2006

Ando, T., Konishi, S., Imoto, S. Nonlinear regression modeling via regularized radial basis function networks. J. Statistical Planning and Inference. In press.

Doi, A., Nagasaki, M., Matsuno, H., Miyano, S. Simulation based validation of the p53 transcriptional activity with hybrid functional Petri net. In Silico Biology. 6(1-2): 1-13, 2006.

Doi, A., Nagasaki, M., Ueno, K., Matsuno, H., Miyano, S. A combined pathway to simulate CDK-dependent phosphorylation and ARF-dependent stabilization for p53 transcriptional activity. Genome Informatics 17(1): 112-123, 2006.

Imoto, S., Tamada, Y., Araki, H., Yasuda, K., Print, C.G., Charnock-Jones, S.D., Sanders, D., Savoie, C.J., Tashiro, K., Kuhara, S., Miyano, S. Computational strategy for discovering druggable gene networks from genome-wide RNA expression profiles. Pacific Symposium on Biocomputing. 11: 559-571, 2006.

Imoto, S., Higuchi, T., Goto, T., Miyano, S. Error tolerant model for incorporating biological knowledge with expression data in estimating gene networks. Statistical Methodology, 3(1):1-16, 2006.

Jeong, E., Miyano, S. A weighted profile based method for protein-RNA interacting residue prediction. Transactions on Computational Systems Biology. Lecture Notes in Computer Science. 3939: 123-139, 2006.

Li, C., Suzuki, S., Ge, Q.-W., Nakata, M., Matsuno, H., Miyano, S. Structural modeling and analysis of signaling pathways based on petri nets. J. Bioinformatics and Computional Biology. 4(5):1119-1140, 2006.

Matsuno, H., Inouye, S.-T., Okitsu, Y., Fujii, Y., Miyano, S. A new regulatory interactions suggested by simulations for circadian genetic control mechanism in mammals. J. Bioinformatics and Computional Biology. 4(1): 139-154, 2006.

Matsuno, H., Li, C., Miyano, S. Petri net based description for systematic understanding of biological pathways. IEICE Trans. Fundamentals, E89-A (11): 3166-3174, 2006.

Nagasaki, M., Yamaguchi, R., Yoshida, R., Imoto, S., Doi, A., Tamada, Y., Matsuno, H., Miyano, S., Higuchi, T. Genomic data assimilation for estimating hybrid functional Petri net from time-course gene expression data. Genome Informatics. 17(1). 46-61, 2006.

Nakamichi, R., Imoto, S., Miyano, S. Statistical model selection method to analyze combinatorial effects of SNPs and environmental factors for binary disease. International J. Artificial Intelligence Tools, 15(5), 711-724, 2006.

Okada, R., Sugii, M., Matsuno, H., Miyano, S. Machine learning prediction of amino acid patterns in protein N-myristoylation. Lecture Notes in Bioinformatics. 4146: 4-14, 2006.

Saito, A., Nagasaki, M., Doi, A., Ueno, K., Miyano, S. Cell fate simulation model of gustatory neurons with microRNAs double-negative feedback loops by hybrid functional Petri net with extension. Genome Informatics 17(1): 100-111, 2006.

Takei, Y., Kawakoshi, A., Tsukada, T., Yuge, S., Ogoshi, M., Inoue, K., Hyodo, S., Bannai, H., Miyano, S. Contribution of comparative fish studies to general endocrinology: structure and function of some osmoregulatory hormones. J. Experimental Zoology. Part A, Comparative Experimental Biology. 305(9):787-798, 2006.

Tamada, Y., Imoto, S., Miyano, S. Estimating gene networks from gene expression data utilizing biological information. Proc. Inst. Statist. Math. 54(2): 333-356, 2006.

Tasaki, S., Nagasaki, M., Oyama, M., Hata, H., Ueno, K., Yoshida, R., Higuchi, T., Sugano, S., Miyano, S. Modeling and estimation of dynamic EGFR pathway by data assimilation approach using time series proteomic data. Genome Informatics. 17(2): 226-228, 2006.

Termier, A., Tamada, Y., Imoto, S., Washio, T., Higuchi, T. From closed tree mining towards closed DAG mining. Proc. International Workshop on Data Mining and Statistical Science, 1-7, 2006.

Washio, T., Higuchi, T., Imoto, S., Tamada, Y., Sato, K., Motoda, H. Graph mining and its application to statistical modeling. Proc. Inst. Statist. Math. 54(2): 315-332, 2006.

Yoshida, R., Higuchi, T., Imoto, S., Miyano, S. ArrayCluster: an analytic tool for clustering, data visualization and module finder on gene expression profiles. Bioinformatics. 22(12):1538-1539, 2006.

Yoshida, R., Numata, K., Imoto, S., Nagasaki, M., Doi, A., Ueno, K., Miyano, S. A statistical framework for genome-wide discovery of biomarker splice variations with GeneChip Human Exon 1.0 ST arrays. Genome Informatics 17(1): 88-99, 2006.