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
11622014
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
2912018
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
2302013
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
2032014
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
1822016
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
1582010
EpiFactors: a comprehensive database of human epigenetic factors and complexes
YA Medvedeva, A Lennartsson, R Ehsani, IV Kulakovskiy, IE Vorontsov, ...
Database 2015, bav067, 2015
1332015
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
902010
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
602013
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
502013
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
452015
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
432016
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
372014
Motif discovery and motif finding from genome-mapped DNase footprint data
IV Kulakovskiy, AV Favorov, VJ Makeev
Bioinformatics 25 (18), 2318-2325, 2009
362009
Discovery of DNA motifs recognized by transcription factors through integration of different experimental sources
IV Kulakovskiy, VJ Makeev
Biophysics 54 (6), 667-674, 2009
352009
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
292012
PERFECTOS-APE-predicting regulatory functional effect of SNPs by approximate P-value estimation
IE Vorontsov, IV Kulakovskiy, G Khimulya, DD Nikolaeva, VJ Makeev
International Conference on Bioinformatics Models, Methods and Algorithms 2 …, 2015
262015
Sequence-based model of gap gene regulatory network
K Kozlov, V Gursky, I Kulakovskiy, M Samsonova
BMC Genomics 15 (Suppl 12), S6, 2014
262014
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
252020
High‐quality genome assembly of Capsella bursa‐pastoris reveals asymmetry of regulatory elements at early stages of polyploid genome evolution
AS Kasianov, AV Klepikova, IV Kulakovskiy, ES Gerasimov, AV Fedotova, ...
The Plant Journal 91 (2), 278-291, 2017
222017
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