Contact

- Hidetoshi Shimodaira, Ph. D.
- Associate Professor
- Department of Mathematical and Computing Sciences
- Tokyo Institute of Technology
- 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8552, Japan.

- shimo (a) is.titech.ac.jp
- http://www.is.titech.ac.jp/~shimo/

- 1990 B.S. Degree in Engineering, Department of Mathematical Engineering and Information Physics, University of Tokyo
- 1992 M.S. Degree in Engineering, Department of Mathematical Engineering and Information Physics, University of Tokyo
- 1995 Ph.D. Degree in Engineering, Department of Mathematical Engineering and Information Physics, University of Tokyo

- 1995-1996 Research Fellow of the Japan Society for the Promotion of Science at
**University of Tokyo** - 1995-1996 Visiting Scholar at Department of Genetics,
**University of Washington**(post-doc at Felsenstein laboratory) - 1996-2002 Assistant Professor (joshu) at
**The Institute of Statistical Mathematics** - 1999-2001 Visiting Scholar at Department of Statistics,
**Stanford University**(Brad Efron) - 2002-2005 Lecturer at Department of Mathematical and Computing Sciences,
**Tokyo Institute of Technology** - 2005-present Associate Professor at Department of Mathematical and Computing Sciences,
**Tokyo Institute of Technology**

**ISI New Hot Papers (Computer Science 2003-07)**for H. Shimodaira and M. Hasegawa (2001). CONSEL: for assessing the confidence of phylogenetic tree selection,*Bioinformatics,*17, 1246-1247.**Tokyo Tech Award for Challenging Research (2004)**for "Highly accurate resampling methods and applications to Bioinformatics".**Fujino Prize, Tejima Seiichi Commemorative Foundation (2005).****Young Scientist Award by Ministry of Education, Culture, Sports, Science and Technology of Japan (2006).****SICE (Society of Instrument and Control Engineers) Award for Publication (2008) jointly to Akaike, Amari, Kitagawa, Kabashima, Shimodaira, Murota, and Tsuchiya.****Japanese Statitical Society Award for Research (2010).**

**1678 times (1640). H. Shimodaira and M. Hasegawa (1999). Multiple comparisons of log-likelihoods with applications to phylogenetic inference,***Molecular Biology and Evolution,*16, 1114-1116.**440 times (455). H. Shimodaira and M. Hasegawa (2001). CONSEL: for assessing the confidence of phylogenetic tree selection,***Bioinformatics,*17, 1246-1247.**ISI New Hot Papers in Computer Science (2003) .****440 times (438). H. Shimodaira (2002). An approximately unbiased test of phylogenetic tree selection,***Systematic Biology,*51, 492-508.**131 times (182).**M.Tanaka et al. (2004). Mitochondrial Genome Variation in Eastern Asia and the Peopling of Japan,*Genome Research,***14**, 1832-1850.**56 times (58).**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.**53times (67).****R. Suzuki and H. Shimodaira (2006). pvclust: an R package for assessing the uncertainty in hierarchical clustering,***Bioinformatics,*22, 1540-1542.**50 times (54).**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.**35 times (52). H. Shimodaira (2004). Approximately unbiased tests of regions using multistep-multiscale bootstrap resampling,***Annals of Statistics*, 32, 2616-2641.**32 times (111). H. Shimodaira (2000). Improving predictive inference under covariate shift by weighting the log-likelihood function,***Journal of Statistical Planning and Inference,*90, 227-244.

**1421 times. H. Shimodaira and M. Hasegawa (1999). Multiple comparisons of log-likelihoods with applications to phylogenetic inference,***Molecular Biology and Evolution,*16, 1114-1116.**330 times. H. Shimodaira and M. Hasegawa (2001). CONSEL: for assessing the confidence of phylogenetic tree selection,***Bioinformatics,*17, 1246-1247.**ISI New Hot Papers in Computer Science (2003) .****327 times. H. Shimodaira (2002). An approximately unbiased test of phylogenetic tree selection,***Systematic Biology,*51, 492-508.**98 times.**M.Tanaka et al. (2004). Mitochondrial Genome Variation in Eastern Asia and the Peopling of Japan,*Genome Research,***14**, 1832-1850.**47 times.**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.**45 times.**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.

- 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