| Transcription factors play an important role in transcriptional gene regulation, a process in which the quantity and pattern of gene expression is controlled through the binding of a transcription factor to DNA near target genes. DNA sequences bound by transcription factors are referred to as transcription factor binding sites, and are organized in a modular fashion. The composition, configuration, and mutation of transcription factor binding sites in a module diversify the expression profile of the target genes, and therefore constitute an important genotypic basis that is a potential target of natural selection on gene expression.;Biological experiments and computational methods have been developed to study transcription regulation through the genome-wide identification and prediction of DNA binding sequences of transcription factors. Toward the ultimate goal of identification of functional transcription factor binding sites, I have studied computational strategies for considering two main issues: biophysical binding energy models and evolutionary models for transcription factor binding sites. With the availability of relevant data resources, I have attempted to correctly represent transcription factor binding sites by developing exact binding energy models and to describe dynamic evolutionary processes using these energy models for the ultimate goal of integrating these approaches. |
