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Data Mining in Bioinformatics

Edited by

Jason T. L. Wang
Mohammed J. Zaki
Hannu T. T. Toivonen
Dennis Shasha

Springer, 2005, ISBN 1-85233-671-4

Book Cover

Table of Contents at Springer

Part I: Overview
  • Chapter 1. Introduction to Data Mining in Bioinformatics; Jason T. L. Wang, Mohammed J. Zaki, Hannu T. T. Toivonen, Dennis Shasha (New Jersey Institute of Technology, Rensselaer Polytechnic Institute, University of Helsinki, Courant Institute, New York University), 3 - 8.
  • Chapter 2. Survey of Biodata Analysis from a Data Mining Perspective; Peter Bajcsy, Jiawei Han, Lei Liu, Jiong Yang (University of Illinois at Urbana-Champaign), 9 - 39.

Part II: Sequence and Structure Alignment

  • Chapter 3. AntiClustAl: Multiple Sequence Alignment by Antipole Clustering; Cinzia Di Pietro, Alfredo Ferro, Giuseppe Pigola, Alfredo Pulvirenti, Michele Purrello, Marco Ragusa, Dennis Shasha (University of Catania, Italy, Courant Institute, New York University), 43 - 57.
  • Chapter 4. RNA Structure Comparison and Alignment; Kaizhong Zhang (University of Western Ontario, Canada), 59 - 81.

Part III: Biological Data Mining

  • Chapter 5. Piecewise Constant Modeling of Sequential Data Using Reversible Jump Markov Chain Monte Carlo; Marko Salmenkivi, Heikki Mannila (University of Helsinki, Helsinki University of Technology, Finland), 85 - 103.
  • Chapter 6. Gene Mapping by Pattern Discovery; Petteri Sevon, Hannu T. T. Toivonen, Paivi Onkamo (University of Helsinki, Finland), 105 - 126.
  • Chapter 7. Predicting Protein Folding Pathways; Mohammed J. Zaki, Vinay Nadimpally, Deb Bardhan, Chris Bystroff (Rensselaer Polytechnic Institute), 127 - 141.
  • Chapter 8. Data Mining Methods for a Systematics of Protein Subcellular Location; Kai Huang, Robert F. Murphy (Carnegie Mellon University), 143 - 187.
  • Chapter 9. Mining Chemical Compounds; Mukund Deshpande, Michihiro Kuramochi, George Karypis (University of Minnesota), 189 - 215.

Part IV: Biological Data Management

  • Chapter 10. Phyloinformatics: Toward a Phylogenetic Database; Roderic D. M. Page (University of Glasgow, United Kingdom), 219 - 241.
  • Chapter 11. Declarative and Efficient Querying on Protein Secondary Structures; Jignesh M. Patel, Donald P. Huddler, Laurie Hammel (University of Michigan), 243 - 273.
  • Chapter 12. Scalable Index Structures for Biological Data; Ambuj K. Singh (University of California at Santa Barbara), 275 - 296.

Glossary, 297 - 301.

References, 303 - 326.

Biographies, 327 - 336.

Index, 337 - 340.

If you have questions, have found bugs or typos, or want to comment on the presentation or content of the book, please send email to wangj@njit.edu.