ArticleProtein science : a publication of the Protein Society2022
CHARMING: Harmonizing synonymous codon usage to replicate a desired codon usage pattern.
Article in Protein science : a publication of the Protein Society, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed, 28 citations in OpenAlex.
- VeloHARMO: a deep learning framework for mRNA coding sequence generation and design via translation velocity harmonization.Briefings in bioinformatics · 2026Article
- Multilayered nucleotide organization reveals purifying selection and host-driven adaptation in CPV and FPV.BMC veterinary research · 2026Article
- Transfer learning with pre-trained language models for protein expression level prediction inSynthetic and systems biotechnology · 2026Article
- Phycocyanobilin biosynthesis in Galdieria sulphuraria requires isomerization of phycoerythrobilin synthesized by bilin reductases.The FEBS journal · 2026Article
- Evolution and Functional Implications of Codon Usage Bias in Eukaryotes.Journal of molecular evolution · 2026Review
- Morphological traits and mitogenome of Thaumapsylla breviceps orientalis endemic to China provide insight into the evolution of the order Siphonaptera.Scientific reports · 2025Article
- Uncovering position-specific patterns in codon and codon-pair usage in candidate genes associated with blood coagulation diseases.NAR genomics and bioinformatics · 2025Article
- Predicting gene sequences with AI to study codon usage patterns.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Synonymous codon substitutions modulate transcription and translation of a divergent upstream gene by modulating antisense RNA production.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- The Effects of Codon Usage on Protein Structure and Folding.Annual review of biophysics · 2024Review
- Profiling expression strategies for a type III polyketide synthase in a lysate-based, cell-free system.Scientific reports · 2024Article
- Modifications of the 5' region of the CASPONMicrobial cell factories · 2024Article
- Codon-optimization in gene therapy: promises, prospects and challenges.Frontiers in bioengineering and biotechnology · 2024Review
- An exploratory in silico comparison of open-source codon harmonization tools.Microbial cell factories · 2023Article
- An outlook to sophisticated technologies and novel developments for metabolic regulation in theFrontiers in bioengineering and biotechnology · 2023Review
- CHARMING: Harmonizing synonymous codon usage to replicate a desired codon usage pattern.Protein science : a publication of the Protein Society · 2022Article
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
There is a growing appreciation that synonymous codon usage, although historically regarded as phenotypically silent, can instead alter a wide range of mechanisms related to functional protein production, a term we use here to describe the net effect of transcription (mRNA synthesis), mRNA half-life, translation (protein synthesis) and the probability of a protein folding correctly to its active, functional structure. In particular, recent discoveries have highlighted the important role that sub-optimal codons can play in modifying co-translational protein folding. These results have drawn increased attention to the patterns of synonymous codon usage within coding sequences, particularly in light of the discovery that these patterns can be conserved across evolution for homologous proteins. Because synonymous codon usage differs between organisms, for heterologous gene expression it can be desirable to make synonymous codon substitutions to match the codon usage pattern from the original organism in the heterologous expression host. Here we present CHARMING (for Codon HARMonizING), a robust and versatile algorithm to design mRNA sequences for heterologous gene expression and other related codon harmonization tasks. CHARMING can be run as a downloadable Python script or via a web portal at http://www.codons.org.
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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.