A5030967753- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- RNA Research and Splicing
- Genomics and Chromatin Dynamics
- Bacteriophages and microbial interactions
- Viral Infections and Immunology Research
- Enzyme Structure and Function
- Genetic Associations and Epidemiology
- Genomics and Phylogenetic Studies
- DNA and Nucleic Acid Chemistry
- RNA regulation and disease
- Genomic variations and chromosomal abnormalities
- Genomics and Rare Diseases
- Gene expression and cancer classification
- Viral gastroenteritis research and epidemiology
- Protein Structure and Dynamics
- Protist diversity and phylogeny
- Cancer Genomics and Diagnostics
- Animal Virus Infections Studies
International Institute of Molecular and Cell Biology
2022-2025
Moscow Institute of Physics and Technology
2016-2024
Keldysh Institute of Applied Mathematics
2020-2023
Institute of Mathematical Problems of Biology
2015-2023
Moscow Power Engineering Institute
2020
Moscow Aviation Institute
2020
National Research University Higher School of Economics
2013-2014
Sequence variants in gene regulatory regions alter expression and contribute to phenotypes of individual cells the whole organism, including disease susceptibility progression. Single-nucleotide enhancers or promoters may affect transcription by altering factor binding sites. Differential heterozygous genomic loci provides a natural source information on such variants. We present novel approach call allele-specific events at single-nucleotide ChIP-Seq data, taking into account joint...
RNA-Puzzles is a collective endeavor dedicated to the advancement and improvement of RNA three-dimensional structure prediction. With agreement from structural biologists, structures are predicted by modeling groups before publication experimental structures. We report large-scale set predictions 18 for 23 RNA-Puzzles: 4 elements, 2 Aptamers, Viral 5 Ribozymes 8 Riboswitches. describe automatic assessment protocols comparisons between prediction experiment. Our analyses reveal some critical...
Abstract Designing RNA sequences that form a specific structure remains challenge. Current computational methods often struggle with the complexity of structures, especially when considering pseudoknots or restrictions related to function. We developed DesiRNA, tool for design based on Replica Exchange Monte Carlo approach. It finds minimize multiobjective scoring function, fulfill user-defined constraints and violation restraints. DesiRNA handles pseudoknots, designs RNA–RNA complexes...
We present ANANASTRA, https://ananastra.autosome.org, a web server for the identification and annotation of regulatory single-nucleotide polymorphisms (SNPs) with allele-specific binding events. ANANASTRA accepts list dbSNP IDs or VCF file reports (ASB) sites particular transcription factors in specific cell types, highlighting those ASBs significantly enriched at SNPs query list. is built on top systematic analysis allelic imbalance ChIP-Seq experiments performs ASB enrichment test against...
High-throughput sequencing facilitates large-scale studies of gene regulation and allows tracing the associations individual genomic variants with changes in expression. Compared to classic association studies, assessment an allelic imbalance at heterozygous captures functional variant effects smaller sample sizes, higher sensitivity, better resolution. Yet, identification allele-specific from read counts remains challenging due data-dependent biases overdispersion arising technical...
Abstract Betacoronaviruses are a genus within the Coronaviridae family of RNA viruses. They capable infecting vertebrates and causing epidemics as well global pandemics in humans. Mitigating threat posed by requires an understanding their molecular diversity. The development novel antivirals hinges on key regulatory elements viral genomes, particular 5′-proximal region, which is pivotal for protein synthesis. Using combination cryo-electron microscopy, atomic force chemical probing,...
Understanding the 3D structure of RNA is key to understanding function. modular and can be seen as a composition building blocks various sizes called tertiary motifs. Currently, long-range motifs formed between distant loops helical regions are largely less studied than local determined by secondary structure. We surveyed interactions in non-redundant set non-coding structures. A new dataset annotated LOng-RAnge modules (LORA) was built using an approach that does not rely on automatic...
Ribonucleic acid (RNA) molecules serve as master regulators of cells by encoding their biological function in the ribonucleotide sequence, particularly ability to interact with other molecules. To understand how RNA perform tasks and design new sequences specific functions, it is great benefit be able computationally predict folds interacts cellular environment. Our workflow for computational modeling 3D structures its interactions uses a set methods developed our laboratory, including...
The recent upgrade of nucleic acid–protein interaction database (NPIDB, http://npidb.belozersky.msu.ru/) includes a newly elaborated classification complexes protein domains with double-stranded DNA and families related complexes. Our classifications are based on contacting structural elements both DNA: the major groove, minor groove backbone; protein: helices, beta-strands unstructured segments. We took into account hydrogen bonds hydrophobic interaction. analyzed material contains 1942...
The Universe of RNA Structures DataBase (URSDB) stores information obtained from all RNA-containing PDB entries (2935 in October 2015). content the database is updated regularly. consists 51 tables containing indexed data on various elements structures. provides a web interface allowing user to select subset structures with desired features and obtain statistical for selected or In particular, one can easily statistics geometric parameters base pairs, structural motifs (stems, loops, etc.)...
ABSTRACT The functions of non-coding RNAs are largely defined by their three-dimensional structures. RNA 3D structure is organized hierarchically and consists recurrent building blocks called tertiary motifs. computational problem motif search remains unsolved, as standard approaches restrained sequence, interaction network, or backbone topology. We developed the ARTEM superposition algorithm, which free from these limitations. Here, we present a version that allows automated searches...
Along with nucleobase pairing, base-base stacking interactions are one of the two main types strong non-covalent that define unique secondary and tertiary structure RNA. In this paper we studied subfamilies nucleobase-inserted structures: (i) any base intercalated between neighboring nucleotide residues (base-intercalated element, BIE, i + 1); (ii) wedged into a hydrophobic cavity formed by heterocyclic bases nucleotides which apart in sequence (base-wedged BWE, 2). We have exploited growing...
Noncoding RNAs play a crucial role in various cellular processes living organisms, and RNA functions heavily depend on molecule structures composed of stems, loops, tertiary motifs. Among those, the most frequent are A-minor interactions, which often involved formation more complex motifs such as kink-turns pseudoknots. We present novel classification A-minors terms secondary structure where each nucleotide an is attributed to stem or loop, pair nucleotides their relative position within...
ABSTRACT Non-coding RNAs play a major role in diverse processes living cells with their sequence and spatial structure serving as the principal determinants of function. Superposition RNA 3D structures is most accurate method for comparative analysis molecules inferring alignments. Topology-independent superposition particularly relevant, evidenced by structurally similar permutations such tRNA Y RNA. To date, state-of-the-art methods rely on intricate heuristics, potential...
The biologically relevant structures of proteins and nucleic acids their complexes are dynamic. They include a combination regions ranging from rigid structural segments to switches that almost always disordered, which interact with each other in various ways. Comparing conformational changes variation contacts between different states is essential understand the biological functions proteins, acids, complexes. Here, we describe new computational tool, 1D2DSimScore, for comparing contact...
Abstract High-throughput sequencing facilitates large-scale studies of gene regulation and allows tracing the associations individual genomic variants with changes in expression. Compared to classic association studies, allelic imbalance at heterozygous captures functional effects regulatory genome variation smaller sample sizes higher sensitivity. Yet, identification allele-specific events from read counts remains non-trivial due multiple sources technical biological variability, which...
Intronic gene regions are mostly considered in the scope of expression regulation, such as alternative splicing. However, relations between basic statistical properties introns much rarely studied detail, despite vast available data. Particularly, little is known regarding relationship intron length and phase. Intron phase distribution significantly different at thresholds. In this study, we performed GO enrichment analysis sets with a particular varying thresholds using list 13823...
Abstract Sequence variants in gene regulatory regions alter expression and contribute to phenotypes of individual cells the whole organism, including disease susceptibility progression. Single-nucleotide enhancers or promoters may affect transcription by altering factor binding sites. Differential heterozygous genomic loci provides a natural source information on such variants. We present novel approach call allele-specific events at single-nucleotide ChIP-Seq data, taking into account joint...
Abstract Non-coding RNAs play a major role in diverse processes living cells with their sequence and spatial structure serving as the principal determinants of function. Superposition RNA 3D structures is most accurate method for comparative analysis molecules inferring structure-based alignments. Topology-independent superposition particularly relevant, evidenced by structurally similar permutations such tRNA Y RNA. To date, state-of-the-art methods rely on intricate heuristics, potential...
RNA secondary structure prediction including pseudoknotted structures of arbitrary types is a well-known NP-hard problem computational biology. By limiting the possible pseudoknots can be solved in polynomial time. According to empirical thermodynamic parameters, formation stem starts decrease free energy only after third stack base pairs. Thus, short stems may unstable and provide limited contribution overall folded molecule. Therefore, detailed analysis could facilitate reducing...