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Vsevolod J. Makeev
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- affiliation: Vavilov Institute of General Genetics (VIGG), Department of Computational Systems Biology
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2020 – today
- 2024
- [j23]Guguchkin Egor, Kasianov Artem, Belenikin Maksim, Zobkova Gaukhar, Kosova Ekaterina, Vsevolod J. Makeev
, Karpulevich Evgeny:
Enhancing SNV identification in whole-genome sequencing data through the incorporation of known genetic variants into the minimap2 index. BMC Bioinform. 25(1): 238 (2024) - [j22]Guguchkin Egor, Kasianov Artem, Belenikin Maksim, Zobkova Gaukhar, Kosova Ekaterina, Vsevolod J. Makeev
Correction: Enhancing SNV identification in whole-genome sequencing data through the incorporation of known genetic variants into the minimap2 index. BMC Bioinform. 25(1): 268 (2024) - 2022
- [j21]Alexandr Boytsov
ANANASTRA: annotation and enrichment analysis of allele-specific transcription factor binding at SNPs. Nucleic Acids Res. 50(W1): 51-56 (2022) - 2021
- [j20]Semyon Kolmykov
GTRD: an integrated view of transcription regulation. Nucleic Acids Res. 49(Database-Issue): D104-D111 (2021)
2010 – 2019
- 2018
- [j19]Ivan V. Kulakovskiy
HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis. Nucleic Acids Res. 46(Database-Issue): D252-D259 (2018) - 2016
- [j18]Ivan V. Kulakovskiy
HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models. Nucleic Acids Res. 44(Database-Issue): 116-125 (2016) - 2015
- [c5]Ilya E. Vorontsov, Ivan V. Kulakovskiy, Grigory Khimulya, Daria D. Nikolaeva, Vsevolod J. Makeev:
PERFECTOS-APE - Predicting Regulatory Functional Effect of SNPs by Approximate P-value Estimation. BIOINFORMATICS 2015: 102-108 - 2014
- [j17]The Fantom Consortium, RIKEN PMII, RIKEN CLST (DGT), Alistair R. R. Forrest, Hideya Kawaji, Michael Rehli, J. Kenneth Baillie, Michiel J. L. de Hoon, Vanja Haberle, Timo Lassmann, Ivan V. Kulakovskiy, Marina Lizio, Masayoshi Itoh, Robin Andersson, Christopher J. Mungall, Terrence F. Meehan, Sebastian Schmeier, Nicolas Bertin, Mette Jørgensen, Emmanuel Dimont, Erik Arner, Christian Schmidl, Ulf Schaefer, Yulia A. Medvedeva
A promoter-level mammalian expression atlas. Nat. 507(7493): 462-470 (2014) - 2013
- [j16]Ilya E. Vorontsov
Jaccard index based similarity measure to compare transcription factor binding site models. Algorithms Mol. Biol. 8: 23 (2013) - [j15]Ivan V. Kulakovskiy
From binding motifs in Chip-seq Data to Improved Models of transcription factor binding Sites. J. Bioinform. Comput. Biol. 11(1) (2013) - [j14]Ivan V. Kulakovskiy
HOCOMOCO: a comprehensive collection of human transcription factor binding sites models. Nucleic Acids Res. 41(Database-Issue): 195-202 (2013) - [c4]Ivan V. Kulakovskiy, Victor G. Levitsky, Dmitry G. Oschepkov, Ilya E. Vorontsov, Vsevolod J. Makeev:
Learning Advanced TFBS Models from Chip-Seq Data - diChIPMunk: Effective Construction of Dinucleotide Positional Weight Matrices. BIOINFORMATICS 2013: 146-150 - 2012
- [j13]Alexander V. Favorov, Loris Mularoni
Exploring Massive, Genome Scale Datasets with the GenometriCorr Package. PLoS Comput. Biol. 8(5) (2012) - [c3]Anna A. Nilulova, Alexander V. Favorov, Vsevolod J. Makeev, Andrey A. Mironov:
A Generalized Hidden Markov Model for Prediction of Cis-regulatory Modules in Eukaryote Genomes and Description of Their Internal Structure. BIOINFORMATICS 2012: 34-41 - 2011
- [j12]Ivan V. Kulakovskiy
A deeper look into transcription regulatory code by preferred pair distance templates for transcription factor binding sites. Bioinform. 27(19): 2621-2624 (2011) - 2010
- [j11]Ivan V. Kulakovskiy
Deep and wide digging for binding motifs in ChIP-Seq data. Bioinform. 26(20): 2622-2623 (2010) - [j10]Sergei Rahmanov, Ivan V. Kulakovskiy
Empirical Potentials for ion Binding in proteins. J. Bioinform. Comput. Biol. 8(3): 427-435 (2010)
2000 – 2009
- 2009
- [j9]Ivan V. Kulakovskiy
Motif discovery and motif finding from genome-mapped DNase footprint data. Bioinform. 25(18): 2318-2325 (2009) - 2007
- [j8]Valentina Boeva
Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modules. Algorithms Mol. Biol. 2 (2007) - 2006
- [j7]Valentina Boeva
Short fuzzy tandem repeats in genomic sequences, identification, and possible role in regulation of gene expression. Bioinform. 22(6): 676-684 (2006) - 2005
- [j6]Alexander V. Favorov, Mikhail S. Gelfand
A Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length. Bioinform. 21(10): 2240-2245 (2005) - 2003
- [j5]Mathias Vandenbogaert, Vsevolod J. Makeev:
Analysis of bacterial RM-Systems through genome-scale analysis and related taxonomic issues. Silico Biol. 3(1-2): 127-143 (2003) - [j4]Olga V. Kalinina, Vsevolod J. Makeev, Roman A. Sutormin, Mikhail S. Gelfand, Aleksandra B. Rakhmaninova:
The channel in transporters is formed by residues that are rare in transmembrane helices. Silico Biol. 3(1-2): 197-204 (2003) - 2001
- [j3]Vasily Ramensky
Segmentation of long genomic sequences into domains with homogeneous composition with BASIO software. Bioinform. 17(11): 1065-1066 (2001) - 2000
- [j2]Vasily Ramensky
DNA Segmentation Through the Bayesian Approach. J. Comput. Biol. 7(1-2): 215-231 (2000) - [c2]Mireille Régnier, Alexandre Lifanov, Vsevolod J. Makeev:
Three Variations on Word Counting. German Conference on Bioinformatics 2000: 75-82 - [c1]Vsevolod J. Makeev
Bayesian Approach to DNA Segmentation into Regions with Different Average Nucleotide Composition. JOBIM 2000: 57-73
1990 – 1999
- 1996
- [j1]Vsevolod J. Makeev
Search of periodicities in primary structure of biopolymers: a general Fourier approach. Comput. Appl. Biosci. 12(1): 49-54 (1996)
Coauthor Index
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