Bioinformatics for Biologists

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.

• 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.

'This volume contains a remarkable collection of individually-authored chapters cutting a wide swathe across the field as it is currently constituted. What is noteworthy, aside from the wide angle of the snapshot of today's bioinformatics, something the editors promise to update in future editions, is the innovative and effective pedagogical emphasis apparent throughout … The editors set out to provide a resource for teaching bioinformatics to life science undergraduates, and this is reflected in the language, organization and mathematical restraint of the different chapters … It is highly suitable as a text or reference for bioinformatics courses at the graduate level, for biologists, medical students and computer scientists. Biological naïveté in thinking and writing plagues bioinformatics, and Pevzner and Shamir's Bioinformatics for Biologists offers a wonderful therapy for that condition as well as an effective palliative for life science students' math phobias.' Professor David Sankoff, University of Ottawa