Andrey Prjibelski

Research Fellow

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

Introduction to Linux (in Russian)

Interests

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

Hobbies

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

Software

Publications

Elena Bushmanova, Dmitry Antipov, Alla Lapidus, Andrey D Prjibelski rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data GigaScience, 2019
Alla Mikheenko, Andrey Prjibelski, Vladislav Saveliev, Dmitry Antipov, Alexey Gurevich Versatile genome assembly evaluation with QUAST-LG Bioinformatics, 2018
Olga Kunyavskaya , Andrey D. Prjibelski SGTK: a toolkit for visualization and assessment of scaffold graphs. Bioinformatics, 2018
Bushmanova E., Antipov D., Lapidus A., Suvorov V., Prjibelski A. rnaQUAST: a quality assessment tool for de novo transcriptome assemblies. Bioinformatics, 2016
Mikheenko A., Valin G., Prjibelski A., Saveliev V., Gurevich A. Icarus: visualizer for de novo assembly evaluation. Bioinformatics, 2016
Vasilinetc I., Prjibelski A., Gurevich A., Korobeynikov A., Pevzner P. A. Assembling Short Reads from Jumping Libraries with Large Insert Sizes. Bioinformatics, 2015
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
Prjibelski A., Vasilinetc I., Bankevich A., Gurevich A., Krivosheeva T., Nurk S., Pham S., Korobeynikov A., Lapidus A., Pevzner P. A. ExSPAnder: a universal repeat resolver for DNA fragment assembly. Bioinformatics, 2014
Nurk S., Bankevich A., Antipov D., Gurevich A., Korobeynikov A., Lapidus A., Prjibelski A., Pyshkin A., Sirotkin A., Sirotkin Y., Stepanauskas R., Clingenpeel S. R., Woyke T., Mclean J. S., Lasken R., Tesler G., Alekseyev M. A., Pevzner P. A. Assembling single-cell genomes and mini-metagenomes from chimeric MDA products. Journal of Computational Biology, 2013
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
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
Bankevich A., Nurk S., Antipov D., Gurevich A., Dvorkin M., Kulikov A. S., Lesin V., Nikolenko S., Pham S., Prjibelski A., Pyshkin A., Sirotkin A., Vyahhi N., Tesler G., Alekseyev M. A., Pevzner P. A. SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing. Journal of Computational Biology, 2012
Prjiblelski A., Miloslavskaya V., Lebed D., Trifonov P. Usage of Field Extensions in Wiedemann Algorithm. Fundamental Research and Innovations in Technical Universities, 2009