Vsevolod J. Makeev

28 papers Journal 23Unranked 5
YearRankTypeTitle / Venue / Authors
2025 J jnl
Exclusive functional signatures for gene annotation with vast OpenOrd layout.
Algorithms Mol. Biol.
Gleb S. Buzanov, Vsevolod J. Makeev
2024 J jnl
Correction: Enhancing SNV identification in whole-genome sequencing data through the incorporation of known genetic variants into the minimap2 index.
BMC Bioinform.
Egor Guguchkin, Artem Kasianov, Maksim Belenikin, Gaukhar Zobkova, Ekaterina Kosova, Vsevolod J. Makeev, Evgeny Karpulevich
2024 J jnl
Enhancing SNV identification in whole-genome sequencing data through the incorporation of known genetic variants into the minimap2 index.
BMC Bioinform.
Egor Guguchkin, Artem Kasianov, Maksim Belenikin, Gaukhar Zobkova, Ekaterina Kosova, Vsevolod J. Makeev, Evgeny Karpulevich
2022 J jnl
ANANASTRA: annotation and enrichment analysis of allele-specific transcription factor binding at SNPs.
Nucleic Acids Res.
Alexandr Boytsov, Sergey Abramov, Ariuna Z. Aiusheeva, Alexandra M. Kasianova, Eugene Baulin, Ivan A. Kuznetsov, Yurii S. Aulchenko, Semyon Kolmykov, Ivan S. Yevshin, Fedor A. Kolpakov, Ilya E. Vorontsov, Vsevolod J. Makeev, Ivan V. Kulakovskiy
2021 J jnl
GTRD: an integrated view of transcription regulation.
Nucleic Acids Res.
Semyon Kolmykov, Ivan S. Yevshin, Mikhail Kulyashov, Ruslan N. Sharipov, Yury V. Kondrakhin, Vsevolod J. Makeev, Ivan V. Kulakovskiy, Alexander E. Kel, Fedor A. Kolpakov
2018 J jnl
HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis.
Nucleic Acids Res.
Ivan V. Kulakovskiy, Ilya E. Vorontsov, Ivan S. Yevshin, Ruslan N. Sharipov, Alla D. Fedorova, Eugene I. Rumynskiy, Yulia A. Medvedeva, Arturo Magana-Mora, Vladimir B. Bajic, Dmitri A. Papatsenko, Fedor A. Kolpakov, Vsevolod J. Makeev
2016 J jnl
HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models.
Nucleic Acids Res.
Ivan V. Kulakovskiy, Ilya E. Vorontsov, Ivan S. Yevshin, Anastasiia V. Soboleva, Artem S. Kasianov, Haitham Ashoor, Wail Ba-alawi, Vladimir B. Bajic, Yulia A. Medvedeva, Fedor A. Kolpakov, Vsevolod J. Makeev
2015 — conf
PERFECTOS-APE - Predicting Regulatory Functional Effect of SNPs by Approximate P-value Estimation.
BIOINFORMATICS
Ilya E. Vorontsov, Ivan V. Kulakovskiy, Grigory Khimulya, Daria D. Nikolaeva, Vsevolod J. Makeev
2013 J jnl
From binding motifs in Chip-seq Data to Improved Models of transcription factor binding Sites.
J. Bioinform. Comput. Biol.
Ivan V. Kulakovskiy, Victor G. Levitsky, Dmitry Yu. Oshchepkov, Leonid Bryzgalov, Ilya E. Vorontsov, Vsevolod J. Makeev
2013 J jnl
HOCOMOCO: a comprehensive collection of human transcription factor binding sites models.
Nucleic Acids Res.
Ivan V. Kulakovskiy, Yulia A. Medvedeva, Ulf Schaefer, Artem S. Kasianov, Ilya E. Vorontsov, Vladimir B. Bajic, Vsevolod J. Makeev
2013 J jnl
Jaccard index based similarity measure to compare transcription factor binding site models.
Algorithms Mol. Biol.
Ilya E. Vorontsov, Ivan V. Kulakovskiy, Vsevolod J. Makeev
2013 — conf
Learning Advanced TFBS Models from Chip-Seq Data - diChIPMunk: Effective Construction of Dinucleotide Positional Weight Matrices.
BIOINFORMATICS
Ivan V. Kulakovskiy, Victor G. Levitsky, Dmitry G. Oschepkov, Ilya E. Vorontsov, Vsevolod J. Makeev
2012 — conf
A Generalized Hidden Markov Model for Prediction of Cis-regulatory Modules in Eukaryote Genomes and Description of Their Internal Structure.
BIOINFORMATICS
Anna A. Nilulova, Alexander V. Favorov, Vsevolod J. Makeev, Andrey A. Mironov
2012 J jnl
Exploring Massive, Genome Scale Datasets with the GenometriCorr Package.
PLoS Comput. Biol.
Alexander V. Favorov, Loris Mularoni, Leslie M. Cope, Yulia A. Medvedeva, Andrey A. Mironov, Vsevolod J. Makeev, Sarah J. Wheelan
2011 J jnl
A deeper look into transcription regulatory code by preferred pair distance templates for transcription factor binding sites.
Bioinform.
Ivan V. Kulakovskiy, A. A. Belostotsky, Artem S. Kasianov, Natalia G. Esipova, Yulia A. Medvedeva, I. A. Eliseeva, Vsevolod J. Makeev
2010 J jnl
Deep and wide digging for binding motifs in ChIP-Seq data.
Bioinform.
Ivan V. Kulakovskiy, Valentina Boeva, Alexander V. Favorov, Vsevolod J. Makeev
2010 J jnl
Empirical Potentials for ion Binding in proteins.
J. Bioinform. Comput. Biol.
Sergei Rahmanov, Ivan V. Kulakovskiy, Leonid Uroshlev, Vsevolod J. Makeev
2009 J jnl
Motif discovery and motif finding from genome-mapped DNase footprint data.
Bioinform.
Ivan V. Kulakovskiy, Alexander V. Favorov, Vsevolod J. Makeev
2007 J jnl
Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of
Algorithms Mol. Biol.
Valentina Boeva, Julien Clément, Mireille Régnier, Mikhail A. Roytberg, Vsevolod J. Makeev
2006 J jnl
Short fuzzy tandem repeats in genomic sequences, identification, and possible role in regulation of gene expression.
Bioinform.
Valentina Boeva, Mireille Régnier, Dmitri A. Papatsenko, Vsevolod J. Makeev
2005 J jnl
A Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length.
Bioinform.
Alexander V. Favorov, Mikhail S. Gelfand, Anna V. Gerasimova, Dmitry A. Ravcheev, Andrey A. Mironov, Vsevolod J. Makeev
2003 J jnl
Analysis of bacterial RM-Systems through genome-scale analysis and related taxonomic issues.
Silico Biol.
Mathias Vandenbogaert, Vsevolod J. Makeev
2003 J jnl
The channel in transporters is formed by residues that are rare in transmembrane helices.
Silico Biol.
Olga V. Kalinina, Vsevolod J. Makeev, Roman A. Sutormin, Mikhail S. Gelfand, Aleksandra B. Rakhmaninova
2001 J jnl
Segmentation of long genomic sequences into domains with homogeneous composition with BASIO software.
Bioinform.
Vasily Ramensky, Vsevolod J. Makeev, Mikhail A. Roytberg, Vladimir G. Tumanyan
2000 — conf
Bayesian Approach to DNA Segmentation into Regions with Different Average Nucleotide Composition.
JOBIM
Vsevolod J. Makeev, Vasily Ramensky, Mikhail S. Gelfand, Mikhail A. Roytberg, Vladimir G. Tumanyan
2000 J jnl
DNA Segmentation Through the Bayesian Approach.
J. Comput. Biol.
Vasily Ramensky, Vsevolod J. Makeev, Mikhail A. Roytberg, Vladimir G. Tumanyan
2000 — conf
Three Variations on Word Counting.
German Conference on Bioinformatics
Mireille Régnier, Alexandre Lifanov, Vsevolod J. Makeev
1996 J jnl
Search of periodicities in primary structure of biopolymers: a general Fourier approach.
Comput. Appl. Biosci.
Vsevolod J. Makeev, Vladimir G. Tumanyan