Work

Mathematical Modeling of Biomolecular Network Dynamics

Year: 2011

Type: book-chapter

Abstract: Mathematical and computational models have become indispensable tools for integrating and interpreting heterogeneous biological data, understanding fundamental principles of biological system functions, genera-ting 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.

Source: Methods in molecular biology

DOI: 10.1007/978-1-61779-276-2_21

Authors: Alexander V. Ratushny, Stephen A. Ramsey, John D. Aitchison

Institution: Institute for Systems Biology

Language: English

Topic: Gene Regulatory Network Analysis

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: green

Funders: National Heart, Lung, and Blood Institute, National Institute of General Medical Sciences, National Center for Research Resources

Awards: Natl Resource for Mass Spectrom of Biolog Macromolecules, Systems analysis of transcriptional interactions underlying foam cell formation, New Tools for Exploring the Dynamic Interactome (Renewal), Oleate-responsive gene regulatory networks governing peroxisome proliferation, Quantitative Systems Biology