Pattern Recognition in Bioinformatics: Second IAPR International Workshop, PRIB 2007, Singapore, October 1-2, 2007. Proceedings

Xu-Ning Tang, Zhi-Chao Lian, Zhi-Li Pei, Yan-Chun Liang (auth.), Jagath C. Rajapakse, Bertil Schmidt, Gwenn Volkert (eds.)3540752854, 9783540752851

The advancements of computational and informational techniques have enabled in silico testing of many lab-based experiments in life sciences before performing them in in vitro or in vivo. Though computational techniques are not capable of mimicking all wet-lab experiments, bioinformatics will inevitably play a major role in future medical practice. For example, in the pursuit of new drugs it can reduce the costs and complexity involved in expensive wet-lab experiments. It is expected that by 2010, sequencing of individual genomes will be affordable generating an unprecedented increase of life sciences data, in the form of sequences, expressions, networks, images, literature. Pattern recognition techniques lie at the heart of discovery of new insights into biological knowledge, as the presence of particular patterns or structure is often an indication of its function. The aim of the workshop series Pattern Recognition in Bioinformatics (PRIB) is to bring pattern recognition scientists and life scientists together to promote pattern recognition applications to solve life sciences problems. This volume presents the proceedings of the 2nd IAPR Workshop PRIB 2007 held in Singapore, October 1–2, 2007. It includes 38 technical contributions that were selected by the International Program Committee from 125 submissions. Each of these rigorously reviewed papers was presented orally at the workshop. The proceedings consists of six parts. Part 1: Sequence Analysis; Part 2: Prediction of Protein Structure, Interaction, and Localization; Part 3: Gene Expression Analysis; Part 4: Pathway Analysis; Part 5: Medical Informatics; and Part 6: Bioimaging.

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Table of contents :
Front Matter….Pages –
Automated Methods of Predicting the Function of Biological Sequences Using GO and Rough Set….Pages 1-10
C-Based Design Methodology for FPGA Implementation of ClustalW MSA….Pages 11-18
A Two-Phase ANN Method for Genome-Wide Detection of Hormone Response Elements….Pages 19-29
An Expert Knowledge-Guided Mutation Operator for Genome-Wide Genetic Analysis Using Genetic Programming….Pages 30-40
cDNA-Derived Amino Acid Sequence from Rat Brain A 2a R Possesses Conserved Motifs PMNYM of  TM 5 Domain, Which May Be Involved in Dimerization of A 2a R….Pages 41-50
Strong GC and AT Skew Correlation in Chicken Genome….Pages 51-59
Comparative Analysis of a Hierarchical Bayesian Method for Quantitative Trait Loci Analysis for the Arabidopsis Thaliana….Pages 60-70
Using Decision Templates to Predict Subcellular Localization of Protein….Pages 71-83
Generalized Schemata Theorem Incorporating Twin Removal for Protein Structure Prediction….Pages 84-97
Using Fuzzy Support Vector Machine Network to Predict Low Homology Protein Structural Classes….Pages 98-107
SVM-BetaPred: Prediction of Right-Handed ß-Helix Fold from Protein Sequence Using SVM….Pages 108-119
Protein Fold Recognition Based Upon the Amino Acid Occurrence….Pages 120-131
Using Efficient RBF Network to Identify Interface Residues Based on PSSM Profiles and Biochemical Properties….Pages 132-141
Dynamic Outlier Exclusion Training Algorithm for Sequence Based Predictions in Proteins Using Neural Network….Pages 142-147
Bioinformatics on β -Barrel Membrane Proteins: Sequence and Structural Analysis, Discrimination and Prediction….Pages 148-157
Estimation of Evolutionary Average Hydrophobicity Profile from a Family of Protein Sequences….Pages 158-165
APMA Database for Affymetrix Target Sequences Mapping, Quality Assessment and Expression Data Mining….Pages 166-177
Ensemble of Dissimilarity Based Classifiers for Cancerous Samples Classification….Pages 178-188
Gene Expression Analysis of Leukemia Samples Using Visual Interpretation of Small Ensembles: A Case Study….Pages 189-197
Ant-MST: An Ant-Based Minimum Spanning Tree for Gene Expression Data Clustering….Pages 198-205
Integrating Gene Expression Data from Microarrays Using the Self-Organising Map and the Gene Ontology….Pages 206-217
Order Preserving Clustering by Finding Frequent Orders in Gene Expression Data….Pages 218-229
Correlation-Based Relevancy and Redundancy Measures for Efficient Gene Selection….Pages 230-241
SVM-RFE with Relevancy and Redundancy Criteria for Gene Selection….Pages 242-252
In Silico Expression Profiles of Human Endogenous Retroviruses….Pages 253-263
A Framework for Path Analysis in Gene Regulatory Networks….Pages 264-273
Transcriptional Gene Regulatory Network Reconstruction Through Cross Platform Gene Network Fusion….Pages 274-285
Reconstruction of Protein-Protein Interaction Pathways by Mining Subject-Verb-Objects Intermediates….Pages 286-299
Validation of Gene Regulatory Networks from Protein-Protein Interaction Data: Application to Cell-Cycle Regulation….Pages 300-310
Rough Sets and Fuzzy Sets Theory Applied to the Sequential Medical Diagnosis….Pages 311-322
In silico Identification of Putative Drug Targets in Pseudomonas aeruginosa Through Metabolic Pathway Analysis….Pages 323-336
Understanding Prediction Systems for HLA-Binding Peptides and T-Cell Epitope Identification….Pages 337-348
Predicting Binding Peptides with Simultaneous Optimization of Entropy and Evolutionary Distance….Pages 349-355
3D Automated Nuclear Morphometric Analysis Using Active Meshes….Pages 356-367
Time-Frequency Method Based Activation Detection in Functional MRI Time-Series….Pages 368-377
High Performance Classification of Two Imagery Tasks in the Cue-Based Brain Computer Interface….Pages 378-390
Human Brain Anatomical Connectivity Analysis Using Sequential Sampling and Resampling….Pages 391-400
Classification of CT Brain Images of Head Trauma….Pages 401-408
Back Matter….Pages –