Codon usage bias: an endless tale
Since the genetic code is degenerate, several codons are translated to the same amino
acid. Although these triplets were historically considered to be “synonymous” and therefore …
acid. Although these triplets were historically considered to be “synonymous” and therefore …
[HTML][HTML] Codon-based indices for modeling gene expression and transcript evolution
S Bahiri-Elitzur, T Tuller - Computational and Structural Biotechnology …, 2021 - Elsevier
Codon usage bias (CUB) refers to the phenomena that synonymous codons are used in
different frequencies in most genes and organisms. The general assumption is that codon …
different frequencies in most genes and organisms. The general assumption is that codon …
In silico methods for predicting functional synonymous variants
Single nucleotide variants (SNVs) contribute to human genomic diversity. Synonymous
SNVs are previously considered to be “silent,” but mounting evidence has revealed that …
SNVs are previously considered to be “silent,” but mounting evidence has revealed that …
Sequence analysis of SARS-CoV-2 genome reveals features important for vaccine design
As the SARS-CoV-2 pandemic is rapidly progressing, the need for the development of an
effective vaccine is critical. A promising approach for vaccine development is to generate …
effective vaccine is critical. A promising approach for vaccine development is to generate …
Nucleotide composition and codon usage across viruses and their respective hosts
The genetic material of the three domains of life (Bacteria, Archaea, and Eukaryota) is
always double-stranded DNA, and their GC content (molar content of guanine plus cytosine) …
always double-stranded DNA, and their GC content (molar content of guanine plus cytosine) …
Analysis of 3.5 million SARS-CoV-2 sequences reveals unique mutational trends with consistent nucleotide and codon frequencies
Background Since the onset of the SARS-CoV-2 pandemic, bioinformatic analyses have
been performed to understand the nucleotide and synonymous codon usage features and …
been performed to understand the nucleotide and synonymous codon usage features and …
Using protein-per-mRNA differences among human tissues in codon optimization
Background Codon usage and nucleotide composition of coding sequences have profound
effects on protein expression. However, while it is recognized that different tissues have …
effects on protein expression. However, while it is recognized that different tissues have …
[HTML][HTML] The structural plasticity of polyglutamine repeats
From yeast to humans, polyglutamine (polyQ) repeat tracts are found frequently in the
proteome and are particularly prominent in the activation domains of transcription factors …
proteome and are particularly prominent in the activation domains of transcription factors …
Optimizing protein expression in heterologous system: Strategies and tools
Heterologous expression involves the introduction of gene encoding for a protein of interest
from one species into the cell of another species, thus allowing for the host cells to express …
from one species into the cell of another species, thus allowing for the host cells to express …
A path toward SARS-CoV-2 attenuation: metabolic pressure on CTP synthesis rules the virus evolution
In the context of the COVID-19 pandemic, we describe here the singular metabolic
background that constrains enveloped RNA viruses to evolve toward likely attenuation in the …
background that constrains enveloped RNA viruses to evolve toward likely attenuation in the …