Andrey Prjibelski

Senior Research Fellow

Career

  • Algorithmic Bioinformatics group, University of Helsinki, 2022 – present time
  • SPbU, Teacher Assistant, 2016 – 2022
  • Center for Algorithmic Biotechnology, SPbU, Senior Research Fellow, 2015 – 2022
  • Bioinformatics Institute, Lecturer, 2014 – 2023
  • SPbAU, Lecturer, 2012 – 2018
  • Algorithmic Biology Lab,SPbAU, Junior Research Fellow, 2011 – 2015
  • Algorithmic Biology Lab, SPbAU, Intern, 2011

Education

  • St. Petersburg State University, PhD, 2020
  • 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

  • Prjibelski, A.D., Mikheenko, A., Joglekar, A., Smetanin, A., Jarroux, J., Lapidus, A.L. and Tilgner, H.U., 2023. Accurate isoform discovery with IsoQuant using long reads. Nature Biotechnology, pp.1-4.
  • Alla Mikheenko, Andrey D Prjibelski, Anoushka Joglekar, Hagen U Tilgner, 2022. Sequencing of individual barcoded cDNAs on Pacific Biosciences and Oxford Nanopore reveals platform-specific error patterns Genome Research, 32(4), pp.726-737.
  • Anoushka Joglekar, Andrey Prjibelski, Ahmed Mahfouz, Paul Collier, … , M Elizabeth Ross, Hagen U Tilgner, 2021. A spatially resolved brain region-and cell type-specific isoform atlas of the postnatal mouse brain, Nature Communications, 12 (1), 1-16.

    • A Prjibelski, D Antipov, D Meleshko, A Lapidus, A Korobeynikov, 2020. Using SPAdes De Novo Assembler. Current Protocols in Bioinformatics 70 (1), e102

  • Prjibelski, A., Bushmanova, E., Giordano, D., Mikheenko, A., Puglia, G., Antipov, D., Viatale, D. and Lapidus, A., 2020. Extending rnaSPAdes functionality for hybrid transcriptome assembly. BMC Bioinformatics, 20.
  • Prjibelski, A., Bushmanova, E., Giordano, D., Mikheenko, A., Puglia, G., Antipov, D., Viatale, D. and Lapidus, A., Extending rnaSPAdes functionality for hybrid transcriptome assembly. BMC Bioinformatics, 20, 2019.
  • Elena Bushmanova, Dmitry Antipov, Alla Lapidus, Andrey D Prjibelski, rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data GigaScience, 2019
  • 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. and Prjibelski, A.D., 2016. rnaQUAST: a quality assessment tool for de novo transcriptome assemblies. Bioinformatics, 32(14), pp.2210-2212.
  • 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.
  • 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.
  • 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.

Conference talks

  • Transcriptome assembly with spISO-seq data, MCCMB 2019, Moscow, Russia, July 2019
  • Hybrid transcriptome assembly and its application to artichoke data, BiATA 2019, St. Petersburg, Russia, June 2019
  • Assembling barcoded RNA sequencing data, BiATA 2018, St. Petersburg, Russia, July 2018
  • Algorithmic challenges in de novo transcriptome assembly, BiATA 2017, St. Petersburg, Russia, August 2017
  • ExSPAnder: a Universal Repeat Resolver for DNA Fragment Assembly, 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

Grants & Awards

  • Assembly and analysis of barcoded RNA sequencing data, Russian Foundation for Basic Research Best projects in basic research (A), 2019-2021
  • Ian Lawson Van Toch Memorial Award for Outstanding Student Paper, ISMB 2014, Boston, USA, July 2014

Teaching

 Full courses

  • NGS Data Analysis, Bioinformatics Institute, 2012 – present time
  • Introduction to Bioinformatics for Biologists, SPbU, 2016 – present time
  • Algorithms in Bioinformatics, SPbAU, 2014-2015

  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, disc golf, alpine skiing, volleyball, water tourism, trekking, hiking

Software

SGTK
QUAST-LG
rnaSPAdes
rnaQUAST
SPAdes

Publications

  1. Andrey D Prjibelski , Alla Mikheenko , Anoushka Joglekar, Dmitry Meleshko , Alla L Lapidus , Hagen Tilgner IsoQuant: isoform analysis and quantification with long error-prone transcriptomic reads (talk), 2020
  3. Prjibelski A. , Meleshko D. Transcriptome assembly with spISO-seq data (talk), 2019
  4. Antipov D. , Bushmanova E. , Dvorkina T. , Gurevich A. , Kunyavskaya O. , Shlemov A., Lapidus A. , Meleshko D. , Nurk S. , Prjibelski A. , Korobeynikov A. SPAdes Family of Tools for Genome Assembly and Analysis (poster), 2019
  5. Korobeynikov A. , Antipov D. , Bushmanova E. , Gurevich A. , Lapidus A. L. , Meleshko D. , Mikheenko A. , Nurk S. , Prjibelski A. , and Pevzner P. A. SPAdes Family of Tools for Genome Assembly and Analysis: Current Status (poster), 2018
  6. Korobeynikov A. , Antipov D. , Bushmanova E. , Gurevich A. , Lapidus A. , Meleshko D. , Mikheenko A. , Nurk S. , Prjibelski A. , Pevzner P. A. SPAdes Family of Tools for Genome Assembly and Analysis: What’s New? (poster), 2018
  7. Prjibelski A. Algorithms for nucleic sequence alignment (talk), 2018
  10. Korobeynikov A. , Antipov D. , Bankevich A. , Bushmanova E. , Gurevich A. , Lapidus A. , Meleshko D. , Nurk S. , Prjibelski A. , Pevzner P. A. SPAdes Family of Tools for Genome Assembly and Analysis: What’s New? (poster), 2017
  11. Lapidus A. , Antipov D. , Bankevich A. , Bushmanova E. , Korobeynikov A. , Meleshko D. , Nurk S. , Prjibelski A. , Pevzner P. A. SPAdes Family of Tools for Genome Assembly and Analysis: What’s New? (poster), 2017
  12. Korobeynikov A. , Antipov D. , Bankevich A. , Bushmanova E. , Lapidus A. , Meleshko D. , Nurk S. , Prjibelski A. , Pevzner P. A. SPAdes: is there anything new we could develop? (talk), 2017
  16. 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
  18. 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
  20. 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
  22. Prjiblelski A., Miloslavskaya V., Lebed D., Trifonov P. Usage of Field Extensions in Wiedemann Algorithm. Fundamental Research and Innovations in Technical Universities, 2009