Kinetic Modelling in Systems Biology

About this book

Providing a comprehensive overview of traditional and modern techniques in computational systems biology, Kinetic Modelling in Systems Biology offers a systematic presentation of the principles and algorithms guiding this process. Combining mathematical theory with practical applications, the book demonstrates how to integrate techniques that enable the collection, modeling, simulation, analysis, and hypothesis of temporal data. With an accompanying CD-ROM of tables, illustrations, and other supporting materials, this text presents a complete understanding of the fundamental principles and basic techniques for mathematical modeling, data analysis, and visualization.

Contents

Introduction; Systems Biology, Biological Knowledge, and Kinetic Modelling Dependence of enzyme reaction rate on the substrate concentration What are the model limitations? Or, in other words, what can be modeled? Cellular Networks Reconstruction and Static Modelling Pathway reconstruction The high-quality network reconstruction: description of the process Visual notations: three categories; Edinburgh Pathway Editor (EPE) Introduction Feature summary of EPE A flexible visual representation Conclusion; Construction and Verification of Kinetic Models Introduction Basic principles of kinetic model construction Basic principles of kinetic model verification Study of dynamic and regulatory properties of the kinetic model; Introduction to DBSolve Creation and analysis of the models using DBSolve: functional description; Enzyme Kinetics Modelling Introduction Basic principles of modeling individual enzymes and transporters "Hyperbolic" enzymes Allosteric enzymes Transporters; Kinetic Models of Biochemical Pathways Modelling of the mitochondrial Krebs cycle Modelling of the Escherichia coli branched-chain amino acid biosynthesis; Modelling of Mitochondrial Energy Metabolism Oxidative phosphorylation and superoxide production in mitochondria Development of kinetic models Description of individual processes of the model Model predictions; Application of the Kinetic Modelling Approach to Problems in Biotechnology and Biomedicine Study of the mechanisms of salicylate-hepatotoxic effect Multiple target identification analysis for antituberculosis drug discovery Application of the kinetic model of E. coli branched-chain amino acid biosynthesis to optimize production of isoleucine and valine; Conclusion and Discussion; References; Index

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Biography

Moscow State University, Moscow, Russia University of Edinburgh, Scotland, UK