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   - Chalkidis, G., Nagasaki, M., Miyano, S. High performance hybrid functional Petri net simulations of biological pathway models on CUDA. IEEE/ACM Transactions on Computational Biology and Bioinformatics. In press.
   - Do, J.H., Nagasaki, M., Miyano, S. The systems approach to the prespore-specific activation of sigma factor SigF in //Bacillus subtilis//. Biosystems. 100: 178-184, 2010.
+  - Fujimoto, A., Nakagawa, H., Hosono, N., Nakano, K., Abe, G., Boroevich, K.A., Nagasaki, M., Yamaguchi, R., Shibuya, T., Kubo, M., Miyano, S., Nakamura, Y., Tsunoda, T. Whole-genome sequencing and comprehensive variant analysis of a Japanese individual using massively parallel sequencing. Nature Genetics. In press. [[http://www.nature.com/ng/journal/vaop/ncurrent/abs/ng.691.html|Link]]
   - Fujita, A., Kojima, K., Patriota, A.G., Sato, J.R., Severino, P., Miyano, S. A fast and robust statistical test based on likelihood ratio with Bartlett correction to identify Granger causality between gene sets. Bioinformatics. 26(18):2349-2351, 2010.
   - Fujita, A., Nagasaki, M., Imoto, S., Saito, A., Ikeda, E., Shimamura, T., Yamaguchi, R., Hayashizaki, Y., Miyano, S. Comparison of gene expression profiles produced by CAGE, illumina microarray and Real Time RT-PCR. Genome Informatics. 24: 56-68, 2010.
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   - Higashigaki,T., Kojima, K., Yamaguchi, R., Inoue, M., Imoto, S., Miyano, S. Identifying hidden confounders in gene networks by Bayesian networks, Proc. 10th IEEE Bioinformatics and Bioengineering. 168-173, 2010.
   - International Cancer Genome Consortium, Hudson, T.J. et al. International network of cancer genome projects. Nature. 464(7291):993-998, 2010. [[http://www.nature.com/nature/journal/v464/n7291/full/nature08987.html|Link]]
+  - Jeong, E., Nagasaki, M., Ueno, K., Miyano, S. Ontology-based instance data validation for high-quality curated biological pathways. BMC Bioinformatics. In press.
   - Koh, C.H., Nagasaki, M., Saito, A., Wong, L., Miyano, S. DA 1.0: parameter estimation of biological pathways using data assimilation approach. Bioinformatics. 26(14):1794-1796, 2010.
   - Kojima, K., Imoto, S., Nagasaki, M., Miyano, S. Gene regulatory network clustering for graph layout based on microarray gene expression data, Genome Informatics. 24: 84-95, 2010.
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   - Nagasaki, M., Saito, A., Jeong, E., Li, C., Kojima, K., Ikeda, E., Miyano, S. Cell Illustrator 4.0: A computational platform for systems biology. In Silico Biol. 10: 0002, 2010. [[http://www.bioinfo.de/isb/2010/10/0002/|Link]]
   - Niida, A., Imoto, S., Yamaguchi, R., Nagasaki, M., Miyano, S. Gene set-based module discovery decodes cis-regulatory codes governing diverse gene expression across human multiple tissues. PLoS ONE. 5(6):e10910, 2010.
-  - Niida, A., Imoto, S., Yamaguchi, R., Nagasaki, M., Fujita, A., Shimamura, T., Miyano, S. Model-free unsupervised gene set screening based on information enrichment in expression profiles. Bioinformatics. In press.
+  - Niida, A., Imoto, S., Yamaguchi, R., Nagasaki, M., Fujita, A., Shimamura, T., Miyano, S. Model-free unsupervised gene set screening based on information enrichment in expression profiles. Bioinformatics. In press.[[http://bioinformatics.oxfordjournals.org/content/early/2010/10/19/bioinformatics.btq592.abstract.html?|Link]]
   - Sato, H, Nakada, H., Yamaguchi, R., Imoto, S., Miyano, S., Kami, M. When should we intervene to control the 2009 influenza A(H1N1) pandemic? Euro Surveill. 7:15(1), pii: 19455, 2010.
   - Shimamura, T., Imoto, S., Yamaguchi, R., Nagasaki, M., Miyano, S. Inferring dynamic gene networks under varying conditions for transcriptomic network comparison. Bioinformatics. 26(8):1064-1072, 2010.
   - Shimamura, T., Imoto, S., Nagasaki, M., Yamauchi, M., Yamaguchi, R., Fujita, A., Tamada, Y., Gotoh, N., Miyano, S. Collocation-based sparse estimation for constructing dynamic gene networks. Genome Informatics. 24: 164-178, 2010.
   - Tamada, Y., Imoto, S., Araki, H., Nagasaki, M., Print, C., Charnock-Jones, D.S., Miyano, S. Estimating genome-wide gene networks using nonparametric Bayesian network models on massively parallel computers. IEEE/ACM Transactions on Computational Biology and Bioinformatics. In press.
+  - Tasaki, S., Nagasaki, M., Kozuka-Hata, H., Semba, K., Gotoh, N., Hattori, S., Inoue, J., Yamamoto, T., Miyano, S., Sugano, S., Oyama, M. Phosphoproteomics-based modeling defines the regulatory mechanism underlying aberrant EGFR signaling. PLoS ONE. In press.
   - Yamaguchi, R., Imoto, S., Miyano, S. Network-based predictions and simulations by biological state space models: Search for drug mode of action. J. Computer Science and Technology. 25(1): 13-153, 2010.
   - Yuji, K., Matsumura, T., Miyano, S., Tsuchiya, R., Kami, M. Human papillomavirus vaccine coverage. Lancet. 376(9738):329-330, 2010.
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 ====== Books ======
-  - Nagasaki, M., Saito, A., Doi, A., Matsuno, H., Miyano, S. "Foundations of Systems Biology - Using Cell Illustrator and Pathway Databases". Springer, 2009. [[http://www.springer.com/computer/computational+biology+and+bioinformatics/book/978-1-84882-022-7|Springerへのリンク]]
+  - Nagasaki, M., Saito, A., Doi, A., Matsuno, H., Miyano, S. "Foundations of Systems Biology - Using Cell Illustrator and Pathway Databases". Springer, 2009. [[http://www.springer.com/computer/computational+biology+and+bioinformatics/book/978-1-84882-022-7|Springer]]
   - Kurata, H., Miyano, S. （Japanese Translation). Uri Alon. An Introduction to Systems Biology: Design Principles of Biological Circuits. Chapman & Hall/CRC, 2007）. Kyoritsu Shuppan Co. Ltd., 2008.
   - Doi, A., Nagasaki, M., Saito, A., Matsuno, H., Miyano, S. "Yes, We Can Understand Systems Biolog! - Let's use Cell Illustrator" (in Japanese). Kyoritsu Shuppan, Co. Ltd., 2007.