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MS in mathematics

Username: lexeyka

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Location: Saint Petersburg, Russian Federation

Member since: November 2013



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Researcher/Software Engineer

Jun 2011 - Sep 2013 (2 years)

Algorithmic Biology Laboratory

Developing SPAdes genome assembler, which was<br />one of the first genome assemblers, specified for single-cell bacterial data. Duties particularly included preparing current release using C++, also optimizing time and memory consumption.<br />In addition a set of tools for an assembly quality assessment was developed using Java and Python.


MS in mathematics

Sankt-Peterburgskij Gosudarstvennyj Universitet



Anton Bankevich, Sergey Nurk, Dmitry Antipov, Alexey A. Gurevich, Mikhail Dvorkin, Alexander S. Kulikov, Valery M. Lesin, Sergey I. Nikolenko, Son Pham, Andrey D. Prjibelski, Alexey V. Pyshkin, Alexander V. Sirotkin, Nikolay Vyahhi, Glenn Tesler, Max A. A

Journal of Computational Biology

The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard

Nikolay Vyahhi, Alexey Pyshkin, Son K. Pham, Pavel Pevzner. From de Bruijn Graphs to Rectangle Graphs for Genome Assembly, Lecture Notes in Bioinformatics 7534 (2012), pp. 249-261. doi:10.1007/978-3-642-33122-0_20

Lecture Notes in Computer Science

Jigsaw puzzles were originally constructed by painting a picture on a rectangular piece of wood and further cutting it into smaller pieces with a jigsaw. The Jigsaw Puzzle Problem is to find an arrangement of these pieces that fills up the rectangle in such a way that neighboring pieces have “matching” boundaries with respect to color and texture. While the general Jigsaw Puzzle Problem is NP-complete [6], we discuss its simpler version (called Rectangle Puzzle Problem) and study the rectangle graphs, recen