2007

Affara, M., Dunmore, B., Savoie, C.J., Imoto, S., Tamada, Y., Araki, H., Charnock-Jones, D.S., Miyano, S., Print, C. Understanding endothelial cell apoptosis: What can the transcriptome glycome and proteome reveal? Philosophical Transactions of Royal Society. 362(1484):1469-1487, 2007.

Akutsu, T., Bannai, H., Miyano, S., Ott, S. On the complexity of deriving position specific score matrices from positive and negative sequences. Discrete Applied Mathematics.155: 676-685, 2007.

Fujita, A., Sato, J.R., Garay-Malpartida, H.M., Yamaguchi, R., Miyano, S., Sogayar, M.C., Ferreira, C.E.　Modeling gene expression regulatory networks with the sparse vector autoregressive model. BMC Systems Biology 2007, 1:39 (doi:10.1186/1752-0509-1-39)

Gupta, P.K., Yoshida, R., Imoto, S., Yamaguchi, R., Miyano, S. Statistical absolute evaluation of gene ontology terms with gene expression data. Lecture Notes in Bioinformatics. 4463:146-157, 2007.

Hirose, O., Yoshida, R., Imoto, S., Yamaguchi, R., Higuchi, T., Charnock-Jones, D.S., Print, C., Miyano, S. Statistical inference of transcriptional module-based gene networks from time course gene expression profiles by using state space models. Bioinformatics. In press.

Hirose, O., Yoshida, R., Yamaguchi, R., Imoto, S., Higuchi, T., Miyano, S. Clustering with time course gene expression profiles and the mixture of state space models. Genome Informatics. 18:258-266, 2007.

Imoto, S. Knowledge discovery of causal relations among genes from microarray gene expression data, Journal of Japan Statistical Society. 37(1): 55-70, 2007.

Imoto, S., Tamada, Y., Savoie, C.J., Miyano, S., Analysis of gene networks for drug target discovery and validation. Methods in Molecular Biology. 360:33-56, 2007.

Jeong, E., Nagasaki, M., Miyano, S. Conversion from BioPAX to CSO for system dynamics and visualization of biological pathway. Genome Informatics. 18:225-236, 2007.

Jeong, E., Nagasai, M., Saito, A., Miyano, S. Cell System Ontology: Representation for modeling, visualizing, and simulating biological pathways. In Silico Biology 7, 0055, 2007.

Kojima, K., Nagasaki, M., Jeong, E., Kato, M., Miyano, S. An efficient grid layout algorithm for biological networks utilizing various biological attributes. BMC Bioinformatics. 8:76, 2007.

Li, C., Ge, Q.-W., Nakata, M., Matsuno, H., Miyano, S. Modeling and simulation of signal transductions in an apoptosis pathway by using timed Petri nets. J. Biosciences. 32(1):113-125, 2007.

Numata, K., Imoto, S., Miyano, S. A structure learning algorithm for inference of gene networks from microarray gene expression data using Bayesian networks. Proc. IEEE 7th International Symposium on Bioinformatics & Bioengineering. 1280-1284, 2007. (BIBE2007: Refereed conference; Digital Object Identifier 10.1109/BIBE.2007.4375731)

Saito, A., Nagasaki, M., Oyama, M., Kozuka-Hata, H., Semba, K., Sugano, S., Yamamoto, T., Miyano, S. AYUMS: an algorithm for completely automatic quantitation based on LC-MS/MS proteome data and its application to the analysis of signal transduction. BMC Bioinformatics. 8:15, 2007.

Shimamura, T., Yamaguchi, R., Imoto, S., Miyano, S. Weighted lasso in graphical Gaussian modeling for large gene network estimation based on microarray data. Genome Informatics. 19:142-153, 2007.

Sugii, M., Okada, R., Matsuno, H., Miyano, S. Performance improvement in protein N-myristoyl classification by BONSAI with insignificant indexing symbol. Genome Informatics. 18:277-286, 2007.

Termier, A., Tamada, Y., Numata, K., Imoto, S., Washio, T., Higuchi, T., DIGDAG, a first algorithm to mine closed frequent embedded sub-DAGs. Proc. 5th International Workshop on Mining and Learning with Graphs, in press, 2007.

Yamaguchi, R., Yamamoto, M., Imoto, S., Nagasaki, M., Yoshida, R., Tsujii, K., Ishiga, A., Asou, H., Watanabe, K., Miyano, S. Identification of activated transcription factors from microarray gene expression data of Kampo-medicine treated mice. Genome Informatics. 18:119-129, 2007.

Yamaguchi, R., Yoshida, R., Imoto, S., Higuchi, T., Miyano, S. Finding module-based gene networks with state-space models? Mining high-dimensional and short time-course gene expression data. IEEE Signal Processing Magazine, 24(1): 37-46, 2007.

Yoshida, R., Numata, K., Imoto, S., Nagasaki, M., Doi, A., Ueno, K., Miyano, S. Computational discovery of aberrant splice variations with genome-wide exon expression profiles. Proc. IEEE 7th International Symposium on Bioinformatics & Bioengineering. 715-722, 2007. (IEEE BIBE2007: Refereed conference; Digital Object Identifier 10.1109/BIBE.2007.4375639)