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Rule-based modeling of transcriptional attenuation at the tryptophan operon. (English) Zbl 1275.92024
Priami, Corrado (ed.) et al., Transactions on Computational Systems Biology XII. Special issue on modeling methodologies. Berlin: Springer (ISBN 978-3-642-11711-4/pbk). Lecture Notes in Computer Science 5945. Lecture Notes in Bioinformatics. Journal Subline, 199-228 (2010).
Summary: Transcriptional attenuation at E.coli’s tryptophan operon is a prime example of RNA-mediated gene regulation. In this paper, we present a discrete stochastic model of the fine-grained control of attenuation, based on chemical reactions. Stochastic simulation of our model confirms results that were previously obtained by master or differential equations. Our approach is easier to understand than master equations, although mathematically well founded. It is compact due to rule schemas that define finite sets of chemical reactions. Object-centered languages based on the \(\pi \)-calculus would yield less intelligible models. Such languages are confined to binary interactions, whereas our model heavily relies on reaction rules with more than two reactants, in order to concisely capture the control of attenuation.
For the entire collection see [Zbl 1204.92037].

92C42 Systems biology, networks
68Q85 Models and methods for concurrent and distributed computing (process algebras, bisimulation, transition nets, etc.)
92C40 Biochemistry, molecular biology
Full Text: DOI
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