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Author Details

Ivan V Kulakovskiy
Vavilov Institute of General Genetics, Russian Academy of Sciences
2009
67
21
PMIDPaper TitleJournal TitlePublished Year
37971293HOCOMOCO in 2024: a rebuild of the curated collection of binding models for human and mouse transcription factors.Nucleic Acids Res2024
36350659EpiFactors 2022: expansion and enhancement of a curated database of human epigenetic factors and complexes.Nucleic Acids Res2023
37490428LegNet: a best-in-class deep learning model for short DNA regulatory regions.Bioinformatics2023
37762093rs71327024 Associated with COVID-19 Hospitalization Reduces <i>CXCR6</i> Promoter Activity in Human CD4<sup>+</sup> T Cells via Disruption of c-Myb Binding.Int J Mol Sci2023
37176068Human Tissues Exhibit Diverse Composition of Translation Machinery.Int J Mol Sci2023
35018467Ribosomal leaky scanning through a translated uORF requires eIF4G2.Nucleic Acids Res2022
35501986Diverse Regulation of YB-1 and YB-3 Abundance in Mammals.Biochemistry (Mosc)2022
35516002RNA-Seq data of ALKBH5 and FTO double knockout HEK293T human cells.Data Brief2022
35446421ANANASTRA: annotation and enrichment analysis of allele-specific transcription factor binding at SNPs.Nucleic Acids Res2022
33231677GTRD: an integrated view of transcription regulation.Nucleic Acids Res2021
33765281Assessing Ribosome Distribution Along Transcripts with Polarity Scores and Regression Slope Estimates.Methods Mol Biol2021
34900236Ribo-Seq and RNA-Seq of <i>TMA46</i> ( <i>DFRP1</i>) and <i>GIR2</i> ( <i>DFRP2</i>) knockout yeast strains.F1000Res2021
34673265A GO catalogue of human DNA-binding transcription factors.Biochim Biophys Acta Gene Regul Mech2021
34606617A standard knockout procedure alters expression of adjacent loci at the translational level.Nucleic Acids Res2021
34107262Enhanced C/EBP binding to G·T mismatches facilitates fixation of CpG mutations in cancer and adult stem cells.Cell Rep2021
34016706Annotation of the local context of the RNA secondary structure improves the classification and prediction of A-minors.RNA2021
34070801<i>VTC4</i> Polyphosphate Polymerase Knockout Increases Stress Resistance of <i>Saccharomyces cerevisiae</i> Cells.Biology (Basel)2021
33980847Landscape of allele-specific transcription factor binding in the human genome.Nat Commun2021
34260924Enhanced C/EBP binding to G·T mismatches facilitates fixation of CpG mutations in cancer and adult stem cells.Cell Rep2021
32470086Brain-related genes are specifically enriched with long phase 1 introns.PLoS One2020
31785408Minor C allele of the SNP rs7873784 associated with rheumatoid arthritis and type-2 diabetes mellitus binds PU.1 and enhances TLR4 expression.Biochim Biophys Acta Mol Basis Dis2020
33138777A holistic view of mouse enhancer architectures reveals analogous pleiotropic effects and correlation with human disease.BMC Genomics2020
32576685Multifaceted deregulation of gene expression and protein synthesis with age.Proc Natl Acad Sci U S A2020
32393327Insights gained from a comprehensive all-against-all transcription factor binding motif benchmarking study.Genome Biol2020
30815525Translatome and transcriptome analysis of TMA20 (MCT-1) and TMA64 (eIF2D) knockout yeast strains.Data Brief2019
31737053What Do Neighbors Tell About You: The Local Context of Cis-Regulatory Modules Complicates Prediction of Regulatory Variants.Front Genet2019
30841857svist4get: a simple visualization tool for genomic tracks from sequencing experiments.BMC Bioinformatics2019
30813912An update to database TraVA: organ-specific cold stress response in Arabidopsis thaliana.BMC Plant Biol2019
30709331CpG traffic lights are markers of regulatory regions in human genome.BMC Genomics2019
31096715The Reduced Level of Inorganic Polyphosphate Mobilizes Antioxidant and Manganese-Resistance Systems in <i>Saccharomyces cerevisiae</i>.Cells2019
31106481Integration of multiple epigenomic marks improves prediction of variant impact in saturation mutagenesis reporter assay.Hum Mutat2019
28024445Role of structural water for prediction of cation binding sites in apoproteins.J Biomol Struct Dyn2018
29989583[The Novel Short Isoform of Securin Stimulates the Expression of Cyclin D3 and Angiogenesis Factors VEGFA and FGF2, but Does Not Affect the Expression of MYC Transcription Factor].Mol Biol (Mosk)2018
30352610Genome-wide map of human and mouse transcription factor binding sites aggregated from ChIP-Seq data.BMC Res Notes2018
29140464HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis.Nucleic Acids Res2018
27876533Multiple single nucleotide polymorphisms in the first intron of the IL2RA gene affect transcription factor binding and enhancer activity.Gene2017
28387959High-quality genome assembly of Capsella bursa-pastoris reveals asymmetry of regulatory elements at early stages of polyploid genome evolution.Plant J2017
28128390Transcriptome profile of yeast reveals the essential role of PMA2 and uncharacterized gene YBR056W-A (MNC1) in adaptation to toxic manganese concentration.Metallomics2017
28234966The single nucleotide variant rs12722489 determines differential estrogen receptor binding and enhancer properties of an IL2RA intronic region.PLoS One2017
29104781The Minor Variant of the Single-Nucleotide Polymorphism rs3753381 Affects the Activity of a SLAMF1 Enhancer.Acta Naturae2017
29297306De novo assembling and primary analysis of genome and transcriptome of gray whale Eschrichtius robustus.BMC Evol Biol2017
28898266Translating natural genetic variation to gene expression in a computational model of the Drosophila gap gene regulatory network.PLoS One2017
27137890Architectural proteins Pita, Zw5,and ZIPIC contain homodimerization domain and support specific long-range interactions in Drosophila.Nucleic Acids Res2016
26586801HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models.Nucleic Acids Res2016
27424222Early B-cell factor 1 (EBF1) is critical for transcriptional control of SLAMF1 gene in human B cells.Biochim Biophys Acta2016
27356864Negative selection maintains transcription factor binding motifs in human cancer.BMC Genomics2016
26153137EpiFactors: a comprehensive database of human epigenetic factors and complexes.Database (Oxford)2015
26267829Single-Cell Analyses of ESCs Reveal Alternative Pluripotent Cell States and Molecular Mechanisms that Control Self-Renewal.Stem Cell Reports2015
26694511Analysis of functional importance of binding sites in the Drosophila gap gene network model.BMC Genomics2015
24472686Application of experimentally verified transcription factor binding sites models for computational analysis of ChIP-Seq data.BMC Genomics2014
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Collaborators

Vsevolod J Makeev
Vavilov Institute of General Genetics, Russian Academy of Sciences
Co-authored papers 28
Ilya E Vorontsov
Vavilov Institute of General Genetics, Russian Academy of Sciences
Co-authored papers 24
Yulia A Medvedeva
Research Center of Biotechnology RAS, Russian Academy of Sciences
Co-authored papers 11
Artem S Kasianov
Institute for Information Transmission Problems of the Russian Academy of Sciences
Co-authored papers 8
Vladimir B Bajic
King Abdullah University of Science and Technology (KAUST)
Co-authored papers 6
Alexander V Favorov
Johns Hopkins School of Medicine
Co-authored papers 5
Vadim N Gladyshev
Brigham and Women's Hospital
Co-authored papers 4
Dmitri Papatsenko
Co-authored papers 4
Andreas Lennartsson
Karolinska Institute
Co-authored papers 3
Finn Drabl??s
NTNU - Norwegian University of Science and Technology
Co-authored papers 3
Alistair R R Forrest
RIKEN Center for Integrative Medical Sciences
Co-authored papers 2
Matthias Harbers
CellFree Sciences Co.
Co-authored papers 2
Oriol Fornes
BC Children's Hospital Research Institute, University of British Columbia
Co-authored papers 2
Ulf Schaefer
Co-authored papers 2
Timo Lassmann
Telethon Kids Institute, University of Western Australia
Co-authored papers 2
Takeya Kasukawa
RIKEN Center for Integrative Medical Sciences
Co-authored papers 2
Wail Ba-Alawi
Princess Margaret Cancer Centre, University Health Network, University Ave.
Co-authored papers 2
Hideya Kawaji
RIKEN Center for Integrative Medical Sciences
Co-authored papers 2
Robin Andersson
University of Copenhagen
Co-authored papers 1
Stefano Gustincich
Istituto Italiano di Tecnologia
Co-authored papers 1
Haruhiko Koseki
RIKEN Research Center for Allergy and Immunology
Co-authored papers 1
Yosuke Mizuno
Yokohama National University
Co-authored papers 1
Guojun Sheng
International Research Center for Medical Sciences (IRCMS), Kumamoto University
Co-authored papers 1
Christophe Simon
RIKEN Yokohama Institute
Co-authored papers 1
Silvano Piazza
International Centre for Genetic Engineering and Biotechnology
Co-authored papers 1
Hiroo Toyodo
Co-authored papers 1
Emily J Wood
Center for Molecular Medicine and Genetics, Wayne State University
Co-authored papers 1
Martin S Taylor
Institute of Genetics and Cancer, University of Edinburgh
Co-authored papers 1
Martin Kircher
Berlin Institute of Health (BIH) at Charite-Universitatsmedizin Berlin
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Release 1.2