IEEE journal of biomedical and health informatics
35998169
The effect of mutations has been traditionally predicted by studying what may happen due to the substitution of one amino acid for another one. This approach may be effective for mutations with impact in the function of the protein, but ineffective f...
In this study, we investigate how an organism's codon usage bias can serve as a predictor and classifier of various genomic and evolutionary traits across the domains of life. We perform secondary analysis of existing genetic datasets to build severa...
It has been known for decades that codon usage contributes to translation efficiency and hence to protein production levels. However, its role in protein synthesis is still only partly understood. This lack of understanding hampers the design of synt...
Translation elongation is essential for maintaining cellular proteostasis, and alterations in the translational landscape are associated with a range of diseases. Ribosome profiling allows detailed measurements of translation at the genome scale. How...
Codon usage bias (CUB), the uneven usage of synonymous codons encoding the same amino acid, differs among genes within and across bacteria genomes. CUB is known to be influenced by gene expression and accordingly, CUB differs between the high-express...
Long non-coding RNAs (lncRNAs) play crucial roles in numerous biological processes and are involved in complex human diseases through interactions with proteins. Accurate identification of lncRNA-protein interactions (LPI) can help elucidate the func...
Methods in molecular biology (Clifton, N.J.)
39527213
Machine learning is a powerful tool for analyzing biological data and making useful predictions. The surge of biological data from high-throughput omics technologies has raised the need for modeling approaches capable of tackling such amounts of data...
Species-specific differences in protein translation can affect the design of protein-based drugs. Consequently, efficient expression of recombinant proteins often requires codon optimization. Publicly available optimization tools do not always result...
Viral codon fitness (VCF) of the host and the VCF shifting has seldom been studied under quantitative measurements, although they could be concepts vital to understand pathogen epidemiology. This study demonstrates that the relative synonymous codon ...
Degeneracy in the genetic code allows many possible DNA sequences to encode the same protein. Optimizing codon usage within a sequence to meet organism-specific preferences faces combinatorial explosion. Nevertheless, natural sequences optimized thro...