Bioinformatics Research and Applications: Third International Symposium, ISBRA 2007, Atlanta, GA, USA, May 7-10, 2007. Proceedings [1 ed.] 3540720308, 9783540720300

Table of contents :
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 -