- 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
- 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
- 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.
- 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.
A Prjibelski, D Antipov, D Meleshko, A Lapidus, A Korobeynikov, 2020. Using SPAdes De Novo Assembler. Current Protocols in Bioinformatics 70 (1), e102
- 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
- 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
- Introduction to Linux (in Russian)
Algorithms, bioinformatics, genomics, transcriptomics, genome assembly, software engineering
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