====== 2000 - 年 ======

  - 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. In press. (Extended abstract: Proceedings of 13th Annual Symposium on Combinatorial Pattern Matching (CPM 2002). Lecture Notes in Computer Science. 2373:168-177, 2002.)
  - Bannai, H., Hyyro, H., Shinohara, A., Takeda, M., Nakai, K., Miyano, S. An O (N2) algorithm for discovering optimal Boolean pattern pairs. IEEE/ACM Transactions on Computational Biology and Bioinformatics. In press. (Extended abstract: Bannai, H., Hyyro, H., Shinohara, A., Takeda, M., Nakai, K., Miyano, S. Finding optimal pairs of patterns. Proc. 4th International Workshop on Algorithms in Bioinformatics (WABI 2004). Lecture Notes in Bioinformatics. 3240:450-462, 2004.)
  - 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. Proc. 1st International Workshop on Data Mining and Bioinformatics. Lecture Note in Comupter Science. In press.
  - Imoto, S., Higuchi, T., Kim, S., Jeong, E., Miyano, S. Residual bootstrapping and median filtering for robust estimation of gene networks from microarray data. Proc. 2nd Computational Methods in Systems Biology. Lecture Note in Bioinformatics. In press.
  - 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. Proc. The 3rd Asia-Pacific Bioinformatics Conference 2005, Imperial College Press, In press.
  - Nagasaki, M., Doi, A., Matsuno, H., Miyano, S. Computational modeling of biological processes with Petri net based architecture. In "Bioinformatics Technologies" (Y.P. Chen, ed). Springer Press. 179-243, 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., and 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.
  - Ando, T., Imoto, S., Miyano, S. Bayesian network and radial basis function network regression for nonlinear modeling of genetic network. Proc. Third International Conference on Information. 561-564, 2004.
  - Ando, T., Imoto, S., Miyano, S. Functional data analysis of the dynamics of gene regulatory networks. Proc. Knowledge Exploration in Life Science Informatics KELSI2004. Lecture Notes in Artificial Intelligence. 3303: 69-83, 2004.
  - Ando, T., Imoto, S., Miyano, S. Kernel mixture survival models for identifying cancer subtypes, predicting patient's cancer types and survival probabilities. Genome Informatics. 15(2):201-210, 2004.
  - Bannai, H., Inenaga, S., Shinohara, A., Takeda, M., Miyano, S. Efficiently finding regulatory elements using correlation with gene expression. J. Bioinformatics and Computational Biology. 2(2):273-288, 2004.
  - De Hoon, M.J.L., Imoto, S., Kobayashi, K., Ogasawara, N., Miyano, S. Predicting the operon structure of Bacillus subtilis using operon length, intergene distance, and gene expression information. Pacific Symposium on Biocomputing. 9:276-287, 2004.
  - De Hoon, M.J.L., Imoto, S., Nolan, J., Miyano, S. Open source clustering software. Bioinformatics. 20(9):1453-1454, 2004.
  - De Hoon, M.J.L., Makita, Y., Imoto, S., Kobayashi, K., Ogasawara, N., Nakai, K., Miyano, S. Predicting gene regulation by sigma factors in Bacillus subtilis from genome-wide data. Bioinformatics, 20(Suppl.1):i101-i108, 2004.
  - Doi, A., Fujita, S., Matsuno, H., Nagasaki, M., Miyano, S. Constructing biological pathway models with hybrid functional Petri nets. In Silico Biology. 4(3):271-291, 2004.
  - Fujita, S., Matsui, M., Matsuno, H., Miyano, S. Modeling and simulation of fission yeast cell cycle on hybrid functional Petri net. IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences. E87-A(11):2919-2928, 2004.
  - Imoto, S., Higuchi, T., Goto, T., Tashiro, K., Kuhara, S., Miyano, S. Combining microarrays and biological knowledge for estimating gene networks via Bayesian networks. J. Bioinformatics and Computational Biology. 2(1):77-98, 2004.
  - Inenaga, S., Bannai, H., Hyyro, H., Shinohara, A., Takeda, M., Nakai, K., Miyano, S. Finding optimal pairs of cooperative and competing patterns with bounded distance. Proc. 7th International Conference on Discovery Science (DS 2004). Lecture Notes in Artificial Intelligence. 3245:32-46, 2004.
  - Jeong, E., Chung, I., Miyano, S. A neural network method for identification of RNA-interacting residues in protein. Genome Informatics. 15(1):105-116, 2004.
  - Kim, S., Imoto, S., Miyano, S. Dynamic Bayesian network and nonparametric regression for nonlinear modeling of gene networks from time series gene expression data. Biosystems, 75(1-3), 57-65, 2004. (Extended abstract: Proceedings of First Computational Methods in Systems Biology. Lecture Note in Computer Science. 2602:104-113, 2003.)
  - Matsui, M., Fujita, S., Suzuki, S., Matsuno, H., Miyano, S. Simulated cell division processes of the Xenopus cell cycle pathway by Genomic Object Net. J. Integrative Bioinformatics. 3: http://journal.imbio.de/index.php?paper_id=3, 2004.
  - Miyano, S. Computational systems biology. Proc. Third International Conference on Information (Li, L. and Yen, K.K., eds.). 9-14, 2004.
  - Nagasaki, M., Doi, A., Matsuno, H., Miyano, S. Genomic Object Net: a platform for modeling and simulating biopathways. Applied Bioinformatics. 2:181-184, 2004.
  - Nagasaki, M., Doi, A., Matsuno, H., Miyano, S. Integrating biopathway databases for large-scale modeling and simulation. Proc. Second Asia-Pacific Bioinformatics Conference (APBC2004) (Y.P. Chen, ed). Conferences in Research and Practice in Information Technology. 29: 43-52, 2004.
  - Nagasaki, M., Doi, A., Matsuno, H., Miyano, S. A versatile Petri net based architecture for modeling and simulation of complex biological processes. Genome Informatics, 15(1):180-197, 2004.
  - Nakamichi, R., Imoto, S., Miyano, S. Case-control study of binary trait considering interactions between SNPs and environmental effects using logistic regression. Proc. 4th IEEE Bioinformatics and Bioengineering. 73-78, 2004. IEEE Press.
  - Nakano, M., Noda, R., Kitakaze, H., Matsuno, H., Miyano, S. XML pathway file conversion between Genomic Object Net and SBML. Proc. The Third International Conference on Information. 585-588, 2004.
  - Nariai, N., Kim, S., Imoto, S., Miyano, S. Using protein-protein interactions for refining gene networks estimated from microarray data by Bayesian networks. Pacific Symposium on Biocomputing. 9:336-347, 2004.
  - Ott, S., Imoto, S., Miyano, S. Finding optimal models for small gene networks. Pacific Symposium on Biocomputing. 9:557-567, 2004.
  - Takei, Y., Inoue, K., Ogoshi, M., Kawahara, T., Bannai, H., and Miyano, S. Identification of novel adrenomedullin in mammals: a potent cardiovascular and renal regulator. FEBS Letters, 556:53-58, 2004.
  - Akutsu, T., Kuhara, S., Maruyama, O., Miyano, S. Identification of genetic networks by strategic gene disruptions and gene overexpressions under a boolean model. Theoretical Computer Science. 298(1):235-251, 2003. (Extended abstract: Proceedings of 9th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA'98), 695-702, 1998.)
  - Akutsu, T., Miyano, S., Kuhara, S. A simple greedy algorithm for finding functional relations: efficient implementation and average case analysis. Theoretical Computer Science. 292(2):481-495, 2003. (Extended abstract: Proceedings of Third International Conference on Discovery Science. Lecture Notes in Artificial Intelligence. 1967:86-98, 2000.)
  - De Hoon, M., Imoto, S., Kobayashi, K., Ogasawara, N., Miyano, S. Inferring gene regulatory networks from time-ordered gene expression data of Bacillus subtilis using differential equations. Pacific Symposium on Biocomputing. 8:17-28, 2003.
  - Doi, A., Nagasaki, M., Matsuno, H., Miyano, S. Genomic Object Net: II. Modelling biopathways by hybrid functional Petri net with extension. Applied Bioinformatics. 2(3):185-188, 2003.
  - Imoto, S., Kim, S., Goto, T., Aburatani, S., Tashiro, K., Kuhara, S., Miyano, S. Bayesian network and nonparametric heteroscedastic regression for nonlinear modeling of genetic network. Journal of Bioinformatics and Computational Biology. 1(2):231-252, 2003. (Extended abstract: Proceedings of IEEE Computer Society Bioinformatics Conference. 219-227, 2002.) (Extended abstract: Proceedings of Second Computational Systems Bioinformatics, 104-113, 2003.)
  - Imoto, S., Savoie, C.J., Aburatani, S., Kim, S., Tashiro, K., Kuhara, S., Miyano, S. Use of gene networks for identifying and validating drug targets. Journal of Bioinformatics and Computational Biology. 1(3):459-474, 2003.
  - Kim, S., Imoto, S., Miyano, S. Inferring gene networks from time series microarray data using dynamic Bayesian networks. Briefings in Bioinformatics. 4(3):228-235, 2003.
  - Nagasaki, M. Doi, A., Matsuno, H., Miyano, S. Genomic Object Net: I. a platform for modeling and simulating biopathways. Applied Bioinformatics. 2(3):181-184, 2003.
  - Matsuno, H., Murakami, R., Yamane, R., Yamasaki, N., Fujita, S., Yoshimori, H., Miyano, S. Boundary formation by notch signaling in Drosophila multicellular systems: experimental observations and gene network modeling by Genomic Object Net. Pacific Symposium on Biocomputing. 8:152-163, 2003.
  - Matsuno, H., Tanaka, Y., Aoshima, H., Doi, A., Matsui, M., Miyano, S. Biopathways representation and simulation on hybrid functional Petri net. In Silico Biology. 3(3): 389-404, 2003. (No. 0032)
  - Matsuno, H., Fujita, S., Doi, A., Nagasaki, M., Miyano, S. Towards biopathway modeling and simulation. Proceedings of 24th International Conference on Applications and Theory of Petri Nets (ICATPN 2003). Lecture Notes in Computer Science. 2679:3-22, 2003.
  - Miyano, S. Inference, Modeling and Simulation of Gene Networks. Proceedings of International Workshop on Computational Methods in Systems Biology. Lecture Notes in Computer Science. 2602:207-211, 2003.
  - Nagasaki, M., Doi, A., Matsuno, H., Miyano, S. Recreating biopathway databases towards simulation. Proceedings of International Workshop on Computational Methods in Systems Biology. Lecture Notes in Computer Science. 2602:191-192, 2003.
  - Obara, W., Iida, A., Suzuki, Y., Tanaka, T., Akiyama, F., Maeda, S., Ohnishi, Y., Yamada, R., Tsunoda, T., Takei, T., Ito, K., Honda, K., Uchida, K., Tsuchiya, K., Yumura, W., Ujiie, T., Nagane, Y., Nitta, K., Miyano, S., Narita, I., Gejyo, F., Nihei, H., Fujioka, T., Nakamura, Y. Association of single-nucleotide polymorphisms in the polymeric immunoglobulin receptor gene with immunoglobulin A nephropathy (IgAN) in Japanese patients. J Hum Genet. 48(6):293-299, 2003.
  - Ott, S., Tamada, Y., Bannai, H., Nakai, K., Miyano, S. Intrasplicing - analysis of long intron sequences. Pacific Symposium on Biocomputing. 8:339-350, 2003.
  - Ott, S., Miyano, S. Finding optimal gene networks using biological constraints. Genome Informatics. 14:124-133, 2003.
  - Savoie, C.J., Aburatani, S., Watanabe, S., Eguchi, Y., Muta, S., Imoto, S., Miyano, S., Kuhara, S., Tashiro, K. Use of gene networks from full genome microarray libraries to identify functionally relevant drug-affected genes and gene regulation cascades. DNA Research. 10(1):19-25, 2003.
  - Tamada, Y., Kim, S., Bannai, H., Imoto, S., Tashiro, K., Kuhara, S., Miyano, S. Estimating gene networks from gene expression data by combining Bayesian network model with promoter element detection. Bioinformatics. 19(Suppl.2):ii227-ii236, 2003.
  - Takei, Y., Inoue, K., Ogoshi, M., Kawahara, T., Bannai, H., Miyano, S. Identification of novel adrenomedullin in mammals: a potent cardiovascular and renal regulator. FEBS Letters, 556(1-3):53-58, 2003.
  - Akiyama, F., Tanaka, T., Yamada, R., Ohnishi, Y., Tsunoda, T., Maeda, S., Takei, T., Obara, W., Ito, K., Honda, K., Uchida, K., Tsuchiya, K., Nitta, K., Yumura, W., Nihei, H., Ujiie, T., Nagane, Y., Miyano, S., Suzuki, Y., Fujioka, T., Narita, I., Gejyo, F., Nakamura, Y. Single-nucleotide polymorphisms in the class II region of the major histocompatibility complex in Japanese patients with immunoglobulin A nephropathy. J. Hum. Genet. 47(10):532-538, 2002.
  - Akutsu, T., Miyano, S. Selecting informative genes for cancer classification using gene expression data. Computational and Statistical Approaches to Genomics (W. Zhang and I. Shmulevich eds.). Kluwer Academic Pub. 79-92, 2002.
  - Bannai, H. Inenaga, S., Shinohara, A., Takeda, M., Miyano, S. A string pattern regression algorithm and its application to pattern discovery in long introns. Genome Informatics. 13:3-11, 2002.
  - Bannai, H., Tamada, Y., Maruyama, O., Nakai, K., Miyano, S. Extensive feature detection of N-terminal protein sorting signals. Bioinformatics. 18(2):298-305, 2002.
  - De Hoon, M., Imoto, S., Miyano, S. Inferring gene regulatory networks from time-ordered gene expression data using differential equations. Proceedings of Fifth International Conference on Discovery Science. Lecture Notes in Artificial Intelligence. 2534:267-274, 2002.
  - De Hoon, M.J.L., Imoto, S., Miyano, S. Statistical analysis of a small set of time-ordered gene expression data using linear splines. Bioinformatics. 18(11):1477-1485, 2002.
  - Imoto, S., Goto, T., Miyano, S. Estimation of genetic networks and functional structures between genes by using Bayesian network and nonparametric regression. Pacific Symposium on Biocomputing. 7:175-186, 2002.
  - Maruyama, O., Bannai, H., Tamada, Y., Kuhara, S., Miyano, S. Fast algorithm for extracting multiple unordered short motifs using bit operations. Information Sciences. 146(1-4):115-126, 2002.
  - Maruyama, O., Shoudai, T., Miyano, S. Toward drawing an atlas of hypothesis classes: approximating a hypothesis via another hypothesis model. Proc. 5th International Conference on Discovery Science (DS2002). Lecture Notes in Computer Science. 2534:220-232, 2002.
  - Takei, T., Iida, A., Nitta, K., Tanaka, T., Ohnishi, Y., Yamada, R., Maeda, S., Tsunoda, T., Takeoka, S., Ito, K., Honda, K., Uchida, K., Tsuchiya, K., Suzuki, Y., Fujioka, T., Ujiie, T., Nagane, Y., Miyano, S., Narita, I., Gejyo, F., Nihei, H., Nakamura, Y. Association between single-nucleotide polymorphisms in selectin genes and immunoglobulin A nephropathy. Am. J. Hum. Genet. 70(3):781-786, 2002.
  - Tamada, Y., Bannai, H., Maruyama, O., Miyano, S. Foundations of designing computational knowledge discovery processes. Progress in Discovery Science. Lecture Notes in Computer Science. 2281:459-470, 2002.
  - Bannai, H., Tamada, Y., Maruyama, O., Miyano, S. VML: a view modeling language for computational knowledge discovery. Proceedings of Fourth International Conference on Discovery Science. Lecture Notes in Artificial Intelligence 2226:30-44, 2001.
  - Bannai, H., Tamada, Y., Maruyama, O., Miyano, S. HypothesisCreator: Concepts for accelerating the computational knowledge discovery process. Electronic Transactions on Artificial Intelligence. 5:73-83, 2001. (Electronic version: Linkoping Electronic Articles in Computer and Information Science. Issue: Vol. 6 (2001), No. 019. URL: http://www.ep.liu.se/ea/cis/2001/019/.)
  - Bannai, H., Tamada, Y., Maruyama, O., Nakai, K., Miyano, S. Views: fundamental building blocks in the process of knowledge discovery. Proceedings of the 14th International FLAIRS Conference. AAAI Press. 233-238, 2001.
  - Maruyama, O., Shoudai, T., Furuichi, E., Kuhara, S., Miyano, S. Learning conformation rules. Proceedings of Fourth International Conference on Discovery Science. Lecture Notes in Artificial Intelligence 2226:243-257, 2001.
  - Matsuno, H., Doi, A., Hirata, Y., Miyano, S. XML Documentation of biopathways and their simulations in Genomic Object Net. Genome Informatics. 12:54-62, 2001.
  - Onami, S., Hamahashi, S., Nagasaki, M., Miyano, S., Kitano, H. Automatic acquisition of cell lineage through 4D micorscopy and analysis of early C. elegans embryogenesis. Foundations of Systems Biology, Kitano, H. (ed.), MIT Press. 39-55, 2001.
  - Sim, K.L., Uchida, T., Miyano, S. ProDDO: a database of disordered proteins form the Protein Data Bank (PDB). Bioinformatics 17(4):379-380, 2001.
  - Sim, K.L., Uchida, T., Miyano, S. ProDDO: a database of disordered proteins from the Protein Data Bank (PDB). Bioinformatics. 17(4):379-380, 2001.
  - Akutsu, T., Miyano, S., Kuhara, S. Inferring qualitative relations in genetic networks and metabolic pathways. Bioinformatics. 16(8):727-734, 2000.
  - Akutsu, T., Miyano, S., Kuhara, S. Algorithms for identifying Boolean networks and related biological networks based on matrix multiplication and fingerprint function. Journal of Computational Biology. 7(3-4):331-343, 2000. (Extended abstract: Proceedings of Fourth Annual International Conference on Computational Molecular Biology. 8-24, 2000.)
  - Akutsu, T., Miyano, S., Kuhara, S. Algorithms for inferring qualitative models of biological networks. Pacific Symposium on Biocomputing. 5:293-304, 2000.
  - Maruyama, O., Miyano, S. Design sspects of discovery systems. IEICE Transactions on Information and Systems. E83-D(1):61-70, 2000.
  - Matsuno, H., Doi, A., Nagasaki, M., Miyano, S. Hybrid Petri net representation of gene regulatory network. Pacific Symposium on Biocomputing. 5:341-352, 2000.
  - Miyano, S., Shinohara, A., Shinohara, T. Polynomial-time learning of elementary formal systems. New Generation Computing. 18(3):217-242, 2000.
  - Tanaka, M., Nakazono, S., Matsuno, H., Tsujimoto, H., Kitamura, Y., Miyano, S. Intelligent system for topic survery in MEDLINE by keyword recommendation and learning text characteristics. Genome Informatics. 11:73-82, 2000.