Evolutionary Computation in Bioinformatics

Erscheinungsjahr 2002
ISBN: 978-1-55860-797-2
Verlag: Elsevier Science

Buch, Englisch, 393 Seiten, Format (B × H): 187 mm x 246 mm, Gewicht: 912 g

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.

Zielgruppe

Researchers and graduate students in computer science and biology

Autoren/Hrsg.

Fogel, Gary B

Corne, David W

Fachgebiete

• Naturwissenschaften Biowissenschaften Biowissenschaften Evolutionsbiologie
• Technische Wissenschaften Elektronik | Nachrichtentechnik Nachrichten- und Kommunikationstechnik
• Mathematik | Informatik EDV | Informatik Informatik Künstliche Intelligenz

Inhaltsverzeichnis

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

Über Autor(innen)

Corne, David W
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.

Fogel, Gary B
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.