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Research Output 2006 2020

2020

MGnify: the microbiome analysis resource in 2020

Mitchell, A. L., Almeida, A., Beracochea, M., Boland, M., Burgin, J., Cochrane, G., Crusoe, M. R., Kale, V., Potter, S. C., Richardson, L. J., Sakharova, E., Scheremetjew, M., Korobeynikov, A., Shlemov, A., Kunyavskaya, O., Lapidus, A. & Finn, R. D., 8 Jan 2020, In : Nucleic Acids Research. 48, D1, p. D570-D578 9 p.

Research output

Open Access
Metagenomics
Microbiota
Molecular Sequence Annotation
Protein Databases
Workflow
2019
1 Citation (Scopus)

BiosyntheticSPAdes: reconstructing biosynthetic gene clusters from assembly graphs

Meleshko, D., Mohimani, H., Tracanna, V., Hajirasouliha, I., Medema, M. H., Korobeynikov, A. & Pevzner, P. A., 1 Aug 2019, In : Genome Research. 29, 8, p. 1352-1362

Research output

Open Access
Multigene Family
Metagenomics
Genome
Microbial Genome
Firearms

MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities

Cao, L., Gurevich, A., Alexander, K. L., Naman, C. B., Leão, T., Glukhov, E., Luzzatto-Knaan, T., Vargas, F., Quinn, R., Bouslimani, A., Nothias, L. F., Singh, N. K., Sanders, J. G., Benitez, R. A. S., Thompson, L. R., Hamid, M. N., Morton, J. T., Mikheenko, A., Shlemov, A., Korobeynikov, A. & 8 others, Friedberg, I., Knight, R., Venkateswaran, K., Gerwick, W. H., Gerwick, L., Dorrestein, P. C., Pevzner, P. A. & Mohimani, H., 18 Dec 2019, In : Cell Systems. 9, 6, p. 600-608.e4 13 p.

Research output

Biological Products
Microbiota
Peptides
Social Networking
Metagenomics

PathRacer: Racing Profile HMM Paths on Assembly Graph

Shlemov, A. & Korobeynikov, A., 25 May 2019, 6th International Conference on Algorithms for Computational Biology. Vega-Rodríguez, M. A., Holmes, I. & Martín-Vide, C. (eds.). Springer, p. 80-94 15 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 11488 LNBI).

Research outputpeer-review

Hidden Markov models
Markov Model
Path
Genes
Graph in graph theory

Sequence Analysis

Пржибельский, А. Д., Коробейников, А. И. & Лапидус, А. Л., 2019, Encyclopedia of Bioinformatics and Computational Biology: Reference Module in Life Sciences. Elsevier, Vol. 3. p. 292-322

Research outputpeer-review

2018
2 Citations (Scopus)

Autoprobiotics as an Approach for Restoration of Personalised Microbiota

Суворов, А. Н., Карасева, А. Б., Котылева, М. П., Кондратенко, Ю. Д., Лавренова, Н., Коробейников, А. И., Козырев, П. А., Крамская, Т. А., Леонтьева, Г., Кудрявцев, И. В., Guo, D., Лапидус, А. Л. & Ермоленко, Е. И., 12 Sep 2018, In : Frontiers in Microbiology. 9, 1869.

Research output

Open Access
21 Citations (Scopus)

Dereplication of microbial metabolites through database search of mass spectra

Mohimani, H., Гуревич, А. А., Шлемов, А. Ю., Михеенко, А. А., Коробейников, А. И., Cao, L., Щербин, Е., Nothias, L-F., Dorrestein, P. C. & Певзнер, П. А., 1 Dec 2018, In : Nature Communications. 9, 1, 12 p., 4035.

Research output

Open Access
metabolites
Metabolites
Biological Products
mass spectra
Databases
19 Citations (Scopus)
Biological Products
Databases
Metabolomics
Social Networking
Bacteria
2 Citations (Scopus)

Ketoreductase domain dysfunction expands chemodiversity: malyngamide biosynthesis in the cyanobacterium Okeania hirsuta

Moss, N., Leao, T., Rankin, M., McCullough, T. M., Qu, P., Коробейников, А. И., Smith, J. L., Gerwick, L. & Gerwick, W. H., 16 Nov 2018, In : ACS Chemical Biology.

Research output

Open Access
Biosynthesis
Biosynthetic Pathways
Cyanobacteria
Genes
Peptide Synthases

Singular Spectrum Analysis with R

Golyandina, N., Korobeynikov, A. & Zhigljavsky, A., 2018, Berlin Heidelberg: Springer. 272 p. (Use R!)

Research output

2017
6 Citations (Scopus)

A Maldiisotopic Approach to Discover Natural Products: Cryptomaldamide, a Hybrid Tripeptide from the Marine Cyanobacterium Moorea producens

Kinnel, R. B., Esquenazi, E., Leao, T., Moss, N., Mevers, E., Pereira, A. R., Monroe, E. A., Korobeynikov, A., Murray, T. F., Sherman, D., Gerwick, L., Dorrestein, P. C. & Gerwick, W. H., 26 May 2017, In : Journal of Natural Products. 80, 5, p. 1514-1521 8 p.

Research output

Cyanobacteria
Biological Products
Genes
Biosynthesis
Amidinotransferases

Assessing the significance of peptide spectrum match scores

Abramova, A. & Korobeynikov, A., 1 Aug 2017, 17th International Workshop on Algorithms in Bioinformatics, WABI 2017. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, Vol. 88. 14. (Leibniz International Proceedings in Informatics, LIPIcs; vol. 88).

Research outputpeer-review

Peptides
Antibiotics
Markov processes
Mass spectrometry
Amino acids
24 Citations (Scopus)

Comparative genomics uncovers the prolific and distinctive metabolic potential of the cyanobacterial genus Moorea

Leao, T., Castelão, G., Korobeynikov, A., Monroe, E. A., Podell, S., Glukhov, E., Allen, E. E., Gerwick, W. H. & Gerwick, L., 21 Mar 2017, In : Proceedings of the National Academy of Sciences of the United States of America. 114, 12, p. 3198-3203 6 p.

Research output

genomics
secondary metabolites
genome
Cyanobacteria
multigene family
282 Citations (Scopus)

MetaSPAdes: A new versatile metagenomic assembler

Nurk, S., Мелешко, Д. А., Korobeynikov, A. & Pevzner, P. A., 1 May 2017, In : Genome Research. 27, 5, p. 824-834 11 p.

Research output

Metagenomics
Metagenome
Benchmarking
Diploidy
Population
2016
6 Citations (Scopus)

A novel uncultured heterotrophic bacterial associate of the cyanobacterium Moorea producens JHB

Cummings, S. L., Barbé, D., Leao, T. F., Korobeynikov, A., Engene, N., Glukhov, E., Gerwick, W. H. & Gerwick, L., 2016, In : BMC Microbiology. 16, 1

Research output

Cyanobacteria
Genome
Bacteria
Acidobacteria
Transposases
93 Citations (Scopus)
Nanopores
Genome
Technology
Costs and Cost Analysis
Benchmarking
18 Citations (Scopus)

Sequencing Rare Marine Actinomycete Genomes Reveals High Density of Unique Natural Product Biosynthetic Gene Clusters

Schorn, M. A., Alanjary, M. M., Aguinaldo, K., Korobeynikov, A., Podell, S., Patin, N. V., Lincecum, T., Jensen, P. R., Ziemert, N. & Moore, B. S., 2016, In : Microbiology.

Research output

15 Citations (Scopus)

The Phormidolide Biosynthetic Gene Cluster: A trans-AT PKS Pathway Encoding a Toxic Macrocyclic Polyketide

Bertin, M. J., Vulpanovici, A., Monroe, E. A., Korobeynikov, A., Sherman, D. H., Gerwick, L. & Gerwick, W. H., 2016, In : Chembiochem : a European journal of chemical biology. 17, 2, 10 p.

Research output

Polyketide Synthases
Polyketides
Acyltransferases
Poisons
Multigene Family
2015
9 Citations (Scopus)

Assembling short reads from jumping libraries with large insert sizes

Vasilinetc, I., Prjibelski, A. D., Gurevich, A., Korobeynikov, A. & Pevzner, P. A., 2015, In : Bioinformatics. 31, 20, p. 3262-3268

Research output

Libraries
Bacterial Genomes
Sequencing
Preparation
Genome
70 Citations (Scopus)

Combining Mass Spectrometric Metabolic Profiling with Genomic Analysis: A Powerful Approach for Discovering Natural Products from Cyanobacteria

Kleigrewe, K., Almaliti, J., Tian, I. Y., Kinnel, R. B., Korobeynikov, A., Monroe, E. A., Duggan, B. M., Di Marzo, V., Sherman, D. H., Dorrestein, P. C., Gerwick, L. & Gerwick, W. H., 2015, In : Journal of Natural Products. 78, 7, p. 1671-1682

Research output

Cyanobacteria
Biological Products
Genes
Genome
Multigene Family
13 Citations (Scopus)

Expanding the Described Metabolome of the Marine Cyanobacterium Moorea producens JHB through Orthogonal Natural Products Workflows

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., 2015, In : PLoS ONE. 10, 7

Research output

Moorea producens
metabolome
Metabolome
Workflow
Cyanobacteria
17 Citations (Scopus)

Spongosine production by a vibrio harveyi strain associated with the sponge tectitethya crypta

Bertin, M. J., Schwartz, S. L., Lee, J., Korobeynikov, A., Dorrestein, P. C., Gerwick, L. & Gerwick, W. H., 2015, In : Journal of Natural Products. 78, 3, p. 493-499

Research output

Arabinofuranosyluracil
Vibrio
Porifera
Non-Steroidal Anti-Inflammatory Agents
Bioactivity
74 Citations (Scopus)

Characterization of Cyanobacterial Hydrocarbon Composition and Distribution of Biosynthetic Pathways

Coates, R. C., Podell, S., Korobeynikov, A., Lapidus, A., Pevzner, P., Sherman, D. H., Allen, E. E., Gerwick, L. & Gerwick, W. H., 2014, In : PLoS ONE. 9, 1, p. e85140

Research output

50 Citations (Scopus)

ExSPAnder: a universal repeat resolver for DNA fragment assembly

Prjibelski, A. D., Vasilinetc, I., Bankevich, A., Gurevich, A., Krivosheeva, T., Nurk, S., Pham, S., Korobeynikov, A., Lapidus, A. & Pevzner, P. A., 2014, In : Bioinformatics. 30, 12, p. I293-I301

Research output

31 Citations (Scopus)

Single cell genome analysis of an uncultured heterotrophic stramenopile

Roy, R. S., Price, D. C., Schliep, A., Cai, G., Korobeynikov, A., Yoon, H. S., Yang, E. C. & Bhattacharya, D., 2014, In : Scientific Reports. 4, p. Art.No.4780

Research output

2013
172 Citations (Scopus)

Assembling Genomes and mini-metagenomes from highly chimeric reads

Nurk, S., Bankevich, A., Antipov, D., Gurevich, A., Korobeynikov, A., Lapidus, A., Prjibelsky, A., Pyshkin, A., Sirotkin, A., Sirotkin, Y., Stepanauskas, R., McLean, J., Lasken, R., Clingenpeel, S. R., Woyke, T., Tesler, G., Alekseyev, M. A. & Pevzner, P. A., 2013, Research in Computational Molecular Biology - 17th Annual International Conference, RECOMB 2013, Beijing, China, April 7-10, 2013. Proceedings. Lecture Notes in Computer Science 7821. p. 158-170

Research output

429 Citations (Scopus)

Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products

Nurk, S., Bankevich, A., Antipov, D., Gurevich, A. A., Korobeynikov, A., Lapidus, A., Prjibelski, A. D., 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., 2013, In : Journal of Computational Biology. 20, 10, p. 714-737

Research output

164 Citations (Scopus)

BayesHammer: Bayesian clustering for error correction in single-cell sequencing

Nikolenko, S. I., Korobeynikov, A. I. & Alekseyev, M. A., 2013, In : BMC Genomics. 14, S7, p. 1-11

Research output

2012
Interval Censoring
Maximum likelihood estimation
Inspection
Maximum likelihood
Parametric Model

Наглядная статистика. Используем R!

Шипунов, А. Б., Балдин, E. М., Волкова, П. А., Коробейников, А. И., Назарова, С. А., Петров, С. В. & Суфиянов, В. Г., 2012, ДМК Пресс. 298 p.

Research output

Open Access