Mohamed N. Nounou

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This paper considers the problem of learning the structure of gene regulatory networks from gene expression time series data. A more realistic scenario when the state space model representing a gene network evolves nonlinearly is considered while a linear model is assumed for the microarray data. To capture the nonlinearity, a particle filter-based state(More)
Network component analysis (NCA) is an efficient method of reconstructing the transcription factor activity (TFA), which makes use of the gene expression data and prior information available about transcription factor (TF) - gene regulations. We propose ROBust Network Component Analysis (ROBNCA), a novel iterative algorithm that explicitly models the(More)
The problems of node localization and clock synchronization in wireless sensor networks are naturally tied from a statistical signal processing perspective. In this work, we consider the joint estimation of an unknown node's location and clock parameters by incorporating the effect of imperfections in node oscillators, which render a time varying nature to(More)
The large influx of data from high-throughput genomic and proteomic technologies has encouraged the researchers to seek approaches for understanding the structure of gene regulatory networks and proteomic networks. This work reviews some of the most important statistical methods used for modeling of gene regulatory networks (GRNs) and protein-protein(More)
A central challenge in computational modeling of biological systems is the determination of the model parameters. In such cases, estimating these variables or parameters from other easily obtained measurements can be extremely useful. For example, time-series dynamic genomic data can be used to develop models representing dynamic genetic regulatory(More)
Recent years have witnessed extensive research activity in modeling biological phenomena as well as in developing intervention strategies for such phenomena. S-systems, which offer a good compromise between accuracy and mathematical flexibility, are a promising framework for modeling the dynamical behavior of biological phenomena. In this paper, two(More)
This paper proposes a novel algorithm for inferring gene regulatory networks which makes use of cubature Kalman filter (CKF) and Kalman filter (KF) techniques in conjunction with compressed sensing methods. The gene network is described using a state-space model. A nonlinear model for the evolution of gene expression is considered, while the gene expression(More)