Yuriy L. Orlov
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View article: Genes Encoding Heat Shock Proteins Are Associated with Risk and Clinical Course of Severe COVID-19: A Pilot Study
Genes Encoding Heat Shock Proteins Are Associated with Risk and Clinical Course of Severe COVID-19: A Pilot Study Open
In viral infections human heat shock proteins (HSPs) play a dual role by either protecting host cells or acting on viruses’ needs. The roles of HSPs have been extensively studied in various human pathologies, but their involvement in the p…
View article: The Potential of Universal Primers for Barcoding of Subtropical Crops: Actinidia, Feijoa, Citrus, and Tea
The Potential of Universal Primers for Barcoding of Subtropical Crops: Actinidia, Feijoa, Citrus, and Tea Open
The molecular identification of valuable genotypes is an important problem of germplasm management. In this study, we evaluated the potential of 11 universal primer pairs for the DNA barcoding of locally derived cultivars of subtropical cr…
View article: Special Issue “25 Anniversary of Bioinformatics of Genome Regulation and Structure Conference Series”
Special Issue “25 Anniversary of Bioinformatics of Genome Regulation and Structure Conference Series” Open
This article overviews historical trends in studies on gene expression regulation published in “25 Anniversary of Bioinformatics of Genome Regulation and Structure Conference Series” (https://www [...]
View article: New Sights into Bioinformatics of Gene Regulations and Structure
New Sights into Bioinformatics of Gene Regulations and Structure Open
This article overviews recent findings on molecular mechanisms of gene expression regulation published in the “New Sights into Bioinformatics of Gene Regulations and Structure” (https://www [...]
View article: Bioinformatic analysis of the regulatory potential of tagging SNPs provides evidence of the involvement of genes encoding the heat-resistant obscure (Hero) proteins in the pathogenesis of cardiovascular diseases
Bioinformatic analysis of the regulatory potential of tagging SNPs provides evidence of the involvement of genes encoding the heat-resistant obscure (Hero) proteins in the pathogenesis of cardiovascular diseases Open
Although multiple aspects of molecular pathology underlying cardiovascular diseases (CVDs) have been revealed, the complete picture has yet to be elucidated. In this respect, annotation of the novel links between genes and atherosclerosis …
View article: Computational identification of promising genetic markers associated with molecular mechanisms of reduced rice resistance to Rhizoctonia solani under excess nitrogen fertilization using gene network reconstruction and analysis methods
Computational identification of promising genetic markers associated with molecular mechanisms of reduced rice resistance to Rhizoctonia solani under excess nitrogen fertilization using gene network reconstruction and analysis methods Open
Although nitrogen fertilizers increase rice yield, their excess can impair plant resistance to diseases, particularly sheath blight caused by Rhizoctonia solani . This pathogen can destroy up to 50 % of the crop, but the mechanisms underly…
View article: Reconstruction and computational analysis of the microRNA regulation gene network in wheat drought response mechanisms
Reconstruction and computational analysis of the microRNA regulation gene network in wheat drought response mechanisms Open
Drought is a critical factor limiting the productivity of bread wheat ( Triticum aestivum L.), one of the key agricultural crops. Wheat adaptation to water deficit is ensured by complex molecular genetic mechanisms, including the coordinat…
View article: Deregulation mechanisms and therapeutic opportunities of p53-responsive microRNAs in diffuse large B-cell lymphoma
Deregulation mechanisms and therapeutic opportunities of p53-responsive microRNAs in diffuse large B-cell lymphoma Open
Here, we have discussed the molecular mechanisms of p53-responsive microRNAs dysregulation in response to genotoxic stress in diffuse large B-cell lymphoma (DLBCL) patients. The role of micro ribonucleic acids (microRNAs) in p53-signaling …
View article: Computer reconstruction of the interaction of genes associated with Angelman syndrome.
Computer reconstruction of the interaction of genes associated with Angelman syndrome. Open
Reconstruction of the structure of the gene network for a set of genes associated with the disease makes it possible to determine the effectiveness of diagnosis and therapy, and to study the possibilities of targeted drug effects on target…
View article: Structural Features of DNA in tRNA Genes and Their Upstream Sequences
Structural Features of DNA in tRNA Genes and Their Upstream Sequences Open
RNA polymerase III (Pol III) transcribes tRNA genes using type II promoters. The internal control regions contain a Box A and a Box B, which are recognized by TFIIIC. The 5′-flanking regions of tRNA genes clearly play a role in the regulat…
View article: In Vitro vs. In Vivo Transcriptomic Approach Revealed Core Pathways of Nitrogen Deficiency Response in Tea Plant (Camellia sinensis (L.) Kuntze)
In Vitro vs. In Vivo Transcriptomic Approach Revealed Core Pathways of Nitrogen Deficiency Response in Tea Plant (Camellia sinensis (L.) Kuntze) Open
For the first time, we used an in vitro vs. in vivo experimental design to reveal core pathways under nitrogen deficiency (ND) in an evergreen tree crop. These pathways were related to lignin biosynthesis, cell redox homeostasis, the defen…
View article: GWAS-significant loci and severe COVID-19: analysis of associations, link with thromboinflammation syndrome, gene-gene, and gene-environmental interactions
GWAS-significant loci and severe COVID-19: analysis of associations, link with thromboinflammation syndrome, gene-gene, and gene-environmental interactions Open
Objective The aim of this study was to replicate associations of GWAS-significant loci with severe COVID-19 in the population of Central Russia, to investigate associations of the SNPs with thromboinflammation parameters, to analyze gene-g…
View article: Overexpression of RPOTmp Being Targeted to Either Mitochondria or Chloroplasts in Arabidopsis Leads to Overall Transcriptome Changes and Faster Growth
Overexpression of RPOTmp Being Targeted to Either Mitochondria or Chloroplasts in Arabidopsis Leads to Overall Transcriptome Changes and Faster Growth Open
The transcription of Arabidopsis organellar genes is performed by three nuclear-encoded RNA polymerases: RPOTm, RPOTmp, and RPOTp. The RPOTmp protein possesses ambiguous transit peptides, allowing participation in gene expression control i…
View article: Associations between SNPs and vegetation indices: unraveling molecular insights for enhanced cultivation of tea plant (<i>Camellia sinensis</i> (L.) O. Kuntze)
Associations between SNPs and vegetation indices: unraveling molecular insights for enhanced cultivation of tea plant (<i>Camellia sinensis</i> (L.) O. Kuntze) Open
Background Breeding programs for nutrient-efficient tea plant varieties could be advanced by the combination of genotyping and phenotyping technologies. This study was aimed to search functional SNPs in key genes related to the nitrogen-as…
View article: RECONSTRUCTION OF GENE AND ASSOCIATIVE NETWORKS OF DISEASES TO SEARCH FOR TARGET GENES
RECONSTRUCTION OF GENE AND ASSOCIATIVE NETWORKS OF DISEASES TO SEARCH FOR TARGET GENES Open
Computer reconstruction of gene networks—sets of interacting macromolecules with common functions – is a complex task in bioinformatics. Gene networks, presented as graphical structures, offer a convenient means of visualization and provid…
View article: WEB-SERVICES FOR MICRORNA TARGET PREDICTION USING NEURAL NETWORKS
WEB-SERVICES FOR MICRORNA TARGET PREDICTION USING NEURAL NETWORKS Open
The pursuit of microRNA target genes necessitates the creation of novel software and web services. MicroRNAs, abbreviated as short non-coding RNA molecules, hold a pivotal role in metabolic regulation, plant responses to environmental stre…
View article: COMPUTATIONAL TOOLS FOR THE DNA TEXT COMPLEXITY ESTIMATES FOR MICROBIAL GENOMES STRUCTURE ANALYSIS
COMPUTATIONAL TOOLS FOR THE DNA TEXT COMPLEXITY ESTIMATES FOR MICROBIAL GENOMES STRUCTURE ANALYSIS Open
One of the fundamental tasks in bioinformatics involves searching for repeats, which are statistically heterogeneous segments within DNA sequences and complete genomes of microorganisms. Theoretical approaches to analyzing the complexity o…
View article: Editorial: Applications of artificial intelligence, machine learning, and deep learning in plant breeding
Editorial: Applications of artificial intelligence, machine learning, and deep learning in plant breeding Open
Editorial: Applications of artificial intelligence, machine learning, and deep learning in plant breeding
View article: Explainable models using transcription factor binding and epigenome patterns at promoters reveal disease-associated genes and their regulators in the context of cell-types
Explainable models using transcription factor binding and epigenome patterns at promoters reveal disease-associated genes and their regulators in the context of cell-types Open
Understanding genome-wide epigenetic regulation of diseases is important in establishing pathogenic factors and could aid in disease diagnosis, prognosis, and therapeutics. In this study, we have utilized transcription factors (TFs) and co…
View article: A Principal Components Analysis and Functional Annotation of Differentially Expressed Genes in Brain Regions of Gray Rats Selected for Tame or Aggressive Behavior
A Principal Components Analysis and Functional Annotation of Differentially Expressed Genes in Brain Regions of Gray Rats Selected for Tame or Aggressive Behavior Open
The process of domestication, despite its short duration as it compared with the time scale of the natural evolutionary process, has caused rapid and substantial changes in the phenotype of domestic animal species. Nonetheless, the genetic…
View article: Unveiling the methionine cycle: a key metabolic signature and NR4A2 as a methionine-responsive oncogene in esophageal squamous cell carcinoma
Unveiling the methionine cycle: a key metabolic signature and NR4A2 as a methionine-responsive oncogene in esophageal squamous cell carcinoma Open
Esophageal squamous cell carcinoma (ESCC) is a deadly malignancy with notable metabolic reprogramming, yet the pivotal metabolic feature driving ESCC progression remains elusive. Here, we show that methionine cycle exhibits robust activati…
View article: Deciphering the Molecular Mechanism of the Intermediate Secondary Growth and Internode Elongation of the Castor Bean (Ricinus communis L.) by the Combined Analysis of the Transcriptome and Metabolome
Deciphering the Molecular Mechanism of the Intermediate Secondary Growth and Internode Elongation of the Castor Bean (Ricinus communis L.) by the Combined Analysis of the Transcriptome and Metabolome Open
The length of internodes plays a crucial role in determining the height of the castor plant (Ricinus communis L.). However, the specific mechanisms underlying internode elongation, particularly in the main stem of the castor plant, remain …
View article: AthRiboNC: an Arabidopsis database for ncRNAs with coding potential revealed from ribosome profiling
AthRiboNC: an Arabidopsis database for ncRNAs with coding potential revealed from ribosome profiling Open
Non-coding RNAs (ncRNAs) are traditionally considered incapable of encoding proteins, but new evidence suggests that small open reading frames (sORFs) within ncRNAs can actually encode biologically functional small peptides. Despite growin…
View article: Reconstruction and analysis of the gene regulatory network for cell wall function in <i>Arabidopsis thaliana</i> L. leaves in response to water deficit
Reconstruction and analysis of the gene regulatory network for cell wall function in <i>Arabidopsis thaliana</i> L. leaves in response to water deficit Open
The plant cell wall represents the outer compartment of the plant cell, which provides a physical barrier and triggers signaling cascades under the influence of biotic and abiotic stressors. Drought is a factor that negatively affects both…
View article: Glutathione Non-Covalent Binding Sites on Hemoglobin and Major Glutathionylation Target betaCys93 Are Conservative among Both Hypoxia-Sensitive and Hypoxia-Tolerant Mammal Species
Glutathione Non-Covalent Binding Sites on Hemoglobin and Major Glutathionylation Target betaCys93 Are Conservative among Both Hypoxia-Sensitive and Hypoxia-Tolerant Mammal Species Open
Intracellular tripeptide glutathione is an important agent of cell survival under hypoxia. Glutathione covalently binds to SH groups of hemoglobin cysteine residues, protecting them from irreversible oxidation, and changes its affinity to …