@article {bioinflmu-516,
	title = {{Assigning functional linkages to proteins using phylogenetic profiles and continuous phenotypes}},
	journal = {Bioinformatics},
	volume = {24},
	number = {10},
	year = {2008},
	pages = {1257-63},
	abstract = {MOTIVATION: A class of non-homology-based methods for protein

function prediction relies on the assumption that genes linked to a phenotypic

trait are preferentially conserved among organisms that share the trait. These

methods typically compare pairs of binary strings, where one string encodes the

phylogenetic distribution of a trait and the other of a protein. In this work, we

extended the approach to automatically deal with continuous phenotypes. RESULTS:

Rather than use a priori rules, which can be very subjective, to construct binary

profiles from continuous phenotypes, we propose to systematically explore

thresholds which can meaningfully separate the phenotype values. We illustrate

our method by analyzing optimal growth temperatures, and demonstrate its

usefulness by automatically retrieving genes which have been associated with

thermophilic growth. We also apply the general approach, for the first time, to

optimal growth pH, and make novel predictions. Finally, we show that our method

can also be applied to other properties which may not be classically considered

as phenotypes. Specifically, we studied correlations between genome size and the

distribution of genes.},
	doi = {10.1093/bioinformatics/btn106 },
	author = {Orland Gonzalez and Ralf Zimmer}
}