I. Kulakovskiy

发表

DNA sequence motif: a jack of all trades for ChIP-Seq data.

V. Makeev, I. Kulakovskiy, Vsevolod J Makeev, 2013, Advances in protein chemistry and structural biology.

Landscape of allele-specific transcription factor binding in the human genome

Dmitry D. Penzar, V. Makeev, A. Favorov, 2020, Nature Communications.

Architectural proteins Pita, Zw5,and ZIPIC contain homodimerization domain and support specific long-range interactions in Drosophila

I. Kulakovskiy, A. Penin, I. Eliseeva, 2016, Nucleic acids research.

Role of structural water for prediction of cation binding sites in apoproteins

V. Makeev, V. Tumanyan, I. Kulakovskiy, 2018, Journal of biomolecular structure & dynamics.

Early B-cell factor 1 (EBF1) is critical for transcriptional control of SLAMF1 gene in human B cells.

K. V. Korneev, Anna V Klepikova, I. Kulakovskiy, 2016, Biochimica et biophysica acta.

Effects of cytosine methylation on transcription factor binding sites

Hideya Kawaji, Wail Ba-Alawi, Vladimir B Bajic, 2014, BMC Genomics.

Discovery of DNA motifs recognized by transcription factors through integration of different experimental sources

V. Makeev, I. Kulakovskiy, 2009 .

Translating natural genetic variation to gene expression in a computational model of the Drosophila gap gene regulatory network

Paul Marjoram, Konstantin N Kozlov, David S. Lawrie, 2017, PloS one.

Analysis of functional importance of binding sites in the Drosophila gap gene network model

Konstantin Kozlov, Maria Samsonova, K. Kozlov, 2015, BMC Genomics.

Sequence-based model of gap gene regulatory network

K. Kozlov, M. Samsonova, V. Gursky, 2015, bioRxiv.

The single nucleotide variant rs12722489 determines differential estrogen receptor binding and enhancer properties of an IL2RA intronic region

M. A. Afanasyeva, V. Makeev, I. Kulakovskiy, 2017, PloS one.

What Do Neighbors Tell About You: The Local Context of Cis-Regulatory Modules Complicates Prediction of Regulatory Variants

Vsevolod J. Makeev, Ivan V. Kulakovskiy, Ilya E. Vorontsov, 2019, Front. Genet..

A holistic view of mouse enhancer architectures reveals analogous pleiotropic effects and correlation with human disease

Steve D. M. Brown, S. Greenaway, A. Mallon, 2020, BMC genomics.

Functional annotation of human long noncoding RNAs using chromatin conformation data

Jay W. Shin, Jordan A. Ramilowski, C. Hon, 2021 .

VTC4 Polyphosphate Polymerase Knockout Increases Stress Resistance of Saccharomyces cerevisiae Cells

I. Kulakovskiy, A. Tomashevsky, T. Kulakovskaya, 2021, Biology.

The Reduced Level of Inorganic Polyphosphate Mobilizes Antioxidant and Manganese-Resistance Systems in Saccharomyces cerevisiae

I. Kulakovskiy, V. Ostroumov, I. Eliseeva, 2019, Cells.

Functional annotation of human long noncoding RNAs via molecular phenotyping.

Boris Lenhard, Lusy Handoko, Piero Carninci, 2020, Genome research.

Corrigendum: Functional annotation of human long noncoding RNAs via molecular phenotyping

Howard Y. Chang, Martin S. Taylor, Jay W. Shin, 2020 .

Enhanced C/EBPs binding to C>T mismatches facilitates fixation of CpG mutations

I. Kulakovskiy, O. Nikonov, I. Vorontsov, 2020, bioRxiv.

Functional annotation of human long noncoding RNAs via molecular phenotyping

Howard Y. Chang, Martin S. Taylor, Jay W. Shin, 2019, bioRxiv.

CpG traffic lights are markers of regulatory regions in human genome

Abdullah M. Khamis, V. Bajic, V. Ramensky, 2019, BMC genomics.

Intergenic, gene terminal, and intragenic CpG islands in the human genome

E. O. Ermakova, V. Makeev, A. Heinzel, 2010, BMC Genomics.

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

I. Kulakovskiy, D. Kuprash, K. Korneev, 2018 .

ANANASTRA: annotation and enrichment analysis of allele-specific transcription factor binding at SNPs

V. Makeev, F. Kolpakov, Y. Aulchenko, 2022, Nucleic Acids Res..

The Minor Variant of the Single-Nucleotide Polymorphism rs3753381 Affects the Activity of a SLAMF1 Enhancer

I. Kulakovskiy, I. Vorontsov, D. Kuprash, 2017, Acta naturae.

De novo assembling and primary analysis of genome and transcriptome of gray whale Eschrichtius robustus

V. V. Sharov, S. Feranchuk, V. Fraifeld, 2017, BMC Evolutionary Biology.

Systematic identification of cis-interacting lncRNAs and their targets

Howard Y. Chang, Jay W. Shin, Jordan A. Ramilowski, 2022, bioRxiv.

Alternative Forms of Y-Box Binding Protein 1 and YB-1 mRNA

I. Kulakovskiy, L. Ovchinnikov, I. Eliseeva, 2014, PloS one.

In silico motif analysis suggests an interplay of transcriptional and translational control in mTOR response

F. Kondrashov, I. Kulakovskiy, I. Vorontsov, 2013, Translation.

Insights gained from a comprehensive all-against-all transcription factor binding motif benchmarking study

Dmitry D. Penzar, Jan Grau, P. Bucher, 2020, Genome Biology.

Transcriptome profile of yeast reveals the essential role of PMA2 and uncharacterized gene YBR056W-A (MNC1) in adaptation to toxic manganese concentration.

I. Kulakovskiy, I. Eliseeva, N. Andreeva, 2017, Metallomics : integrated biometal science.

Potential Markers of Autoimmune Diseases, Alleles rs115662534(T) and rs548231435(C), Disrupt the Binding of Transcription Factors STAT1 and EBF1 to the Regulatory Elements of Human CD40 Gene

A. S. Kasyanov, I. Kulakovskiy, D. Kuprash, 2018, Biochemistry (Moscow).

Diverse Regulation of YB-1 and YB-3 Abundance in Mammals

I. Kulakovskiy, I. Eliseeva, D. Lyabin, 2022, Biochemistry (Moscow).

HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis

F. A. Kolpakov, Vladimir B. Bajic, Arturo Magana-Mora, 2017, Nucleic Acids Res..

A promoter-level mammalian expression atlas

Cesare Furlanello, Finn Drabløs, Carsten O. Daub, 2015 .

Multiple single nucleotide polymorphisms in the first intron of the IL2RA gene affect transcription factor binding and enhancer activity.

Ivan V. Kulakovskiy, Ilya E. Vorontsov, A. S. Kasyanov, 2017, Gene.

An update to database TraVA: organ-specific cold stress response in Arabidopsis thaliana

I. Kulakovskiy, M. Logacheva, A. Penin, 2019, BMC plant biology.

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Martin S. Taylor, Jay W. Shin, Thomas J. Ha, 2021, Nature Communications.

Translatome and transcriptome analysis of TMA20 (MCT-1) and TMA64 (eIF2D) knockout yeast strains

D. Andreev, I. Kulakovskiy, I. Terenin, 2019, Data in brief.

Sequence-based model of gap gene regulatory network

Konstantin Kozlov, Maria Samsonova, K. Kozlov, 2014, bioRxiv.

The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome

Robert S. Young, J. Blake, T. Meehan, 2015, PLoS biology.

GTRD: an integrated view of transcription regulation

Alexander E. Kel, Vsevolod J. Makeev, Fedor A. Kolpakov, 2020, Nucleic Acids Res..

Multifaceted deregulation of gene expression and protein synthesis with age

V. Gladyshev, I. Kulakovskiy, S. Dmitriev, 2020, Proceedings of the National Academy of Sciences.

HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models

Vladimir B. Bajic, Haitham Ashoor, Wail Ba-alawi, 2015, Nucleic Acids Res..

Minor C allele of the SNP rs7873784 associated with rheumatoid arthritis and type-2 diabetes mellitus binds PU.1 and enhances TLR4 expression.

M. A. Afanasyeva, I. Kulakovskiy, D. Kuprash, 2019, Biochimica et biophysica acta. Molecular basis of disease.

An atlas of transcribed human cardiac promoters and enhancers reveals an important role of regulatory elements in heart failure

T. Tatarinova, I. Kulakovskiy, Ramesh Singh, 2023, Nature Cardiovascular Research.

Jaccard index based similarity measure to compare transcription factor binding site models

Vsevolod J. Makeev, Ivan V. Kulakovskiy, Ilya E. Vorontsov, 2013, Algorithms for Molecular Biology.

HOCOMOCO: a comprehensive collection of human transcription factor binding sites models

Vladimir B. Bajic, Ulf Schaefer, Vsevolod J. Makeev, 2012, Nucleic Acids Res..

High‐quality genome assembly of Capsella bursa‐pastoris reveals asymmetry of regulatory elements at early stages of polyploid genome evolution

A. Kondrashov, I. Kulakovskiy, M. Logacheva, 2017, The Plant journal : for cell and molecular biology.

EpiFactors: a comprehensive database of human epigenetic factors and complexes

Rezvan Ehsani, Finn Drabløs, Takeya Kasukawa, 2015, Database J. Biol. Databases Curation.

The Gene Regulation Knowledge Commons: The action area of GREEKC.

Juan M. Vaquerizas, Pedro T. Monteiro, D. Zerbino, 2021, Biochimica et biophysica acta. Gene regulatory mechanisms.

A GO catalogue of human DNA-binding transcription factors

A. Ignatchenko, A. Lægreid, M. Kuiper, 2020, bioRxiv.

Application of experimentally verified transcription factor binding sites models for computational analysis of ChIP-Seq data

V. Makeev, T. Merkulova, V. Levitsky, 2014, BMC Genomics.

Application of experimentally verified transcription factor binding sites models for computational analysis of ChIP-Seq data

V. Makeev, T. Merkulova, V. Levitsky, 2014, BMC Genomics.

From binding motifs in Chip-seq Data to Improved Models of transcription factor binding Sites

Victor G. Levitsky, Vsevolod J. Makeev, Dmitry Yu. Oshchepkov, 2013, J. Bioinform. Comput. Biol..

Deep and wide digging for binding motifs in ChIP-Seq data

Vsevolod J. Makeev, Alexander V. Favorov, Valentina Boeva, 2010, Bioinform..

A holistic view of mouse enhancer architectures reveals analogous pleiotropic effects and correlation with human disease

Steve D. M. Brown, S. Greenaway, A. Mallon, 2020, BMC genomics.

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

I. Kulakovskiy, D. Kuprash, K. Korneev, 2018, Molecular Biology.

Integration of multiple epigenomic marks improves prediction of variant impact in saturation mutagenesis reporter assay

Nir Yosef, Anat Kreimer, Jay Shendure, 2019, Human mutation.

Human Tissues Exhibit Diverse Composition of Translation Machinery

I. Kulakovskiy, S. Dmitriev, A. Anisimova, 2023, bioRxiv.

M. Roytberg, I. Kulakovskiy, E. Baulin, 2020, PloS one.

Motif discovery and motif finding from genome-mapped DNase footprint data

Vsevolod J. Makeev, Alexander V. Favorov, Ivan V. Kulakovskiy, 2009, Bioinform..

PERFECTOS-APE - Predicting Regulatory Functional Effect of SNPs by Approximate P-value Estimation

Vsevolod J. Makeev, Ivan V. Kulakovskiy, Ilya E. Vorontsov, 2015, BIOINFORMATICS.

A deeper look into transcription regulatory code by preferred pair distance templates for transcription factor binding sites

Vsevolod J. Makeev, Natalia G. Esipova, Ivan V. Kulakovskiy, 2011, Bioinform..

Negative selection maintains transcription factor binding motifs in human cancer

V. Makeev, I. Kulakovskiy, E. Lukianova, 2015, BMC Genomics.

Diverse Regulation of YB-1 and YB-3 Abundance in Mammals

I. Kulakovskiy, I. Eliseeva, D. Lyabin, 2022, Biochemistry (Moscow).

YB-3 substitutes YB-1 in global mRNA binding

I. Kulakovskiy, L. Ovchinnikov, I. Eliseeva, 2020, RNA biology.

Systematic Identification of Post-Transcriptional Regulatory Modules

M. Corces, I. Kulakovskiy, H. Goodarzi, 2023, bioRxiv.

svist4get: a simple visualization tool for genomic tracks from sequencing experiments

Vadim N. Gladyshev, Ivan V. Kulakovskiy, Sergey E. Dmitriev, 2019, BMC Bioinformatics.

Ribo-Seq and RNA-Seq of TMA46 ( DFRP1) and GIR2 ( DFRP2) knockout yeast strains

I. Kulakovskiy, S. Dmitriev, D. S. Makeeva, 2021, F1000Research.

Enhanced C/EBP binding to G·T mismatches facilitates fixation of CpG mutations in cancer and adult stem cells.

I. Kulakovskiy, O. Nikonov, I. Vorontsov, 2021, Cell reports.

Multifaceted deregulation of gene expression and protein synthesis with age

V. Gladyshev, I. Kulakovskiy, S. Dmitriev, 2020, Proceedings of the National Academy of Sciences.

RNA-Seq data of ALKBH5 and FTO double knockout HEK293T human cells

I. Kulakovskiy, I. Eliseeva, D. Lyabin, 2022, Data in brief.

Ribosomal leaky scanning through a translated uORF requires eIF4G2

I. Kulakovskiy, I. Terenin, I. Shatsky, 2022, Nucleic acids research.

Effects of extracellular YB-1 protein on cultured cells of human breast cancer

I. Kulakovskiy, L. Ovchinnikov, I. Eliseeva, 2013, Biochemistry (Moscow) Supplement Series A: Membrane and Cell Biology.

Positional weight matrices have sufficient prediction power for analysis of noncoding variants

V. Makeev, I. Kulakovskiy, Sergey Abramov, 2022, F1000Research.

Single-Cell Analyses of ESCs Reveal Alternative Pluripotent Cell States and Molecular Mechanisms that Control Self-Renewal

Ben D. MacArthur, Dmitri Papatsenko, Vsevolod J. Makeev, 2015, Stem cell reports.

Preferred distances between transcription factor binding sites

Vsevolod J. Makeev, Ivan V. Kulakovskiy, Artem S. Kasianov, 2011 .

Spi-1/PU.1 activates transcription through clustered DNA occupancy in erythroleukemia

Emmanuel Barillot, Alain Nicolas, Philippe Hupé, 2012, Nucleic acids research.

Assessing Ribosome Distribution Along Transcripts with Polarity Scores and Regression Slope Estimates.

V. Makeev, V. Gladyshev, I. Kulakovskiy, 2021, Methods in molecular biology.

Jaccard index based similarity measure to compare transcription factor binding site models

V. Makeev, I. Kulakovskiy, I. Vorontsov, 2013, Algorithms for Molecular Biology.

Crol contributes to PRE-mediated repression and Polycomb group proteins recruitment in Drosophila

I. Kulakovskiy, P. Georgiev, D. Chetverina, 2023, Nucleic acids research.

Insights gained from a comprehensive all-against-all transcription factor binding motif benchmarking study

Jan Grau, P. Bucher, V. Makeev, 2020, Genome Biology.

Coat color allele and mtDNA haplotype distributions in Russian cat populations: a citizen-science research

Y. Aulchenko, I. Kulakovskiy, M. Logacheva, 2017, bioRxiv.

De novo assembling and primary analysis of genome and transcriptome of gray whale Eschrichtius robustus

V. V. Sharov, S. Feranchuk, V. Fraifeld, 2017, BMC Evolutionary Biology.

A standard knockout procedure alters expression of adjacent loci at the translational level

V. Gladyshev, I. Kulakovskiy, S. Dmitriev, 2021, bioRxiv.

Genome-wide map of human and mouse transcription factor binding sites aggregated from ChIP-Seq data

V. Makeev, F. Kolpakov, I. Yevshin, 2018, BMC Research Notes.

Annotation of the local context of RNA secondary structure improves the classification and prediction of A-minors

I. Kulakovskiy, E. Baulin, L. Fakhranurova, 2021, RNA.

EpiFactors 2022: expansion and enhancement of a curated database of human epigenetic factors and complexes

A. Lennartsson, I. Kulakovskiy, Y. Medvedeva, 2022, Nucleic Acids Res..

LegNet: a best-in-class deep learning model for short DNA regulatory regions

Carl G. de Boer, I. Kulakovskiy, A. Lando, 2023, bioRxiv.

svist4get: a simple visualization tool for genomic tracks from sequencing experiments

V. Gladyshev, I. Kulakovskiy, S. Dmitriev, 2019, BMC Bioinformatics.

Invited Talks and Posters Abstracts

Y. Ponty, M. Régnier, I. Kulakovskiy, 2010 .

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Thomas J. Ha, L. K. Nielsen, Kelly J. Hitchens, 2021 .

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Thomas J. Ha, L. K. Nielsen, Kelly J. Hitchens, 2021 .

Functional Annotation of Human Long Non-Coding RNAs via Molecular Phenotyping 1

Howard Y. Chang, Martin S. Taylor, Jay W. Shin, 2019 .

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Thomas J. Ha, L. K. Nielsen, Kelly J. Hitchens, 2022 .

Evaluation and optimization of sequence-based gene regulatory deep learning models

Carl G. de Boer, A. Regev, Payman Yadollahpour, 2023, bioRxiv.

Analysis of functional importance of binding sites in the Drosophila gap gene network model

K. Kozlov, M. Samsonova, V. Gursky, 2015, BMC Genomics.

Functional annotation of human long noncoding RNAs using chromatin conformation data

Jay W. Shin, Jordan A. Ramilowski, C. Hon, 2021 .

The Minor Variant of the Single-Nucleotide Polymorphism rs3753381 Affects the Activity of a SLAMF1 Enhancer

I. Kulakovskiy, I. Vorontsov, A. Klepikova, 2017, Acta Naturae.

Multiple single nucleotide polymorphisms in the first intron of the IL2RA gene affect transcription factor binding and enhancer activity.

A. S. Kasyanov, I. Kulakovskiy, I. Vorontsov, 2017, Gene.

Integration of multiple epigenomic marks improves prediction of variant impact in saturation mutagenesis reporter assay

John E. Reid, Michael A. Beer, Aashish N. Adhikari, 2019, Human mutation.

CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods

Silvio C. E. Tosatto, Julius O. B. Jacobsen, Nicholas A. Sinnott-Armstrong, 2024, Genome biology.

A promoter-level mammalian expression atlas

Martin S. Taylor, Jay W. Shin, Thomas J. Ha, 2014, Nature.

LegNet: resetting the bar in deep learning for accurate prediction of promoter activity and variant effects from massive parallel reporter assays

Carl G. de Boer, I. Kulakovskiy, Arsenii Zinkevich, 2022 .

Y-Box-Binding Proteins Have a Dual Impact on Cellular Translation

I. Kulakovskiy, I. Eliseeva, D. Lyabin, 2024, International journal of molecular sciences.

HOCOMOCO in 2024: a rebuild of the curated collection of binding models for human and mouse transcription factors

V. Makeev, A. Jolma, I. Yevshin, 2023, Nucleic acids research.

CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods

Nicholas A. Sinnott-Armstrong, Jonathan M. Mudge, Hui Ting Grace Yeo, 2022, Genome biology.