Section “Reconstruction, computational analysis and modeling of gene networks and metabolic pathways”

The section “Reconstruction, computational analysis and modeling of gene networks and metabolic pathways” is an interdisciplinary platform for presenting and discussing modern advances in research of structural and functional organization of gene networks and metabolic pathways of humans, animals, plants, microorganisms and viruses, based on integration of experimental and computational approaches.

The central objects of the section are (a) gene networks, ensembles of coordinately functioning genes that control the formation of phenotypic characteristics of human, animal, plant and microorganism organisms, based on information encoded in genomes, and (b) functional modules of gene networks—signal transduction pathways, networks of intermolecular interactions, metabolic pathways, transcriptional and microRNA regulatory modules, etc.).

The central questions of the section include:

• De novo reconstruction of gene networks (and their basic modules) functioning at the level of cells, tissues, organs and organisms, based on analysis of large omics data (genomic, transcriptomic, proteomic, metabolomic, etc.), including using machine learning and artificial intelligence methods;
• Computer modeling of the temporal and spatial dynamics of functioning of gene networks and their functional modules using: (a) systems of ordinary differential equations (ODEs), (b) partial differential equations (for spatially distributed systems), (c) stochastic models, (d) Petri nets (to describe gene network dynamics in a discrete approximation), etc.
• Parametric analysis of computational/mathematical models of gene networks, including: (a) solving inverse modeling problems—identification of parameters (constants) in computational/mathematical models of gene network dynamics; and (b) assessment of parametric robustness of models of gene network functioning (sensitivity of models to variations of their parameters);
• creation of knowledge bases on computational models of gene networks (and their functional modules) and dynamics characteristics;
• works combining computational methods of reconstruction, analysis and modeling with experimental approaches to solve problems of systems biology of humans, animals, plants and microorganisms.
• applied aspects of systems computational biology (in biotechnology, biomedicine, pharmacology, agrobiotechnology and other fields).