State estimation for gene networks with intrinsic and extrinsic noise: a case study on E.coli arabinose uptake dynamics

Alfonso Carta 1, * Eugenio Cinquemani 2
* Auteur correspondant
1 BIOCORE - Biological control of artificial ecosystems
LOV - Laboratoire d'océanographie de Villefranche, CRISAM - Inria Sophia Antipolis - Méditerranée , INRA - Institut National de la Recherche Agronomique
2 IBIS - Modeling, simulation, measurement, and control of bacterial regulatory networks
LAPM - Laboratoire Adaptation et pathogénie des micro-organismes [Grenoble], Inria Grenoble - Rhône-Alpes, Institut Jean Roget
Abstract : We address state estimation for gene regulatory networks at the level of single cells. We consider models that include both intrinsic noise, in terms of stochastic dynamics, and extrinsic noise, in terms of random parameter values. We take the Chemical Master Equation (CME) with random parameters as a reference modeling approach, and investigate the use of stochastic differential model approximations for the construction of practical real-time filters. To this aim we consider a Square-Root Unscented Kalman Filter (SRUKF) built on a Chemical Langevin Equation (CLE) approximation of the CME. Using arabinose uptake regulation in Escherichia coli bacteria as a case study, we show that performance is comparable to that of a (computationally heavier) particle filter built directly on the CME, and that the use of information about parameter uncertainty allows one to improve state estimation performance.
Type de document :
Communication dans un congrès
ECC13 - European Control Conference - 2013, Jul 2013, Zurich, Switzerland. 2013, 〈http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=6669467&isnumber=6669080〉
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Soumis le : lundi 29 avril 2013 - 15:25:52
Dernière modification le : mardi 29 mai 2018 - 12:50:54

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Alfonso Carta, Eugenio Cinquemani. State estimation for gene networks with intrinsic and extrinsic noise: a case study on E.coli arabinose uptake dynamics. ECC13 - European Control Conference - 2013, Jul 2013, Zurich, Switzerland. 2013, 〈http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=6669467&isnumber=6669080〉. 〈hal-00818902〉

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