Oleg Shpynov
Research Groups
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 postgraduate student in SPbSU. Graduated from Bioinformatics Institute in 2012, where he studied Molecular Biology and Bioinformatics.
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 machine learning, information retrieval, and bioinformatics.
From 2018 Oleg takes part in Systems Biology Seminars organized together with ITMO University and Washington University in St.Louis. From 2019 he teaches “Computational methods of epigenetics data analysis” in Bioinformatics and Systems Biology Master’s Program at ITMO University. Oleg regularly speaks at schools and seminars on Bioinformatics and mentors students in Bioinformatics Institute, Higher School of Economics, and Computer Science Center.
Professional Activity
- Speaker at Bioinformatics Institute Summer School, 2020
- Speaker at Math Winter School URFU Mathematics in Biology, 2020
- Certificate Deep Learning nanodegree program at Udacity, 2019
- Speaker at Bioinformatics Institute Summer School, Moscow, 2019
- Speaker at Systems Biology Workshop by IFMO university, Bioinformatics Insitute and Washington University in St.Louis, 2019
- Lectures on epigenetics data analysis for system biology masters program at IFMO university: https://research.jetbrains.org/news/epigenetics-data-analysis-tutorial, 2019
- Semi-supervised solution for robust peak calling of Low Input ChIP-Seq, a poster at ECCB, 2018
- Semi-supervised peak calling solution, a poster at Biata: The Second Annual Scientific Conference, from algorithms to applications, 2018
- Machine Learning and Intelligence School, Microsoft Research, 2015
- Yandex school of Data Analysis Conference, Yandex, 2014
Publications
SPAN and JBR: analysis and visualization toolkit for peak calling
August 2021
Oleg Shpynov , Roman Chernyatchik, Petr Tsurinov, Maxim Artyomov
FARM: hierarchical association rule mining and visualization method
August 2021
Petr Tsurinov, Oleg Shpynov, Nina Lukashina, Daria Likholetova, Maxim Artyomov
PubTrends: a scientific literature explorer
August 2021
Oleg Shpynov, Kapralov Nikolai
Semi-supervised peak calling with SPAN and JBR Genome Browser
May 2021
Oleg Shpynov, Aleksei Dievskii, Roman Chernyatchik, Petr Tsurinov, Maxim N Artyomov
Automatic generation of reviews of scientific papers
December 2020
Anna Nikiforovskaya, Nikolai Kapralov, Anna Vlasova, Oleg Shpynov, Aleksei Shpilman
Comprehensive Profiling of an Aging Immune System Reveals Clonal GZMK+ CD8+ T Cells as Conserved Hallmark of Inflammaging
December 2020
Denis A. Mogilenko, Oleg Shpynov, Prabhakar Sairam Andhey, Laura Arthur, Amanda Swain, Ekaterina Esaulova, Simone Brioschi, Irina Shchukina, Martina Kerndl, Monika Bambouskova, Zhangting Yao, Anwesha Laha, Konstantin Zaitsev, Samantha Burdess, Susan Gillfilan, Sheila A. Stewart, Marco Colonna, Maxim N.Artyomov
Enhanced epigenetic profiling of classical human monocytes reveals a specific signature of healthy aging in the DNA methylome
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
Epigenetic aging of classical monocytes from healthy individuals
May 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
Bioinformatics Institute 2018/19 project abstracts
June 2019
O. Shpynov, A. Dievskii, P. Tsurinov, et al
POSTER: Semi-supervised solution for robust peak calling of Low Input ChIP-Seq
September 2018
Oleg Shpynov, Aleksei Dievskii, Roman Chernyatchik, Evgeny Kurbatsky, Petr Tsurinov and Maxim Artyomov
POSTER: Semi-supervised solution for peak calling
July 2018
Oleg Shpynov, Aleksei Dievskii, Roman Chernyatchik, Evgeny Kurbatsky, Petr Tsurinov, Maxim N. Artyomov
Bhlhe40 is an essential repressor of IL-10 during Mycobacterium tuberculosis infection
May 2018
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
POSTER: Systems Level Characterization of the Epigenomic Changes During Healthy Aging in the Human Blood Monocyte
October 2016
Bagaitkar Juhi, Bambouskova Monica, Oltz Eugene, Porter Sofia, Collins Patrick, Shpynov Oleg, German Demidov, Konstantin Zaytsev