Algebraic Statistics for Computational Biology

The title of this book reflects who we are: a computational biologist and an algebraist who share a common interest in statistics. Our collaboration sprang from the desire to find a mathematical language for discussing biological sequence analysis, with the initial impetus being provided by the introductory workshop on Discrete and Computational Geometry at the Mathematical Sciences Research Institute (MSRI) held at Berkeley in August 2003. At that workshop we began exploring the similarities between tropical matrix multiplication and the Viterbi algorithm for hidden Markov models. Our discussions ultimately led to two articles [Pachter and Sturmfels, 2004a,b] which are explained and further developed in various chapters of this book.