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Robustification as a tool in modeling biochemical reaction networks
KTH, School of Electrical Engineering (EES), Automatic Control.
KTH, School of Electrical Engineering (EES), Automatic Control.
2011 (English)In: Journal of Process Control, ISSN 0959-1524, Vol. 21, no 10, 1517-1525 p.Article in journal (Refereed) Published
Abstract [en]

Biological functions have evolved to become robust against a multitude of perturbations such as gene mutations, intracellular noise and changes in the physical and chemical environment. This robustness should be reflected in models of the underlying biochemical networks, and robustness analysis has consequently been established as an important tool for model validation in systems biology. However, while robustness analysis can be used to invalidate a given model, it does not support the postulation of model modifications that can serve to improve the robustness. Herein we propose a method for this purpose, based on computing the sensitivity of the robustness with respect to generic dynamic perturbations applied to the individual network edges. To quantify robustness we compute the smallest simultaneous change in the activity of the network nodes that induces a bifurcation in the network, resulting in a qualitative change in the network behavior. The proposed method can be used to identify network interactions with the most significant impact on the overall robustness of a given function. By considering the impact of adding new nodes and edges, the method can also be used to postulate the presence of important unmodeled components and interactions. The focus here is on biological functions related to bistable switches and sustained oscillations, and the proposed methodology is demonstrated through application to metabolic oscillations in white blood cells and bistable switching in MAPK signal transduction. The classical Goodwin model of oscillations in a simple gene regulatory network is used for illustration throughout the paper.

Place, publisher, year, edition, pages
2011. Vol. 21, no 10, 1517-1525 p.
Keyword [en]
Systems biology, Gene regulatory networks, Modeling, Dynamic behavior, Biochemical networks, Robustness, Bifurcations
National Category
Electrical Engineering, Electronic Engineering, Information Engineering
URN: urn:nbn:se:kth:diva-53396DOI: 10.1016/j.jprocont.2011.05.009ISI: 000297394100016ScopusID: 2-s2.0-80054725308OAI: diva2:470283
QC 20111228Available from: 2011-12-28 Created: 2011-12-28 Last updated: 2011-12-28Bibliographically approved

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Jacobsen, Elling W.Nenchev, Vladislav
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