TY - GEN
T1 - Comprehensive pharmacogenomic pathway screening by data assimilation
AU - Hasegawa, Takanori
AU - Yamaguchi, Rui
AU - Nagasaki, Masao
AU - Imoto, Seiya
AU - Miyano, Satoru
PY - 2011
Y1 - 2011
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=79955822489&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=79955822489&partnerID=8YFLogxK
U2 - 10.1007/978-3-642-21260-4_18
DO - 10.1007/978-3-642-21260-4_18
M3 - Conference contribution
AN - SCOPUS:79955822489
SN - 9783642212598
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 160
EP - 171
BT - Bioinformatics Research and Applications - 7th International Symposium, ISBRA 2011, Proceedings
T2 - 7th International Symposium on Bioinformatics Research and Applications, ISBRA 2011
Y2 - 27 May 2011 through 29 May 2011
ER -