Using multiple interdependency to separate functional from phylogenetic correlations in protein alignments
By Elisabeth R. M. Tillier, T. W. Lui. 2003
137 citations recorded by the source corpus.
Subfields: Materials Chemistry, Molecular Biology
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Materials Chemistry
- Lukas Burger
- E. van Nimwegen
- Alfonso Valencia
- Florencio Pazos
- David de Juan
- ChristopherA. Miller
- David S. Eisenberg
- G. Gloor
In Molecular Biology
- E. van Nimwegen
- David de Juan
- Florencio Pazos
- Alfonso Valencia
- Lukas Burger
- A. Pineda-Peña
- Anne-Mieke Vandamme
- ChristopherA. Miller
Citations in the corpus
- Using inferred residue contacts to distinguish between correct and incorrect protein models (2008, background): “3 Alignments augmented by metagenomics data produce slightly more accurate predictions Other investigators have reported an improved ability to predict residue contacts with increased alignment size (e.g. Martin et al., 2005; Shackelford and Karplus, 2007; Tillier and Lui, 2003).”
- Disentangling Direct from Indirect Co-Evolution of Residues in Protein Alignments (2010, methodology): “As mentioned in the introduction, the phylogenetic relationships of the underlying sequences is a major confounding factor when determining the statistical dependency between several residues (nicely explained in eg [9,13]) and it is a difficult task to ‘subtract’ from the apparent statistical depen”
- A new ensemble coevolution system for detecting HIV-1 protein coevolution (2015, methodology): “Important coevolving residues were also found in HIV-1 Env [11], Vif [12] and Gag [5].”
- Emerging methods in protein co-evolution (2013, background): “These problems have been addressed in subsequent versions 25,28,29 that improved contact predic‑ tion performance 25 (represented as ‘Mutual information corrected’ in FIG.”
- Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction (2008, methodology): “Initially, we ensured that the entropy of both positions exceeded 0.3 since previous work showed that positions with an entropy below this value often display MI because of insufficient variability (Fodor and Aldrich, 2004a; Martin et al ., 2005; Tillier and Lui, 2003).”