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EURASIP J Bioinform Syst Biol. 2011;2011:572876. doi: 10.1155/2011/572876. Epub 2010 Dec 29.

Inference of kinetic parameters of delayed stochastic models of gene expression using a markov chain approximation.

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1
Computational Systems Biology Research Group, Department of Signal Processing, Tampere University of Technology, P.O. Box 553, 33101 Tampere, Finland.

Abstract

We propose a Markov chain approximation of the delayed stochastic simulation algorithm to infer properties of the mechanisms in prokaryote transcription from the dynamics of RNA levels. We model transcription using the delayed stochastic modelling strategy and realistic parameter values for rate of transcription initiation and RNA degradation. From the model, we generate time series of RNA levels at the single molecule level, from which we use the method to infer the duration of the promoter open complex formation. This is found to be possible even when adding external Gaussian noise to the RNA levels.

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