Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium

Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development

(2010) Jennifer I Deegan (née Clark) et al.   BMC BIOINFORMATICS

GIGA: a simple, efficient algorithm for gene tree inference in the genomic age

(2010) Paul D Thomas   BMC BIOINFORMATICS

The Gene Ontology in 2010: extensions and refinements

(2009)   NUCLEIC ACIDS RESEARCH

PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium

(2009) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

How confident can we be that orthologs are similar, but paralogs differ?

(2009) Romain A. Studer et al.   TRENDS IN GENETICS

The Gene Ontology's Reference Genome Project: A Unified Framework for Functional Annotation across Species

(2009)   PLoS Computational Biology

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates

(2008) A. J. Vilella et al.   GENOME RESEARCH