Pacific Symposium on Biocomputing 2000,9789810241889

Pacific Symposium on Biocomputing 2000

by ; ; ; ;
ISBN13: 9789810241889
ISBN10: 9810241887
Format: Hardcover
Pub. Date: 1999-09-01
Publisher(s): WORLD SCIENTIFIC PUB CO INC
List Price: $235.20

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Summary

Proceedings of the Pacific Symposium on Bio- computing 2000 held in Honolulu, Hawaii, U.S.A., January 4-9, 2000.

Table of Contents

Preface v
PROTEIN EVOLUTION AND STRUCTURAL GENOMICS
Session Introduction
3(3)
D. Frishman
R. A. Goldstein
D. D. Pollock
Enzyme Evolution Explained (Sort Of)
6(12)
A. M. Dean
G. B. Golding
Modeling Evolution at the Protein Level Using an Adjustable Amino Acid Fitness Model
18(12)
M. W. Dimmic
D. P. Mindell
R. A. Goldstein
Protein Folds in the Worm Genome
30(12)
M. Gerstein
J. Lin
H. Hegyi
Sensitive Sequence Comparison as Protein Function Predictor
42(12)
K. Pawlowski
L. Jaroszewski
L. Rychlewski
A. Godzik
High-Throughput Functional Annotation of Novel Gene Products Using Document Clustering
54(15)
A. Renner
A. Aszodi
The Evolution of Duplicated Genes Considering Protein Stability Constraints
69(12)
D. M. Taverna
R. M. Goldstein
Relating Physicochemmical Properties of Amino Acids to Variable Nucleotide Substitution Patterns Among Sites
81(12)
Z. Yang
PROTEIN STRUCTURE PREDICTION IN BIOLOGY AND MEDICINE
Session Introduction
93(2)
R. L. Dunbrack Jr.
K. Dunker
A. Godzik
Algorithmic Approach to Quantifying the Hydrophobic Force Contribution in Protein Folding
95(12)
R. Backofen
S. Will
P. Clote
Eliminating Superfluous Neighbor Pairs While Threading Fold Models
107(12)
J. R. Bienkowska
R. G. Rogers Jr.
T. F. Smith
Hybrid Fold Recognition: Combining Sequence Derived Properties with Evolutionary Information
119(12)
D. Fischer
Folding Nuclei in 3D Protein Structures
131(12)
O. V. Galzitskaya
A. V. Skoogarev
D. N. Ivankov
A. V. Finkelstein
How Universal Are Fold Recognition Parameters. A Comprehensive Study of Alignment and Scoring Function Parameters Influence on Recognition of Distant Folds
143(12)
K. A. Olszewski
Pinpointing the Putative Heparin/Sialic Acid-Binding Residues in the `Sushi' Domain 7 of Factor H: A Molecular Modeling Study
155(13)
S. Ranganathan
D. A. Male
R. J. Ormsby
E. Giannakis
D. L. Gordon
Recognition of Protein Structure: Determining the Relative Energetic Contributions of β-strands, α-helices and Loops
168(11)
B. Reva
S. Topiol
Probing Structure-Function Relationships of the DNA Polymerase Alpha-Associated Zinc-Finger Protein Using Computational Approaches
179(12)
R. Samudrala
Y. Xia
M. Levitt
N. J. Cotton
E. S. Huang
R. Davis
Flexibility and Critical Hydrogen Bonds in Cytochrome C
191(12)
M. F. Thorpe
B. M. Hespenheide
Y. Yang
L. A. Kuhn
MOLECULES TO MAPS: TOOLS FOR VISUALIZATION AND INTERACTION IN COMPUTATIONAL BIOLOGY
Session Introduction
203(3)
E. T. Kraemer
T. E. Ferrin
MappetShow: Non-Linear Visualization for Genome Data
206(12)
F. Guyon
G. Vaysseix
E. Barillot
ProFeel: Low Cost Visual-Haptic Perceptualization of Protein Structure-Structure Alignments
218(12)
M. D. Hansen
S. Lodha
A. Pang
Integrated Tools for Structural and Sequence Alignment and Analysis
230(12)
C. C. Huang
W. R. Novak
P. C. Babbitt
A. I. Jewett
T. E. Ferrin
T. E. Klein
In Vest: Interactive and Visual Edge Selection Tool for Constructing Evolutionary Trees
242(12)
P. Kearney
A. Secord
H. Zhang
The Ensemble/Legacy Chimera Extension: Standardized User and Programmer Interface to Molecular Ensemble Data and Legacy Modeling Programs
254(12)
D. E. Konerding
Generating Interactive Molecular Documentaries Using a Library of Graphical Actions
266(12)
P. Pulavarthi
R. Chiang
R. B. Altman
Visual Management of Large Scale Data Mining Projects
278(13)
I. Shah
L. Hunter
MOLECULAR NETWORK MODELING AND DATA ANALYSIS
Session Introduction
291(2)
R. Somogyi
H. Kitano
S. Miyano
Q. Zheng
Algorithms for Inferring Qualitative Models of Biological Networks
293(12)
T. Akutsu
S. Miyano
S. Kuhara
Discovery of Regulatory Interactions Through Perturbation: Inference and Experimental Design
305(12)
T. E. Ideker
V. Thorsson
R. M. Karp
Construction of a Generalized Simulator for Multi-Cellular Organisms and its Application to SMAD Signal Transduction
317(12)
K. M. Kyoda
M. Muraki
H. Kitano
Delta-Notch Lateral Inhibitory Patterning in the Emergence of Ciliated Cells in Xenopus: Experimental Observations and a Gene Network Model
329(12)
G. Marnellos
G. A. Deblandre
E. Mjolsness
C. Kinter
Hybrid Petri Net Representation of Gene Regulatory Network
341(12)
H. Matsuno
A. Doi
M. Nagasaki
S. Miyano
The Effect of Dynamic Receptor Clustering on the Sensitivity of Biochemical Signaling
353(12)
C. Zhang
S. H. Kim
DATA MINING AND KNOWLEDGE DISCOVERY IN MOLECULAR DATABASES
Session Introduction
365(2)
J. Glasgow
I. Jurisica
R. Ng
Mining the Quantitative Trait Loci Associated with Oral Glucose Tolerance in the Oletf Rat
367(13)
A. Nakaya
H. Hishigaki
S. Morishita
Stochastic Segment Models of Eukaryotic Promoter Regions
380(12)
U. Ohler
G. Stemmer
S. Harbeck
H. Niemann
Stochastic Heuristic Algorithms for Target Motif Identification (Extended Abstract)
392(12)
H. T. Wareham
T. Jiang
X. Zhang
C. G. Trendall
Identifying Amino Acid Residues in Medium Resolution Critical Point Graphs Using Instance Based Query Generation
404(12)
K. Whelan
J. Glasgow
IDENTIFICATION OF COORDINATED GENE EXPRESSION AND REGULATORY SEQUENCES
Session Introduction
416(2)
Gary Stormo
Mutual Information Relevance Networks: Functional Genomic Clustering Using Pairwise Entropy Measurements
418(12)
A. J. Butte
I. S. Kohane
EST Databases as Multi-Conditional Gene Expression Datasets
430(13)
R. M. Ewing
J-M. Claverie
In Silico Analysis of Gene Expression Patterns During Early Development of Xenopus laevis
443(12)
N. Pollet
H. A. Schmidt
V. Gawantka
C. Niehrs
M. Vingrom
Principal Components Analysis to Summarize Microarray Experiments: Application to Sporulation Time Series
455(12)
S. Raychaudhuri
J. M. Stuart
R. B. Altman
ANN-Spec: A Method for Discovering Transcription Factor Binding Sites with Improved Specificity
467(12)
C. T. Workman
G. D. Stormo
Cluster, Function and Promoter:Analysis of Yeast Expression Array
479(12)
J. Zhu
M. Q. Zhang
NATURAL LANGUAGE PROCESSING FOR BIOLOGY
Session Introduction
491(2)
T. Tsunoda
L. Wong
Knowledge Representation and Indexing Using the Unified Medical Language System
493(12)
K. Baclawski
J. Cigna
M. M. Kokar
P. Mager
B. Indurkhya
Two Applications of Information Extraction to Biological Science Journal Articles: Enzyme Interactions and Protein Structures
505(12)
K. Humphreys
G. Demetriou
R. Gaizauskas
EDGAR: Extraction of Drugs, Genes and Relations from the Biomedical Literature
517(12)
T. C. Rindflesch
L. Tanabe
J. N. Weinstein
L. Hunter
Biobibliometrics: Information Retrieval and Visualization from Co-Occurrences of Gene Names in Medline Abstracts
529(12)
B. J. Stapley
G. Benoit
Automatic Extraction of Protein Interactions from Scientific Abstracts
541(12)
J. Thomas
D. Milward
C. Ouzounis
S. Pulman
M. Carroll
COMPUTER-AIDED COMBINATORIAL CHEMISTRY AND CHEMINFORMATICS
Session Introduction
553(2)
A. Tropsha
R. S. Pearlman
Compound Acquisition Strategies
555(11)
J. B. Dunbar Jr.
Searching for Molecules with Similar Biological Activity: Analysis by Fingerprint Profiling
566(10)
J. W. Godden
L. Xue
F. L. Stahura
J. Bajorath
Library Design and Virtual Screening Using Multiple 4-Point Pharmacophore Fingerprints
576(12)
J. S. Mason
D. L. Cheney
Piccolo: A Tool for Combinatorial Library Design Via Multicriterion Optimization
588(12)
W. Zheng
S. T. Hung
J. T. Saunders
G. L. Seibel
APPLICATIONS OF INFORMATION THEORY TO BIOLOGY
Session Introduction
600(2)
T. G. Dewey
H. Herzel
Information Dynamics of In Vitro Selection-Amplification Systems
602(12)
T. G. Dewey
Average Mutual Information of Coding and Noncoding DNA
614(10)
I. Grosse
S. V. Buldyrev
H. E. Stanley
D. Holste
H. Herzel
Finite-Temperature Sequence Alignment
624(12)
M. Kschischo
M. Lassing
HUMAN GENOME VARIATION: ANALYSIS, MANAGEMENT AND APPLICATION OF SNP DATA
Session Introduction
636(3)
F. M. De la Vega
M. Kreitman
ALFRED: A Web-Accessible Allele Frequency Database
639(12)
K-H. Cheung
P. L. Miller
J. R. Kidd
K. K. Kidd
M. V. Osier
A. J. Paksits
Linkage Disequilibrium Mapping Using Single Nucleotide Polymorphisms-Which Population?
651(12)
A. Collins
An Analytic Solution to Single Nucleotide Polymorphism Error-Detection Rates in Nuclear Families: Implications for Study Design
663(12)
D. Gordon
S. M. Leal
S. C. Heath
J. Ott
The Haplotype Linkage Disequilibrium Test for Genome-Wide Screens: Its Power and Study Design
675
M. Xiong
J. Akey
L. Jin

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