4. PSB 1999: Big Island of Hawaii, USA

• Preface.
  

Gene Expression and Genetic Networks

• Roland Somogyi, Hiroaki Kitano:
  Gene Expression and Genetic Networks - Session Introduction. 3-4
  
• Zoltan Szallasi:
  Genetic Network Analysis in Light of Massively Parallel Biological Data Acquisition. 5-16
  
• Tatsuya Akutsu, Satoru Miyano, Satoru Kuhara:
  Identification of Genetic Networks from a Small Number of Gene Expression Patterns Under the Boolean Network Model. 17-28
  
• Ting Chen, Hongyu L. He, George M. Church:
  Modeling Gene Expression with Differential Equations. 29-40
  
• Patrik D'haeseleer, X. Wen, Stefanie Fuhrman, Roland Somogyi:
  Linear Modeling of mRNA Expression Levels During CNS Development and Injury. 41-52
  
• Robert S. Erb, George S. Michaels:
  Sensitivity of Biological Models to Errors in Parameter Estimates. 53-64
  
• P. J. E. Goss, Jean Peccoud:
  Analysis of the Stabilizing Effect of ROM on the Genetic Network Controlling ColE1 Plasmid Replication. 65-76
  
• Koji Kyoda, Hiroaki Kitano:
  Simulation of Genetic Interaction for Drosophila Leg Formation. 77-89
  
• Sylvia B. Nagl, James Freeman, Temple F. Smith:
  Evolutionary Constraint Networks in Ligand-Binding Domains: An Information-Theoretic Approach. 90-101
  
• Maria Samsonova, V. N. Serov:
  NetWork: An Interactive Interface to the Tools for Analysis of Genetic Network Structure and Dynamics. 102-111
  
• D. C. Weaver, Christopher T. Workman, Gary D. Stormo:
  Modeling Regulatory Networks with Weight Matrices. 112-123
  

Data Mining and Knowledge Discovery in Molecular Databases

• Janice I. Glasgow, Raymond T. Ng:
  Data Mining and Knowledge Discovery in Molecular Databases - Session Introduction. 124-125
  
• Robert Giegerich, Dirk Haase, Marc Rehmsmeier:
  Prediction and Visualization of Structural Switches in RNA. 126-137
  
• J. Hudak, M. A. McClure:
  A Comparative Analysis of Computational Motif-Detection Methods. 138-149
  
• Betty Lazareva-Ulitsky, David Haussler:
  A Probabilistic Approach to a Consensus Multiple Alignment. 150-161
  
• M. A. McClure, J. Kowlaski:
  The Effects of Ordered-Series-of-Motifs Anchoring and Sub-Class Modeling on the Generation of HMMs Representing Highly Divergent Protein Sequences. 162-170
  
• K. Murakami, T. Takagi:
  Clustering and Detection of 5' Splice Sites of mRNA by k Weight-Matrices Model. 171-181
  
• Christopher J. Savoie, Nobuhiro Kamikawaji, Takehiko Sasazuki, Satoru Kuhara:
  Use of Bonsai Decision Trees for the Identification of Potential MHC Class I Peptide Epitope Motifs. 182-189
  
• Shaobing Su, Diane J. Cook, Lawrence B. Holder:
  Application of Knowledge Discovery to Molecular Biology: Identifying Structural Regularities in Proteins. 190-201
  
• Tatsuhiko Tsunoda, Masao Fukagawa, Toshihisa Takagi:
  Time and Memory Efficient Algorithm for Extracting Palindromic and Repetitive Subsequences in Nucleic Acid Sequences. 202-213
  
• Hugh E. Williams:
  Effective Query Filtering for Fast Homology Searching. 214-225
  

Computer Modeling in Physiology: From Cell to Tissue

• Andrej Bugrim, Joel Keizer, Leon Glass, Arthur Winfree:
  Computer Modeling in Physiology: From Cell to Tissue - Session Introduction. 226-227
  
• James C. Schaff, Leslie M. Loew:
  The Virtual Cell. 228-239
  
• Natalia A. Trayanova, Felipe Aguel, K. Skouibine:
  Extension of Refractoriness in a Model of Cardiac Defibrillation. 240-251
  

Information Theoretic Approaches to Biology

• David L. Dowe, Klaus Prank: Information Theoretic Approaches to Biology - Session Introduction. 252-253
• Olivier Delgrange, Max Dauchet, Eric Rivals:
  Location of Repetitive Regions in Sequences By Optimizing A Compression Method. 254-265
  
• T. Gregory Dewey:
  MDL and the Statistical Mechanics of Protein Potentials. 266-277
  
• Jacquelyn S. Fetrow, George Berg:
  Using Information Theory to Discover Side Chain Rotamer Classes: Analysis of the Effects of Local Backbone Structure. 278-289
  
• Eric Lemoine, David Merceron, Jean Sallantin, Engelbert Mephu Nguifo:
  Improving the Efficiency of a User-Driven Learning System with Reconfigurable Hardware. Application to DNA Splicing. 290-301
  
• Rolf Olsen, Terence Hwa, Michael Lässig:
  Optimizing Smith-Waterman Alignments. 302-313
  
• Guoqi Qian:
  Computing Minimum Description Length for Robust Linear Regression Model Selection. 314-325
  
• Hiroshi Tanaka, Fengrong Ren, Toshitsugu Okayama, Takashi Gojobori:
  Topology Selection in Unrooted Molecular Phylogenetic Tree By Minimum Model-Based Complexity Method. 326-337
  

Molecules to Maps: Tools for Visualization & Interaction

• Thomas E. Ferrin, Eileen Kraemer:
  Molecules to Maps: Tools for Visualization & Interaction - Session Introduction. 338-340
  
• S. Meiyappan, R. Raghavan, R. Viswanathan, Y. Yu, W. Lawton:
  Proteinmorphosis: A Mechanical Model for Protein Conformational Changes. 341-353
  
• Doanna Meads, Marc D. Hansen, Alex Pang:
  ProtAlign: A 3-Dimensional Protein Alignment Assessment Tool. 354-367
  
• Marc D. Hansen, Erik Charp, Suresh K. Lodha, Doanna Meads, Alex Pang:
  PROMUSE: A System for Multi-Media Data Presentation of Protein Structural Alignments. 368-379
  
• Greg B. Quinn, H.-P. Wang, D. Martinez, Philip E. Bourne:
  Developing Protein Documentaries and Other Multimedia Presentations for Molecular Biology. 380-391
  
• Wayne Salamonsen, Kevin Yee Chuen Mok, Prasanna R. Kolatkar, S. Subbiah:
  BioJAKE: A Tool for the Creation, Visualization and Manipulation of Metabolic Pathways. 392-400
  
• Michel F. Sanner, Bruce S. Duncan, C. J. Carrillo, Arthur J. Olson:
  Integrating Computation and Visualization for Biomolecular Analysis: An Example Using Python and AVS. 401-412
  

Computer-Aided Drug Design

• Jürgen Bajorath, Teri E. Klein, Terry P. Lybrand, Jiri Novotny:
  Computer-Aided Drug Design - Session Introduction. 413-414
  
• James R. Blinn, Douglas C. Rohrer, Gerald M. Maggiora:
  Field-Based Similarity Forcing in Energy Minimization and Molecular Matching. 415-425
  
• Djamal Bouzida, Sandra Arthurs, Anthony B. Colson, Stephan T. Freer, Daniel K. Gehlhaar, Veda Larson, Brock A. Luty, Paul A. Rejto, Peter W. Rose, Gennady Verkhivker:
  Thermodynamics and Kinetics of Ligand-Protein Binding Studied with the Weighted Histogram Analysis Method and Simulated Annealing. 426-437
  
• Peter Gund:
  Empirical vs. "Rational" Methods of Discovering New Drugs. 438-443
  
• Paul Labute:
  Binary QSAR: A New Method for the Determination of Quantitative Structure Activity Relationships. 444-455
  
• Jonathan S. Mason, Daniel L. Cheney:
  Ligand-Receptor 3-D Similarity Studies Using Multiple 4-Point Pharmacophores. 456-467
  
• I. A. Shkel, S. Kim:
  Two-Dimensional Reaction of Biological Molecules Studied by Weighted-Ensemble Brownian Dynamics. 468-479
  

Protein Structure Prediction

• Jeffrey Skolnick, Richard H. Lathrop:
  Protein Structure Prediction - Session Introduction. 480-481
  
• Christian Lemmen, Alexander Zien, Ralf Zimmer, Thomas Lengauer:
  Application of Parameter Optimization to Molecular Comparison Problems. 482-493
  
• O. B. Ptitsyn:
  Protein Evolution and Protein Folding: Non-Functional Conserved Residues and Their Probable Role. 494-504
  
• Ram Samudrala, Yu Xia, M. Levitt, Enoch S. Huang:
  A Combined Approach for Ab Initio Construction of Low Resolution Protein Tertiary Structures from Sequence. 505-516
  

Disorder in Protein Structure and Function

• C. Kissinger, A. Keith Dunker, Eugene I. Shakhnovich:
  Disorder in Protein Structure and Function - Session Introduction. 517-519
  
• S. J. Landry, N. K. Steede, A. M. Garaudy, K. Maskos, P. V. Viitanen:
  Chaperonin Function Depends on Structure and Disorder in Co-Chaperonin Mobile Loops. 520-531
  
• Diane J. Rodi, Lee Makowski:
  Similarity Between the Sequences of Taxol-Selected Peptides and the Disordered Loop of the Anti-Apoptotic Protein, BCL-2. 532-541
  
• Stuart I. Mathieson, Christopher J. Penkett, Lorna J. Smith:
  Characterisation of Side-Chain Conformational Preferences in a Biologically Active But Unfolded Protein. 542-553
  
• B. S. Nieslanik, E. C. Dietze, W. M. Atkins, I. Le Trong, E. Adman: The Locally Denatured State of Glutathione S-Transferase A1-1: Transition State Analysis of Ligand-Dependent Formation of the C-Terminal Helix. 554-565
• R. B. Sessions, M. V. Hayes, A. J. Murray, A. R. Clarke, R. L. Brady: One Sequence, Four Folds: Transitions Between an Ensemble of Metastable Folds for the N-Terminal Domain of CD2. 566-577
• W.-L. Shaiu, T. Hu, T.-S. Hsieh: The Hydrophilic, Protease-Sensitive Terminal Domains of Eucaryotic DNA Topoisomerases Have Essential Intracellular Functions. 578-589
• X.-M. Yang, R. E. Georgescu, J.-H. Li, W.-F. Yu, Haierhan, M. L. Tasayco:
  Recognition Between Disordered Polypeptide Chains from Cleavage of an a/B Domain: Self- versus Non-Self-Association. 590-600
  

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