To enable personalized medicine, it is important yet highly challenging to accurately predict disease-causing mutations in target proteins at high throughput. Previous computational methods have been developed using evolutionary information in combin...
Predicting the strength of promoters and guiding their directed evolution is a crucial task in synthetic biology. This approach significantly reduces the experimental costs in conventional promoter engineering. Previous studies employing machine lear...
Gene expression is temporally and spatially regulated by the interaction of transcription factors (TFs) and cis-regulatory elements (CREs). The uneven distribution of TF binding sites across the genome poses challenges in understanding how this distr...
Phylogenetic tree reconstruction with molecular data is important in many fields of life science research. The gold standard in this discipline is the phylogenetic tree reconstruction based on the Maximum Likelihood method. In this study, we present ...
The Plant journal : for cell and molecular biology
39133828
Deep learning offers new approaches to investigate the mechanisms underlying complex biological phenomena, such as subgenome dominance. Subgenome dominance refers to the dominant expression and/or biased fractionation of genes in one subgenome of all...
A phylogenetic tree represents hypothesized evolutionary history for a set of taxa. Besides the branching patterns (i.e., tree topology), phylogenies contain information about the evolutionary distances (i.e. branch lengths) between all taxa in the t...
Interdisciplinary sciences, computational life sciences
39348072
The sluggish pace of new antibacterial drug development reflects a vulnerability in the face of the current severe threat posed by bacterial resistance. Microbial natural products (NPs), as a reservoir of immense chemical potential, have emerged as t...
Invertible promoters (invertons) are crucial regulatory elements in bacteria, facilitating gene expression changes under stress. Despite their importance, their prevalence and the range of regulated gene functions are largely unknown. We introduced D...
Amino acid substitution models play an important role in studying the evolutionary relationships among species from protein sequences. The amino acid substitution model consists of a large number of parameters; therefore, it is estimated from hundred...