ReviewComputational and structural biotechnology journal2021
Codon-based indices for modeling gene expression and transcript evolution.
Review in Computational and structural biotechnology journal, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
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Who cites it
60 citing papers in PubMed, 134 citations in OpenAlex.
- Genomic indicators of gene function: a systematic assessment of the human genome.G3 (Bethesda, Md.) · 2026Article
- Synonymous codon usage shapes ERα function through specialized translational programs during breast cancer progression.Oncogene · 2026Article
- Evidence for Non-optimal Codon Choice in Highly Transcribed Sex-Biased Genes of Drosophila melanogaster.Genome biology and evolution · 2026Article
- Temporal and gene-specific dynamics of codon usage evolution in SARS-CoV-2 genomes.BMC genomics · 2026Article
- Synonymous codon usage defines functional gene families.BMC biology · 2026Article
- Article
- Hurdles to horizontal gene transfer: species-specific effects of synonymous variation and plasmid copy number determine antibiotic resistance phenotype.Microbiology (Reading, England) · 2026Article
- RNA editing signatures and codon adaptation reveal potential translational compatibility between Hendra virus and its natural host Pteropus Alecto.Archives of microbiology · 2025Article
- DeepCodon: A deep learning codon-optimization model to enhance protein expression.Biodesign research · 2025Article
- Proteogenomic Discovery of Novel Open Reading Frames With HLA Immune Presentation on Human β-Cells.Diabetes · 2025Article
- Translation elongation: measurements and applications.RNA biology · 2025Review
- A computational investigation into the role of tRNAs encoded by Shigella phage Sf14.BMC genomics · 2025Article
- Article
- CocoVax: a web server for codon-based deoptimization of viral genes in live attenuated vaccine design.Nucleic acids research · 2025Article
- Modeling coding sequence design for virus-based expression in tobacco.Synthetic and systems biotechnology · 2025Article
- Traces of a Primitive RNA Ring in Current Genomes.Biology · 2025Article
- Article
- CaLMPhosKAN: prediction of general phosphorylation sites in proteins via fusion of codon aware embeddings with amino acid aware embeddings and wavelet-based Kolmogorov-Arnold network.Bioinformatics (Oxford, England) · 2025Article
- The differential effect of SARS-CoV-2 NSP1 on mRNA translation and stability reveals new insights linking ribosome recruitment, codon usage, and virus evolution.Nucleic acids research · 2025Article
- Untranslated region engineering strategies for gene overexpression, fine-tuning, and dynamic regulation.Journal of microbiology (Seoul, Korea) · 2025Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Codon usage bias (CUB) refers to the phenomena that synonymous codons are used in different frequencies in most genes and organisms. The general assumption is that codon biases reflect a balance between mutational biases and natural selection. Today we understand that the codon content is related and can affect all gene expression steps. Starting from the 1980s, codon-based indices have been used for answering different questions in all biomedical fields, including systems biology, agriculture, medicine, and biotechnology. In general, codon usage bias indices weigh each codon or a small set of codons to estimate the fitting of a certain coding sequence to a certain phenomenon (e.g., bias in codons, adaptation to the tRNA pool, frequencies of certain codons, transcription elongation speed, etc.) and are usually easy to implement. Today there are dozens of such indices; thus, this paper aims to review and compare the different codon usage bias indices, their applications, and advantages. In addition, we perform analysis that demonstrates that most indices tend to correlate even though they aim to capture different aspects. Due to the centrality of codon usage bias on different gene expression steps, it is important to keep developing new indices that can capture additional aspects that are not modeled with the current indices.
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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.