ReviewGenomics insights2016
Inferring Orthologs: Open Questions and Perspectives.
Review in Genomics insights, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
34 citing papers in PubMed, 85 citations in OpenAlex.
- Phyling: phylogenetic inference from annotated genomes.G3 (Bethesda, Md.) · 2026Article
- Comparative functional and evolutionary analysis of essential germline stem cell genes across the genus Drosophila and two outgroup species.G3 (Bethesda, Md.) · 2025Article
- Yeast Pseudozyma hubeiensis potential for aflatoxin B1 decontamination and its genetic properties.World journal of microbiology & biotechnology · 2025Article
- Generalization of Classification of AlkB Family Alkane Monooxygenases fromInternational journal of molecular sciences · 2025Article
- Article
- Detection of colinear blocks and synteny and evolutionary analyses based on utilization of MCScanX.Nature protocols · 2024Review
- First Genome Sequence of the Microcolonial Black FungusMicroorganisms · 2024Article
- Sequencing and Characterization ofGenes · 2023Article
- OrthoPhy: A Program to Construct Ortholog Data Sets Using Taxonomic Information.Genome biology and evolution · 2023Article
- A Phylogenetic Framework to Simulate Synthetic Interspecies RNA-Seq Data.Molecular biology and evolution · 2023Article
- Phylogenomic Analyses of 2,786 Genes in 158 Lineages Support a Root of the Eukaryotic Tree of Life between Opisthokonts and All Other Lineages.Genome biology and evolution · 2022Article
- Gene Structure-Based Homology Search Identifies Highly Divergent Putative Effector Gene Family.Genome biology and evolution · 2022Article
- The rise of genomics in snake venom research: recent advances and future perspectives.GigaScience · 2022Article
- Review
- Does effective population size affect rates of molecular evolution: Mitochondrial data for host/parasite species pairs in bees suggests not.Ecology and evolution · 2022Article
- Hybrid Deep Learning Based on a Heterogeneous Network Profile for Functional Annotations ofInternational journal of molecular sciences · 2021Article
- Total Ortholog Median Matrix as an alternative unsupervised approach for phylogenomics based on evolutionary distance between protein coding genes.Scientific reports · 2021Article
- Orthology and synteny analysis of receptor-like kinases "RLK" and receptor-like proteins "RLP" in legumes.BMC genomics · 2021Article
- Immunologic Profiling of the Atlantic Salmon Gill by Single Nuclei Transcriptomics.Frontiers in immunology · 2021Article
- The genetic factors of bilaterian evolution.eLife · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
1 author at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
With the increasing number of sequenced genomes and their comparisons, the detection of orthologs is crucial for reliable functional annotation and evolutionary analyses of genes and species. Yet, the dynamic remodeling of genome content through gain, loss, transfer of genes, and segmental and whole-genome duplication hinders reliable orthology detection. Moreover, the lack of direct functional evidence and the questionable quality of some available genome sequences and annotations present additional difficulties to assess orthology. This article reviews the existing computational methods and their potential accuracy in the high-throughput era of genome sequencing and anticipates open questions in terms of methodology, reliability, and computation. Appropriate taxon sampling together with combination of methods based on similarity, phylogeny, synteny, and evolutionary knowledge that may help detecting speciation events appears to be the most accurate strategy. This review also raises perspectives on the potential determination of orthology throughout the whole species phylogeny.
Indexed as
Identifiers
What OpenQuestion holds
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.