ArticlePloS one2012
On the limitations of using ribosomal genes as references for the study of codon usage: a rebuttal.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 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
10 citing papers in PubMed.
- Intragenomic variation in non-adaptive nucleotide biases causes underestimation of selection on synonymous codon usage.PLoS genetics · 2022Article
- Evolution of Genomic Base Composition: From Single Cell Microbes to Multicellular Animals.Computational and structural biotechnology journal · 2019Review
- The Codon Usage of Lowly Expressed Genes Is Subject to Natural Selection.Genome biology and evolution · 2018Article
- Translational Selection for Speed Is Not Sufficient to Explain Variation in Bacterial Codon Usage Bias.Genome biology and evolution · 2018Article
- Switches in Genomic GC Content Drive Shifts of Optimal Codons under Sustained Selection on Synonymous Sites.Genome biology and evolution · 2017Article
- Codon and Amino Acid Usage Are Shaped by Selection Across Divergent Model Organisms of the Pancrustacea.G3 (Bethesda, Md.) · 2015Article
- Mutation--The Engine of Evolution: Studying Mutation and Its Role in the Evolution of Bacteria.Cold Spring Harbor perspectives in biology · 2015Review
- GC-Content evolution in bacterial genomes: the biased gene conversion hypothesis expands.PLoS genetics · 2015Article
- Article
- scnRCA: a novel method to detect consistent patterns of translational selection in mutationally-biased genomes.PloS one · 2013Article
Corrections and comments
- Comment on
Authors and funding
2 authors.
Funding
Abstract
In a recent paper published in PLOS ONE, Wang et al. challenge our finding that the identity of optimal codons in different genomes follows a set of clear rules. Here we provide a rebuttal of their paper and demonstrate that the results of our original PLOS Genetics paper stand. This provides us with an opportunity to bring up an aspect of how codon usage has been studied that should be of general interest. The Wang et al. study, as well as many other studies, used ribosomal genes as a reference set for the study of patterns of codon usage. We discuss here the assumptions that are made in order to justify using ribosomal genes to study codon bias, suggest that this practice can at times be problematic, and discuss its limitations.
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.