Separation of phylogenetic and functional associations in biological sequences by using the parametric bootstrap.

By K. Wollenberg, W. Atchley. 2000

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Citations in the corpus

Direct-coupling analysis of residue coevolution captures native contacts across many protein families (2011, background): “The problem has been discussed extensively in the literature (10, 23-26).”
Using multiple interdependency to separate functional from phylogenetic correlations in protein alignments (2003, background): “Methods to find constrained regions in the alignment (Aimon et al., 2002) or to find correlations between sites (Shindyalov et al., 1994; Pollock et al., 1999; Atchley et al., 2000; Wollenberg and Atchley, 2000) assume a phylogeny and substitution model.”
Using inferred residue contacts to distinguish between correct and incorrect protein models (2008, background): “…effects of sample size or skewed phylogeny by performing many randomized trials, recalculating the test statistic of covariation and comparing the resulting distribution with the observed value (Korber et al., 1993; Noivirt et al., 2005; Shackelford and Karplus, 2007; Wollenberg and Atchley, 2000).”
Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction (2008, methodology): “…and Ranganathan, 1999), Mutual Interdependency (Tillier and Lui, 2003), Coevolution Analysis using Protein Sequence (Fares and Travers, 2006) and Mutual Information ( MI ) based methods (Chiu and Kolodziejczak, 1991; Cover and Thomas, 1991; Korber et al ., 1993; Wollenberg and Atchley, 2000).”
Origins of coevolution between residues distant in protein 3D structures (2017, background): “It has been proposed that coevolution between distant sites can arise from residue–residue interactions through allosteric interaction networks (20), negative design (21), codon effects (22), and spurious phylogenetic correlations (23, 24).”
Disentangling Direct from Indirect Co-Evolution of Residues in Protein Alignments (2010, methodology): “…computationally tractable way for treating the phylogenetic dependencies in a rigorous manner, i.e. by explicitly modeling the evolution of the sequences including arbitrary dependencies, several procedures have been proposed that can correct at least for the main phylogenetic signal [8,9,14,15].”
Prevalence of Epistasis in the Evolution of Influenza A Surface Proteins (2011, methodology): “Various corrections for the phylogenetic non-independence have been proposed [52–54], and their performance has been shown to be satisfactory in some cases [55–57].”