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Emerging trends in applications and infrastructures for computational biology, bioinformatics, and systems biology : systems and applications / Quoc Nam Tran, Hamid R. Arabnia. -- Cambridge : Morgan Kaufmann / Elsevier Ltd., c2016. – (58.105/T772)

Contents

List of Contributors  xix

Preface  xxvii

Introduction

Acknowledgments  xxxm

SECTION I  COMPUTATIONAL BIOLOGY- METHODOLOGIES AND ALGORITHMS

CHAPTER 1  Using Methylation Patterns for Reconstructing Cell Division Dynamics: Assessing Validation Experiments  3

CHAPTER 2 A Directional Cellular Dynamic Under the Control of a Diffusing Energy for Tissue Morphogenesis: Phenotype and Genotype  17

CHAPTER 3 A Feature Learning Framework for Histology Images Classification  37

CHAPTER 4 Spontaneous Activity Characterization in Spiking Neural Systems with Log-Normal Synaptic Weight Distribution  49

CHAPTER 5 Comparison between OpenMP and MPICH Optimized Parallel Implementations of a Cellular Automaton that Simulates the Skin Pigmentation Evolution  61

SECTION II  BIOINFORMATICS, SIMULATION, DATA MINING, PATTERN DISCOVERY, AND PREDICTION METHODS

CHAPTER 6 Structure Calculation of a, a/p, p Proteins from Residual Dipolar Coupling Data Using REDCRAFT  75

CHAPTER 7 Architectural Topography of the a-Subunit Cytoplasmic Loop in the GABAA Receptor  91

CHAPTER 8 Finding Long-Term Influence and Sensitivity of Genes Using Probabilistic Genetic Regulatory Networks  lO7

CHAPTER 9 The Application of Grammar Space Entropy in RNA Secondary Structure Modeling  121

CHAPTER 10 Effects of Excessive Water Intake on Body-Fluid Homeostasis and the Cardiovascular System -- A Computer Simulation  1:39

CHAPTER 11 A DNA-Based Migration Modeling of the Lizards in Florida Scrub Habitat  157

CHAPTER 12 Reconstruction of Gene Regulatory Networks Using Principal Component Analysis  171

CHAPTER 13 nD-PDPA: n-Dimensional Probability Density Profile Analysis  181

CHAPTER 14 Biomembranes Under Oxidative Stress: Insights from Molecular Dynamics Simulations  197

CHAPTER 15 Feature Selection and Classification of Microarray Data Using Machine Learning Techniques  213

CHAPTER 16 New Directions in Deterministic Metabolism Modeling of Sheep  243

CHAPTER 17 Differentiating Cancer from Normal Protein-Protein Interactions Through Network Analysis  253

CHAPTER 18 Predicting the Co-Receptors of the Viruses that Cause AIDS (HIV-1) in CD4 Cells  271

SECTION III    SYSTEMS BIOLOGY AND BIOLOGICAL PROCESSES

CHAPTER 19 Cellular Automata-Based Modeling of Three-Dimensional Multicellular Tissue Growth  287

CHAPTER 20 A Combination of Protein-Protein Interaction Network Topological and Biological Process Features for Multiprotein Complex Detection  305

CHAPTER 21 Infogenomics: Genomes as Information Sources  317

SECTION IV  DATA ANALYTICS AND NUMERICAL MODELING IN COMPUTATIONAL BIOLOGY AND BIOINFORMATICS

CHAPTER 22 Analysis of Large Data Sets: A Cautionary Tale of the Perils of Binning Data  327

CHAPTER 23 Structural and Percolation Models of Intelligence: To the Question of the Reduction of the Neural Network  333

SECTION V    MEDICAL APPLICATIONS AND SYSTEMS

CHAPTER 24 Analyzing TCGA Lung Cancer Genomic and Expression Data Using SVM with Embedded Parameter Tuning  343

CHAPTER 25 State-of-the-Art Mock Human Blood Circulation Loop: Prototyping and Introduction of a New Heart Simulator  357

CHAPTER 26 Framework for an Interactive Assistance in Diagnostic Processes Based on Probabilistic Modeling of Clinical Practice Guidelines  3"/1

CHAPTER 27 Motion Artifacts Compensation in DCE-MRI Framework Using Active Contour Model  391

CHAPTER 28 Phase III Placebo-Controlled, Randomized Clinical Trial with Synthetic Crohn's Disease Patients to Evaluate Treatment Response  411

CHAPTER 29 Pathological Tissue Permittivity Distribution Difference Imaging: Near-Field Microwave Tomographic Image for Breast Tumor Visualization  429

CHAPTER 30 A System for the Analysis of EEG Data and Brain State Modeling  447

CHAPTER 31 Using Temporal Logic to Verify the Blood Supply Chain Safety  467

CHAPTER 32 Evaluation of Window Parameters of CT Brain Images with Statistical Central Moments  493

CHAPTER 33 An Improved Balloon Snake Algorithm for Ultrasonic Image Segmentation

CHAPTER 34 Brain Ventricle Detection Using Hausdorff Distance  523

CHAPTER 35 Tumor Growth Emergent Behavior Analysis Based on Cancer Hallmarks and in a Cancer Stem Cell Context  533

Index  545