Beisi Xu

Learn More
Standard normal mode analysis (NMA) method is able to calculate vibrational entropy of proteins, but it is computationally intensive, especially for large proteins. To evaluate vibrational entropy efficiently and accurately, we, here, propose computation schemes based on coarse-grained NMA methods. This can be achieved by rescaling coarse-grained results(More)
DNA methylation patterns are initiated by de novo DNA methyltransferases DNMT3a/3b adding methyl groups to CG dinucleotides in the hypomethylated genome of early embryos. These patterns are faithfully maintained by DNMT1 during DNA replication to ensure epigenetic inheritance across generations. However, this two-step model is based on limited data. We(More)
Scanning through genomes for potential transcription factor binding sites (TFBSs) is becoming increasingly important in this post-genomic era. The position weight matrix (PWM) is the standard representation of TFBSs utilized when scanning through sequences for potential binding sites. However, many transcription factor (TF) motifs are short and highly(More)
Retinal development requires precise temporal and spatial coordination of cell cycle exit, cell fate specification, cell migration and differentiation. When this process is disrupted, retinoblastoma, a developmental tumor of the retina, can form. Epigenetic modulators are central to precisely coordinating developmental events, and many epigenetic processes(More)
  • 1