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Rule-based Modeling of Transcriptional Attenuation at the Tryptophan Operon
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Dagstuhl Seminar Proceedings, Volume 9091
Series: Dagstuhl Seminar Proceedings (DagSemProc) - License:
Creative Commons Attribution 4.0 International license
- Publication Date: 2009-05-05
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Céline Kuttler, Cédric Lhoussaine, and Mirabelle Nebut. Rule-based Modeling of Transcriptional Attenuation at the Tryptophan Operon. In Formal Methods in Molecular Biology. Dagstuhl Seminar Proceedings, Volume 9091, pp. 1-22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2009)
https://doi.org/10.4230/DagSemProc.09091.6
https://doi.org/10.4230/DagSemProc.09091.6
Abstract
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 for this phenomenon based on
chemical reactions. Our model is compact and intelligible,
due to n-ary reactions (which preclude object-centric
approaches) and to rule schemas that define finite
sets of chemical reactions. Stochastic simulations
with our model confirm results that were previously
obtained by master equations or differential equations.
In addition, our approach permits to reflect
mutation experiments by simple model modifications,
and to re-use model components for transcriptional attenuation
in other genes and organisms.
Keywords
- Systems biology
- rule-based modeling languages
- stochastic simulation
- kappa.
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