TEXT MINING BIOMEDICAL LITERATURE FOR CONSTRUCTING GENE REGULATORY NETWORKS By YONGLING SONG A DISSERTATION PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY UNIVERSITY OF FLORIDA

3 To my family 4 ACKNOWLEDGMENTS I acknowledge the assistance of my advisor Dr. Su-Shing Chen. I appreciate his valuable academic advice, his kindness, help and support without which, it would have been impossible for me to assume the process toward my Ph.D. degree. I would like to thank all of my Ph.D. Chris Jermaine, whose teaching I have enjoyed immensely and I have learnt a lot from his course. I would like to thank Dr. Shouguang Jin for providing me with this interesting research topic and continually helping me on it. I want to thank all of my colleagues, especially Weihui Wu for his help and collaboration and Hyunki Kim for all the useful advice on my research. Most of all I would like to thank my husband, Yuan Guo, for his continued encouragement and help during these years.