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.
Author(s): Dan L. Nicolae, Omar De la Cruz, William Wen (auth.), Ion Măndoiu, Raj Sunderraman, Alexander Zelikovsky (eds.)
Series: Lecture Notes in Computer Science 4983 : Lecture Notes in Bioinformatics
Edition: 1
Publisher: Springer-Verlag Berlin Heidelberg
Year: 2008
Language: English
Pages: 510
Tags: Computational Biology/Bioinformatics; Computation by Abstract Devices; Pattern Recognition; Data Mining and Knowledge Discovery
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 -
