The rampant spread of COVID-19, an infectious disease caused by SARS-CoV-2, all over the world has led to over millions of deaths, and devastated the social, financial and political entities around the world. Without an existing effective medical the...
In genetics and related fields, huge amounts of data, such as genome sequences, are accumulating, and the use of artificial intelligence (AI) suitable for big data analysis has become increasingly important. Unsupervised AI that can reveal novel know...
Proteins are responsible for most physiological processes, and their abundance provides crucial information for systems biology research. However, absolute protein quantification, as determined by mass spectrometry, still has limitations in capturing...
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...
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...
Accurate annotation of coding regions in RNAs is essential for understanding gene translation. We developed a deep neural network to directly predict and analyze translation initiation and termination sites from RNA sequences. Trained with human tran...
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...