| Preface | |
| Design of a High-Throughput Assay for Alternative Splicing Using Polymerase Colonies | p. 5 |
| The Effects of Alternative Splicing on Transmembrane Proteins in the Mouse Genome | p. 17 |
| Genome-Wide Detection of Alternative Splicing in Expressed Sequences Using Partial Order Multiple Sequence Alignment Graphs | p. 29 |
| Detection of Novel Splice Forms in Human and Mouse Using Cross-Species Approach | p. 42 |
| Extensive Search for Discriminative Features of Alternative Splicing | p. 54 |
| Transcriptome and Genome Conservation of Alternative Splicing Events in Humans and Mice | p. 66 |
| A Database Designed to Computationally Aid an Experimental Approach to Alternative Splicing | p. 78 |
| Pedigree Generation for Analysis of Genetic Linkage and Association | p. 93 |
| A Markov Chain Approach to Reconstruction of Long Haplotypes | p. 104 |
| Tradeoff Between No-Call Reduction in Genotyping Error Rate and Loss of Sample Size for Genetic Case/Control Association Studies | p. 116 |
| A Comparison of Different Strategies for Computing Confidence Intervals of the Linkage Disequilibrium Measure D' | p. 128 |
| Multiplexing Schemes for Generic SNP Genotyping Assays | p. 140 |
| Haplotype Block Definition and Its Application | p. 152 |
| Part-of Relations in Anatomy Ontologies: A Proposal for RDFS and OWL Formalisations | p. 166 |
| Building Mouse Phenotype Ontologies | p. 178 |
| An Evidence Ontology for Use in Pathway/Genome Databases | p. 190 |
| Terminological Mapping for High Throughput Comparative Biology of Phenotypes | p. 202 |
| The Compositional Structure of Gene Ontology Terms | p. 214 |
| Defaults, Context, and Knowledge: Alternatives for OWL-Indexed Knowledge Bases | p. 226 |
| Biological Nomenclatures: A Source of Lexical Knowledge and Ambiguity | p. 238 |
| Investigating Implicit Knowledge in Ontologies with Application to the Anatomical Domain | p. 250 |
| ProGreSS: Simultaneous Searching of Protein Databases by Sequence and Structure | p. 264 |
| Predicting the Operon Structure of Bacillus subtilis Using Operon Length, Intergene Distance, and Gene Expression Information | p. 276 |
| Combining Text Mining and Sequence Analysis to Discover Protein Functional Regions | p. 288 |
| Kernel-Based Data Fusion and Its Application to Protein Function Prediction in Yeast | p. 300 |
| Discovery of Binding Motif Pairs from Protein Complex Structural Data and Protein Interaction Sequence Data | p. 312 |
| Phylogenetic Motif Detection by Expectation-Maximization on Evolutionary Mixtures | p. 324 |
| Using Protein-Protein Interactions for Refining Gene Networks Estimated from Microarray Data by Bayesian Networks | p. 336 |
| Motif Discovery in Heterogeneous Sequence Data | p. 348 |
| Negative Information for Motif Discovery | p. 360 |
| The Status of Structural Genomics Defined Through the Analysis of Current Targets and Structures | p. 375 |
| Protein Structure and Fold Prediction Using Tree-Augmented Naive Bayesian Classifier | p. 387 |
| Clustering Protein Sequence and Structure Space with Infinite Gaussian Mixture Models | p. 399 |
| Accurate Classification of Protein Structural Families Using Coherent Subgraph Analysis | p. 411 |
| Identifying Good Predictions of RNA Secondary Structure | p. 423 |
| Exploring Bias in the Protein Data Bank Using Contrast Classifiers | p. 435 |
| Geometric Analysis of Cross-Linkability for Protein Fold Discrimination | p. 447 |
| Protein Fold Recognition Through Application of Residual Dipolar Coupling Data | p. 459 |
| A Mixed Integer Linear Programming (MILP) Framework for Inferring Time Delay in Gene Regulatory Networks | p. 474 |
| Robust Identification of Large Genetic Networks | p. 486 |
| Reconstructing Chain Functions in Genetic Networks | p. 498 |
| Inferring Gene Regulatory Networks from Raw Data - A Molecular Epistemics Approach | p. 510 |
| A Biospi Model of Lymphocyte-Endothelial Interactions in Inflamed Brain Venules | p. 521 |
| Modeling Cellular Processes with Variational Bayesian Cooperative Vector Quantizer | p. 533 |
| Symbolic Inference of Xenobiotic Metabolism | p. 545 |
| Finding Optimal Models for Small Gene Networks | p. 557 |
| Pathway Logic Modeling of Protein Functional Domains in Signal Transduction | p. 568 |
| Modeling Gene Expression from Microarray Expression Data with State-Space Equations | p. 581 |
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