Single-stranded DNA (ssDNA) binding proteins are crucial for biological processes including replication, transcription, and genomic integrity. We can better comprehend th[...]

Computational modeling of protein–DNA complex structures has important implications in biomedical applications such as structure-based, computer aided drug design. A key [...]

The recent advance of single-cell technologies has provided an unprecedented opportunity to bring new insights into many complex biological phenomena, such as the regulat[...]

The Flexibility and Stability Test (FAST) is a C++ class library designed in the early 2000’s to execute free energy decomposition and reconstitution operations applied t[...]

Although transcription is one of the most important biological functions of cells, our understanding of its regulation is still limited. In this dissertation, we have st[...]

Gene regulation networks (GRNs) are the bases for virtually all biological processes. To gain a global understanding of GRNs encoded in a genome, we first need to identif[...]

Falling has become one of the leading causes to both fatal and non-fatal injuries among the elder adults and patients with dysfunctional mobility. The following consequen[...]

Gene annotation is a critical step for understanding functions of genomes and host organisms. However, accurately annotating thousands of sequenced genomes can be a chall[...]

Transcription factors (TFs) regulate gene expression through binding to specific target DNA sites. Accurate annotation of transcription factor binding sites (TFBSs) at ge[...]

Recent advancements in single-cell RNA sequencing have revolutionized our understanding of gene expression regulation under various biological contexts, providing higher [...]