Bioinformatics Research and Applications: Fourth International Symposium, Isbra 2008, Atlanta, Ga, USA, May 6-9, 2008, Proceedings

by Mandoiu, Ion; Sunderraman, Raj; Zelikovsky, Alexander

• ISBN13: 9783540794493
• ISBN10: 3540794492
• Format: Paperback
• Copyright: 2008-06-30
• Publisher: Springer-Verlag New York Inc

Summary

"This book constitutes the refereed proceedings of the Fourth International Symposium on Bioinformatics Research and Applications, ISBRA 2008, held in Atlanta, GA, USA in May 2008. The 35 revised full papers presented together with 6 workshop papers and 6 invited papers were carefully reviewed and selected from a total of 94 submissions. The papers cover a wide range of topics, including clustering and classification, gene expression analysis, gene networks, genome analysis, motif finding, pathways, protein structure prediction, protein domain interactions, phylogenetics, and software tools."--BOOK JACKET.

Table of Contents

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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