This second edition is aimed at researchers and graduate students in the quantitative sciences needing an introduction to the application of mathematical, statistical and computational methods in molecular biology. It is well known for the quality of the exposition and the perfect balance of mathematical theory and biological aspects. The text includes the necessary mathematical details with lots of detailed real examples, without overburdening the reader with unnecessary proofs and formalisms. This new edition has been substantially updated and now includes new chapters on genome rearrangements, motif finding, gene prediction, gene and protein networks and future research directions.