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This article is part of the supplement: The 2010 International Conference on Bioinformatics and Computational Biology (BIOCOMP 2010): Systems Biology

Open Access Highly Accessed Research article

Bayesian parameter estimation for nonlinear modelling of biological pathways

Omid Ghasemi1, Merry L Lindsey2, Tianyi Yang1, Nguyen Nguyen1, Yufei Huang1* and Yu-Fang Jin1*

Author Affiliations

1 Department of Electrical and Computer Engineering, University of Texas at San Antonio, San Antonio, TX, USA

2 Barshop Institute of Longevity and Aging Studies and the Division of Geriatrics, Gerontology and Palliative Medicine, Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA

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BMC Systems Biology 2011, 5(Suppl 3):S9  doi:10.1186/1752-0509-5-S3-S9

Published: 23 December 2011

Abstract

Background

The availability of temporal measurements on biological experiments has significantly promoted research areas in systems biology. To gain insight into the interaction and regulation of biological systems, mathematical frameworks such as ordinary differential equations have been widely applied to model biological pathways and interpret the temporal data. Hill equations are the preferred formats to represent the reaction rate in differential equation frameworks, due to their simple structures and their capabilities for easy fitting to saturated experimental measurements. However, Hill equations are highly nonlinearly parameterized functions, and parameters in these functions cannot be measured easily. Additionally, because of its high nonlinearity, adaptive parameter estimation algorithms developed for linear parameterized differential equations cannot be applied. Therefore, parameter estimation in nonlinearly parameterized differential equation models for biological pathways is both challenging and rewarding. In this study, we propose a Bayesian parameter estimation algorithm to estimate parameters in nonlinear mathematical models for biological pathways using time series data.

Results

We used the Runge-Kutta method to transform differential equations to difference equations assuming a known structure of the differential equations. This transformation allowed us to generate predictions dependent on previous states and to apply a Bayesian approach, namely, the Markov chain Monte Carlo (MCMC) method. We applied this approach to the biological pathways involved in the left ventricle (LV) response to myocardial infarction (MI) and verified our algorithm by estimating two parameters in a Hill equation embedded in the nonlinear model. We further evaluated our estimation performance with different parameter settings and signal to noise ratios. Our results demonstrated the effectiveness of the algorithm for both linearly and nonlinearly parameterized dynamic systems.

Conclusions

Our proposed Bayesian algorithm successfully estimated parameters in nonlinear mathematical models for biological pathways. This method can be further extended to high order systems and thus provides a useful tool to analyze biological dynamics and extract information using temporal data.