Ph.D.
Associate Professor
Saint Petersburg State University,
Faculty of Mathematics and Mechanics, Department of Statistical Modelling
Universitetskiy 28
198504, Stary Peterhof, Saint Petersburg, Russia
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Olga Kunyavskaya*, Azat M Tagirdzhanov*, Andrés Mauricio Caraballo-Rodríguez, Louis-Félix Nothias, Pieter C Dorrestein, Anton Korobeynikov, Hosein Mohimani, Alexey Gurevich
Nerpa: A Tool for Discovering Biosynthetic Gene Clusters of Bacterial Nonribosomal Peptides Metabolites,
2021
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Mitchell AL, Almeida A, Beracochea M, Boland M, Burgin J, Cochrane G, Crusoe MR, Kale V, Potter SC, Richardson LJ, Sakharova E, Scheremetjew M, Korobeynikov A, Shlemov A, Kunyavskaya O, Lapidus A and Finn RD.
MGnify: the microbiome analysis resource in 2020 Nucleic Acids Research,
2020
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Korobeynikov A.
Tools for assembly graph analysis via SPAdes toolbox and more (talk),
2019
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Antipov D. , Rayko M. , Lapidus A. L. , Korobeynikov A.
metaplasmidSPAdes: Plasmid Detection and Assembly in Genomic and Metagenomic Datasets (talk),
2019
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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
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Shlemov A. , Dvorkina T. , Antipov D. , Nurk S. , Korobeynikov A.
Tools for assembly graph analysis via SPAdes toolbox and more (talk),
2019
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Shlemov A., Korobeynikov A.
PathRacer: racing profile HMM paths on assembly graph (talk),
2019
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Shlemov A., Korobeynikov A.
PathRacer: racing profile HMM paths on assembly graph (poster),
2019
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Dmitry Meleshko , Hosein Mohimani, Vittorio Tracanna, Iman Hajirasouliha, Marnix H. Medema, Anton Korobeynikov , and Pavel A. Pevzner
BiosyntheticSPAdes: Reconstructing Biosynthetic Gene Clusters From Assembly Graphs Genome Research,
2019
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Alexander Shlemov, Anton Korobeynikov
PathRacer: Racing Profile HMM Paths on Assembly Graph Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics),
2019
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Liu Cao, Alexey Gurevich , Kelsey L Alexander, C. Benjamin Naman, Tiago Leao, Evgenia Glukhov, Nathan A Moss, Tal Luzzatto Knaan, Fernando Vargas, Robby Quinn, Amina Bouslimani, Louis-Felix Nothias, Nitin K Singh, John G Sanders, Rodolfo A S Benitez, Luke R Thompson, Md-Nafiz Hamid, James T Morton, Alla Mikheenko , Alexander Shlemov , Anton Korobeynikov , Iddo Friedberg, Rob Knight, Kasthuri Venkateswaran, William Gerwick, Lena Gerwick, Peter C. Dorrestein, Pavel A. Pevzner , Hosein Mohimani
MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities Cell Systems,
2019
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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
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Hosein Mohimani, Alexey Gurevich, Alexander Shlemov, Alla Mikheenko, Anton Korobeynikov, Liu Cao, Egor Shcherbin, Louis-Felix Nothias, Pieter Dorrestein, Pavel Pevzner
Dereplication of Microbial Metabolites Through Database Search of Mass Spectra Nature Communications,
2018
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Gurevich A. , Mikheenko A. , Shlemov A. , Korobeynikov A. , Pevzner P. A.
Variable Identification and De Novo Sequencing of Cyclopeptides via Computational Processing of Tandem Mass Spectra (talk),
2018
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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
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Korobeynikov A.
Challenges of metagenome assemblies: how to deal with them and how to live with them? (talk),
2018
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Korobeynikov A. , Shlemov A., Bzikadze A.
Accurate targeted assembly and variant calling from NanoString Hyb & Seq data (poster),
2017
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Korobeynikov A.
SPAdes Toolbox (tallk),
2017
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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
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Korobeynikov A. , Abramova A.
Assessing Significance of Peptide Spectrum Match Scores (talk),
2017
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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
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Gurevich A. , Shlemov A., Mikheenko A. , Korobeynikov A. , Pevzner P. A.
Identification of novel peptidic antibiotics via large scale scoring of mass spectra against natural products databases (poster),
2017
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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
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Gurevich A. , Shlemov A., Mikheenko A. , Korobeynikov A. , Pevzner P. A.
VarQuest: modification-tolerant identification of novel variants of peptidic antibiotics and other natural products. (poster),
2017
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Nurk S., Meleshko D., Korobeynikov A., Pevzner P. A.
metaSPAdes: a new versatile de novo metagenomics assembler. Genome Research,
2017
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Boudreau P. D., Monroe E. A., Mehrotra S., Desfor S., Korobeynikov A., Sherman D. H., Murray T. F., Gerwick L., Dorrestein P. C., Gerwick W. H.
Expanding the Described Metabolome of the Marine Cyanobacterium Moorea producens JHB through Orthogonal Natural Products Workflows. PLoS One,
2016
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Antipov D., Korobeynikov A., McLean J. S., Pevzner P. A.
hybridSPAdes: an algorithm for hybrid assembly of short and long reads. Bioinformatics,
2016
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Vasilinetc I., Prjibelski A., Gurevich A., Korobeynikov A., Pevzner P. A.
Assembling Short Reads from Jumping Libraries with Large Insert Sizes. Bioinformatics,
2015
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Bertin M. J., Vulpanovici A., Monroe E. A., Korobeynikov A., Sherman D. H., Gerwick L., Gerwick W. H.
The Phormidolide Biosynthetic Gene Cluster: A trans‐AT PKS Pathway Encoding a Toxic Macrocyclic Polyketide. Chembiochem.,
2015
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Kleigrewe K., Almaliti J., Tian I. Y., Korobeynikov A., Monroe E. A., Duggan B.M., Di Marzo V., Sherman D. H., Dorrestein P. C., Gerwick L., Gerwick W. H.
Combining Mass Spectrometric Metabolic Profiling with Genomic Analysis: A Powerful Approach for Discovering Natural Products from Cyanobacteria. Journal of natural products,
2015
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Bertin M. J., Schwartz S. L., Lee J., Korobeynikov A., Dorrestein P. C., Gerwick L., Gerwick W. H.
Spongosine Production by a Vibrio harveyi Strain Associated with the Sponge Tectitethya crypta Journal of natural products,
2015
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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
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Coates R. C., Podell S., Korobeynikov A., Lapidus A., Pevzner P. A., Sherman D. H., Allen E. E., Gerwick L., Gerwick W. H.
Characterization of Cyanobacterial Hydrocarbon Composition and Distribution of Biosynthetic Pathways. PLoS One,
2014
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Roy R. S., Price D. C., Schliep A., Cai G., Korobeynikov A., Yoon H. S., Yang E. C., Bhattacharya D.
Single cell genome analysis of an uncultured heterotrophic stramenopile. Scientific Reports,
2014
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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
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Nikolenko S., Korobeynikov A., Pevzner P. A.
BayesHammer: Bayesian clustering for error correction in single-cell sequencing. BMC Genomics,
2013
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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
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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
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Nikolenko S., Korobeynikov A., Pevzner P. A.
BayesHammer: Bayesian clustering for error correction in single-cell sequencing. BMC Genomics,
2013