Abstract. Given the substantial computational requirements of stochastic simulation, approximation is essential for efficient analysis of any realistic biochemical system. This pap...
—We are developing a framework for computation with biochemical reactions with a focus on synthesizing specific logical functionality, a task analogous to technology-independent...
The simulation of chemical reacting systems is one of the most challenging topics in Systems Biology, due to their complexity and inherent randomness. The Gillespie's Stochas...
Background: Intrinsic fluctuations due to the stochastic nature of biochemical reactions can have large effects on the response of biochemical networks. This is particularly true ...
David Adalsteinsson, David McMillen, Timothy C. El...
Abstract. We propose a computational method for reconstructing metabolic networks. The method utilizes optimization techniques and graph traversal algorithms to discover a set of b...