A5082117531- Genomics and Phylogenetic Studies
- Genomics and Chromatin Dynamics
- RNA and protein synthesis mechanisms
- Bioinformatics and Genomic Networks
- RNA Research and Splicing
- Genetics, Bioinformatics, and Biomedical Research
- Gene expression and cancer classification
- Chromosomal and Genetic Variations
- Vestibular and auditory disorders
- Hearing, Cochlea, Tinnitus, Genetics
- Hearing Impairment and Communication
- Scientific Computing and Data Management
- Gene Regulatory Network Analysis
- Research Data Management Practices
- Microbial Community Ecology and Physiology
- Material Properties and Applications
- Plant nutrient uptake and metabolism
- Bacterial Genetics and Biotechnology
- Machine Learning in Bioinformatics
- Engineering Technology and Methodologies
- Bacteriophages and microbial interactions
- Genetic Mapping and Diversity in Plants and Animals
Siberian Branch of the Russian Academy of Sciences
2019-2025
Institute of Cytology and Genetics
2019-2025
Novosibirsk State University
2019-2025
Russian Academy of Sciences
2024
Kurchatov Institute
2024
Transcription factors (TFs) are the main regulators of eukaryotic gene expression. The cooperative binding at least two TFs to genomic DNA is a major mechanism transcription regulation. Massive analysis co-occurrence overrepresented pairs motifs for different target studied in ChIP-seq experiments can clarify mechanisms TF cooperation. We categorized from M. musculus and A. thaliana ChIP-seq/DAP-seq according structure their DNA-binding domains (DBDs) into classes. homotypic motifs, using...
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...
(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...
Gene expression profiling data contains more information than is routinely extracted with standard approaches. Here we present Fold-Change-Specific Enrichment Analysis (FSEA), a new method for functional annotation of differentially expressed genes from transcriptome respect to their fold changes. FSEA identifies Ontology (GO) terms, which are shared by the group similar magnitude response, and assesses these GO terms found fold-change-specifically (e.g., weakly, moderately, or strongly)...
Gene expression profiling data contains more information than is routinely extracted with standard approaches. Here we present Fold-change-Specific Enrichment Analysis (FSEA), a new method for functional annotation of differentially expressed genes from transcriptome respect to their fold changes. FSEA identifies GO terms, which are shared by the group similar magnitude response, and assesses these terms found fold-change-specifically (e.g. weakly, moderately or strongly) affected stimulus...
(1) Background: Transcription factors (TFs) are main regulators of eukaryotic gene expression. The cooperative binding at least two TFs to genomic DNA is the widespread mechanism transcription regulation. Massive analysis co-occurrence overrepresented pairs motifs (composite elements, CEs) for different target studied in ChIP-seq experiments can clarify mechanisms TF cooperation. (2) Methods: We focused on homotypic CEs representing same motif models and considered only with spacers....
A list of the main operational and morphological properties heat sound insulating materials (HSIM) is selected, which makes it possible to improve energy efficiency production working conditions for personnel in press heat-treating shops. From properties, taking into account range changes their values, classification codes are formed. The code system used form a task selection HSIM, displaying priority, composition values required solve specific problem insulation design. structure HSIM...
As areas of application terahertz (THz) radiation expand in science and practice, evidence is accumulating that this type can affect not only biological molecules directly, but also cellular processes as a whole. In study, the transcriptome cells thermophilic bacterium
An increase in the prevalence of autosomal recessive deafness 1A (DFNB1A) populations European descent was shown to be promoted by assortative marriages among deaf people. Assortative became possible with widespread introduction sign language, resulting increased genetic fitness individuals and, thereby, relaxing selection against deafness. However, effect this phenomenon not previously studied different structures. We developed an agent-based computer model for analysis spread DFNB1A. Using...
The transcriptome sequencing experiment (RNA-seq) has become almost a routine procedure for studying both model organisms and crops. As result of bioinformatics processing such experimental output, huge heterogeneous data are obtained, representing nucleotide sequences transcripts, amino acid sequences, their structural functional annotation. It is important to present the obtained wide range researchers in form databases. This article proposes hybrid approach creating molecular genetic...
Modern investigations in biology often require the efforts of one or more groups researchers. Often these are specialists from various scientific fields who generate and share data different formats sizes. Without modern approaches to work automation versioning (where collaborators stored at points time), teamwork quickly devolves into unmanageable confusion. In this review, we present a number information systems designed solve problems. Their application organization activity helps manage...
Regulation of eukaryotic gene transcription is controlled by specific proteins factors. Transcription factors bind certain regions genomic DNA (binding sites or motives). Common action two more widespread mechanism factor action. Hence, the term ‘composite element’ implied closely located and frequently occurred in motives. Composite elements are partitioned onto those with overlapped motifs, these motifs separated a spacer. Currently, chromatin immunoprecipitation high throughput approach...
Transcription regulation plays an important role in bacterial activity. The operon concept coined by François Jacob and Jacques Monod has had a considerable effect on investigations into gene expression regulation, including modeling. However, most such studies have considered the models devised manually for one or several operons. For that reason, objective of present study was automated genome model reconstruction different bacteria. suggested algorithm accounted all possible interactions...
ABSTRACT It was evidenced, that the increase in prevalence of autosomal recessive deafness 1A (DFNB1A) populations European descent promoted by assortative marriages among deaf people. Assortative become possible with a widespread introduction sign language resulting increased genetic fitness individuals, thus relaxing selection against deafness. Currently, cochlear implantation is becoming common method rehabilitation for patients, restoring their hearing ability and promoting acquirement...