2007 [李　晨]

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====== 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)