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 Puigb# 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 Natasa Przulj
16. Regulatory network inference Russell Schwartz

Index

Pavel Pevzner is Ronald R. Taylor Professor of Computer Science and Director of the Bioinformatics and Systems Biology Program at the University of California, San Diego. He was named a Howard Hughes Medical Institute Professor in 2006.

Ron Shamir is the Raymond and Beverly Sackler Professor of Bioinformatics and Head of the Edmond J. Safra Bioinformatics Program at Tel Aviv University. He founded the joint Life Sciences/Computer Science undergraduate degree program in Bioinformatics at Tel Aviv University.