Alexey Gurevich

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:

Algorithmic Biology Lab/Center for Algorithmic Biotechnology, Research Scientist, 2011 – present time

Algorithmic Biology Lab, Intern, 2011

St. Petersburg State Polytechnic University, Research Fellow, 2009-2010

Education:

Saint Petersburg Academic University of the Russian Academy of Sciences, MSc in Software Engineering (summa cum laude), 2010 – 2012

Saint Petersburg State Polytechnic University, BSc in Information Technologies (summa cum laude), 2006 – 2010

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

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 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]

Awards

Press releases

Conferences

Teaching

  • Introduction to Bioinformatics at St. Petersburg State University, Fall 2016 & Fall 2017
  • 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:

  • 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 Evaluation, Metabolomics, Software Engineering

Hobbies:

Football (soccer), snowboard, travelling.

Software

Publications

  1. 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