Bioinformatics Research and Applications: Fourth International Symposium, ISBRA 2008, Atlanta, GA, USA, May 6-9, 2008. Proceedings

Front Matter....Pages -
 Invited Keynote Talk: Set-Level Analyses for Genome-Wide Association Data....Pages 1-1
Hierarchical Clustering Using Constraints....Pages 2-13
The Gene-Duplication Problem: Near-Linear Time Algorithms for NNI Based Local Searches....Pages 14-25
A Distance-Based Method for Detecting Horizontal Gene Transfer in Whole Genomes....Pages 26-37
An Approach for Determining Evolutionary Distance in Network-Based Phylogenetic Analysis....Pages 38-49
Pairwise Statistical Significance Versus Database Statistical Significance for Local Alignment of Protein Sequences....Pages 50-61
Estimating Pairwise Statistical Significance of Protein Local Alignments Using a Clustering-Classification Approach Based on Amino Acid Composition....Pages 62-73
Gapped Extension for Local Multiple Alignment of Interspersed DNA Repeats....Pages 74-86
Improved Alignment of Protein Sequences Based on Common Parts....Pages 87-99
 Invited Keynote Talk: Computing P-Values for Peptide Identifications in Mass Spectrometry....Pages 100-109
PFP: A Computational Framework for Phylogenetic Footprinting in Prokaryotic Genomes....Pages 110-121
Accelerating the Neighbor-Joining Algorithm Using the Adaptive Bucket Data Structure....Pages 122-133
Generalized Gene Adjacencies, Graph Bandwidth and Clusters in Yeast Evolution....Pages 134-145
Physicochemical Correlation between Amino Acid Sites in Short Sequences under Selective Pressure....Pages 146-158
HCV Quasispecies Assembly Using Network Flows....Pages 159-170
A Dynamic Programming Algorithm for De Novo Peptide Sequencing with Variable Scoring....Pages 171-182
 Invited Keynote Talk: Haplotype Sharing for Genome-Wide Case-Control Association Studies....Pages 183-183
Incorporating Literature Knowledge in Bayesian Network for Inferring Gene Networks with Gene Expression Data....Pages 184-195
Integrative Network Component Analysis for Regulatory Network Reconstruction....Pages 196-207
A Graph-Theoretic Method for Mining Overlapping Functional Modules in Protein Interaction Networks....Pages 208-219
Identification of Transcription Factor Binding Sites in Promoter Regions by Modularity Analysis of the Motif Co-occurrence Graph....Pages 220-231
Mean Squared Residue Based Biclustering Algorithms....Pages 232-243
Sparse Decomposition of Gene Expression Data to Infer Transcriptional Modules Guided by Motif Information....Pages 244-255
A Novel Metric for Redundant Gene Elimination Based on Discriminative Contribution....Pages 256-267
Network-Based Inference of Cancer Progression from Microarray Data....Pages 268-279
 Invited Keynote Talk: Quiet Revolution: Connectivity in the Cancer Research Community....Pages 280-280
Wavelet-Based 3-D Multifractal Spectrum with Applications in Breast MRI Images....Pages 281-292
Accurate Inverse Consistent Non-rigid Image Registration and Its Application on Automatic Re-contouring....Pages 293-304
GlycoBrowser: A Tool for Contextual Visualization of Biological Data and Pathways Using Ontologies....Pages 305-316
Pattern Matching in RNA Structures....Pages 317-330
The Use of a Conformational Alphabet for Fast Alignment of Protein Structures....Pages 331-342
On-the-Fly Rotamer Pair Energy Evaluation in Protein Design....Pages 343-354
 Invited Keynote Talk: Integrative Viral Molecular Epidemiology: Hepatitis C Virus Modeling....Pages 355-366
Multiple Kernel Support Vector Regression for siRNA Efficacy Prediction....Pages 367-378
Hierarchical Clustering Support Vector Machines for Classifying Type-2 Diabetes Patients....Pages 379-389
Computational Mutagenesis of E. coli Lac Repressor: Insight into Structure-Function Relationships and Accurate Prediction of Mutant Activity....Pages 390-401
Evaluating Genetic Algorithms in Protein-Ligand Docking....Pages 402-413
A Hidden Markov Model Approach for Prediction of Genomic Alterations from Gene Expression Profiling....Pages 414-425
Evolutionary Algorithm for Feature Subset Selection in Predicting Tumor Outcomes Using Microarray Data....Pages 426-433
Incorporating Knowledge of Topology Improves Reconstruction of Interaction Networks from Microarray Data....Pages 434-443
 Invited Keynote Talk: Data Mining and Statistical Methods for Analyzing Microarray Experiments....Pages 444-444
Seven Variations of an Alignment Workflow - An Illustration of Agile Process Design and Management in Bio-jETI....Pages 445-456
Supporting Computational Systems Science: Genomic Analysis Tool Federations Using Aspects and AOP....Pages 457-468
BioDQ: Data Quality Estimation and Management for Genomics Databases....Pages 469-480
Stepped Linear Regression to Accurately Assess Statistical Significance in Batch Confounded Differential Expression Analysis....Pages 481-491
Bagging Multiple Comparisons from Microarray Data....Pages 492-503
Human Blood-Brain Differential Gene-Expression Correlates with Dipeptide Frequency of Gene Products....Pages 504-508
Back Matter....Pages -