Oleg Shpynov

Biography

Oleg leads bioinfomatics group at JetBrains Research laboratory. Works in the laboratory since 2013.

In 2008 Oleg graduated cum laude from the Mathematics and Mechanics Faculty of the St. Petersburg State University. In 2008-2010 he was a Ph.D. student in SPbSU, faculty of mathematics and mechanics, system programming department. Graduated from Bioinformatics Institute in 2012, where he studied Molecular Biology and Bioinformatics. At the moment Oleg is a Ph.D. candidate.

Previously he took part in the development of major JetBrains products: flagship tool IntellIJ IDEA, PyCharm, IdeaVIM (vim emulation plugin, 7+mln downloads), etc. Creator of the Rubymine Integrated Development Environment for Ruby programming language. His main focus was on the analysis of source code in programming languages, starting from lexical analysis to advanced type system development and source code semantic verifications.

His research interests include bioinformatics, machine learning, and information retrieval.

Oleg teaches "Bioinformatics methods for epigenetics data" in Bioinformatics Institute, and mentors student projects in Bioinformatics Institute, Higher School of Economics, and Computer Science Center.

Professional Activity

Academic Advising

More than 10 projects including 2 master dissertations were successfully defended under Oleg's supervision.

Projects

  • Epigenetic changes in aging human monocytes - joint research project of Healthy Aging in collaboration with Maxim Artyomov’s laboratory at Washington University in St. Louis.
  • Semisupervised Peak Analyzer
  • JBR - genome browser with peak calling functionality, multiple locations mode, and more
  • 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.
  • Automated Ishikawa Fishbone Diagram construction for epigenetics data
  • Pubtrends is a new scientific publications analysis service. http://bit.ly/pubtrends
  • 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
    bioRxiv preprint, May 2020
  • O. Shpynov, A. Dievskii, P. Tsurinov, et al
    Saint-Petersburg, ISBN 978-5-6043094-2-1, 2019
  • Jeremy P. Huynh, Chih-Chung Lin, Jacqueline M. Kimmey, Nicholas N. Jarjour, Elizabeth A. Schwarzkopf, Tara R. Bradstreet, Irina Shchukina, Oleg Shpynov, Casey T. Weaver, Reshma Taneja, Maxim N. Artyomov, Brian T. Edelson, Christina L. Stallings
    Journal of Experimental Medicine, May 2018
  • BioLabs Head of group, Researcher