A5001721170- Evolution and Genetic Dynamics
- Bioinformatics and Genomic Networks
- Genomics and Phylogenetic Studies
- Microbial Community Ecology and Physiology
- Gene Regulatory Network Analysis
- Microbial Metabolic Engineering and Bioproduction
- RNA and protein synthesis mechanisms
- Bacteriophages and microbial interactions
- Genetics, Bioinformatics, and Biomedical Research
- Evolutionary Game Theory and Cooperation
- Hearing, Cochlea, Tinnitus, Genetics
- RNA modifications and cancer
- Genetics and Neurodevelopmental Disorders
- Machine Learning in Bioinformatics
- Mental Health Research Topics
- Hearing Impairment and Communication
- Scientific Computing and Data Management
- Gene expression and cancer classification
- Autism Spectrum Disorder Research
- Insect Resistance and Genetics
- Gut microbiota and health
- Vestibular and auditory disorders
- Viral Infectious Diseases and Gene Expression in Insects
- Research Data Management Practices
- Microbial Natural Products and Biosynthesis
Siberian Branch of the Russian Academy of Sciences
2015-2025
Institute of Cytology and Genetics
2016-2025
Novosibirsk State University
2016-2025
Institute of Clinical and Experimental Lymphology
2025
Kurchatov Institute
2021-2024
Russian Academy of Sciences
2012-2013
Autism spectrum disorder (ASD) has a strong and complex genetic component with an estimate of more than 1000 genes implicated cataloged in SFARI (Simon′s Foundation Research Initiative) gene database. A significant part both syndromic idiopathic autism cases can be attributed to disorders caused by the mechanistic target rapamycin (mTOR)-dependent translation deregulation. We conducted gene-set analyses revealed that 606 out 1053 (58%) included Gene database 179 281 (64%) first three...
Technologies for the production of a range compounds using microorganisms are becoming increasingly popular in industry. The creation highly productive strains whose metabolism is aimed to synthesis specific desired product impossible without complex directed modifications genome mathematical and computer modeling methods. One bacterial species actively used biotechnological Corynebacterium glutamicum . There already 5 whole-genome flux balance models it, which can be metabolism research...
In this work, we for the first time performed a comprehensive bioinformatics analysis of 568 human genes that, according to NCBI Gene database as on September 15, 2024, were associated with pain generation, perception and anesthesia. The SCN9A gene encoding sodium voltage-gated channel α subunit 9 expressed in sensory neurons transferring signals central nervous system about tissue damage was only one involved all processes interest at once hub gene. First, our tool called OrthoWeb,...
Cholesterol is an essential structural component of cell membranes and a precursor vitamin D, as well steroid hormones. Humans other animal species can absorb cholesterol from food. also synthesized de novo in the cells many tissues. We have previously reconstructed gene network regulating intracellular levels, which included regulatory circuits involving transcription factors SREBP (Sterol Regulatory Element-Binding Proteins) subfamily. The activity regulated inversely depending on...
Data on the genetics and molecular biology of diabetes are accumulating rapidly. This poses challenge creating research tools for a rapid search for, structuring analysis information in this field. We have developed web resource, GlucoGenes ® , which includes database an Internet portal genes proteins associated with high glucose (hyperglycemia), low (hypoglycemia), both metabolic disorders. The data were collected using text mining publications indexed PubMed Central gene networks...
This article introduces Orthoweb (https://orthoweb.sysbio.cytogen.ru/), a software package developed for the calculation of evolutionary indices, including phylostratigraphic indices and divergence (K /K s ) individual genes as well gene networks. The age index (PAI) allows stage gene’s emergence (and thus indirectly approximate time its origin, known “evolutionary age”) to be assessed based on analysis orthologous across closely distantly related taxa. Additionally, supports transcriptome...
Multiscale approaches for integrating submodels of various levels biological organization into a single model became the major tool systems biology. In this paper, we have constructed and simulated set multiscale models spatially distributed microbial communities study an influence unevenly environmental factors on genetic diversity evolution community members. Haploid Evolutionary Constructor software http://evol-constructor.bionet.nsc.ru/ was expanded by adding spatial modeling (1D, 2D 3D...
Plants constantly fight with stressful factors as high or low temperature, drought, soil salinity and flooding. have evolved a set of stress response mechanisms, which involve physiological biochemical changes that result in adaptive morphological changes. At molecular level, plants is performed by genetic networks, also undergo the process evolution. The study network structure evolution may highlight mechanisms adaptation to adverse conditions, well their stresses help discovery functional...
Wheat heading time is primarily governed by two loci: VRN-1 (response to vernalization) and PPD-1 photoperiod). Five sets of near-isogenic lines (NILs) were studied with the aim investigating effect aforementioned genes on wheat vegetative period duration 14 yield-related traits. Every NIL was sown in hydroponic greenhouse Institute Cytology Genetics, SB RAS. To assess their allelic composition at loci, molecular markers used. It shown that HT plants Vrn-A1vrn-B1vrn-D1 genotype reduced 29 21...
There are many available software tools for visualization and analysis of biological networks. Among them, Cytoscape ( http://cytoscape.org/ ) is one the most comprehensive packages, with plugins applications which extends its functionality by providing protein-protein interaction, gene regulatory co-expression networks, metabolic, signaling, neural as well ecological-type networks including food webs, communities etc. Nevertheless, only three tagged 'network evolution' found in official app...
Bacteriophages are known to be one of the driving forces bacterial evolution. Besides promoting horizontal transfer genes between cells, they may induce directional selection cells (for instance, according more or less resistance phage infection). Switching lysogenic and lytic pathways results in various types (co)evolution host-phage systems. Spatial (more generally, ecological) organization living environment is another factor affecting In this study, we have simulated analyzed a series...
In this study, we collected and systemized diverse information related to depressive anxiety disorders as the first step on way investigate associations between molecular genetics, electrophysiological, behavioral, psychological characteristics of people. Keeping that in mind, developed an internet resource including a database tools for primary presentation data genetic factors, results electroencephalography (EEG) tests, questionnaires. The sample our study was 1010 people from different...
Protein synthesis is not a straight forward process and one gene locus can produce many isoforms, for example, by starting mRNA translation from alternative start sites. altORF evaluator (altORFev) predicts open reading frames within eukaryotic translated linear scanning mechanism its modifications (leaky reinitiation). The program reveals the efficiently altORFs recognized majority of 40S ribosomal subunits landing on 5'-end an mRNA. This information aids to reveal functions genes connected...
Autism spectrum disorder (ASD) is characterized by uncommon genetic heterogeneity and a high heritability concurrently. Most autoimmune disorders (AID), similarly to ASD, are impressive heritability. We conducted gene-set analyses revealed that 584 out of 992 genes (59%) included in new release the SFARI Gene database 439 871 AID-associated (50%) could be attributed one four groups: 1. FMRP (fragile X mental retardation protein) target genes, 2. mTOR signaling network 3. mTOR-modulated 4....
Motivation: Living systems have a complex hierarchical organization that can be viewed as set of dynamically interacting subsystems. Thus, to simulate the internal nature and dynamics entire biological system, we should use iterative way for model reconstruction, which is consistent composition combination its elementary In accordance with this bottom-up approach, developed MAthematical Models bioMOlecular sysTems (MAMMOTh) tool consists database containing manually curated MAMMOTh fitted...
Motility is a key adaptation factor in scarce marine environments inhabited by bacteria. The question of how capacity for adaptive migrations influences the success microbial population various conditions challenge addressed this study. We employed agent-based model competition motile and sedentary populations confined aquatic environment supplied with periodic batch nutrient source to assess fitness both. Such factors as concentration batch, period, mortality type energetic costs migration...
We propose an original program "Evolutionary constructor" that is capable of computationally efficient modeling both population-genetic and ecological problems, combining these directions in one model required detail level. also present results comparative stability, adaptability biodiversity dynamics populations unicellular haploid organisms which form symbiotic ecosystems. The advantages disadvantages two evolutionary strategies biota formation--a few generalists' taxa-based formation...
In this paper we consider the recent advances in methodology for modeling of prokaryotic communities evolution and new features software package "Haploid evolutionary constructor" (http://evol-constructor.bionet.nsc.ru). We show principles
The main goal of this study was to examine the effect long-term meditation practice on behavioral indicators and ERP peak characteristics during an error-recognition task, where participants were presented with emotionally negative (evoking anxiety or aggression) written sentences describing self-related non-self-related emotional state personality traits. In total, 200 in Russian varying coloring half containing a grammatical error that asked identify. EEG recorded age-matched control...
Cydia pomonella granulovirus is a natural pathogen for that used as biocontrol agent of insect populations. The study virulence particular interest since the development resistance in populations C. has been observed during long-term use Mexican isolate CpGV. In our study, we present genomes 18 CpGV strains endemic to southern Russia and from Kazakhstan, well strain included commercial preparation "Madex Twin", which were sequenced analyzed. We performed comparative genomic analysis using...
Phylostratigraphic analysis is an approach to the study of gene evolution that makes it possible determine time origin genes by analyzing their orthologous groups. The age a belonging group def ined as most recent ancestor all species represented in group. Such can reveal important stages both organism whole and groups functionally related genes, particular networks. In addition investigating gene, level its genetic variability what type selection subject relation closely organisms studied....
Background/Aim: We compared the therapeutic efficacy of two recently developed experimental anticancer technologies: 1) in situ vaccination based on local immunotherapy with CpG oligonucleotides and anti-OX40 antibodies to activate antitumor immune response 2) "Karanahan" technology [from Sanskrit kāraṇa ('source') + han ('to kill')] combined injection cyclophosphamide double-stranded DNA eradicate cancer stem cells. Materials Methods: The approaches were three types mouse malignant tumors...
(1) Background: The widespread application of ChIP-seq technology requires annotation cis-regulatory modules through the search co-occurred motifs. (2) Methods: We present web server Motifs Co-Occurrence Tool (Web-MCOT) that for a single dataset detects composite elements (CEs) or overrepresented homo- and heterotypic pairs motifs with spacers overlaps, any mutual orientations, uncovering various similarities to recognition models within first (Anchor) motif in CEs respects target...