Ebook: Advances in Computational Biology

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.

---

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.

---

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.
Content:
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
The Application of Regular Expression-Based Pattern Matching to Profiling the Developmental Factors that Contribute to the Development of the Inner Ear....Pages 157-164
Functionally Informative Tag SNP Selection Using a Pareto-Optimal Approach....Pages 165-171
Front Matter....Pages 173-180
KMeans Greedy Search Hybrid Algorithm for Biclustering Gene Expression Data....Pages 137-137
FM-GA and CM-GA for Gene Microarray Analysis....Pages 181-188
Front Matter....Pages 189-197
Novel Features for Automated Cell Phenotype Image Classification....Pages 199-204
A Relational Fuzzy C-Means Algorithm for Detecting Protein Spots in Two-Dimensional Gel Images....Pages 205-205
Assigning Probabilities to Mascot Peptide Identification Using Logistic Regression....Pages 207-213
Genome-Wide EST Data Mining Approaches to Resolving Incongruence of Molecular Phylogenies....Pages 215-227
Building a Parallel Between Structural and Topological Properties....Pages 229-236
GNCPro: Navigate Human Genes and Relationships Through Net-Walking....Pages 237-243
Small-Scale Modeling Approach and Circuit Wiring of the Unfolded Protein Response in Mammalian Cells....Pages 245-251
Random-Walk Mechanism in the Genetic Recombination....Pages 253-259
Critical Assessment of Side Chain Conformation Prediction in Modelling of Single Point Amino Acid Mutation....Pages 261-274
Temporal Anomaly Detection: An Artificial Immune Approach Based on T Cell Activation, Clonal Size Regulation and Homeostasis....Pages 275-282
An Integrated Methodology for Mining Promiscuous Proteins: A Case Study of an Integrative Bioinformatics Approach for Hepatitis C Virus Non-structural 5a Protein....Pages 283-289
Enhanced Prediction of Conformational Flexibility and Phosphorylation in Proteins....Pages 291-298
Why Are MD Simulated Protein Folding Times Wrong?....Pages 299-305
Automatic TEM Image Analysis of Membranes for 2D Crystal Detection....Pages 307-319
High Performance Computing Approaches for 3D Reconstruction of Complex Biological Specimens....Pages 321-326
Protein Identification Using Receptor Arrays and Mass Spectrometry....Pages 327-333
Front Matter....Pages 335-342
Assessing Consistency Between Versions of Genotype-Calling Algorithm Birdseed for the Genome-Wide Human SNP Array 6.0 Using HapMap Samples....Pages 343-351
Front Matter....Pages 353-353
An Overview of the BioExtract Server: A Distributed, Web-Based System for Genomic Analysis....Pages 355-360
A Deterministic DNA Database Search....Pages 353-353
Taxonomic Parsing of Bacteriophages Using Core Genes and In Silico Proteome-Based CGUG and Applications to Small Bacterial Genomes....Pages 361-369
Analysis of Gene Translation Using a Communications Theory Approach....Pages 371-378
A Fast and Efficient Algorithm for Mapping Short Sequences to a Reference Genome....Pages 379-385
Sequence Analysis and Homology Modeling Gallus gallus Glutathione S-transferase (Q08392)....Pages 387-397
Toward Optimizing the Cache Performance of Suffix Trees for Sequence Analysis Algorithms Suffix Tree Cache Performance Optimization....Pages 399-403
Toward a Visualization of DNA Sequences....Pages 405-410
A Practical Approach for Computing the Active Site of the Ribonucleoside Hydrolase of E. coli Encoded by rihC....Pages 411-417
Front Matter....Pages 419-435
Addressing the Docking Problem: Finding Similar 3-D Protein Envelopes for Computer-Aided Drug Design....Pages 437-443
Simultaneous Pathogen Detection and Antibiotic Resistance Characterization Using SNP-Based Multiplexed Oligonucleotide Ligation-PCR (MOL-PCR)....Pages 445-445
Specification and Verification of Pharmacokinetic Models....Pages 447-454
Dehydron Analysis: Quantifying the Effect of Hydrophobic Groups on the Strength and Stability of Hydrogen Bonds....Pages 455-464
Docking to Large Allosteric Binding Sites on Protein Surfaces....Pages 465-472
Modeling of ATP-Sensitive Inward Rectifier Potassium Channel 11 and Inhibition Mechanism of the Natural Ligand, Ellagic Acid, Using Molecular Docking....Pages 473-479
GPU Acceleration of Dock6’s Amber Scoring Computation....Pages 481-488
Front Matter....Pages 489-495
Discriminative Distance Functions and the Patient Neighborhood Graph for Clinical Decision Support....Pages 497-511
A Scalable and Integrative System for Pathway Bioinformatics and Systems Biology....Pages 513-513
Registration of In Vivo Fluorescence Endomicroscopy Images Based on Feature Detection....Pages 515-522
Kinetic Models for Cancer Imaging....Pages 523-534
Front Matter....Pages 535-548
Using Web and Social Media for Influenza Surveillance....Pages 549-557
CodeSlinger: A Case Study in Domain-Driven Interactive Tool Design for Biomedical Coding Scheme Exploration and Use....Pages 513-513
DigitalLung: Application of High-Performance Computing to Biological System Simulation....Pages 559-564
Consideration of Indices to Evaluate Age-Related Muscle Performance by Using Surface Electromyography....Pages 565-572
A Study on Discrete Wavelet-Based Noise Removal from EEG Signals....Pages 573-584
Enhancing the Communication Flow Between Alzheimer Patients, Caregivers, and Neuropsychologists....Pages 585-591
An Improved 1-D Gel Electrophoresis Image Analysis System....Pages 593-599
A Fuzzy Approach for Contrast Enhancement of Mammography Breast Images....Pages 601-607
Computational Modeling of a New Thrombectomy Device for the Extraction of Blood Clots....Pages 609-617
NEURONSESSIONS: A Web-Based Collaborative Tool to Create Brain Computational Models....Pages 619-626
Front Matter....Pages 627-633
Toward Automating an Inference Model on Unstructured Terminologies: OXMIS Case Study....Pages 635-642
Semantic Content-Based Recommendations Using Semantic Graphs....Pages 643-643
Modeling Membrane Localization: Case Study of a Ras Signaling Model....Pages 645-651
A Study on Distributed PACS....Pages 653-659
Epileptic EEG: A Comprehensive Study of Nonlinear Behavior....Pages 661-667
Computational Energetic Model of Morphogenesis Based on Multi-agent Cellular Potts Model....Pages 669-676
Standardizing the Next Generation of Bioinformatics Software Development with BioHDF (HDF5)....Pages 677-683
Multisensor Smart System on a Chip....Pages 685-692
Visual Presentation as a Welcome Alternative to Textual Presentation of Gene Annotation Information....Pages 693-700
Automatic FRAP Analysis with Inhomogeneous Fluorescence Distribution and Movement Compensation....Pages 701-708
Front Matter....Pages 709-715
Sorting Circular Permutations by Bounded Transpositions....Pages 717-724
Annotating Patents with Medline MeSH Codes via Citation Mapping....Pages 643-643
Some New Measures of Entropy, Useful Tools in Biocomputing....Pages 725-736
Erratum to: Kinetic Models for Cancer Imaging....Pages 737-744
Back Matter....Pages 745-750
....Pages E1-E1