ISI Science Citation Index 2010-01-08 (with google scholar in parentheses)

1. 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.
2. 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) .
3. 440 times (438). H. Shimodaira (2002). An approximately unbiased test of phylogenetic tree selection, Systematic Biology, 51, 492-508.
4. 131 times (182). M.Tanaka et al. (2004).  Mitochondrial Genome Variation in Eastern Asia and the Peopling of Japan, Genome Research, 14, 1832-1850.
5. 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.
6. 53times (67). R. Suzuki and H. Shimodaira (2006). pvclust: an R package for assessing the uncertainty in hierarchical clustering, Bioinformatics, 22, 1540-1542.
7. 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.
8. 35 times (52). H. Shimodaira (2004). Approximately unbiased tests of regions using multistep-multiscale bootstrap resampling, Annals of Statistics, 32, 2616-2641.
9. 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.

過去の被引用回数　ISI Science Citation Index (2009/01/07)

1. 1421回　H. Shimodaira and M. Hasegawa (1999). Multiple comparisons of log-likelihoods with applications to phylogenetic inference, Molecular Biology and Evolution, 16, 1114-1116. Shimodaira-Hasegawa testの論文です．
2. 330回　H. Shimodaira and M. Hasegawa (2001). CONSEL: for assessing the confidence of phylogenetic tree selection, Bioinformatics, 17, 1246-1247. ISI New Hot Papers (2003-07) にコンピュータサイエンス部門で選ばれました．
3. 327回　H. Shimodaira (2002). An approximately unbiased test of phylogenetic tree selection, Systematic Biology, 51, 492-508.
4. 98回　M.Tanaka et al. (2004).  Mitochondrial Genome Variation in Eastern Asia and the Peopling of Japan, Genome Research, 14, 1832-1850.
5. 47回　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.
6. 45回　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.

• 中野馨, 廣田誠, 下平英寿, 衛作人, 銅谷賢治　編著 (1992). Cでつくる脳の情報システム, 啓学出版（近代科学社から1995年に再出版）.
• 下平英寿 (1993). モデルの信頼集合と地図によるモデル探索, 統計数理, 41, 131-147.　[PDF] Shimodaira-Hasegawa testの原形を提案しました．
• 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. Shimodaira-Hasegawa testを提案しました．
• H. Shimodaira and M. Hasegawa (1999). Multiple comparisons of log-likelihoods with applications to phylogenetic inference, Molecular Biology and Evolution, 16, 1114-1116. 下平(1993)，Shimodaira (1998)の方法を分子系統樹推定に用いることを提唱しました．この手法はShimodaira-Hasegawa testと後ほど呼ばれるようになり，国際的な標準手法として定着しつつあります．
• 下平英寿 (1999). モデル選択理論の新展開, 統計数理, 47, 3-27. [PDF]
• 下平英寿 (1999). 統計的仮説検定は有効か？, 日本統計学会会報, 100, 12-15.
• 下平英寿 (1999). 信頼集合と予測分布地図による統計的モデル選択の診断法, 計測と制御, 38, 433-438.
• H. Shimodaira (2000). Improving predictive inference under covariate shift by weighting the log-likelihood function, Journal of Statistical Planning and Inference, 90, 227-244. [ソフトウエア]
• 金森敬文, 下平英寿 (2000). 重み付き最尤推定量の情報量規準を用いた能動学習の最適化, 統計数理, 48, 197-212.
• 下平英寿 (2000). ゲノムの統計解析（５）モデル選択のバラツキを評価する, ESTRELA, 80, 76-80.
• 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) ラオ先生，とても元気でした．
• H. Shimodaira and M. Hasegawa (2001). CONSEL: for assessing the confidence of phylogenetic tree selection, Bioinformatics, 17, 1246-1247. [ソフトウエア] マルチスケール・ブートストラップ法のソフトウエアに関する論文です．アルゴリズム・理論の論文よりまずこれが最初にpublishされました．
• 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. マルチスケール・ブートストラップ法のアルゴリズムを最初に提案した論文．統計の方法論の論文だが，生物系の雑誌でまずpublishされた．
• 下平英寿 (2002). ブートストラップ法によるクラスタ分析のバラツキ評価, 統計数理, 50, 33-44. [PDF]
• 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.
• 下平英寿 (2002). データからの「発見」と新しいブートストラップ法，数理科学, 474, 14-20.
• 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.
• 下平英寿 (2004). 情報量規準によるモデル選択とその信頼性評価, モデル選択 ─ 予測・検定・推定の交差点, 統計科学のフロンティア 3, 岩波書店.
• H. Shimodaira (2004). Approximately unbiased tests of regions using multistep-multiscale bootstrap resampling, Annals of Statistics, 32, 2616-2641. [PDF] [この方法論のページ] マルチスケール・ブートストラップ法とその拡張に関する理論を与える論文です．
• 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. Simodaira 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]
• 下平英寿 (2007). モデル選択とブートストラップ，赤池情報量規準 AIC ― モデリング・予測・知識発見，共立出版．
• H. Shimodaira (2008). Testing Regions with Nonsmooth Boundaries via Multiscale Bootstrap, Journal of Statistical Planning and Inference, 138, 1227-1241. http://dx.doi.org/10.1016/j.jspi.2007.04.001
• 下平英寿　(2008)．ブートストラップ，書籍 21世紀の統計科学３ （第III部 第８章）， 東京大学出版会．
• T. Kanamori and H. Shimodaira (2008). Geometry of Covariate Shift with Applications to Active Learning, Dataset Shift in Machine Learning (eds. J. Quinonero-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.
• 下平英寿 (2008). 滑らかでない境界をもつ領域のためのマルチスケール・ブートストラップ法の理論と実装, 統計数理, 56, 3-18. [PDF]
• 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