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