Comprehensive pharmacogenomic pathway screening by data assimilation

Takanori Hasegawa, Rui Yamaguchi, Masao Nagasaki, Seiya Imoto, Satoru Miyano

Research output: Chapter in Book/Report/Conference proceedingConference contribution

6 Citations (Scopus)


We propose a computational method to comprehensively screen for pharmacogenomic pathway simulation models. A systematic model generation strategy is developed; candidate pharmacogenomic models are automatically generated from some prototype models constructed from existing literature. The parameters in the model are automatically estimated based on time-course observed gene expression data by data assimilation technique. The candidate simulation models are also ranked based on their prediction power measured by Bayesian information criterion. We generated 53 pharmacogenomic simulation models from five prototypes and applied the proposed method to microarray gene expression data of rat liver cells treated with corticosteroid. We found that some extended simulation models have higher prediction power for some genes than the original models.

Original languageEnglish
Title of host publicationBioinformatics Research and Applications - 7th International Symposium, ISBRA 2011, Proceedings
Number of pages12
Publication statusPublished - 2011
Event7th International Symposium on Bioinformatics Research and Applications, ISBRA 2011 - Changsha, China
Duration: 2011 May 272011 May 29

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume6674 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349


Other7th International Symposium on Bioinformatics Research and Applications, ISBRA 2011

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)


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