The journal of physical chemistry letters
33104327
Chemical similarity-based approaches employed to repurpose or develop new treatments for emerging diseases, such as COVID-19, correlates molecular structure-based descriptors of drugs with those of a physiological counterpart or clinical phenotype. W...
Advanced materials (Deerfield Beach, Fla.)
33615570
Insights into the fascinating molecular world of biological processes are crucial for understanding diseases, developing diagnostics, and effective therapeutics. These processes are complex as they involve interactions between four major classes of b...
Promoter is a region of DNA that determines the transcription of a particular gene. There are several σ factors in the RNA polymerase, which has the function of identifying the promoter and facilitating the binding of the RNA polymerase to the promot...
This study used k-mer embeddings as effective feature to identify DNA N6-Methyladenine sites in plant genomes and obtained improved performance without substantial effort in feature extraction, combination and selection. Identification of DNA N6-meth...
Precise identification of target sites of RNA-binding proteins (RBP) is important to understand their biochemical and cellular functions. A large amount of experimental data is generated by in vivo and in vitro approaches. The binding preferences det...
MOTIVATION: Structural genomic variants account for much of human variability and are involved in several diseases. Structural variants are complex and may affect coding regions of multiple genes, or affect the functions of genomic regions in differe...
PURPOSE: Prior studies have demonstrated the significance of specific cis-regulatory variants in retinal disease; however, determining the functional impact of regulatory variants remains a major challenge. In this study, we utilized a machine learni...
MOTIVATION: The interactions between proteins and other molecules are essential to many biological and cellular processes. Experimental identification of interface residues is a time-consuming, costly and challenging task, while protein sequence data...
IEEE journal of biomedical and health informatics
34613923
Deciphering the relationship between transcription factors (TFs) and DNA sequences is very helpful for computational inference of gene regulation and a comprehensive understanding of gene regulation mechanisms. Transcription factor binding sites (TFB...
IEEE/ACM transactions on computational biology and bioinformatics
35471887
The binding of DNA sequences to cell type-specific transcription factors is essential for regulating gene expression in all organisms. Many variants occurring in these binding regions play crucial roles in human disease by disrupting the cis-regulati...