Advances in Computational Biology (Advances in Experimental Medicine and Biology Book 680)

Proceedings of The 2009 International Conference on Bioinformatics and Computational Biology in Las Vegas, NV, July 13-16, 2009. Recent advances in Computational Biology are covered through a variety of topics. Both inward research (core areas of computational biology and computer science) and outward research (multi-disciplinary, Inter-disciplinary, and applications) will be covered during the conferences. These include: Gene regulation, Gene expression databases, Gene pattern discovery and identification, Genetic network modeling and inference, Gene expression analysis, RNA and DNA structure and sequencing, Biomedical engineering, Microarrays, Molecular sequence and structure databases, Molecular dynamics and simulation, Molecular sequence classification, alignment and assembly, Image processing In medicine and biological sciences, Sequence analysis and alignment, Informatics and Statistics in Biopharmaceutical Research, Software tools for computational biology and bioinformatics, Comparative genomics; and more. Front Matter....Pages i-xvii Front Matter....Pages 1-1 A Classification Method Based on Similarity Measures of Generalized Fuzzy Numbers in Building Expert System for Postoperative Patients....Pages 3-10 Efficient Support Vector Machine Method for Survival Prediction with SEER Data....Pages 11-18 Searching Maximal Degenerate Motifs Guided by a Compact Suffix Tree....Pages 19-26 Exploring Motif Composition of Eukaryotic Promoter Regions....Pages 27-34 Large-Scale Analysis of Phylogenetic Search Behavior....Pages 35-42 Silicosection and Elucidation of the Plant Circadian Clock Using Bayesian Classifiers and New Genemining Algorithm....Pages 43-56 ChemBrowser: A Flexible Framework for Mining Chemical Documents....Pages 57-64 Experimental Study of Modified Voting Algorithm for Planted ( l , d )-Motif Problem....Pages 65-73 Prediction of Severe Sepsis Using SVM Model....Pages 75-81 Online Multi-divisive Hierarchical Clustering for On-Body Sensor Data....Pages 83-88 On Quality Assurance and Assessment of Biological Datasets and Related Statistics....Pages 89-97 Pattern Recognition-Informed Feedback for Nanopore Detector Cheminformatics....Pages 99-108 An MLP Neural Network for ECG Noise Removal Based on Kalman Filter....Pages 109-116 Discovery of Structural Motifs Using Protein Structural Alphabets and 1D Motif-Finding Methods....Pages 117-123 Biological Databases at DNA Data Bank of Japan in the Era of Next-Generation Sequencing Technologies....Pages 125-135 Front Matter....Pages 137-137 Comparison of Microarray Preprocessing Methods....Pages 139-147 A Robust Ensemble Classification Method Analysis....Pages 149-155 k -NN for the Classification of Human Cancer Samples Using the Gene Expression Profiles....Pages 157-164 The Application of Regular Expression-Based Pattern Matching to Profiling the Developmental Factors that Contribute to the Development of the Inner Ear....Pages 165-171 Functionally Informative Tag SNP Selection Using a Pareto-Optimal Approach....Pages 173-180 Front Matter....Pages 137-137 KMeans Greedy Search Hybrid Algorithm for Biclustering Gene Expression Data....Pages 181-188 Robust Stability Analysis and Design Under Consideration of Multiple Feedback Loops of the Tryptophan Regulatory Network of Escherichia coli ....Pages 189-197 FM-GA and CM-GA for Gene Microarray Analysis....Pages 199-204 Front Matter....Pages 205-205 Novel Features for Automated Cell Phenotype Image Classification....Pages 207-213 A Relational Fuzzy C -Means Algorithm for Detecting Protein Spots in Two-Dimensional Gel Images....Pages 215-227 Assigning Probabilities to Mascot Peptide Identification Using Logistic Regression....Pages 229-236 Genome-Wide EST Data Mining Approaches to Resolving Incongruence of Molecular Phylogenies....Pages 237-243 Building a Parallel Between Structural and Topological Properties....Pages 245-251 GNCPro: Navigate Human Genes and Relationships Through Net-Walking....Pages 253-259 Small-Scale Modeling Approach and Circuit Wiring of the Unfolded Protein Response in Mammalian Cells....Pages 261-274 Random-Walk Mechanism in the Genetic Recombination....Pages 275-282 Critical Assessment of Side Chain Conformation Prediction in Modelling of Single Point Amino Acid Mutation....Pages 283-289 Temporal Anomaly Detection: An Artificial Immune Approach Based on T Cell Activation, Clonal Size Regulation and Homeostasis....Pages 291-298 An Integrated Methodology for Mining Promiscuous Proteins: A Case Study of an Integrative Bioinformatics Approach for Hepatitis C Virus Non-structural 5a Protein....Pages 299-305 Enhanced Prediction of Conformational Flexibility and Phosphorylation in Proteins....Pages 307-319 Why Are MD Simulated Protein Folding Times Wrong?....Pages 321-326 Automatic TEM Image Analysis of Membranes for 2D Crystal Detection....Pages 327-333 High Performance Computing Approaches for 3D Reconstruction of Complex Biological Specimens....Pages 335-342 Protein Identification Using Receptor Arrays and Mass Spectrometry....Pages 343-351 Front Matter....Pages 353-353 Assessing Consistency Between Versions of Genotype-Calling Algorithm Birdseed for the Genome-Wide Human SNP Array 6.0 Using HapMap Samples....Pages 355-360 Front Matter....Pages 353-353 An Overview of the BioExtract Server: A Distributed, Web-Based System for Genomic Analysis....Pages 361-369 A Deterministic DNA Database Search....Pages 371-378 Taxonomic Parsing of Bacteriophages Using Core Genes and In Silico Proteome-Based CGUG and Applications to Small Bacterial Genomes....Pages 379-385 Analysis of Gene Translation Using a Communications Theory Approach....Pages 387-397 A Fast and Efficient Algorithm for Mapping Short Sequences to a Reference Genome....Pages 399-403 Sequence Analysis and Homology Modeling Gallus gallus Glutathione S-transferase (Q08392)....Pages 405-410 Toward Optimizing the Cache Performance of Suffix Trees for Sequence Analysis Algorithms Suffix Tree Cache Performance Optimization....Pages 411-417 Toward a Visualization of DNA Sequences....Pages 419-435 A Practical Approach for Computing the Active Site of the Ribonucleoside Hydrolase of E. coli Encoded by rihC....Pages 437-443 Front Matter....Pages 445-445 Addressing the Docking Problem: Finding Similar 3-D Protein Envelopes for Computer-Aided Drug Design....Pages 447-454 Simultaneous Pathogen Detection and Antibiotic Resistance Characterization Using SNP-Based Multiplexed Oligonucleotide Ligation-PCR (MOL-PCR)....Pages 455-464 Specification and Verification of Pharmacokinetic Models....Pages 465-472 Dehydron Analysis: Quantifying the Effect of Hydrophobic Groups on the Strength and Stability of Hydrogen Bonds....Pages 473-479 Docking to Large Allosteric Binding Sites on Protein Surfaces....Pages 481-488 Modeling of ATP-Sensitive Inward Rectifier Potassium Channel 11 and Inhibition Mechanism of the Natural Ligand, Ellagic Acid, Using Molecular Docking....Pages 489-495 GPU Acceleration of Dock6’s Amber Scoring Computation....Pages 497-511 Front Matter....Pages 513-513 Discriminative Distance Functions and the Patient Neighborhood Graph for Clinical Decision Support....Pages 515-522 A Scalable and Integrative System for Pathway Bioinformatics and Systems Biology....Pages 523-534 Registration of In Vivo Fluorescence Endomicroscopy Images Based on Feature Detection....Pages 535-548 Kinetic Models for Cancer Imaging....Pages 549-557 Front Matter....Pages 513-513 Using Web and Social Media for Influenza Surveillance....Pages 559-564 CodeSlinger: A Case Study in Domain-Driven Interactive Tool Design for Biomedical Coding Scheme Exploration and Use....Pages 565-572 DigitalLung: Application of High-Performance Computing to Biological System Simulation....Pages 573-584 Consideration of Indices to Evaluate Age-Related Muscle Performance by Using Surface Electromyography....Pages 585-591 A Study on Discrete Wavelet-Based Noise Removal from EEG Signals....Pages 593-599 Enhancing the Communication Flow Between Alzheimer Patients, Caregivers, and Neuropsychologists....Pages 601-607 An Improved 1-D Gel Electrophoresis Image Analysis System....Pages 609-617 A Fuzzy Approach for Contrast Enhancement of Mammography Breast Images....Pages 619-626 Computational Modeling of a New Thrombectomy Device for the Extraction of Blood Clots....Pages 627-633 NEURONSESSIONS: A Web-Based Collaborative Tool to Create Brain Computational Models....Pages 635-642 Front Matter....Pages 643-643 Toward Automating an Inference Model on Unstructured Terminologies: OXMIS Case Study....Pages 645-651 Semantic Content-Based Recommendations Using Semantic Graphs....Pages 653-659 Modeling Membrane Localization: Case Study of a Ras Signaling Model....Pages 661-667 A Study on Distributed PACS....Pages 669-676 Epileptic EEG: A Comprehensive Study of Nonlinear Behavior....Pages 677-683 Computational Energetic Model of Morphogenesis Based on Multi-agent Cellular Potts Model....Pages 685-692 Standardizing the Next Generation of Bioinformatics Software Development with BioHDF (HDF5)....Pages 693-700 Multisensor Smart System on a Chip....Pages 701-708 Visual Presentation as a Welcome Alternative to Textual Presentation of Gene Annotation Information....Pages 709-715 Automatic FRAP Analysis with Inhomogeneous Fluorescence Distribution and Movement Compensation....Pages 717-724 Front Matter....Pages 643-643 Sorting Circular Permutations by Bounded Transpositions....Pages 725-736 Annotating Patents with Medline MeSH Codes via Citation Mapping....Pages 737-744 Some New Measures of Entropy, Useful Tools in Biocomputing....Pages 745-750 Erratum to: Kinetic Models for Cancer Imaging....Pages E1-E1 Back Matter....Pages 751-759 Bioinformatics Databases, Data Mining, And Pattern Discovery -- Microarray, Gene Expression Analysis, And Gene Regulatory Networks -- Protein Classification & Structure Prediction, And Computational Structural Biology -- Comparative Sequence, Genome Analysis, Genome Assembly, And Genome Scale Computational Methods -- Drug Design, Drug Screening, And Related Topics -- Computational Methods And Diagnostic Tools In Biomedical -- General Topics In Bioinformatics. Hamid R. Arabnia, Editor. The Book Is Composed Of A Collection Of Papers Received In Response To An Announcement ... In The Broad Area Of Computational Biology. Also, Selected Authors Of Accepted Papers Of Biocomp'09 Proceedings (international Conference On Bioinformatics And Computational Biology: July 13-16, 2009; Las Vegas, Nv, Usa) Were Invited To Submit The Extended Versions Of Their Papers For Evaluation.--pref. Includes Bibliographical References And Index.