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