Mathematical modeling and dynamic simulation of metabolic reaction systems using metabolome time series data

Kansuporn Sriyudthsak, Fumihide Shiraishi, Masami Yokota Hirai

Research output: Contribution to journalReview article

8 Citations (Scopus)

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.

Original languageEnglish
Article number15
JournalFrontiers in Molecular Biosciences
Volume3
Issue numberMAY
DOIs
Publication statusPublished - May 3 2016

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Metabolome
Metabolites
Metabolic Networks and Pathways
Time series
Computer simulation
Theoretical Models
Metabolism
Technology
Benchmarking
Metabolomics
Mathematical models
Merging
Throughput
Research

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Biochemistry
  • Biochemistry, Genetics and Molecular Biology (miscellaneous)

Cite this

Mathematical modeling and dynamic simulation of metabolic reaction systems using metabolome time series data. / Sriyudthsak, Kansuporn; Shiraishi, Fumihide; Hirai, Masami Yokota.

In: Frontiers in Molecular Biosciences, Vol. 3, No. MAY, 15, 03.05.2016.

Research output: Contribution to journalReview article

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