Clustering and Network Analysis with Biological Applications

Acknowledgments My experience as a graduate student at Boston University has been excellent. Having been an undergraduate here as well, I already knew a lot of the faculty when I decided to enroll in the Ph.D. program. Throughout the years I have felt at home here, and was always greeted with a smile whenever I saw professors around the building. My interest in interdisciplinary research began as an undergraduate when I enrolled in an Undergraduate Research Opportunities Program during the summer between my junior and senior year. I was placed in the Tolan lab in the Biology department, where Professor Dean Tolan needed a programmer to implement some of their algorithms. That summer I created a small application that implemented their routines, which was used by me and the other people in the lab. Dean's enthusiasm for what I was doing encouraged me to continue my education as a computer scientist and showed me the value of interdisciplinary collaboration. It was also during my junior year that I first met Professor Shang-Hua Teng. Shang-Hua was teaching an introductory algorithms course, and I was impressed by the elegance of many of the techniques that we studied, as well as the arguments for their correctness. During my senior year I told Shang-Hua that I was thinking about applying to the Ph.D. program at Boston University, and asked him to write a letter of recommendation for me. He told me that he was looking for another graduate student, and asked me about my research interests. I told him about my experience in the Tolan lab, and he told me that he was very interested in bioinformatics. At the time Shang-Hua was considering several other students, but I am very glad that he chose me, and he became my advisor. Over the years Shang-Hua has been a great mentor, and has challenged me to think about many questions, a lot of which I had no good answers to. Still, he has taught me that research involves posing concrete problems and trying to solve them. I have gotten much more disciplined in my thinking, which is mainly because of him. During my second year as a graduate student I sought the help of Professor Yu (Bran-don) Xia with our bioinformatics research. Brandon was very friendly and we started to meet iv on a regular basis; later he formally became my co-advisor. He has taught me …