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URN: urn:nbn:de:0030-drops-19938
URL: http://drops.dagstuhl.de/opus/volltexte/2009/1993/
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Kuttler, CÚline ; Lhoussaine, CÚdric ; Nebut, Mirabelle

Rule-based Modeling of Transcriptional Attenuation at the Tryptophan Operon

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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.

BibTeX - Entry

@InProceedings{kuttler_et_al:DSP:2009:1993,
  author =	{C{\'e}line Kuttler and C{\'e}dric Lhoussaine and Mirabelle Nebut},
  title =	{Rule-based Modeling of Transcriptional Attenuation at the Tryptophan Operon},
  booktitle =	{Formal Methods in Molecular Biology},
  year =	{2009},
  editor =	{Rainer Breitling and David Roger Gilbert and Monika Heiner and Corrado Priami},
  number =	{09091},
  series =	{Dagstuhl Seminar Proceedings},
  ISSN =	{1862-4405},
  publisher =	{Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik, Germany},
  address =	{Dagstuhl, Germany},
  URL =		{http://drops.dagstuhl.de/opus/volltexte/2009/1993},
  annote =	{Keywords: Systems biology, rule-based modeling languages, stochastic  simulation, kappa.}
}

Keywords: Systems biology, rule-based modeling languages, stochastic simulation, kappa.
Seminar: 09091 - Formal Methods in Molecular Biology
Issue Date: 2009
Date of publication: 05.05.2009


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