title: Mathematical Modeling and Dynamic Simulation of Metabolic Reaction Systems Using Metabolome Time Series Data.
abstract: The high-throughput acquisition of metabolome data is greatly anticipated for the complete understanding of cellular metabolism in living organisms. A variety of analytical technologies have been developed to acquire large-scale metabolic profiles under different biological or environmental conditions. Time series data are useful for predicting the most likely metabolic pathways because they provide important information regarding the accumulation of metabolites, which implies causal relationships in the metabolic reaction network. Considerable effort has been undertaken to utilize these data for constructing a mathematical model merging system properties and quantitatively characterizing a whole metabolic system in toto. However, there are technical difficulties between benchmarking the provision and utilization of data. Although, hundreds of metabolites can be measured, which provide information on the metabolic reaction system, simultaneous measurement of thousands of metabolites is still challenging. In addition, it is nontrivial to logically predict the dynamic behaviors of unmeasurable metabolite concentrations without sufficient information on the metabolic reaction network. Yet, consolidating the advantages of advancements in both metabolomics and mathematical modeling remain to be accomplished. This review outlines the conceptual basis of and recent advances in technologies in both the research fields. It also highlights the potential for constructing a large-scale mathematical model by estimating model parameters from time series metabolome data in order to comprehensively understand metabolism at the systems level.
authors.affiliation: RIKEN Center for Sustainable Resource Science Yokohama, Japan.
authors.forename: Kansuporn
authors.initials: K
authors.lastname: Sriyudthsak
authors.affiliation: Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Science, Kyushu University Fukuoka, Japan.
authors.forename: Fumihide
authors.initials: F
authors.lastname: Shiraishi
authors.affiliation: RIKEN Center for Sustainable Resource Science Yokohama, Japan.
authors.forename: Masami Yokota
authors.initials: MY
authors.lastname: Hirai
keywords: biochemical systems theory; bottleneck ranking indicator; dynamic simulation; mathematical model; metabolic reaction network; metabolome; sensitivity analysis; time series data