Calculating the Secrets of Life Contributions of the Mathematical Sciences to Molecular Biology (1995) / Chapter Skim

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Select Another Chapter Chapter 1 The Secrets of Life: A Mathematician's Introduction..., pages 1-1 BIOCHEMISTRY, pages 2-4 CLASSICAL GENETICS, pages 5-6 MOLECULAR BIOLOGY, pages 7-12 THE RECOMBINANT DNA REVOLUTION, pages 13-15 MOLECULAR GENETICS IN THE 1990S, pages 16-17 THE HUMAN GENOME PROJECT, pages 18-21 COMING ATTRACTIONS, pages 22-23 REFERENCES, pages 24-24 Chapter 2 Mapping Heredity: Using Probabilistic Models..., pages 25-26 The Concept of Genetic Maps, pages 27-29 Challenges of Genetic Mapping: Human Families and Complex..., pages 30-33 MAXIMUM LIKELIHOOD ESTIMATION, pages 34-34 Efficient Algorithms, pages 35-36 Excursion: Susceptibility to Colon Cancer in Mice and..., pages 37-41 Assembling Physical Maps by "Fingerprinting"..., pages 42-46 Excursion: Designing a Strategy to Map the Human Genome, pages 47-50 CONCLUSION, pages 51-53 REFERENCES, pages 54-55 Chapter 3 Seeing Conserved Signals: Using Algorithms..., pages 56-57 FINDING GLOBAL SIMILARITIES, pages 58-58 Visualizing Alignments: Edit Graphs, pages 59-59 The Basic Dynamic Programming Algorithm, pages 60-64 FINDING LOCAL SIMILARITIES, pages 65-69 Variations in Gap Cost Penalties, pages 70-71 The Duality Between Similarity and Difference Measures, pages 72-72 Aligning More Than Two Sequences at a Time, pages 73-75 K-Best Alignments, pages 76-77 Approximate Pattern Matching, pages 78-78 Parallel Computing, pages 79-80 COMPARING ONE SEQUENCE AGAINST A DATABASE, pages 81-81 Heuristic Algorithms, pages 82-83 Sublinear Similarity Searches, pages 84-85 OPEN PROBLEMS, pages 86-87 REFERENCES, pages 88-89 Chapter 4 Hearing Distant Echoes: Using Extremal Statistics..., pages 90-93 Sequence Alignment, pages 94-94 Alignment Given, pages 95-95 Alignment Unknown, pages 96-98 Alignment Given, pages 99-104 Alignment Unknown, pages 105-105 APPLICATION TO RNA EVOLUTION, pages 106-107 TWO BEHAVIORS SUFFICE, pages 108-109 RNA EVOLUTION REVISITED, pages 110-111 REFERENCES, pages 112-113 Chapter 5 Calibrating the Clock: Using Stochastic Processes..., pages 114-116 OVERVIEW, pages 117-118 THE COALESCENT AND MUTATION, pages 119-121 The Ewens Sampling Formula, pages 122-123 Top-down, pages 124-124 Bottom-up, pages 125-126 The Infinitely-Many-Sites Model, pages 127-129 K-Allele Models, pages 130-131 The Finitely-Many-Sites Models, pages 132-135 Approximations for the Ewens Sampling Formula, pages 136-138 Combinatorial Assemblies, pages 139-141 Other Combinatorial Structures, pages 142-143 The Large Components, pages 144-144 WHERE TO NEXT?, pages 145-145 Likelihood Methods, pages 146-147 Discussion, pages 148-148 General-Purpose References, pages 149-149 Detailed References, pages 150-152 Chapter 6 Winding the Double Helix: Using Geometry,..., pages 153-154 DNA GEOMETRY AND TOPOLOGY: LINKING, TWISTING, AND WRITHING, pages 155-162 APPLICATIONS TO DNA TOPOISOMERASE REACTIONS, pages 163-165 DNA ON PROTEIN COMPLEXES, pages 166-166 THE SURFACE LINKING NUMBER, pages 167-170 THE WINDING NUMBER AND HELICAL REPEAT, pages 171-172 RELATIONSHIP BETWEEN LINKING, SURFACE LINKING, AND..., pages 173-173 APPLICATION TO THE STUDY OF THE MINICHROMOSOME, pages 174-176 REFERENCES, pages 177-178 Chapter 7 Unwinding the Double Helix: Using Differential..., pages 179-180 DNA SUPERHELICITY - MATHEMATICS AND BIOLOGY, pages 181-183 STATEMENT OF THE PROBLEM, pages 184-185 THE ENERGETICS OF A STATE, pages 186-186 ANALYSIS OF SUPERHELICAL EQUILIBRIA, pages 187-191 Evaluation of Free-Energy Parameters, pages 192-193 Accuracy of the Calculated Results, pages 194-194 APPLYING THE METHOD TO STUDY INTERESTING GENES, pages 195-198 DISCUSSION AND OPEN PROBLEMS, pages 199-199 REFERENCES, pages 200-201 Chapter 8 Lifting the Curtain: Using Topology to Probe..., pages 202-202 THE TOPOLOGY OF DNA, pages 203-206 SITE-SPECIFIC RECOMBINATION, pages 207-211 TOPOLOGICAL TOOLS FOR DNA ANALYSIS, pages 212-221 THE TANGLE MODEL FOR SITE-SPECIFIC RECOMBINATION, pages 222-224 THE TOPOLOGY OF TN3 RESOLVASE, pages 225-229 SOME UNSOLVED PROBLEMS, pages 230-231 Application of Geometry and Topology to Biology, pages 232-232 REFERENCES, pages 233-235 Chapter 9 Folding the Sheets: Using Computational Methods..., pages 236-236 A PRIMER ON PROTEIN STRUCTURE, pages 237-240 BASIC INSIGHTS ABOUT PROTEIN STRUCTURE, pages 241-247 THREADING METHODS, pages 248-253 PREDICTING HIV PROTEASE STRUCTURE:AN EXCURSION, pages 254-254 HIERARCHICAL APPROACHES, pages 255-264 PREDICTING MYOGLOBIN STRUCTURE:AN EXCURSION, pages 265-265 ACKNOWLEDGMENTS, pages 266-266 REFERENCES, pages 267-271 Appendix - Chapter Authors, pages 272-276 Index, pages 277-285

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