Name
Title | ||
|---|---|---|
A general computational method for robustness analysis with applications to synthetic gene networks. |
Abstract | ||
|---|---|---|
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.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.Version 2.8 of BIOCHAM and the transcriptional cascade model are available at http://contraintes.inria.fr/BIOCHAM/. |
Year | DOI | Venue |
|---|---|---|
2009 | 10.1093/bioinformatics/btp200 | Bioinformatics |
Keywords | Field | DocType |
biological function expressible,biological relevance,general computational method,synthetic gene network,broad model class,computational approach,biological robustness,synthetic transcriptional cascade,biological timer,robustness analysis,biological system,linear temporal logic,synthetic biology application,computational biology,synthetic biology,gene network,gene expression profiling,systems biology,gene regulatory networks,algorithms,gene networks | Computer science,Systems biology,Linear temporal logic,Theoretical computer science,Robustness (computer science),Software,Timer,Bioinformatics,Temporal logic,Gene regulatory network,Synthetic biology | Journal |
Volume | Issue | ISSN |
25 | 12 | 1367-4811 |
Citations | PageRank | References |
32 | 1.33 | 14 |
Authors | ||
4 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Aurélien Rizk | 1 | 149 | 8.72 |
| Gregory Batt | 2 | 92 | 4.78 |
| François Fages | 3 | 1383 | 126.46 |
| Sylvain Soliman | 4 | 484 | 35.02 |