Acknowledgment

It is said that only a military general fielding an army in the frontier could truly appreciate and fully acknowledge the contribution of the comrades in arms protecting his left and right, and the logistics department backing him up from behind. Not being a general and having never been close to becoming one, it seems inevitable that my acknowledgement is to be inadequate and defective.

But I do have comrades in arms protecting me and friends and family members helping me with logistics. I am fortunate to have Stephan Aris-Brosou, Linda Bonen, Andre Dabrowski, Christian Detellier, Marc Ekker, Guy Drouin, Donal Hickey, Stan Matwin, Youlian Pan, Steve Perry, Marcel Turcotte, Vance Trudeau, Morris Zhang, and David Zhou as colleagues and friends who have helped me not only in the role of comrades in arms but also as an essential component of my logistics department.

Much of the book is based on my two undergraduate courses and a graduate course on bioinformatics and molecular evolution at University of Ottawa. My students, especially graduate students, have supplied me with constant challenges and pedagogical insights. The following graduate students have commented on various chapters and corrected typing errors: Malisa Carullo, Sam Khalouei, Pinchao, Ma, Jan Mennigen, Gareth Polidwor, Jason Popescu, Ziyu Song, Huiling Xiong, Xiaoquan Yao.

The internet has helped me keep contact with colleagues far and wide.  Many concepts and methods in the book were included as a consequence of my discussions with Esther Betran, Adam Eyre-Walker, Joe Felsenstein, Youngbi Fu, Olivier Gascuel, Brian Golding, Paul Higgs, King Jordan, Sudhir Kumar, Wen-Hsiung Li, Jean Lobry, Manyuan Long, Axel Meyer, Etsuko Moriyama, Eduardo Rocha, Eduardo Roman, Marco Salemi, Anne-Mieke Vandamme, and Reiner Veitia.

While many people have read and commented on some parts of the book, Stephan Aris-Brosou and Yongbi Fu have read almost every chapter and provided detailed comments and suggestions. Joe Felsenstein suggested, upon a quick reading of an earlier draft, adding the EM algorithm for maximum likelihood calculation and MCMC algorithm for evaluating posterior probabilities in Bayesian inference. As a little known fact, it is also Joe who, together with Ben Hall, got me started with molecular evolution and phylogenetics when I developed severe allergic response to deer mice that I used to study.

The patience of my editors, Joseph Burns and Marcia Kidston, are much appreciated. As an embarrassing manifestation of my naivety, I promised, in late 2003, to deliver the book to the publisher before February 15, 2005, and I thought it was a conservative estimate. After all, I had been teaching these computational methods for many years and producing a book seemed to require little more than simply dumping my lectures to a printer. What a humbling experience in writing the book!

I also wish to take this opportunity to thank my wife, Zheng, my daughter Kimberley, and my sons Jeffery, Jeremy and Jadon, for their love, support and entertainment. Without their constant demand for walks, talks and outdoor activities, Daddy would probably have spent all his time in front of computers and consequently ruined his health many years ago.

A family of increasing size has helped me better appreciate the importance of financial matters, so that I will not forget to acknowledge the grant support I have received from University of Ottawa and from Canadian National Science and Engineering Research Council’s Discovery Grant, Research Tools and Instrument Grant, and Strategic Grant for doing research in bioinformatics and molecular evolution. While our funding agencies will inevitably focus on research projects aiming to turn the white and light from the sky into the golden and heavy in the bank, I am glad that there is still some leftover for other enquiries.

From: Xia, X. 2007. Bioinformatics and the cell: modern computational approaches in genomics, proteomics and transcriptomics. Springer URL link. 361 pp.