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  • PhD Student
  • Physician
  • Post-doc
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  • Technician
  • Undergraduate Student
  • Veterinary
  • Visiting Scientist
  • Deputy Director of Center
  • Deputy Director of Department
  • Deputy Director of National Reference Center
  • Deputy Head of Facility
  • Director of Center
  • Director of Department
  • Director of Institute
  • Director of National Reference Center
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About

A computer scientist by training, I am applying this knowledge to solve biological problems and am particularly interested in modelling of biological systems, phylodynamics, phylogeography, knowledge inference and data visualisation.

Courses

09:30
18
Dec 2017
Course

INTRODUCTION À LA PHYLOGÉNIE MOLÉCULAIRE : CONCEPTS, METHODES ET OUTILS

Nous proposons une formation classique à la phylogénie moléculaire avec des cours théoriques portant sur les trois méthodes de construction d’arbres phylogénétiques : distance, parcimonie et maximum de vraisemblance. Nous expliquerons les concepts généraux […]
Evolutionary Bioinformatics
Bioinformatics and Biostatistics HUB
Olivier Gascuel
Frédéric Lemoine
Julien Guglielmini
Anna Zhukova
Alexis Criscuolo
Catherine Dauga
2017-12-18 09:30:00 2017-12-22 17:30:00 Europe/Paris INTRODUCTION À LA PHYLOGÉNIE MOLÉCULAIRE : CONCEPTS, METHODES ET OUTILS Nous proposons une formation classique à la phylogénie moléculaire avec des cours théoriques portant sur les trois méthodes de construction d’arbres phylogénétiques : distance, parcimonie et maximum de vraisemblance. Nous expliquerons les concepts généraux […] 25-28 Rue du Dr Roux, 75015 Paris, France
09:30
06
Mar 2017
Course

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 […]
Bioinformatics and Biostatistics HUB
Biomics
Bertrand Néron
Thomas Cokelaer
François Laurent
Anna Zhukova
Jean-Baptiste Masson
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
09:30
04
Jun 2018
Course

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 […]
Bioinformatics and Biostatistics HUB
Bertrand Néron
Anna Zhukova
Benoît Lelandais
Nicolas Maillet
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
09:00
16
Jan 2017
Course

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 […]
Bioinformatics and Biostatistics HUB
Stéphane Descorps-Declère
Marie-Agnès Dillies
Gaël Millot
Anne Biton
Stevenn Volant
Quentin Giai Gianetto
Vincent Guillemot
Nicolas Maillet
Blaise Li
Anna Zhukova
Hugo Varet
Amandine Perrin
Eric Deveaud
Bertrand Néron
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
08:00
22
Oct 2018
Course

C3BI Course: Introduction to Molecular Phylogenetics – Hong Kong 2018

General Information: This introductory course aims to give the basic theoretical and practical concepts, best practices, and software necessary to start working on molecular phylogenetics and its applications to epidemiology. The course will have […]
Bioinformatics and Biostatistics HUB
Evolutionary Bioinformatics
Hong Kong University-Pasteur Research Pole
Olivier Gascuel
Anna Zhukova
Frédéric Lemoine
Julien Guglielmini
Sebastian Duchene
2018-10-22 08:00:00 2018-10-27 19:00:00 Europe/Paris C3BI Course: Introduction to Molecular Phylogenetics – Hong Kong 2018 General Information: This introductory course aims to give the basic theoretical and practical concepts, best practices, and software necessary to start working on molecular phylogenetics and its applications to epidemiology. The course will have […] HKU-Pasteur Research Pole HKJC Building for Interdisciplinary Research 5 Sassoon Road, Pokfulam, Hong Kong

Projects

project
Ongoing
5 Members

The phylodynamics of partner notification and contact tracing in HIV epidemics

Olivier Gascuel (PI)

We develop phylodynamics models and methods to study viral epidemics, in particular HIV. This new, trendy domain is in between usual mathematical epidemiology, typically based on compartment models, and phylogenetics. The models used in […]
project
Ongoing
16 Members

Bioconvert

Thomas Cokelaer (PI)

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another. Life science uses many different formats. They may be old, or with complex syntax and converting […]
project
Ongoing
4 Members

PastML: A Fast Likelihood Method to Reconstruct and Visualize Ancestral Scenarios

Olivier Gascuel (PI)

The reconstruction of ancestral scenarios is widely used to study the evolution of characters along a phylogenetic tree, for example to infer ancestral molecular characters and their changes in time, or in phylogeography to […]
project
Ongoing
2 Members

Modelling the emergence and transmission of HIV-1 drug resistance mutations

Olivier Gascuel (PI)

Drug resistance mutations (DRM) emerge in HIV-1 viruses through selective pressure during antiviral treatment (ART). Acquired drug resistance rates vary depending on duration of ART and type of prescribed regimen. Drug resistance can then […]
project
Ongoing
6 Members

Virogenesis

Olivier Gascuel (PI)

Virus discovery and epidemic tracing from high throughput metagenomic sequencing VIROGENESIS is a research project under the EC H2020 framework (2015-2018), that will develop bioinformatics software applications to fully exploit the potential of high-throughput Next-Generation-Sequencing […]
project
Ongoing
3 Members

Systems biology of cell infection by the bacterial pathogen Listeria monocytogenes

Javier Pizarro-Cerda (PI)

In the context of the Swiss consortium InfectX (www.infectx.ch), we have previously performed siRNA, microRNA and drug screens  to investigate signaling pathways modulating invasion of host cells by the bacterial pathogen Listeria monocytogenes. In […]

CV

(EN)

Experience

since 2015, Paris FR Research Engineer @ Institut Pasteur phylodynamics, phylogeography
2014-15, Bordeaux FR Postdoc @ IBGC CNRS UMR 5095/U. of Bordeaux modelling mitochondrial metabolism
2011-14, Bordeaux FR Doctoral researcher @ Inria/U. of Bordeaux/CNRS joint project-team MAGNOME knowledge-based generalization and visualization for metabolic models
2011, Cambridge, UK Intern @ EMBL-EBI, Comp. Systems Neurobiology group Kinetic Simulation Algorithm Ontology (KiSAO) and libKiSAO
2010, Bordeaux, FR Intern @ Inria/U. of Bordeaux/CNRS joint project-team MAGNOME Magus genome annotation system
2009, Cambridge, UK Intern @ EMBL-EBI, Functional Genomics group Experimental Factor Ontology extension of search in ArrayExpress
2008-10, St. Petersburg, RU Junior software developer @ SwiftTeams

Education

2011-14 PhD, Computer Science University of Bordeaux, FR
2005-10 Specialist (BSc+MSc), Software Engineering & Math St. Petersburg State University, RU
2007-09 Alumna, Software Engineering Academy of Modern Software Engineering, RU

Publications

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