A Tight Link between Orthologs and Bidirectional Best Hits in Bacterial and Archaeal Genomes

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

Resolving the Ortholog Conjecture: Orthologs Tend to Be Weakly, but Significantly, More Similar in Function than Paralogs

(2012) Adrian M. Altenhoff et al.   PLoS Computational Biology

Domain architecture conservation in orthologs

(2011) Kristoffer Forslund et al.   BMC BIOINFORMATICS

Positional orthology: putting genomic evolutionary relationships into context

(2011) C. N. Dewey   BRIEFINGS IN BIOINFORMATICS

Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication

(2011) J. Huerta-Cepas et al.   BRIEFINGS IN BIOINFORMATICS

Computational methods for Gene Orthology inference

(2011) D. M. Kristensen et al.   BRIEFINGS IN BIOINFORMATICS

RAxML and FastTree: Comparing Two Methods for Large-Scale Maximum Likelihood Phylogeny Estimation

(2011) Kevin Liu et al.   PLoS One

Testing the Ortholog Conjecture with Comparative Functional Genomic Data from Mammals

(2011) Nathan L. Nehrt et al.   PLoS Computational Biology

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Evolutionary constraints on structural similarity in orthologs and paralogs

(2009) Mark E. Peterson et al.   PROTEIN SCIENCE

Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods

(2009) Adrian M. Altenhoff et al.   PLoS Computational Biology

Evolution of genome architecture

(2008) Eugene V. Koonin   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY