ArticleScientific reports2022
iCodon customizes gene expression based on the codon composition.
Article in Scientific reports, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed, 67 citations in OpenAlex.
- Tunable AMPA receptor function via recurrent evolution of heterotetramers.The Journal of general physiology · 2026Article
- Codon Optimality Modulates Cellular Stress and Innate Immune Responses Triggered by Exogenous RNAs.Journal of molecular biology · 2026Article
- Global Regulatory Functions of the Human CCR4-NOT Complex in mRNA Deadenylation and Decay.bioRxiv : the preprint server for biology · 2026Article
- NNature · 2026Article
- Dynamic interactions between epithelial skin cells and a sensory cavity sculpt the growing olfactory orifice.Nature communications · 2026Article
- An Efficient TetR/TetO-Integrated Packaging System for Fowl Adenovirus 4 Vector Carrying Toxic Transgene.Methods and protocols · 2026Article
- Versatile CRISPR-Cas Tools for Gene Regulation in Zebrafish via an Enhanced Q Binary System.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Evolution and Functional Implications of Codon Usage Bias in Eukaryotes.Journal of molecular evolution · 2026Review
- CellCousin2: an optimized system for partial ablation and tracing of regenerative lineages.NPJ Regenerative medicine · 2026Article
- Pichia-CLM: A language model-based codon optimization pipeline forProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Evaluation of eef1a1l1 expression stability and promoter-driven reporter activity during zebrafish development.microPublication biology · 2026Article
- Uncovering position-specific patterns in codon and codon-pair usage in candidate genes associated with blood coagulation diseases.NAR genomics and bioinformatics · 2025Article
- DeepCodon: A deep learning codon-optimization model to enhance protein expression.Biodesign research · 2025Article
- Translation elongation: measurements and applications.RNA biology · 2025Review
- Jam2 Signaling Functions Downstream of Hand2 To Initiate The Formation Of Organ-Specific Vascular Progenitors In Zebrafish.bioRxiv : the preprint server for biology · 2025Article
- mRNA folding algorithms for structure and codon optimization.Briefings in bioinformatics · 2025Review
- Genetically encoded affinity reagents are a toolkit for visualizing and manipulating endogenous protein function in vivo.Nature communications · 2025Article
- Comparative analysis of chloroplast genomes and phylogenetic relationships of different pitaya cultivars.BMC genomics · 2025Article
- Enhanced RNA-targeting CRISPR-Cas technology in zebrafish.Nature communications · 2025Article
- Targeting refractory diffuse large B cell lymphoma by CAR-WEE1 T-cells: In vitro evaluation.Annals of hematology · 2025Article
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
Messenger RNA (mRNA) stability substantially impacts steady-state gene expression levels in a cell. mRNA stability is strongly affected by codon composition in a translation-dependent manner across species, through a mechanism termed codon optimality. We have developed iCodon ( www.iCodon.org ), an algorithm for customizing mRNA expression through the introduction of synonymous codon substitutions into the coding sequence. iCodon is optimized for four vertebrate transcriptomes: mouse, human, frog, and fish. Users can predict the mRNA stability of any coding sequence based on its codon composition and subsequently generate more stable (optimized) or unstable (deoptimized) variants encoding for the same protein. Further, we show that codon optimality predictions correlate with both mRNA stability using a massive reporter library and expression levels using fluorescent reporters and analysis of endogenous gene expression in zebrafish embryos and/or human cells. Therefore, iCodon will benefit basic biological research, as well as a wide range of applications for biotechnology and biomedicine.
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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.