A5032139596- Genomics and Chromatin Dynamics
- RNA Research and Splicing
- Cell Image Analysis Techniques
- Gene Regulatory Network Analysis
- Developmental Biology and Gene Regulation
- Plant Reproductive Biology
- Chromosomal and Genetic Variations
- 3D Printing in Biomedical Research
- Genetic and Environmental Crop Studies
- Plant Molecular Biology Research
- Plant Genetic and Mutation Studies
- Legume Nitrogen Fixing Symbiosis
- Evolution and Genetic Dynamics
- Pluripotent Stem Cells Research
- CRISPR and Genetic Engineering
- Soybean genetics and cultivation
- Nonlinear Waves and Solitons
- Bioinformatics and Genomic Networks
- Genetic Mapping and Diversity in Plants and Animals
- Cellular Mechanics and Interactions
- RNA and protein synthesis mechanisms
- Botanical Research and Chemistry
- Photosynthetic Processes and Mechanisms
- Seed Germination and Physiology
- Nonlinear Photonic Systems
Ioffe Institute
2014-2024
Peter the Great St. Petersburg Polytechnic University
2014-2024
Physical and Technical Institute
2009-2024
Institute of Cytology
2022-2024
St Petersburg University
2020
BIOCAD (Russia)
2020
Physico-Technical Institute
2004-2016
Russian Academy of Sciences
2004-2015
Computing Center
1999-2001
Developing embryos exhibit a robust capability to reduce phenotypic variations that occur naturally or as result of experimental manipulation. This reduction in variation occurs by an epigenetic mechanism called canalization, phenomenon which has resisted understanding because lack necessary molecular data and appropriate gene regulation models. In recent years, quantitative expression have become available for the segment determination process Drosophila blastoderm, revealing specific...
The variation in the expression patterns of gap genes blastoderm fruit fly Drosophila melanogaster reduces over time as a result cross regulation between these genes, fact that we have demonstrated an accompanying article PLoS Biology (see Manu et al., doi:10.1371/journal.pbio.1000049). This biologically essential process is example phenomenon known canalization. It has been suggested developmental trajectory wild-type organism inherently stable, and canalization manifestation this property....
Extensive variation in early gap gene expression the Drosophila blastoderm is reduced over time because of cross regulation. This phenomenon a manifestation canalization, ability an organism to produce consistent phenotype despite variations genotype or environment. The canalization can be understood as arising from actions attractors dynamical system. In order better understand processes developmental robustness and embryo, we investigated effects varying spatial profiles Bicoid protein...
Initiation of flowering moves plants from vegetative to reproductive development. The time when this transition happens (flowering time), an important indicator productivity, depends on both endogenous and environmental factors. core genetic regulatory network canalizing the signals decision flower has been studied extensively in model plant Arabidopsis thaliana shown preserve its main blocks other species. It integrates activation FLOWERING LOCUS T (FT) gene or homologs expressed as high...
The detailed analysis of transcriptional regulation is crucially important for understanding biological processes. gap gene network in Drosophila attracts large interest among researches studying mechanisms regulation. It implements the most upstream regulatory layer segmentation network. knowledge molecular involved far less complete than that genetics system. Mathematical modeling goes beyond insights gained by and approaches. allows us to reconstruct wild-type expression patterns silico,...
The ability of human pluripotent stem cells for unlimited proliferation and self-renewal promotes their application in the fields regenerative medicine. morphological assessment growing colonies cells, as a non-invasive method, allows best clones further clinical applications to be safely selected. For this purpose, we analyzed seven parameters both extracted from phase-contrast images embryonic cell line H9, control induced (hiPSC) AD3, hiPSC HPCASRi002-A (CaSR) various passages during...
As an RNA virus, hepatitis C virus (HCV) is able to rapidly acquire drug resistance, and for this reason the design of effective anti-HCV drugs a real challenge. The HCV subgenomic replicon-containing cells are widely used experimental studies genome replication mechanisms, testing in vitro resistance. NS3/4A protease essential and, therefore, it one most attractive targets developing specific antiviral agents against HCV. We have developed stochastic model replicon replication, which...
The statistical thermodynamics based approach provides a promising framework for construction of the genotype-phenotype map in many biological systems. Among important aspects good model connecting DNA sequence information with that molecular phenotype (gene expression) is selection regulatory interactions and relevant transcription factor bindings sites. As may predict different levels functional importance specific binding sites genomic contexts, it essential to formulate study such models...
Human pluripotent stem cells (hPSCs) are an important tool in the field of regenerative medicine due to their ability differentiate towards all tissues adult organism. An task study hPSCs is understand factors that influence maintenance and clonal characteristics colonies represented by morphological phenotype. Such include migrate during growth. In this work, we measured analyzed migration trajectories hPSC obtained from bright-field images three cell lines, including induced lines AD3...
Human pluripotent stem cells (hPSCs) attract tremendous attention due to their unique properties. Manual extraction of trajectories cell colonies in experimental image time series is labor intensive and subjective, thus the aim work was develop a computer semi-automated protocol for colony tracking. The developed procedure consists three major stages, namely, registration, object detection Registration using discrete Fourier transform tracking based on solution linear assignment problem...
Human pluripotent stem cells are promising for a wide range of research and therapeutic purposes. Their maintenance in culture requires the deep control their clonal status. A non-invasive method such involves day-to-day observation morphological changes, along with imaging colonies, subsequent automatic assessment colony phenotype using image analysis by machine learning methods. We developed classifier convolutional neural network applied it to discriminate between images human embryonic...
Human pluripotent stem cells have the potential for unlimited proliferation and controlled differentiation into various somatic cells, making them a unique tool regenerative personalized medicine. Determining best clone selection is challenging problem in this field requires new sensing instruments methods able to automatically assess state of growing colony ('phenotype') make decisions about its destiny. One possible solution such label-free, non-invasive assessment phase-contrast images...
In many plant species, flowering is promoted by the cold treatment or vernalization. The mechanism of vernalization-induced has been extensively studied in
We consider a mathematical formulation of the problem protein production during segment determination in Drosophila blastoderm, together with some preliminary results its analytical study. reformulate spatial difference equations as set nonlinear partial differential and obtain their dimensionless form continuum limit. Using previous obtained by gene circuit method, we find an asymptotic statement small parameter. Some comparison method applied to model are obtained, exact stationary upper...
Cis-regulatory sequences are often composed of many low-affinity transcription factor binding sites (TFBSs). Determining the evolutionary and functional importance regulatory sequence composition is impeded without a detailed knowledge genotype-phenotype map.
Annotating the genotype-phenotype relationship, and developing a proper quantitative description of requires understanding impact natural genomic variation on gene expression. We apply sequence-level model gap expression in early development Drosophila to analyze single nucleotide polymorphisms (SNPs) panel sequenced D. melanogaster lines. Using thermodynamic modeling framework, we provide both analytical computational descriptions how single-nucleotide variants affect The analysis reveals...
Transition to flowering is an important stage of plant development. Many regulatory modules that control floral transition are conservative across plants. This process best studied for the model Arabidopsis thaliana . The homologues genes responsible initiation in legumes have been identified, and available data on their expression provide a good basis gene network modeling. In this study, we developed several dynamical models controlling pea ( Pisum sativum ) using two different approaches....