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ICOR: improving codon optimization with recurrent neural networks
BackgroundIn protein sequences—as there are 61 sense codons but only 20 standard amino acids—most amino acids are encoded by more than one codon....
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Using protein-per-mRNA differences among human tissues in codon optimization
BackgroundCodon usage and nucleotide composition of coding sequences have profound effects on protein expression. However, while it is recognized...
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Tailoring Codon Usage to the Underlying Biology for Protein Expression Optimization
For heterologous gene expression, codon optimization is required to enhance the quality and quantity of the protein product. Recently, we introduced...
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Assessing optimal: inequalities in codon optimization algorithms
BackgroundCustom genes have become a common resource in recombinant biology over the last 20 years due to the plummeting cost of DNA synthesis. These...
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Effects of codon optimization, N-terminal truncation and gene dose on the heterologous expression of berberine bridge enzyme
Morphine, sanguinarine and chelerythrine are benzylisoquinoline alkaloids (BIAs), and these compounds possess strong biological activities. ( S )-scoule...
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Codon optimization of the synthetic 3-ketosphinganine reductase (3KSR) protein for enhancing sphingolipid biosynthetic enzyme expression
BackgroundSphinganine is a key precursor for the synthesis of ceramide during sphingolipid biosynthesis in eukaryotes. In the sphinganine...
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Influence of codon optimization, promoter, and strain selection on the heterologous production of a β-fructofuranosidase from Aspergillus fijiensis ATCC 20611 in Pichia pastoris
Fructooligosaccharides (FOS) are compounds possessing various health properties and are added to functional foods as prebiotics. The commercial...
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Large-scale in silico mutagenesis experiments reveal optimization of genetic code and codon usage for protein mutational robustness
BackgroundHow, and the extent to which, evolution acts on DNA and protein sequences to ensure mutational robustness and evolvability is a...
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Optimized transgene expression in the red alga Porphyridium purpureum and efficient recombinant protein secretion into the culture medium
Microalgae represent a promising but yet underexplored production platform for biotechnology. The vast majority of studies on recombinant protein...
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Efficient heterologous expression of bovine lactoferrin in Pichia pastoris and characterization of antibacterial activity
The low-expression level of lactoferrin (LF) in the production process poses a significant challenge. This study aimed to efficiently express bovine...
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Harnessing the potential of microalgae for the production of monoclonal antibodies and other recombinant proteins
Monoclonal antibodies (mAbs) have become indispensable tools in various fields, from research to therapeutics, diagnostics, and industries. However,...
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Heterologous protein production in filamentous fungi
AbstractFilamentous fungi are able to produce a wide range of valuable proteins and enzymes for many industrial applications. Recent advances in...
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The Influence of the Nucleotide Composition of Genes and Gene Regulatory Elements on the Efficiency of Protein Expression in Escherichia coli
AbstractRecombinant proteins expressed in Escherichia coli are widely used in biochemical research and industrial processes. At the same time,...
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Codon usage bias
Codon usage bias is the preferential or non-random use of synonymous codons, a ubiquitous phenomenon observed in bacteria, plants and animals....
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Enhanced editing efficiency in Arabidopsis with a LbCas12a variant harboring D156R and E795L mutations
Cas12a (Cpf1), a Class 2 Type V CRISPR/Cas nuclease, has several unique attributes for genome editing and may provide a valuable alternative to Cas9....
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Efficient genetic transformation of rice using Agrobacterium with a codon-optimized chromoprotein reporter gene (ChromoP) and introducing an optimized iPCR method for transgene integration site detection
Rice ( Oryza sativa L.) is a vital staple food for a significant portion of the global population. Meeting the demand and enhancing productivity in...
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Evaluating the effect of codon optimization on expression of bar gene in transgenic tobacco plants
Information of codon usage bias has been used for modifying genes for improved expression in heterologous systems. Codon modifications are carried...
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Bacillus subtilis: current and future modification strategies as a protein secreting factory
Bacillus subtilis is regarded as a promising microbial expression system in bioengineering due to its high stress resistance, nontoxic, low codon...
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Codon usage optimization in pluripotent embryonic stem cells
BackgroundThe uneven use of synonymous codons in the transcriptome regulates the efficiency and fidelity of protein translation rates. Yet, the...
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Peptide based vaccine designing against endemic causing mammarenavirus using reverse vaccinology approach
The rodent-borne Arenavirus in humans has led to the emergence of regional endemic situations and has deeply emerged into pandemic-causing viruses....
