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Briefings in Bioinformatics Advance Access published online on April 26, 2006
Briefings in Bioinformatics, doi:10.1093/bib/bbl007
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© The Author 2006. Published by Oxford University Press. For Permissions, please email: journals.permissions@oxfordjournals.org

Original Papers

Flux balance analysis in the era of metabolomics

Jong Min Lee, Erwin P. Gianchandani, and Jason A. Papin *

* To whom correspondence should be addressed.
Jason A. Papin, E-mail: papin{at}virginia.edu


  Abstract

Flux balance analysis (FBA) has emerged as an effective means to analyse biological networks in a quantitative manner. Much progress has been made on the extension of FBA to incorporate a priori biological knowledge, provide more practical descriptions of observed cell behaviours, and predict the outcome of network perturbations. Metabolomics is independently advancing as a set of high-throughput data acquisition tools providing dynamic profiles of metabolites in an unbiased manner. These data sets are neither yet sufficiently comprehensive nor accurate enough for generating large-scale kinetic models. Thus, there is a pressing need to develop quantitative techniques that can make use of the emerging data and embrace the associated uncertainties. This article reviews recent advances in FBA to meet this need and discusses the utility of FBA as a complement to metabolomics and the expected synergy as a result of combining these two techniques.

Keywords: metabolism; metabolome; genome scale analysis; network reconstruction; objective function; optimization.

Jong Min Lee is a postdoctoral research associate in the Department of Biomedical Engineering at the University of Virginia. His research interests include dynamic analysis of integrated cellular networks and machine learning approaches to the understanding of signal transduction.

Erwin P. Gianchandani is a graduate student in the Department of Biomedical Engineering at the University of Virginia. His research interests include applying systems analyses to the integration of metabolic, regulatory and signalling networks for the characterization of whole-cell properties.

Jason A. Papin is an Assistant Professor of Biomedical Engineering at the University of Virginia. His group has ongoing projects on polymicrobial interactions in human disease, signalling networks in cancer and the integration of signalling, regulatory and metabolic networks in embryogenesis.


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