ArticlePeerJ2017
Differential bicodon usage in lowly and highly abundant proteins.
Article in PeerJ, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Genomic AT Bias Coupled with Amino Acid Metabolism Modulates Codon Usage.Journal of molecular evolution · 2025Article
- Investigations on genomic, topological and structural properties of diguanylate cyclases involved inCurrent research in structural biology · 2025Article
- Influence of Nucleophosmin (Journal of clinical oncology : official journal of the American Society of Clinical Oncology · 2025Article
- SARS-CoV-2 CoCoPUTs: analyzing GISAID and NCBI data to obtain codon statistics, mutations, and free energy over a multiyear period.Virus evolution · 2025Article
- Mouse embryo CoCoPUTs: novel murine transcriptomic-weighted usage website featuring multiple strains, tissues, and stages.BMC bioinformatics · 2024Article
- mRNAid, an open-source platform for therapeutic mRNA design and optimization strategies.NAR genomics and bioinformatics · 2024Article
- Dicodon-based measures for modeling gene expression.Bioinformatics (Oxford, England) · 2023Article
- Distal nucleotides affect the rate of stop codon read-through.Quantitative biology (Beijing, China) · 2023Article
- Codon-specific Ramachandran plots show amino acid backbone conformation depends on identity of the translated codon.Nature communications · 2022Article
- Bias at the third nucleotide of codon pairs in virus and host genomes.Scientific reports · 2022Article
- Plasma cell-free RNA characteristics in COVID-19 patients.Genome research · 2022Article
- The Dynamic Codon Biaser: calculating prokaryotic codon usage biases.Microbial genomics · 2021Article
- SARS-CoV-2 Codon Usage Bias Downregulates Host Expressed Genes With Similar Codon Usage.Frontiers in cell and developmental biology · 2020Article
- COSMO: A dynamic programming algorithm for multicriteria codon optimization.Computational and structural biotechnology journal · 2020Article
- Effects of codon optimization on coagulation factor IX translation and structure: Implications for protein and gene therapies.Scientific reports · 2019Article
- The link between adjacent codon pairs and mRNA stability.BMC genomics · 2017Article
- Bicodon bias can determine the role of synonymous SNPs in human diseases.BMC genomics · 2017Article
- [Synonymous Codon Usage-a Guide for Co-Translational Protein Folding in the Cell].Molekuliarnaia biologiiaReview
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Authors and funding
1 author.
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No grant is acknowledged in the PubMed record.
Abstract
Degeneracy in the genetic code implies that different codons can encode the same amino acid. Usage preference of synonymous codons has been observed in all domains of life. There is much evidence suggesting that this bias has a major role on protein elongation rate, contributing to differential expression and to co-translational folding. In addition to codon usage bias, other preference variations have been observed such as codon pairs. In this paper, I report that codon pairs have significant different frequency usage for coding either lowly or highly abundant proteins. These usage preferences cannot be explained by the frequency usage of the single codons. The statistical analysis of coding sequences of nine organisms reveals that in many cases bicodon preferences are shared between related organisms. Furthermore, it is observed that misfolding in the drug-transport protein, encoded by
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