Publications by authors named "Shashkova T"

Article Synopsis
  • The text discusses the creation of SEMA 2.0, a web platform designed to predict conformational B-cell epitopes, which are vital for vaccine development.
  • SEMA 2.0 utilizes advanced protein language models and offers tools for both sequence- and structure-based predictions, along with identifying N-glycosylation sites.
  • The platform is freely accessible to everyone without needing a login, and its source code is available on GitHub.
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Article Synopsis
  • * The authors introduce PROSTATA, a new predictive model that outperforms existing neural network solutions due to its innovative architecture and a high-quality training dataset.
  • * PROSTATA is available for use and implementation at the provided URLs, offering a promising tool for future protein stability assessments.
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Introduction: The WHO regularly updates influenza vaccine recommendations to maximize their match with circulating strains. Nevertheless, the effectiveness of the influenza A vaccine, specifically its H3N2 component, has been low for several seasons. The aim of the study is to develop a mathematical model of cross-immunity based on the array of published WHO hemagglutination inhibition assay (HAI) data.

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  • Interpretation of noncoding genomic variants is a major challenge in human genetics, and recent machine learning methods have shown promise in predicting their effects.
  • Current methods rely on specific experimental data for training, which limits their applicability across different cell types with unmeasured features.
  • The new DeepCT neural network architecture can learn from sparse epigenetic data, infer missing information, and provide cell type-specific predictions regarding the impact of noncoding variations in the genome.
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Article Synopsis
  • * Researchers developed a new model named SEMA using transfer learning with pretrained deep learning models to enhance prediction of antibody-antigen interactions.
  • * SEMA outperformed existing tools, achieving an ROC AUC of 0.76, and was able to effectively rank key regions in the SARS-CoV-2 RBD domain; the model is publicly accessible online.
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In recent years, the number of genome-wide association studies (GWAS) carried out for various economically important animal traits has been increasing. GWAS discoveries provide summary statistics that can be used both for targeted marker-oriented selection and for studying the genetic control of economically important traits of farm animals. In contrast to research in human genetics, GWAS on farm animals often does not meet generally accepted standards (availability of information about effect and reference alleles, the size and direction of the effect, etc.

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A biosafety study was carried out concerning the metabolites of strain 19/97 M. This strain is a promising producer of biological preparations and shows antagonistic properties against fungi, which cause Fusarium wilt disease. The strain has a pronounced biological activity against conifers, cereals and legumes.

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Background: Understanding the influence of genetic variants on DNA methylation is fundamental for the interpretation of epigenomic data in the context of disease. There is a need for systematic approaches not only for determining methylation quantitative trait loci (methQTL), but also for discriminating general from cell type-specific effects.

Results: Here, we present a two-step computational framework MAGAR ( https://bioconductor.

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Background And Hypothesis: Physical activity (PA) is an important behavioral factor associated with the quality of life and healthy longevity. We hypothesize that extremely low and extremely high levels of daily PA (including occupational PA) may have a negative impact on sleep quality and psychological well-being.

Objective: The aim of the study is to investigate the association between the level and type of PA and sleep problems in adult population.

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Article Synopsis
  • Adult height has been a key focus in studies of heritability and helped develop the classical polygenic model for understanding complex traits.
  • The traditional model assumes that effects are additive and residuals are normally distributed, but this may not hold true in larger studies involving many individuals.
  • Findings suggest that for large-scale analyses, incorporating non-additive interactions among sex, environment, and genes is essential, or alternatively, using a log-normal approximation can maintain the robustness of the additive model.
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  • The gut microbiome is crucial for human health, and while its structure varies, its functional capacity is key; improved functional prediction methods can enhance understanding of its role in diseases.
  • Researchers used advanced feature engineering based on microbial phenotypes from 16S rRNA sequencing to analyze gut microbes in patients with inflammatory bowel disease (IBD) and found specific metabolic functions tied to health and disease.
  • Machine learning techniques distinguished microbiome profiles between healthy individuals and those with Crohn's disease or ulcerative colitis, offering insights into disease mechanisms and potential biomarkers for personalized medicine.
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Hundreds of genome-wide association studies (GWAS) of human traits are performed each year. The results of GWAS are often published in the form of summary statistics. Information from summary statistics can be used for multiple purposes - from fundamental research in biology and genetics to the search for potential biomarkers and therapeutic targets.

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Genome-wide association studies have provided a vast array of publicly available SNP × phenotype association results. However, they are often in disparate repositories and formats, making downstream analyses difficult and time consuming. PheLiGe (https://phelige.

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Genomic selection is routinely used worldwide in agricultural breeding. However, in Russia, it is still not used to its full potential partially due to high genotyping costs. The use of genotypes imputed from the low-density chips (LD-chip) provides a valuable opportunity for reducing the genotyping costs.

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Genome-wide association studies have led to a significant progress in identification of genomic loci affecting coronary artery disease (CAD) risk. However, revealing the causal genes responsible for the observed associations is challenging. In the present study, we aimed to prioritize CAD-relevant genes based on cumulative evidence from the published studies and our own study of colocalization between eQTLs and loci associated with CAD using SMR/HEIDI approach.

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Varicose veins of lower extremities (VVs) are a common multifactorial vascular disease. Genetic factors underlying VVs development remain largely unknown. Here we report the first large-scale study of VVs performed on a freely available genetic data of 408,455 European-ancestry individuals.

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Background: Metagenomic surveys of human microbiota are becoming increasingly widespread in academic research as well as in food and pharmaceutical industries and clinical context. Intuitive tools for investigating experimental data are of high interest to researchers.

Results: Knomics-Biota is a web-based resource for exploratory analysis of human gut metagenomes.

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Personalized nutrition is of increasing interest to individuals actively monitoring their health. The relations between the duration of diet intervention and the effects on gut microbiota have yet to be elucidated. Here we examined the associations of short-term dietary changes, long-term dietary habits and lifestyle with gut microbiota.

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Alternative splicing (AS) can significantly impact the transcriptome and proteome of a eukaryotic cell. Here, using transcriptome and proteome profiling data, we analyzed AS in two life forms of the model moss Physcomitrella patens, namely protonemata and gametophores, as well as in protoplasts. We identified 12 043 genes subject to alternative splicing and analyzed the extent to which AS contributes to proteome diversity.

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Background: Intestinal microbiota plays an important role in the human health. It is involved in the digestion and protects the host against external pathogens. Examination of the intestinal microbiome interactions is required for understanding of the community influence on host health.

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Using the pTrc99A/P450scc vector, a plasmid was constructed in which cDNAs for cytochrome P450scc, adrenodoxin reductase, and adrenodoxin are situated in a single expression cassette. This plasmid was shown to direct the synthesis of all the above proteins in Escherichia coli. Their localization in the E.

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X-ray and endoscopic examinations were made in the course of follow-up of patients surgically treated for gastroduodenal ulcer (n = 134). X-ray investigations of postoperative stomach make it possible to assess it functionally, to determine its relations with other parts of gastrointestinal tract. Endoscopy is helpful in revealing changes in gastric mucosa, anastomosis capable of producing diverse motor and evacuatory disturbances of the stomach.

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