Stochastic S-system modeling of gene regulatory network

Modeling gene regulatory networks: Classical models, optimal perturbation for identification of network

Deep understanding of molecular biology has allowed emergence of new technologies like DNA decryption.  On the other hand, advancements of molecular biology have made manipulation of genetic systems simpler than ever; this promises extraordinary progress in biological, medical and biotechnological applications.  This is not an unrealistic goal since genes which are regulated by gene regulatory ...

Estimation of Gene Regulatory Network Using Stochastic Differential Equation Model

Stochastic neural network models for gene regulatory networks

Recent advances in gene-expression profiling technologies provide large amounts of gene expression data. This raises the possibility for a functional understanding of genome dynamics by means of mathematical modelling. As gene expression involves intrinsic noise, stochastic models are essential for better descriptions of gene regulatory networks. However, stochastic modelling for large scale ge...

Modeling and Simulation of Gene Regulatory Network: A Comprehensive Survey

The Gene Regulatory Network (GRN) specifies the series of regulatory interactions between different genes. A target gene is interacted by a signal which is originated from the expression of its regulator gene. A gene is known to be expressed when it synthesizes a protein and the degree of synthesizing the protein determines the level of its expression. The same gene can behave as a 'target' in ...

Constraint-based modeling of the Drosophila Gap-gene regulatory network

We present a constraint-based assistant for the modeling of the dynamics of biological networks. The global aim is to automate some modeling tasks by providing high-level functionalities to biologists. Network dynamics is represented by the discrete abstraction of R. Thomas (Thomas and Kaufman (2001)), which is briefly introduced. We explain how this formalism is cast into Constraint Logic Prog...