TY  - JOUR
T1  - A general computational method for robustness analysis with applications to synthetic gene networks
AU  - Rizk, Aurélien
AU  - Batt, Gregory
AU  - Fages, François
AU  - Soliman, Sylvain
Y1  - 2009/06/15
N1  - 10.1093/bioinformatics/btp200
JO  - Bioinformatics
SP  - i169
EP  - i178
VL  - 25
IS  - 12
N2  - Motivation: Robustness is the capacity of a system to maintain a function in the face of perturbations. It is essential for the correct functioning of natural and engineered biological systems. Robustness is generally defined in an ad hoc, problem-dependent manner, thus hampering the fruitful development of a theory of biological robustness, recently advocated by Kitano.Results: In this article, we propose a general definition of robustness that applies to any biological function expressible in temporal logic LTL (linear temporal logic), and to broad model classes and perturbation types. Moreover, we propose a computational approach and an implementation in BIOCHAM 2.8 for the automated estimation of the robustness of a given behavior with respect to a given set of perturbations. The applicability and biological relevance of our approach is demonstrated by testing and improving the robustness of the timed behavior of a synthetic transcriptional cascade that could be used as a biological timer for synthetic biology applications.Availability: Version 2.8 of BIOCHAM and the transcriptional cascade model are available at http://contraintes.inria.fr/BIOCHAM/Contact:gregory.batt@inria.fr
SN  - 1367-4803
M3  - doi: 10.1093/bioinformatics/btp200
UR  - http://dx.doi.org/10.1093/bioinformatics/btp200
ER  -