Oleg Shpynov

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.

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

Publications

PubTrends: a scientific literature explorer

August 2021

Oleg Shpynov, Kapralov Nikolai

BCB '21: Proceedings of the 12th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, Article No.: 72, Pages 1

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FARM: hierarchical association rule mining and visualization method

August 2021

Petr Tsurinov, Oleg Shpynov, Nina Lukashina, Daria Likholetova, Maxim Artyomov

BCB '21: Proceedings of the 12th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, Article No.: 70, Pages 1

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SPAN and JBR: analysis and visualization toolkit for peak calling

August 2021

Oleg Shpynov , Roman Chernyatchik, Petr Tsurinov, Maxim Artyomov

BCB '21: Proceedings of the 12th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, Article No.: 69, Pages 1

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Semi-supervised peak calling with SPAN and JBR Genome Browser

May 2021

Oleg Shpynov, Aleksei Dievskii, Roman Chernyatchik, Petr Tsurinov, Maxim N Artyomov

Bioinformatics, btab376

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Automatic generation of reviews of scientific papers

December 2020

Anna Nikiforovskaya, Nikolai Kapralov, Anna Vlasova, Oleg Shpynov, Aleksei Shpilman

ICMLA2020

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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

Immunity

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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

Nature Aging

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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

bioRxiv preprint

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Bioinformatics Institute 2018/19 project abstracts

June 2019

O. Shpynov, A. Dievskii, P. Tsurinov, et al

Saint-Petersburg, ISBN 978-5-6043094-2-1

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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

Proceedings of the 17th European conference on computational biology

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POSTER: Semi-supervised solution for peak calling

July 2018

Oleg Shpynov, Aleksei Dievskii, Roman Chernyatchik, Evgeny Kurbatsky, Petr Tsurinov, Maxim N. Artyomov

Proceedings of Biata2018 Bioinformatics: from algorithms to applications

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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

Journal of Experimental Medicine

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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

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