Bioinformatics research and applications : third international symposium, ISBRA 2007, Atlanta, GA, USA, May 7-10, 2007 : proceedings

Table of Contents

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   Book Overview
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   Chapter 1 GFBA: A Biclustering Algorithm for Discovering Value-Coherent Biclusters
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   Chapter 2 Significance Analysis of Time-Course Gene Expression Profiles
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   Chapter 3 Data-Driven Smoothness Enhanced Variance Ratio Test to Unearth Responsive Genes in 0-Time Normalized Time-Course Microarray Data
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   Chapter 4 Efficiently Finding the Most Parsimonious Phylogenetic Tree Via Linear Programming
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   Chapter 5 A Multi-Stack Based Phylogenetic Tree Building Method
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   Chapter 6 A New Linear-Time Heuristic Algorithm for Computing the Parsimony Score of Phylogenetic Networks: Theoretical Bounds and Empirical Performance
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   Chapter 7 A Bootstrap Correspondence Analysis for Factorial Microarray Experiments with Replications
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   Chapter 8 Clustering Algorithms Optimizer: A Framework for Large Datasets
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    Chapter 9 Ranking Function Based on Higher Order Statistics (RF-HOS) for Two-Sample Microarray Experiments
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    Chapter 10 Searching for Recombinant Donors in a Phylogenetic Network of Serial Samples
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    Chapter 11 Algorithm for Haplotype Inferring Via Galled-Tree Networks with Simple Galls
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    Chapter 12 Estimating Bacterial Diversity from Environmental DNA: A Maximum Likelihood Approach
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    Chapter 13 Invited Talk: Modern Homology Search
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    Chapter 14 Statistical Absolute Evaluation of Gene Ontology Terms with Gene Expression Data
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    Chapter 15 Discovering Relations Among GO-Annotated Clusters by Graph Kernel Methods
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    Chapter 16 An Empirical Comparison of Dimensionality Reduction Methods for Classifying Gene and Protein Expression Datasets
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    Chapter 17 NEURONgrid: A Toolkit for Generating Parameter-Space Maps Using NEURON in a Grid Environment
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    Chapter 18 An Adaptive Resolution Tree Visualization of Large Influenza Virus Sequence Datasets
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    Chapter 19 Wavelet Image Interpolation (WII): A Wavelet-Based Approach to Enhancement of Digital Mammography Images
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    Chapter 20 High Level Programming Environment System for Protein Structure Data
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    Chapter 21 Finding Minimal Sets of Informative Genes in Microarray Data
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    Chapter 22 Noise-Based Feature Perturbation as a Selection Method for Microarray Data
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    Chapter 23 Efficient Generation of Biologically Relevant Enriched Gene Sets
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    Chapter 24 Space and Time Efficient Algorithms to Discover Endogenous RNAi Patterns in Complete Genome Data
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    Chapter 25 A Fast Approximate Covariance-Model-Based Database Search Method for Non-coding RNA
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    Chapter 26 Extensions of Naive Bayes and Their Applications to Bioinformatics
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    Chapter 27 The Solution Space of Sorting by Reversals
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    Chapter 28 A Fast and Exact Algorithm for the Perfect Reversal Median Problem
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    Chapter 29 Genomic Signatures from DNA Word Graphs
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    Chapter 30 Enhancing Motif Refinement by Incorporating Comparative Genomics Data
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    Chapter 31 Mining Discriminative Distance Context of Transcription Factor Binding Sites on ChIP Enriched Regions
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    Chapter 32 Enhanced Prediction of Cleavage in Bovine Precursor Sequences
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    Chapter 33 Invited Talk: A Computational Study of Bidirectional Promoters in the Human Genome
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    Chapter 34 The Identification of Antisense Gene Pairs Through Available Software
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    Chapter 35 Inferring Weak Adaptations and Selection Biases in Proteins from Composition and Substitution Matrices
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    Chapter 36 Markov Model Variants for Appraisal of Coding Potential in Plant DNA
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    Chapter 37 Predicting Palmitoylation Sites Using a Regularised Bio-basis Function Neural Network
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    Chapter 38 A Novel Kernel-Based Approach for Predicting Binding Peptides for HLA Class II Molecules
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    Chapter 39 A Database for Prediction of Unique Peptide Motifs as Linear Epitopes
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    Chapter 40 A Novel Greedy Algorithm for the Minimum Common String Partition Problem
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    Chapter 41 An Efficient Algorithm for Finding Gene-Specific Probes for DNA Microarrays
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    Chapter 42 Multiple Sequence Local Alignment Using Monte Carlo EM Algorithm
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    Chapter 43 Cancer Class Discovery Using Non-negative Matrix Factorization Based on Alternating Non-negativity-Constrained Least Squares
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    Chapter 44 A Support Vector Machine Ensemble for Cancer Classification Using Gene Expression Data
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    Chapter 45 Combining SVM Classifiers Using Genetic Fuzzy Systems Based on AUC for Gene Expression Data Analysis
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    Chapter 46 A BP-SCFG Based Approach for RNA Secondary Structure Prediction with Consecutive Bases Dependency and Their Relative Positions Information
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    Chapter 47 Delta: A Toolset for the Structural Analysis of Biological Sequences on a 3D Triangular Lattice
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    Chapter 48 Statistical Estimate for the Size of the Protein Structural Vocabulary
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    Chapter 49 Coclustering Based Parcellation of Human Brain Cortex Using Diffusion Tensor MRI
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    Chapter 50 An Algorithm for Hierarchical Classification of Genes of Prokaryotic Genomes
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    Chapter 51 Using Multi Level Nearest Neighbor Classifiers for G-Protein Coupled Receptor Sub-families Prediction
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    Chapter 52 Invited Talk: Ab Initio Gene Finding Engines: What Is Under the Hood
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    Chapter 53 Reconstruction of 3D Structures from Protein Contact Maps
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    Chapter 54 A Feature Selection Algorithm Based on Graph Theory and Random Forests for Protein Secondary Structure Prediction
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    Chapter 55 DNA Sites Buried in Nucleosome Become Accessible at Room Temperature: A Discrete-Event-Simulation Based Modeling Approach
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    Chapter 56 Comparative Analysis of Gene-Coexpression Networks Across Species
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    Chapter 57 Comparative Pathway Prediction Via Unified Graph Modeling of Genomic Structure Information
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    Chapter 58 Extending the Calculus of Looping Sequences to Model Protein Interaction at the Domain Level