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