Preface; Acknowledgements; Introduction Pavel Pevzner and Ron Shamir; Part I. Genomes: 1. Identifying the genetic basis of disease Vineet Bafna; 2. Pattern identification in a haplotype block Kun-Mao Chao; 3. Genome reconstruction: a puzzle with a billion pieces Phillip Compeau and Pavel Pevzner; 4. Dynamic programming: one algorithmic key for many biological locks Mikhail Gelfand; 5. Measuring evidence: who's your daddy? Christopher Lee; Part II. Gene Transcription and Regulation: 6. How do replication and transcription change genomes? Andrei Grigoriev; 7. Modeling regulatory motifs Sridhar Hannenhalli; 8. How does influenza virus jump from animals to humans? Haixu Tang; Part III. Evolution: 9. Genome rearrangements Steffen Heber and Brian Howard; 10. The crisis of the tree of life concept and the search for order in the phylogenetic forest Eugene Koonin, Pere Puigbò and Yuri Wolf; 11. Reconstructing the history of large-scale genomic changes: biological questions and computational challenges Jian Ma; Part IV. Phylogeny: 12. Figs, wasps, gophers, and lice: a computational exploration of coevolution Ran Libeskind-Hadas; 13. Big cat phylogenies, consensus trees, and computational thinking Seung-Jil Sun and Tiffani Williams; 14. Algorithm design for large-scale phylogeny Tandy Warnow; Part V. Regulatory Networks: 15. Biological networks uncover evolution, disease, and gene functions Nataša Pržulj; 16. Regulatory network inference Russell Schwartz; Index.