Bayes empirical bayes inference of amino acid sites under positive selection.

By Ziheng Yang, Wendy S. W. Wong, Rasmus Nielsen. Molecular biology and evolution, 2005

2,264 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/f9f27bee818c3ae23e943201ef27c60fed062558

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In Molecular Biology

Citations in the corpus

A random effects branch-site model for detecting episodic diversifying selection. (2011, background): “Sixth, naive, or Bayes empirical Bayes approaches developed for rBS for detecting individual sites subject to episodic diversifying selection (Yang et al. 2005), need to be adapted to and evaluated in the context of uBS.”
EasyCodeML: A visual tool for analysis of selection using CodeML (2019, positive): “These models can be used to identify signals of episodic selection occurring along a specified branch after gene duplication (Yang & Nielsen, 2002; Zhang, Nielsen, & Yang, 2005).”
Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. (2005, methodology): “For a discussion of the Bayesian and frequentist measures of performance in detecting positively selected sites, see Yang, Wong, and Nielsen (2005), who also demonstrated that the BEB procedure had excellent frequentist properties in site-based analysis.”
Mutations in smooth muscle α-actin (ACTA2) lead to thoracic aortic aneurysms and dissections (2007, background): “Using Bayesian estimates of the probability of positive selection for each codon in these six protein”
Class of multiple sequence alignment algorithm affects genomic analysis. (2013, methodology): “Sites above a BEB cutoff of > 0.5 were regarded to correspond to positive selection (Yang et al. 2005).”
INDELible: A Flexible Simulator of Biological Sequence Evolution (2009, methodology): “Although the branch-site model described by Yang et al. (2005) allows only two types of branches (the foreground and background branches) and four site classes, INDELible allows an arbitrary number of site classes and branch types.”
Distinguishing importation from diversification of quinolone-resistant Neisseria gonorrhoeae by molecular evolutionary analysis (2007, methodology): “We applied the empirical Bayesian approach [42] to identify the potential sites under diversifying selection as indicated by a posterior probability (pP) > 0.”
PAML 4: phylogenetic analysis by maximum likelihood. (2007, background): “genes or proteins in extinct ancestors on a phylogeny ( Yang et al. 1995; Koshi and Goldstein 1996).”
Three Members of the 6-cys Protein Family of Plasmodium Play a Role in Gamete Fertility (2010, methodology): “berghei genes are under positive selection we performed a Bayes Empirical Bayes analysis (BEB; [49]).”
Survey of Branch Support Methods Demonstrates Accuracy, Power, and Robustness of Fast Likelihood-based Approximation Schemes (2011, background): “Alternatively, using a branch length prior with higher weighting for near-zero values has been suggested (Yang et al. 2005; Yang 2007).”
Selecton 2007: advanced models for detecting positive and purifying selection using a Bayesian inference approach (2007, background): “Recently two alternatives have been proposed: the full Bayesian estimation (32) and the hierarchical Bayesian estimation (33).”