Ran Libeskind-HadasCambridge University PressEdition: Illustrated, 9/22/2014EAN 9781107642188, ISBN10: 1107642183Paperback, 218 pages, 24.6 x 19 x 1 cmLanguage: EnglishComputing is revolutionizing the practice of biology. This book, which assumes no prior computing experience, provides students with the tools to write their own Python programs and to understand fundamental concepts in computational biology and bioinformatics. Each major part of the book begins with a compelling biological question, followed by the algorithmic ideas and programming tools necessary to explore it: the origins of pathogenicity are examined using gene finding, the evolutionary history of sex determination systems is studied using sequence alignment, and the origin of modern humans is addressed using phylogenetic methods. In addition to providing general programming skills, this book explores the design of efficient algorithms, simulation, NP-hardness, and the maximum likelihood method, among other key concepts and methods. Easy-to-read and designed to equip students with the skills to write programs for solving a range of biological problems, the book is accompanied by numerous programming exercises, available at www.cs.hmc.edu/CFB.PrefaceMeet pythonPart I. Python versus Pathogens1. Computing GC content2. Pathogenicity islands3. Open reading frames and genes4. Finding genes (at last!)Part II. Sequence Alignment and Sex Determination5. Recursion6. The use-it-or-lose-it principle7. Dictionaries, memoization, and speed8. Sequence alignments and the evolution of sex chromosomesPart III. Phylogenetic Reconstruction and the Origin of Modern Humans9. Representing and working with trees10. Drawing trees11. The UPGMA algorithmPart IV. Additional Topics12. RNA secondary structure prediction13. Gene regulatory networks and the maximum likelihood method14. Birds, bees, and genetic algorithmsWhere to go from hereIndex.
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