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Ivan Kulakovskiy
Ivan Kulakovskiy
Institute of Protein Research RAS
Verified email at vigg.ru - Homepage
Title
Cited by
Cited by
Year
A promoter-level mammalian expression atlas
TF Consortium
Nature 507 (7493), 462-470, 2014
13702014
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
4422018
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
2512013
Effects of cytosine methylation on transcription factor binding sites
YA Medvedeva, AM Khamis, IV Kulakovskiy, W Ba-Alawi, MSI Bhuyan, ...
BMC Genomics 15 (1), 119, 2014
2282014
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
2102016
EpiFactors: a comprehensive database of human epigenetic factors and complexes
YA Medvedeva, A Lennartsson, R Ehsani, IV Kulakovskiy, IE Vorontsov, ...
Database 2015, bav067, 2015
1752015
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
1712010
Intergenic, gene terminal, and intragenic CpG islands in the human genome
Y Medvedeva, M Fridman, N Oparina, D Malko, E Ermakova, ...
BMC genomics 11 (1), 48, 2010
952010
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
752020
From binding motifs in ChIP-seq data to improved models of transcription factor binding sites
I KULAKOVSKIY, V LEVITSKY, D OSHCHEPKOV, L BRYZGALOV, ...
Journal of Bioinformatics and Computational Biology, 2013
712013
Jaccard index based similarity measure to compare transcription factor binding site models
IE Vorontsov, IV Kulakovskiy, VJ Makeev
Algorithms for Molecular Biology 8 (1), 23, 2013
662013
Architectural proteins Pita, Zw5, and ZIPIC contain homodimerization domain and support specific long-range interactions in Drosophila
N Zolotarev, A Fedotova, O Kyrchanova, A Bonchuk, AA Penin, AS Lando, ...
Nucleic acids research 44 (15), 7228-7241, 2016
552016
Single-Cell Analyses of ESCs Reveal Alternative Pluripotent Cell States and Molecular Mechanisms that Control Self-Renewal
D Papatsenko, H Darr, IV Kulakovskiy, A Waghray, VJ Makeev, ...
Stem Cell Reports 5 (2), 207-220, 2015
492015
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
462021
Application of experimentally verified transcription factor binding sites models for computational analysis of ChIP-Seq data
VG Levitsky, IV Kulakovskiy, NI Ershov, DY Oshchepkov, VJ Makeev, ...
BMC genomics 15 (1), 80, 2014
432014
Discovery of DNA motifs recognized by transcription factors through integration of different experimental sources
IV Kulakovskiy, VJ Makeev
Biophysics 54 (6), 667-674, 2009
392009
Motif discovery and motif finding from genome-mapped DNase footprint data
IV Kulakovskiy, AV Favorov, VJ Makeev
Bioinformatics 25 (18), 2318-2325, 2009
382009
Sequence-based model of gap gene regulatory network
K Kozlov, V Gursky, I Kulakovskiy, M Samsonova
BMC Genomics 15 (Suppl 12), S6, 2014
322014
Spi-1/PU. 1 activates transcription through clustered DNA occupancy in erythroleukemia
M Ridinger-Saison, V Boeva, P Rimmelé, I Kulakovskiy, I Gallais, ...
Nucleic Acids Research 40 (18), 8927-8941, 2012
312012
Multifaceted deregulation of gene expression and protein synthesis with age
AS Anisimova, MB Meerson, MV Gerashchenko, IV Kulakovskiy, ...
PNAS 117 (27), 15581-15590, 2020
302020
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