This book constitutes the refereed proceedings of the Third International Symposium on Bioinformatics Research and Applications, ISBRA 2007, held in Atlanta, GA, USA in May 2007.
The 55 revised full papers presented together with three invited talks were carefully reviewed and selected from a total of 146 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): Xubo Fei, Shiyong Lu, Horia F. Pop (auth.), Ion Măndoiu, Alexander Zelikovsky (eds.)
Series: Lecture Notes in Computer Science 4463 : Lecture Notes in Bioinformatics
Edition: 1
Publisher: Springer-Verlag Berlin Heidelberg
Year: 2007
Language: English
Pages: 656
Tags: Computational Biology/Bioinformatics; Computation by Abstract Devices; Pattern Recognition; Data Mining and Knowledge Discovery
Front Matter....Pages -
GFBA: A Biclustering Algorithm for Discovering Value-Coherent Biclusters....Pages 1-12
Significance Analysis of Time-Course Gene Expression Profiles....Pages 13-24
Data-Driven Smoothness Enhanced Variance Ratio Test to Unearth Responsive Genes in 0-Time Normalized Time-Course Microarray Data....Pages 25-36
Efficiently Finding the Most Parsimonious Phylogenetic Tree Via Linear Programming....Pages 37-48
A Multi-Stack Based Phylogenetic Tree Building Method....Pages 49-60
A New Linear-Time Heuristic Algorithm for Computing the Parsimony Score of Phylogenetic Networks: Theoretical Bounds and Empirical Performance....Pages 61-72
A Bootstrap Correspondence Analysis for Factorial Microarray Experiments with Replications....Pages 73-84
Clustering Algorithms Optimizer: A Framework for Large Datasets....Pages 85-96
Ranking Function Based on Higher Order Statistics (RF-HOS) for Two-Sample Microarray Experiments....Pages 97-108
Searching for Recombinant Donors in a Phylogenetic Network of Serial Samples....Pages 109-120
Algorithm for Haplotype Inferring Via Galled-Tree Networks with Simple Galls....Pages 121-132
Estimating Bacterial Diversity from Environmental DNA: A Maximum Likelihood Approach....Pages 133-144
Invited Talk: Modern Homology Search....Pages 145-145
Statistical Absolute Evaluation of Gene Ontology Terms with Gene Expression Data....Pages 146-157
Discovering Relations Among GO-Annotated Clusters by Graph Kernel Methods....Pages 158-169
An Empirical Comparison of Dimensionality Reduction Methods for Classifying Gene and Protein Expression Datasets....Pages 170-181
NEURONgrid: A Toolkit for Generating Parameter-Space Maps Using NEURON in a Grid Environment....Pages 182-191
An Adaptive Resolution Tree Visualization of Large Influenza Virus Sequence Datasets....Pages 192-202
Wavelet Image Interpolation (WII): A Wavelet-Based Approach to Enhancement of Digital Mammography Images....Pages 203-214
High Level Programming Environment System for Protein Structure Data....Pages 215-226
Finding Minimal Sets of Informative Genes in Microarray Data....Pages 227-236
Noise-Based Feature Perturbation as a Selection Method for Microarray Data....Pages 237-247
Efficient Generation of Biologically Relevant Enriched Gene Sets....Pages 248-259
Space and Time Efficient Algorithms to Discover Endogenous RNAi Patterns in Complete Genome Data....Pages 260-269
A Fast Approximate Covariance-Model-Based Database Search Method for Non-coding RNA....Pages 270-281
Extensions of Naive Bayes and Their Applications to Bioinformatics....Pages 282-292
The Solution Space of Sorting by Reversals....Pages 293-304
A Fast and Exact Algorithm for the Perfect Reversal Median Problem....Pages 305-316
Genomic Signatures from DNA Word Graphs....Pages 317-328
Enhancing Motif Refinement by Incorporating Comparative Genomics Data....Pages 329-337
Mining Discriminative Distance Context of Transcription Factor Binding Sites on ChIP Enriched Regions....Pages 338-349
Enhanced Prediction of Cleavage in Bovine Precursor Sequences....Pages 350-360
Invited Talk: A Computational Study of Bidirectional Promoters in the Human Genome....Pages 361-371
The Identification of Antisense Gene Pairs Through Available Software....Pages 372-381
Inferring Weak Adaptations and Selection Biases in Proteins from Composition and Substitution Matrices....Pages 382-393
Markov Model Variants for Appraisal of Coding Potential in Plant DNA....Pages 394-405
Predicting Palmitoylation Sites Using a Regularised Bio-basis Function Neural Network....Pages 406-417
A Novel Kernel-Based Approach for Predicting Binding Peptides for HLA Class II Molecules....Pages 418-429
A Database for Prediction of Unique Peptide Motifs as Linear Epitopes....Pages 430-440
A Novel Greedy Algorithm for the Minimum Common String Partition Problem....Pages 441-452
An Efficient Algorithm for Finding Gene-Specific Probes for DNA Microarrays....Pages 453-464
Multiple Sequence Local Alignment Using Monte Carlo EM Algorithm....Pages 465-476
Cancer Class Discovery Using Non-negative Matrix Factorization Based on Alternating Non-negativity-Constrained Least Squares....Pages 477-487
A Support Vector Machine Ensemble for Cancer Classification Using Gene Expression Data....Pages 488-495
Combining SVM Classifiers Using Genetic Fuzzy Systems Based on AUC for Gene Expression Data Analysis....Pages 496-505
A BP-SCFG Based Approach for RNA Secondary Structure Prediction with Consecutive Bases Dependency and Their Relative Positions Information....Pages 506-517
Delta: A Toolset for the Structural Analysis of Biological Sequences on a 3D Triangular Lattice....Pages 518-529
Statistical Estimate for the Size of the Protein Structural Vocabulary....Pages 530-538
Coclustering Based Parcellation of Human Brain Cortex Using Diffusion Tensor MRI....Pages 539-550
An Algorithm for Hierarchical Classification of Genes of Prokaryotic Genomes....Pages 551-563
Using Multi Level Nearest Neighbor Classifiers for G-Protein Coupled Receptor Sub-families Prediction....Pages 564-576
Invited Talk: Ab Initio Gene Finding Engines: What Is Under the Hood....Pages 577-577
Reconstruction of 3D Structures from Protein Contact Maps....Pages 578-589
A Feature Selection Algorithm Based on Graph Theory and Random Forests for Protein Secondary Structure Prediction....Pages 590-600
DNA Sites Buried in Nucleosome Become Accessible at Room Temperature: A Discrete-Event-Simulation Based Modeling Approach....Pages 601-614
Comparative Analysis of Gene-Coexpression Networks Across Species....Pages 615-626
Comparative Pathway Prediction Via Unified Graph Modeling of Genomic Structure Information....Pages 627-637
Extending the Calculus of Looping Sequences to Model Protein Interaction at the Domain Level....Pages 638-649
Back Matter....Pages -
