Zakhar Mustafin

• PhD
• Institute of Cytology and Genetics, Russian Academy of Sciences

This article introduces Orthoweb (https://orthoweb.sysbio.cytogen.ru/), a software package developed for the calculation of evolutionary indices, including phylostratigraphic indices and divergence indices (K a /K s ) for individual genes as well as for gene networks. The phylostratigraphic age index (PAI) allows the evolutionary stage of a gene’s...

Genes encoding cell surface receptors make up a significant portion of the human genome (more than a thousand genes) and play an important role in gene networks. Cell surface receptors are transmembrane proteins that interact with molecules (ligands) located outside the cell. This interaction activates signal transduction pathways in the cell. A la...

Simple Summary Bacteria belonging to the Ralstonia genus are of great interest for study since this genus includes both phytopathogenic species and soil opportunistic human pathogens, forming two phylogenetic branches. The difference in phenotype of related species is formed by differences in how proteins and other molecules bacteria synthesize, as...

To overcome immune tolerance to cancer, the immune system needs to be exposed to a multi-target action intervention. Here, we investigated the activating effect of CpG oligodeoxynucleotides (ODNs), mesyl phosphoramidate CpG ODNs, anti-OX40 antibodies, and OX40 RNA aptamers on major populations of immunocompetent cells ex vivo. Comparative analysis...

Autism spectrum disorder (ASD) is a neurodevelopmental condition characterized by the early onset of communication and behavioral problems. ASD is highly heritable; however, environmental factors also play a considerable role in this disorder. A significant part of both syndromic and idiopathic autism cases could be attributed to disorders caused b...

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 and 2) "Karanahan" technology [from the Sanskrit kāraṇa ('source') + han ('to kill')] based...

Autism spectrum disorder (ASD) is characterized by uncommon genetic heterogeneity and a high heritability concurrently. Most autoimmune disorders (AID), similarly to ASD, are characterized by impressive genetic heterogeneity and heritability. We conducted gene-set analyses and revealed that 584 out of 992 genes (59%) included in a new release of th...

Active polar transport of the plant hormone auxin carried out by its PIN transporters is a key link in the formation and maintenance of auxin distribution, which, in turn, determines plant morphogenesis. The plasticity of auxin distribution is largely realized through the molecular genetic regulation of the expression of its transporters belonging...

Phylostratigraphic analysis is an approach to the study of gene evolution that makes it possible to determine the time of the origin of genes by analyzing their orthologous groups. The age of a gene belonging to an orthologous group is def ined as the age of the most recent ancestor of all species represented in that group. Such an analysis can rev...

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 Autism Research Initiative) gene database. A significant part of both syndromic and idiopathic autism cases can be attributed to disorders caused by the mechanistic target of rapamycin...

Plants constantly fight with stressful factors as high or low temperature, drought, soil salinity and flooding. Plants have evolved a set of stress response mechanisms, which involve physiological and biochemical changes that result in adaptive or morphological changes. At a molecular level, stress response in plants is performed by genetic network...

Background: Net blotch caused by Pyrenophra teres f. teres is a major foliar disease of barley. Infection can result in significant yield losses of susceptible cultivars of up to 40%. Of the two forms of net blotch (P. teres f. teres and P. teres f. maculata), P. teres f. teres (net form of net blotch) is the dominant one in Russia. The goal of th...

Phylostratigraphic analysis is a way to look anew on phylogenetic data in the evolutionary aspect. It allows counting the evolutionary age based on the analysis of genes, their orthologs and finding the last common ancestor. We performed phylostratigraphic analysis of Arabidopsis thaliana genes associated with several types of abiotic stresses (hea...

Background There are many available software tools for visualization and analysis of biological networks. Among them, Cytoscape (http://cytoscape.org/) is one of the most comprehensive packages, with many plugins and applications which extends its functionality by providing analysis of protein-protein interaction, gene regulatory and gene co-expres...

Bacterial communities are closely interrelated systems consisting of numerous species making it challenging to analyze their structure and relations. At present, there are several experimental techniques providing heterogeneous data, concerning various aspects of this research object. The recent avalanche of available metagenomic data challenges no...

Bacterial communities are tightly interconnected systems consisting of numerous species making it challenging to analyze their structure and relations. There are several experimental techniques providing heterogeneous data concerning various aspects of this object. A recent avalanche of metagenomic data challenges not only biostatisticians but also...

Three high-performance versions of the Haploid Evolutionary Constructor program are presented (http://evol-constructor.bionet.nsc.ru). The software was designed for simulating the functioning and evolution of microbial communities. These high-performance versions are to be run on systems with shared and distributed memory, using CPU and/or GPU. Alm...

В работе приведены результаты разработки высокопроизводительной версии программного комплекса «Гаплоидный эволюционный конструктор» (http://evol-constructor.bionet.nsc.ru), предназначенного для моделирования функционирования и эволюции прокариотических сообществ. Разработана па- раллельная версия программы, предназначенная для работы на высокопрои...