Laboratory for Biological Systems Analysis
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Parameter Estimation and Structure Identification

Modern molecular biology is generating data of unprecedented quantity and quality. Particularly exciting for biochemical pathway modeling and proteomics are comprehensive, time-dense profiles of metabolites and proteins that are measurable with mass spectrometry and nuclear magnetic resonance. These profiles contain a wealth of information about the structure and dynamics of the pathway or network from which the data were obtained. The retrieval of this information requires a combination of computational methods and mathematical models, which are typically represented as systems of ordinary differential equations. This long-term project explores different means of identifying parameters from biological time series data.

Selected Recent References:

Chou, I-C., and E.O. Voit: Estimation of dynamic flux profiles from metabolic time series data, BMC Syst. Biol. ##:###, 2012.

Chou, I-C., Z. Qi, M.L. Kemp, and E.O. Voit: Metabolic System Identification from Different Experimental Data. In: W. Dubitzky, O. Wolkenhauer, K. Cho, and H. Yokota (Eds.) Encyclopedia of Systems Biology. (invited) Springer Science + Business Media, LLC 2012.

Voit, E.O.: What if the fit is unfit? Criteria for biological systems estimation beyond residual errors. In: M. Dehmer, F. Emmert-Streib and A. Salvador (Eds.): Applied Statistics for Biological Networks. J. Wiley and Sons, New York, pp. 183-200, 2011.

Ndukum, J. L.L. Fonseca, H. Santos, E.O. Voit, and S. Datta: Statistical inference methods for sparse biological time series data. BMC Syst. Biol. 5:57, 2011.

Voit, E.O. and I-C. Chou: Parameter estimation in canonical biological systems models. Int. J. Syst. Synth. Biol. 1(1), 1-19, 2010.

Chou, I-C. and E.O. Voit: Recent developments in parameter estimation and structure identification of biochemical and genomic systems. Math. Biosc. 219, 57-83, 2009.

Voit, E.O., G. Goel , I-C. Chou, and L. da Fonseca: Estimation of metabolic pathway systems from different data sources. IET Systems Biol. 3(6), 513-522, 2009.

Vilela, M., S. Vinga, M. A. Grivet Mattoso Maia, E. O. Voit, J. S. Almeida: Identification of neutral sets of biochemical systems models from time series data. BMC Systems Biology 3:47, 2009.

Goel, G., I-C. Chou, and E.O. Voit: System estimation from metabolic time series data. Bioinformatics 24, 2505-2511, 2008.

Chou, I-C., H. Martens, and E.O. Voit. Parameter estimation in biochemical systems models with alternating regression. BMC Theoretical Biology and Medical Modelling 3:25, 2006.

Click image to view:
Modeling Paradigms Modeling Paradigms

from Voit, E.O.: The dawn of a new era of metabolic systems analysis, Drug Discovery Today BioSilico 2(5), 182-189, 2004

Click image to view:
Alternating Regression Alternating Regression

from Chou, Martens, Voit, 2006