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An approximately unbiased test of phylogenetic tree selection.
Shimodaira H. Shimodaira H. Syst Biol. 2002 Jun;51(3):492-508. doi: 10.1080/10635150290069913. Syst Biol. 2002. PMID: 12079646
The AU test, like the Shimodaira-Hasegawa (SH) test, adjusts the selection bias overlooked in the standard use of the bootstrap probability and Kishino-Hasegawa tests. ...
The AU test, like the Shimodaira-Hasegawa (SH) test, adjusts the selection bias overlooked in the standard use of the bootstrap proba …
Pvclust: an R package for assessing the uncertainty in hierarchical clustering.
Suzuki R, Shimodaira H. Suzuki R, et al. Among authors: shimodaira h. Bioinformatics. 2006 Jun 15;22(12):1540-2. doi: 10.1093/bioinformatics/btl117. Epub 2006 Apr 4. Bioinformatics. 2006. PMID: 16595560
Evaluating hypotheses on the origin and evolution of the New Zealand alpine cicadas (Maoricicada) using multiple-comparison tests of tree topology.
Buckley TR, Simon C, Shimodaira H, Chambers GK. Buckley TR, et al. Among authors: shimodaira h. Mol Biol Evol. 2001 Feb;18(2):223-34. doi: 10.1093/oxfordjournals.molbev.a003796. Mol Biol Evol. 2001. PMID: 11158381
Therefore, we examined the stability of the inferred phylogenetic placement of these two species using the newly developed Shimodaira-Hasegawa test (SH test) implemented in a maximum-likelihood framework. ...
Therefore, we examined the stability of the inferred phylogenetic placement of these two species using the newly developed Shimodaira
Appropriate likelihood ratio tests and marginal distributions for evolutionary tree models with constraints on parameters.
Ota R, Waddell PJ, Hasegawa M, Shimodaira H, Kishino H. Ota R, et al. Among authors: shimodaira h. Mol Biol Evol. 2000 May;17(5):798-803. doi: 10.1093/oxfordjournals.molbev.a026358. Mol Biol Evol. 2000. PMID: 10779540
., H(0): homogeneous site rates, and H(1): site rates follow a gamma distribution with variance 1/k, then asymptotically as sequence length increases, the distribution under H(0) becomes a mixture of chi distributions, in this case 50% chi(0), and 50% chi(1) …
., H(0): homogeneous site rates, and H(1): site rates follow a gamma distribution with variance 1/k, then asymptotically as se …
Consistency of SINE insertion topology and flanking sequence tree: quantifying relationships among cetartiodactyls.
Lum JK, Nikaido M, Shimamura M, Shimodaira H, Shedlock AM, Okada N, Hasegawa M. Lum JK, et al. Among authors: shimodaira h. Mol Biol Evol. 2000 Oct;17(10):1417-24. doi: 10.1093/oxfordjournals.molbev.a026242. Mol Biol Evol. 2000. PMID: 11018149
CONSEL: for assessing the confidence of phylogenetic tree selection.
Shimodaira H, Hasegawa M. Shimodaira H, et al. Bioinformatics. 2001 Dec;17(12):1246-7. doi: 10.1093/bioinformatics/17.12.1246. Bioinformatics. 2001. PMID: 11751242
This p-value is less biased than the other conventional p-values such as the Bootstrap Probability (BP), the Kishino-Hasegawa (KH) test, the Shimodaira-Hasegawa (SH) test, and the Weighted Shimodaira-Hasegawa (WSH) test. ...
This p-value is less biased than the other conventional p-values such as the Bootstrap Probability (BP), the Kishino-Hasegawa (KH) test, the …
A scale-free structure prior for graphical models with applications in functional genomics.
Sheridan P, Kamimura T, Shimodaira H. Sheridan P, et al. Among authors: shimodaira h. PLoS One. 2010 Nov 5;5(11):e13580. doi: 10.1371/journal.pone.0013580. PLoS One. 2010. PMID: 21079769 Free PMC article.
PAFit: A Statistical Method for Measuring Preferential Attachment in Temporal Complex Networks.
Pham T, Sheridan P, Shimodaira H. Pham T, et al. Among authors: shimodaira h. PLoS One. 2015 Sep 17;10(9):e0137796. doi: 10.1371/journal.pone.0137796. eCollection 2015. PLoS One. 2015. PMID: 26378457 Free PMC article.
Joint estimation of preferential attachment and node fitness in growing complex networks.
Pham T, Sheridan P, Shimodaira H. Pham T, et al. Among authors: shimodaira h. Sci Rep. 2016 Sep 7;6:32558. doi: 10.1038/srep32558. Sci Rep. 2016. PMID: 27601314 Free PMC article.
Cross-validation of matching correlation analysis by resampling matching weights.
Shimodaira H. Shimodaira H. Neural Netw. 2016 Mar;75:126-40. doi: 10.1016/j.neunet.2015.12.007. Epub 2015 Dec 22. Neural Netw. 2016. PMID: 26775131
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