Advances in Computational Biology

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