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This hands-on tutorial text for non-experts demonstrates biological applications of a versatile modeling and optimization technique.
List of contents
Preface; Part I: 1. A fly-over introduction; 2. Biological networks and graphs; 3. Character compatibility; 4. Near-cliques; 5. Parsimony in phylogenetics; 6. RNA folding; 7. Protein problems; 8. Tanglegrams; 9. TSP in genomics; 10. Molecular sequence analysis; 11. Metabolic networks and engineering; 12. ILP idioms; Part II: 13. Communities and cuts; 14. Corrupted data and extensions in phylogenetics; 15. More tanglegrams and trees; 16. Return to Steiner-trees; 17. Exploiting protein networks; 18. More strings and sequences; 19. Max-likelihood pedigrees; 20. Haplotyping; 21. Extended exercises; 22. What's next?; Epilogue: opinionated comments.
About the author
Dan Gusfield is Distinguished Professor of Computer Science at the University of California, Davis, and a Fellow of the IEEE, the ACM, and the International Society of Computational Biology (ISCB). His previous books include The Stable Marriage Problem (1989, with Robert W. Irving), Algorithms on Strings, Trees and Sequences (Cambridge, 1997) and ReCombinatorics (2014). He has served as chair of the computer science department at UCD (2000–04), and was the founding Editor-in-Chief of the IEEE/ACM Transactions of Computational Biology and Bioinformatics until January 2009. He has been instrumental in the definition and development of the intersection between computer science and computational biology.
Summary
Integer linear programming is a versatile modeling and optimization technique with potential to transform biological computation. This hands-on text, designed for students, researchers, and professionals in both biology and computational fields, demonstrates applications in genomics, RNA and protein folding, DNA sequencing, phylogenetics, and more.
