Integer linear programming in computational and systems biology: an entry-level text and course

Cover......Page 1
Front Matter ......Page 3
INTEGER LINEAR PROGRAMMING IN COMPUTATIONAL AND SYSTEMS BIOLOGY:An Entry-Level Text and Course......Page 5
Copyright......Page 6
Dedication......Page 7
Contents......Page 9
Introduction to the Book and Course......Page 13
Part I......Page 21
1 A Flyover Introduction to Integer LinearProgramming......Page 23
2 Biological Networks, Graphs, andHigh-Density Subgraphs......Page 35
3 Maximum Character Compatibilityin Phylogenetics......Page 69
4 Near Cliques, Dense Subgraphs, and Motifsin Biological Networks......Page 85
5 Convergent and Maximum ParsimonyProblems in Phylogenetics......Page 109
6 The RNA-Folding Problem......Page 125
7 Protein Problems Solved By IntegerProgramming......Page 142
8 Tanglegrams and Coevolution......Page 162
9 Traveling Salesman Problems in Genomics......Page 176
10 Integer Programming in MolecularSequence Analysis......Page 206
11 Metabolic Networks and MetabolicEngineering......Page 225
12......Page 241
Part II......Page 253
13 Communities, Cuts, and High-DensitySubgraphs......Page 255
14 Character Compatibility with Corrupted Dataand Generalized Phylogenetic Models......Page 280
15 More Tanglegrams, More Trees, More ILPs......Page 293
16 Return to Steiner Trees and MaximumParsimony......Page 307
17 Exploiting and Leveraging ProteinNetworks......Page 315
18 More String and Sequence ProblemsSolved by ILP......Page 333
19 Maximum Likelihood PedigreeReconstruction......Page 351
20 Two DNA Haplotyping Problems......Page 363
21 More Extended Exercises......Page 377
22What’s Next?......Page 402
23 Epilogue: Some Very OpinionatedComments for Advanced Readers......Page 405
24 Bibliography......Page 413
Index......Page 425