Vsevolod Makeev - researchr alias

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Viewing Publication 1 - 20 from 20

2013

From binding motifs in Chip-seq Data to Improved Models of transcription factor binding SitesIvan V. Kulakovskiy, Victor G. Levitsky, Dmitry Yu. Oshchepkov, Leonid Bryzgalov, Ilya E. Vorontsov, Vsevolod Makeev. jbcb, 11(1), 2013. [doi]

HOCOMOCO: a comprehensive collection of human transcription factor binding sites modelsIvan V. Kulakovskiy, Yulia A. Medvedeva, Ulf Schaefer, Artem S. Kasianov, Ilya E. Vorontsov, Vladimir B. Bajic, Vsevolod Makeev. nar, 41(Database-Issue):195-202, 2013. [doi]

Learning Advanced TFBS Models from Chip-Seq Data - diChIPMunk: Effective Construction of Dinucleotide Positional Weight MatricesIvan V. Kulakovskiy, Victor G. Levitsky, Dmitry G. Oschepkov, Ilya E. Vorontsov, Vsevolod Makeev. biostec 2013: 146-150

Jaccard index based similarity measure to compare transcription factor binding site modelsIlya E. Vorontsov, Ivan V. Kulakovskiy, Vsevolod Makeev. almob, 8:23, 2013. [doi]

2012

Exploring Massive, Genome Scale Datasets with the GenometriCorr PackageAlexander V. Favorov, Loris Mularoni, Leslie M. Cope, Yulia A. Medvedeva, Andrey A. Mironov, Vsevolod Makeev, Sarah J. Wheelan. ploscb, 8(5), 2012. [doi]

A Generalized Hidden Markov Model for Prediction of Cis-regulatory Modules in Eukaryote Genomes and Description of Their Internal StructureAnna A. Nilulova, Alexander V. Favorov, Vsevolod Makeev, Andrey A. Mironov. biostec 2012: 34-41

2011

A deeper look into transcription regulatory code by preferred pair distance templates for transcription factor binding sitesIvan V. Kulakovskiy, A. A. Belostotsky, Artem S. Kasianov, Natalie G. Esipova, Yulia A. Medvedeva, I. A. Eliseeva, Vsevolod Makeev. bioinformatics, 27(19):2621-2624, 2011. [doi]

2010

Deep and wide digging for binding motifs in ChIP-Seq dataIvan V. Kulakovskiy, Valentina Boeva, Alexander V. Favorov, Vsevolod Makeev. bioinformatics, 26(20):2622-2623, 2010. [doi]

Empirical Potentials for ion Binding in proteinsSergei Rahmanov, Ivan V. Kulakovskiy, Leonid Uroshlev, Vsevolod Makeev. jbcb, 8(3):427-435, 2010. [doi]

2009

Motif discovery and motif finding from genome-mapped DNase footprint dataIvan V. Kulakovskiy, Alexander V. Favorov, Vsevolod Makeev. bioinformatics, 25(18):2318-2325, 2009. [doi]

2007

Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of ::::cis::::-regulatory modulesValentina Boeva, Julien ClÃ©ment, Mireille RÃ©gnier, Mikhail A. Roytberg, Vsevolod Makeev. almob, 2, 2007. [doi]

2006

Short fuzzy tandem repeats in genomic sequences, identification, and possible role in regulation of gene expressionValentina Boeva, Mireille Régnier, Dmitri A. Papatsenko, Vsevolod Makeev. bioinformatics, 22(6):676-684, 2006. [doi]

2005

A Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal lengthAlexander V. Favorov, Mikhail S. Gelfand, Anna V. Gerasimova, Dmitry A. Ravcheev, Andrey A. Mironov, Vsevolod Makeev. bioinformatics, 21(10):2240-2245, 2005. [doi]

2003

The channel in transporters is formed by residues that are rare in transmembrane helicesOlga V. Kalinina, Vsevolod Makeev, Roman A. Sutormin, Mikhail S. Gelfand, Aleksandra B. Rakhmaninova. isb, 3:17, 2003. [doi]

Analysis of bacterial RM-Systems through genome-scale analysis and related taxonomic issuesMathias Vandenbogaert, Vsevolod Makeev. isb, 3:12, 2003. [doi]

2001

Segmentation of long genomic sequences into domains with homogeneous composition with BASIO softwareVasily Ramensky, Vsevolod Makeev, Mikhail A. Roytberg, Vladimir G. Tumanyan. bioinformatics, 17(11):1065-1066, 2001.

2000

Bayesian Approach to DNA Segmentation into Regions with Different Average Nucleotide CompositionVsevolod Makeev, Vasily Ramensky, Mikhail S. Gelfand, Mikhail A. Roytberg, Vladimir G. Tumanyan. jobim 2001: 57-73 [doi]

DNA Segmentation Through the Bayesian ApproachVasily Ramensky, Vsevolod Makeev, Mikhail A. Roytberg, Vladimir G. Tumanyan. jcb, 7(1-2):215-231, 2000.

Three Variations on Word CountingMireille Régnier, Alexandre Lifanov, Vsevolod Makeev. gcb 2000: 75-82

1996

Search of periodicities in primary structure of biopolymers: a general Fourier approachVsevolod Makeev, Vladimir G. Tumanyan. bioinformatics, 12(1):49-54, 1996.

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