| Invited Keynote Talk: Set-Level Analyses for Genome-Wide Association Data (Abstract) | p. 1 |
| Hierarchical Clustering Using Constraints | p. 2 |
| The Gene-Duplication Problem: Near-Linear Time Algorithms for NNI Based Local Searches | p. 14 |
| A Distance-Based Method for Detecting Horizontal Gene Transfer in Whole Genomes | p. 26 |
| An Approach for Determining Evolutionary Distance in Network-Based Phylogenetic Analysis | p. 38 |
| Pairwise Statistical Significance Versus Database Statistical Significance for Local Alignment of Protein Sequences | p. 50 |
| Estimating Pairwise Statistical Significance of Protein Local Alignments Using a Clustering-Classification Approach Based on Amino Acid Composition | p. 62 |
| Gapped Extension for Local Multiple Alignment of Interspersed DNA Repeats | p. 74 |
| Improved Alignment of Protein Sequences Based on Common Parts | p. 87 |
| Invited Keynote Talk: Computing P-Values for Peptide Identifications in Mass Spectrometry | p. 100 |
| PFP: A Computational Framework for Phylogenetic Footprinting in Prokaryotic Genomes | p. 110 |
| Accelerating the Neighbor-Joining Algorithm Using the Adaptive Bucket Data Structure | p. 122 |
| Generalized Gene Adjacencies, Graph Bandwidth and Clusters in Yeast Evolution | p. 134 |
| Physicochemical Correlation between Amino Acid Sites in Short Sequences under Selective Pressure | p. 146 |
| HCV Quasispecies Assembly Using Network Flows | p. 159 |
| A Dynamic Programming Algorithm for De Novo Peptide Sequencing with Variable Scoring | p. 171 |
| Invited Keynote Talk: Haplotype Sharing for Genome-Wide Case-Control Association Studies (Abstract) | p. 183 |
| Incorporating Literature Knowledge in Bayesian Network for Inferring Gene Networks with Gene Expression Data | p. 184 |
| Integrative Network Component Analysis for Regulatory Network Reconstruction | p. 196 |
| A Graph-Theoretic Method for Mining Overlapping Functional Modules in Protein Interaction Networks | p. 208 |
| Identification of Transcription Factor Binding Sites in Promoter Regions by Modularity Analysis of the Motif Co-occurrence Graph | p. 220 |
| Mean Squared Residue Based Biclustering Algorithms | p. 232 |
| Sparse Decomposition of Gene Expression Data to Infer Transcriptional Modules Guided by Motif Information | p. 244 |
| A Novel Metric for Redundant Gene Elimination Based on Discriminative Contribution | p. 256 |
| Network-Based Inference of Cancer Progression from Microarray Data | p. 268 |
| Invited Keynote Talk: Quiet Revolution: Connectivity in the Cancer Research Community (Abstract) | p. 280 |
| Wavelet-Based 3-D Multifractal Spectrum with Applications in Breast MRI Images | p. 281 |
| Accurate Inverse Consistent Non-rigid Image Registration and Its Application on Automatic Re-contouring | p. 293 |
| GlycoBrowser: A Tool for Contextual Visualization of Biological Data and Pathways Using Ontologies | p. 305 |
| Pattern Matching in RNA Structures | p. 317 |
| The Use of a Conformational Alphabet for Fast Alignment of Protein Structures | p. 331 |
| On-the-Fly Rotamer Pair Energy Evaluation in Protein Design | p. 343 |
| Invited Keynote Talk: Integrative Viral Molecular Epidemiology: Hepatitis C Virus Modeling | p. 355 |
| Multiple Kernel Support Vector Regression for siRNA Efficacy Prediction | p. 367 |
| Hierarchical Clustering Support Vector Machines for Classifying Type-2 Diabetes Patients | p. 379 |
| Computational Mutagenesis of E. Coli Lac Repressor: Insight into Structure-Function Relationships and Accurate Prediction of Mutant Activity | p. 390 |
| Evaluating Genetic Algorithms in Protein-Ligand Docking | p. 402 |
| A Hidden Markov Model Approach for Prediction of Genomic Alterations from Gene Expression Profiling | p. 414 |
| Evolutionary Algorithm for Feature Subset Selection in Predicting Tumor Outcomes Using Microarray Data | p. 426 |
| Incorporating Knowledge of Topology Improves Reconstruction of Interaction Networks from Microarray Data | p. 434 |
| Invited Keynote Talk: Data Mining and Statistical Methods for Analyzing Microarray Experiments (Abstract) | p. 444 |
| Seven Variations of an Alignment Workflow - An Illustration of Agile Process Design and Management in Bio-jETI | p. 445 |
| Supporting Computational Systems Science: Genomic Analysis Tool Federations Using Aspects and AOP | p. 457 |
| BioDQ: Data Quality Estimation and Management for Genomics Databases | p. 469 |
| Stepped Linear Regression to Accurately Assess Statistical Significance in Batch Confounded Differential Expression Analysis | p. 481 |
| Bagging Multiple Comparisons from Microarray Data | p. 492 |
| Human Blood-Brain Differential Gene-Expression Correlates with Dipeptide Frequency of Gene Products | p. 504 |
| Author Index | p. 509 |
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