TitleMathematical modeling of biomolecular network dynamics.
Publication TypeJournal Article
Year of Publication2011
AuthorsRatushny, AV, Ramsey, SA, Aitchison, JD
JournalMethods Mol Biol
Date Published2011
KeywordsAlgorithms, Computational Biology, Computer Simulation, Gene Regulatory Networks, Models, Biological, Protein Interaction Maps, Proteins, Transcription Factors

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.

Alternate JournalMethods Mol Biol
PubMed ID21877294
PubMed Central IDPMC4482237
Grant ListP50-GM076547 / GM / NIGMS NIH HHS / United States
K25-HL098807 / HL / NHLBI NIH HHS / United States
P41 RR000862 / RR / NCRR NIH HHS / United States
U54 RR022220 / RR / NCRR NIH HHS / United States
P50 GM076547 / GM / NIGMS NIH HHS / United States
R01 GM075152 / GM / NIGMS NIH HHS / United States
R01-GM075152 / GM / NIGMS NIH HHS / United States
K25 HL098807 / HL / NHLBI NIH HHS / United States
U54-RR022220 / RR / NCRR NIH HHS / United States