Publications

1. 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
2. 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
3. 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
4. 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
5. 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
6. Shlemov A., Korobeynikov A. PathRacer: racing profile HMM paths on assembly graph (poster), 2019
7. Shlemov A., Korobeynikov A. PathRacer: racing profile HMM paths on assembly graph (talk), 2019
8. Shlemov A. , Dvorkina T. , Antipov D. , Nurk S. , Korobeynikov A. Tools for assembly graph analysis via SPAdes toolbox and more (talk), 2019
9. 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
10. Antipov D. , Rayko M. , Lapidus A. L. , Korobeynikov A. metaplasmidSPAdes: Plasmid Detection and Assembly in Genomic and Metagenomic Datasets (talk), 2019
11. Korobeynikov A. Tools for assembly graph analysis via SPAdes toolbox and more (talk), 2019
12. 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
13. 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
14. 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
15. 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
16. Korobeynikov A. Challenges of metagenome assemblies: how to deal with them and how to live with them? (talk), 2018
17. Nurk S., Meleshko D., Korobeynikov A., Pevzner P. A. metaSPAdes: a new versatile de novo metagenomics assembler. Genome Research, 2017
18. 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
19. 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
20. 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
21. 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
22. 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
23. Korobeynikov A. , Abramova A. Assessing Significance of Peptide Spectrum Match Scores (talk), 2017
24. Korobeynikov A. SPAdes Toolbox (tallk), 2017
25. Korobeynikov A. , Shlemov A., Bzikadze A. Accurate targeted assembly and variant calling from NanoString Hyb & Seq data (poster), 2017
26. 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
27. Antipov D., Korobeynikov A., McLean J. S., Pevzner P. A. hybridSPAdes: an algorithm for hybrid assembly of short and long reads. Bioinformatics, 2016
28. 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
29. 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
30. 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
31. Vasilinetc I., Prjibelski A., Gurevich A., Korobeynikov A., Pevzner P. A. Assembling Short Reads from Jumping Libraries with Large Insert Sizes. Bioinformatics, 2015
32. 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
33. 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
34. 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
35. 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
36. 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
37. 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
38. Nikolenko S., Korobeynikov A., Pevzner P. A. BayesHammer: Bayesian clustering for error correction in single-cell sequencing. BMC Genomics, 2013
39. Nikolenko S., Korobeynikov A., Pevzner P. A. BayesHammer: Bayesian clustering for error correction in single-cell sequencing. BMC Genomics, 2013