Explanipedia

Identification of proteins regulating phenotype-associated genes of M2 macrophages: a bioinformatic analysis Open

Е. А. Ощепкова, I. V. Yatsyk, П. С. Деменков, Timofey Ivanisenko, В. А. Иванисенко · 2025

Macrophages are immune system cells that perform various, often opposing, functions in the organism depending on the incoming microenvironment signals. This is possible due to the plasticity of macrophages, which allows them to radically a…

Gene networks and metabolomic screening analysis revealed specific pathways of amino acid and acylcarnitine profile alterations in blood plasma of patients with Parkinson’s disease and vascular parkinsonism Open

A. A. Makarova, P. M. Melnikova, Artem D. Rogachev, П. С. Деменков, Timofey Ivanisenko , et al. · 2025

Parkinson’s disease (PD) and vascular parkinsonism (VP) are characterized by similar neurological syndromes but differ in pathogenesis, morphology, and therapeutic approaches. The molecular genetic mechanisms of these pathologies are multi…

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

Е. А. Ощепкова, A. R. Volyanskaya, A. V. Adamovskaya, П. С. Деменков, I. V. Yatsyk , et al. · 2025

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…

Investigation of metabolic features of glioblastoma tissue and the peritumoral environment using targeted metabolomics screening by LC-MS/MS and gene network analysis Open

N. V. Basov, A. V. Adamovskaya, Artem D. Rogachev, E. V. Gaisler, П. С. Деменков , et al. · 2025

The metabolomic profiles of glioblastoma and surrounding brain tissue, comprising 17 glioblastoma samples and 15 peritumoral tissue samples, were thoroughly analyzed in this investigation. The LC-MS/MS method was used to analyze over 400 m…

Reconstruction and computational analysis of the microRNA regulation gene network in wheat drought response mechanisms Open

M. A. Kleshchev, Anastasia Maltseva, Е. А. Ощепкова, П. С. Деменков, Timofey Ivanisenko , et al. · 2025

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…

AI-Assisted Identification of Primary and Secondary Metabolomic Markers for Postoperative Delirium Open

В. А. Иванисенко, Artem D. Rogachev, A. A. Makarova, N. V. Basov, E. V. Gaisler , et al. · 2024

Despite considerable investigative efforts, the molecular mechanisms of postoperative delirium (POD) remain unresolved. The present investigation employs innovative methodologies for identifying potential primary and secondary metabolic ma…

An Accurate and Efficient Approach to Knowledge Extraction from Scientific Publications Using Structured Ontology Models, Graph Neural Networks, and Large Language Models Open

Timofey Ivanisenko, П. С. Деменков, В. А. Иванисенко · 2024

The rapid growth of biomedical literature makes it challenging for researchers to stay current. Integrating knowledge from various sources is crucial for studying complex biological systems. Traditional text-mining methods often have limit…

AI-Assisted Identification of Primary and Secondary Metabolomic Markers for Post-Operative Delirium Open

В. В. Ломиворотов, В. А. Иванисенко, A. A. Makarova, Artem D. Rogachev, N. V. Basov , et al. · 2024

Despite considerable investigative efforts, the molecular mechanisms of postoperative delirium (POD) remain unresolved. The present investigation employs innovative methodologies for identifying potential primary and secondary metabolic ma…

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

A. R. Volyanskaya, Е. А. Ощепкова, У. С. Зубаирова, П. С. Деменков, A. S. Venzel , et al. · 2023

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…

Prioritization of potential pharmacological targets for the development of anti-hepatocarcinoma drugs modulating the extrinsic apoptosis pathway: the reconstruction and analysis of associative gene networks help Open

П. С. Деменков, Е. А. Ощепкова, A. V. Adamovskaya, Elena Mishchenko, Т. М. Хлебодарова , et al. · 2023

Hepatocellular carcinoma (HCC) is a common severe type of liver cancer characterized by an extremely aggressive course and low survival rates. It is known that disruptions in the regulation of apoptosis activation are some of the key featu…

Gene networks for use in metabolomic data analysis of blood plasma from patients with postoperative delirium Open

В. А. Иванисенко, N. V. Basov, A. A. Makarova, A. S. Venzel, Artem D. Rogachev , et al. · 2023

Postoperative delirium (POD) is considered one of the most severe complications, resulting in impaired cognitive function, extended hospitalization, and higher treatment costs. The challenge of early POD diagnosis becomes particularly sign…

Molecular-genetic pathways of hepatitis C virus regulation of the expression of cellular factors PREB and PLA2G4C, which play an important role in virus replication Open

E. L. Mishchenko, A. A. Makarova, Е. А. Ощепкова, A. S. Venzel, Timofey Ivanisenko , et al. · 2023

The participants of Hepatitis C virus (HCV) replication are both viral and host proteins. Therapeutic approaches based on activity inhibition of viral non-structural proteins NS3, NS5A, and NS5B are undergoing clinical trials. However, rap…

Reconstruction of the regulatory hypermethylation network controlling hepatocellular carcinoma development during hepatitis C viral infection Open

Е. А. Ощепкова, Т. М. Хлебодарова, П. С. Деменков, Anastasiia R. Volianskaia, A. S. Venzel , et al. · 2023

Hepatocellular carcinoma (HCC) has been associated with hepatitis C viral (HCV) infection as a potential risk factor. Nonetheless, the precise genetic regulatory mechanisms triggered by the virus, leading to virus-induced hepatocarcinogene…

Accurate noise-robust classification of Bacillus species from MALDI-TOF MS spectra using a denoising autoencoder Open

Yulia E. Uvarova, П. С. Деменков, Irina N. Kuzmicheva, A. S. Venzel, E. Mischenko , et al. · 2023

Bacillus strains are ubiquitous in the environment and are widely used in the microbiological industry as valuable enzyme sources, as well as in agriculture to stimulate plant growth. The Bacillus genus comprises several closely related gr…

Primary and Secondary micro-RNA Modulation the Extrinsic Pathway of Apoptosis in Hepatocellular Carcinoma Open

Т. М. Хлебодарова, П. С. Деменков, Timofey Ivanisenko, Е. А. Ощепкова, Inna N. Lavrik , et al. · 2023

Abstract-One of the most common malignant liver diseases is hepatocellular carcinoma, which has a high recurrence rate and a low five-year survival rate. It is very heterogeneous both in structure and between patients, which complic…

Computer analysis of regulation of hepatocarcinoma marker genes hypermethylated by HCV proteins Open

Е. А. Ощепкова, Т. М. Хлебодарова, П. С. Деменков, A. S. Venzel, Nikita V. Ivanisenko , et al. · 2023

Hepatitis C virus (HCV) is a risk factor that leads to hepatocellular carcinoma (HCC) development. Epigenetic changes are known to play an important role in the molecular genetic mechanisms of virus-induced oncogenesis. Aber rant DNA methy…

The New Version of the ANDDigest Tool with Improved AI-Based Short Names Recognition Open

Timofey Ivanisenko, П. С. Деменков, Н. А. Колчанов, В. А. Иванисенко · 2022

The body of scientific literature continues to grow annually. Over 1.5 million abstracts of biomedical publications were added to the PubMed database in 2021. Therefore, developing cognitive systems that provide a specialized search for in…

Plasma metabolomics and gene regulatory networks analysis reveal the role of nonstructural SARS-CoV-2 viral proteins in metabolic dysregulation in COVID-19 patients Open

В. А. Иванисенко, E. V. Gaisler, N. V. Basov, Artem D. Rogachev, С. В. Чересиз , et al. · 2022

The New Version of the Anddigest Tool with Improved AI-Based Short Names Recognition Open

Timofey Ivanisenko, П. С. Деменков, Н. А. Колчанов, В. А. Иванисенко · 2022

The body of scientific literature continues to grow annually. Over 1.5 million abstracts of biomedical publications were added to the PubMed database in 2021. Therefore, developing cognitive systems that provide a specialized search for in…

Metabolomics analysis reveals a potential role SARS-CoV-2 viral proteins in the regulation/perturbation of metabolic pathways associated with altered plasma metabolites in COVID-19 patients Open

В. А. Иванисенко, E. V. Gaisler, N. V. Basov, Artem D. Rogachev, С. В. Чересиз , et al. · 2022

Metabolomic analysis of patient`s plasma is a promising approach to the study of molecular mechanisms of viral infections, identification of diagnostic and prognostic biomarkers, and improvement of the current therapies. However, metabolom…

Prioritization of biological processes based on the reconstruction and analysis of associative gene networks describing the response of plants to adverse environmental factors Open

П. С. Деменков, Е. А. Ощепкова, Timofey Ivanisenko, В. А. Иванисенко · 2021

Methods for prioritizing or ranking candidate genes according to their importance based on specific criteria via the analysis of gene networks are widely used in biomedicine to search for genes associated with diseases and to predict bioma…

ANDDigest: A web tool for finding information in scientific publications and patents in the biological field Open

Timofey Ivanisenko, П. С. Деменков, В. А. Иванисенко · 2021

Reconstruction of associative gene networks using text mining methods Open

В. А. Иванисенко, Е. А. Ощепкова, Timofey Ivanisenko, П. С. Деменков · 2021

Young «oil site» of the Uzon Caldera as a habitat for unique microbial life Open

S. E. Peltek, A. V. Bryanskaya, Yuliya E. Uvarova, А. С. Розанов, Timofey Ivanisenko , et al. · 2020

ANDDigest: a new web-based module of ANDSystem for the search of knowledge in the scientific literature Open

Timofey Ivanisenko, Olga Saik, П. С. Деменков, Nikita V. Ivanisenko, Alexander N. Savostianov , et al. · 2020

Background The rapid growth of scientific literature has rendered the task of finding relevant information one of the critical problems in almost any research. Search engines, like Google Scholar, Web of Knowledge, PubMed, Scopus, and othe…

Additional file 2 of Young «oil site» of the Uzon Caldera as a habitat for unique microbial life Open

S. E. Peltek, A. V. Bryanskaya, Yuliya E. Uvarova, А. С. Розанов, Timofey Ivanisenko , et al. · 2020

Additional file 2: Table S1. Water samples. Note: b.d.l. – below detected limit, n.d. – no data.

Additional file 8 of Young «oil site» of the Uzon Caldera as a habitat for unique microbial life Open

S. E. Peltek, A. V. Bryanskaya, Yuliya E. Uvarova, А. С. Розанов, Timofey Ivanisenko , et al. · 2020

Additional file 8: Figure S4-A, Additional file 7: Fig. S4-B. Completeness of the naphthalene degradation (А) and benzoate degradation (B) metabolic pathways for the U3.4.10 sample. Red borders indicate the proteins found in U3.4.10 sample…

Prioritization of potato genes involved in the formation of agronomically valuable traits using the SOLANUM TUBEROSUM knowledge base Open

П. С. Деменков, Olga Saik, Timofey Ivanisenko, Н. А. Колчанов, А. В. Кочетов , et al. · 2019

The development of highly efficient technologies in genomics, transcriptomics, proteomics and metabolomics, as well as new technologies in agriculture has led to an “information explosion” in plant biology and crop production, including po…

Prioritization of genes involved in endothelial cell apoptosis by their implication in lymphedema using an analysis of associative gene networks with ANDSystem Open

Olga Saik, Vadim Nimaev, Dilovarkhuja Usmonov, П. С. Деменков, Timofey Ivanisenko , et al. · 2019

A new version of the ANDSystem tool for automatic extraction of knowledge from scientific publications with expanded functionality for reconstruction of associative gene networks by considering tissue-specific gene expression Open

В. А. Иванисенко, П. С. Деменков, Timofey Ivanisenko, E. L. Mishchenko, Olga Saik · 2019

Timofey Ivanisenko YOU? Author Swipe