PSB 99 On-Line Proceedings

PSB 99 On-Line Proceedings

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CONTENTS


Preface

GENE EXPRESSION AND GENETIC NETWORKS

Session Introduction
R. Somogyi and H. Kitano; Pacific Symposium on Biocomputing 4:3-4 (1999).

Genetic Network Analysis in Light of Massively Parallel Biological Data Acquisition
Z. Szallasi; Pacific Symposium on Biocomputing 4:5-16 (1999).

Identification of Genetic Networks from a Small Number of Gene Expression Patterns Under the Boolean Network Model
T. Akutsu, S. Miyano, and S. Kuhara; Pacific Symposium on Biocomputing 4:17-28 (1999).

Modeling Gene Expression with Differential Equations
T. Chen, H. L. He, and G.M. Church; Pacific Symposium on Biocomputing 4:29-40 (1999).

Linear Modeling of mRNA Expression Levels During CNS Development and Injury
P. D'haeseleer, X. Wen, S. Fuhrman, and R. Somogyi; Pacific Symposium on Biocomputing 4:41-52 (1999).

Sensitivity of Biological Models to Errors in Parameter Estimates
R.S. Erb and G.S. Michaels; Pacific Symposium on Biocomputing 4:53-64 (1999).

Analysis of the Stabilizing Effect of ROM on the Genetic Network Controlling ColE1 Plasmid Replication
P.J.E. Goss and J. Peccoud; Pacific Symposium on Biocomputing 4:65-76 (1999).

Simulation of Genetic Interaction for Drosophila Leg Formation
K. Kyoda and H. Kitano; Pacific Symposium on Biocomputing 4:77-89 (1999).

Evolutionary Constraint Networks in Ligand-Binding Domains: An Information- Theoretic Approach
S.B. Nagl, J. Freeman, and T.F. Smith; Pacific Symposium on Biocomputing 4:90-101 (1999).

NetWork: An Interactive Interface to the Tools for Analysis of Genetic Network Structure and Dynamics
M.G. Samsonova and V.N. Serov; Pacific Symposium on Biocomputing 4:102-111 (1999).

Modeling Regulatory Networks with Weight Matrices
D.C. Weaver, C.T. Workman, G.D. Stormo; Pacific Symposium on Biocomputing 4:112-123 (1999).

DATA MINING AND KNOWLEDGE DISCOVERY IN MOLECULAR DATABASES

Session Introduction
J. Glasgow and R. Ng; Pacific Symposium on Biocomputing 4:124-125 (1999).

Prediction and Visualization of Structural Switches in RNA
R. Giegerich, D. Haase, and M. Rehmsmeier; Pacific Symposium on Biocomputing 4:126-137 (1999).

A Comparative Analysis of Computational Motif-Detection Methods
J. Hudak and M.A. McClure; Pacific Symposium on Biocomputing 4:138-149 (1999).

A Probabilistic Approach to a Consensus Multiple Alignment
B. Lazareva-Ulitsky and D. Haussler; Pacific Symposium on Biocomputing 4:150-161 (1999).

The Effects of Ordered-Series-of-Motifs Anchoring and Sub-Class Modeling on the Generation of HMMs Representing Highly Divergent Protein Sequences
M.A. McClure and J. Kowlaski; Pacific Symposium on Biocomputing 4:162-170 (1999).

Clustering and Detection of 5' Splice Sites of mRNA by k Weight-Matrices Model
K. Murakami and T. Takagi; Pacific Symposium on Biocomputing 4:171-181 (1999).

Use of Bonsai Decision Trees for the Identification of Potential MHC Class I Peptide Epitope Motifs
C.J. Savoie, N. Kamikawaji, T. Sasazuki, and S. Kuhara; Pacific Symposium on Biocomputing 4:182-189 (1999).

Application of Knowledge Discovery to Molecular Biology: Identifying Structural Regularities in Proteins
S. Su, D.J. Cook, and L.B. Holder; Pacific Symposium on Biocomputing 4:190-201 (1999).

Time and Memory Efficient Algorithm for Extracting Palindromic and Repetitive Subsequences in Nucleic Acid Sequences
T. Tsunoda, M. Fukagawa, and T. Takagi; Pacific Symposium on Biocomputing 4:202-213 (1999).

Effective Query Filtering for Fast Homology Searching
H.E. Williams; Pacific Symposium on Biocomputing 4:214-225 (1999).

COMPUTER MODELING IN PHYSIOLOGY: FROM CELL TO TISSUE

Session Introduction
A. Bugrim, J. Keizer, L. Glass, and A. Winfree; Pacific Symposium on Biocomputing 4:226-227 (1999).

The Virtual Cell
J. Schaff and L.M. Loew; Pacific Symposium on Biocomputing 4:228-239 (1999).

Extension of Refractoriness in a Model of Cardiac Defibrillation
N.A. Trayanova, F. Aguel, and K. Skouibine; Pacific Symposium on Biocomputing 4:240-251 (1999).

INFORMATION THEORETIC APPROACHES TO BIOLOGY

Session Introduction
D. L. Dowe and K. Prank; Pacific Symposium on Biocomputing 4:252-253 (1999).

Location of Repetitive Regions in Sequences By Optimizing A Compression Method
O. Delgrange, M. Dauchet, and E. Rivals; Pacific Symposium on Biocomputing 4:254-265 (1999).

MDL and the Statistical Mechanics of Protein Potentials
T.G. Dewey; Pacific Symposium on Biocomputing 4:266-277 (1999).

Using Information Theory to Discover Side Chain Rotamer Classes: Analysis of the Effects of Local Backbone Structure
J. S. Fetrow and G. Berg; Pacific Symposium on Biocomputing 4:278-289 (1999).

Improving the Efficiency of a User-Driven Learning System with Reconfigurable Hardware. Application to DNA Splicing.
E. Lemoine, D. Merceron, J. Sallantin, and E. Mephu-Nguifo; Pacific Symposium on Biocomputing 4:290-301 (1999).

Optimizing Smith-Waterman Alignments
R. Olsen, T. Hwa, and M. Lässig; Pacific Symposium on Biocomputing 4:302-313 (1999).

Computing Minimum Description Length for Robust Linear Regression Model Selection
G. Qian; Pacific Symposium on Biocomputing 4:214-325 (1999).

Topology Selection in Unrooted Molecular Phylogenetic Tree By Minimum Model-Based Complexity Method
H. Tanaka, F. Ren, T. Okayama, and T. Gojobori; Pacific Symposium on Biocomputing 4: 326-337 (1999).

MOLECULES TO MAPS: TOOLS FOR VISUALIZATION & INTERACTION

Session Introduction
T. Ferrin and E. Kraemer; Pacific Symposium on Biocomputing 4:338-340 (1999).

Proteinmorphosis: A Mechanical Model for Protein Conformational Changes
S. Meiyappan, R. Raghavan, R. Viswanathan, Y. Yu, and W. Lawton; Pacific Symposium on Biocomputing 4:341-353 (1999).

ProtAlign: A 3-Dimensional Protein Alignment Assessment Tool
D. Meads, M.C. Hansen, and A. Pang; Pacific Symposium on Biocomputing 4:354-367 (1999).

PROMUSE: A System for Multi-Media Data Presentation of Protein Structural Alignments
M.C. Hansen, E. Charp, S. Lodha, D. Meads, and A. Pang; Pacific Symposium on Biocomputing 4:368-379 (1999).

Developing Protein Documentaries and Other Multimedia Presentations for Molecular Biology
G. Quinn, H-P Wang, D. Martinez, and P.E. Bourne; Pacific Symposium on Biocomputing 4:380-391 (1999).

BioJAKE: A Tool for the Creation, Visualization and Manipulation of Metabolic Pathways
W. Salamonsen, K.Y.C. Mok, P. Kolatkar, and S. Subbiah; Pacific Symposium on Biocomputing 4:392-400 (1999).

Integrating Computation and Visualization for Biomolecular Analysis: An Example Using Python and AVS
M.F. Sanner, B.S. Duncan, C.J. Carrillo, and A.J. Olson; Pacific Symposium on Biocomputing 4:401-412 (1999).

COMPUTER-AIDED DRUG DESIGN

Session Introduction
J. Bajorath , T.E. Klein, T.P. Lybrand, and J. Novotny; Pacific Symposium on Biocomputing 4:413-414 (1999).

Field-Based Similarity Forcing in Energy Minimization and Molecular Matching
J.R. Blinn, D.C. Rohrer, and G.M. Maggiora; Pacific Symposium on Biocomputing 4:415-425 (1999).

Thermodynamics and Kinetics of Ligand-Protein Binding Studied with the Weighted Histogram Analysis Method and Simulated Annealing
D. Bouzida, S. Arthurs, A.B. Colson, S.T. Freer, D.K. Gehlhaar, V. Larson, B.A. Luty, P.A. Rejto, P.W. Rose, and G.M. Verkhivker; Pacific Symposium on Biocomputing 4:426-437 (1999).

Empirical vs. "Rational" Methods of Discovering New Drugs
P. Gund; Pacific Symposium on Biocomputing 4:438-443 (1999).

Binary QSAR: A New Method for the Determination of Quantitative Structure Activity Relationships
P. Labute; Pacific Symposium on Biocomputing 4:444-455 (1999).

Ligand-Receptor 3-D Similarity Studies Using Multiple 4-Point Pharmacophores
J.S. Mason and D.L. Cheney; Pacific Symposium on Biocomputing 4:456-467 (1999).

Two-Dimensional Reaction of Biological Molecules Studied by Weighted- Ensemble Brownian Dynamics
I.A. Shkel and S. Kim; Pacific Symposium on Biocomputing 4:468-479 (1999).

PROTEIN STRUCTURE PREDICTION

Session Introduction
J. Skolnick and R. Lathrop; Pacific Symposium on Biocomputing 4:480-481 (1999).

Application of Parameter Optimization to Molecular Comparison Problems
C. Lemmen, A. Zien, R. Zimmer, and T. Lengauer; Pacific Symposium on Biocomputing 4:482-493 (1999).

Protein Evolution and Protein Folding: Non-Functional Conserved Residues and Their Probable Role
O.B. Ptitsyn; Pacific Symposium on Biocomputing 4:494-504 (1999).

A Combined Approach for Ab Initio Construction of Low Resolution Protein Tertiary Structures from Sequence
R. Samudrala, Y. Xia, M. Levitt, and E. S. Huang; Pacific Symposium on Biocomputing 4:505-516 (1999).

DISORDER IN PROTEIN STRUCTURE AND FUNCTION

Session Introduction
C. Kissinger, A.K. Dunker, and E. Shakhnovich; Pacific Symposium on Biocomputing 4:517-519 (1999).

Chaperonin Function Depends on Structure and Disorder in Co-Chaperonin Mobile Loops
S.J. Landry, N.K. Steede, A.M. Garaudy, K. Maskos, and P.V. Viitanen; Pacific Symposium on Biocomputing 4:520-531 (1999).

Similarity Between the Sequences of Taxol-Selected Peptides and the Disordered Loop of the Anti-Apoptotic Protein, BCL-2
D.J. Rodi and L. Makowski; Pacific Symposium on Biocomputing 4:532-541 (1999).

Characterisation of Side-Chain Conformational Preferences in a Biologically Active But Unfolded Protein
S. I. Mathieson, C. J. Penkett, and L. J. Smith; Pacific Symposium on Biocomputing 4:542-553 (1999).

The Locally Denatured State of Glutathione S-Transferase A1-1: Transition State Analysis of Ligand-Dependent Formation of the C-Terminal Helix
B.S. Nieslanik, E.C. Dietze, W.M. Atkins, I. Le Trong, and E. Adman; Pacific Symposium on Biocomputing 4:554-565 (1999).

One Sequence, Four Folds: Transitions Between an Ensemble of Metastable Folds for the N-Terminal Domain of CD2
R.B. Sessions, M.V. Hayes, A.J. Murray, A.R. Clarke, and R.L. Brady; Pacific Symposium on Biocomputing 4:566-577 (1999).

The Hydrophilic, Protease-Sensitive Terminal Domains of Eucaryotic DNA Topoisomerases Have Essential Intracellular Functions
W.-L. Shaiu, T. Hu, and T.-S. Hsieh; Pacific Symposium on Biocomputing 4:578-589 (1999).

Recognition Between Disordered Polypeptide Chains from Cleavage of an a/B Domain: Self- versus Non-Self-Association
X.-M. Yang, R.E. Georgescu, J.-H. Li, W.-F. Yu, Haierhan, and M.L. Tasayco; Pacific Symposium on Biocomputing 4:590-600 (1999).