning session – Introduction to NGS data analysis
The Hub of Bioinformatics and Biostatistics at the Institut Pasteur organizes thematic courses open to everybody. The second session, entitled “Introduction to NGS data analysis” will take place every Tuesday, from the May 10th […]
2016-05-10 09:00:00
2016-06-28 12:00:00
Europe/Paris
Morning session – Introduction to NGS data analysis
The Hub of Bioinformatics and Biostatistics at the Institut Pasteur organizes thematic courses open to everybody. The second session, entitled “Introduction to NGS data analysis” will take place every Tuesday, from the May 10th […]
28 Rue du Dr Roux, Paris, France
Projects
Software
Tools
Former Teams
CV
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2013PhD in Bioinformatics
Genscale team, Inria/IRISA, Université de Rennes 1, Rennes, France
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2010Research Master’s Degree of Science
Université de Rennes 1, Rennes, France
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2008Bachelor’s Degree in Computer Science
Université de Bretagne Sud, Vannes, France
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2006Higher National Diploma of Computer Science
IUT Informatique, Université de Bretagne Sud, Vannes, France
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2004French Scientific Baccalaureate
Lycée Joubert, Ancenis, France
Experiences
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2015Research engineer
Pasteur (HUB, department C3BI)
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2014Postdoctoral position in Bioinformatics
Stazione Zoologica Anton Dohrn of Naples, Italy (Laboratory of Ecology and Evolution of Plankton)
Publications
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2022Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems., Elife 2022 Aug; 11(): .
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2019Rapid Peptides Generator: fast and efficient in silico protein digestion, NAR Genomics and Bioinformatics 2020 Mar;2(1):lqz004.
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2019Community‐Level Responses to Iron Availability in Open Ocean Plankton Ecosystems, Global Biogeochemical Cycles 2019 Jan;33(3):391-419.
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2017Marine diatoms change their gene expression profile when exposed to microscale turbulence under nutrient replete conditions, Sci. Rep. 7, 016303–11 (2017).
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2017Listeriomics: an Interactive Web Platform for Systems Biology of Listeria, mSystems 2017 Mar-Apr;2(2).
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2014COMMET: comparing and combining multiple metagenomic datasets, BIBM, IEEE 2014 Nov.
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2013Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species, Gigascience 2013;2(1):10.
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2012Compareads: comparing huge metagenomic experiments, BMC Bioinformatics 2012;13 Suppl 19:S10.
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2012Genome-wide patterns of divergence during speciation: the lake whitefish case study, Philos. Trans. R. Soc. Lond., B, Biol. Sci. 2012 Feb;367(1587):354-63.
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2011Assemblathon 1: a competitive assessment of de novo short read assembly methods, Genome Res. 2011 Dec;21(12):2224-41.
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+View full list of publications