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.
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Courses
Behind Evolutionary Trees: Mathematics and Algorithms in Phylogenetics – Montevideo 2019
Evolutionary trees are used in many domains, to reveal the function of genes, study the outbreak of epidemics, and set up inventories of biodiversity and its decline, among other things. Phylogenetic software programs for […]
2019-10-22 09:00:00
2019-10-24 17:00:00
Europe/Paris
Behind Evolutionary Trees: Mathematics and Algorithms in Phylogenetics – Montevideo 2019
Evolutionary trees are used in many domains, to reveal the function of genes, study the outbreak of epidemics, and set up inventories of biodiversity and its decline, among other things. Phylogenetic software programs for […]
Institut Pasteur de Montevideo, Mataojo, Montevideo Montevideo Department, Uruguay
Mathematical and Computational methods for Phylogenetics and Evolutionary Epidemiology – Havana 2019
Mathematical and Computational concepts and models are essentials in new developments of the evolutionary studies related to outbreaks of infectious diseases pandemics. Predicting, assessing and controlling potential outbreaks are key aspects of the worldwide […]
2019-10-14 09:00:00
2019-10-18 16:00:00
Europe/Paris
Mathematical and Computational methods for Phylogenetics and Evolutionary Epidemiology – Havana 2019
Mathematical and Computational concepts and models are essentials in new developments of the evolutionary studies related to outbreaks of infectious diseases pandemics. Predicting, assessing and controlling potential outbreaks are key aspects of the worldwide […]
Institute of Tropical Medicine “Pedro Kourí” (IPK), Havana, Cuba
Introduction à la Phylogénie Moléculaire : Concepts, méthodes et interprétation
Ce cours a pour objectif de donner les bases théoriques et pratiques, ainsi que les bonnes pratiques nécessaires au démarrage de travaux en phylogénie et épidémiologie moléculaires. Les sessions théoriques donneront les bases du […]
2019-10-07 09:30:00
2019-11-11 17:30:00
Europe/Paris
Introduction à la Phylogénie Moléculaire : Concepts, méthodes et interprétation
Ce cours a pour objectif de donner les bases théoriques et pratiques, ainsi que les bonnes pratiques nécessaires au démarrage de travaux en phylogénie et épidémiologie moléculaires. Les sessions théoriques donneront les bases du […]
28 Rue du Dr Roux, Paris, France
Introduction à la phylogénie moléculaire
Ce cours d’introduction à la phylogénie a pour objectif d’apporter les connaissances théoriques et les bonnes pratiques d’analyse de données par les logiciels de phylogénie. Il est ouvert aux formations doctorales et aux professionnels […]
2019-02-18 09:00:00
2019-02-22 17:00:00
Europe/Paris
Introduction à la phylogénie moléculaire
Ce cours d’introduction à la phylogénie a pour objectif d’apporter les connaissances théoriques et les bonnes pratiques d’analyse de données par les logiciels de phylogénie. Il est ouvert aux formations doctorales et aux professionnels […]
28 Rue du Dr Roux, Paris, France
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 […]
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
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 […]
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
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
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 […]
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
Transversal Projects
Projects
Software
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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2019A Fast Likelihood Method to Reconstruct and Visualize Ancestral Scenarios, Mol. Biol. Evol. 2019 Sep;36(9):2069-2085.
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2017The Role of Phylogenetics as a Tool to Predict the Spread of Resistance, J. Infect. Dis. 2017 12;216(suppl_9):S820-S823.
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2017Genome-Wide Transcriptional Start Site Mapping and sRNA Identification in the Pathogen Leptospira interrogans, Front Cell Infect Microbiol 2017;7:10.
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2016Toward community standards and software for whole-cell modeling, IEEE Trans Biomed Eng 2016 Jun;.
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2015Mimoza: web-based semantic zooming and navigation in metabolic networks, BMC Syst Biol 2015;9:10.
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2015Pantograph: A template-based method for genome-scale metabolic model reconstruction, J Bioinform Comput Biol 2015 Apr;13(2):1550006.
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2014Knowledge-based generalization of metabolic models, J. Comput. Biol. 2014 Jul;21(7):534-47.
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2014Knowledge-based generalization of metabolic networks: a practical study, J Bioinform Comput Biol 2014 Apr;12(2):1441001.
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2012LibKiSAO: a Java library for Querying KiSAO, BMC Res Notes 2012;5:520.
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2011Controlled vocabularies and semantics in systems biology, Mol. Syst. Biol. 2011;7:543.
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