This monograph synthesizes several studies in average-case analysis of algorithms and in computational biology. Several works, spanning from the study of problems on sequences to systems biology, are presented. A unifying thread is followed: whatever the applications are, probabilistic sources of words plays the central role. These works find applications both in biological sequence analysis with a focus on the improvement of pattern matching algorithms and in the design of precise statistical tests, and in systems biology where strong collaborations with biologists permit to apply the developed methods to real living systems.
