Alexey Gurevich

Research Scientist at Center for Algorithmic Biotechnology, Saint Petersburg State University

 

Personal:

E-mail: gurevich@bioinf.spbau.ru

Birthday: 21 March 1989. Married, has a daughter (born in 2015).

 

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, PhD student in Bioinformatics, 2012 –  present time

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 

 

Projects:

Natural Products Discovery: Dereplicator and other projects (since 2015, ongoing)
Genome Assembly Evaluation: QUAST (since 2011, ongoing) and MetaQUAST (2015)
Genome Assembly: SPAdes (since 2011, ongoing)
Cancer Genomics: collaboration with AstraZeneca Oncology (2014-2015)
 

Publications

  • Alla Mikheenko, Gleb Valin, Andrey Prjibelski, Vladislav Saveliev, Alexey Gurevich. Icarus: visualizer for de novo assembly evaluation. Submitted.
  • Hosein Mohimani, Alexey Gurevich, Pieter C. Dorrestein, and Pavel A. Pevzner. In silico Identification of Peptidic Natural Products Through Database Search of Mass Spectra. Submitted.
  • Alla Mikheenko, Vladislav Saveliev, Alexey Gurevich. MetaQUAST: evaluation of metagenome assemblies, Bioinformatics (2015). doi: 10.1093/bioinformatics/btv697. First published online: November 26, 2015
  • Irina Vasilinetc, Andrey D. Prjibelski, Alexey Gurevich, Anton Korobeynikov and Pavel Pevzner. Assembling Short Reads from Jumping Libraries with Large Insert Sizes, Bioinformatics, 2015, 31 (12): pp. 3262-3268.
  • Andrey D. Prjibelski, Irina Vasilinetc, Anton Bankevich, Alexey Gurevich, Tatiana Krivosheeva, Sergey Nurk, Son Pham, Anton Korobeynikov, Alla Lapidus and Pavel A. Pevzner. ExSPAnder: a universal repeat resolver for DNA fragment assembly. Bioinformatics (2014) 30 (12): i293-i301. doi: 10.1093/bioinformatics/btu266
  • Sergey Nurk, Anton Bankevich, Dmitry Antipov, Alexey A Gurevich, Anton Korobeynikov, Alla Lapidus, Andrey D Prjibelski, Alexey Pyshkin, Alexander Sirotkin, Yakov Sirotkin, Ramunas Stepanauskas, Scott R Clingenpeel, Tanja Woyke, Jeffrey S Mclean, Roger Lasken, Glenn Tesler, Max A Alekseyev, Pavel A Pevzner. Assembling single-cell genomes and mini-metagenomes from chimeric MDA products. Journal of Computational Biology 20(10) (2013), pp. 714-737.

  • Alexey Gurevich, Vladislav Saveliev, Nikolay Vyahhi, and Glenn Tesler. QUAST: quality assessment tool for genome assemblies. Bioinformatics 29(8) (2013), pp. 1072-1075. doi:10.1093/bioinformatics/btt086

  • Anton Bankevich, Sergey Nurk, Dmitry Antipov, Alexey A. Gurevich, Mikhail Dvorkin, Alexander S. Kulikov, Valery M. Lesin, Sergey I. Nikolenko, Son Pham, Andrey D. Prjibelski, Alexey V. Pyshkin, Alexander V. Sirotkin, Nikolay Vyahhi, Glenn Tesler, Max A. Alekseyev, and Pavel A. Pevzner. SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing. Journal of Computational Biology 19(5) (2012), 455-477. doi:10.1089/cmb.2012.0021

 

Conferences

Translational Biomedicine, St. Petersburg, Russia, November 2015 (talk: Software pipeline for Oncology NGS data analysis)

CAMI evaluation meeting, Berlin, Germany, May 2015 (talk: metaQUAST: evaluating metagenome assemblies)

RECOMB & RECOMB-Seq, Beijing, China, April 2013 (poster: quality assessment of genome assemblies (web tool))

RECOMB-AB & RECOMB-BE, St. Petersburg, Russia, August 2012 

RECOMB & RECOMB-Seq, Barcelona, Spain, April 2012

 

Teaching

  • Informatics/Programming (Java/Python/Delphi) at Lyceum "Physical-Technical High School",  2012-2015

  • 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:

  • 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. Peterbsurg Academic University, first year Bachelor student), Spring 2015
  • Anna Lioznova, "Misassemblies detection without reference" (St. Peterbsurg 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, Antibiotics Sequencing, Software Engineering

Hobbies:

Soccer, snowboard