Andrey Prjibelski

Junior Research Fellow
ap@bioinf.spbau.ru

Career

  • SPbU, Teacher assistant, 2016 – present time
  • Center for Algorithmic Biotechnology, SPbU, Junior Researcher, 2015 – present time
  • SPbAU, Teacher, 2012 – present time
  • Algorithmic Biology Lab,SPbAU, Researcher, 2011 – 2016
  • Algorithmic Biology Lab, SPbAU, Intern, 2011

Education

  • St. Petersburg Staet University, expected degree: PhD, 2017
  • 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

Selected publications

  • Bankevich, A., Nurk, S., Antipov, D., Gurevich, A.A., Dvorkin, M., Kulikov, A.S., Lesin, V.M., Nikolenko, S.I., Pham, S., Prjibelski, A.D. and Pyshkin, A.V., 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. Journal of computational biology, 19(5), pp.455-477.
  • Prjibelski, A.D., Vasilinetc, I., Bankevich, A., Gurevich, A., Krivosheeva, T., Nurk, S., Pham, S., Korobeynikov, A., Lapidus, A. and Pevzner, P.A., 2014. ExSPAnder: a universal repeat resolver for DNA fragment assembly.Bioinformatics, 30(12), pp.i293-i301.
  • Vasilinetc, I., Prjibelski, A.D., Gurevich, A., Korobeynikov, A. and Pevzner, P.A., 2015. Assembling short reads from jumping libraries with large insert sizes. Bioinformatics, 31(20), pp.3262-3268.
  • Bushmanova, E., Antipov, D., Lapidus, A., Suvorov, V. and Prjibelski, A.D., 2016. rnaQUAST: a quality assessment tool for de novo transcriptome assemblies. Bioinformatics, 32(14), pp.2210-2212.

Talks & posters

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

 Full courses

  • NGS Data Analysis, Spring 2017
  • Introduction to Bioinformatics for Biologists, Fall 2017
  • NGS Data Analysis, Fall 2016
  • 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

  Workshops and schools 

  • Short Read Alignment, Genomic Bioinformatics Workshop, St. Petersburg, Russia, April 2017
  • Assembling Bacterial Genomes with SPAdes, Genomic Bioinformatics Workshop, St. Petersburg, Russia, April 2017
  • Assembling Bacterial Genomes with SPAdes, Genomic Bioinformatics Workshop, St. Petersburg, Russia, November 2016
  • Assembling Bacterial Genomes Workshop, Pisa, Italy, April 2016
  • Assembling Bacterial Genomes with SPAdes, Genomic Bioinformatics Workshop, St. Petersburg, Russia, November 2015
  • Assembling Bacterial Genomes: SPAdes, QUAST, Genomic Bioinformatics Workshop, Moscow, Russia, November 2015
  • Introduction to NGS, Introduction to Algorithms in Bioinformatics, Bioinformatics Summer School 2015, Moscow, July 2015
  • Assembling Bacterial Genomes with SPAdes, Genomic Bioinformatics Workshop, St. Petersburg, Russia, April 2015
  • Assembling Bacterial Genomes with SPAdes, Working with Bacterial Genomes Workshop, Helsinki, Finland, October 2014
  • Genome Assembly Future, Bioinformatics Summer School 2014, St. Petersburg, August 2014
  • Introduction to NGS, Bioinformatics Summer School 2013, Moscow, August 2013
  • Introduction to Genome Assembly, System biology and Bioinformatics School, Novosibirsk, Russia, July 2013

Online courses

Interests

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

Hobbies

Ultimate frisbee, alpine skiing, volleyball, water tourism, trekking, hiking

Software

QUAST-LG
rnaSPAdes
rnaQUAST
SPAdes

Publications

  6. Lapidus A., Antipov D., Bankevich A., Gurevich A., Korobeynikov A., Nurk S., Prjibelski A., Safonova Y., Vasilinetc I., Pevzner P. A. New Frontiers of Genome Assembly with SPAdes 3.0. (poster), 2014
  8. 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
  10. Prjibelski A., Krivosheeva T., Bankevich A., Nurk S., Pham S., Pevzner P. A. Path-Extend: An Approach for Repeat Resolution in de novo Genome Assembly. , 2012
  11. Prjiblelski A., Miloslavskaya V., Lebed D., Trifonov P. Usage of Field Extensions in Wiedemann Algorithm. Fundamental Research and Innovations in Technical Universities, 2009