Biocomputing 2003 : Proceedings of the Pacific Symposium, Hawaii, USA, 3-7 January 2003

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  • Format: Hardcover
  • Copyright: 2002-12-01
  • Publisher: World Scientific Pub Co Inc

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Supplemental Materials

What is included with this book?


The Pacific Symposium on Biocomputing (PSB 2003) is an international, multidisciplinary conference for the presentation and discussion of current research in the theory and application of computational methods in problems of biological significance. The rigorously peer-reviewed papers and presentations are collected in this archival proceedings volume.PSB 2003 brings together top researchers from the US, the Asia-Pacific region and around the world to exchange research findings and address open issues in all aspects of computational biology. PSB is a forum for the presentation of work in databases, algorithms, interfaces, visualization, modeling and other computational methods, as applied to biological problems, with emphasis on applications in data-rich areas of molecular biology.

Table of Contents

Session Introductionp. 3
Multiclass Cancer Classification Using Gene Expression Profiling and Probabilistic Neural Networksp. 5
Inferring Gene Regulatory Networks from Time-Ordered Gene Expression Data of Bacillus subtilis Using Differential Equationsp. 17
Genome-Wide Analysis of Bacterial Promoter Regionsp. 29
MOPAC: Motif Finding by Preprocessing and Agglomerative Clustering from Microarraysp. 41
Improved Gene Selection for Classification of Microarraysp. 53
Kernel Cox Regression Models for Linking Gene Expression Profiles to Censored Survival Datap. 65
Extracting Conserved Gene Expression Motifs from Gene Expression Datap. 77
Decomposing Gene Expression into Cellular Processesp. 89
Session Introductionp. 101
Suitability and Utility of Computational Analysis Tools: Characterization of Erythrocyte Parameter Variationp. 104
Foundations of a Query and Simulation System for the Modeling of Biochemical and Biological Processesp. 116
Incorporating Biological Knowledge into Evaluation of Causal Regulatory Hypothesesp. 128
Assessment of the Reliability of Protein-Protein Interactions and Protein Function Predictionp. 140
Boundary Formation by Notch Signaling in Drosophila Multicellular Systems: Experimental Observations and Gene Network Modeling by Genomic Object Netp. 152
Influence of Network Topology and Data Collection on Network Inferencep. 164
Session Introductionp. 176
Simultaneous Sequence Alignment and Tree Construction Using Hidden Markov Modelsp. 180
Towards Discovering Structural Signatures of Protein Folds Based on Logical Hidden Markov Modelsp. 192
Automated Construction of Structural Motifs for Predicting Functional Sites on Protein Structuresp. 204
Prediction of Boundaries Between Intrinsically Ordered and Disordered Protein Regionsp. 216
Identifying Structural Motifs in Proteinsp. 228
A Path Planning-Based Study of Protein Folding with a Case Study of Hairpin Formation in Protein G and Lp. 240
Profile-Profile Alignment: A Powerful Tool for Protein Structure Predictionp. 252
Protein Threading by Linear Programmingp. 264
Session Introductionp. 276
Towards Identifying Lateral Gene Transfer Eventsp. 279
Whole Genome Human/Mouse Phylogenetic Footprinting of Potential Transcription Regulatory Signalsp. 291
MAP: Searching Large Genome Databasesp. 303
Towards the Development of Computational Tool for Evaluating Phylogenetic Network Reconstruction Methodsp. 315
Identification of Regulatory Binding Sites Using Minimum Spanning Treesp. 327
Intrasplicing - Analysis of Long Intron Sequencesp. 339
Trajectory Clustering: A Non-Parametric Method for Grouping Gene Expression Time Courses, with Applications to Mammary Developmentp. 351
Algorithms for Multiple Genome Rearrangement by Signed Reversalsp. 363
DIGIT: A Novel Gene Finding Program by Combining Gene-Findersp. 375
Session Introductionp. 388
Evaluation of the Vector Space Representation in Text-Based Gene Clusteringp. 391
Playing Biology's Name Game: Identifying Protein Names in Scientific Textp. 403
Mining Terminological Knowledge in Large Biomedical Corporap. 415
A Biological Named Entity Recognizerp. 427
Linking Biomedical Language Information and Knowledge Resources: GO and UMLSp. 439
A Simple Algorithm for Identifying Abbreviation Definitions in Biomedical Textp. 451
Session Introductionp. 463
Selection of Minimum Subsets of Single Nucleotide Polymorphisms to Capture Haplotype Block Diversityp. 466
On the Power to Detect SNP/Phenotype Association in Candidate Quantitative Trait Loci Genomic Regions: A Simulation Studyp. 478
Errors and Linkage Disequilibrium Interact Multiplicatively when Computing Sample Sizes for Genetic Case-Control Association Studiesp. 490
An MDL Method for Finding Haplotype Blocks and for Estimating the Strength of Haplotype Block Boundariesp. 502
PyPop: A Software Framework for Population Genomics: Analyzing Large-Scale Multi-Locus Genotype Datap. 514
Joint Bayesian Estimation of Mutation Location and Age Using Linkage Disequilibriump. 526
SNP Analysis and Presentation in the Pharmacogenetics of Membrane Transporters Projectp. 535
Methods for Analysis and Visualization of SNP Genotype Data for Complex Diseasesp. 548
Session Introductionp. 562
Functional Discrimination of Gene Expression Patterns in Terms of the Gene Ontologyp. 565
Towards a Broad-Coverage Biomedical Ontology Based on Description Logicsp. 577
Evaluation of Ontology Merging Tools in Bioinformaticsp. 589
Semantic Similarity Measures as Tools for Exploring the Gene Ontologyp. 601
Linking Molecular Imaging Terminology to the Gene Ontology (GO)p. 613
A Methodology to Migrate the Gene Ontology to a Description Logic Environment Using DAML + OILp. 624
Development Under Extreme Conditions: Forensic Bioinformatics in the Wake of the World Trade Center Disasterp. 638
Table of Contents provided by Blackwell. All Rights Reserved.

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