Efficient Computational Techniques for Tag SNP Selection, Epistasis Analysis, and Genome-Wide Association Study

2012 Declaration I hereby declare that this thesis is my original work and it has been written by me in its entirety. I have duly acknowledged all the sources of information which have been used in the thesis. This thesis has also not been submitted for any degree in any university previously. i I would like to dedicate this thesis to my loving mother Zhang Meiying and father Wang Yisong. ii Acknowledgements I would like to extend my deep gratitude to every person in my life who has helped me during the past four years of my PhD studies. Foremost, I thank my mentor, Professor Wong Limsoon. He has given me the academic freedom to explore a variety of topics in bioinformatics, which brings me to the field of genome-wide association studies. He guided me in developing ideas rigorously and logically through our regular meetings over the past four years. I especially appreciate his encouragement and patience towards me so that I can finish this thesis while supporting my family. I thank also my other two Thesis Advisory Committee members: Professor Tan Kian-Lee and Professor Wynne Hsu. Professor Tan Kian-Lee introduced and explained Hadoop technology to me, which, later, is used in my research. I am grateful to both of them for providing invaluable comments at our regular TAC meetings. I am extremely grateful to my two seniors: Dr Liu Guimei and Dr Feng Mengling. Dr Liu Guimei has been very supportive and would always inspire me to find solutions when I faced difficulties at the early stages of my PhD. Dr Feng Mengling introduced me to many data mining techniques and has been like an older brother, who cares about my leisure life and taught me street dance. I would also like to express special thanks to Dr Giovanni Montana and Professor Philip Keith Moore, who gave me an opportunity to do research at Imperial College London. I thank the NUS Graduate School for Integrative Sciences and Engineering (NGS) for providing a generous scholarship and abundant opportunities to attend conferences, as well as the School of Computing for providing software and hardware facilities to me. Also, I would like to extend my appreciation to my dear Computational Biology Lab mates like and other members. We had a wonderful time discussing and exchanging ideas with each other over the past four years. Last but not the least, I deeply thank …