MOTIVATION The development of an annotated global database suitable for a wide range of investigations is a challenging and labor-intensive task. Thus, the development of databases tailored for specific applications remains necessary. For example, in the field of toxicology, no annotated gene array databases are now available that may assist in the… (More)
Recent studies indicate that during tumorigenic transformations, cells may generate mutations by themselves as a result of error-prone cell division with participation of error-prone polymerases and aberrant mitosis. These mechanisms may be activated in cells by continuing proliferative and survival signaling in a sustained stress environment (SSE). The… (More)
MOTIVATION Many current studies of complex microbial communities rely on the isolation of community genomic DNA, amplification of 16S ribosomal RNA genes (rDNA) and subsequent examination of community structure through interrogation of the amplified 16S rDNA pool by high-throughput sequencing, phylogenetic microarrays or quantitative PCR. RESULTS Here we… (More)
BACKGROUND In recent years, several stochastic simulation algorithms have been developed to generate Monte Carlo trajectories that describe the time evolution of the behavior of biomolecular reaction networks. However, the effects of various stochastic simulation and data analysis conditions on the observed dynamics of complex biomolecular reaction networks… (More)
We developed a software package called Biomolecular Network Simulator (BNS) to model and simulate complex biomolecular reaction networks. The software uses the Gillespie stochastic simulation algorithm for generating Monte Carlo trajectories that describe the evolution of a system of biochemical reactions. This software uses a combination of MATLAB and… (More)
reaction event that occurs in the system, the accuracy of the method comes at a high computational cost. This is At the functional level, all biological processes in especially true for systems with a large number of cells can be represented as a series of biochemical molecular species, where reactions occur numerous times reactions that are stochastic in… (More)
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