Computational Methods in Molecular Biology


Edited by Steven Salzberg, David Searls, and Simon Kasif
Published by Elsevier Science, 1998
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The on-line list of software and databases for computational biology on the Internet is maintained here.

Table of Contents

Preface

Section I: Introduction and Tutorial Background
  1. Grand Challenges in Computational Biology
    David Searls
    SmithKline Beecham Pharmaceuticals
    and the University of Pennsylvania

  2. A Tutorial Introduction to Computation for Biologists
    Steven L. Salzberg
    Dept. of Computer Science
    Johns Hopkins University
    and
    The Institute for Genomic Research
    Rockville, Maryland

  3. A Tutorial Introduction to Biological Sequence Analysis
    Kenneth H. Fasman(1) and Steven L. Salzberg
    (1) Whitehead Institute/MIT Center for Genome Research
    (2) Johns Hopkins University and TIGR


Section II: Learning and Pattern Discovery in Sequence Databases

  1. An Introduction to Hidden Markov Models for Biological Sequences
    Anders Krogh
    Center for Biological Sequence Analysis (CBS)
    Technical University of Denmark

  2. Case-Based Reasoning Driven Gene Annotation
    G. Christian Overton and Juergen Haas
    Computational Biology and Informatics Laboratory
    Dept. of Genetics, University of Pennsylania

  3. Classification Based Molecular Sequence Analysis
    David J. States and William C. Reisdorf, Jr.
    Institute for Biomedical Computing
    Washington University

  4. Computational Gene Prediction Using Neural Networks and Similarity Search
    Ying Xu and Edward C. Uberbacher
    Oak Ridge National Laboratory

  5. Modeling Dependencies in Pre-mRNA Splicing Signals
    Christopher Burge
    Center for Cancer Research
    Massachusetts Institute of Technology

  6. Evolutionary Approaches to Computational Biology
    Rebecca J. Parsons
    Dept. of Computer Science
    University of Central Florida

  7. Decision Trees and Markov Chains for Gene Finding
    Steven L. Salzberg
    Dept. of Computer Science
    Johns Hopkins University
    and
    The Institute for Genomic Research
    Rockville, Maryland


Section III: Protein Structure Modeling and Prediction

  1. Statistical Analysis of Protein Structures: Using Environmental Features for Multiple Purposes
    Liping Wei, Jeffrey T. Chang, and Russ B. Altman
    Section on Medical Informatics
    Department of Medicine
    Stanford University

  2. Analysis and Algorithms for Protein Sequence-Structure Alignment
    Richard H. Lathrop(1),Robert G. Rogers Jr.(2),Jadwiga Bienkowska(2), Barbara K. M. Bryant(3),Ljubomir J. Buturovic(4), Chrysanthe Gaitatzes(2), Raman Nambudripad(5), James V. White(6), and Temple F. Smith>(2)
    (1) Department of Information and Computer Science,
    University of California, Irvine
    (2) BioMolecular Engineering Research Center
    Boston University
    (3) Millennium Pharmaceuticals, Inc.
    Cambridge, MA
    (4) Incyte Pharmaceuticals, Inc.
    Palo Alto, CA 94304
    (5) Molecular Computing Facility
    Beth Israel Hospital
    Boston, MA 02215
    (6) TASC, Inc.
    Reading, MA 01867

  3. THREADER : Protein Sequence Threading by Double Dynamic Programming
    David Jones
    Department of Biological Sciences
    University of Warwick (UK)

  4. From Computer Vision to Protein Structure and Association
    Haim J. Wolfson and Ruth Nussinov
    Computer Science Department
    Tel Aviv University (Israel)

  5. Modeling Biological Data and Structure with Probabilistic Networks
    Simon Kasif(1) and Arthur L. Delcher(2)
    (1) Department of Electrical Engineering and Computer Science
    University of Illinois, Chicago
    (2) Department of Computer Science
    Loyola College in Maryland


Section IV: Reference Materials

A. Internet Resources: Software and Databases for Computational Biology

B. Suggestions for Further Reading in Computational Biology

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