Bioinformatics Research and Applications

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.