Computer Sciences Department Novel Uses for Machine Learning and Other Computational Methods for the Design and Interpretation of Genetic Microarrays

ACKNOWLEDGMENTS First I would like to acknowledge my advisor, Jude Shavlik, for his patient guidance throughout. His careful attention and rigorous approach have not only helped to develop my work, but have also set the ideal example of how to perform meaningful professional research. Next, I would like to thank the other members of my thesis committee: Fred Blattner, David Page, Mark Craven and Chuck Dyer. They all provided important suggestions and insights that improved the thesis dramatically. They provided a community and an environment in which I could thrive. Since 2001, NimbleGen Systems Inc. (now Roche Nimblegen) has provided me with not only a series of interesting problems to work on, and, through my consulting, the funding to work on them, but NimbleGen has also provided superb collaborators too numerous to mention. I would like to specifically acknowledge several who were of special help with regard to my thesis work: Kitzman and Matt Rosesch have all been very helpful along the way. I would like to thank Peter Andrae for joining and substantially improving our text mining project; and John Tobler for his part in our joint work on microarray design. I would also like to thank my close friend Eric Haag for allowing me to join his work in compensatory evolution. I also received three years of support from the Biotechnology Training Program (BTP, NIH Grant 5T32GM08349) and 3 months of support from the Computation and Informatics in Biology and Medicine (CIBM) Training Program (NLM Grant 5T15LM007359). I would also like to acknowledge Timothy Donohue and Beth Holden of the BTP and Louise Pape of the CIBM program for their kind assistance during and since my participation in these training programs. Finally, I would like to acknowledge my family. My wife, Rebecca, and my children Celia and Eva have been constant sources of inspiration and support. My parents' love and generosity have helped to make this possible. I would also like to thank Rebecca's parents for their gracious encouragement and advice throughout.

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