I would like to thank three important groups of people, without whom this dissertation would not have been possible: my committee, my wonderful lab-mates, and my family.
I would like to first thank the members of my dissertation committee - not only for their time and extreme patience, but for their intellectual contributions to my development as a scientist. I am indebted to Kathleen Hall, who first taught me that RNA genes were ``cool'' in my favorite section of the Nucleic Acids core graduate course. Without the appreciation and excitement in RNA research inspired by those lectures, I may not have ever pursued this challenging area of biology overlooked by many. To Tim Schedl, I thank for being a supportive, strong guiding force as Chair of my committee. I am particularly appreciative to Tim for agreeing to head a committee dominated by computational biologists; he offered a welcome, balancing perspective as a rigorous experimental geneticist. To Warren Gish, who helped train me as a budding computational biologist even before I arrived at graduate school. My experience working with Warren on dbEST at the National Center for Biotechnology Information was extremely positive and fun (Ultimate and Friday TGIFs sipping margaritas certainly included). To Michael Zuker, for kindly sharing his decades of wisdom in the RNA field. The tRNAscan-SE website was enhanced with his help creating graphic representations of tRNA secondary structures. To Steve Johnson, whom I am most appreciative for agreeing to serve on the committee on short notice, and knowing he would probably have less than two weeks to read my thesis. I earnestly hope to have the chance to contribute to vertebrate genomics in the future through active collaborations with Steve.
Most of all, I would like to thank my thesis advisor, Sean Eddy, a talented teacher and passionate scientist. For a young researcher who had never before taken on a graduate student, Sean seemed to be wise beyond his experience. Sean took me into his lab after I had left my first thesis lab under less-than-favorable conditions, without questions or prejudgement - for that, I am indebted and thankful for the fresh new opportunities he offered. At several points during my thesis work, Sean put my interests as a student ahead of his own - as a young, unestablished faculty member, his ultimate concern for the welfare of his students is noteworthy. I also thank Sean for appreciating my research strengths and patiently encouraging me to improve in my weaker areas. His strong support of my own ideas and research directions, and confidence in my abilities were benefits not all thesis students enjoy (but should). Graduate school can be a difficult, draining experience. I am proud to say my experience in the Eddy lab was intellectually exciting and fun, and has energized me to continue in academic research. I sincerely hope I continue to have opportunities to interact with Sean for the rest of my research career.
To my lab-mates, thanks for the fun and support. My experience in the lab was greatly enhanced as it filled out from just Sean, Mindi, and me. I greatly look forward to having all of you as colleagues in the years ahead. To Mindi and Cheryl, many thanks for help at the bench and great company. Of all the people I have worked with in the ``wet-lab'' environment, I will easily miss hanging out with you two the most. I only hope my future wet-lab mates have a similarly adventurous taste in music. Lastly, I wish to sincerely thank Linda Lutfiyya. Linda was a best friend, a source of great emotional support, and the best ``fun stuff'' organizer I knew in grad school. Linda was also critical in the success of my main thesis project. She helped train me in yeast bench technique, sharing her excellent advice, reagents, and protocols eagerly through dozens of gene disruptions and tetrad dissections. Without her expertise and other valuable resources from the Johnston lab, my project might not have ever come to fruition. I cannot adequately express how thankful I am.
Finally, but not least, I want to thank my parents and my identical twin brother Robert (with whom I shared so much growing up, hence the ``us'' in this section). My parents always encouraged us to ask questions, to be curious about how things work. Thanks for watching endless Nova, Nature, and The Body Human programs on PBS with us when we were little. Thanks for encouraging us to be independent thinkers, and having confidence in our abilities to go after new things that inspired us. Thanks Dad for taking us into lab with you to see those cool pictures you called ``electron micrographs'' when we were just five or six - and showing us how marvelously exciting biological research can be by your excitement. Thanks for teaching us that it is important to try to leave the world just a little better than when you came into it, and how a career in research can be a worthy part of that pursuit. And, of course, thank you both for your constant support through the ups and downs of my academic career. It has been bumpy at times, but your confidence in me has enhanced my ability to get through it all and succeed in the end.
And my most heartfelt thanks to my brother Robert. Without a doubt, my interest in genetics started when I realized we had the same DNA, down to the base pair, and yet we were still so different in some ways. I sometimes consider our lives a life-long experiment, in which chance and the interesting people we interact with split us on different paths. Our intense, yet positive academic and athletic competition up through high school pushed me to always strive for more. I cannot imagine being the person I am today without such a great brother through the years. Thanks for everything that helped me get to this day.