Network Biology

Volume 781 of the series Methods in Molecular Biology pp 415-433


Mathematical Modeling of Biomolecular Network Dynamics

  • Alexander V. RatushnyAffiliated withInstitute for Systems Biology
  • , Stephen A. RamseyAffiliated withInstitute for Systems Biology
  • , John D. AitchisonAffiliated withInstitute for Systems Biology Email author 

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Mathematical and computational models have become indispensable tools for integrating and interpreting heterogeneous biological data, understanding fundamental principles of biological system functions, genera­ting reliable testable hypotheses, and identifying potential diagnostic markers and therapeutic targets. Thus, such tools are now routinely used in the theoretical and experimental systematic investigation of biological system dynamics. Here, we discuss model building as an essential part of the theoretical and experimental analysis of biomolecular network dynamics. Specifically, we describe a procedure for defining kinetic equations and parameters of biomolecular processes, and we illustrate the use of fractional activity functions for modeling gene expression regulation by single and multiple regulators. We further discuss the evaluation of model complexity and the selection of an optimal model based on information criteria. Finally, we discuss the critical roles of sensitivity, robustness analysis, and optimal experiment design in the model building cycle.

Key words

Biomolecular network Differential equation Dynamical system Inverse problem Mathematical model Systems biology