Alexey Gurevich

Senior Research Fellow

Full name in native language: Алексей Александрович Гуревич

Birthday: 21 March 1989. Married, has a daughter (born in May 2015) and a son (born in December 2017).

Profiles: Google Scholar, LinkedIn.

Career

Center for Algorithmic Biotechnology, St. Petersburg State University, Senior Research Scientist, 2019–present time

Center for Algorithmic Biotechnology, St. Petersburg State University, Research Scientist, 2018–2019

Center for Algorithmic Biotechnology, St. Petersburg State University, Junior Research Fellow, 2015–2017

Algorithmic Biology Lab, St. Petersburg Academic University, Junior Research Fellow, 2011–2015

Algorithmic Biology Lab, St. Petersburg Academic University, Intern, 2011

St. Petersburg State Polytechnic University, Researcher, 2009-2010

Visiting Research

The Kohlbacher lab (Applied Bioinformatics Group), Universität Tübingen, Germany, September-December 2019 (DAAD & SPbSU visiting scholar program)

Education

Saint Petersburg State University, Ph.D. in Bioinformatics, 2018

Saint Petersburg Academic University of the Russian Academy of Sciences, M.Sc. in Software Engineering (summa cum laude, 5.0 GPA), 2010 – 2012

Saint Petersburg State Polytechnic University, B.Sc. in Information Technologies (summa cum laude, 5.0 GPA), 2006 – 2010

Lyceum “Physical-Technical High School” of the Russian Academy of Sciences (4.9 GPA), 2002 – 2006

Awards

Skills

  • Languages: Russian (native), English (fluent), German (beginner)
  • OS: Linux, macOS, Windows
  • Programming languages: commonly used: Python, C++, bash; have experience in: Java, JavaScript, HTML, C#
  • Tools & technologies: git, svn, cmake, PyCharm, CLion, Eclipse, VisualStudio
  • Other: algorithms, data structures, design patterns, OOP, writing documentation

Projects

  • Natural Products Discovery: Dereplicator, VarQuest, Dereplicator+ and other projects (since 2015, ongoing) [leading and developement]
  • Genome Assembly Evaluation: QUAST (since 2011, ongoing), including MetaQUAST (2015), Icarus (2016) and QUAST-LG (2017-2018) [leading and developement]
  • Genome Assembly: SPAdes (2011-2015) [creation and support of command line interface]
  • Collaboration with AstraZeneca (2014-2015) [developement of NGS data processing pipelines]

Press releases/interviews

Conferences

Teaching

  • Introduction to Bioinformatics at St. Petersburg State University, Fall 2016, 2017, 2018
  • Informatics/Programming (Java/Python/Delphi) at Lyceum “Physical-Technical High School”,  2012-2017
  • Linux for Beginners (MOOC at Stepic, in Russian), 2014
  • Journal Club in Algorithmic Bioinformatics at St. Petersburg Academic University, Fall 2014
  • Scientific Software Design at St. Petersburg Academic University, Spring 2014
  • Python for Beginners, Bioinformatics Summer School 2013, Moscow, August 2013

Supervising

  • Olga Kunyavskaya,  “NRPmatcher: an automated approach for NRP biosynthetic gene cluster identification” (St. Petersburg Academic University, Bachelor student + Internship at the Lab), Spring, Summer, 2018
  • Vladimir Sukhov, “Retention time for identification of natural products” (student of Bioinformatics Institute), Fall 2017
  • Azat Tagirdzhanov, “Enhancement of scoring functions for antibiotics discovery” (Internship at the Lab), Summer 2017
  • Sergey Chernov, “Application of SILAC data in antibiotic discovery” (St. Petersburg Academic University, Master student + Internship at the Lab), Summer, Fall 2016, Spring 2017
  • Denis Konoplev, “Finding structural motifs in Natural Products” (St. Petersburg Academic University, first-year Bachelor student), Spring 2016
  • Andrey Slabodkin, “Optimization of spectral network parameters” (St. Petersburg Academic University, first-year Bachelor student), Spring 2016
  • Nikolay Kapralov, “Evaluating Quality and Enhancing Optical Chemical Structure Recognition Tools” (student of Bioinformatics Institute), Fall 2015
  • Alla Mikheenko, “MetaQUAST: Quality Assessment Tool for Metagenome Assemblies”  (Internship at the Lab), Summer 2015
  • Gleb Valin, “Interactive contig alignment browser” (St. Petersburg Academic University, first-year Bachelor student), Spring 2015
  • Anna Lioznova, “Misassemblies detection without reference” (St. Petersburg Academic University, first-year Master student), Spring 2014
  • Maxim Stepachev, “Interactive visualization of contig alignment” (student of Bioinformatics Institute), Spring 2013
  • Vlad Saveliev, “Web-interface for QUAST” (Internship at the Lab), Summer 2012

Scientific Interests

Genome Assembly, Metabolomics, Natural Products, Computational Mass Spectrometry, Software Engineering

Hobbies

Football (soccer), snowboard, traveling.

Software

Publications

  1. Liu Cao, Alexey Gurevich , Kelsey L Alexander, C. Benjamin Naman, Tiago Leao, Evgenia Glukhov, Nathan A Moss, Tal Luzzatto Knaan, Fernando Vargas, Robby Quinn, Amina Bouslimani, Louis-Felix Nothias, Nitin K Singh, John G Sanders, Rodolfo A S Benitez, Luke R Thompson, Md-Nafiz Hamid, James T Morton, Alla Mikheenko , Alexander Shlemov ,  Anton Korobeynikov , Iddo Friedberg, Rob Knight, Kasthuri Venkateswaran, William Gerwick, Lena Gerwick, Peter C. Dorrestein, Pavel A. Pevzner , Hosein Mohimani MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities Cell Systems, 2019
  2. Tagirdzhanov A. , Shlemov A., Gurevich A. NPS: scoring and evaluating the statistical significance of peptidic natural product–spectrum matches (talk, poster), 2019
  3. Antipov D. , Bushmanova E. , Dvorkina T. , Gurevich A. , Kunyavskaya O. , Shlemov A., Lapidus A. , Meleshko D. , Nurk S. , Prjibelski A. , Korobeynikov A. SPAdes Family of Tools for Genome Assembly and Analysis (poster), 2019
  4. Gurevich A. , Mikheenko A. , Shlemov A. , Korobeynikov A. , Pevzner P. A. Variable Identification and De Novo Sequencing of Cyclopeptides via Computational Processing of Tandem Mass Spectra (talk), 2018
  5. Mikheenko A. , Prjibelski A. , Saveliev V. , Antipov D. , Gurevich A. Versatile genome assembly evaluation with QUAST-LG (talk, poster), 2018
  6. Korobeynikov A. , Antipov D. , Bushmanova E. , Gurevich A. , Lapidus A. , Meleshko D. , Mikheenko A. , Nurk S. , Prjibelski A. , Pevzner P. A. SPAdes Family of Tools for Genome Assembly and Analysis: What’s New? (poster), 2018
  7. Korobeynikov A. , Antipov D. , Bushmanova E. , Gurevich A. , Lapidus A. L. , Meleshko D. , Mikheenko A. , Nurk S. , Prjibelski A. , and Pevzner P. A. SPAdes Family of Tools for Genome Assembly and Analysis: Current Status (poster), 2018
  8. Gurevich A. , Shlemov A., Mikheenko A. , Korobeynikov A. , Pevzner P. A. VarQuest: modification-tolerant identification of novel variants of peptidic antibiotics and other natural products. (poster), 2017
  9. Gurevich A. , Shlemov A., Mikheenko A. , Korobeynikov A. , Pevzner P. A. Identification of novel peptidic antibiotics via large scale scoring of mass spectra against natural products databases (poster), 2017
  10. Gurevich A. Genome assembly evaluation with QUAST (talk), 2017
  11. Nurk S., Bankevich A., Antipov D., Gurevich A., Korobeynikov A., Lapidus A., Prjibelski A., Pyshkin A., Sirotkin A., Sirotkin Y., Stepanauskas R., McLean J., Lasken R., Clingenpeel S., Woyke T., Tesler G., Alekseyev M. A., Pevzner P. A. Assembling Genomes and Mini-metagenomes from Highly Chimeric Reads. Lecture Notes in Computer Science, 2013