Research Output 1974 2020

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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., TalLuzzatto-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., 16 Oct 2019, In : Cell Systems.

Research output

Biological Products
Microbiota
Peptides
Social Networking
Metagenomics

Monte Carlo Method for Solving ODE Systems

Ермаков, С. М. & Товстик, Т. М., 2019, Vestnik St. Petersburg University: Mathematics, 52, 3, p. 272-280 9 p.

Research output

Open Access
Monte Carlo method
System of Integral Equations
Transition Density
Cubic equation
Linear Ordinary Differential Equations

Noise model estimation with application to gene expression

Zhornikova, P., Golyandina, N. & Spirov, A., 1 Apr 2019, In : Journal of Bioinformatics and Computational Biology. 17, 2, 20 p., 1950009.

Research output

Gene expression
Gene Expression
Noise
Singular Spectrum Analysis
Multiplicative Model
3 Downloads (Pure)
Open Access
File
Markov processes
Integral equations
Stochastic Equations
Differential equations
Monte Carlo methods
Positive Matrices
Optimization Methods
Approximation Problem
Approximation
Semifield
Polynomial Regression
Intercept
Chebyshev System
Regression Function
Coefficient
Robust Design
Regression Model
Maximin
Circular function
Optimization Problem
1 Downloads (Pure)
Optimal Scheduling
Optimization Problem
Objective function
Idempotent
Semiring
Basin of Attraction
Vertical
Vibration
Asymptotic Methods
Perturbation
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
1 Citation (Scopus)
Semifield
Optimization Problem
Solution Set
Irreducible Matrix
Subset
14 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
1 Citation (Scopus)

Excess of locally D-optimal designs for Cobb–Douglas model

Шпилев, П. В., Мелас, В. Б. & Григорьев, Ю. Д., Dec 2018, In : Statistical Papers. Volume 59, Issue 4, p. 1425-1439 15 p.

Research output

15 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
Newton-Raphson method
Time series
Costs
1 Citation (Scopus)

Optimal discrimination designs for semiparametric models

Мелас, В. Б., Гученко, Р. А., Dette, H. & Wong, W. K., 2018, In : Biometrika. 105, 1, p. 185-197 13 p.

Research output

1 Citation (Scopus)
Positive Matrices
Max-algebra
Matrix Approximation
Low-rank Approximation
Low-rank Matrices
1 Citation (Scopus)
Random number
Randomisation
Monte Carlo methods
Quasi-Monte Carlo Methods
Random Sequence

Rod Vibrations Caused by Axial Impact

Morozov, N. F., Belyaev, A. K., Tovstik, P. E., Tovstik, T. P. & Shurpatov, A. O., 1 May 2018, In : Doklady Physics. 63, 5, p. 208-212 5 p.

Research output

Elastic waves
Vibrations (mechanical)
transverse oscillation
rods
vibration
Optimization Problem
Semifield
Entire Solution
Subset
Chebyshev
2 Citations (Scopus)
rods
Axial compression
longitudinal waves
Hinges
vibration
2 Citations (Scopus)
Vibration
Vertical
Pendulum
Critical Load
Pivoting
1 Citation (Scopus)
Analytical Hierarchy Process
Pairwise Comparisons
Solution Set
Chebyshev Approximation
Entire Solution
3 Citations (Scopus)
Elasticity
shear
elastic properties

Two-Exponential Models of Gene Expression Patterns for Noisy Experimental Data

Alexandrov, T., Golyandina, N., Holloway, D., Shlemov, A. & Spirov, A., 1 Nov 2018, In : Journal of Computational Biology. 25, 11, p. 1220–1230 11 p.

Research output

Exponential Model
Noisy Data
Gene expression
Gene Expression
Experimental Data
Bicriteria
Decision problem
Optimization Techniques
Pairwise Comparisons
Optimization Problem