Publications

• H. Shimodaira (1993). A model search technique based on confidence set and map of models, Proc. Inst. Statist. Math., 41, 131-147. (in Japanese)
• H. Shimodaira (1994). A new criterion for selecting models from partially observed data, Selecting Models from Data: AI and Statistics IV (eds. P. Cheeseman and R. W. Oldford), Lecture Notes in Statistics, 89, 21-30, Springer-Verlag.
• H. Shimodaira (1997). Assessing the error probability of the model selection test, Annals of the Institute of Statistical Mathematics, 49, 395-410.
• H. Shimodaira (1998). An application of multiple comparison techniques to model selection, Annals of the Institute of Statistical Mathematics, 50, 1-13.
• H. Shimodaira and M. Hasegawa (1999). Multiple comparisons of log-likelihoods with applications to phylogenetic inference, Molecular Biology and Evolution, 16, 1114-1116.
• H. Shimodaira (1999). Recent Developments in Model Selection Theory, Proc. Inst. Statist. Math., 47, 3-27. (in Japanese)
• H. Shimodaira (1999). Is statistical hypothesis testing useful?, Newsletters of Japan Statistical Society, 100, 12-15. (in Japanese)
• H. Shimodaira (1999). Diagnostics for statistical model selection using the confidence set and predictive density map, Journal of the Society of Instrument and Control Engineers, 38, 433-438. (in Japanese)
• H. Shimodaira (2000). Improving predictive inference under covariate shift by weighting the log-likelihood function, Journal of Statistical Planning and Inference, 90, 227-244. [SOFTWARE]
• T. Kanamori, and H. Shimodaira (2000). An active learning algorithm using an information criterion for the maximum weighted log-likelihood estimator, Proc. Inst. Statist. Math., 48, 197-212. (in Japanese)
• H. Shimodaira (2000). Statistical analysis in genomics (5) Assessing the uncertainty in model selection, ESTRELA, 80, 76-80. (in Japanese)
• J. K. Lum, M. Nikaido, M. Shimamura, H. Shimodaira, A. M. Shedlock, N. Okada, and M. Hasegawa (2000). Consistency of SINE insertion topology and flanking sequence tree: Quantifying relationships among cetartiodactyls, Molecular Biology and Evolution, 17, 1417-1424.
• R. Ota, P. Waddell, M. Hasegawa, H. Shimodaira, and H. Kishino (2000). Appropriate likelihood ratio tests and marginal distributions for evolutionary tree models with constraints on parameters, Molecular Biology and Evolution, 17, 798-803.
• T. Buckley, C. Simon, H. Shimodaira, and G. Chambers (2001). Evaluating hypotheses on the origin and evolution of the New Zealand alpine cicadas (Maoricicada) using multiple-comparison tests of tree topology, Molecular Biology and Evolution, 18, 223-234.
• H. Shimodaira (2001). Multiple comparisons of log-likelihoods and combining nonnested models with applications to phylogenetic tree selection, Communications in Statistics, Part A-Theory and Methods, 30, 1751-1772. (Special Issue in Honor of the 80th Birthday of CR Rao)
• H. Shimodaira and M. Hasegawa (2001). CONSEL: for assessing the confidence of phylogenetic tree selection, Bioinformatics, 17, 1246-1247. [SOFTWARE]
• S. Kuriki, H. Shimodaira, and T. Hayter (2002). On the isotonic range statistic for testing against an ordered alternative, Journal of Statistical Planning and Inference, 105, 347-362.
• H. Shimodaira (2002). An approximately unbiased test of phylogenetic tree selection, Systematic Biology, 51, 492-508.
• H. Shimodaira (2002). Assessing the uncertainty of the cluster analysis using the bootstrap resampling, Proc. Inst. Statist. Math., 50, 33-44. (in Japanese)
• S.Imoto, S.Kim, H.Shimodaira, S.Aburatani, K.Tashiro, S.Kuhara, S.Miyano (2002). Bootstrap Analysis of Gene Networks Based on Byesian Networks and Nonparametric Regression, Genome Informatics, 13, 369-370.
• H. Shimodaira (2003). "Discovery" from data and a novel bootstrap method, Suuri-kagaku, 474, 14-20. (in Japanese)
• T. Kamimura, H. Shimodaira, S. Imoto, S. Kim, K. Tashiro, S. Kuhara, S. Miyano (2003). Multiscale Bootstrap Analysis of Gene Networks Based on Bayesian Networks and Nonparametric Regression, Genome Informatics, 14, 350-351.
• T. Kanamori and H. Shimodaira (2003). Active learning algorithm using the maximum weighted log-likelihood estimator, Journal of Statistical Planning and Inference, 116, 149-162.
• H. Shimodaira (2003). Asymptotic analysis of the bootstrap methods. Mathematica notebook document. Department of Mathematical and Computing Sciences, Tokyo Institute of Technology, Tokyo, Japan. (Available in HTML, PDF, and Mathematica Notebook.)
• H. Shimodaira (2004). Technical details of the multistep-multiscale bootstrap resampling. Research Reports B-403. Department of Mathematical and Computing Sciences, Tokyo Institute of Technology, Tokyo, Japan. [PDF]
• Y. Yamamoto, H. Nakada, H. Shimodaira and S. Matsuoka (2004). Parallelization of phylogenetic tree inference using Grid technologies, Proceedings of the First International Workshop on Life Science Grid (LSGRID 2004), 109 - 122.
• H. Shimodaira (2004). Information theoretic model selection and its confidence evaluation (in Japanese), a book in the series of Frontier of Statistical Science, Iwanami-Shoten.
• H. Shimodaira (2004). Approximately unbiased tests of regions using multistep-multiscale bootstrap resampling, Annals of Statistics, 32, 2616-2641. [PDF] [SUPPLEMENT]
• M.Tanaka, V. M. Cabrera, A. M. Gonzalez, J. M. Larruga, T. Takeyasu, N. Fuku, L. J. Guo, R. Hirose, Y. Fujita, M. Kurata, K. Shinoda, K. Umetsu, Y. Yamada, Y. Oshida, Y. Sato, N. Hattori, Y. Mizuno, Y. Arai, N. Hirose, S. Ohta, O. Ogawa, Y. Tanaka, R. Kawamori, M. Nagai, W. Maruyama, H. Shimokata, R. Suzuki and H. Shimodaira (2004).  Mitochondrial Genome Variation in Eastern Asia and the Peopling of Japan, Genome Research, 14, 1832-1850.
• H. Shimodaira and M. Hasegawa (2005). Assessing the uncertainty in phylogenetic inference, Statistical Methods in Molecular Evolution (ed. R. Nielsen), Statistics for Biology and Health, Springer Verlag, 463-492.
• R. Suzuki and H. Shimodaira (2006). pvclust: an R package for assessing the uncertainty in hierarchical clustering, Bioinformatics, 22, 1540-1542. [SOFTWARE]
• T. Nagashima, H. Shimodaira, K. Ide, T. Nakakuki, Y. Tani, K. Takahashi, N. Yumoto and M. Hatakeyama (2007). Quantitative transcriptional control of ERBB receptor signaling undergoes graded to biphasic response for cell differentiation, Journal of Biological Chemistry, 282, 4045-4056 [journal website]
• H. Shimodaira (2008). Testing Regions with Nonsmooth Boundaries via Multiscale Bootstrap, Journal of Statistical Planning and Inference, 138, 1227-1241, 2008. http://dx.doi.org/10.1016/j.jspi.2007.04.001
• T. Kanamori and H. Shimodaira (2008). Geometry of Covariate Shift with Applications to Active Learning, Dataset Shift in Machine Learning (eds. J. Quiñonero-Candela, M. Sugiyama, A. Schwaighofer and N. D. Lawrence), Neural Information Procesing Series, MIT Press, 87-105 (Chapter 6).
• P. Sheridan, Y. Yagahara, and H. Shimodaira (2008). A preferential attachment model with Poisson growth for scale-free networks, Annals of the Institute of Statistical Mathematics, 60, 747-761.
• H. Shimodaira (2010). Frequentist and Bayesian measures of confidence via multiscale bootstrap for testing three regions, Annals of the Institute of Statistical Mathematics, 62, 189-208. (Special issue in honor of Dr. Hirotugu Akaike)
• P. Sheridan, T. Kamimura, H. Shimodaira (2010). A scale-free structure prior for graphical models with applications in functional genomics, PLoS ONE, 5(11), e13580. doi:10.1371/journal.pone.0013580

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