Related papers: Signal Propagation in Nonlinear Stochastic Gene Re…

The structure of a genetic network is uncovered by studying its response to external stimuli (input signals). We present a theory of propagation of an input signal through a linear stochastic genetic network. It is found that there are…

We investigate the stochastic resonance phenomenon in a physical system based on a tunnel diode. The experimental control parameters are set to allow the control of the frequency and amplitude of the deterministic modulating signal over an…

Regulatory networks describe the interactions between molecular or cellular regulators, like transcription factors and genes in gene regulatory networks, kinases and their receptors in signalling networks, or neurons in neural networks. A…

Biological structure and function depend on complex regulatory interactions between many genes. A wealth of gene expression data is available from high-throughput genome-wide measurement technologies, but effective gene regulatory network…

Gene regulatory networks must relay information from extracellular signals to downstream genes in an efficient, timely and coherent manner. Many complex functional tasks such as the immune response require system-wide broadcasting of…

Modelling gene regulatory networks not only requires a thorough understanding of the biological system depicted but also the ability to accurately represent this system from a mathematical perspective. Throughout this chapter, we aim to…

Genetic regulatory networks enable cells to respond to the changes in internal and external conditions by dynamically coordinating their gene expression profiles. Our ability to make quantitative measurements in these biochemical circuits…

In this review, we give an introduction to the structural and functional properties of the biological networks. We focus on three major themes: topology of complex biological networks like the metabolic and protein-protein interaction…

Single-cell studies often show significant phenotypic variability due to the stochastic nature of intra-cellular biochemical reactions. When the numbers of molecules, e.g., transcription factors and regulatory enzymes, are in low abundance,…

Stochastic reaction network models are widely utilized in biology and chemistry to describe the probabilistic dynamics of biochemical systems in general, and gene interaction networks in particular. Most often, statistical analysis and…

Genetic regulatory networks with adaptive responses are widely studied in biology. Usually, models consisting only of a few nodes have been considered. They present one input receptor for activation and one output node where the adaptive…

It is by now established that, remarkably, the addition of noise to a nonlinear system may sometimes facilitate, rather than hamper the detection of weak signals. This phenomenon, usually referred to as stochastic resonance, was originally…

We typically think of cells as responding to external signals independently by regulating their gene expression levels, yet they often locally exchange information and coordinate. Can such spatial coupling be of benefit for conveying…

Regulatory gene networks contain generic modules like those involving feedback loops, which are essential for the regulation of many biological functions. We consider a class of self-regulated genes which are the building blocks of many…

Stochastic resonance holds much promise for the detection of weak signals in the presence of relatively loud noise. Following the discovery of nondynamical and of aperiodic stochastic resonance, it was recently shown that the phenomenon can…

Biological systems and processes are networks of complex nonlinear regulatory interactions between nucleic acids, proteins, and metabolites. A natural way in which to represent these interaction networks is through the use of a graph. In…

Many biological, technological, and social systems can be effectively described as networks of interacting subsystems. Typically, these networks are not isolated objects, but interact with their environment through both signals and…

Recent progress in experimental techniques has enabled us to quantitatively study stochastic and flexible behavior of biological systems. For example, gene regulatory networks perform stochastic information processing and their…

Signal transduction is an important and basic mechanism to cell life activities. The stochastic state transition of receptor induces the release of signaling molecular, which triggers the state transition of other receptors. It constructs a…

We present computer-assisted methods for analyzing stochastic models of gene regulatory networks. The main idea that underlies this equation-free analysis is the design and execution of appropriately-initialized short bursts of stochastic…