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4. PSB 1999: Big Island of Hawaii, USA
- Russ B. Altman, A. Keith Dunker, Lawrence Hunter, Teri E. Klein:
Proceedings of the 4th Pacific Symposium on Biocomputing, PSB 1999, The Orchid at Mauna Lani, Big Island of Hawaii, USA, January 4-9, 1999. 1999 - 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, Vassili 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 - Katsuhiko Murakami, Toshihisa 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, Kirill B. 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. Pacific Symposium on Biocomputing 1999: 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 Q. 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 T. 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, David Martínez, 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. Pacific Symposium on Biocomputing 1999: 554-565 - Richard B. Sessions, M. V. Hayes, A. J. Murray, A. R. Clarke, R. Leo Brady:
One Sequence, Four Folds: Transitions Between an Ensemble of Metastable Folds for the N-Terminal Domain of CD2. Pacific Symposium on Biocomputing 1999: 566-577 - W.-L. Shaiu, T. Hu, T.-S. Hsieh:
The Hydrophilic, Protease-Sensitive Terminal Domains of Eucaryotic DNA Topoisomerases Have Essential Intracellular Functions. Pacific Symposium on Biocomputing 1999: 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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