Vsevolod Makeev
Vsevolod Makeev
Cancer Research UK, Manchester
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A promoter-level mammalian expression atlas
Nature 507 (7493), 462-470, 2014
Assessing computational tools for the discovery of transcription factor binding sites
M Tompa, N Li, TL Bailey, GM Church, B De Moor, E Eskin, AV Favorov, ...
Nature biotechnology 23 (1), 137-144, 2005
HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis
IV Kulakovskiy, IE Vorontsov, IS Yevshin, RN Sharipov, AD Fedorova, ...
Nucleic acids research 46 (D1), D252-D259, 2018
An integrated expression atlas of miRNAs and their promoters in human and mouse
D De Rie, I Abugessaisa, T Alam, E Arner, P Arner, H Ashoor, G Åström, ...
Nature biotechnology 35 (9), 872-878, 2017
HOCOMOCO: a comprehensive collection of human transcription factor binding sites models
IV Kulakovskiy, YA Medvedeva, U Schaefer, AS Kasianov, IE Vorontsov, ...
Nucleic acids research 41 (D1), D195-D202, 2013
HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models
IV Kulakovskiy, IE Vorontsov, IS Yevshin, AV Soboleva, AS Kasianov, ...
Nucleic acids research 44 (D1), D116-D125, 2016
Homotypic regulatory clusters in Drosophila
AP Lifanov, VJ Makeev, AG Nazina, DA Papatsenko
Genome research 13 (4), 579-588, 2003
Identification of proteins associated with murine cytomegalovirus virions
LM Kattenhorn, R Mills, M Wagner, A Lomsadze, V Makeev, ...
Journal of virology 78 (20), 11187-11197, 2004
Exploring massive, genome scale datasets with the GenometriCorr package
A Favorov, L Mularoni, LM Cope, Y Medvedeva, AA Mironov, VJ Makeev, ...
PLoS computational biology 8 (5), e1002529, 2012
Deep and wide digging for binding motifs in ChIP-Seq data
IV Kulakovskiy, VA Boeva, AV Favorov, VJ Makeev
Bioinformatics 26 (20), 2622-2623, 2010
De novo sequencing and characterization of floral transcriptome in two species of buckwheat (Fagopyrum)
MD Logacheva, AS Kasianov, DV Vinogradov, TH Samigullin, ...
BMC genomics 12, 1-17, 2011
A Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length
AV Favorov, MS Gelfand, AV Gerasimova, DA Ravcheev, AA Mironov, ...
Bioinformatics 21 (10), 2240-2245, 2005
GTRD: an integrated view of transcription regulation
S Kolmykov, I Yevshin, M Kulyashov, R Sharipov, Y Kondrakhin, ...
Nucleic acids research 49 (D1), D104-D111, 2021
Functional annotation of human long noncoding RNAs via molecular phenotyping
JA Ramilowski, CW Yip, S Agrawal, JC Chang, Y Ciani, IV Kulakovskiy, ...
Genome research 30 (7), 1060-1072, 2020
A novel model system for design of biomaterials based on recombinant analogs of spider silk proteins
VG Bogush, OS Sokolova, LI Davydova, DV Klinov, KV Sidoruk, ...
Journal of neuroimmune pharmacology 4, 17-27, 2009
Distance preferences in the arrangement of binding motifs and hierarchical levels in organization of transcription regulatory information
VJ Makeev, AP Lifanov, AG Nazina, DA Papatsenko
Nucleic acids research 31 (20), 6016-6026, 2003
Extraction of functional binding sites from unique regulatory regions: the Drosophila early developmental enhancers
DA Papatsenko, VJ Makeev, AP Lifanov, M Régnier, AG Nazina, ...
Genome research 12 (3), 470-481, 2002
Short fuzzy tandem repeats in genomic sequences, identification, and possible role in regulation of gene expression
V Boeva, M Regnier, D Papatsenko, V Makeev
Bioinformatics 22 (6), 676-684, 2006
Intergenic, gene terminal, and intragenic CpG islands in the human genome
YA Medvedeva, MV Fridman, NJ Oparina, DB Malko, EO Ermakova, ...
BMC genomics 11, 1-16, 2010
Jaccard index based similarity measure to compare transcription factor binding site models
IE Vorontsov, IV Kulakovskiy, VJ Makeev
Algorithms for Molecular Biology 8, 1-11, 2013
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