A5037628539- SARS-CoV-2 and COVID-19 Research
- MicroRNA in disease regulation
- COVID-19 Clinical Research Studies
- vaccines and immunoinformatics approaches
- RNA Research and Splicing
- Cancer-related molecular mechanisms research
- RNA modifications and cancer
- Extracellular vesicles in disease
- Bladder and Urothelial Cancer Treatments
- Advanced Statistical Methods and Models
- RNA and protein synthesis mechanisms
- RNA Interference and Gene Delivery
- interferon and immune responses
- Immunotherapy and Immune Responses
- Ferroptosis and cancer prognosis
- Molecular Biology Techniques and Applications
- Epigenetics and DNA Methylation
- Monoclonal and Polyclonal Antibodies Research
- Auction Theory and Applications
- Consumer Market Behavior and Pricing
- Prostate Cancer Treatment and Research
- Advanced biosensing and bioanalysis techniques
- T-cell and B-cell Immunology
- Supply Chain and Inventory Management
- Long-Term Effects of COVID-19
National Research University Higher School of Economics
2021-2024
Institute of Bioorganic Chemistry
2021-2023
Yandex (Russia)
2020
Rapidly appearing SARS-CoV-2 mutations can affect T cell epitopes, which help the virus to evade either CD8 or CD4 T-cell responses. We developed COVID-19 Atlas (T-CoV, https://t-cov.hse.ru) - comprehensive web portal, allows one analyze how alter presentation of viral peptides by HLA molecules. The data are presented for common variants and most frequent class I II alleles. Binding affinities molecules were assessed with accurate in silico methods. obtained results highlight importance...
The T-cell immune response is a major determinant of effective SARS-CoV-2 clearance. Here, using the recently developed T-CoV bioinformatics pipeline ( https://t-cov.hse.ru ) we analyzed peculiarities viral peptide presentation for Omicron, Delta and Wuhan variants SARS-CoV-2. First, showed absence significant differences in SARS-CoV-2-derived peptides by most frequent HLA class I/II alleles corresponding haplotypes. Then, analysis was limited to set originating from Spike proteins...
We propose a homogeneity test closely related to the concept of linear separability between two samples. Using one can answer question whether classifier is merely ``random'' or effectively captures differences classes. focus on establishing upper bounds for test's \emph{p}-value when applied two-dimensional Specifically, normally distributed samples we experimentally demonstrate that bound highly accurate. this bound, evaluate classifiers designed detect ER-positive breast cancer recurrence...
Several performance measures can be used for evaluating classification results: accuracy, F-measure, and many others. Can we say that some of them are better than others, or, ideally, choose one measure is best in all situations? To answer this question, conduct a systematic analysis measures: formally define list desirable properties theoretically analyze which satisfy properties. We also prove an impossibility theorem: cannot simultaneously satisfied. Finally, propose new family satisfying...
MiRNA isoforms (isomiRs) are single stranded small RNAs originating from the same pri-miRNA hairpin as a result of cleavage by Drosha and Dicer enzymes. Variations at 5'-end miRNA alter seed region molecule, thus affecting targetome miRNA. In this manuscript, we analysed distribution positions across 31 different cancers using sequencing data TCGA project. As result, found that processing not tissue specific all miRNAs could be correctly classified ones exhibiting homogeneous or...
Inaccurate cleavage of pri- and pre-miRNA hairpins by Drosha Dicer results in the generation miRNA isoforms known as isomiRs. isomiRs with 5′-end variations (5′-isomiRs) create a new dimension research since they have different seed regions distinct targetomes. We developed isomiRTar ( https://isomirtar.hse.ru )—a comprehensive portal that allows one to analyze expression profiles targeting activity 5′-isomiRs cancer. Using Cancer Genome Atlas sequencing data, we compiled list 1022 expressed...
One of the standard methods high-throughput RNA sequencing analysis is differential expression. However, it does not detect changes in molecular regulation. In contrast to expression analysis, co-expression one aims pairs or clusters whose mutual between two conditions.We developed Differential Co-expression Network Analysis (DCoNA)-an open-source statistical tool that allows identify pair interactions, which correlation significantly conditions. Comparing DCoNA with state-of-the-art analog,...
ABSTRACT Rapidly appearing SARS-CoV-2 mutations can affect T cell epitopes, which help the virus to evade either CD8 or CD4 T-cell responses. We developed COVID-19 Atlas (T-CoV, https://t-cov.hse.ru ) – comprehensive web portal, allows one analyze how alter presentation of viral peptides by HLA molecules. The data are presented for common variants and most frequent class I II alleles. Binding affinities molecules were assessed with accurate in silico methods. obtained results highlight...
A widely used procedure for selecting significant miRNA-mRNA or isomiR-mRNA pairs out of predicted interactions involves calculating the correlation between expression levels miRNAs/isomiRs and mRNAs in a series samples. In this manuscript, we aimed to assess validity by comparing profiles sets sequence-based target non-target (negative controls). Target prediction was carried using RNA22 TargetScan algorithms. Spearman's analysis conducted miRNA mRNA sequencing data The Cancer Genome Atlas...
Abstract The T-cell immune response is a major determinant of effective SARS-CoV-2 clearance. Here, using the recently developed T-CoV bioinformatics pipeline ( https://t-cov.hse.ru ) we analyzed peculiarities viral peptide presentation for Omicron, Delta and Wuhan variants SARS-CoV-2. First, showed absence significant differences in SARS-CoV-2-derived peptides by most frequent HLA class I/II alleles corresponding haplotypes. Then, analysis was limited to set originating from Spike proteins...
Gemcitabine monophosphate (dFdCMP), one of the intracellular forms phosphorylated gemcitabine, determines its antitumor activity. A pharmaco-molecular model for determining gemcitabine relative levels has been developed based on assessment activity ENT1, ENT2 channels and dCK, CDA enzymes in tumor tissue. is a more relevant predictive factor resistance bladder cancer when compared with expression individual markers related to dFdCMP formation.
Abstract In somatic cells, microRNAs (miRNAs) bind to the genomes of RNA viruses and influence their translation replication. Here we demonstrate that a significant number miRNA binding sites locate in NSP4 region SARS-CoV-2 genome, intestinal human miRNAs exert evolutionary pressure on this region. Notably, infected promotes formation double-membrane vesicles, which serve as scaffolds for replication-transcriptional complexes protect viral from intracellular destruction. three years...
Abstract In somatic cells, microRNAs (miRNAs) bind to the genomes of RNA viruses and influence their translation replication. London Berlin samples represented in GISAID database, we traced severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) lineages divided these sequenced two groups, “Ancestral variants” “Omicrons,” analyzed them through prism tissue‐specific binding between host miRNAs viral messenger RNAs. We demonstrate a significant number miRNA‐binding sites NSP4 region...
Abstract We developed DCoNA – a statistical tool that allows one to identify pair interactions, which correlation significantly changes between two conditions. Comparing with the state-of-the-art analog, we showed is faster, more accurate, and less memory-consuming tool. applied prostate mRNA/miRNA-seq data collected from The Cancer Genome Atlas (TCGA) compared predicted regulatory interactions of miRNA isoforms (isomiRs) their target mRNAs normal cancer samples. As result, almost all highly...