Bioinformatics and Computational Biology

Invited Talks.- Association Analysis Techniques for Bioinformatics Problems.- Analyzing and Interrogating Biological Networks (Abstract).- From Architecture to Function (and Back) in Bio-networks.- A New Machine Learning Approach for Protein Phosphorylation Site Prediction in Plants.- Assembly of Large Genomes from Paired Short Reads.- Amino Acid Classification and Hash Seeds for Homology Search.- Genotype and Haplotype Reconstruction from Low-Coverage Short Sequencing Reads.- Gene Networks Viewed through Two Models.- Identifying Evolutionarily Conserved Protein Interaction Modules Using GraphHopper.- The 2-Interval Pattern Matching Problems and Its Application to ncRNA Scanning.- Refereed Papers.- RNA Pseudoknot Folding through Inference and Identification Using TAGRNA.- Comparing Bacterial Genomes by Searching Their Common Intervals.- Generalized Binary Tanglegrams: Algorithms and Applications.- Three-Dimensional Multimodality Modelling by Integration of High-Resolution Interindividual Atlases and Functional MALDI-IMS Data.- Detecting Motifs in a Large Data Set: Applying Probabilistic Insights to Motif Finding.- A Biclustering Method to Discover Co-regulated Genes Using Diverse Gene Expression Datasets.- Computational Protocol for Screening GPI-anchored Proteins.- Towards Large-Scale Molecular Dynamics Simulations on Graphics Processors.- An Agent-Based Model of Solid Tumor Progression.- Deciphering Drug Action and Escape Pathways: An Example on Nasopharyngeal Carcinoma.- Selection of Multiple SNPs in Case-Control Association Study Using a Discretized Network Flow Approach.- Biclustering Expression Data Based on Expanding Localized Substructures.- Constrained Fisher Scores Derived from Interaction Profile Hidden Markov Models Improve Protein to Protein Interaction Prediction.- Improving Protein Localization Prediction Using Amino Acid Group Based Physichemical Encoding.- The Impact of Gene Selection on Imbalanced Microarray Expression Data.- Spatial Information and Boolean Genetic Regulatory Networks.- Modeling of Genetic Regulatory Network in Stochastic ?-Calculus.- fMRI Activation Detection by MultiScale Hidden Markov Model.- cnF2freq: Efficient Determination of Genotype and Haplotype Probabilities in Outbred Populations Using Markov Models.- A Comprehensive Analysis Workflow for Genome-Wide Screening Data from ChIP-Sequencing Experiments.- A Fitness Distance Correlation Measure for Evolutionary Trees.- Alignment and Analysis of Closely Related Genomes.- Computational Prediction of Genes Translationally Regulated by Cytoplasmic Polyadenylation Elements.- Multiple Sequence Alignment System for Pyrosequencing Reads.- A Bayesian Approach to High-Throughput Biological Model Generation.- Parallel Selection of Informative Genes for Classification.- Simulation Methods in Uncovering New Regulatory Mechanisms in Signaling Pathways.- GridSPiM: A Framework for Simple Locality and Containment in the Stochastic ?-Calculus.- Mutual Information Based Extrinsic Similarity for Microarray Analysis.- Graph Spectral Approach for Identifying Protein Domains.