Alexey Gurevich

Senior Research Fellow

Full name in native language: Алексей Александрович Гуревич

Birthday: 21 March 1989.

Interests: Bioinformatics, Genome Assembly Evaluation, Metabolomics, Natural Products, Computational Mass Spectrometry, Software Engineering

Profiles: Google Scholar, LinkedIn. CV in PDF.

Career

since 2022        Junior Professor at the Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) and Saarland University

2019–2022       Senior Research Scientist at Center for Algorithmic Biotechnology, St. Petersburg State University

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

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

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

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

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

Visiting Research

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

Jul-Aug 2016     The Pevzner lab, University of California San Diego (short-term research visit)

Mar 2015            The Pevzner lab, University of California San Diego (short-term research visit)

Education

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

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

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

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

Grants as PI

  • System Biology Fellowship (accept rate ~17%) “Integration of genomics and metabolomics data for discovery of small natural products”, 2020-2022 (personal grant, 0.6M RUB per year)
  • RSF grant (accept rate ~19%) “Creation of a web-database of hypothetical peptidic secondary metabolites”, 2020-2022 (2 members, 1.5M RUB per year)
  • RFBR grant (accept rate ~19%) “Development of computational methods for mass spectrometry-based identification of plant secondary metabolites”, 2020-2021 (4 members, 1.2M RUB per year)

Awards

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]

Teaching

  • Bioinformatics Algorithms at St. Petersburg State University (for CS Bachelor’s students), Spring 2021 (as a part of the Multi-University class)
  • Introduction to Bioinformatics at St. Petersburg State University (for Biology/Bioinformatics Master’s students), Fall 2016, 2017, 2018, 2020
  • Informatics/Programming (Java/Python/Delphi) at Lyceum “Physical-Technical High School”,  2012-2017
  • Linux for Beginners (MOOC at Stepik, in Russian, 120K+ enrolled users), 2014
  • Journal Club in Algorithmic Bioinformatics at St. Petersburg Academic University (for Bioinformatics Master’s students), Fall 2014
  • Scientific Software Design at St. Petersburg Academic University (for Bioinformatics Master’s students), 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

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, Latex
  • Other: algorithms, data structures, design patterns, OOP, writing documentation

Press releases/interviews

Conferences

Software

NPvis
Nerpa
TandemTools
NPDtools
NPS
Dereplicator+
MetaMiner
QUAST-LG
VarQuest
Dereplicator

Publications

  3. Alla Mikheenko , Andrey V Bzikadze, Alexey Gurevich , Karen H Miga, Pavel A Pevzner TandemTools: mapping long reads and assessing/improving assembly quality in extra-long tandem repeats (talk), 2020
  5. 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
  6. Tagirdzhanov A. , Shlemov A., Gurevich A. NPS: scoring and evaluating the statistical significance of peptidic natural product–spectrum matches (talk, poster), 2019
  7. 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
  11. Mikheenko A. , Prjibelski A. , Saveliev V. , Antipov D. , Gurevich A. Versatile genome assembly evaluation with QUAST-LG (talk, poster), 2018
  12. 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
  13. 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
  14. 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
  16. 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
  17. 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
  18. Gurevich A. Genome assembly evaluation with QUAST (talk), 2017
  26. 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