Phylogenetic Profiling: How Much Input Data Is Enough?

CAFA and the Open World of protein function predictions

(2013) Christophe Dessimoz et al.   TRENDS IN GENETICS

Phyletic Profiling with Cliques of Orthologs Is Enhanced by Signatures of Paralogy Relationships

(2013) Nives Škunca et al.   PLoS Computational Biology

Shared Protein Complex Subunits Contribute to Explaining Disrupted Co-occurrence

(2013) Adrian Schneider et al.   PLoS Computational Biology

Automatic selection of reference taxa for protein–protein interaction prediction with phylogenetic profiling

(2012) Martin Simonsen et al.   BIOINFORMATICS

Effect of Reference Genome Selection on the Performance of Computational Methods for Genome-Wide Protein-Protein Interaction Prediction

(2012) Vijaykumar Yogesh Muley et al.   PLoS One

Quality of Computationally Inferred Gene Ontology Annotations

(2012) Nives Škunca et al.   PLoS Computational Biology

On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report

(2012) Paul D. Thomas et al.   PLoS Computational Biology

The what, where, how and why of gene ontology--a primer for bioinformaticians

(2011) L. du Plessis et al.   BRIEFINGS IN BIOINFORMATICS

The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata

(2011) I. Pagani et al.   NUCLEIC ACIDS RESEARCH

Predicting gene function using hierarchical multi-label decision tree ensembles

(2010) Leander Schietgat et al.   BMC BIOINFORMATICS

Comparison of eukaryotic phylogenetic profiling approaches using species tree aware methods

(2009) Valentín Ruano-Rubio et al.   BMC BIOINFORMATICS

Algorithm of OMA for large-scale orthology inference

(2008) Alexander CJ Roth et al.   BMC BIOINFORMATICS

Decision trees for hierarchical multi-label classification

(2008) Celine Vens et al.   MACHINE LEARNING

Phylogenetic profiles reveal evolutionary relationships within the "twilight zone" of sequence similarity

(2008) G. S. Chang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution

(2007) P. R Kensche et al.   Journal of the Royal Society Interface