Literature DB >> 16984084

Robustness analysis of biochemical network models.

J Kim1, D G Bates, I Postlethwaite, L Ma, P A Iglesias.   

Abstract

Biological systems that have been experimentally verified to be robust to significant changes in their environments require mathematical models that are themselves robust. In this context, a necessary condition for model robustness is that the model dynamics should not be sensitive to small variations in the model's parameters. Robustness analysis problems of this type have been extensively studied in the field of robust control theory and have been found to be very difficult to solve in general. The authors describe how some tools from robust control theory and nonlinear optimisation can be used to analyse the robustness of a recently proposed model of the molecular network underlying adenosine 3',5'-cyclic monophosphate (cAMP) oscillations observed in fields of chemotactic Dictyostelium cells. The network model, which consists of a system of seven coupled nonlinear differential equations, accurately reproduces the spontaneous oscillations in cAMP observed during the early development of D. discoideum. The analysis by the authors reveals, however, that very small variations in the model parameters can effectively destroy the required oscillatory dynamics. A biological interpretation of the analysis results is that correct functioning of a particular positive feedback loop in the proposed model is crucial to maintaining the required oscillatory dynamics.

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Year:  2006        PMID: 16984084     DOI: 10.1049/ip-syb:20050024

Source DB:  PubMed          Journal:  Syst Biol (Stevenage)        ISSN: 1741-2471


  16 in total

1.  A systems engineering approach to validation of a pulmonary physiology simulator for clinical applications.

Authors:  A Das; Z Gao; P P Menon; J G Hardman; D G Bates
Journal:  J R Soc Interface       Date:  2010-06-10       Impact factor: 4.118

2.  Sensitivity Measures for Oscillating Systems: Application to Mammalian Circadian Gene Network.

Authors:  Stephanie R Taylor; Rudiyanto Gunawan; Linda R Petzold; Francis J Doyle
Journal:  IEEE Trans Automat Contr       Date:  2008-01-01       Impact factor: 5.792

3.  A method for determining the robustness of bio-molecular oscillator models.

Authors:  Reza Ghaemi; Jing Sun; Pablo A Iglesias; Domitilla Del Vecchio
Journal:  BMC Syst Biol       Date:  2009-09-21

4.  Geometry and topology of parameter space: investigating measures of robustness in regulatory networks.

Authors:  Madalena Chaves; Anirvan Sengupta; Eduardo D Sontag
Journal:  J Math Biol       Date:  2008-11-06       Impact factor: 2.259

5.  Efficient estimation of the robustness region of biological models with oscillatory behavior.

Authors:  Mochamad Apri; Jaap Molenaar; Maarten de Gee; George van Voorn
Journal:  PLoS One       Date:  2010-04-01       Impact factor: 3.240

6.  Bayesian design strategies for synthetic biology.

Authors:  Chris P Barnes; Daniel Silk; Michael P H Stumpf
Journal:  Interface Focus       Date:  2011-10-05       Impact factor: 3.906

7.  Translational recoding as a feedback controller: systems approaches reveal polyamine-specific effects on the antizyme ribosomal frameshift.

Authors:  Claudia Rato; Svetlana R Amirova; Declan G Bates; Ian Stansfield; Heather M Wallace
Journal:  Nucleic Acids Res       Date:  2011-02-07       Impact factor: 16.971

8.  A computational framework for qualitative simulation of nonlinear dynamical models of gene-regulatory networks.

Authors:  Liliana Ironi; Luigi Panzeri
Journal:  BMC Bioinformatics       Date:  2009-10-15       Impact factor: 3.169

9.  Validation of a model of the GAL regulatory system via robustness analysis of its bistability characteristics.

Authors:  Luca Salerno; Carlo Cosentino; Alessio Merola; Declan G Bates; Francesco Amato
Journal:  BMC Syst Biol       Date:  2013-05-17

10.  Threshold-dominated regulation hides genetic variation in gene expression networks.

Authors:  Arne B Gjuvsland; Erik Plahte; Stig W Omholt
Journal:  BMC Syst Biol       Date:  2007-12-06
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