Stepan Nersisyan
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View article: Organism-Specific Sequence Motifs Link Ribosomal RNAs to Brain Disorders
Organism-Specific Sequence Motifs Link Ribosomal RNAs to Brain Disorders Open
We report that in humans, mice, fruit flies, and worms, the ribosomal RNAs and the transcribed spacers of 45S are densely packed with organism-specific sequence motifs that are primarily shared with nervous system genes. The human ribosoma…
View article: CorrAdjust unveils biologically relevant transcriptomic correlations by efficiently eliminating hidden confounders
CorrAdjust unveils biologically relevant transcriptomic correlations by efficiently eliminating hidden confounders Open
Correcting for confounding variables is often overlooked when computing RNA–RNA correlations, even though it can profoundly affect results. We introduce CorrAdjust, a method for identifying and correcting such hidden confounders. CorrAdjus…
View article: CorrAdjust unveils biologically relevant transcriptomic correlations by efficiently eliminating hidden confounders
CorrAdjust unveils biologically relevant transcriptomic correlations by efficiently eliminating hidden confounders Open
Correcting for confounding variables is often overlooked when computing RNA-RNA correlations, even though it can profoundly affect results. We introduce CorrAdjust, a method for identifying and correcting such hidden confounders. CorrAdjus…
View article: Comprehensive profiling of small RNAs and their changes and linkages to mRNAs in schizophrenia and bipolar disorder
Comprehensive profiling of small RNAs and their changes and linkages to mRNAs in schizophrenia and bipolar disorder Open
We investigated small non-coding RNAs (sncRNAs) from the prefrontal cortex of 93 individuals diagnosed with schizophrenia (SCZ) or bipolar disorder (BD) and 77 controls. We uncovered recurring complex sncRNA profiles, with 98% of all sncRN…
View article: All ribosomal RNAs and 45S spacers from humans to worms are packed with organism-specific motifs whose other copies are found predominantly in numerous nervous system genes including many associated with human disorders
All ribosomal RNAs and 45S spacers from humans to worms are packed with organism-specific motifs whose other copies are found predominantly in numerous nervous system genes including many associated with human disorders Open
The nucleotide sequences of ribosomal RNAs (rRNAs) and the spacers of 45S are tuned to fulfill optimally their respective roles during ribosome biosynthesis and function. We report that these sequences satisfy additional genome-wide constr…
View article: Spontaneous metastasis xenograft models link CD44 isoform 4 to angiogenesis, hypoxia, EMT and mitochondria‐related pathways in colorectal cancer
Spontaneous metastasis xenograft models link CD44 isoform 4 to angiogenesis, hypoxia, EMT and mitochondria‐related pathways in colorectal cancer Open
Hematogenous metastasis limits the survival of colorectal cancer (CRC) patients. Here, we illuminated the roles of CD44 isoforms in this process. Isoforms 3 and 4 were predominantly expressed in CRC patients. CD44 isoform 4 indicated poor …
View article: MINRbase: a comprehensive database of nuclear- and mitochondrial-ribosomal-RNA-derived fragments (rRFs)
MINRbase: a comprehensive database of nuclear- and mitochondrial-ribosomal-RNA-derived fragments (rRFs) Open
We describe the Mitochondrial and Nuclear rRNA fragment database (MINRbase), a knowledge repository aimed at facilitating the study of ribosomal RNA-derived fragments (rRFs). MINRbase provides interactive access to the profiles of 130 238 …
View article: Development of a novel mathematical model that explains SARS-CoV-2 infection dynamics in Caco-2 cells
Development of a novel mathematical model that explains SARS-CoV-2 infection dynamics in Caco-2 cells Open
Mathematical modeling is widely used to study within-host viral dynamics. However, to the best of our knowledge, for the case of SARS-CoV-2 such analyses were mainly conducted with the use of viral load data and for the wild type (WT) vari…
View article: Differential co-expression network analysis with DCoNA reveals isomiR targeting aberrations in prostate cancer
Differential co-expression network analysis with DCoNA reveals isomiR targeting aberrations in prostate cancer Open
Motivation One of the standard methods of high-throughput RNA sequencing analysis is differential expression. However, it does not detect changes in molecular regulation. In contrast to the standard differential expression analysis, differ…
View article: <i>HLA-A*01:01</i> allele diminishing in COVID-19 patients population associated with non-structural epitope abundance in CD8+ T-cell repertoire
<i>HLA-A*01:01</i> allele diminishing in COVID-19 patients population associated with non-structural epitope abundance in CD8+ T-cell repertoire Open
In mid-2021, the SARS-CoV-2 Delta variant caused the third wave of the COVID-19 pandemic in several countries worldwide. The pivotal studies were aimed at studying changes in the efficiency of neutralizing antibodies to the spike protein. …
View article: A novel approach for a joint analysis of isomiR and mRNA expression data reveals features of isomiR targeting in breast cancer
A novel approach for a joint analysis of isomiR and mRNA expression data reveals features of isomiR targeting in breast cancer Open
A widely used procedure for selecting significant miRNA-mRNA or isomiR-mRNA pairs out of predicted interactions involves calculating the correlation between expression levels of miRNAs/isomiRs and mRNAs in a series of samples. In this manu…
View article: Differences in Presentation of SARS-CoV-2 Omicron Strain Variant BA.1–BA.5 Peptides by HLA Molecules
Differences in Presentation of SARS-CoV-2 Omicron Strain Variant BA.1–BA.5 Peptides by HLA Molecules Open
In this work, we analyzed the binding affinities of mutated peptides of Omicron strain variants BA.1-BA.5 and the worldwide prevalent HLA alleles. Bioinformatics analysis was conducted with the use of T-CoV web portal. We showed that, for …
View article: isomiRTar: a comprehensive portal of pan-cancer 5′-isomiR targeting
isomiRTar: a comprehensive portal of pan-cancer 5′-isomiR targeting Open
Inaccurate cleavage of pri- and pre-miRNA hairpins by Drosha and Dicer results in the generation of miRNA isoforms known as isomiRs. isomiRs with 5′-end variations (5′-isomiRs) create a new dimension in miRNA research since they have diffe…
View article: Induction of Hypoxic Response in Caco-2 Cells Promote the Expression of Genes Involved in SARS-CoV-2 Endocytosis and Transcytosis
Induction of Hypoxic Response in Caco-2 Cells Promote the Expression of Genes Involved in SARS-CoV-2 Endocytosis and Transcytosis Open
In the present manuscript we analyzed the influence of hypoxic response in Caco-2 cells on the expression of genes and miRNAs involved in the mechanisms of intracellular transport of SARS-CoV-2 viral particles, especially endocytosis and t…
View article: HLA-A*01:01 allele vanishing in COVID-19 patients population associated with non-structural epitope abundance in CD8<sup>+</sup> T-cell repertoire
HLA-A*01:01 allele vanishing in COVID-19 patients population associated with non-structural epitope abundance in CD8<sup>+</sup> T-cell repertoire Open
In mid-2021, the SARS-CoV-2 Delta variant caused the third wave of the COVID-19 pandemic in several countries worldwide. The pivotal studies were aimed at studying changes in the efficiency of neutralizing antibodies to the spike protein. …
View article: Isoforms of miR-148a and miR-203a are putative suppressors of colorectal cancer
Isoforms of miR-148a and miR-203a are putative suppressors of colorectal cancer Open
MicroRNAs are short non-coding molecules which regulate translation in a gene-specific manner. MicroRNA isoforms that differ by few extra or missing nucleotides at the 5'-terminus (5'-isomiR) show strikingly different target specificity. T…
View article: Alterations in SARS-CoV-2 Omicron and Delta peptides presentation by HLA molecules
Alterations in SARS-CoV-2 Omicron and Delta peptides presentation by HLA molecules Open
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 the peculiarities of the viral peptide presentation …
View article: Immunogenic epitope panel for accurate detection of non-cross-reactive T cell response to SARS-CoV-2
Immunogenic epitope panel for accurate detection of non-cross-reactive T cell response to SARS-CoV-2 Open
The ongoing COVID-19 pandemic calls for more effective diagnostic tools. T cell response assessment serves as an independent indicator of prior COVID-19 exposure while also contributing to a more comprehensive characterization of SARS-CoV-…
View article: ExhauFS: exhaustive search-based feature selection for classification and survival regression
ExhauFS: exhaustive search-based feature selection for classification and survival regression Open
Feature selection is one of the main techniques used to prevent overfitting in machine learning applications. The most straightforward approach for feature selection is an exhaustive search: one can go over all possible feature combination…
View article: Alterations in SARS-CoV-2 Omicron and Delta peptides presentation by HLA molecules
Alterations in SARS-CoV-2 Omicron and Delta peptides presentation by HLA molecules Open
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 the peculiarities of the viral peptide presentation …
View article: RNA22 and TargetScan predictions, negative controls
RNA22 and TargetScan predictions, negative controls Open
Custom RNA22 and TargetScan predictions for 139 5'-isomiR, which are highly expressed in breast cancer. The dataset also includes negative controls for isomiRs.
View article: Immunogenic epitope panel for accurate detection of non-cross-reactive T cell response to SARS-CoV-2
Immunogenic epitope panel for accurate detection of non-cross-reactive T cell response to SARS-CoV-2 Open
The ongoing COVID-19 pandemic calls for more effective diagnostic tools, and T cell response assessment can serve as an independent indicator of prior COVID-19 exposure while also contributing to a more comprehensive characterization of SA…
View article: ECM–Receptor Regulatory Network and Its Prognostic Role in Colorectal Cancer
ECM–Receptor Regulatory Network and Its Prognostic Role in Colorectal Cancer Open
Interactions of the extracellular matrix (ECM) and cellular receptors constitute one of the crucial pathways involved in colorectal cancer progression and metastasis. With the use of bioinformatics analysis, we comprehensively evaluated th…
View article: Endocytosis and Transcytosis of SARS-CoV-2 Across the Intestinal Epithelium and Other Tissue Barriers
Endocytosis and Transcytosis of SARS-CoV-2 Across the Intestinal Epithelium and Other Tissue Barriers Open
Since 2003, the world has been confronted with three new betacoronaviruses that cause human respiratory infections: SARS-CoV, which causes severe acute respiratory syndrome (SARS), MERS-CoV, which causes Middle East respiratory syndrome (M…
View article: ExhauFS: exhaustive search-based feature selection for classification and survival regression
ExhauFS: exhaustive search-based feature selection for classification and survival regression Open
Motivation Feature selection is one of the main techniques used to prevent overfitting in machine learning applications. The most straightforward approach for feature selection is exhaustive search: one can go over all possible feature com…
View article: T-CoV: a comprehensive portal of HLA-peptide interactions affected by SARS-CoV-2 mutations
T-CoV: a comprehensive portal of HLA-peptide interactions affected by SARS-CoV-2 mutations Open
Rapidly appearing SARS-CoV-2 mutations can affect T cell epitopes, which can help the virus to evade either CD8 or CD4 T-cell responses. We developed T-cell COVID-19 Atlas (T-CoV, https://t-cov.hse.ru) – the comprehensive web portal, which…