De Hoon, Michiel J. L., Makita, Y., Nakai, K., Miyano, S. Prediction of transcriptional terminators in Bacillus subtilis and related species. PLoS Computational Biology. 1(3): e25, 2005.

Hirose, O., Nariai, N., Tamada, Y., Bannai, H., Imoto, S., Miyano, S. Estimating gene networks from expression data and binding location data via boolean networks. Lecture Notes in Computer Science. 3482: 349-356, 2005.

Kato, M., Nagasaki, M., Doi, A., Miyano, S. Automatic drawing of biological networks using cross cost and subcomponent data. Genome Informatics 16(2): 22-31, 2005.

Kitakaze, H., Matsuno, H., Ikeda, N., Miyano, S. Prediction of debacle points for robustness of biological pathways by using recurrent neural networks. Genome Informatics. 16(1): 192-202, 2005.

Li, C., Suzuki, S., Ge, Q.-W., Nakata, M., Matsuno, H., Miyano, S. On modeling and analyzing signaling pathways with inhibitory interactions based on Petri net. BIOINFO2005, 348-353, 2005.

Makita, Y., De Hoon, M.J., Ogasawara, N., Miyano, S., Nakai, K. Bayesian joint prediction of associated transcription factors in Bacillus subtilis. Pacific Symposium on Biocomputing. 10: 507-518, 2005.

Nagasaki, M., Doi, A., Matsuno, H., Miyano, S. Petri net modeling of biological pathways. Proc. Algebraic Biology 2005, Universal Academy Press, 19-31, 2005.

Nariai, N., Tamada, Y., Imoto, S., Miyano, S. Estimating gene regulatory networks and protein-protein interactions of Saccharomyces cerevisiae from multiple genome-wide data. Bioinformatics. 21: ii206-ii212, 2005.

Ohtsubo, S., Iida, A., Nitta, K., Tanaka, T., Yamada, R., Ohnishi, Y., Maeda, S., Tsunoda, T., Takei, T., Obara, W., Akiyama, F., Ito, K., Honda, K., Uchida, K., Tsuchiya, K., Yumura, W., Ujiie, T., Nagane, Y., Miyano, S., Suzuki, Y., Narita, I., Gejyo, F., Fujioka, T., Nihei, H., Nakamura, Y. Association of a single-nucleotide polymorphism in the immunoglobulin mu-binding protein 2 gene with immunoglobulin A nephropathy. J. Hum. Genet. 50(1): 30-35, 2005.

Ott, S., Hansen, A., Kim, S.-Y., Miyano, S. Superiority of network motifs over optimal networks and an application to the revelation of gene network evolution. Bioinformatics. 21(2): 227-238, 2005.

Tamada, Y., Bannai, H., Imoto, S., Katayama, T., Kanehisa, M., Miyano, S. Utilizing evolutionary information and gene expression data for estimating gene networks with Bayesian network models. J. Bioinformatics and Computational Biology. 3(6): 1295-1313, 2005.

Tamada, Y., Imoto, S., Tashiro, K., Kuhara, S., Miyano, S. Identifying drug active pathways from gene networks estimated by gene expression data. Genome Informatics. 16(1): 182-191, 2005.

Yoshida, R., Higuchi, T., Imoto, S. Estimating time-dependent gene networks from time series DNA microarray data by dynamic linear model with Markov switching. Proc. IEEE 4th Computational Systems Bioinformatics. IEEE Press. 289-298, 2005.

Yoshida, R., Imoto, S., Higuchi, T. A penalized likelihood estimation on transcriptional module-based clustering. Lecture Notes in Computer Science. 3482: 389-401, 2005.