Evolutionary Computation in Bioinformatics

Evolutionary Computation in Bioinformatics

1st Edition - September 16, 2002

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  • Editors: Gary Fogel, David Corne
  • eBook ISBN: 9780080506081
  • Hardcover ISBN: 9781558607972

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Description

Bioinformatics has never been as popular as it is today. The genomics revolution is generating so much data in such rapid succession that it has become difficult for biologists to decipher. In particular, there are many problems in biology that are too large to solve with standard methods. Researchers in evolutionary computation (EC) have turned their attention to these problems. They understand the power of EC to rapidly search very large and complex spaces and return reasonable solutions. While these researchers are increasingly interested in problems from the biological sciences, EC and its problem-solving capabilities are generally not yet understood or applied in the biology community.This book offers a definitive resource to bridge the computer science and biology communities. Gary Fogel and David Corne, well-known representatives of these fields, introduce biology and bioinformatics to computer scientists, and evolutionary computation to biologists and computer scientists unfamiliar with these techniques. The fourteen chapters that follow are written by leading computer scientists and biologists who examine successful applications of evolutionary computation to various problems in the biological sciences.

Key Features

* Describes applications of EC to bioinformatics in a wide variety of areas including DNA sequencing, protein folding, gene and protein classification, drug targeting, drug design, data mining of biological databases, and biodata visualization.
* Offers industrial and academic researchers in computer science, biology, and bioinformatics an important resource for applying evolutionary computation.
* Includes a detailed appendix of biological data resources.

Readership

Researchers and graduate students in computer science and biology

Table of Contents

  • PART I - Introduction to the Concepts of Bioinformatics and Evolutionary Computation

    Chapter 1. An Introduction to Bioinformatics for Computer Scientists
    By David W. Corne and Gary B. Fogel
    Chapter 2. An Introduction to Evolutionary Computation for Biologists
    By Gary B. Fogel and David W. Corne

    PART II - Sequence and Structure Alignment
    Chapter 3. Determining Genome Sequences from Experimental Data Using Evolutionary Computation
    By Jacek Blazewic and Marta Kasprzak
    Chapter 4. Protein Structure Alignment Using Evolutionary Computation
    By Joseph D. Szustakowski and Zhipeng Weng

    Chapter 5. Using Genetic Algorithms for Pairwise and Multiple Sequence Alignments
    By Cédric Notredame

    PART III - Protein Folding
    Chapter 6. On the Evolutionary Search for Solutions to the Protein Folding Problem
    By Garrison W. Greenwood and Jae-Min Shin
    Chapter 7. Toward Effective Polypeptide Structure Prediction with Parallel Fast Messy Genetic Algorithms
    By Gary B. Lamont and Laurence D. Merkle

    Chapter 8. Application of Evolutionary Computation to Protein Folding with Specialized Operators
    By Steffen Schulze-Kremer

    PART IV - Machine Learning and Inference
    Chapter 9. Identification of Coding Regions in DNA Sequences Using Evolved Neural Networks
    By Gary B. Fogel, Kumar Chellapilla, and David B. Fogel
    Chapter 10. Clustering Microarray Data with Evolutionary Algorithms
    By Emanuel Falkenauer and Arnaud Marchand

    Chapter 11. Evolutionary Computation and Fractal Visualization of Sequence Data
    By Dan Ashlock and Jim Golden

    Chapter 12. Identifying Metabolic Pathways and Gene Regulation Networks with Evolutionary Algorithms
    By Junji Kitagawa and Hitoshi Iba

    Chapter 13. Evolutionary Computational Support for the Characterization of Biological Systems
    By Bogdan Filipic and Janez Strancar

    PART V - Feature Selection
    Chapter 14. Discovery of Genetic and Environmental Interactions in Disease Data Using Evolutionary Computation
    By Laetitia Jourdan, Clarisse Dhaenens[AQ2], and El-Ghazali Talbi
    Chapter 15. Feature Selection Methods Based on Genetic Algorithms for in Silico Drug Design
    By Mark J. Embrechts, Muhsin Ozdemir, Larry Lockwood, Curt Breneman, Kristin Bennet, Dirk Devogelaere, and Marcel Rijkaert

    Chapter 16. Interpreting Analytical Spectra with Evolutionary Computation
    By Jem J. Rowland

    Appendix: Internet Resources for Bioinformatics Data and Tools

Product details

  • No. of pages: 393
  • Language: English
  • Copyright: © Morgan Kaufmann 2002
  • Published: September 16, 2002
  • Imprint: Morgan Kaufmann
  • eBook ISBN: 9780080506081
  • Hardcover ISBN: 9781558607972

About the Editors

Gary Fogel

Gary B. Fogel is a senior staff scientist at Natural Selection, Inc., in La Jolla, California.His research interests include the application of evolutionary computationto problems in the biomedical sciences and evolutionary biology. He received aB.A. in biology from the University of California, Santa Cruz, in 1991 and a Ph.D.in biology from the University of California, Los Angeles, in 1998 with a focus onevolutionary biology. While at UCLA, Dr. Fogel was a fellow of the Center for theStudy of Evolution and the Origin of Life and earned several teaching and researchawards. He is a current member of the International Society for the Studyof the Origin of Life, the Society for the Study of Evolution, IEEE, Sigma Xi, andthe Evolutionary Programming Society. He currently serves as an associate editorfor IEEE Transactions on Evolutionary Computation and BioSystems and was a technicalco-chair for the recent 2000 Congress on Evolutionary Computation. He is alsoa senior staff scientist at the Center for Excellence in Evolutionary Computation,a nonprofit organization that promotes scientific research and development ofevolutionary algorithms.

Affiliations and Expertise

Natural Selection, Inc.

David Corne

David W. Corne is a reader in evolutionary computation (EC) at the University of Reading. His early research on evolutionary timetabling (with Peter Ross) resultedin the first freely available and successful EC-based general timetabling programfor educational and other institutions. His later EC work has been in suchareas as DNA pattern mining, promoter modeling, phylogeny, scheduling, layoutdesign, telecommunications, data mining, algorithm comparison issues, and multiobjectiveoptimization. Recent funded work (with Douglas Kell) applies EC directlyto the in vivo optimization of proteins. He is an associate editor of the IEEETransactions on Evolutionary Computation and a founding co-editor of the Journal ofScheduling. Dr. Corne is on the editorial boards of Applied Soft Computing and the InternationalJournal of Systems Science, and he serves on a host of international conferenceprogram committees. Other recent edited books include New Ideas in Optimization(with Marco Dorigo and Fred Glover), Telecommunications Optimization: Heuristic andAdaptive Techniques (with Martin Oates and George Smith), and Creative EvolutionarySystems (with Peter Bentley). He is also a director of Evosolve (United Kingdomregistered charity number 1086384, with Jeanne Lynch-Aird, Paul Marrow, GlenysOates, and Martin Oates), a nonprofit organization that promotes the use of advancedcomputation technologies to enhance the quality of life.

Affiliations and Expertise

University of Reading

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