Pacific Symposium on Biocomputing 2001: Mauna Lani, Hawaii 3-7 January 2001 2000

by Altman, Russ B.

• ISBN13: 9789810245153
• ISBN10: 9810245157
• Format: Hardcover
• Copyright: 2001-04-01
• Publisher: WORLD SCIENTIFIC PUB CO INC

Summary

Proceedings of the Pacific Symposium on Computing 2001, held in Mauna Lani, Hawaii, January 3-7, 2001. Topics covered at the symposium include high performance computing for computational biology, structures, phylogenies, and genomes, genome, pathway, and interaction in bioinformatics, and other related subjects.

Table of Contents

Preface	v
HUMAN GENOME VARIATION: LINKING GENOTYPES TO CLINICAL PHENOTYPES
Session Introduction	3	(3)
F. M. De la Vega
M. Kreitman
I. S. Kohane
Determining Significant Fold Differences in Gene Expression Analysis	6	(12)
A. J. Butte
J. Ye
H. U. Haring
M. Stumvoll
M. F. White
I. S. Kohane
Assessment and Management of Single Nucleotide Polymorphism Genotype Errors in Genetic Association Analysis	18	(12)
D. Gordon
J. Ott
Unsupervised Learning from Complex Data: The Matrix Incision Tree Algorithm	30	(12)
J. H. Kim
L. Ohno-Machado
I. S. Kohane
Mutual Information Analysis as a Tool to Assess the Role of Aneuploidy in the Generation of Cancer-Associated Differential Gene Expression Patterns	42	(10)
G. T. Klus
A. Song
A. Schick
M. Wahde
Z. Szallasi
A Nonparametric Scoring Algorithm for Identifying Informative Genes from Microarray Data	52	(15)
P. J. Park
M. Pagano
M. Bonetti
DISORDER AND FLEXIBILITY IN PROTEIN STRUCTURE AND FUNCTION
Session Introduction	64	(3)
C. Bracken
M. M. Young
K. Dunker
An NMR-Based Quenched Hydrogen Exchange Investigation of Model Amyloid Fibrils Formed by Cold Shock Protein A	67	(12)
A. T. Alexandrescu
Collective Reorientational Motion and Nuclear Spin Relaxation in Proteins	79	(10)
J. J. Prompers
S. F. Lienin
R. Bruschweiler
The Protein Non-Folding Problem: Amino Acid Determinants of Intrinsic Order and Disorder	89	(14)
R. M. Williams
Z. Obradovic
V. Mathura
W. Braun
E. C. Garner
J. Young
S. Takayama
C. J. Brown
A. K. Dunker
DNA STRUCTURE, PROTEIN-DNA INTERACTIONS, AND DNA-PROTEIN EXPRESSION
Session Introduction	101	(2)
P. F. Baldi
R. H. Lathrop
Stress-Induced DNA Duplex Destabilization in Transcriptional Initiation	103	(12)
C. J. Benham
SAMIE: Statistical Algorithm for Modeling Interaction Energies	115	(12)
P. V. Benos
A. S. Lapedes
D. S. Fields
G. D. Stormo
BioProspector: Discovering Conserved DNA Motifs in Upstream Regulatory Regions of Co-Expressed Genes	127	(12)
X. Liu
D. L. Brutlag
J. S. Liu
A Structure-Based Approach for Prediction of Protein Binding Sites in Gene-Upstream Regions	139	(12)
Y. Mandel-Gutfreund
A. Baron
H. Margalit
Promoter Region-Based Classification of Genes	151	(16)
P. Pavlidis
T. S. Furey
M. Liberto
D. Haussler
W. N. Grundy
STRUCTURES, PHYLOGENIES, AND GENOMES: THE INTEGRATED STUDY OF PROTEIN EVOLUTION
Session Introduction	164	(3)
R. A. Goldstein
D. D. Pollock
J. L. Thorne
Nucleotide Substitutions and the Evolution of Duplicate Genes	167	(12)
J. S. Conery
M. Lynch
An Algorithm for Statistical Alignment of Sequences Related by a Binary Tree	179	(12)
J. Hein
Analyzing Site Heterogeneity During Protein Evolution	191	(12)
J. M. Koshi
R. A. Goldstein
Markov Chain Monte Carlo Computation of Confidence Intervals for Substitution-Rate Variation in Proteins	203	(12)
A. Rzhetsky
P. Morozov
A Model for Phylogenetic Inference Using Structural and Chemical Covariates	215	(11)
S. Tavare
D. C. Adams
O. Fedrigo
G. J. P. Naylor
Maximum Likelihood Analysis of Adaptive Evolution in HIV-1 GP120 ENV Gene	226	(14)
Z. Yang
HIGH PERFORMANCE COMPUTING FOR COMPUTATIONAL BIOLOGY
Session Introduction	238	(2)
T. Ferrin
B. A. Foster
R. Hughey
View Feature: Integrated Feature Analysis and Visualization	240	(11)
D. R. Banatao
C. C. Huang
P. C. Babbitt
R. B. Altman
T. E. Klein
Analyzing Sensory Systems with the Information Distortion Function	251	(12)
A. G. Dimitrov
J. P. Miller
Sequence Analysis With the Kestrel SIMD Parallel Processor	263	(12)
L. Grate
M. Diekhans
D. Dahle
R. Hughey
A New Algorithm for the Alignment of Multiple Protein Structures Using Monte Carlo Optimization	275	(12)
C. Guda
E. D. Scheeff
P. E. Bourne
I. N. Shindyalov
Gene Verification and Discovery by Walking Tree Method	287	(12)
T. Hsu
P. Cull
Predicting Gene Function from Gene Expressions and Ontologies	299	(12)
T. R. Hvidsten
J. Komorowski
A. K. Sandvik
A. Laegreid
A Multithreaded Parallel Implementation of a Dynamic Programming Algorithm for Sequence Comparison	311	(12)
W. S. Martins
J. B. Del Cuvillo
F. J. Useche
K. B. Theobald
G. R. Gao
Molecular Fingerprinting on the SIMD Parallel Processor Kestrel	323	(12)
E. Rice
R. Hughey
Percolation Clustering: A Novel Approach to the Clustering of Gene Expression Patterns in Dictyostelium Development	335	(13)
R. Sasik
T. Hwa
N. Iranfar
W. F. Loomis
Quality Control in Manufacturing Oligo Arrays: A Combinatorial Design Approach	348	(12)
R. Sengupta
M. Tompa
Using Metacomputing Tools to Facilitate Large Scale Analyses of Biological Databases	360	(14)
A. Waugh
G. A. Williams
L. Wei
R. B. Altman
NATURAL LANGUAGE PROCESSING AND INFORMATION EXTRACTION IN BIOLOGY
Session Introduction	372	(2)
J.-I. Tsujii
L. Wong
Including Biological Literature Improves Homology Search	374	(10)
J. T. Chang
S. Raychaudhuri
R. B. Altman
Textquest: Document Clustering of Medline Abstracts For Concept Discovery In Molecular Biology	384	(12)
I. Iliopoulos
A. J. Enright
C. A. Ouzounis
Bidirectional Incremental Parsing for Automatic Pathway Identification with Combinatory Categorial Grammar	396	(12)
J. C. Park
H. S. Kim
J. J. Kim
Event Extraction from Biomedical Papers Using a Full Parser	408	(14)
A. Yakushiji
Y. Tateisi
Y. Miyao
J.-I. Tsujii
GENOME, PATHWAY, AND INTERACTION BIOINFORMATICS
Session Introduction	420	(2)
P. Karp
E. Neumann
P. Romero
Using Graphical Models and Genomic Expression Data to Statistically Validate Models of Genetic Regulatory Networks	422	(12)
A. J. Hartemink
D. K. Gifford
T. S. Jaakkola
R. A. Young
Reverse Engineering of Metabolic Pathways from Observed Data Using Genetic Programming	434	(12)
J. R. Koza
W. Mydlowec
G. Lanza
J. Yu
M. A. Keane
Development of a System for the Inference of Large Scale Genetic Networks	446	(13)
Y. Maki
D. Tominaga
M. Okamoto
S. Watanabe
Y. Eguchi
Representation and Simulation of Biochemical Processes Using the π-Calculus Process Algebra	459	(12)
A. Regev
W. Silverman
E. Shapiro
Nutrient-Related Analysis of Pathway/Genome Databases	471	(12)
P. R. Romero
P. Karp
Detecting Gene Relations from Medline Abstracts	483	(13)
M. Stephens
M. Palakal
S. Mukhopadhyay
R. Raje
J. Mostafa
On Reporting Fold Differences	496	(12)
C. L. Tsien
T. A. Libermann
X. Gu
I. S. Kohane
A Comparison of Genetic Network Models	508	(12)
L. F. A. Wessels
E. P. Van Someren
M. J. T. Reinders
PIES, A Protein Interaction Extraction System	520	(12)
L. Wong
Simulating the Growth of Viruses	532	(15)
L. You
J. Yin
PHYLOGENETICS IN THE POST-GENOMIC ERA
Session Introduction	544	(3)
J. E. Steinbachs
P. Kearney
Scaling of Accuracy in Extremely Large Phylogenetic Trees	547	(12)
O. R. P. Bininda-Emonds
S. G. Brady
J. Kim
M. J. Sanderson
Exact Algorithms for Computing Pairwise Alignments and 3-Medians From Structure-Annotated Sequences (Extended Abstract)	559	(12)
P. A. Evans
H. T. Wareham
A Tree Obscured By Vines: Horizontal Gene Transfer and the Median Tree Method of Estimating Species Phylogeny	571	(12)
J. Kim
B. A. Salisbury
A New Implementation and Detailed Study of Breakpoint Analysis	583	(12)
B. M. E. Moret
S. Wyman
D. A. Bader
T. Warnow
M. Yan
A New Algorithm for Analysis of Within-Host HIV-1 Evolution	595	(11)
F. Ren
S. Ogishima
H. Tanaka
Efficiencies of Genes and Accuracy of Tree-Building Methods in Recovering a Known Drosophila Genealogy	606
J. E. Steinbachs
N. V. Schizas
W. O. Ballard
BIOETHICS, FICTION SCIENCE, AND THE FUTURE OF MANKIND
Session Introduction	618
P. Baldi
S. Brunak