Bayesian learning of biological pathways on genomic data assimilation

Ryo Yoshida, Masao Nagasaki, Rui Yamaguchi, Seiya Imoto, Satoru Miyano, Tomoyuki Higuchi

Research output: Contribution to journalArticlepeer-review

12 Citations (Scopus)

Abstract

Motivation: Mathematical modeling and simulation, based on biochemical rate equations, provide us a rigorous tool for unraveling complex mechanisms of biological pathways. To proceed to simulation experiments, it is an essential first step to find effective values of model parameters, which are difficult to measure from in vivo and in vitro experiments. Furthermore, once a set of hypothetical models has been created, any statistical criterion is needed to test the ability of the constructed models and to proceed to model revision. Results: The aim of our research is to present a new statistical technology towards data-driven construction of in silico biological pathways. The method starts with a knowledge-based modeling with hybrid functional Petri net. It then proceeds to the Bayesian learning of model parameters for which experimental data are available. This process exploits quantitative measurements of evolving biochemical reactions, e.g. gene expression data. Another important issue that we consider is statistical evaluation and comparison of the constructed hypothetical pathways. For this purpose, we have developed a new Bayesian information-theoretic measure that assesses the predictability and the biological robustness of in silico pathways.

Original languageEnglish
Pages (from-to)2592-2601
Number of pages10
JournalBioinformatics
Volume24
Issue number22
DOIs
Publication statusPublished - 2008 Nov

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

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