Quantitative Biology - Quantitative Methods LCC:Science LCC:Q Methodology Article LCC:Biology (General) DOAJ:Biology LCC:QH301-705.5 DOAJ:Biology and Life Sciences 2009-10-19 BioMed Central BMC Bioinformatics <p>Abstract</p> <p>Background</p> <p>Fluorescent and luminescent gene reporters allow us to dynamically quantify changes in molecular species concentration over time on the single cell level. The mathematical modeling of their interaction through multivariate dynamical models requires the deveopment of effective statistical methods to calibrate such models against available data. Given the prevalence of stochasticity and noise in biochemical systems inference for stochastic models is of special interest. In this paper we present a simple and computationally efficient algorithm for the estimation of biochemical kinetic parameters from gene reporter data.</p> <p>Results</p> <p>We use the linear noise approximation to model biochemical reactions through a stochastic dynamic model which essentially approximates a diffusion model by an ordinary differential equation model with an appropriately defined noise process. An explicit formula for the likelihood function can be derived allowing for computationally efficient parameter estimation. The proposed algorithm is embedded in a Bayesian framework and inference is performed using Markov chain Monte Carlo.</p> <p>Conclusion</p> <p>The major advantage of the method is that in contrast to the more established diffusion approximation based methods the computationally costly methods of data augmentation are not necessary. Our approach also allows for unobserved variables and measurement error. The application of the method to both simulated and experimental data shows that the proposed methodology provides a useful alternative to diffusion approximation based methods.</p> BMC Bioinformatics, Vol 10, Iss 1, p 343 (2009) oai:doaj.org/article:4de1e859536641a6869d7a725d99868c oai:europepmc.org:1889871 oai:arXiv.org:0907.0759 10.1186/1471-2105-10-343 oai:doaj.org/article:4de1e859536641a6869d7a725d99868c oai:europepmc.org:1889871 oai:arXiv.org:0907.0759 PMC2774326 19840370 true false 0.9 dedup-similarity-result doajarticles::ca4753db9feca61b453dbb362c35b342 2 Komorowski Michał doajarticles::a07265fa744e66e9c5ec7b77c0851f89 4 Rand David A doajarticles::e1cad832939799d3048e316c22782174 1 Finkenstädt Bärbel doajarticles::381604e57032b94c4848b4f74f746d8e 3 Harper Claire V wt__________::faa5036a74ad4f433adcf94213f14cf2 067252 wt__________::WT::UNKNOWN wt__________::WT::Physiological Sciences 2009-10-19 BioMed Central 2009-10-01 BioMed Central 2009-07-04 http://www.biomedcentral.com/1471-2105/10/343 http://arxiv.org/abs/0907.0759 http://europepmc.org/articles/PMC2774326 Arnold, L. 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