ArticleScientific reports2019
Optimizing the dynamics of protein expression.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 22 papers.
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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
22 citing papers in PubMed.
- Accelerate the Highly Efficient Development of mRNA Vaccines Through Advanced Computational Methods.MedComm · 2026Review
- ColiFormer: A Transformer-Based Codon Optimization Model Balancing Multiple Objectives for EnhancedBioengineering (Basel, Switzerland) · 2026Article
- Bacterial gene 5' ends have unusual mutation rates that can mislead tests of selection.PLoS biology · 2025Article
- Near-cognate tRNAs dominate codon decoding times in simulated ribosomes.Nucleic acids research · 2025Article
- Less is more: slow-codon windows enhance eGFP mRNA resilience against RNA interference.Journal of the Royal Society, Interface · 2025Article
- Recombinant multiepitope proteins expressed in Escherichia coli cells and their potential for immunodiagnosis.Microbial cell factories · 2024Review
- Cellular energy regulates mRNA degradation in a codon-specific manner.Molecular systems biology · 2024Article
- Designing of a multi-epitopes based vaccine againstFrontiers in immunology · 2024Article
- Decoding stoichiometric protein synthesis inBiophysical reports · 2023Article
- Physical modeling of ribosomes along messenger RNA: Estimating kinetic parameters from ribosome profiling experiments using a ballistic model.PLoS computational biology · 2023Article
- Modelling genetic stability in engineered cell populations.Nature communications · 2023Article
- ICOR: improving codon optimization with recurrent neural networks.BMC bioinformatics · 2023Article
- Integrated mRNA sequence optimization using deep learning.Briefings in bioinformatics · 2023Article
- Modelling ribosome kinetics and translational control on dynamic mRNA.PLoS computational biology · 2023Article
- Proteomics Identifies Substrates and a Novel Component in hSnd2-Dependent ER Protein Targeting.Cells · 2022Article
- Tailoring Codon Usage to the Underlying Biology for Protein Expression Optimization.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Overcoming the Solubility Problem in E. coli: Available Approaches for Recombinant Protein Production.Methods in molecular biology (Clifton, N.J.) · 2022Review
- Assessing optimal: inequalities in codon optimization algorithms.BMC biology · 2021Article
- A Modelling Framework Linking Resource-Based Stochastic Translation to the Optimal Design of Synthetic Constructs.Biology · 2021Article
- Learning the Regulatory Code of Gene Expression.Frontiers in molecular biosciences · 2021Review
Corrections and comments
- Erratum issued
Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Heterologously expressed genes require adaptation to the host organism to ensure adequate levels of protein synthesis, which is typically approached by replacing codons by the target organism's preferred codons. In view of frequently encountered suboptimal outcomes we introduce the codon-specific elongation model (COSEM) as an alternative concept. COSEM simulates ribosome dynamics during mRNA translation and informs about protein synthesis rates per mRNA in an organism- and context-dependent way. Protein synthesis rates from COSEM are integrated with further relevant covariates such as translation accuracy into a protein expression score that we use for codon optimization. The scoring algorithm further enables fine-tuning of protein expression including deoptimization and is implemented in the software OCTOPOS. The protein expression score produces competitive predictions on proteomic data from prokaryotic, eukaryotic, and human expression systems. In addition, we optimized and tested heterologous expression of manA and ova genes in Salmonella enterica serovar Typhimurium. Superiority over standard methodology was demonstrated by a threefold increase in protein yield compared to wildtype and commercially optimized sequences.
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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.