ArticleJournal of the Royal Society, Interface2020
Hidden patterns of codon usage bias across kingdoms.
Article in Journal of the Royal Society, Interface, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
What it found
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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.
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.
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Who cites it
12 citing papers in PubMed, 26 citations in OpenAlex.
- Patterns and drivers of genome-wide codon usage bias in the fungal order Sordariales.DNA research : an international journal for rapid publication of reports on genes and genomes · 2025Article
- Near-cognate tRNAs dominate codon decoding times in simulated ribosomes.Nucleic acids research · 2025Article
- CodonTransformer: a multispecies codon optimizer using context-aware neural networks.Nature communications · 2025Article
- SARS-CoV-2 Displays a Suboptimal Codon Usage Bias for Efficient Translation in Human Cells Diverted by Hijacking the tRNA Epitranscriptome.International journal of molecular sciences · 2024Article
- Synthetic genomes unveil the effects of synonymous recoding.bioRxiv : the preprint server for biology · 2024Article
- Intraspecific and interspecific variations in the synonymous codon usage in mitochondrial genomes of 8 pleurotus strains.BMC genomics · 2024Article
- Comprehensive analysis of codon bias in 13Frontiers in microbiology · 2023Article
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- Codon usage bias.Molecular biology reports · 2022Review
- Analysis of codon usage patterns in open reading frame 4 of hepatitis E viruses.Beni-Suef University journal of basic and applied sciences · 2022Article
- Comparative study of codon usage profiles of Zingiber officinale and its associated fungal pathogens.Molecular genetics and genomics : MGG · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
The genetic code is necessarily degenerate with 64 possible nucleotide triplets being translated into 20 amino acids. Eighteen out of the 20 amino acids are encoded by multiple synonymous codons. While synonymous codons are clearly equivalent in terms of the information they carry, it is now well established that they are used in a biased fashion. There is currently no consensus as to the origin of this bias. Drawing on ideas from stochastic thermodynamics we derive from first principles a mathematical model describing the statistics of codon usage bias. We show that the model accurately describes the distribution of codon usage bias of genomes in the fungal and bacterial kingdoms. Based on it, we derive a new computational measure of codon usage bias-the distance
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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.