Andrey Prjibelski

Contact information

E-mail: ap (at) bioinf.spbau.ru

 

Education

  • St. Petersburg University of the Russian Academy of Sciences, expected degree: PhD, 2016

  • St. Petersburg University of the Russian Academy of Sciences, MSc in software engineering,  2010-2012

  • Academy of Modern Software Engineering, 2009 - 2011

  • St. Petersburg State Technical University, BSc in information technologies (magna cum laude), 2006 - 2010

  • Lyceum "Physical-Technical High School" of the Russian Academy of Sciences, 2004-2006

  • Giles School, Toronto, Canada, 2003-2004

 

Career

  • St. Petersburg University of the Russian Academy of Sciences, Teacher, 2012 - present time

  • Algorithmic Biology Lab, Researcher, 2011 - present time

  • Algorithmic Biology Lab, Intern, 2011

  • JetBrains, Part-time intern, 2010-2011

 

Publications

  • Elena Bushmanova, Dmitry Antipov, Alla Lapidus, Vladimir Suvorov and Andrey D. Prjibelski. rnaQUAST: a quality assessment tool for de novo transcriptome assemblies, Bioinformatics, 2016.
  • 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):.
  • 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.
  • Sergey Nurk, Anton Bankevich, Dmitry Antipov, Alexey Gurevich, Anton Korobeynikov, Alla Lapidus, Andrey Prjibelski, Alexey Pyshkin, Alexander Sirotkin, Yakov Sirotkin, Ramunas Stepanauskas, Jeffrey McLean, Roger Lasken, Scott Clingenpeel, Tanja Woyke, Glenn Tesler, Max Alekseyev, and Pavel Pevzner. Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products. Journal of Computational Biology. October 2013, 20(10): 714-737. 
  • 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. 2013, 19(5), 455-477.
  • A.D. Prjiblelski, V.D. Miloslavskaya, D.O. Lebed and P.V. Trifonov. Usage of Field Extensions in Wiedemann Algorithm. Fundamental Research and Innovations in Technical Universities, 2009.

 

Talks & posters

  • Assembling Bacterial Genomes with SPAdes, Bioinformatics short course, St. Petersburg, Russia, April 2015

  • Assembling Bacterial Genomes with SPAdes, Working with Bacterial Genomes course, Helsinki, Finland, October 2014

  • Genome Assembly Future, Bioinformatics Summer School 2014, St. Petersburg, August 2014

  • ExSPAnder: a Universal Repeat Resolver for DNA Fragment Assembly, ISMB 2014, Boston, USA, July 2014

  • New Features in SPAdes Genome Assembler (Poster), ISMB 2014, Boston, USA, July 2014

  • New Frontiers of Genome Assembly with SPAdes 3.1, BOSC 2014, Boston, USA, July 2014

  • Introduction to NGS, Biological seminar, St. Petersburg State University, Russia, December 2013

  • Introduction to NGS, Bioinformatics Summer School 2013, Moscow, August 2013

  • Genome Draft Assembly Algorithms: From the Very Beginning till Present-day Problems, High-Throughput Sequencing in Genomics, Novosibirsk, Russia, July 2013

  • Introduction to Genome Assembly, System biology and Bioinformatics School, Novosibirsk, Russia, July 2013

  • Path-Extend: A New Approach for Repeat Resolution in Genome Assembly (Poster), WABI 2012, Ljubljana, Slovenia, August 2012

 

Awards

  • Ian Lawson Van Toch Memorial Award for Outstanding Student Paper, ISMB 2014, Boston, USA, July 2014

 

Teaching

  • NGS Data Analysis, Spring 2015

  • Algorithms in Bioinformatics, Fall 2014

  • Algorithms in Bioinformatics, Spring 2014

  • NGS Data Analysis, Fall 2013

  • NGS Data Analysis, Fall 2012

  • NGS Data Analysis, Spring 2012

 

Interests

Algorithms, bioinformatics, genomics, transcriptomics, genome assembly, software engineering

 

Hobbies

Volleyball, soccer, alpine skiing, cycling, water tourism, trekking