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Pattern Discovery in Biomolecular Data

Tools, Techniques, and Applications

Edited by

Jason T. L. Wang
Bruce A. Shapiro
Dennis Shasha

Oxford University Press, 1999, ISBN 0-19-511940-1

The aim of this book is to introduce you to some of the best techniques of pattern discovery in molecular biology in the hope that you will build on them to make new discoveries on your own. The techniques draw from many fields of mathematical science ranging from graph theory to information theory to statistics to computer vision. We hope you find the book as fascinating to read as we have found it to write and edit.

Book Cover

Table of Contents at Oxford University Press

Part I: Finding Patterns in Sequences
  • Chapter 1. Discovering Patterns in DNA Sequences by the Algorithmic Significance Method; Aleksandar Milosavljevic (Genometrix Inc.), 3 - 23.
  • Chapter 2. Assembling Blocks; Jorja G. Henikoff (Fred Hutchinson Cancer Research Center), 24 - 29.
  • Chapter 3. MEME, MAST, and Meta-MEME: New Tools for Motif Discovery in Protein Sequences; Timothy Bailey, Michael E. Baker, Charles P. Elkan, William N. Grundy (San Diego Supercomputer Center, University of California at San Diego Department of Medicine and Department of Computer Science and Engineering, Columbia University), 30 - 54.
  • Chapter 4. Pattern Discovery and Classification in Biosequences; Jason T. L. Wang, Thomas G. Marr, Steve Rozen, Dennis Shasha, et al. (NJIT, Genomica Corporation, MIT Whitehead Institute for Biomedical Research, NYU Courant Institute), 55 - 74.

Part II: Finding Patterns in 3D Structures

  • Chapter 5. Motif Discovery in Protein Structure Databases; Janice Glasgow, Evan Steeg, Suzanne Fortier (Queen's University Department of Computing and Information Science and Department of Chemistry, Canada), 77 - 96.
  • Chapter 6. Systematic Detection of Protein Structural Motifs; Kentaro Tomii, Minoru Kanehisa (Kyoto University Institute for Chemical Research, Japan), 97 - 110.
  • Chapter 7. Representation and Matching of Small Flexible Molecules in Large Databases of 3D Molecular Information; Isidore Rigoutsos, Daniel Platt, Andrea Califano, David Silverman (IBM T. J. Watson Research Center), 111 - 129.

Part III: System Components for Discovery

  • Chapter 8. A Framework for Biological Pattern Discovery on Networks of Workstations; Bin Li, Dennis Shasha, Jason T. L. Wang (NYU Courant Institute, NJIT), 133 - 144.
  • Chapter 9. Discovering Concepts in Structural Data; Diane J. Cook, Lawrence B. Holder, Gehad Galal (University of Texas at Arlington Department of Computer Science and Engineering), 145 - 159.
  • Chapter 10. Overview: A System for Tracking and Managing the Results from Sequence Comparison Programs; David P. Yee, Judith Bayard Cushing, Tim Hunkapiller, Elizabeth Kutter, et al. (Zymogenetics Inc., Evergreen State College, University of Washington Department of Molecular Biotechnology), 160 - 182.
  • Chapter 11. RNA Structure Analysis: A Multifaceted Approach; Bruce A. Shapiro, Wojciech Kasprzak, Jin Chu Wu, Kathleen Currey (National Cancer Institute, University of Maryland Medical School), 183 - 215.

Glossary, 216 - 225.

References, 226 - 247.

Index, 248 - 251.

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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 jason@cis.njit.edu.