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A practical introduction to stochastic modelling of reaction-diffusion processes is presented. No prior knowledge of stochastic simulations is assumed. The methods are explained using illustrative… Expand
Bacterial chemotaxis is widely studied from both the microscopic (cell) and macroscopic (population) points of view, and here we connect these very different levels of description by deriving the… Expand
Several stochastic simulation algorithms (SSAs) have recently been proposed for modelling reaction-diffusion processes in cellular and molecular biology. In this paper, two commonly used SSAs are… Expand
Among the most striking aspects of the movement of many animal groups are their sudden coherent changes in direction. Recent observations of locusts and starlings have shown that this directional… Expand
The collective behavior of bacterial populations provides an example of how cell-level decision making translates into population-level behavior and illustrates clearly the difficult multiscale mat...
Many cellular and subcellular biological processes can be described in terms of diffusing and chemically reacting species (e.g. enzymes). Such reaction-diffusion processes can be mathematically… Expand
Nonlinear independent component analysis is combined with diffusion-map data analysis techniques to detect good observables in high-dimensional dynamic data. These detections are achieved by… Expand
Spatial organization and noise play an important role in molecular systems biology. In recent years, a number of software packages have been developed for stochastic spatio-temporal simulation,… Expand
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… Expand
Polyadenylation of pre-mRNAs, a critical step in eukaryotic gene expression, is mediated by cis elements collectively called the polyadenylation signal. Genome-wide analysis of such polyadenylation… Expand