Bioinformatics and Computational Biology: First International Conference, BICoB 2009, New Orleans, LA, USA, April 8-10, 2009. Proceedings

Front Matter....Pages -
Association Analysis Techniques for Bioinformatics Problems....Pages 1-13
Analyzing and Interrogating Biological Networks (Abstract)....Pages 14-15
From Architecture to Function (and Back) in Bio-networks....Pages 16-17
A New Machine Learning Approach for Protein Phosphorylation Site Prediction in Plants....Pages 18-29
Assembly of Large Genomes from Paired Short Reads....Pages 30-43
Amino Acid Classification and Hash Seeds for Homology Search....Pages 44-51
Genotype and Haplotype Reconstruction from Low-Coverage Short Sequencing Reads....Pages 52-53
Gene Networks Viewed through Two Models....Pages 54-66
Identifying Evolutionarily Conserved Protein Interaction Modules Using GraphHopper....Pages 67-78
The 2-Interval Pattern Matching Problems and Its Application to ncRNA Scanning....Pages 79-89
RNA Pseudoknot Folding through Inference and Identification Using TAG RNA ....Pages 90-101
Comparing Bacterial Genomes by Searching Their Common Intervals....Pages 102-113
Generalized Binary Tanglegrams: Algorithms and Applications....Pages 114-125
Three-Dimensional Multimodality Modelling by Integration of High-Resolution Interindividual Atlases and Functional MALDI-IMS Data....Pages 126-138
Detecting Motifs in a Large Data Set: Applying Probabilistic Insights to Motif Finding....Pages 139-150
A Biclustering Method to Discover Co-regulated Genes Using Diverse Gene Expression Datasets....Pages 151-163
Computational Protocol for Screening GPI-anchored Proteins....Pages 164-175
Towards Large-Scale Molecular Dynamics Simulations on Graphics Processors....Pages 176-186
An Agent-Based Model of Solid Tumor Progression....Pages 187-198
Deciphering Drug Action and Escape Pathways: An Example on Nasopharyngeal Carcinoma....Pages 199-210
Selection of Multiple SNPs in Case-Control Association Study Using a Discretized Network Flow Approach....Pages 211-223
Biclustering Expression Data Based on Expanding Localized Substructures....Pages 224-235
Constrained Fisher Scores Derived from Interaction Profile Hidden Markov Models Improve Protein to Protein Interaction Prediction....Pages 236-247
Improving Protein Localization Prediction Using Amino Acid Group Based Physichemical Encoding....Pages 248-258
The Impact of Gene Selection on Imbalanced Microarray Expression Data....Pages 259-269
Spatial Information and Boolean Genetic Regulatory Networks....Pages 270-281
Modeling of Genetic Regulatory Network in Stochastic π -Calculus....Pages 282-294
fMRI Activation Detection by MultiScale Hidden Markov Model....Pages 295-306
 cnF2freq : Efficient Determination of Genotype and Haplotype Probabilities in Outbred Populations Using Markov Models....Pages 307-319
A Comprehensive Analysis Workflow for Genome-Wide Screening Data from ChIP-Sequencing Experiments....Pages 320-330
A Fitness Distance Correlation Measure for Evolutionary Trees....Pages 331-342
Alignment and Analysis of Closely Related Genomes....Pages 343-352
Computational Prediction of Genes Translationally Regulated by Cytoplasmic Polyadenylation Elements....Pages 353-361
Multiple Sequence Alignment System for Pyrosequencing Reads....Pages 362-375
A Bayesian Approach to High-Throughput Biological Model Generation....Pages 376-387
Parallel Selection of Informative Genes for Classification....Pages 388-399
Simulation Methods in Uncovering New Regulatory Mechanisms in Signaling Pathways....Pages 400-408
GridSPiM: A Framework for Simple Locality and Containment in the Stochastic π-Calculus....Pages 409-423
Mutual Information Based Extrinsic Similarity for Microarray Analysis....Pages 424-436
Graph Spectral Approach for Identifying Protein Domains....Pages 437-448
Back Matter....Pages -