Table of contents
    1. 1. Acknowledgments
    2. 2. Preface

    Acknowledgments

     
    It is my great honor to be surrounded by many inspirational and friendly people during my whole graduate study at Purdue. I first would like to thank my Ph.D. advisor Michael Gribskov, for his unlimited encouragement over the years. His educational philosophy fosters a truly academic freedom that supports me to think about the questions I am really interested in. I am also grateful to my committee members: Daisuke Kihara, Henry Chang, and Jennifer Neville for their helpful comments. I am also indebted to David Gleich for his numerous discussions on many technical details of my research since he came to Purdue in 2011. I would also like to thank Chun-Ju Chang for offering the collaboration opportunity which widens the scope of my research. Of course, I cannot forget the supports from my research collaborators: Yong Wang who led me to the field of bioinformatics, and Kyle Kloster for his patient discussions and revision of our manuscript. Most of all, I owe my deepest gratitude to my family for their endless love in my whole life.
     

    Preface

     
    Computational biology is still in its infancy. It had not been included in any college curriculum until the end of last century. That means every young researcher in computational biology has his/her own story about how to transition to this new field of study. Here, I would like to share my story about how I become a computational biologist step by step.
      
    My major in college was pharmaceutical engineering whose curriculum is a combination of chemistry, chemical engineering and pharmacology. At that time, I had very poor ability to keep tons of chemical reaction formulas in mind, and therefore gained very little academic achievement in my major. In 2007, I accidentally registered a course on mathematical modeling when I was a sophomore. The first project was to use mathematical models to predict the Chinese population in the future. I still remember I used a logistic regression model to fit the given population data in the past. As a result, my report received a top grade, which deeply encouraged me to do something bigger in this field. In that summer, I founded a team with Yuanhai Xue from computer science and Yongzhuo Li from optoelectronics to participate in a five-round campus-wide competition in order to represent our college for the international contest. One of the problems we were given was to design a power supply network that connects hundreds of villages with minimal lengths. Yuanhai taught me Kruskal's algorithm, a classical algorithm in graph theory for finding the minimal spanning tree in a graph, to solve this problem. This was the beginning of my journey in graph theory, and eventually led me to my graduate research: using network models to understand molecular functions and behaviors. Our team was finally awarded meritorious winner in the international Mathematical Contest in Modeling in 2008, and the two teammates become my lifelong friends.
     
    After graduating from college, I went to the Academy of Mathematics and Systems Science in the Chinese Academy of Sciences as a research intern for one year, under Yong Wang's supervision. During that time, I utilized the PageRank algorithm to study the relevance of proteins to Type 2 Diabetes in different tissues. At that time, I wrote my first PageRank program using a very time-consuming power method. Two years later, I took David Gleich's class: Network and Matrix Computation, and learned how to accelerate PageRank by formulating it as a linear system and solving it faster by taking advantage of network sparseness. All these experiences benefit my graduate research in this thesis about how to use PageRank to predict protein functions and to partition a network into small modules. I suddenly realize that everything is ultimately interconnected, which reminds me of a speech given by Steve Jobs at Stanford University in 2005:
     
    "Again, you can't connect the dots looking forward; you can only connect them looking backwards. So you have to trust that the dots will somehow connect in your future. You have to trust in something---your gut, destiny, life, karma, whatever. Because believing that the dots will connect down the road will give you the confidence to follow your heart even when it leads you off the well-worn path and that will make all the difference."
     
     
    Biaobin Jiang
    West Lafayette, Indiana
    July 22, 2016
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