Biocomputing 2002 : Proceedings of the Pacific Symposium Kauai, Hawaii, USA 3 - 7 January 2002

by Altman, Russ B.; Dunker, A. Keith; Hunter, Lawrence; Lauderdale, Kevin; Klein, T. E. D.

• ISBN13: 9789810247775
• ISBN10: 981024777X
• Format: Hardcover
• Copyright: 2002-03-01
• Publisher: WORLD SCIENTIFIC PUB CO INC

Summary

Proceedings of the Pacific Symposium, held January 3-7, 2002, in Kauai, Hawaii. The symposium brings together key researchers from the international biocomputing community. Contains peer-reviewed articles in computational biology.

Table of Contents

Preface	v
HUMAN GENOME VARIATION: DISEASE, DRUG RESPONSE, AND CLINICAL PHENOTYPES
Session Introduction	3	(3)
I. Kohane
C. Stephens
J. Schneider
F. De La Vega
A Stability Based Method for Discovering Structure in Clustered Data	6	(12)
A. Ben-Hur
A. Elisseeff
I. Guyon
Singular Value Decomposition Regression Models for Classification of Tumors from Microarray Experiments	18	(12)
D. Ghosh
An Automated Computer System to Support Ultra High Throughput SNP Genotyping	30	(11)
J. Heil
S. Glanowski
J. Scott
E. Winn-Deen
I. McMullen
L. Wu
C. Gire
A. Sprague
Inferring Genotype from Clinical Phenotype through a Knowledge Based Algorithm	41	(12)
B.A. Malin
L.A. Sweeney
A Cellular Automata Approach to Detecting Interactions Among Single-nucleotide Polymorphisms in Complex Multifactorial Diseases	53	(12)
J.H. Moore
L.W. Hahn
Ontology Development for a Pharmacogenetics Knowledge Base	65	(12)
D.E. Oliver
D.L. Rubin
J.M. Stuart
M. Hewett
T.E. Klein
R.B. Altman
A SOFM Approach to Predicting HIV Drug Resistance	77	(11)
R.B. Potter
S. Draghici
Automating Data Acquisition into Ontologies from Pharmacogenetics Relational Data Sources Using Declarative Object Definitions and XML	88	(12)
D.L. Rubin
M. Hewett
D.E. Oliver
T.E. Klein
R.B. Altman
On a Family-Based Haplotype Pattern Mining Method for Linkage Disequilibrium Mapping	100	(15)
S. Zhang
K. Zhang
J. Li
H. Zhao
GENOME-WIDE ANALYSIS AND COMPARATIVE GENOMICS
Session Introduction	112	(3)
I. Dubchak
L. Pachter
L. Wei
Scoring Pairwise Genomic Sequence Alignments	115	(12)
F. Chiaromonte
V.B. Yap
W. Miller
Structure-Based Comparison of Four Eukaryotic Genomes	127	(12)
M. Cline
G. Liu
A.E. Loraine
R. Shigeta
J. Cheng
G. Mei
D. Kulp
M.A. Siani-Rose
Constructing Comparative Genome Maps with Unresolved Marker Order	139	(12)
D. Goldberg
S. McCouch
J. Kleinberg
Representation and Processing of Complex DNA Spatial Architecture and its Annotated Genomic Content	151	(12)
R. Gherbi
J. Herisson
Pairwise RNA Structure Comparison with Stochastic Context-Free Grammars	163	(12)
I. Holmes
G.M. Rubin
Estimation of Genetic Networks and Functional Structures Between Genes by Using Bayesian Networks and Nonparametric Regression	175	(12)
S. Imoto
T. Goto
S. Miyano
Automatic Annotation of Genomic Regulatory Sequences by Searching for Composite Clusters	187	(12)
O.V. Kel-Margoulis
T.G. Ivanova
E. Wingender
A.E. Kel
Euler-PCR: Finishing Experiments for Repeat Resolution	199	(12)
Z. Mulyukov
P.A. Pevzner
The Accuracy of Fast Phylogenetic Methods for Large Datasets	211	(12)
L. Nakhleh
B.M.E. Moret
U. Roshan
K. St. John
J. Sun
T. Warnow
Pre-mRNA Secondary Structure Prediction Aids Splice Site Prediction	223	(12)
D.J. Patterson
K. Yasuhara
W.L. Ruzzo
Finding Weak Motifs in DNA Sequences	235	(12)
S.-H. Sze
M.S. Gelfand
P.A. Pevzner
Evidence for Sequence-Independent Evolutionary Traces in Genomics Data	247	(12)
W. Volkmuth
N. Alexandrov
Multiple Genome Rearrangement by Reversals	259	(12)
S. Wu
X. Gu
High Speed Homology Search with FPGAs	271	(14)
Y. Yamaguchi
T. Maruyama
A. Konagaya
EXPANDING PROTEOMICS TO GLYCOBIOLOGY
Session Introduction	283	(2)
C.-W. von der Lieth
Glycosylation of Proteins: A Computer Based Method for the Rapid Exploration of Comformational Space of N-Glycans	285	(12)
A. Bohne
C.-W. von der Lieth
Data Standardisation in GlycoSuiteDB	297	(13)
C.A. Cooper
M.J. Harrison
J.M. Webster
M.R. Wilkins
N.H. Packer
Prediction of Glycosylation Across the Human Proteome and the Correlation to Protein Function	310	(16)
R. Gupta
S. Brunak
LITERATURE DATA MINING FOR BIOLOGY
Session Introduction	323	(3)
L. Hirschman
J. C. Park
J. Tsujii
C. Wu
L. Wong
Mining MEDLINE: Abstracts, Sentences, or Phrases?	326	(12)
J. Ding
D. Berleant
D. Nettleton
E. Wurtele
Creating Knowledge Repositories from Biomedical Reports: The Medsyndikate Text Mining System	338	(12)
U. Hahn
M. Romacker
S. Schulz
Filling Preposition-Based Templates to Capture Information from Medical Abstracts	350	(12)
G. Leroy
H. Chen
Robust Relational Parsing Over Biomedical Literature: Extracting Inhibit Relations	362	(12)
J. Pustejovsk
J. Castano
J. Zhang
M. Kotecki
B. Cochran
Predicting the Sub-Cellular Location of Proteins from Text Using Support Vector Machines	374	(12)
B.J. Stapley
L.A. Kelley
M.J.E. Sternberg
A Thematic Analysis of the AIDS Literature	386	(14)
W.J. Wilbur
GENOME, PATHWAY AND INTERACTION BIOINFORMATICS
Session Introduction	398	(2)
P. Karp
P. Romero
E. Neumann
Pathway Logic: Symbolic Analysis of Biological Signaling	400	(13)
S. Eker
M. Knapp
K. Laderoute
P. Lincoln
J. Meseguer
K. Sonmez
Towards the Prediction of Complete Protein-Protein Interaction Networks	413	(12)
S.M. Gomez
A. Rzhetsky
Identifying Muscle Regulatory Elements and Genes in the Nematode Caenorhabditis Elegans	425	(12)
D. Guhathakurta
L.A. Schriefer
M.C. Hresko
R.H. Waterston
G.D. Stormo
Combining Location and Expression Data for Principled Discovery of Genetic Regulatory Network Models	437	(13)
A.J. Hartemink
D.K. Gifford
T.S. Jaakkola
R.A. Young
The ERATO Systems Biology Workbench: Enabling Interaction and Exchange Between Software Tools for Computational Biology	450	(12)
M. Hucka
A. Finney
H.M. Sauro
H. Bolouri
J. Doyle
H. Kitano
Genome-Wide Pathway Analysis and Visualization Using Gene Expression Data	462	(12)
M.P. Kurhekar
S. Adak
S. Jhunjhunwala
K. Raghupathy
Exploring Gene Expression Data with Class Scores	474	(12)
P. Pavlidis
D.P. Lewis
W.S. Noble
Guiding Revision of Regulatory Models with Expression Data	486	(12)
J. Shrager
P. Langley
A. Pohorille
Discovery of Causal Relationships in a Gene-Regulation Pathway from a Mixture of Experimental and Observational DNA Microarray Data	498	(14)
C. Yoo
V. Thorsson
G.F. Cooper
PHYLOGENETIC GENOMICS AND GENOMIC PHYLOGENETICS
Session Introduction	510	(2)
S. Stanley
B.A. Salisbury
Shallow Genomics, Phylogenetics, and Evolution in the Family Drosophilidae	512	(12)
M. Zilversmit
P. O'Grady
R. Desalle
Fast Phylogenetic Methods for the Analysis of Genome Rearrangement Data: An Empirical Study	524	(12)
L.-S. Wang
R.K. Jansen
B.M.E. Moret
L.A. Raubeson
T. Warnow
Vertebrate Phylogenomics: Reconciled Trees and Gene Duplications	536	(16)
R.D.M. Page
J.A. Cotton
PROTEINS: STRUCTURE, FUNCTION AND EVOLUTION
Session Introduction	548	(4)
P. Clote
G.J.P. Naylor
Z. Yang
Screened Charge Electrostatic Model in Protein-Protein Docking Simulations	552	(12)
J. Fernandez-Recio
M. Totrov
R. Abagyan
The Spectrum Kernel: A String Kernel for SVM Protein Classification	564	(12)
C. Leslie
E. Eskin
W.S. Noble
Detecting Positively Selected Amino Acid Sites Using Posterior Predictive P-Values	576	(13)
R. Nielsen
J. P Huelsenbeck
Improving Sequence Alignments For Intrinsically Disordered Proteins	589	(12)
P. Radivojac
Z. Obradovic
C.J. Brown
A.K. Dunker
ab initio Folding of Multiple-Chain Proteins	601	(12)
J.A. Saunders
K.D. Gibson
H.A. Scheraga
Investigating Evolutionary Lines of Least Resistance Using the Inverse Protein-Folding Problem	613	(12)
J. Schonfeld
O. Eulenstein
K. Vander Velden
G.J.P. Naylor
Using Evolutionary Methods to Study G-Protein Coupled Receptors	625	(12)
O. Soyer
M.W. Dimmic
R.R. Neubig
R.A. Goldstein
Progress in Predicting Protein Function from Structure: Unique Features of O-Glycosidases	637	(12)
E.W. Stawiski
Y. Mandel-Gutfreund
A.C. Lowenthal
L. M. Gregoret
Support Vector Machine Prediction of Signal Peptide Cleavage Site Using a New Class of Kernels for Strings	649	(12)
J.-P. Vert
Constraint-Based Hydrophobic Core Construction for Protein Structure Prediction in the Face-Centered-Cubic Lattice	661	(12)
S. Will
Detecting Native Protein Folds Among Large Decoy Sets with Hydrophobic Moment Profiling	673
R. Zhou
B.D. Silverman