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 E.C. Compeau and Pavel A. 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 E. Howard; 10. Comparison of phylogenetic trees and search for a central trend in the "Forest of Life" / Eugene V. Koonin, Pere Puigbò, and Yuri I. 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 L. Williams; 14. Phylogenetic estimation: optimization problems, heuristics, and performance analysis / Tandy Warnow
Part V. Regulatory Networks: 15. Biological networks uncover evolution, disease, and gene functions / Nataša Pržulj; 16. Regulatory network inference / Russell Schwartz.
