Structural Identification of Piecewise-Linear Models of Genetic Regulatory Networks
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We propose an extension of secant methods for nonlinear equations using a population of previous iterates. Contrarily to classical secant methods, where exact interpolation is used, we prefer a least squares approach to calibrate the linear model. We propo ...
This paper considers piecewise affine models of genetic regulatory networks and focuses on the problem of detecting switches among different modes of operation in gene expression data. This task constitutes the first step of a procedure for the complete id ...
Background: Identifying large gene regulatory networks is an important task, while the acquisition of data through perturbation experiments (e.g., gene switches, RNAi, heterozygotes) is expensive. It is thus desirable to use an identification ...
We propose an extension of secant methods for nonlinear equations using a population of previous iterates. Contrarily to classical secant methods, where exact interpolation is used, we prefer a least squares approach to calibrate the linear model. We propo ...
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 ge ...
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 technical report, we present an approach for the identification of PieceWise-Affine (PWA) m ...
Motivation: MicroRNAs (miRNAs) are small endogenous RNAs that can play important regulatory roles via the RNA-interference pathway by targeting mRNAs for cleavage or translational repression. We propose a computational method to predict mi ...
Background: Proteins are the primary regulatory agents of transcription even though mRNA expression data alone, from systems like DNA microarrays, are widely used. In addition, the regulation process in genetic systems is inherently non-linear in nature, a ...
This tutorial paper considers the problem of reconstructing Genetic Regulatory Networks (GRNs) from gene expression measurements. Among various modeling frameworks that have been proposed for these biological systems, we focus on PieceWise Affine (PWA) mod ...
Motivation: MicroRNAs are small endogenous RNAs that can play important regulatory roles via the RNA-interference pathway by targeting mRNAs for cleavage or translational repression. We propose a computational method to predict miRNA regulatory modules or ...
