Ivan V Kulakovskiy
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Explore the profile of Ivan V Kulakovskiy including associated specialties, affiliations and a list of published articles.
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2903
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Recent Articles
11.
Rafi A, Nogina D, Penzar D, Lee D, Lee D, Kim N, et al.
Nat Biotechnol
. 2024 Oct;
PMID: 39394483
A systematic evaluation of how model architectures and training strategies impact genomics model performance is needed. To address this gap, we held a DREAM Challenge where competitors trained models on...
12.
Khoroshkin M, Buyan A, Dodel M, Navickas A, Yu J, Trejo F, et al.
Nat Commun
. 2024 Sep;
15(1):7872.
PMID: 39251607
In our cells, a limited number of RNA binding proteins (RBPs) are responsible for all aspects of RNA metabolism across the entire transcriptome. To accomplish this, RBPs form regulatory units...
13.
Deviatiiarov R, Gams A, Kulakovskiy I, Buyan A, Meshcheryakov G, Syunyaev R, et al.
Nat Cardiovasc Res
. 2024 Aug;
2(1):58-75.
PMID: 39196209
A deeper knowledge of the dynamic transcriptional activity of promoters and enhancers is needed to improve mechanistic understanding of the pathogenesis of heart failure and heart diseases. In this study,...
14.
Agrawal S, Buyan A, Severin J, Koido M, Alam T, Abugessaisa I, et al.
PLoS One
. 2024 May;
19(5):e0295971.
PMID: 38709794
The human genome is pervasively transcribed and produces a wide variety of long non-coding RNAs (lncRNAs), constituting the majority of transcripts across human cell types. Some specific nuclear lncRNAs have...
15.
Rafi A, Nogina D, Penzar D, Lee D, Lee D, Kim N, et al.
bioRxiv
. 2024 Feb;
PMID: 38405704
Neural networks have emerged as immensely powerful tools in predicting functional genomic regions, notably evidenced by recent successes in deciphering gene regulatory logic. However, a systematic evaluation of how model...
16.
Eliseeva I, Buyan A, Smolin E, Kaliadzenka K, Popov S, Kulakovskiy I, et al.
Int J Mol Sci
. 2024 Feb;
25(3).
PMID: 38339016
Y-box-binding proteins (YB proteins) are multifunctional DNA- and RNA-binding proteins that play an important role in the regulation of gene expression. The high homology of their cold shock domains and...
17.
Vorontsov I, Eliseeva I, Zinkevich A, Nikonov M, Abramov S, Boytsov A, et al.
Nucleic Acids Res
. 2023 Nov;
52(D1):D154-D163.
PMID: 37971293
We present a major update of the HOCOMOCO collection that provides DNA binding specificity patterns of 949 human transcription factors and 720 mouse orthologs. To make this release, we performed...
18.
Uvarova A, Stasevich E, Ustiugova A, Mitkin N, Zheremyan E, Sheetikov S, et al.
Int J Mol Sci
. 2023 Sep;
24(18).
PMID: 37762093
Single-nucleotide polymorphism rs71327024 located in the human 3p21.31 locus has been associated with an elevated risk of hospitalization upon SARS-CoV-2 infection. The 3p21.31 locus contains several genes encoding chemokine receptors...
19.
Penzar D, Nogina D, Noskova E, Zinkevich A, Meshcheryakov G, Lando A, et al.
Bioinformatics
. 2023 Jul;
39(8).
PMID: 37490428
Motivation: The increasing volume of data from high-throughput experiments including parallel reporter assays facilitates the development of complex deep-learning approaches for modeling DNA regulatory grammar. Results: Here, we introduce LegNet,...
20.
Anisimova A, Kolyupanova N, Makarova N, Egorov A, Kulakovskiy I, Dmitriev S
Int J Mol Sci
. 2023 May;
24(9).
PMID: 37176068
While protein synthesis is vital for the majority of cell types of the human body, diversely differentiated cells require specific translation regulation. This suggests the specialization of translation machinery across...