Computational Biology : New Research.

Intro -- Computational Biology: New Research -- Contents -- Preface -- Expressed Sequence Tags in Cancer Genomics -- Abstract -- Introduction -- Gene Expression -- SNPs -- Databases -- Advantages and Limitations -- Conclusions -- Acknowledgement -- References -- Short Commentaries -- Protein Bioinformatics for Drug Discovery Concavity Druggability and Antibody Druggability -- Abstract -- Introduction -- Protein Sequence and Structure Analysis -- Concavity Druggability -- Antibody Modeling and Druggability -- Conclusion -- References -- A Linkage Disequilibrium-Based Statistical Approach to Discovering Interactions among SNP Alleles at Multiple Loci Contributing to Human Skin Pigmentation Variation -- Abstract -- Introduction -- Materials and Methods -- Results -- Conclusion -- References -- Sufficient Conditions for Exact Penalty in Constrained Optimization on Complete Metric Spaces -- Abstract -- Introduction -- The Main Results -- Proofs of Theorems 2.1 and 2.2 -- References -- How to Create a Computational Medicine Study -- Abstract -- Introduction -- Research Design: The First Step -- Database and Tool for Manipulation -- Simulation Experiment -- References -- Identifying Related Cancer Types -- Abstract -- Introduction -- Methods -- Results -- Conclusion -- Acknowledgment -- References -- Research and Review Studies -- Sample Size Calculation and Power in Genomics Studies -- Introduction -- Preliminaries -- General Simulation-Based Approaches to Sample Size and Power Planning -- Methods Assuming Independence in Gene Expression -- Methods Accounting for Dependence in Gene Expression -- Methods for Controlling Family-Wise Error -- Other Approaches and Relevant Literature -- Discussion -- Acknowledgment -- References.

Coupling Computational and Experimental Analysis for the Prediction of Transcription Factor E2F Regulatory Elements in the Human Gene Promoter -- Abstract -- Introduction -- DNA Microarray and Bioinformatics -- Computational Prediction of E2F Binding Site Locations -- Experimental Verification of E2F Binding Site Locations -- ChIP-on-Chip -- Systems Biology -- Conclusion -- Acknowledgement -- References -- Solving a Stochastic Generalized Assignment Problem with Branch and Price -- Abstract -- Introduction -- Literature Review -- Mathematical Formulation -- Reformulating the Stochastic GAP -- Branch-and-Price Algorithm -- Computational Results -- Summary and Conclusions -- Acknowledgments -- References -- Reconstruction and Analysis of Large-Scale Phylogenetic Data, Challenges abd Opportunities -- Abstract -- Introduction -- The Standard Phylogenetic Analysis Pipeline -- Scaling up the Pipeline -- Challenges in the Analysis and Interpretation of Large-Scale Datasets -- Addressing Biological Questions Through Phylogenomics -- References -- Chromatin Fiber: 30 Years of Models -- Abstract -- Introduction -- Nucleosome/Chromatosome as the Chromatin Fundamental Subunit -- Nucleosome Computation -- Nucleosomal Arrays and the "30 nm Fiber -- From Hard Models to In Silico Chromatin Fibers -- Why So Many Models? -- Conclusion -- References -- Fast Modelling of Protein Structures Through Multi-Level Contact Maps -- Abstract -- Introduction -- Representing Protein Structures -- Modelling Structures with Contact Maps -- Contact Map Prediction -- Conclusions -- Acknowledgments -- References -- Coarse-Grained Structural Model of Protein Molecules -- Abstract -- Introduction -- Molecular Simulation: Normal Mode Analysis (NMA) -- Go Model -- Trion's Model: Elastic Network Model (ENM) -- Coarse-Grained Elastic Network Model -- Conformational Fluctuation Dynamics.

Lowest-Frequency Normal Mode -- Collective and Correlated Motion of Proteins -- Conformational Transition -- Conclusion -- Acknowledgement -- References -- Differentiating Superficial and Advanced Urothelial Bladder Carcinomas Based on Gene Expression Profiles Analyzed Using Self-Organizing Maps -- Abstract -- Introduction -- Materials and Methods -- Results -- Discussion -- Conclusion -- References -- Full Sibling Reconstruction in Wild Populations from Microsatellite Genetic Markers -- Abstract -- Introduction -- Sibling Reconstruction Problem -- Genetic of Sibship -- Methods for Full Sibling Reconstruction -- Experimental Validation -- Conclusion -- Acknowledgments -- References -- Recent Issues and Computational Approaches for Developing Prognostic Gene Signatures from Gene Expression Data -- Abstract -- Introduction -- Current Issues in the Development of Prognostic Gene Signatures -- Current Computational Approaches for Developing Prognostic Gene Signatures -- Conclusion -- Acknowledgements -- References -- Comparison of Φ-Values and Folding Time Predictions by Using Monte-Carlo and Dynamic Programming Approaches -- Abstract -- Introduction -- Results -- Discussion -- Acknowledgments -- References -- Computational Methods for Protein Structural Class Prediction -- Abstract -- Introduction -- Structural Class Definitions -- Methods for Evaluating the Prediction Quality -- Prediction of Secondary Structure Content -- Methods of Secondary Structural Class Prediction -- Conclusion -- References -- Fundamental of Natural Computation in Living Systems -- Abstract -- Introduction: Grounds for Computability and the Peircean Paradigm -- Quantum Mechanical Basis of Computability -- Robert Rosen's Theory of (M,R) Systems and Autopoiesis -- Organizational Invariance as the Principle of Optimal Design -- Internal Computability of Metabolic Systems.

Computability of the Evolutionary Process -- Computable Structures in Psychology -- Conclusion: Rosen's "Central Result" and Computability -- References -- Extraction of Position-Sensitive Promoter Constituents -- Abstract -- Introduction -- LDSS Strategy -- Procedure of LDSS Analysis -- Advantage and Limitation -- Examples of LDSS Analysis -- Other Application of LDSS Analysis -- Conclusion -- References -- Deconvolution of Positional Scanning Synthetic Combinatorial Libraries: Mathematical Models and Bioinformatics Approaches -- Abstract -- Introduction -- Mathematical Model -- Model Evaluation -- Support Vector Machine -- Bioinformatical Approach -- Applications -- Acknowledgement -- References -- Scripting of Molecular Structure Viewer for Data Analysis Using Lua Language Interpreter -- Abstract -- Introduction -- Introduction to Lua -- Embedding a Lua Interpreter -- An Application to Molecular Graphics -- Discussion -- Conclusion -- Acknowledgements -- References -- Computational Medicine Research in Hematology: A Study on Hemoglobin and Prothrombin Disorders -- Abstract -- Introduction to Computational Hematology -- Computational Medicine Research on Hemoglobin Disorder -- Computational Medicine Research on Prothrombin Disorder -- References -- Index.

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Electronic reproduction. Ann Arbor, Michigan : ProQuest Ebook Central, 2024. Available via World Wide Web. Access may be limited to ProQuest Ebook Central affiliated libraries.