How to infer the interactive large scale regulatory network in 'omic' studies

Asako Komori, Yukihiro Maki, Isao Ono, Masahiro Okamoto

Research output: Contribution to journalConference article

2 Citations (Scopus)

Abstract

Inferring regulatory networks in genetic systems and metabolic pathways is one of the most important problems in systems biology. Inferring network structure from experimentally observed time series data is an inverse problem. To deal with such problems, we have developed an efficient numerical optimization method called the hybrid method, which is a combination of real-coded genetic algorithms and the modified Powell method using the S-system representation. In general, a large regulatory network comprises numerous interactive system components and requires the optimization of a large number of parameters with non-zero interaction coefficients between them. To date, we have succeeded in optimizing 272 real-valued parameters using the hybrid method. Although compared with conventional numerical optimization methods, the hybrid method is powerful but is still insufficient for inferring large-scale networks. Here we discuss the inference of interactive large-scale regulatory networks in 'omics' studies based on our hybrid numerical optimization method.

Original languageEnglish
Pages (from-to)44-52
Number of pages9
JournalProcedia Computer Science
Volume23
DOIs
Publication statusPublished - Jan 1 2013
Event4th International Conference on Computational Systems-Biology and Bioinformatics, CSBio 2013 - Seoul, Korea, Republic of
Duration: Nov 7 2013Nov 9 2013

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Inverse problems
Time series
Genetic algorithms
Systems Biology
Metabolic Networks and Pathways

All Science Journal Classification (ASJC) codes

  • Computer Science(all)

Cite this

How to infer the interactive large scale regulatory network in 'omic' studies. / Komori, Asako; Maki, Yukihiro; Ono, Isao; Okamoto, Masahiro.

In: Procedia Computer Science, Vol. 23, 01.01.2013, p. 44-52.

Research output: Contribution to journalConference article

Komori, Asako ; Maki, Yukihiro ; Ono, Isao ; Okamoto, Masahiro. / How to infer the interactive large scale regulatory network in 'omic' studies. In: Procedia Computer Science. 2013 ; Vol. 23. pp. 44-52.
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