Title | Mathematical modeling of biomolecular network dynamics. |
Publication Type | Journal Article |
Year of Publication | 2011 |
Authors | Ratushny, AV, Ramsey, SA, Aitchison, JD |
Journal | Methods Mol Biol |
Volume | 781 |
Pagination | 415-33 |
Date Published | 2011 |
ISSN | 1940-6029 |
Keywords | Algorithms, Computational Biology, Computer Simulation, Gene Regulatory Networks, Models, Biological, Protein Interaction Maps, Proteins, Transcription Factors |
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. |
DOI | 10.1007/978-1-61779-276-2_21 |
Alternate Journal | Methods Mol Biol |
PubMed ID | 21877294 |
PubMed Central ID | PMC4482237 |
Grant List | P50-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 |