Bioinformatics Research and Applications

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.