ArticleNature methods2016
Standardized benchmarking in the quest for orthologs.
Article in Nature methods, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 125 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
125 citing papers in PubMed, 233 citations in OpenAlex.
- Gene Observability Limits Comparative Genomic Inference of Vertebrate Lifespan Evolution.Journal of molecular evolution · 2026Article
- REvolutionH-tl 2.0: A fast and robust tool for decoding evolutionary gene histories.PLoS computational biology · 2026Article
- OrthoFinder: improved phylogenetic orthology inference with enhanced accuracy and scalability.Nature methods · 2026Article
- A protein interactome for the last eukaryotic common ancestor illuminates the biochemical basis of modern genetic diseases.Cell genomics · 2026Article
- Evolutionary History and Functional Divergence of Hydroxycarboxylic Acid Receptors in Primates.Genome biology and evolution · 2026Article
- Genome-wide identification and alkaline stress response analysis of the class III peroxidase (PRX) gene family in Castanea mollissima.BMC plant biology · 2026Article
- Article
- eggNOG v7: phylogeny-based orthology predictions and functional annotations.Nucleic acids research · 2026Article
- Quest for Orthologs in the era of Data Deluge and AI: Challenges and Innovations in Orthology Prediction and Data Integration.Journal of molecular evolution · 2025Review
- Reconstructing Evolutionary Histories with Hierarchical Orthologous Groups.Journal of molecular evolution · 2025Review
- OrthoGrafter: Rapid Identification of Orthologs from Precomputed Placement in Phylogenetic Trees.Journal of molecular evolution · 2025Article
- Amino Acid Frequency in the Proteome Is Not Associated With Realised Thermal Limit nor Dietary Niche Breadth in 35 Lepidoptera Species.Ecology and evolution · 2025Article
- Quantifying Hierarchical Conflicts in Homology Statements.Journal of molecular evolution · 2025Article
- Orthology and near-cographs in the context of phylogenetic networks.Algorithms for molecular biology : AMB · 2025Article
- Evolution and Functional Dynamics of the BAG Gene Family in Passion Fruit (Plants (Basel, Switzerland) · 2025Article
- Review
- Annotation matters: the effect of structural gene annotation on orthology inference.Bioinformatics (Oxford, England) · 2025Article
- Biparental inheritance of germline-specific chromosomes in the sea lamprey and their roles in oocytes.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- SOI: robust identification of orthologous synteny with the Orthology Index and broad applications in evolutionary genomics.Nucleic acids research · 2025Article
- Article
65 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
28 authors at 18 institutions in 9 countries.
Funding
Abstract
Achieving high accuracy in orthology inference is essential for many comparative, evolutionary and functional genomic analyses, yet the true evolutionary history of genes is generally unknown and orthologs are used for very different applications across phyla, requiring different precision-recall trade-offs. As a result, it is difficult to assess the performance of orthology inference methods. Here, we present a community effort to establish standards and an automated web-based service to facilitate orthology benchmarking. Using this service, we characterize 15 well-established inference methods and resources on a battery of 20 different benchmarks. 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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.