Results 1 - 10 of 69

A.: Reconstruction of switching thresholds in piecewise-affine models of genetic regulatory networks

by S. Drulhe, G. Ferrari-trecate, H. Dejong, A. Viari , 2005
"... Abstract. Recent advances of experimental techniques in biology have led to the production of enormous amounts of data on the dynamics of genetic regulatory networks. In this paper, we present an approach for the identification of PieceWise-Affine (PWA) models of genetic regulatory networks from exp ..."
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Abstract. Recent advances of experimental techniques in biology have led to the production of enormous amounts of data on the dynamics of genetic regulatory networks. In this paper, we present an approach for the identification of PieceWise-Affine (PWA) models of genetic regulatory networks from

Identification of piecewise affine models of genetic regulatory networks: the data classification problem

by Riccardo Porreca, Giancarlo Ferrari-trecate
"... Abstract: In this paper we consider the identification of PieceWise Affine (PWA) models of Genetic Regulatory Networks (GRNs) and focus on data classification that is a task of the whole identification process. By assuming that gene expression profiles have been split into segments generated by a si ..."
Abstract - Cited by 2 (2 self) - Add to MetaCart
Abstract: In this paper we consider the identification of PieceWise Affine (PWA) models of Genetic Regulatory Networks (GRNs) and focus on data classification that is a task of the whole identification process. By assuming that gene expression profiles have been split into segments generated by a

1The Switching Threshold Reconstruction Problem for Piecewise Affine Models of Genetic Regulatory Networks

by Samuel Drulhe, Giancarlo Ferrari-trecate, Hidde De Jong
"... Abstract — Recent advances of experimental techniques in bi-ology have led to the production of enormous amounts of data on the dynamics of genetic regulatory networks. We present an approach for the identification of PieceWise-Affine (PWA) models of genetic regulatory networks from experimental dat ..."
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thresholds in a PWA model of the carbon starvation response in the bacterium Escherichia coli. Index Terms — hybrid systems, system identification, systems biology, genetic regulatory networks, piecewise-affine models, switching thresholds. I.

The identification of dynamic gene-protein networks

by Ronald L. Westra, Goele Hollanders, Geert Jan Bex, Marc Gyssens, Karl Tuyls - LNBI , 2007
"... In this study we will focus on piecewise linear state space models for gene-protein interaction networks. We will follow the dynamical systems approach with special interest for partitioned state spaces. From the observation that the dynamics in natural systems tends to punctuated equilibria, we w ..."
Abstract - Cited by 4 (2 self) - Add to MetaCart
will focus on piecewise linear models and sparse and hierarchic interactions, as, for instance, described by Glass, Kauffman, and de Jong. Next, the paper is concerned with the identification (also known as reverse engineering and reconstruction) of dynamic genetic networks from microarray data. We

unknown title

by Riccardo Porreca, Samuel Drulhe, Hidde Jong, Giancarlo Ferrari-trecate
"... Identification of parameters and structure of piecewise affine models of genetic networks ..."
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Identification of parameters and structure of piecewise affine models of genetic networks

O.: Switch detection in genetic regulatory networks

by Riccardo Porreca, Giancarlo Ferrari-trecate, Lalo Magni, Olivier Bernard , 2006
"... Abstract. This paper considers piecewise affine models of genetic regu-latory networks and focuses on the problem of detecting switches among different modes of operation in gene expression data. This task consti-tutes the first step of a procedure for the complete identification of the network. We ..."
Abstract - Cited by 10 (7 self) - Add to MetaCart
Abstract. This paper considers piecewise affine models of genetic regu-latory networks and focuses on the problem of detecting switches among different modes of operation in gene expression data. This task consti-tutes the first step of a procedure for the complete identification of the network. We

Systems biology Stochastic dynamics of genetic networks: modelling and

by Parameter Identification, Eugenio Cinquemani, Andreas Milias-argeitis, Sean Summers, John Lygeros
"... Motivation: Identification of regulatory networks is typically based on deterministic models of gene expression. Increasing experimental evidence suggests that the gene regulation process is intrinsically random. To ensure accurate and thorough processing of the experimental data, stochasticity must ..."
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Motivation: Identification of regulatory networks is typically based on deterministic models of gene expression. Increasing experimental evidence suggests that the gene regulation process is intrinsically random. To ensure accurate and thorough processing of the experimental data, stochasticity

R.: Model checking liveness properties of genetic regulatory networks

by Calin Belta, Ron Weiss
"... Abstract. Recent studies have demonstrated the possibility to build ge-netic regulatory networks that confer a desired behavior to a living organ-ism. However, the design of these networks is difficult, notably because of uncertainties on parameter values. In previous work, we proposed an approach t ..."
Abstract - Cited by 17 (4 self) - Add to MetaCart
to analyze genetic regulatory networks with parameter uncer-tainties. In this approach, the models are based on piecewise-multiaffine (PMA) differential equations, the specifications are expressed in tem-poral logic, and uncertain parameters are given by intervals. Abstrac-tions are used to obtain finite

COMBINED APPROACH OF RBF NEURAL NETWORKS, GENETIC ALGORITHMS AND LOCAL SEARCH AND ITS APPLICATION TO THE IDENTIFICATION OF A NON-LINEAR PROCESS

by André Eugênio Lazzaretti, Fábio Alessandro Guerra, Rodrigo Jardim Riella, Hugo Vieira Neto, Leandro Dos Santos Coelho
"... Abstract. The identification of non-linear systems by artificial neural networks has been successfully applied in many applications. In this context, the radial basis function neural network (RBF-NN) is a powerful approach for non-linear system identification. An RBF neural network has an input laye ..."
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based on a genetic algorithm (GA) and local search is presented. During the identification procedure, the GA guided by local search aims to optimize the parameters of the RBF-NN and the optimal values are regarded as the initial values of the RBF-NN parameters. The validity and accuracy of system

A Simulation Testbed for the Study of Multicellular Development: The Multiple Mechanisms of Morphogenesis

by Kurt Fleischer, Alan H. Barr , 1993
"... This paper presents a simulation framework and computational testbed for studying multicellular pattern formation. The approach combines several developmental mechanisms (chemical, mechanical, genetic and electrical) known to be important for biological pattern formation. The mechanisms are present ..."
Abstract - Cited by 77 (4 self) - Add to MetaCart
genome whose expression is dependent only upon its internal state and its local environment. The changes of each cell's state and of the environment are determined by piecewise continuous differential equations. The current two-dimensional simulation exhibits a variety of multicellular behaviors
Results 1 - 10 of 69