A Novel Methodology for Idenitfying Conserved Regulatory Modules at the Binding Site Level

To my dearly loved wife, Haoxian, with whom enjoyable and difficult times were shared throughout this journey, and to my parents, Zhanfu and Xioumei, for their love and support through my life. iv ACKNOWLEDGMENTS I would like to express my sincere thanks and appreciation to my advisors, Dr. Arunava Banerjee and Dr. Lei Zhou, for their invaluable guidance, support, and encouragement throughout my graduate research and study at the University of Florida. My accomplishments could not have been achieved without their support.