Utilizing high-throughput genomics methodologies to explore transcritomes and exomes

ii ACKNOWLEDGEMENTS The work in this thesis would not have been possible without the aid of a great many people, most importantly my research advisor, Professor John Manak. When I did my second rotation more than four years ago, John showed his great kindness and patience by answering all of my questions regarding the project I was working on. It was his kindness and patience that made me decide to join this lab. I am grateful that he gave me this opportunity to work with him. During my Ph.D. study, John encouraged me to work on several projects at the same time and always trusted me to be able to take on the challenges. John helped me with my projects whenever I needed help. He has a talent in science and discussion with him always generated new thoughts. This work would not have been accomplished without John's tremendous support and invaluable insight. I admire him for his critical thinking, rigorous scientific attitude and things I learned from him will benefit me for the rest of my entire academic career. discussions to help me accomplish my Ph.D. study. I would also like to express my gratitude to all the members in our lab, especially Mrutyunjaya (Rocky) Parida. Rocky helped me a lot for several projects that we were working on together. He is an expert in bioinformatics and always has a positive attitude and eagerness to solve new problems and get better results. During my time here in Iowa, I have met a lot of friends. Without their friendships I would not have gotten through this and I know they will always be an important part of my time in graduate school. Finally I have to thank my parents who iii never questioned whether or not I was going to be successful. No matter what mistakes I made, they were always there to support me and be proud of. I feel so honored to be the first Ph.D. student in my family. It is not only my dream but also theirs. iv ABSTRACT High-throughput genomics methodologies provide us the methods and solutions to the research fields of genomes, transcriptomes and proteomics. In my study, we utilized different high-throughput genomics methodologies to explore the exomes of human patients as well as transcriptomes of Drosophila melanogaster and Daphnia pulex. Exome sequencing, an efficient strategy to sequence the coding regions of the genome, helped …