Ivan Kulakovskiy

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Vsevolod MakeevVavilov Institute of General Genetics, Department of computational systems biologyVerified email at vigg.ru
Ilya VorontsovVavilov Institute of General GeneticsVerified email at vigg.ru
Yulia A MedvedevaResearch Center of Biotechnology RASVerified email at biengi.ac.ru
Eliseeva IrinaInstitute of protein research RASVerified email at vega.protres.ru
Fedor KolpakovBiosoft.RuVerified email at biosoft.ru
Alexander Favorovresearch associate@oncbiostat.jhu.edu; senior fellow reasearcher@vigg.ruVerified email at sensi.org
Dmitry KuprashEngelhardt Institute of Molecular BiologyVerified email at eimb.ru
Anton SchwartzEngelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, RussiaVerified email at eimb.ru
Marina FridmanResearcher of Vavilov Institute of General GeneticsVerified email at vigg.ru
Valentina BoevaAssistant Prof., ETH Zürich, Department of Computer ScienceVerified email at inf.ethz.ch
Wail Ba-alawiPrincess Margaret Cancer Center, UHN; Medical Biophysics, UofTVerified email at uhnresearch.ca
Aleksey PeninThe Institute for Information Transmission Problems of the Russian Academy of SciencesVerified email at de.bio.msu.ru
Grigory KhimulyaPrivateVerified email at alumni.harvard.edu
Sergey DmitrievBelozersky Institute of Physico-Chemical Biology, Moscow State UniversityVerified email at belozersky.msu.ru
Abdullah M KhamisKing Abdullah University of Science and Technology (KAUST)Verified email at kaust.edu.sa
Konstantin KozlovPeter the Great St.Petersburg Polytechnic University (SPbPU)Verified email at spbstu.ru
Maria SamsonovaProfessor, Peter the Great St.Petersburg Polytechnic University (SPbPU)Verified email at spbstu.ru
Nina OparinaGothenburg University, Gothenburg, SwedenVerified email at gu.se
Arturo Magana-MoraLead Data Scientist, Saudi AramcoVerified email at kaust.edu.sa
Kirill KorneevEngelhardt Institute of Molecular BiologyVerified email at eimb.ru

Ivan Kulakovskiy

Institute of Protein Research RAS

Verified email at vigg.ru - Homepage

bioinformatics gene regulation sequence analysis high-throughput sequencing


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A promoter-level mammalian expression atlas TF Consortium Nature 507 (7493), 462-470, 2014	1220	2014
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	335	2018
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	240	2013
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	211	2014
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	194	2016
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	163	2010
EpiFactors: a comprehensive database of human epigenetic factors and complexes YA Medvedeva, A Lennartsson, R Ehsani, IV Kulakovskiy, IE Vorontsov, ... Database 2015, bav067, 2015	140	2015
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	92	2010
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	63	2013
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	53	2013
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	46	2015
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	45	2016
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	41	2020
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	39	2014
Motif discovery and motif finding from genome-mapped DNase footprint data IV Kulakovskiy, AV Favorov, VJ Makeev Bioinformatics 25 (18), 2318-2325, 2009	38	2009
Discovery of DNA motifs recognized by transcription factors through integration of different experimental sources IV Kulakovskiy, VJ Makeev Biophysics 54 (6), 667-674, 2009	37	2009
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	30	2012
Sequence-based model of gap gene regulatory network K Kozlov, V Gursky, I Kulakovskiy, M Samsonova BMC Genomics 15 (Suppl 12), S6, 2014	28	2014
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	26	2015
Early B-cell factor 1 (EBF1) is critical for transcriptional control of SLAMF1 gene in human B cells AM Schwartz, LV Putlyaeva, M Covich, AV Klepikova, KA Akulich, ... Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms 1859 (10 …, 2016	24	2016

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