A computer scientist by training, I am applying this knowledge to solve biological problems and am particularly interested in modelling of biological systems, knowledge inference, ontologies and data visualisation.
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 […]
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 […]
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 […]
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 […]
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 […]
The phylodynamics of partner notification and contact tracing in HIV epidemics
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 […]
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 […]
PastML: A Fast Likelihood Method to Reconstruct and Visualize Ancestral Scenarios
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 […]
Modelling the emergence and transmission of HIV-1 drug resistance mutations
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 […]
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 […]
Systems biology of cell infection by the bacterial pathogen Listeria monocytogenes
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 […]
|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|
|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|
2017The Role of Phylogenetics as a Tool to Predict the Spread of Resistance, J. Infect. Dis. 2017 Oct;.
2017Genome-Wide Transcriptional Start Site Mapping and sRNA Identification in the Pathogen Leptospira interrogans, Front Cell Infect Microbiol 2017;7:10.
2016Toward community standards and software for whole-cell modeling, IEEE Trans Biomed Eng 2016 Jun;.
2015Mimoza: web-based semantic zooming and navigation in metabolic networks, BMC Syst Biol 2015;9:10.
2015Pantograph: A template-based method for genome-scale metabolic model reconstruction, J Bioinform Comput Biol 2015 Apr;13(2):1550006.
2014Knowledge-based generalization of metabolic models, J. Comput. Biol. 2014 Jul;21(7):534-47.
2014Knowledge-based generalization of metabolic networks: a practical study, J Bioinform Comput Biol 2014 Apr;12(2):1441001.
2012LibKiSAO: a Java library for Querying KiSAO, BMC Res Notes 2012;5:520.
2011Controlled vocabularies and semantics in systems biology, Mol. Syst. Biol. 2011;7:543.
2010Modeling sample variables with an Experimental Factor Ontology, Bioinformatics 2010 Apr;26(8):1112-8.
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