Advances in Computational Biology

ISBN-13: 9781461426967 / Angielski / Miękka / 2012 / 759 str.

Hamid R. Arabnia

Opis

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.

Spis treści

Bioinformatics Databases, Data Mining, and Pattern Discovery.- A Classification Method Based on Similarity Measures of Generalized Fuzzy Numbers in Building Expert System for Postoperative Patients.- Efficient Support Vector Machine Method for Survival Prediction with SEER Data.- Searching Maximal Degenerate Motifs Guided by a Compact Suffix Tree.- Exploring Motif Composition of Eukaryotic Promoter Regions.- Large-Scale Analysis of Phylogenetic Search Behavior.- Silicosection and Elucidation of the Plant Circadian Clock Using Bayesian Classifiers and New Genemining Algorithm.- ChemBrowser: A Flexible Framework for Mining Chemical Documents.- Experimental Study of Modified Voting Algorithm for Planted (l,d)-Motif Problem.- Prediction of Severe Sepsis Using SVM Model.- Online Multi-divisive Hierarchical Clustering for On-Body Sensor Data.- On Quality Assurance and Assessment of Biological Datasets and Related Statistics.- Pattern Recognition-Informed Feedback for Nanopore Detector Cheminformatics.- An MLP Neural Network for ECG Noise Removal Based on Kalman Filter.- Discovery of Structural Motifs Using Protein Structural Alphabets and 1D Motif-Finding Methods.- Biological Databases at DNA Data Bank of Japan in the Era of Next-Generation Sequencing Technologies.- Microarray, Gene Expression Analysis, and Gene Regulatory Networks.- Comparison of Microarray Preprocessing Methods.- A Robust Ensemble Classification Method Analysis.- k-NN for the Classification of Human Cancer Samples Using the Gene Expression Profiles.- The Application of Regular Expression-Based Pattern Matching to Profiling the Developmental Factors that Contribute to the Development of the Inner Ear.- Functionally Informative Tag SNP Selection Using a Pareto-Optimal Approach.- KMeans Greedy Search Hybrid Algorithm for Biclustering Gene Expression Data.- Robust Stability Analysis and Design Under Consideration of Multiple Feedback Loops of the Tryptophan Regulatory Network of Escherichia coli.- FM-GA and CM-GA for Gene Microarray Analysis.- Protein Classification & Structure Prediction, and Computational Structural Biology.- Novel Features for Automated Cell Phenotype Image Classification.- A Relational Fuzzy C-Means Algorithm for Detecting Protein Spots in Two-Dimensional Gel Images.- Assigning Probabilities to Mascot Peptide Identification Using Logistic Regression.- Genome-Wide EST Data Mining Approaches to Resolving Incongruence of Molecular Phylogenies.- Building a Parallel Between Structural and Topological Properties.- GNCPro: Navigate Human Genes and Relationships Through Net-Walking.- Small-Scale Modeling Approach and Circuit Wiring of the Unfolded Protein Response in Mammalian Cells.- Random-Walk Mechanism in the Genetic Recombination.- Critical Assessment of Side Chain Conformation Prediction in Modelling of Single Point Amino Acid Mutation.- Temporal Anomaly Detection: An Artificial Immune Approach Based on T Cell Activation, Clonal Size Regulation and Homeostasis.- An Integrated Methodology for Mining Promiscuous Proteins: A Case Study of an Integrative Bioinformatics Approach for Hepatitis C Virus Non-structural 5a Protein.- Enhanced Prediction of Conformational Flexibility and Phosphorylation in Proteins.- Why Are MD Simulated Protein Folding Times Wrong?.- Automatic TEM Image Analysis of Membranes for 2D Crystal Detection.- High Performance Computing Approaches for 3D Reconstruction of Complex Biological Specimens.- Protein Identification Using Receptor Arrays and Mass Spectrometry.- Comparative Sequence, Genome Analysis, Genome Assembly, and Genome Scale Computational Methods.- Assessing Consistency Between Versions of Genotype-Calling Algorithm Birdseed for the Genome-Wide Human SNP Array 6.0 Using HapMap Samples.- An Overview of the BioExtract Server: A Distributed, Web-Based System for Genomic Analysis.- A Deterministic DNA Database Search.- Taxonomic Parsing of Bacteriophages Using Core Genes and In Silico Proteome-Based CGUG and Applications to Small Bacterial Genomes.- Analysis of Gene Translation Using a Communications Theory Approach.- A Fast and Efficient Algorithm for Mapping Short Sequences to a Reference Genome.- Sequence Analysis and Homology Modeling Gallus gallus Glutathione S-transferase (Q08392).- Toward Optimizing the Cache Performance of Suffix Trees for Sequence Analysis Algorithms Suffix Tree Cache Performance Optimization.- Toward a Visualization of DNA Sequences.- A Practical Approach for Computing the Active Site of the Ribonucleoside Hydrolase of E. coli Encoded by rihC.- Drug Design, Drug Screening, and Related Topics.- Addressing the Docking Problem: Finding Similar 3-D Protein Envelopes for Computer-Aided Drug Design.- Simultaneous Pathogen Detection and Antibiotic Resistance Characterization Using SNP-Based Multiplexed Oligonucleotide Ligation-PCR (MOL-PCR).- Specification and Verification of Pharmacokinetic Models.- Dehydron Analysis: Quantifying the Effect of Hydrophobic Groups on the Strength and Stability of Hydrogen Bonds.- Docking to Large Allosteric Binding Sites on Protein Surfaces.- Modeling of ATP-Sensitive Inward Rectifier Potassium Channel 11 and Inhibition Mechanism of the Natural Ligand, Ellagic Acid, Using Molecular Docking.- GPU Acceleration of Dock6’s Amber Scoring Computation.- Computational Methods and Diagnostic Tools in Biomedical.- Discriminative Distance Functions and the Patient Neighborhood Graph for Clinical Decision Support.- A Scalable and Integrative System for Pathway Bioinformatics and Systems Biology.- Registration of In Vivo Fluorescence Endomicroscopy Images Based on Feature Detection.- Kinetic Models for Cancer Imaging.- Using Web and Social Media for Influenza Surveillance.- CodeSlinger: A Case Study in Domain-Driven Interactive Tool Design for Biomedical Coding Scheme Exploration and Use.- DigitalLung: Application of High-Performance Computing to Biological System Simulation.- Consideration of Indices to Evaluate Age-Related Muscle Performance by Using Surface Electromyography.- A Study on Discrete Wavelet-Based Noise Removal from EEG Signals.- Enhancing the Communication Flow Between Alzheimer Patients, Caregivers, and Neuropsychologists.- An Improved 1-D Gel Electrophoresis Image Analysis System.- A Fuzzy Approach for Contrast Enhancement of Mammography Breast Images.- Computational Modeling of a New Thrombectomy Device for the Extraction of Blood Clots.- NEURONSESSIONS: A Web-Based Collaborative Tool to Create Brain Computational Models.- General Topics in Bioinformatics.- Toward Automating an Inference Model on Unstructured Terminologies: OXMIS Case Study.- Semantic Content-Based Recommendations Using Semantic Graphs.- Modeling Membrane Localization: Case Study of a Ras Signaling Model.- A Study on Distributed PACS.- Epileptic EEG: A Comprehensive Study of Nonlinear Behavior.- Computational Energetic Model of Morphogenesis Based on Multi-agent Cellular Potts Model.- Standardizing the Next Generation of Bioinformatics Software Development with BioHDF (HDF5).- Multisensor Smart System on a Chip.- Visual Presentation as a Welcome Alternative to Textual Presentation of Gene Annotation Information.- Automatic FRAP Analysis with Inhomogeneous Fluorescence Distribution and Movement Compensation.- Sorting Circular Permutations by Bounded Transpositions.- Annotating Patents with Medline MeSH Codes via Citation Mapping.- Some New Measures of Entropy, Useful Tools in Biocomputing.- Erratum to: Kinetic Models for Cancer Imaging.- Erratum to: Kinetic Models for Cancer Imaging.