Biography

I Graduated from St. Petersburg State University, the Faculty of Mathematics and Mechanics, Software Engineering Department. In 2012 completed a year-long course on molecular biology and bioinformatics at Bioinformatics Institute.

My main research interests are human aging mechanisms, human epigenetics, DNA methylation, and integrational data analysis of epigenetic data. Also, I'm interested in Deep Learning and develop IoT as hobby projects.

I teach "Epigenetics" in the international Master's Degree Program Bioinformatics and Systems Biology at St. Petersburg ITMO University, "Bioinformatics methods for epigenetics data" in Bioinformatics Institute, and mentor student projects in St. Petersburg ITMO University, Bioinformatics Institute and Higher School of Economics.

2012 – now Researcher at JetBrains Research, BioLabs Group.

2020 now PhD student in computational biology at St. Petersburg ITMO University.

2006 – 2012 Participated in the development of major JetBrains products: IntelliJ IDEA and TeamCity. I was one of the key developers in the RubyMine project, an integrated development environment for Ruby programming language and Ruby-based web frameworks.

2005 – 2006 Developer at the Apache Harmony - an Open Source Java SE Implementation.

2005 – 2008 Participated in various projects related to Domain-Specific Languages and Visual Modeling.

Professional Activity

Academic Advising

Was a mentor in more than 7 student projects including Master's degree supervising:

  • Kalinin V., Masters 'GEO Data Server'

Projects

  • SPAN Peak Analyzer and JBR Genome Browser can be used separately as general-purpose peak caller and genome browser, respectively. However, together, they can serve as a complete solution for peak calling. The semi-supervised peak calling approach is capable of improving peaks consistency in datasets with different signal-to-noise ratio, as well as obtaining the best peak calling results for individual samples.
  • Snakecharm is a plugin for PyCharm and any other IntellIJ platform-based IDEs providing rich editing and refactoring capabilities for Snakemake programming language.
  • JBR - genome browser with peak calling functionality, multiple locations mode, and more
  • CMeth Completed
    CMeth is a tool for analysing and comparing replicated WGBS data

Publications

  • Irina Shchukina, Juhi Bagaitkar, Oleg Shpynov, Ekaterina Loginicheva, Sofia Porter, Denis A. Mogilenko, Erica Wolin, Patrick Collins, German Demidov, Mykyta Artomov, Konstantin Zaitsev, Sviatoslav Sidorov, Christina Camell, Monika Bambouskova, Laura Arthur, Amanda Swain, Alexandra Panteleeva, Aleksei Dievskii, Evgeny Kurbatsky, Petr Tsurinov, Roman Chernyatchik, Vishwa Deep Dixit, Marko Jovanovic, Sheila A. Stewart, Mark J. Daly, Sergey Dmitriev, Eugene M. Oltz & Maxim N. Artyomov
    Nature Aging, November 2020
  • Irina Shchukina, Juhi Bagaitkar, Oleg Shpynov, Ekaterina Loginicheva, Sofia Porter, Denis A. Mogilenko, Erica Wolin, Patrick Collins, German Demidov, Mykyta Artomov, Konstantin Zaitsev, Sviatoslav Sidorov, Christina Camell, Monika Bambouskova, Laura Arthur, Amanda Swain, Alexandra Panteleeva, Aleksei Dievskii, Evgeny Kurbatsky, Petr Tsurinov, Roman Chernyatchik, Vishwa Deep Dixit, Marko Jovanovic, Sheila A. Stewart, Mark J. Daly, Sergey Dmitriev, Eugene M. Oltz, Maxim N. Artyomov
    bioRxiv preprint, May 2020
  • Kalinin Vladislav Il'ich, Cherniatchik Roman Igorevich
    ПРОЦЕССЫ УПРАВЛЕНИЯ И УСТОЙЧИВОСТЬ, 2019
  • Oleg Shpynov, Aleksei Dievskii, Roman Chernyatchik, Evgeny Kurbatsky, Petr Tsurinov and Maxim Artyomov
    Proceedings of the 17th European conference on computational biology, September 2018
  • Oleg Shpynov, Aleksei Dievskii, Roman Chernyatchik, Evgeny Kurbatsky, Petr Tsurinov, Maxim N. Artyomov
    Proceedings of Biata2018 Bioinformatics: from algorithms to applications, July 2018
  • BioLabs Researcher
    • DNA Methylation analysis
    • SPAN Semi-supervised peak calling & JBR Genome browser
    • SnakeCharm Plugin