The Impact of Gene Duplication, Insertion, Deletion, Lateral Gene Transfer and Sequencing Error on Orthology Inference: A Simulation Study

Toward community standards in the quest for orthologs

(2012) C. Dessimoz et al.   BIOINFORMATICS

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

Orthology prediction methods: A quality assessment using curated protein families

(2011) Kalliopi Trachana et al.   BIOESSAYS

OrthoInspector: comprehensive orthology analysis and visual exploration

(2011) Benjamin Linard et al.   BMC BIOINFORMATICS

Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees

(2011) B. Boeckmann et al.   BRIEFINGS IN BIOINFORMATICS

Computational methods for Gene Orthology inference

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

ALF—A Simulation Framework for Genome Evolution

(2011) Daniel A. Dalquen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ecology drives a global network of gene exchange connecting the human microbiome

(2011) Chris S. Smillie et al.   NATURE

Evaluating Ortholog Prediction Algorithms in a Yeast Model Clade

(2011) Leonidas Salichos et al.   PLoS One

A Bayesian Approach for Fast and Accurate Gene Tree Reconstruction

(2010) M. D. Rasmussen et al.   MOLECULAR BIOLOGY AND EVOLUTION

OMA 2011: orthology inference among 1000 complete genomes

(2010) A. M. Altenhoff et al.   NUCLEIC ACIDS RESEARCH

2× genomes - depth does matter

(2010) Michel C Milinkovitch et al.   GENOME BIOLOGY

Horizontal gene transfer in evolution: facts and challenges

(2009) L. Boto   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Probabilistic Orthology Analysis

(2009) Bengt Sennblad et al.   SYSTEMATIC BIOLOGY

Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods

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

Algorithm of OMA for large-scale orthology inference

(2008) Alexander CJ Roth et al.   BMC BIOINFORMATICS

Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution

(2008) T. Dagan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA