Rule-based modeling of transcriptional attenuation at the tryptophan operon

Kuttler, Celine; Lhoussaine, Cedric; Nebut, Mirabelle

Document type :

Article dans une revue scientifique

Title :

Rule-based modeling of transcriptional attenuation at the tryptophan operon

Author(s) :

Kuttler, Celine [Auteur correspondant]

Programming Languages for Biological Modeling and Simulation [BioComputing]
Laboratoire d'Informatique Fondamentale de Lille [LIFL]
Institut de Recherche Interdisciplinaire [Villeneuve d'Ascq] [IRI]
Nebut, Mirabelle [Auteur]
Programming Languages for Biological Modeling and Simulation [BioComputing]
Laboratoire d'Informatique Fondamentale de Lille [LIFL]
Institut de Recherche Interdisciplinaire [Villeneuve d'Ascq] [IRI]

Journal title :

Transactions on Computational Systems Biology

Pages :

199-228

Publisher :

Springer

Publication date :

2010-01-09

HAL domain(s) :

Informatique [cs]/Modélisation et simulation

English abstract : [en]

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 ...
Show more >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.Show less >

Language :

Anglais

Peer reviewed article :

Oui

Audience :

Internationale

Popular science :

Non

ANR Project :

A Uniform Approach for Stochastic Modeling with Spatial Aspects in Systems Biology

Comment :

LNBI 5945