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.
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 […]
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 in the UK
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 […]
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 […]
Institut Pasteur, Paris, France
|2014 – 2015||
|2011 – 2014||
|2008 – 2010||
SwiftTeams, St. Petersburg, Russia
|Junior software developer|
|2011 – 2014||University of Bordeaux, France||PhD, Computer Science|
|2005 – 2010||Saint Petersburg State University,
Mathematics and Mechanics Faculty, Russia
|Specialist (equiv. to BSc+MSc), Software Engineering|
|2007 – 2009||Academy of Modern Software Engineering, St. Petersburg, Russia||Alumnus, Software Engineering|
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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