Ladies and gentlemen, signatures in hand.
(Acknowledgments from the dissertation)
I would like to sincerely thank my advisor Vineet Bafna, for his steady and encouraging guidance. He was instrumental in helping me find my niche in graduate school, and finding research that I could flourish with. Vineet was always available for me and is a generous man.Vineet always focused on getting the correct result, regardless of its affect on the research.
I would also like to thank the members of my committee.I have been blessed with significant scientific interaction with every committee member; each was open, generous, and kind.With each, I felt elevated beyond a graduate student to peer.I thank Bill Loomis for his thoughtful and careful mentoring of a young computer science student. Bill spent many hours helping me understand and appreciate the beauty of molecular biology. His tutoring was invaluable in helping me to be a competent bioinformaticist. He always stressed to me that computation alone would not solve any significant or interesting problems. I thank Steve Briggs, for his guidance and encouragement. I benefited greatly from regularly attending his lab meetings and watching his discerning eye. I thank Betsy Komives for her friendly and informative tutorage in the experimental aspects of mass spectrometry. Finally, I thank Terry Hwa for his respect and solicitation of my ideas.
My work would not have been possible without funding from the National Institutes of Health and the National Science Foundation, both of which supplied training grants that allowed me to research here at UCSD. The NIH bioinformatics training grant gave me the opportunity to rotate through many labs and find the research that interested me. The NSF plant systems biology IGERT helped me find exciting and productive collaborations and allowed me to present my research at conferences. This research was supported in part by the UCSD FWGrid Project, NSF Research Infrastructure Grant Number EIA-0303622.
I would like to thank the many friends and family who supported and influenced my education. First, my wife Mollie has been the standard of unwavering support. She always helped me to focus on what is most important for both my degree and my life. Without her love and support, none of this would have been possible. My two boys, Harrison and Noah, whose energy fills me. I thank my sister, Sara Anderson, for introducing me to bioinformatics. I would like to thank my parent for their support and encouragement. They have also been an example for me in balancing life and work. Finally, I would like to thank my grandfather, John W Payne, who made the educational leap from shepherd to college professor, for his diligence and determination in pursuing education.
I would also like to thank past scientists who had a significant impact on my career. Bryan Morse, at Brigham Young University, and Bernard Heymann, at the National Institutes of Health, both provided research opportunities for me as an undergraduate in biomedical imaging. I would also like to thank Steve Wasserman, at UCSD, for letting me rotate in his lab and learn basic experimental techniques.
I would like to thank past and present members of the Bafna, Briggs and Zhou lab for helping me with my research. Stephen Tanner for mentoring in computational mass spectrometry, and for writing a wonderful software tool, Inspect, which I was able to extend and use for all my research needs. I would like to thank Natalie Castellana for her diligent work with me in the Arabidopsis proteogenomic annotation. Zhouxin Shen, Marcus Smolka, and Claudio Albuquerque all generated the data that I used for my research. I am indebted to them for their gifted knowledge of analytical chemistry and mass spectrometry.
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