PSB 2004 Online Proceedings

PSB Proceedings for All Years

CONTENTS

Preface

Alternative Splicing

Session Introduction
H. Wang, U. Yang, C. Lee, and J. Blume; Pacific Symposium on Biocomputing 9:3-4(2004)
Design of a High-Throughput Assay for Alternative Splicing Using Polymerase Colonies
J.D. Buhler, R.M. Souvenir, W. Zhang, and R.D. Mitra; Pacific Symposium on Biocomputing 9:5-16(2004)
The Effects of Alternative Splicing on Transmembrane Proteins in the Mouse Genome
M.S. Cline, R. Shigeta, R.L. Wheeler, M.A. Siani-Rose, D. Kulp, and A.E. Loraine ; Pacific Symposium on Biocomputing 9:17-28(2004)
Genome-Wide Detection of Alternative Splicing in Expressed Sequences Using Partial Order Multiple Sequence Alignment Graphs
C. Grasso, B. Modrek, Y. Xing, and C. Lee; Pacific Symposium on Biocomputing 9:29-41(2004)
Detection of Novel Splice Forms in Human and Mouse Using Cross-Species Approach
Z. Kan, J. Castle, J. M. Johnson, and N. F. Tsinoremas; Pacific Symposium on Biocomputing 9:42-53(2004)
Extensive Search for Discriminative Features of Alternative Splicing
H. Sakai and O. Maruyama; Pacific Symposium on Biocomputing 9:54-65(2004)
Transcriptome and Genome Conservation of Alternative Splicing Events in Humans and Mice
C.W. Sugnet, W.J. Kent, M. Ares Jr., and D. Haussler; Pacific Symposium on Biocomputing 9:66-77(2004)
A Database Designed to Computationally Aid an Experimental Approach to Alternative Splicing
C.L. Zheng, T.M. Nair, M. Gribskov, Y.S. Kwon, H.R. Li, and X.-D. Fu; Pacific Symposium on Biocomputing 9:78-88(2004)

Computational Tools for Complex Trait Gene Mapping

Session Introduction
F. de la Vega, K. Kidd, and A. Collins; Pacific Symposium on Biocomputing 9:89-92(2004)
Pedigree Generation for Analysis of Genetic Linkage and Association
M.P. Bass, E.R. Martin, and E.R. Hauser; Pacific Symposium on Biocomputing 9:93-103(2004)
A Markov Chain Approach to Reconstruction of Long Haplotypes
L. Eronen, F. Geerts, and H. Toivonen; Pacific Symposium on Biocomputing 9:104-115(2004)
Tradeoff Between No-Call Reduction in Genotyping Error Rate and Loss of Sample Size for Genetic Case/Control Association Studies
S.J. Kang, D. Gordon, A.M. Brown, J. Ott, and S.J. Finch; Pacific Symposium on Biocomputing 9:116-127(2004)
A Comparison of Different Strategies for Computing Confidence Intervals of the Linkage Disequilibrium Measure
S.K. Kim, K. Zhang, and F. Sun; Pacific Symposium on Biocomputing 9:128-139(2004)
Multiplexing Schemes for Generic SNP Genotyping Assays
R. Sharan, A.Ben-Dor, and Z. Yakhini; Pacific Symposium on Biocomputing 9:140-151(2004)
Haplotype Block Definition and Its Application
X. Zhu, S. Zhang, D. Kan, and R. Cooper; Pacific Symposium on Biocomputing 9:152-163(2004)

Biomedical Ontologies

Session Introduction
O. Bodenreider, J.A. Mitchell, and A.T. McCray; Pacific Symposium on Biocomputing 9:164-165(2004)
Part-of Relations in Anatomy Ontologies: A Proposal for RDFS and OWL Formalisations
J.S. Aitken, B.L. Webber, and J.B.L. Bard; Pacific Symposium on Biocomputing 9:166-177(2004)
Building Mouse Phenotype Ontologies
G.V. Gkoutos, E.C.J. Green, A.M. Mallon, J.M. Hancock, and D. Davidson; Pacific Symposium on Biocomputing 9:178-189(2004)
An Evidence Ontology for Use in Pathway/Genome Databases
P.D. Karp, S. Paley, C.J. Krieger, and P. Zhang; Pacific Symposium on Biocomputing 9:190-201(2004)
Terminological Mapping for High Throughput Comparative Biology of Phenotypes
Y.A. Lussier and J. Li; Pacific Symposium on Biocomputing 9:202-213(2004)
The Compositional Structure of Gene Ontology Terms
P.V. Ogren, K.B. Cohen, G.K. Acquaah-Mensah, J. Eberlein, and L. Hunter; Pacific Symposium on Biocomputing 9:214-225(2004)
Defaults, Context, and Knowledge: Alternatives for OWL-Indexed Knowledge Bases
A. Rector; Pacific Symposium on Biocomputing 9:226-237(2004)
Biological Nomenclatures: A Source of Lexical Knowledge and Ambiguity
O. Tuason, L. Chen, H. Liu, J.A Blake, and C. Friedman; Pacific Symposium on Biocomputing 9:238-249(2004)
Investigating Implicit Knowledge in Ontologies with Application to the Anatomical Domain
S. Zhang and O. Bodenreider; Pacific Symposium on Biocomputing 9:250-261(2004)

Joint Learning from Multiple Types of Genomic Data

Session Introduction
A. Hartemink and E. Segal; Pacific Symposium on Biocomputing 9:262-263(2004)
ProGreSS: Simultaneous Searching of Protein Databases by Sequence and Structure
A. Bhattacharya, T. Can, T. Kahveci, A. K. Singh, and Y.-F. Wang; Pacific Symposium on Biocomputing 9:264-275(2004)
Predicting the Operon Structure of Bacillus subtilis Using Operon Length, Intergene Distance, and Gene Expression Information
M.J.L. De Hoon, S. Imoto, K. Kobayashi, N. Ogasawara, and S. Miyano; Pacific Symposium on Biocomputing 9:276-287(2004)
Combining Text Mining and Sequence Analysis to Discover Protein Functional Regions
E. Eskin and E. Agichtein; Pacific Symposium on Biocomputing 9:288-299(2004)
Kernel-Based Data Fusion and Its Application to Protein Function Prediction in Yeast
G. R. G. Lanckriet, M. Deng, N. Cristianini, M. I. Jordan, and W. S. Noble; Pacific Symposium on Biocomputing 9:300-311(2004)
Discovery of Binding Motif Pairs from Protein Complex Structural Data and Protein Interaction Sequence Data
H. Li, J. Li, S.H. Tan, S.-K. Ng; Pacific Symposium on Biocomputing 9:312-323(2004)
Phylogenetic Motif Detection by Expectation-Maximization on Evolutionary Mixtures
A.M. Moses, D.Y. Chiang, and M.B. Eisen; Pacific Symposium on Biocomputing 9:324-335(2004)
Using Protein-Protein Interactions for Refining Gene Networks Estimated from Microarray Data by Bayesian Networks
N. Nariai, S. Kim, S. Imoto, and S. Miyano; Pacific Symposium on Biocomputing 9:336-347(2004)
Motif Discovery in Heterogeneous Sequence Data
A. Prakash, M. Blanchette, S. Sinha, and M. Tompa; Pacific Symposium on Biocomputing 9:348-359(2004)
Negative Information for Motif Discovery
K.T. Takusagawa and D.K. Gifford; Pacific Symposium on Biocomputing 9:360-371(2004)

Informatics Approaches in Structural Genomics

Session Introduction
S.D. Mooney, P.E. Bourne, and P.C. Babbitt; Pacific Symposium on Biocomputing 9:372-374(2004)
The Status of Structural Genomics Defined Through the Analysis of Current Targets and Structures
P.E. Bourne, C.K.J. Allerston, W. Krebs, W. Li, I.N. Shindyalov, A. Godzik, I. Friedberg, T. Liu, D. Wild, S. Hwang, Z. Ghahramani, L. Chen, and J. Westbrook; Pacific Symposium on Biocomputing 9:375-386(2004)
Protein Structure and Fold Prediction Using Tree-Augmented Bayesian Classifier
A. Chinnasamy, W.-K. Sung, and A. Mittal; Pacific Symposium on Biocomputing 9:387-398(2004)
Clustering Protein Sequence and Structure Space with Infinite Gaussian Mixture Models
A. Dubey, S. Hwang, C. Rangel, C.E. Rasmussen, Z. Ghahramani, and D.L. Wild; Pacific Symposium on Biocomputing 9:399-410(2004)
Accurate Classification of Protein Structural Families Using Coherent Subgraph Analysis
J. Huan, W. Wang, A. Washington, J. Prins, R. Shah, and A. Tropsha; Pacific Symposium on Biocomputing 9:411-422(2004)
Identifying Good Predictions of RNA Secondary Structure
M.E. Nebel; Pacific Symposium on Biocomputing 9:423-434(2004)
Exploring Bias in the Protein Data Bank Using Contrast Classifiers
K. Peng, Z. Obradovic, and S. Vucetic; Pacific Symposium on Biocomputing 9:435-446(2004)
Geometric Analysis of Cross-Linkability for Protein Fold Discrimination
S. Potluri, A.A. Khan, A. Kuzminykh, J.M. Bujnicki, A.M. Friedman, and C. Bailey-Kellogg; Pacific Symposium on Biocomputing 9:447-458(2004)
Protein Fold Recognition Through Application of Residual Dipolar Coupling Data
Y. Qu, J.-T. Guo, V. Olman, and Y. Xu; Pacific Symposium on Biocomputing 9:459-470(2004)

Computational and Symbolic Systems Biology

Session Introduction
T. Ideker, E. Neumann, and V. Schachter; Pacific Symposium on Biocomputing 9:471-473(2004)
A Mixed Integer Linear Programming (MILP) Framework for Inferring Time Delay in Gene Regulatory Networks
M. Dasika, A. Gupta, C.D. Maranas, and J.D. Varner; Pacific Symposium on Biocomputing 9:474-485(2004)
Robust Identification of Large Genetic Networks
D. Di Bernardo, T.S. Gardner, and J.J. Collins; Pacific Symposium on Biocomputing 9:486-497(2004)
Reconstructing Chain Functions in Genetic Networks
I. Gat-Viks, R. Shamir, R.M. Karp, and R. Sharan; Pacific Symposium on Biocomputing 9:498-509(2004)
Inferring Gene Regulatory Networks from Raw Data: A Molecular Epistemics Approach
D.A. Kightley, N. Chandra, and K. Elliston; Pacific Symposium on Biocomputing 9:510-520(2004)
A Biospi Model of Lymphocyte-Endothelial Interactions in Inflamed Brain Venules
P. Lecca, C. Priami, C. Laudanna, and G. Constantin; Pacific Symposium on Biocomputing 9:521-532(2004)
Modeling Cellular Processes with Variational Bayesian Cooperative Vector Quantizer
X. Lu, M. Hauskrecht, and R.S. Day; Pacific Symposium on Biocomputing 9:533-544(2004)
Symbolic Inference of Xenobiotic Metabolism
D.C. McShan, M. Upadhyaya, and I. Shah; Pacific Symposium on Biocomputing 9:545-556(2004)
Finding Optimal Models for Small Gene Networks
S. Ott, S. Imoto, and S. Miyano; Pacific Symposium on Biocomputing 9:557-567(2004)
Pathway Logic Modeling of Protein Functional Domains in Signal Transduction
C. Talcott, S. Eker, M. Knapp, P. Lincoln, and K. Laderoute; Pacific Symposium on Biocomputing 9:568-580(2004)
Modeling Gene Expression from Microarray Expression Data with State-Space Equations
F.X. Wu, W.J. Zhang, and A.J. Kusalik; Pacific Symposium on Biocomputing 9:581-592(2004)
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