Preface

HUMAN GENOME VARIATION: LINKING GENOTYPES TO CLINICAL PHENOTYPES

Session Introduction
F.M. De la Vega, M. Kreitman, and I.S. Kohane; Pacific Symposium on Biocomputing 6:3-5 (2001).

Determining Significant Fold Differences in Gene Expression Analysis
A. J. Butte, J.Ye, G. Niederfellner, K. Rett, H.U. Häring, M.F.White, and I. S. Kohane ; Pacific Symposium on Biocomputing 6:6-17 (2001).

Assessment and Management of Single Nucleotide Polymorphism Genotype Errors in Genetic Association
D. Gordon and J. Ott ; Pacific Symposium on Biocomputing 6:18-29 (2001).

Unsupervised Learning from Complex Data: The Matrix Incision Tree Algorithm
J.H. Kim, L. Ohno-Machado, and I.S. Kohane ; Pacific Symposium on Biocomputing 6:30-41 (2001).

Mutual Information Analysis as a Tool to Assess the Role of Aneuploidy in the Generation of Cancer-Associated Differential Gene Expression Patterns
G.T. Klus, A. Song, A. Schick, M. Wahde, and Z. Szallasi ; Pacific Symposium on Biocomputing 6:42-51 (2001).

A Nonparametric Scoring Algorithm for Identifying Informative Genes from Microarray Data
P.J. Park, M. Pagano, and M. Bonetti ; Pacific Symposium on Biocomputing 6:52-63 (2001).

DISORDER AND FLEXIBILITY IN PROTEIN STRUCTURE AND FUNCTION

Session Introduction
C. Bracken, M.M. Young, and K. Dunker; Pacific Symposium on Biocomputing 6:64-66 (2001).

An NMR-Based Quenched Hydrogen Exchange Investigation of Model Amyloid Fibrils Formed by Cold Shock Protein A
A.T. Alexandrescu; Pacific Symposium on Biocomputing 6:67-78 (2001).

Collective Reorientational Motion and Nuclear Spin Relaxation in Proteins
J.J. Prompers, S.F. Lienin, and R. Brüschweiler; Pacific Symposium on Biocomputing 6:79-88 (2001).

The Protein Non-Folding Problem: Amino Acid Determinants of Intrinsic Order and Disorder
R.M. Williams, Z. Obradovic, V. Mathura, W. Braun, E.C. Garner, J. Young, S. Takayama, C. J. Brown, and A.K. Dunker; Pacific Symposium on Biocomputing 6:89-100 (2001).

DNA STRUCTURE, PROTEIN-DNA INTERACTIONS, AND DNA-PROTEIN EXPRESSION

Session Introduction
P.F. Baldi and R.H. Lathrop; Pacific Symposium on Biocomputing 6:101-102 (2001).

Stress-Induced DNA Duplex Destabilization in Transcriptional Initiation
C.J. Benham; Pacific Symposium on Biocomputing 6:103114- (2001).

SAMIE: Statistical Algorithm for Modeling Interaction Energies
P.V. Benos, A.S. Lapedes, D.S. Fields, and G.D. Stormo ; Pacific Symposium on Biocomputing 6:115-126 (2001).

BioProspector: Discovering Conserved DNA Motifs in Upstream Regulatory Regions of Co-Expressed Genes
X. Liu, D.L. Brutlag, and J.S. Liu; Pacific Symposium on Biocomputing 6:127-138 (2001).

A Structure-Based Approach for Prediction of Protein Binding Sites in Gene-Upstream Regions
Y. Mandel-Gutfreund, A. Baron, and H. Margalit; Pacific Symposium on Biocomputing 6:139-150 (2001).

Promoter Region-Based Classification of Genes
P. Pavlidis, T. S. Furey, M. Liberto, D. Haussler, and W. N. Grundy; Pacific Symposium on Biocomputing 6:151-164 (2001).

STRUCTURES, PHYLOGENIES, AND GENOMES: THE INTEGRATED STUDY OF PROTEIN EVOLUTION

Session Introduction
R.A. Goldstein, D.D. Pollock, and J.L. Thorne; Pacific Symposium on Biocomputing 6:164-166 (2001).

Nucleotide Substitutions and the Evolution of Duplicate Genes
J.S. Conery and M. Lynch; Pacific Symposium on Biocomputing 6:167-178 (2001).

An Algorithm for Statistical Alignment of Sequences Related by a Binary Tree
J. Hein; Pacific Symposium on Biocomputing 6:179-190 (2001).

Analyzing Rate Heterogeneity During Protein Evolution
K.M. Koshi and R.A. Goldstein; Pacific Symposium on Biocomputing 6:191-202 (2001).

Markov Chain Monte Carlo Computation of Confidence Intervals for Substitution-Rate Variation in Proteins
A. Rzhetsky and P. Morozov ; Pacific Symposium on Biocomputing 6:203-214 (2001).

A Model for Phylogenetic Inference Using Structural and Chemical Covariates
S. Tavaré, D.C. Adams, O. Fedrigo, and G.J.P. Naylor; Pacific Symposium on Biocomputing 6:215-225 (2001).

Maximum Likelihood Analysis of Adaptive Evolution in HIV-1 Gp120 env Gene
Z. Yang; Pacific Symposium on Biocomputing 6:226-237 (2001).

HIGH PERFORMANCE COMPUTING FOR COMPUTATIONAL BIOLOGY

Session Introduction
T. Ferrin, B.A. Foster, and R. Hughey; Pacific Symposium on Biocomputing 6:238-239 (2001).

ViewFeature: Integrated Feature Analysis and Visualization
D.R. Banatao, C.C. Huang, P.C. Babbitt, R.B. Altman, and T.E. Klein ; Pacific Symposium on Biocomputing 6:240-250 (2001).

Analyzing Sensory Systems with the Information Distortion Function
A.G. Dimitrov and J.P. Miller; Pacific Symposium on Biocomputing 6:251-262 (2001).

Sequence Analysis With the Kestrel SIMD Parallel Processor
L. Grate, M. Diekhans, D. Dahle, and R. Hughey; Pacific Symposium on Biocomputing 6:263-274 (2001).

A New Algorithm for the Alignment of Multiple Protein Structures Using Monte Carlo Optimization
C. Guda, E. D. Scheeff, P. E. Bourne, and I. N. Shindyalov; Pacific Symposium on Biocomputing 6:275-286 (2001).

Gene Verification and Discovery by Walking Tree Method
T. Hsu and P. Cull; Pacific Symposium on Biocomputing 6:287-298 (2001).

Predicting Gene Function from Gene Expressions and Ontologies
T.R. Hvidsten, J. Komorowski, A.K. Sandvik, and A. Lægreid ; Pacific Symposium on Biocomputing 6:299-310 (2001).

A Multithreaded Parallel Implementation of a Dynamic Programming Algorithm for Sequence Comparison
W.S. Martins, J.B. Del Cuvillo, F.J. Useche, K.B. Theobald, and G.R. Gao; Pacific Symposium on Biocomputing 6:311-322 (2001).

Molecular Fingerprinting on the SIMD Parallel Processor Kestrel
E. Rice and R. Hughey ; Pacific Symposium on Biocomputing 6:323-334 (2001).

Percolation Clustering: A Novel Algorithm Applied to the Clustering of Gene Expression Patterns in Dictyostelium Development
R. Sásik, T. Hwa, N. Iranfar, and W.F. Loomis; Pacific Symposium on Biocomputing 6:335-347 (2001).

Quality Control in Manufacturing Oligo Arrays: A Combinatorial Design Approach
R. Sengupta and M. Tompa; Pacific Symposium on Biocomputing 6:348-359 (2001).

Using Metacomputing Tools to Facilitate Large Scale Analyses of Biological Databases
A. Waugh, G.A. Williams, L. Wei, and R.B. Altman; Pacific Symposium on Biocomputing 6:360-371 (2001).

NATURAL LANGUAGE PROCESSING FOR BIOLOGY

Session Introduction
J. Tsujii and L. Wong; Pacific Symposium on Biocomputing 6:372-373 (2001).

Including Biological Literature Improves Homology Search
J.T. Chang, S. Raychaudhuri, and R.B. Altman; Pacific Symposium on Biocomputing 6:374-383 (2001).

TEXTQUEST: Document Clustering of MEDLINE Abstracts For Concept Discovery In Molecular Biology
I. Iliopoulos, A. J. Enright, and C. A. Ouzounis ; Pacific Symposium on Biocomputing 6:384-395 (2001).

Bidirectional Incremental Parsing for Automatic Pathway Identification with Combinatory Categorial Grammar
J. C. Park, H. S. Kim, and J. J. Kim; Pacific Symposium on Biocomputing 6:396-407 (2001).

Event Extraction from Biomedical Papers Using a Full Parser
A. Yakushiji, Y. Tateisi, Y. Miyao, and J. Tsujii; Pacific Symposium on Biocomputing 6:408-419 (2001).

GENOME, PATHWAY AND INTERACTION BIOINFORMATICS

Session Introduction
P. Karp, E. Neumann and P. Romero; Pacific Symposium on Biocomputing 6:420-421 (2001).

Using Graphical Models and Genomic Expression Data to Statistically Validate Models of Genetic Regulatory Networks
A.J. Hartemink, D.K. Gifford, T.S. Jaakkola, and R.A. Young; Pacific Symposium on Biocomputing 6:422-433 (2001).

Reverse Engineering of Metabolic Pathways from Observed Data Using Genetic Programming
J.R. Koza, W. Mydlowec, G. Lanza, J. Yu, and M.A. Keane; Pacific Symposium on Biocomputing 6:434-445 (2001).

Development of a System for the Inference of Large Scale Genetic Networks
Y. Maki, D. Tominaga, M. Okamoto, S. Watanabe, and Y. Eguchi; Pacific Symposium on Biocomputing 6:446-458 (2001).

Representation and Simulation of Biochemical Processes Using the pi- Calculus Process Algebra
A. Regev, W. Silverman, and E. Shapiro; Pacific Symposium on Biocomputing 6:459-470 (2001).

Nutrition-Related Analysis of Pathway/Genome Databases
P.R. Romero and P. Karp; Pacific Symposium on Biocomputing 6:470-482 (2001).

Detecting Gene Relations from MEDLINE Abstracts
M. Stephens, M. Palakal, S. Mukhopadhyay, R. Raje, and J. Mostafa; Pacific Symposium on Biocomputing 6:483-496 (2001).

On Reporting Fold Differences
C.L. Tsien, T.A. Libermann, X. Gu, and I.S. Kohane; Pacific Symposium on Biocomputing 6:496-507 (2001).

A Comparison of Genetic Network Models
L.F.A. Wessels, E.P. Van Someren, and M.J.T. Reinders; Pacific Symposium on Biocomputing 6:508-519 (2001).

PIES, A Protein Interaction Extraction System
L. Wong; Pacific Symposium on Biocomputing 6:520-531 (2001).

Simulating the Growth of Viruses
L. You and J. Yin; Pacific Symposium on Biocomputing 6:532-543 (2001).

PHYLOGENETICS IN THE POST-GENOMIC ERA

Session Introduction
J.E. Steinbachs and P. Kearney; Pacific Symposium on Biocomputing 6:544-546 (2001).

Scaling of Accuracy in Extremely Large Phylogenetic Trees
O.R.P. Bininda-Emonds, S.G. Brady, J. Kim, and M.J. Sanderson; Pacific Symposium on Biocomputing 6:547-558 (2001).

Exact Algorithms for Computing Pairwise Alignments and 3-Medians From Structure-Annotated Sequences (Extended Abstract)
P.A. Evans and H.T. Wareham; Pacific Symposium on Biocomputing 6:559-570 (2001).

A Tree Obscured By Vines: Horizontal Gene Transfer and the Median Tree Method of Estimating Species Phylogeny
J. Kim and B.A. Salisbury ; Pacific Symposium on Biocomputing 6:571-582 (2001).

A New Implmentation and Detailed Study of Breakpoint Analysis
B.M.E. Moret, S. Wyman, D.A. Bader, T. Warnow, and M. Yan; Pacific Symposium on Biocomputing 6:583-594 (2001).

A New Algorithm for Analysis of Within-Host HIV-1 Evolution
F. Ren, S. Ogishima, and H. Tanaka; Pacific Symposium on Biocomputing 6:595-605 (2001).

Efficiencies of Genes and Accuracy of Tree-Building Methods in Recovering a Known Drosophila Genealogy
J.E. Steinbachs, N.V. Schizas, and J.W.O. Ballard; Pacific Symposium on Biocomputing 6:606-617 (2001).

BIOETHICS, FICTION SCIENCE, AND THE FUTURE OF MANKIND

Session Introduction P. Baldi and S. Brunak