Preface

PROTEIN EVOLUTION AND STRUCTURAL GENOMICS

Session Introduction
D. Frishman, R.A. Goldstein, and D.D. Pollock; Pacific Symposium on Biocomputing 5:3-5 (2000).

Enzyme Evolution Explained (Sort Of)
A. M. Dean and G. B. Golding; Pacific Symposium on Biocomputing 5:6-17 (2000).

Modeling Evolution at the Protein Level Using an Adjustable Amino Acid Fitness Model
M.W. Dimmic, D.P. Mindell, and R.A. Goldstein; Pacific Symposium on Biocomputing 5:18-29 (2000).

Protein Folds in the Worm Genome
M. Gerstein, J. Lin, and H. Hegyi; Pacific Symposium on Biocomputing 5:30-41 (2000).

Sensitive Sequence Comparison as Protein Function Predictor
K. Pawlowski, L. Jaroszewski, L. Rychlewski, and A. Godzik; Pacific Symposium on Biocomputing 5:42-53 (2000).

High-throughput Functional Annotation of Novel Gene Products Using Document Clustering
A. Renner and A. Aszódi; Pacific Symposium on Biocomputing 5:54-65 (2000).

The Evolution of Duplicated Genes Considering Protein Stability Constraints
D.M. Taverna and R.M. Goldstein; Pacific Symposium on Biocomputing 5:66-77 (2000).

Relating Physicochemmical Properties of Amino Acids to Variable Nucleotide Substitution Patterns Among Sites
Z. Yang; Pacific Symposium on Biocomputing 5:78-89 (2000).

PROTEIN STRUCTURE PREDICTION IN BIOLOGY AND MEDICINE

Session Introduction
R.L. Dunbrak Jr., K. Dunker, and A. Godzik; Pacific Symposium on Biocomputing 5:90-91 (2000).

Algorithmic Approach to Quantifying the Hydrophobic Force Contribution in Protein Folding
R. Backofen, S. Will, J. Bond, and P. Clote; Pacific Symposium on Biocomputing 5:92-103 (2000).

Eliminating Superfluous Neighbor Pairs While Threading Fold Models
J.R. Bienkowska, R.G. Rogers Jr., and T.F. Smith; Pacific Symposium on Biocomputing 5:104-115 (2000).

Hybrid Fold Recognition: Combining Sequence Derived Properties with Evolutionary Information
D. Fischer; Pacific Symposium on Biocomputing 5:116-127 (2000).

Folding Nuclei in 3D Protein Structures
O.V. Galzitskaya, A.V. Skoogarev, D.N. Uvankov, and A.V. Finkelstein; Pacific Symposium on Biocomputing 5:128-139 (2000).

How Universal Are Fold Recognition Parameters. A Comprehensive Study of Alignment and Scoring Function Parameters Influence on Recognition of Distant Folds
K.A. Olszewski; Pacific Symposium on Biocomputing 5:140-151 (2000).

Pinpointing the Putative Heparin/Sialic Acid-Binding Residues in the 'Sushi' Domain 7 of Factor H: A Molecular Modeling Study
S. Ranganathan, D.A. Male, R.J. Ormsby, E. Giannakis, and D.L. Gordon; Pacific Symposium on Biocomputing 5:152-164 (2000).

Recognition of Protein Structure: Determining the Relative Energetic Contributions of Beta-strands, Alpha-helices and Loops
B. Reva and S. Topiol; Pacific Symposium on Biocomputing 5:165-175 (2000).

Probing Structure-Function Relationships of the DNA Polymerase Alpha-Associated Zinc-Finger Protein Using Computational Approaches
R. Samudrala, Y. Xia, M. Levitt, N.J. Cotton, E.S. Huang, and R. Davis; Pacific Symposium on Biocomputing 5:176-187 (2000).

Flexibility and Critical Hydrogen Bonds in Cytochrome C
M. F. Thorpe, B. M. Hespenheide, Y. Yang and L. A. Kuhn; Pacific Symposium on Biocomputing 5:188-199 (2000).

MOLECULES TO MAPS: TOOLS FOR VISUALIZATION AND INTERACTION IN COMPUTATIONAL BIOLOGY

Session Introduction
E.T. Kraemer and T.E. Ferrin; Pacific Symposium on Biocomputing 5:200-202 (2000).

MappetShow: Non-Linear Visualization for Genome Data
F. Guyon, G. Vaysseix, and E. Barillot; Pacific Symposium on Biocomputing 5:203-214 (2000).

ProFeel: Low Cost Visual-Haptic Perceptualization of Protein Structure-Structure Alignments
M. D. Hansen, S. Lodha, A. Pang; Pacific Symposium on Biocomputing 5:215-226 (2000).

Integrated Tools for Structural and Sequence Alignment and Analysis
C.C. Huang, W.R. Novak, P.C. Babbitt, A.I. Jewett, T.E. Ferrin and T.E. Klein; Pacific Symposium on Biocomputing 5:227-238 (2000).

InVest: Interactive and Visual Edge Selection Tool for Constructing Evolutionary Trees
P. Kearney, A. Secord, and H. Zhang; Pacific Symposium on Biocomputing 5:239-250 (2000).

The Ensemble/Legacy Chimera Extension: Standardized User and Programmer Interface to Molecular Ensemble Data and Legacy Modeling Programs
D.E. Konerding; Pacific Symposium on Biocomputing 5:251-262 (2000).

Generating Interactive Molecular Documentaries Using a Library of Graphical Actions
P. Pulavarthi, R. Chiang, and R.B. Altman; Pacific Symposium on Biocomputing 5:263-274 (2000).

Visual Management of Large Scale Data Mining Projects
I. Shah and L. Hunter; Pacific Symposium on Biocomputing 5:275-287 (2000).

MOLECULAR NETWORK MODELING AND DATA ANALYSIS

Session Introduction
R. Somogyi, H. Kitano, S. Miyano, and Q. Zheng; Pacific Symposium on Biocomputing 5:288-289 (2000).

Algorithms for Inferring Qualitative Models of Biological Networks
T. Akutsu, S. Miyano, and S.Kuhara; Pacific Symposium on Biocomputing 5:290-301 (2000).

Discovery of Regulatory Interactions Through Perturbation: Inference and Experimental Design
T.E. Ideker, V. Thorsson, and R.M. Karp; Pacific Symposium on Biocomputing 5:302-313 (2000).

Construction of a Generalized Simulator for Multi-cellular Organisms and its Application to SMAD Signal Transduction
K. Kyoda, M. Muraki, and H. Kitano; Pacific Symposium on Biocomputing 5:314-325 (2000).

Delta-Notch Lateral Inhibitory Patterning in the Emergence of Ciliated Cells in Xenopus: Experimental Observations and a Gene Network Model
G. Marnellos, G.A. Deblandre, E. Mjolsness, and C. Kintner; Pacific Symposium on Biocomputing 5:326-337 (2000).

Hybrid Petri Net Representation of Gene Regulatory Network
H. Matsuno, A. Doi, M. Nagasaki, and S. Miyano; Pacific Symposium on Biocomputing 5:338-349 (2000).

The Effect of Dynamic Receptor Clustering on the Sensitivity of Biochemical Signaling
C. Zhang and S-H. Kim; Pacific Symposium on Biocomputing 5:350-361 (2000).

DATA MINING AND KNOWLEDGE DISCOVERY IN MOLECULAR DATABASES

Session Introduction
J. Glasgow, I. Jurisica, and R. Ng; Pacific Symposium on Biocomputing 5:362-363 (2000).

Mining the Quantitative Trait Loci Associated with Oral Glucose Tolerance in the Oletf Rat
A. Nakaya, H. Hishigaki, and S. Morishita; Pacific Symposium on Biocomputing 5:364-376 (2000).

Stochastic Segment Models of Eukaroyotic Promoter Regions
U. Ohler, G. Stommer, and S. Harbeck; Pacific Symposium on Biocomputing 5:377-388 (2000).

Stochastic Heuristic Algorithms for Target Motif Identification (Extended Abstract)
H.T. Wareham, T. Jiang, X. Zhang, and C.G. Trendall; Pacific Symposium on Biocomputing 5:389-400 (2000).

Identifying Amino Acid Residues in Medium Resolution Critical Point Graphs Using Instance Based Query Generation
K. Whelan and J. Glasgow; Pacific Symposium on Biocomputing 5:401-412 (2000).

IDENTIFICATION OF COORDIANTED GENE EXPRESSION AND REGULATORY SEQUENCES

Session Introduction
Gary Stormo; Pacific Symposium on Biocomputing 5:413-414 (2000).

Mutual Information Relevance Networks: Functional Genomic Clustering Using Pairwise Entropy Measurements
A. J. Butte and I. S. Kohane; Pacific Symposium on Biocomputing 5:415-426 (2000).

EST Databases as Multi-Conditional Gene Expression Datasets
R.M. Ewing and J-M. Claverie; Pacific Symposium on Biocomputing 5:427-439 (2000).

In Silico Analysis of Gene Expression Patterns During Early Development of Xenopus laevis
N. Pollet, H. Schmidt, V. Gawantka, C. Niehrs, and M. Vingron; Pacific Symposium on Biocomputing 5:440-451 (2000).

Principal Components Analysis to Summarize Microarray Experiments: Application to Sporulation Time Series
S. Raychaudhuri, J.M. Stuart, and R.B. Altman; Pacific Symposium on Biocomputing 5:452-463 (2000).

ANN-Spec: A Method for Discovering Transcription Factor Binding Sites with Improved Specificity
C.T. Workman and G.D. Stormo; Pacific Symposium on Biocomputing 5:464-475 (2000).

Cluster, Function and Promoter: Analysis of Yeast Expression Array
J. Zhu and M. Q. Zhang; Pacific Symposium on Biocomputing 5:476-487 (2000).

NATURAL LANGUAGE PROCESSING FOR BIOLOGY

Session Introduction
T. Tsunoda and L. Wong; Pacific Symposium on Biocomputing 5:488-489 (2000).

Knowledge Representation and Indexing Using the Unified Medical Language System
K. Baclawski, J. Cigna, M.M. Kokar, P. Mager, and B. Indurkhya; Pacific Symposium on Biocomputing 5:490-501 (2000).

Two Applications of Information Extraction to Biological Science Journal Articles: Enzyme Interactions and Protein Structures
K. Humphreys, G. Demetriou and R. Gaizauskas; Pacific Symposium on Biocomputing 5:502-513 (2000).

EDGAR: Extraction of Drugs, Genes and Relations from the Biomedical Literature
T.C. Rindflesch, Lorraine Tanabe, John N. Weinstein, and L. Hunter; Pacific Symposium on Biocomputing 5:514-525 (2000).

Biobibliometrics: Information Retrieval and Visualization from Co-Occurrences of Gene Names in Medline Abstracts
B.J. Stapley and G. Benoit; Pacific Symposium on Biocomputing 5:526-537 (2000).

Automatic Extraction of Protein Interactions from Scientific Abstracts
J. Thomas, D. Milward, C. Ouzounis, S. Pulman, and M. Carroll; Pacific Symposium on Biocomputing 5:538-549 (2000).

COMPUTER-AIDED COMBINATORIAL CHEMISTRY & CHEMINFORMATICS

Session Introduction
A. Tropsha and R.S. Pearlman; Pacific Symposium on Biocomputing 5:550-551 (2000).

Compound Acquisition Strategies
J.B. Dunbar; Pacific Symposium on Biocomputing 5:552-562 (2000).

Searching for Molecules with Similar Biological Activity: Analysis by Fingerprint Profiling
J.W. Godden, L. Xue, F.L. Stahura, and J. Bajorath; Pacific Symposium on Biocomputing 5:563-572 (2000).

Library Design and Virtual Screening Using Multiple 4-Point Pharmacophore Fingerprints
J.S. Mason and D.L. Cheney; Pacific Symposium on Biocomputing 5:573-584 (2000).

Piccolo: A Tool For Combinatorial Library Design Via Multicriterion Optimization
W. Zheng, S. T. Hung, J. T. Saunders, and G. L. Seibel; Pacific Symposium on Biocomputing 5:585-596 (2000).

APPLICATIONS OF INFORMATION THEORY IN BIOLOGY

Session Introduction
T.G. Dewey and H. Herzel; Pacific Symposium on Biocomputing 5:597-598 (2000).

Information Dynamics of In Vitro Selection-Amplification Systems
T.G. Dewey; Pacific Symposium on Biocomputing 5:599-610 (2000).

Average Mutual Information of Coding and Noncoding DNA
I. Grosse, S.V. Buldyrev, H. E. Stanley, D. Holste, and H. Herzel; Pacific Symposium on Biocomputing 5:611-620 (2000).

Finite-temperature Sequence Alignment
M. Kschischo and M. Lässig; Pacific Symposium on Biocomputing 5:621-632 (2000).

HUMAN GENOME VARIATION: ANALYSIS, MANAGEMENT AND APPLICATION OF SNP DATA

Session Introduction
F.M. De la Vega and M. Kreitman; Pacific Symposium on Biocomputing 5:633-635 (2000).

ALFRED: A Web-Accessible Allele Frequency Database [corrected 1/14/00]
K-H. Cheung, P.L. Miller, J.R. Kidd, K.K. Kidd, M.V. Osier, and A. J. Pakstis; Pacific Symposium on Biocomputing 5:636-647 (2000).

ALFRED: A Web-Accessible Allele Frequency Database [original version]
K-H. Cheung, P.L. Miller, J.R. Kidd, K.K. Kidd, M.V. Osier, and A. J. Pakstis; Pacific Symposium on Biocomputing 5:636-647 (2000).

Linkage Disequilibrium Mapping: Using Single Nucleotide Polymorphisms - Which Population?
A. Collins; Pacific Symposium on Biocomputing 5:648-659 (2000).

An Analytic Solution to Single Nucleotide Polymorphism Error-Detection Rates in Nuclear Families: Implications for Study Design
D. Gordon, S.M. Leal, S.C. Heath, and J. Ott; Pacific Symposium on Biocomputing 5:660-671 (2000).

The Haplotype Linkage Disequilibrium Test for Genome-Wide Screens: Its Power and Study
M. Xiong, J. Akey, and L. Jin; Pacific Symposium on Biocomputing 5:672-681 (2000).