publications_en [Satoru Miyano- english]

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====== Publications - Satoru Miyano ======


====== Papers ======
===== 2010 =====
  - 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.
  - 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.
  - Fujita, A., Sato, J.R., Demas, M.A.A, Yamaguchi, R., Shimamura, T., Ferreira, C.E., Sogayar, M.C., Miyano, S. Inferring contagion in regulatory networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics. In press.
  - Fujita, A., Sato, J.R., Kojima, K., Gomes, L.R., Sogayar, M.C., Miyano, S. Identification of Granger causality between gene sets. J. Bioinformatics and Computational Biology. 8(4): 679?701, 2010.
  - Fujita, A., Severino, P., Sato, J.R., Miyano, S. Granger causality in systems biology: modeling gene networks in time series microarray data using vector autoregressive models. Lecture Notes in Bioinformatics. 6268: 13-24, 2010.
  - 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.
  - Kojima, K., Nagasaki, M., Miyano, S. An efficient biological pathway layout algorithm combining grid-layout and spring embedder for complicated cellular location information. BMC Bioinformatics. 11:335, 2010.
  - Kojima, K., Perrier, E., Imoto, S., Miyano, S. Optimal search on clustered structural constraint for learning Bayesian network structure. J. Machine Learning Research.11: 285?310, 2010. [[http://www.jmlr.org/papers/volume11/kojima10a/kojima10a.pdf|Link]]
  - Li, C., Nagasaki, M., Saito, A., Miyano, S. Time-dependent structural transformation analysis to high-level Petri net model with active state transition diagram. BMC Systems Biology. 4:39, 2010.
  - Miwa, Y., Li, C., Ge, Q.W., Matsuno, H., Miyano, S., On determining delay time of transitions for Petri net based signaling pathways by introducing stochastic decision rules. In Silico Biol. 10: 0004, 2010. (*Equally contributed) [[http://www.bioinfo.de/isb/2010/10/0004/|Link]]
  - 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.[[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.


===== 2009 =====
  - Araki, H.*, Tamada, Y.*, Imoto, S.*, Dunmore, B., Sanders, D., Humphrey, S., Nagasaki, M., Doi, A., Nakanishi, Y., Yasuda, K., Tomiyasu, Y., Tashiro, K., Print, C., Charnock-Jones, D.S., Kuhara, S., Miyano, S. Analysis of PPARalpha-dependent and PPARalpha-independent transcript regulation following fenofibrate treatment of human endothelial cells. Angiogenesis. 12(3): 221-229, 2009. (*Equally contributed).
  - Do, J.H., Miyano, S., Choi, D.K. Statistical approaches to genome-wide biological networks. Biochip J.  3(3): 190-202, 2009.
  - Do, J.H., Yamaguchi, R., Miyano, S. Exploring temporal transcription regulation structure of //Aspergillus fumigatus// in heat shock by state space model. BMC Genomics. 10:306, 2009.
  - Fujita, A., Sato, J.R., Demas, M.A.A, Yamaguchi, R., Shimamura, T., Ferreira, C.E., Sogayar, M.C., Miyano, S. Inferring contagion in regulatory networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics. In press.
  - Fujita, A., Sato, J.R., Demas, M.A.A, Sogayar, M.C., Ferreira, C.E., Miyano, S. Comparing Pearson, Spearman and Hoeffding's D measure for gene expressionassociation analysis. J. Bioinformatics and Computational Biology. 7(4): 663-684, 2009.
  - Hashimoto, T.B., Nagasaki, M., Kojima, K., Miyano, S. BFL: a node and edge betweenness based fast layout algorithm for large scale networks. BMC Bioinformatics. 10:19, 2009.
  - Li, C.*, Nagasaki, M.*#, Ueno, K., Miyano, S. Simulation-based model checking approach to cell fate specification during Caenorhabditis elegans vulval development by hybrid functional Petri net with extension. BMC Systems Biology. 3:42, 2009. doi:10.1186/1752-0509-3-42 (*: These authors equally contributed, #: Corresponding author).
  - Miyakawa, C., Sugii, M., Matsuno, H., Miyano, S. Computational predictions for functional proteins working after cleaved in apoptotic pathway. Proc. Second International Workshop on Intelligent Informatics in Biology and Medicine, IEEE Computer Society Press, 807-812, 2009.
  - Miyano, S., Yamaguchi, R., Tamada, Y., Nagasaki, M., Imoto, S. Gene networks viewed through two models. Lecture Notes in Computer Science. 5462: 54-66, 2009. (Proc. First International Conference on Bioinformatics and Computational Biology (BICoB)). doi: 10.1007/978-3-642-00727-9_8.
  - Nakamura, K., Yoshida, R., Nagasaki, M., Miyano, S., Higuchi, T. Parameter estimation of in silico biological pathways with particle filtering towards a petascale computing. Pacific Symposium on Biocomputing. 14: 227-238, 2009.
  - Shimamura, T., Imoto, S., Yamaguchi, R., Fujita, A., Nagasaki, M., Miyano, S. Recursive regularization for inferring gene networks from time-course gene expression profiles. BMC Systems Biology. 3:41, 2009.
  - Tamada, Y., Araki, H., Imoto, S., Nagasaki, M., Doi, A., Nakanishi, Y., Tomiyasu, Y., Yasuda, K., Dunmore, B., Sanders, D., Humphreys, S., Print, C., Charnock-Jones, D.S., Tashiro, K., Kuhara, S., Miyano, S. Unraveling dynamic activities of autocrine pathways that control drug-response transcriptome networks. Pacific Symposium on Biocomputing. 14: 251–263, 2009.
  - Watanabe-Fukuda, Y., Yamamoto, M., Miura, N., Fukutake, M., Ishige, A., Yamaguchi, R., Nagasaki, M., Saito, A., Imoto, S., Miyano, S., Takeda, J., Watanabe, K. Orengedokuto and berberine improve indomethacin-induced small intestinal injury via adenosine. Journal of Gastroenterology. 44(5):380-389, 2009.
  - Yamamoto, T., Miyano, S., Nagasaki, M., Bannai, H. Better decomposition heuristics for the maximum-weight connected graph problem using betweenness centrality. Lecture Notes in Artificial Intelligence. In press.
  - Yashiro, Y., Bannai, H., Minowa, T., Yabiku, T., Miyano, S., Osawa, M., Iwama, A., Nakauchi, H. Transcriptional profiling of hematopoietic stem cells by high-throughput sequencing. I.J. Hematology. 89(1):24-33, 2009. 
  - Yoshikawa, N., Nagasaki, M., Sano, M., Tokudome, S., Ueno, K., Shimizu, N., Imoto, S., Miyano, S., Suematsu, M., Fukuda, K., Morimoto, C., Tanaka, H. Ligand-based gene expression profiling reveals novel roles of glucocorticoid receptor in cardiac metabolism. Am J Physiol Endocrinol Metab. 296(6):E1363-E1373, 2009.



===== 2008 =====
  - Do, J.H., Miyano, S. The GC and window-averaged DNA curvature profile of secondary metabolite gene cluster in Aspergillus fumigatus genome. Applied Microbiology and Biotechnology. 80(5):841-847, 2008.
  - Fujita, A., Gomes, L.R., Sato, J.R., Yamaguchi, R., Thomaz, C.E., Sogayar, M.C., Miyano, S. Multivariate gene expression analysis reveals functional connectivity changes between normal/tumoral prostates. BMC Systems Biology. 2:106, 2008.
  - Fujita, A., Sato, J.R., Garay-Malpartida, H.M., Sogayar, M.C., Ferreira, C.E., Miyano, S. Modeling nonlinear gene regulatory networks from time series gene expression data. J. Bioinformatics and Computational Biology. 6(5): 961 -- 979, 2008.
  - Hatanaka, Y., Nagasai, M., Yamaguchi, R., Obayashi, T., Numata, K., Fujita, A., Shimamura, T., Tamada, Y., Imoto, S., Kinoshita, K., Nakai, K., Miyano, S. A novel strategy to search conserved transcription factor binding sites among coexpressing genes in human. Genome Informatics. 20:212-221, 2008.
  - 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. 24(7): 932-942, 2008.
  - Hirose, O.,Yoshida, R., Yamaguchi, R., Imoto, S., Higuchi, T., Miyano, S. Analyzing time course gene expression data with biological and technical replicates to estimate gene networks by state space models. Proc. 2nd Asia International Conference on Modelling & Simulation, 940-946, 2008. (AMS2008: Refereed conference)
  - Jeong, E., Nagasaki, M., Miyano, S. Rule-based reasoning for system dynamics in cell systems. Genome Informatics. 20:25-36, 2008.
  - Kitakaze, H., Kanda, M., Nakatsuka, H., Ikeda, N., Matsuno, H., Miyano, S. Prediction of fragile points for robustness checking of cell systems. IEICE TRANSACTIONS on Information and Systems D. J91-D(9):2404-2417, 2008.
  - Kojima, K., Fujita, A., Shimamura, T., Imoto, S., Miyano, S. Estimation of nonlinear gene regulatory networks via L1 regularized NVAR from time series gene expression data. Genome Informatics. 20:37-51, 2008.
  - Kojima, K., Nagasaki, M.*, Miyano, S. Fast grid layout algorithm for biological networks with sweep calculation. Bioinformatics. 24(12): 1426-1432, 2008 (*: Corresponding author)
  - Mito, N., Ikegami, Y., Matsuno, H., Miyano, S., Inouye, S. Simulation analysis for the effect of light-dark cycle on the entrainment in circadian rhythm. Genome Informatics. 21:212-223, 2008.
  - Nagasaki, M.*, Saito, A., Chen, L., Jeong, E., Miyano, S. Systematic reconstruction of TRANSPATH data into Cell System Markup Language. BMC Systems Biology.  2:53 (23Jun2008), 2008. (*: Corresponding author)
  - Numata, K., Yoshida, R., Nagasaki, M., Saito, S., Imoto, S., Miyano, S. ExonMiner: Web service for analysis of GeneChip exon array data. BMC Bioinformatics. 9:494, 2008.
  - Numata, K., Imoto, S., Miyano, S. Partial order-based Bayesian network learning algorithm for estimating gene networks. Proc. IEEE 8th International Symposium on Bioinformatics & Bioengineering, IEEE Computer Society, 357-360, 2008. 　(BIBE2008: Refereed conference; Digital Object Identifier 10.1109/BIBM.2008.85)
  - Perrier, E., Imoto, S., Miyano, S. Finding optimal Bayesian network given a super-structure. J. Machine Learning Research. 9: 2251-2286, 2008.
  - Yamaguchi, R., Imoto, S., Yamauchi, M., Nagasaki, M., Yoshida, R., Shimamura, T., Hatanaka, Y., Ueno, K., Higuchi, T., Gotoh, N., Miyano, S. Predicting differences in gene regulatory systems by state space models. Genome Informatics. 21:101-113, 2008.
  - Yoshida, R., Nagasaki, M., Yamaguchi, R., Imoto, S., Miyano, S., Higuchi, T. Bayesian learning of biological pathways on genomic data assimilation. Bioinformatics. 24(22):2592-2601, 2008.


===== 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. (Extended abstract: Proceedings of 13th Annual Symposium on Combinatorial Pattern Matching (CPM 2002). Lecture Notes in Computer Science. 2373:168-177, 2002.)
  - 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. 1:39, 2007. (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., 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., 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. (Target Discovery and Validation, Volume 1, 33-56, 2007 (a volume of "Methods in Molecular Biology" series), Walker, J. and Sioud, M. (Eds.), Humana Press, USA.).
  - Imoto, S., Miyano, S. Bayesian network approach to estimate gene networks. A. Mittal, A. Kassim and T. Tan (Eds.), Bayesian Network Technologies: Applications and Graphical Models, Idea Group Publishers, USA. 269-299, 2007. (Refereed book chapter).
  - 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. (* These authors equally contributed)
  - Jeong, E.*, Nagasaki, M.*, Saito, A., Miyano, S. Cell System Ontology: Representation for modeling, visualizing, and simulating biological pathways. In Silico Biology 7, 0055, 2007. (* These authors equally contributed)
  - Kojima, K.*, Nagasaki, M.*, Jeong, E., Kato, M., Miyano, S. An efficient grid layout algorithm for biological networks utilizing various biological attributes. BMC Bioinformatics 2007, 8:76 (6 March 2007). (* These authors equally contributed)
  - 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.
  - 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)

===== 2006 =====

  - Doi, A., Nagasaki, M., Matsuno, H., Miyano, S. Simulation based validation of the p53 transcriptional activity with hybrid functional Petri net. In Silico Biology. 6(1-2): 1-13, 2006.
  - Doi, A., Nagasaki, M., Ueno, K., Matsuno, H., Miyano, S. A combined pathway to simulate CDK-dependent phosphorylation and ARF-dependent stabilization for p53 transcriptional activity. Genome Informatics. 17(1): 112-123, 2006.
  - Imoto, S., Tamada, Y., Araki, H., Yasuda, K., Print, C.G., Charnock-Jones, S.D., Sanders, D., Savoie, C.J., Tashiro, K., Kuhara, S., Miyano, S.  Computational strategy for discovering druggable gene networks from genome-wide RNA expression profiles. Pacific Symposium on Biocomputing. 11: 559-571, 2006.
  - Imoto, S., Higuchi, T., Goto, T., Miyano, S. Error tolerant model for incorporating biological knowledge with expression data in estimating gene networks. Statistical Methodology, 3(1):1-16, 2006.
  - Jeong, E., Miyano, S. A weighted profile based method for protein-RNA interacting residue prediction. Transactions on Computational Systems Biology. Lecture Notes in Computer Science. 3939: 123-139, 2006.
  - Li, C., Suzuki, S., Ge, Q.-W., Nakata, M., Matsuno, H., Miyano, S. Structural modeling and analysis of signaling pathways based on petri nets. J. Bioinf. Comput. Biol. 4(5):1119-1140, 2006. (On modeling and analyzing signaling pathways with inhibitory interactions based on Petri net. Extended abstract: Proc. The 2005 Internatinal Joint Conference of InCoB, AASBi and KSBI (BIOINFO2005), 348-353, 2005.).
  - 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. J. Bioinf. Comput. Biol.  4(1): 139-154, 2006. (Extended abstract: Matsuno, H., Inouye, S-T., Okitsu, Y., Fujii, Y., Miyano, S. Proc. The 3rd Asia-Pacific Bioinformatics Conference 2005, Imperial College Press.)
  - Matsuno, H., Li, C., Miyano, S. Petri net based description for systematic understanding of biological pathways. IEICE Trans. Fundamentals, E89-A (11): 3166-3174, 2006.
  - Nagasaki, M.*, Yamaguchi, R.*, Yoshida, R., Imoto, S., Doi, A., Tamada, Y., Matsuno, H., Miyano, S., Higuchi, T. Genomic data assimilation for estimating hybrid functional Petri net from time-course gene expression data. Genome Informatics. 17(1): 46-61, 2006. (* These authors equally contributed)
  - Nakamichi, R., Imoto, S., Miyano, S. Statistical model selection method to analyze combinatorial effects of SNPs and environmental factors for binary disease. International J. Artificial Intelligence Tools, 15(5), 711-724, 2006.
  - Okada, R., Sugii, M., Matsuno, H., Miyano, S. Machine learning prediction of amino acid patterns in protein N-myristoylation. Lecture Notes in Bioinformatics. 4146: 4-14, 2006. (2006 Workshop on Pattern Recognition In Bioinformatics (PRIB'06))
  - Saito, A., Nagasaki, M., Doi, A., Ueno, K., Miyano, S. Cell fate simulation model of gustatory neurons with microRNAs double-negative feedback loops by hybrid functional Petri net with extension. Genome Informatics. 17(1): 100-111, 2006.
  - Takei, Y., Kawakoshi, A., Tsukada, T., Yuge, S., Ogoshi, M., Inoue, K., Hyodo, S., Bannai, H., Miyano, S.  Contribution of comparative fish studies to general endocrinology: structure and function of some osmoregulatory hormones. J. Experimental Zoology. Part A, Comparative Experimental Biology. 305(9):787-798, 2006.
  - Tamada, Y., Imoto, S., Miyano, S. Estimating gene networks from gene expression data utilizing biological information. Proc. Inst. Statist. Math. 54(2): 333-356, 2006.
  - Tasaki, S., Nagasaki, M., Oyama, M., Hata, H., Ueno, K., Yoshida, R., Higuchi, T., Sugano, S., Miyano, S. Modeling and estimation of dynamic EGFR pathway by data assimilation approach using time series proteomic data. Genome Informatics. 17(2): 226-228, 2006.
  - Yoshida, R., Higuchi, T., Imoto, S., Miyano, S. ArrayCluster: an analytic tool for clustering, data visualization and module finder on gene expression profiles. Bioinformatics. 22(12):1538-1539, 2006.
  - Yoshida, R., Numata, K., Imoto, S., Nagasaki, M., Doi, A., Ueno, K., Miyano, S. A statistical framework for genome-wide discovery of biomarker splice variations with GeneChip Human Exon 1.0 ST arrays. Genome Informatics. 17(1): 88-99, 2006.

===== 2005 =====

  - 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. (Proc. 1st International Conference on Computational Science and Its Applications (Workshop on Data Mining and Bioinformatics)). 
  - Imoto, S., Matsuno, H., Miyano, S. Gene networks: estimation, modeling and simulation. in R. Eils and A. Kriete (Eds.), Computational Systems Biology, Academic Press, 205-228, 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.
  - 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.
  - 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.
  - 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.



===== 2004 =====

  - 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., Hyyrö, 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. 1(4): 159-170, 2004.  (Extended abstract: Bannai, H., Hyyrö, 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.)
  - 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., 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 Notes in Bioinformatics. 3082:149-160, 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., Hyyrö, 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 Notes 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: 95-104, 2004. (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. 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. IEEE Press. 73-78, 2004. 
  - 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., Miyano, S. Identification of novel adrenomedullin in mammals: a potent cardiovascular and renal regulator. FEBS Letters, 556:53-58, 2004.

===== 2003 =====

  - 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.
  - 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.
  - 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. Genomic Object Net: I. a platform for modeling and simulating biopathways. Applied Bioinformatics. 2(3):181-184, 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.

===== 2002 =====

  - 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.


===== 2001 =====

  - 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.

===== 2000 =====

  - 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.

===== 1999 =====

  - Akutsu, T., Miyano, S. On the approximation of protein threading. Theoretical Computer Science. 210:261-275, 1999. (Extended abstract: Proceedings of the First Annual International Conference on Research in Computational Molecular Biology. 3-8, 1997.)
  - Akutsu, T., Miyano, S., Kuhara, S. Identification of genetic networks from a small number of gene expression patterns under the boolean network model. Pacific Symposium on Biocomputing. 4:17-28, 1999.
  - Bannai, H., Miyano, S. A definition of discovery in terms of generalized descriptional complexity. Proceedings of Second International Conference on Discovery Science. Lecture Notes in Artificial Intelligence. 1721:316-318, 1999.
  - Maruyama, O., Uchida, T., Sim, K.L., Miyano, S. Designing views in HypothesisCreator: System for assisting in discovery. Proceedings of Second International Conference on Discovery Science. Lecture Notes in Artificial Intelligence. 1721:115-127, 1999. 
  - Moriyama, T., Shinohara, A., Takeda, M., Maruyama, O., Goto, T., Miyano, S., Kuhara, S. A system to find genetic networks using weighted network model. Genome Informatics. 10:186-195, 1999.
  - Nagasaki, M., Onami, S., Miyano, S., Kitano, H. Bio-calculus: its concept and molecular interaction. Genome Informatics. 10:133-143, 1999.
  - Yasuda, T.,  Bannai, H., Onami, S.,  Miyano, S., Kitano, H. Towards automatic construction of cell-linearge of C. elegans from Normarski DIC microscope images. Genome Informatics. 10:144-154, 1999.

===== 1998 =====

  - Akutsu, T., Maruyama, O., Miyano, S., Kuhara, S. A system for identifying genetic networks from gene expression patterns produced by gene disruptions and overexpressions. Genome Informatics. 9:151-160, 1998.
  - Maruyama, O., Uchida, T., Shoudai, T., Miyano, S. Toward Genomic Hypothesis Creator: View Designer for Discovery. Proceedings of First International Conference on Discovery Science. Lecture Notes in Artificial Intelligence. 1532:105-116, 1998. 
  - Noda, K., Shinohara, A., Takeda, M., Matsumoto, S., Miyano, S., Kuhara, S. Finding genetic network from experiments by weighted network model. Genome Informatics. 9:141-150, 1998.
  - Usuzaka, S., Sim, K.L., Tanaka, M., Matsuno, H., Miyano, S. A machine learning approach to reducing the work of experts in article selection from database: a case study for regulatory relations of S. cerevisiae genes in MEDLINE. Genome Informatics. 9:91-101, 1998.









===== 1997 - 1978 =====
  - Yamaguchi, A., Nakano, K., Miyano, S. An approximation algorithm for the minimum common supertree problem. Nordic J. Computing. 4(2):303-316, 1997.
  - Miyano, S. Genome Informatics: New Frontiers of Computer Science and Biosciences. Cooperative Databases and Applications (Advances Database Research and Development Series Vol. 7). Edited by Kambayashi, Y. and Yokota, K. (World Scientific). 12-21, 1997.
  - Furukawa, N., Matsumoto, S., Shinohara, A., Shoudai, T., Miyano, S. HAKKE: A multi-strategy prediction system for sequences. Genome Informatics. 7:98-107, 1996.
  - Maruyama, O., Miyano, S. Taking a walk on a graph. Mathematica Japonica. 43(3):595-606, 1996.
  - Maruyama, O., Miyano, S. Inferring a tree from walks. Theoretical Computer Science. 161(1-2):289-300, 1996.
  - Tateishi, E., Miyano, S. A greedy strategy for finding motifs from yes-no examples. Pacific Symposium on Biocomputing. 1:599-613, 1996.
  - Tateishi, E., Maruyama, O., Miyano, S. Extracting best consensus motifs from positive and negative examples. Proceedings of the 13th Annual Symposium on Theoretical Aspects of Computer Science. Lecture Notes in Computer Science. 1046:219-230, 1996.
  - Miyano, S. Learning theory towards genome informatics. IEICE Transactions on Information and Systems. E78-D(5):560-567, 1995. (Invited paper: Miyano, S. Learning theory towards genome informatics. Proc. 4th International Workshop on Algorithmic Learning Theory, Lecture Notes in Computer Science. 744: 19-36, 1993.)
  - Shimozono, S., Miyano, S. Complexity of finding alphabet indexing. IEICE Transactions on Information and Systems. E78-D(1):13-18, 1995.
  - Shoudai, T., Miyano, S. Using maximal independent sets to solve problems in parallel. Theoretical Computer Science. 148(1):57-65, 1995.
  - Uchida, T., Shoudai, T., Miyano, S. Parallel algorithms for refutation tree problem on elementary formal graph systems. IEICE Transactions on Information and Systems. E78-D(2):99-112, 1995.
  - Shoudai, T., Lappe, M., Miyano, S., Shinohara, A., Okazaki, T., Arikawa, S., Uchida, T., Shimozono, S., Shinohara, T., Kuhara, S. BONSAI Garden: parallel knowledge discovery system for amino acid sequences. Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology. AAAI Press. 359-366, 1995.
  - Miyano, S., Shimozono, S., Maruyama, O. Some algorithmic problems arising from genome informatics. Advances in Computing Techniques - Algorithms, Databases and Prallel Processing. World Scientific, 45-59, 1995.
  - Uchida, T., Shoudai, T., Miyano, S. Polynomial time algorithm solving the refutation tree problem for formal graph systems. Bulletin of Informatics and Cybernetics. 26(1-2):55-74, 1994. 
  - Arikawa, S., Kuhara, S., Miyano, S., Mukouchi, Y., Shinohara, A., Shinohara, T. A machine discovery from amino acid sequences by decision trees over regular patterns. New Generation Computing. 11(3):361-375, 1993.
  - Arikawa, S., Shinohara, T., Miyano, S., Shinohara, A. More about learning elementary formal systems. Proceedings of Second International Workshop on Nonmonotonic and Inductive Logic. Lecture Notes in Computer Science. 659:107-117, 1993.
  - Furuya, S., Miyano, S. NP-hard aspects in analogical reasoning. Bulletin of Informatics and Cybernetics. 25(3-4):155-159, 1993. 
  - Shimozono, S., Shinohara, A., Shinohara, T., Miyano, S., Kuhara, S., Arikawa, S. Finding alphabet indexing for decision trees over regular patterns: an approach to bioinformatical knowledge acquisition. Proceedings of the Twenty-Sixth Hawaii International Conference on System Sciences, Vol. I. IEEE Computer Society Press. 763-772, 1993.
  - Shimozono, S., Shinohara, A., Shinohara, T., Miyano, S., Kuhara, S., Arikawa, S. Knowledge acquisition from amino acid sequences by machine learning system BONSAI. Transactions on Information Processing Society of Japan. 35(10):2009-2018, 1993.
  - Shinohara, A., Shimozono, S., Uchida, T., Miyano, S. Kuhara, S., Arikawa, S. Running learning systems in parallel for machine discovery from sequences. Genome Informatics. 4:74-83, 1993.
  - Shoudai, T., Miyano, S. A parallel algorithm for the maximal co-hitting set problem. IEICE Transactions on Information and Systems. E76-D(2):296-298, 1993.
  - Uchida, T., Miyano, S. //O//(log*//n//) time parallel algorithm for computing bounded degree maximal subgraphs. Journal of Information Processing. 16(1):16-20, 1993.
  - Arikawa, S., Kuhara, S., Miyano, S., Shinohara, A., Shinohara, T. A learning algorithm for elementary formal systems and its experiments on identification of transmembrane domains. Proceedings of the Twenty-Fifth Hawaii International Conference on System Science, Vol. I. IEEE Computer Society Press. 675-684, 1992.
  - Arikawa, S., Miyano, S., Shinohara, A., Shimozono, S., Shinohara, T., Kuhara, S. Knowledge acquisition from amino acid sequences by learning algorithms. Proceedings of the Second Japanese Knowledge Acquisition for Knowledge-Based Systems Workshop. 109-128, 1992.
  - Arikawa, S., Miyano, S., Shinohara, A., Shinohara, T., Yamamoto, A. Algorithmic learning theory with elementary formal systems. IEICE Transactions on Information and Systems. E75-D(4):405-414, 1992.
  - Furuya, S., Miyano, S. NP-complete problems on label updating calculation in ATMS. Bulletin of Informatics and Cybernetics. 25(1-2):1-5, 1992.
  - Furuya, S., Miyano, S. Analogy is NP-hard. Proceedings of the Second Workshop on Algorithmic Learning Theory. 207-212, 1991.
  - Miyano, S. <html>&Delta;</html><sup>//p//</sup><sub>//2//</sub>complete lexicographcially first maximal subgraph problems. Theoretical Computer Science. 88(1):33-57, 1991.
  - Miyano, S., Shinohara, A., Shinohara, T. Which classes of elementary formal systems are polynomial-time learnable? Proceedings of the Second Workshop on Algorithmic Learning Theory. 139-150, 1991.
  - Shinohara, A., Miyano, S. Teachability in computational learning. New Generation Computing. 8(4):337-347, 1991.
  - Miyano, S. Systematized approaches to the complexity of subgraph problems. Journal of Information Processing. 13(4):442-448, 1990.
  - Arikawa, S., Haraguchi, M., Inoue, H., Kawasaki, Y., Miyahara, T., Miyano, S., Oshima, K., Sakai, H., Shinohara, T., Shiraishi, S., Takeda, M., Takeya, S., Yamamoto, A., Yuasa, H. The text database management system SIGMA: an improvement of the main engine. Proceedings of Berliner Informatik-Tage. 72-81, 1989.
  - Miyano, S. The lexicographically first maximal subgraph problems - P-completeness and NC algorithms. Mathematical Systems Theory. 22(1):47-73, 1989.
  - Miyano, S. A parallelizable lexicographically first edge-induced subgraph problem. Information Processing Letters. 27(2):75-78, 1988.
  - Miyano, S. Indexing alternating finite automata and binary tree like circuits. Bulletin of Informatics and Cybernetics. 23(1-2):79-88, 1988.
  - Miyano, S. Parallel complexity and P-complete problems. Proceedings of International Conference on Fifth Generation Computer Systems 1988. 532-541, 1988.
  - Hayashi, T., Miyano, S. Finite tree automata on infinite trees. Bulletin of Informatics and Cybernetics. 21(3-4):71-82, 1985.
  - Miyano, S. Remarks on two-way automata with weak-counters. Information Processing Letters. 18(2):105-107, 1984.
  - Miyano, S., Hayashi, T. Alternating finite automata on <html>&omega;</html>-words. Theoretical Computer Science. 32(3):321-330, 1984.
  - Miyano, S. Remarks on multihead pushdown automata and multihead stack automata. Journal of Computer and System Sciences. 27(1):116-124, 1983.
  - Miyano, S. Two-way deterministic multi-weak-counter machines. Theoretical Computer Science. 21(1):27-32, 1982.
  - Miyano, S. A hierarchy theorem for multihead stack-counter automata. Acta Informatica. 17(1):63-67, 1982.
  - Miyano, S., Haraguchi, M. Recovery of incomplete tables under functional dependencies. Bulletin of Informatics and Cybernetics. 20(1-2):25-41, 1982.
  - Miyano, S. One-way weak-stack-counter automata. Journal of Computer and System Sciences. 20(1):59-76, 1980.
  - Miyano, S. On a lower bound of Shepherdson function. Memoirs of the Faculty of Science, Kyushu University, Ser. A. 33(2):257-267, 1979.
  - Hirokawa, S., Miyano, S. A note on the regularity of fuzzy languages. Memoirs of the Faculty of Science, Kyushu University, Ser. A. 32(1):61-66, 1978.
  - Miyano, S. On an automaton which recognizes a family of automata. Memoirs of the Faculty of Science, Kyushu University, Ser. A. 32(1):37-51, 1978.
====== Book Chapter ======
  - Imoto, S., Tamada, Y., Araki, H., Miyano, S. Computational Drug Target Pathway Discovery: A Bayesian Network Approach. in H. Lu, B. Schokop, H. Zhao (Eds.), Handbook of Computational Statistics: Statistical Bioinformatics, Springer. In press.
  - Fujita, A., Sato, J.R., Demasi, M.A.A., Miyano, S., Sogayar, M.C., Ferreira, C.E. An introduction to time-varying connectivity estimation for gene regulatory networks. Frank Emmert-Streib; Matthias Dehmer. (Org.). Medical Biostatistics for complex diseases. Weinheim, Germany: Wiley VCH Verlag, p.205-230, 2010.
  - Mitou, N., Matsuno, H., Miyano, S., Inouye, S. Essential role of Ror gene in the interaction of feedback loops in mammalian circadian clocks. In press.
  - Saito, A., Nagasaki, M., Miyano, S. Hybrid functional Petri net with extension for dynamic pathway modeling. In press.
  - 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. (Target Discovery and Validation, Volume 1, 33-56, 2007 (a volume of "Methods in Molecular Biology" series), Walker, J. and Sioud, M. (Eds.), Humana Press, USA.).
  - Imoto, S., Miyano, S. Bayesian network approach to estimate gene networks. A. Mittal, A. Kassim and T. Tan (Eds.), Bayesian Network Technologies: Applications and Graphical Models, Idea Group Publishers, USA. 269-299, 2007. (Refereed book chapter).
  - 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.
  - 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.
  - 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.
  - Miyano, S. Genome Informatics: New Frontiers of Computer Science and Biosciences. Cooperative Databases and Applications (Advances Database Research and Development Series Vol. 7). edited by Kambayashi, Y. and Yokota, K. (World Scientific), 12-21, 1997.



====== 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]]
  - 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.
  - Miyano, S. "Parallel Algorithms - Theory and Design" (in Japanese). Kindai kagaku sha Co. Ltd., 1993. 
  - Arikawa, S., Miyano, S. "Automata and Computability" (in Japanese). Baifukan Co. Ltd., 1986.

====== Editions ======
  - Ferreira, C.E., Miyano, S., Stadler, P.F. (Eds.) Advances in Bioinformatics and Computational Biology, Springer, 2010.
  - DeLisi, C., Kanehisa, M., Miyano, S., Mohr, S., Wallach, I. (Eds.) Genome Informatics. 22. Imperial College Press, London, 2009.
  - Brazma, A., Miyano, S., Akutsu, T. Proceedings of the 6th Asia-Pacific Bioinformatics Conference (APBC 2008).Imperial College Press, 2008. [[http://www.worldscibooks.com/lifesci/p544.html|Link]]
  - Knapp, E.-W., Benson, G., Holzhütter, H.-G., Kanehisa, M., Miyano, S. (Eds.) Genome Informatics. 20, 2008. [[http://www.jsbi.org/modules/journal1/index.php/GI20.html|Link]]
  - Miyano, S., DeLisi, C., Holzhütter, H.-G., Kanehisa, M. (Eds.) Genome Informatics. 18, 2007. [[http://www.jsbi.org/modules/journal1/index.php/GI18.html|Link]]
  - Sakakibara, Y., Smith, T.F., Kanehisa, M., Miyano, S., Takagi, T. (Eds.) Genome Informatics. 17(2), 2006. [[http://www.jsbi.org/modules/journal1/index.php/GI17_2.html|Link]]
  - DeLisi, C., Kanehisa, M., Heinrich, R., Miyano, S. (Eds.) Genome Informatics. 17(1), 2006. [[http://www.jsbi.org/modules/journal1/index.php/GI17_1.html|Link]]
  - Miyano, S. (Ed.) Special RECOMB 2005 Issue. J. Comp. Biol. 13(2), 2006. 
  - Heinrich, R., Mamitsuka, H., Kanehisa, M., Miyano, S., Takagi, T. (Eds.). Genome Informatics 16(2), 2005. [[http://www.jsbi.org/modules/journal1/index.php/GI16_2.html|Lionk]]
  - Heinrich, T., DeLisi, C., Kanehisa, M., Miyano, S. (Eds.). Genome Informatics 16(1), 2005. [[http://www.jsbi.org/modules/journal1/index.php/GI16_1.html|Link]]
  - Miyano, S., Mesirov, J.P., Kasif, S., Istrail, S., Pevzner, P.A., Waterman, M.S. (Eds.) Proc. 9th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2005), Lecture Notes in Bioinformatics (Springer). Vol. 3500, 2005. [[http://www.springer.com/computer/foundations/book/978-3-540-25866-7|Link]]
  - Akutsu, T., Brusic, V., Miyano, S., Takagi, T., Kanehisa, M. (Eds.) Genome Informatics. 15(2), 2004. [[http://www.jsbi.org/modules/journal1/index.php/GI15_2.html|Link]]
  - Mamitsuka, H., Smith, T.F., Holzhütter, H-G., Kanehisa, M., DeLisi, C., Heinrich, R,  Miyano, S. (Eds.). Genome Informatics. 15(1), 2004. [[http://www.jsbi.org/modules/journal1/index.php/GI15_1.html|Link]]
  - Gribskov, M., Kanehisa, M., Miyano, S., Takagi, T. (Eds.). Genome Informatics. 14, 2003. [[http://www.jsbi.org/modules/journal1/index.php/GI14.html|Link]]
  - Lathrop, R., Nakai, K., Miyano, S., Takagi, T., Kanehisa, M. (Eds.). Genome Informatics. 13, 2002. [[http://www.jsbi.org/modules/journal1/index.php/GI13.html|Link]]
  - Matsuda, H., Miyano, S., Takagi, T., Wong, L. (Eds.) Genome Informatics. 12, 2001. [[http://www.jsbi.org/modules/journal1/index.php/GI12.html|Link]]
  - Dunker, A.K., Konagaya, A., Miyano, S., Takagi, T.  (Eds.) Genome Informatics. 11, 2000. [[http://www.jsbi.org/modules/journal1/index.php/GI11.html|Link]]
  - Asai, K., Miyano, S., Takagi, T. (Eds.) Genome Informatics. 10, 1999. [[http://www.jsbi.org/modules/journal1/index.php/GI10.html|Link]]
  - Miyano, S., Takagi, T. (Eds.) Genome Informatics. 9, 1998. [[http://www.jsbi.org/modules/journal1/index.php/GI09.html|Link]]
  - Miyano, S., Takagi, T. (Eds.) Genome Informatics. 8, 1997. [[http://www.jsbi.org/modules/journal1/index.php/GI08.html|Link]]
  - Akutsu, T., Asai, K., Hagiya, M., Kuhara, S., Miyano, S. and Nakai, K. (Eds.) Genome Informatics. 7, 1996. [[http://www.jsbi.org/modules/journal1/index.php/GI06.html|Link]]
  - Asano, T., Igarashi, Y., Nagamochi, H., Miyano, S., Suri, S. Proc. 7th International Symposium on Algorithms and Computation (ISAAC '96), Lecture Notes in Computer Science. Vol. 1178, 1996. [[http://www.springer.com/computer/foundations/book/978-3-540-62048-8|Link]]
  - Hagiya, M., Miyano, S., Nakai, K., Suyama, A., Yokomori, T., Takagi, T. (Eds.) Genome Informatics. 6, 1995. [[http://www.jsbi.org/modules/journal1/index.php/GI06.html|Link]]
  - Miyano, S., Akutsu, T., Imai, H., Gotoh, O., Takagi, T. (Eds.) Genome Informatics. 5, 1994. [[http://www.jsbi.org/modules/journal1/index.php/GI05.html|Link]]
  - Takagi, T., Imai, H., Miyano, S.,  Mitaku, S., Kanehisa, M. (Eds.) Genome Informatics. 4, 1993. [[http://www.jsbi.org/modules/journal1/index.php/GI04.html|Link]]