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