Editorial: Orthology and applications

  title={Editorial: Orthology and applications},
  author={Christophe Dessimoz},
  journal={Briefings in bioinformatics},
  volume={12 5},
  • C. Dessimoz
  • Published 1 September 2011
  • Biology
  • Briefings in bioinformatics
The accurate inference of orthologous genes underpins almost all biological studies that consider more than a single genome. Indeed, orthology formalizes the intuitive notion of corresponding genes in different species. As such, orthology finds applications in a broad range of research areas, such as functional genomics, comparative genomics, phylogenetics or pharmacology. Accordingly, well over 30 orthology databases have been developed (http://q4o.org/ orthology_databases) and many thousands… 

Standardized benchmarking in the quest for orthologs

Standardized benchmarking provides a way for users to identify the most effective methods for the problem at hand, sets a minimum requirement for new tools and resources, and guides the development of more accurate orthology inference methods.

Improved orthologous databases to ease protozoan targets inference

A methodology to build improved orthologous databases with the potential to aid on protozoan target identification, one of the many tasks which benefit from comparative genomics tools is proposed.

Probabilistic Models for Species Tree Inference and Orthology Analysis

A phylogenetic tree is used to model gene evolution and species evolution using molecular sequence data and may differ from a species tree, aphenom tree, or a phenom tree for artifactual and biological reasons.

Toward community standards in the quest for orthologs

The second ‘Quest for Orthologs’ meeting brought together stakeholders from various communities to address challenges of development and application of orthology inference methods, focusing on topics of particular relevance to the research community at large.



Role of Duplicate Genes in Robustness against Deleterious Human Mutations

This paper investigates in detail the contribution of gene duplicates to back-up against deleterious human mutations and demonstrates that similarity of expression profiles across tissues significantly increases the likelihood of functional compensation by homologs.

Codon bias and base composition are poor indicators of horizontally transferred genes.

A phylogenetic approach was employed to confirm selected examples of horizontal transmission among the novel groups of genes, and determined that a number of genes previously classified as horizontally transferred based on base composition and codon bias were native, and genes previously classification as native appeared to be horizontally transferred.

Genome-wide identification of genes likely to be involved in human genetic disease.

A computational method is developed that allows the detection of genes likely to be involved in hereditary disease in the human genome and moreover can be used to predict novel disease genes.

Joining forces in the quest for orthologs

Better orthology-prediction resources would be beneficial for the whole biological community. A recent meeting discussed how to coordinate and leverage current efforts.