Calculating the secrets of life : applications of the mathematical sciences in molecular biology / Eric S. Lander and Michael S. Waterman, editors.

Format:

Book

Contributor:

Lander, Eric S.

Waterman, Michael S.

Language:

English

Subjects (All):

Genetics--Mathematical models.

Genetics--Statistical methods.

Molecular biology--Mathematical models.

Molecular biology--Statistical methods.

Physical Description:

1 online resource (299 p.)

Edition:

1st ed.

Other Title:

Life

Place of Publication:

Washington, D.C. : National Academy Press, 1995.

Language Note:

English

Summary:

As researchers have pursued biology's secrets to the molecular level, mathematical and computer sciences have played an increasingly important role--in genome mapping, population genetics, and even the controversial search for "Eve," hypothetical mother of the human race. In this first-ever survey of the partnership between the two fields, leading experts look at how mathematical research and methods have made possible important discoveries in biology. The volume explores how differential geometry, topology, and differential mechanics have allowed researchers to "wind" and "unwind" DNA's double helix to understand the phenomenon of supercoiling. It explains how mathematical tools are revealing the workings of enzymes and proteins. And it describes how mathematicians are detecting echoes from the origin of life by applying stochastic and statistical theory to the study of DNA sequences. This informative and motivational book will be of interest to researchers, research administrators, and educators and students in mathematics, computer sciences, and biology.

Contents:

Calculating the Secrets of Life

Copyright

Preface

Contents

Calculating the Secrets of Life

Chapter 1 The Secrets of Life: A Mathematician's Introduction to Molecular Biology

BIOCHEMISTRY

CLASSICAL GENETICS

MOLECULAR BIOLOGY

THE RECOMBINANT DNA REVOLUTION

MOLECULAR GENETICS IN THE 1990S

THE HUMAN GENOME PROJECT

COMING ATTRACTIONS

REFERENCES

Chapter 2 Mapping Heredity: Using Probabilistic Models and Algorithms to Map Genes and Genomes

GENETIC MAPPING

The Concept of Genetic Maps

Challenges of Genetic Mapping: Human Families and Complex Traits

MAXIMUM LIKELIHOOD ESTIMATION

Efficient Algorithms

Statistical Significance

Excursion: Susceptibility to Colon Cancer in Mice and the Large Deviation Theory of Diffusion Processes

PHYSICAL MAPPING

Assembling Physical Maps by "Fingerprinting" Random Clones

Excursion: Designing a Strategy to Map the Human Genome

CONCLUSION

Chapter 3 Seeing Conserved Signals: Using Algorithms to Detect Similarities between Biosequences

FINDING GLOBAL SIMILARITIES

Visualizing Alignments: Edit Graphs

The Basic Dynamic Programming Algorithm

FINDING LOCAL SIMILARITIES

VARIATIONS ON SEQUENCE COMPARISON

Variations in Gap Cost Penalties

The Duality Between Similarity and Difference Measures

Aligning More Than Two Sequences at a Time

K-Best Alignments

Approximate Pattern Matching

Parallel Computing

COMPARING ONE SEQUENCE AGAINST A DATABASE

Heuristic Algorithms

Sublinear Similarity Searches

OPEN PROBLEMS

Chapter 4 Hearing Distant Echoes: Using Extremal Statistics to Probe Evolutionary Origins

GLOBAL SEQUENCE COMPARISONS

Sequence Alignment

Alignment Given

Alignment Unknown

LOCAL SEQUENCE COMPARISONS

APPLICATION TO RNA EVOLUTION.

TWO BEHAVIORS SUFFICE

RNA EVOLUTION REVISITED

Chapter 5 Calibrating the Clock: Using Stochastic Processes to Measure the Rate of Evolution

OVERVIEW

THE COALESCENT AND MUTATION

The Ewens Sampling Formula

Forwards and Backwards in the Tree

Top-down

Bottom-up

The Infinitely-Many-Sites Model

K-Allele Models

The Finitely-Many-Sites Models

MATHEMATICAL VIGNETTE: APPROXIMATING COMBINATORIAL STRUCTURES

Approximations for the Ewens Sampling Formula

Combinatorial Assemblies

Other Combinatorial Structures

The Large Components

WHERE TO NEXT?

Likelihood Methods

Discussion

General-Purpose References

Detailed References

Chapter 6 Winding the Double Helix: Using Geometry, Topology, and Mechanics of DNA

DNA GEOMETRY AND TOPOLOGY: LINKING, TWISTING, AND WRITHING

APPLICATIONS TO DNA TOPOISOMERASE REACTIONS

DNA ON PROTEIN COMPLEXES

THE SURFACE LINKING NUMBER

THE WINDING NUMBER AND HELICAL REPEAT

RELATIONSHIP BETWEEN LINKING, SURFACE LINKING, AND WINDING

APPLICATION TO THE STUDY OF THE MINICHROMOSOME

Chapter 7 Unwinding the Double Helix: Using Differential Mechanics to Probe Conformational Changes...

DNA SUPERHELICITY-MATHEMATICS AND BIOLOGY

STATEMENT OF THE PROBLEM

THE ENERGETICS OF A STATE

ANALYSIS OF SUPERHELICAL EQUILIBRIA

Evaluation of Free-Energy Parameters

Accuracy of the Calculated Results

APPLYING THE METHOD TO STUDY INTERESTING GENES

DISCUSSION AND OPEN PROBLEMS

Chapter 8 Lifting the Curtain: Using Topology to Probe the Hidden Action of Enzymes

THE TOPOLOGY OF DNA

SITE-SPECIFIC RECOMBINATION

TOPOLOGICAL TOOLS FOR DNA ANALYSIS

THE TANGLE MODEL FOR SITE-SPECIFIC RECOMBINATION

THE TOPOLOGY OF TN3 RESOLVASE

SOME UNSOLVED PROBLEMS

ANNOTATED BIBLIOGRAPHY

Knot Theory.

Application of Geometry and Topology to Biology

Chapter 9 Folding the Sheets: Using Computational Methods to Predict the Structure of Proteins

A PRIMER ON PROTEIN STRUCTURE

BASIC INSIGHTS ABOUT PROTEIN STRUCTURE

THREADING METHODS

PREDICTING HIV PROTEASE STRUCTURE:AN EXCURSION

HIERARCHICAL APPROACHES

PREDICTING MYOGLOBIN STRUCTURE:AN EXCURSION

ACKNOWLEDGMENTS

Appendix-Chapter Authors

Index.

Notes:

Bibliographic Level Mode of Issuance: Monograph

Includes bibliographical references and index.

ISBN:

9786610211388

9781280211386

1280211385

9780309556163

0309556163

9780585037233

058503723X

OCLC:

44958986