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A cis-regulatory module often processes multiple regulatory inputs provided by transcription factors that bind to DNA and regulate the expression of the gene in a combinatorial logic manner. Here the authors analyse dynamic cross correlations between the regulator concentrations and the output of the gene using stochastic modelling, and show their characteristics for different logic operations. The...
Codon usage has been reported to be correlated with local recombination rate, which can be explained by two proposed models. In the present study, correspondence analysis was used to investigate the major trends in codon usage variation among S. cerevisiae genes. It was found that the first principle source of codon usage variation in yeast is due to the variance of expressional levels, which is consistent...
We aim at developing a new methodology to model and design periodic oscillators of gene regulatory networks with multiple genes, proteins and time delays, by using multiple time-scale networks (MTN). Multiple time scale properties are exploited to simplify the model according to singular perturbation theory. We show that a MTN has no stable equilibria but stable periodic orbits. Finally, we design...
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