PSB 2003 Online Proceedings

PSB Proceedings for All Years

CONTENTS

Preface

Gene Regulation

Session Introduction
S. Batzoglou and L. Pachter; Pacific Symposium on Biocomputing 8:3-4(2003).
Multiclass Cancer Classification Using Gene Expression Profiling and Probabilistic Neural Networks
D.P. Berrar, C.S. Downes, W. Dubitzky; Pacific Symposium on Biocomputing 8:5-16(2003).
Inferring Gene Regulatory Networks from Time-Ordered Gene Expression Data of Bacillus Subtilis Using Differential Equations
M.J.L. de Hoon, S. Imoto, K. Kobayashi, N. Ogasawara, S. Miyano; Pacific Symposium on Biocomputing 8:17-28(2003).
Genome-Wide Analysis of Bacterial Promoter Regions
E. Eskin, M. Gelfand, P. Pevzner; Pacific Symposium on Biocomputing 8:29-40(2003).
MOPAC: MOtif Finding by Preprocessing and Agglomerative Clustering from Microarrays
R. Ganesh, T.R. Ioerger, D.A. Siegele; Pacific Symposium on Biocomputing 8:41-52(2003).
Improved Gene Selection for Classification of Microarrays
J. Jaeger, R. Sengupta, W.L. Ruzzo; Pacific Symposium on Biocomputing 8:53-64(2003).
Kernel Cox Regression Models for Linking Gene Expression Profiles to Censored Survival Data
H. Li, Y. Luan; Pacific Symposium on Biocomputing 8:65-76(2003).
Extracting Conserved Gene Expression Motifs from Gene Expression Data
T.M. Murali, S. Kasif; Pacific Symposium on Biocomputing 8:77-88(2003).
Decomposing Gene Expression into Cellular Processes
E. Segal, A. Battle, D. Koller; Pacific Symposium on Biocomputing 8:89-100(2003).

Genome, Pathway, and Interaction Bioinformatics

Session Introduction
P. Karp, E. Neumann, A. Hartemink, and P. Romero ; Pacific Symposium on Biocomputing 8:101-103(2003).
Suitability and Utility of Computational Analysis Tools: Characterization of Erythrocyte Parameter Variation
R.E. Altenbaugh, K.J. Kauffman, J.S. Edwards; Pacific Symposium on Biocomputing 8:104-115(2003).
Foundations of a Query and Simulation System for the Modeling of Biochemical and Biological Processes
M. Antoniotti, F. Park, A. Policiriti, N. Ugel, B. Mishra; Pacific Symposium on Biocomputing 8:116-127(2003).
Incorporating Biological Knowledge into Evaluation of Causal Regulatory Hypotheses
L. Chrisman, P. Langley, S. Bay; Pacific Symposium on Biocomputing 8:128-139(2003).
Assessment of the reliability of protein-protein interactions and protein function prediction
M. Deng, F. Sun, T. Chen; Pacific Symposium on Biocomputing 8:140-151(2003).
Boundary Formation by Notch Signaling in Drosophila Multicellular Systems: Experimental Observations and Gene Network Modeling by Genomic Object Net
H. Matsuno, R. Murakani, R. Yamane, N. Yamasaki, S. Fujita, H. Yoshimori, S. Miyano; Pacific Symposium on Biocomputing 8:152-163(2003).
Influence of Network Topology and Data Collection on Network Inference
V.A. Smith, E.D. Jarvis, A.J. Hartemink; Pacific Symposium on Biocomputing 8:164-175(2003).

Informatics Approaches in Structural Genomics

Session Introduction
S.D. Mooney and P.C. Babbitt ; Pacific Symposium on Biocomputing 8:176-179(2003).
Simultaneous Sequence Alignment and Tree Construction Using Hidden Markov Models
R.C. Edgar, K. Sjölander; Pacific Symposium on Biocomputing 8:180-191(2003).
Towards Discovering Structural Signatures of Protein Folds Based on Logical Hidden Markov Models
K. Kersting, T. Raiko, S. Kramer, L. De Raedt; Pacific Symposium on Biocomputing 8:192-203(2003).
Automated Construction of Structural Motifs for Predicting Functional Sites on Protein Structures
M.P. Liang, D.L. Brutlag, R.B. Altman; Pacific Symposium on Biocomputing 8:204-215(2003).
Prediction of Boundaries Between Intrinsically Ordered and Disordered Protein Regions
P. Radivojac, Z. Obradovic, C.J. Brown, A.K. Dunker; Pacific Symposium on Biocomputing 8:216-227(2003).
Identifying Structural Motifs in Proteins
R. Singh, M. Saha; Pacific Symposium on Biocomputing 8:228-239(2003).
A Path Planning-Based Study of Protein Folding with a Case Study of Hairpin Formation in Protein G and L
G. Song, S. Thomas, K.A. Dill, J.M. Scholtz, N.M. Amato; Pacific Symposium on Biocomputing 8:240-251(2003).
Profile-Profile Alignment: A Powerful Tool for Protein Structure Prediction
N. von Öhsen, I. Sommer, R. Zimmer; Pacific Symposium on Biocomputing 8:252-263(2003).
Protein Threading by Linear Programming
J. Xu, M. Li, G. Lin, D. Kim, Y. Xu; Pacific Symposium on Biocomputing 8:264-275(2003).

Genome-wide Analysis and Comparative Genomics

Session Introduction
I. Dubchak, V. Solovyev, and L. Wei; Pacific Symposium on Biocomputing 8:276-278(2003).
Towards Identifying Lateral Gene Transfer Events
L. Addario-Berry, M. Hallett, J. Lagergren; Pacific Symposium on Biocomputing 8:279-290(2003).
Whole Genome Human/Mouse Phylogenetic Footprinting of Potential Transcription Regulatory Signals
E. Cheremushkin, A. Kel; Pacific Symposium on Biocomputing 8:291-302(2003).
MAP: Searching Large Genome Databases
T. Kahveci, A. Singh; Pacific Symposium on Biocomputing 8:303-314(2003).
Towards the Development of Computational Tools for Evaluating Phylogenetic Network Reconstruction Methods
L. Nakhleh, J. Sun, T. Warnow, C.R. Linder, B.M.E. Moret, A. Tholse; Pacific Symposium on Biocomputing 8:315-326(2003).
Identification of Regulatory Binding Sites Using Minimum Spanning Trees
V. Olman, D. Xu, Y. Xu; Pacific Symposium on Biocomputing 8:327-338(2003).
Intrasplicing - Analysis of Long Intron Sequences
S. Ott, Y. Tamada, H. Bannai, K. Nakai, and S. Miyano; Pacific Symposium on Biocomputing 8:339-350(2003).
Trajectory Clustering: A Non-Parametric Method for Grouping Gene Expression Time Courses with Applications to Mammary Development
T.L. Phang, M.C. Neville, M. Rudolph, L. Hunter; Pacific Symposium on Biocomputing 8:351-362(2003).
Algorithms for Multiple Genome Rearrangement by Signed Reversals
S. Wu, X. Gu; Pacific Symposium on Biocomputing 8:363-374(2003).
DIGIT: A Novel Gene Finding Program by Combining Gene-Finders
T. Yada, Y. Totoki, Y. Takaeda, Y. Sakaki, T. Takagi; Pacific Symposium on Biocomputing 8:375-387(2003).

Linking Biomedical Language, Information and Knowledge

Session Introduction
C. Friedman, L. Hirschman, R. McEntire, and C. Wu ; Pacific Symposium on Biocomputing 8:388-390(2003).
Evaluation of the Vector Space Representation in Text-Based Gene Clustering
P. Glenisson, P. Antal, J. Mathys, Y. Moreau, B. De Moor; Pacific Symposium on Biocomputing 8:391-402(2003).
Playing Biology's Name Game: Identifying Protein Names in Scientific Text
D. Hanisch, J. Fluck, HT. Mevissen, R. Zimmer; Pacific Symposium on Biocomputing 8:403-414(2003).
Mining Terminological Knowledge in Large Biomedical Corpora
H. Liu, C. Friedman; Pacific Symposium on Biocomputing 8:415-426(2003).
A Biological Named Entity Recognizer
M. Narayanaswamy, K. E. Ravikumar, K. Vi jay-Shanker; Pacific Symposium on Biocomputing 8:427-438(2003).
Linking Biomedical Language Information and Knowledge Resources in the 21st Century: GO and UMLS
I.N. Sarkar, M.N. Cantor, R. Gelman, F. Hartel, Y.A. Lussier; Pacific Symposium on Biocomputing 8:439-450(2003).
A Simple Algorithm for Identifying Abbreviation Definitions in Biomedical Text
A.S. Schwartz, M.A. Hearst; Pacific Symposium on Biocomputing 8:451-462(2003).

Human Genome Variation: Haplotypes, Linkage Disequilibrium, and Populations

Session Introduction
F.M. De La Vega, K. Kidd, and I. Kohane ; Pacific Symposium on Biocomputing 8:463-465(2003).
Selection of Minimum Subsets of Single Nucleotide Polymorphisms to Capture Haplotype Block Diversity
H.I. Avi-Itzhak, X. Su, F.M. De La Vega; Pacific Symposium on Biocomputing 8:466-477(2003).
On the Power to Detect SNP/Phenotype Association in Candidate Quantitative Trait Loci Genomic Regions: A Simulation Study
J.M. Comeron, M. Kreitman, F.M. De La Vega; Pacific Symposium on Biocomputing 8:478-489(2003).
Errors and Linkage Disequilibrium Interact Multiplicatively When Computing Sample Sizes for Genetic Case-Control Association Studies
D. Gordon, M.A. Levenstien, S.J. Finch, J. Ott; Pacific Symposium on Biocomputing 8:490-501(2003).
An MDL Method for Finding Haplotype Blocks and for Estimating the Strength of Haplotype Block Boundaries
M. Koivisto, M. Perola, T. Varilo, W. Hennah, J. Ekelund, M. Lukk, L. Peltonen, E. Ukkonen, H. Mannila; Pacific Symposium on Biocomputing 8:502-513(2003).
PyPop: A Software Framework for Population Genomics: Analyzing Large-Scale Multi-Locus Genotype Data
A. Lancaster, M. Nelson, D. Meyer, R. Single, G. Thomson; Pacific Symposium on Biocomputing 8:514-525(2003).
Joint Bayesian Estimation of Mutation Location and Age Using Linkage Disequilibrium
B. Rannala, J.P. Reeve; Pacific Symposium on Biocomputing 8:526-534(2003).
SNP Analysis and Presentation in the Pharmacogenetics of Membrane Transporters Project
D. Stryke, C.C. Huang, M. Kawamoto, S.J. Johns, E.J. Carlson, J.A. Deyoung, M.K. Leabman, I. Herskowitz, K.M. Giacomini, T.E. Ferrin; Pacific Symposium on Biocomputing 8:535-547(2003).
Methods for Analysis and Visualization of SNP Genotype Data for Complex Diseases
A. Tsalenko, A. Ben-Dor, N. Cox, Z. Yakhini; Pacific Symposium on Biocomputing 8:548-561(2003).

Biomedical Ontologies

Session Introduction
O. Bodenreider, J.A. Mitchell, and A.T. McCray ; Pacific Symposium on Biocomputing 8:562-564(2003).
Functional Discrimination of Gene Expression Patterns in Terms of the Gene Ontology
L. Badea; Pacific Symposium on Biocomputing 8:565-576(2003).
Towards a Broad-Coverage Biomedical Ontology Based on Description Logics
U. Hahn, S. Schulz; Pacific Symposium on Biocomputing 8:577-588(2003).
Evaluation of Ontology Merging Tools in Bioinformatics
P. Lambrix, A. Edberg; Pacific Symposium on Biocomputing 8:589-600(2003).
Semantic Similarity Measures as Tools for Exploring the Gene Ontology
P.W. Lord, R.D. Stevens, A. Brass, C.A.Goble; Pacific Symposium on Biocomputing 8:601-612(2003).
Linking Molecular Imaging Terminology to the Gene Ontology (GO)
P.K. Tulipano, W. Millar, J.J. Cimino; Pacific Symposium on Biocomputing 8:613-623(2003).
A Methodology to Migrate the Gene Ontology to a Description Logic Environment Using DAML+OIL
C.J. Wroe, R. Stevens, C.A. Goble, M. Ashburner; Pacific Symposium on Biocomputing 8:624-635(2003).

Special Paper

Introduction
R.B. Altman, A.K. Dunker, L. Hunter, T.E. Klein; Pacific Symposium on Biocomputing 8:636-637(2003).
Development Under Extreme Conditions: Forensic Bioinformatics in the Wake of the World Trade Center Disaster
H.D. Cash, J.W. Hoyle, A.J. Sutton; Pacific Symposium on Biocomputing 8:638-653(2003).
Paper is temporarily unavailable per Dr. Howard Cash's request.
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