Similarity of phylogenetic trees as indicator of protein-protein interaction.

By Florencio Pazos, Alfonso Valencia. Protein Engineering, 2001

535 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/02e951f0f3c8c3f86eaa933e4e0ed716c6e93fd6

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Citations in the corpus

Emerging methods in protein co-evolution (2013, methodology): “This approach, which is called MirrorTree, made it possible to evaluate the relationship between tree similarities and physical or functional interaction and to predict poten‑ tial protein–protein interactions on a genomic scale 21 .”
Predicting protein function from sequence and structure (2007, unknown): “Methods to detect similarities in phylogenetic tree”
Predicting protein-protein interactions using signature products (2005, background): “, 1997) and similarity of phylogentic trees (Goh et al., 2000; Pazos and Valencia, 2001).”
Protein network inference from multiple genomic data: a supervised approach (2004, unknown): “…genomic data, such as Bayesian networks (Friedman et al., 2000) and Boolean networks (Akutsu et al., 2000), which aim at inferring gene regulation networks from gene expression data, or the mirror tree method (Pazos et al., 2001), which predicts protein interactions from evolutionary similarities.”
Supervised Graph Inference (2004, background): “In other cases, such as inferring protein interactions from gene sequences or gene expression, these models are less relevant and more direct approaches involving the prediction of edges between “similar” nodes have been tested [5, 6].”
Evolution of proteins and proteomes: a phylogenetics approach (2005, background): “Some authors (Pazos and Valencia 2001, Valencia and Pazos 2003) have applied this property to predict interaction partners in E. coli by detecting signifi cantly correlated positions between the distance matrices used to build the phylogenetic trees.”
Using phylogenetic profiles to predict functional relationships. (2012, methodology): “Another approach used matrices instead of vectors to represent each profile (6).”
Deciphering Protein–Protein Interactions. Part II. Computational Methods to Predict Protein and Domain Interaction Partners (2007, methodology): “The similarity between phylogenetic trees can be quantified by calculating the correlation coefficient between distance matrices used to construct the trees with large values indicating co-evolution between two protein families [29,30] or domain families [31].”
Supervised reconstruction of biological networks with local models (2007, methodology): “, 2000) or the prediction of edges between ‘similar’ vertices (Marcotte et al., 1999; Pazos and Valencia, 2001).”