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Interdisciplinary Research and Applications in Bioinformatics, Computational Biology, and Environmental Sciences

Book Description

The advancement of high-throughput technologies that generate large scale biological data, as well as the development of related computational tools, has united global efforts and brought revolutionary changes to the research of biology during the last decade. Nowadays, biologists work with scientists and engineers from a broad spectrum of disciplines to unravel how complex biological systems work.Interdisciplinary Research and Applications in Bioinformatics, Computational Biology, and Environmental Sciences is a collection of cutting-edge research papers in the field of computational and systems biology contributed by leading researchers from across the globe. The studies range from the atomic/molecular level to the genomic level and present a wide spectrum of important biological problems and applications. It is a must-read for researchers in a broad range of disciplines, including computer science, chemistry, physics, math and statistics, and biological sciences.

Table of Contents

  1. Cover
  2. Title Page
  3. Copyright Page
  4. Editorial Advisory Board and List of Reviewers
    1. LIST OF REVIEWERS
  5. Preface
    1. TARGETS AND OVERALL OBJECTIVES OF THE BOOK
    2. ORGANIZATION OF THE BOOK
  6. Section 1: Method Development and Application in Bioinformatics
    1. Chapter 1: JFeature
      1. ABSTRACT
      2. INTRODUCTION
      3. THE JFEATURE TOOLBOX
      4. APPLICATION
      5. CONCLUSION
    2. Chapter 2: Cross-Platform Microarray Data Integration Combining Meta-Analysis and Gene Set Enrichment Analysis
      1. ABSTRACT
      2. INTRODUCTION AND BACKGROUND
      3. MAIN FOCUS OF THE CHAPTER
      4. DISCUSSIONS AND CONCLUSION
    3. Chapter 3: Chaos Game Representation of Mitochondrial Genomes
      1. ABSTRACT
      2. INTRODUCTION
      3. MATERIALS AND METHODS
      4. RESULTS AND DISCUSSIONS
      5. CONCLUSION
    4. Chapter 4: A Two-Layer Learning Architecture for Multi-Class Protein Folds Classification
      1. ABSTRACT
      2. INTRODUCTION
      3. MATERIALS
      4. METHOD
      5. RESULTS AND DISCUSSION
      6. CONCLUSION
      7. APPENDIX
    5. Chapter 5: Improving PSI-BLAST’s Fold Recognition Performance through Combining Consensus Sequences and Support Vector Machine
      1. ABSTRACT
      2. INTRODUCTION
      3. COMPUTATIONAL MODELS AND METHODS
      4. RESULT
      5. DISCUSSION AND CONCLUSION
    6. Chapter 6: A New Approach for DNA Sequence Similarity Analysis based on Triplets of Nucleic Acid Bases
      1. ABSTRACT
      2. INTRODUCTION
      3. SIMILARITY ANALYSIS
      4. A NEW APPROACH BASED ON TRIPLETS OF NUCLEIC ACIDS BASES
      5. EXPERIMENTS AND RESULT ANALYSIS
      6. CONCLUSION AND FUTURE WORK
    7. Chapter 7: MicroRNA Precursor Prediction Using SVM with RNA Pairing Continuity Feature
      1. ABSTRACT
      2. INTRODUCTION
      3. BACKGROUND
      4. DISCOVERY OF A NOVEL FEATURE FOR MICRORNA PRECURSOR CLASSIFICATION
      5. MATERIALS AND METHODS
      6. RESULTS AND DISCUSSION
      7. CONCLUSION
    8. Chapter 8: Four Long-Chain Acyl-Coenzyme A Synthetase Genes that Might be Involved in the Biosynthesis of Lipids in Brassica Napus
      1. ABSTRACT
      2. INTRODUCTION
      3. MATERIALS AND METHODS
      4. RESULT
      5. CONCLUSION
  7. Section 2: Biological Networks and Systems Biology
    1. Chapter 9: Topological Analysis of Axon Guidance Network for Homo Sapiens
      1. ABSTRACT
      2. INTRODUCTION
      3. MODEL AND ANALYSIS TOOL
      4. RESULTS AND DISCUSSIONS
      5. CONCLUSION
    2. Chapter 10: Evaluation of Coupled Nuclear and Cytoplasmic p53 Dynamics
      1. ABSTRACT
      2. INTRODUCTION
      3. BACKGROUND
      4. MAIN FOCUS OF THE CHAPTER
      5. DISCUSSION
      6. CONCLUSION AND FUTURE WORK
    3. Chapter 11: Agonist Fluctuation Maintained Calcium Signaling in a Mesoscopic System
      1. ABSTRACT
      2. INTRODUCTION
      3. BACKGROUND
      4. RESULTS AND DISCUSSION
      5. CONCLUSION
  8. Section 3: Computational Predictions of Drug Properties
    1. Chapter 12: Theoretical Study on the Antioxidant Activity of Alizarin, Purpurin, and Pseudopurpurin
      1. ABSTRACT
      2. INTRODUCTION
      3. COMPUTATIONAL DETAILS
      4. RESULTS AND DISCUSSION
      5. CONCLUSION
    2. Chapter 13: Human Oral Bioavailability Prediction of Four Kinds of Drugs
      1. ABSTRACT
      2. INTRODUCTION
      3. MATERIALS AND METHODS
      4. CONCLUSION
    3. Chapter 14: In Silico Prediction of Blood Brain Barrier Permeability
      1. ABSTRACT
      2. INTRODUCTION
      3. MATERIALS AND METHODS
      4. RESULTS AND DISCUSSION
      5. CONCLUSION
      6. Appendix
  9. Section 4: Medical Signal Processing and Analysis
    1. Chapter 15: The Study of Transesophageal Oxygen Saturation Monitoring
      1. ABSTRACT
      2. INTRODUCTION
      3. SPO2 MONITORING SYSTEM
      4. EXPERIMENT
      5. DISCUSSION
      6. CONCLUSION
    2. Chapter 16: Digital Auscultation System of Traditional Chinese Medicine and Its Signals Acquisition
      1. ABSTRACT
      2. INTRODUCTION
      3. ANALYSIS METHODS AND FEATURES
      4. PATTERN RECOGNITION METHODS
      5. DIGITAL AUSCULTATION SYSTEM OF TCM
    3. Chapter 17: Pulse Wave Analysis of Traditional Chinese Medicine Based on Hemodynamics Principles
      1. ABSTRACT
      2. INTRODUCTION
      3. HEMODYNAMIC PRINCIPLE BASIS OF TCM PULSE WAVE
      4. WAVE HARMONIC WAVE ANALYSIS OF PULSE WAVE
      5. ANALYSIS OF PULSE WAVE PROPAGATION AND REFLCTION PROPERTY
      6. CONCLUSION
  10. Section 5: Computational Biology
    1. Chapter 18: A New Mechanical Algorithm for Calculating the Amplitude Equation of the Reaction-Diffusion Systems
      1. ABSTRACT
      2. INTRODUCTION
      3. BASIC METHODS
      4. NEW MECHANICAL ALGORITHM
      5. EXAMPLES
      6. CONCLUSION
    2. Chapter 19: Pattern Formation Controlled by External Forcing in a Spatial Harvesting Predator-Prey Model
      1. ABSTRACT
      2. INTRODUCTION
      3. THE MODEL
      4. NUMERICAL RESULTS
      5. CONCLUSION
    3. Chapter 20: Repetitive Firing and Bursting due to Different Bifurcation Mechanism in Unmyelinated Fibre
      1. ABSTRACT
      2. INTRODUCTION
      3. COMPUTATIONAL MODELS AND METHODS
      4. DIFFERENT FIRING PATTERN AND THEIR DYNAMICS
      5. CONCLUSION
    4. Chapter 21: The Mathematical Modeling and Computational Simulation for Error-Prone PCR
      1. ABSTRACT
      2. INTRODUCTION
      3. MODELING FOR ERROR-PRONE PCR
      4. DISCUSSION AND CONCLUSION
  11. Section 6: Structure and Modeling
    1. Chapter 22: Molecular Dynamics Simulation of Interlayer Structure and Hydration Properties of Glycine Intercalated Layered Double Hydroxides
      1. ABSTRACT
      2. INTRODUCTION
      3. COMPUTATIONAL MODELS AND METHODS
      4. CONCLUSION
    2. Chapter 23: Structure of Hydrogenase in Biohydrogen Production Anaerobic Bacteria
      1. ABSTRACT
      2. INTRODUCTION
      3. BACKGROUND
      4. STRUCTURE AND ACTIVE SITE OF HYDROGENASES
      5. FUTURE RESEARCH DIRECTIONS
      6. CONCLUSION
  12. Section 7: Problems and Solutions in Environmental Sciences
    1. Chapter 24: Seasonal Trade-Off between Water- and Nitrogen-Use Efficiency of Constructive Plants in Desert Riparian Forest in Hyperarid Region of China
      1. ABSTRACT
      2. INTRODUCTION
      3. MATERIAL AND METHOD
      4. RESULTS
      5. DISCUSSION
      6. CONCLUSION
    2. Chapter 25: Root Water Uptake Model of Populus Euphratica in Desert Riparian Forest in Extreme Arid Region
      1. ABSTRACT
      2. INTRODUCTION
      3. MATERIALS AND METHODS
      4. RESULTS AND DISCUSSION
      5. CONCLUSION
    3. Chapter 26: The Fuzzy Integrated Energy Prior-warning Model Based on Entropy Weight
      1. ABSTRACT
      2. INTRODUCTION
      3. THE SELECTION OF PRIOR-WARNING INDEXES
      4. THE PRIOR-WARNING MODEL OF ENERGY SYSTEM BASED ON FUZZY SYNTHESIS EVALUATION
      5. THE PRIOR-WARNING MODEL BASED ON THE MULTI-OBJECTIVE OF ENTROPY WEIGHT
      6. DISCUSSION AND CONCLUSION
    4. Chapter 27: A Novel Flowsheet for the Recycling of Valuable Constituents from Waste Printed Circuit Boards
      1. ABSTRACT
      2. INTRODUCTION
      3. EXPERIMENT RESEARCH OF WASTE PCBS SUBSTRATES
      4. EXPERIMENT RESEARCH OF WASTE PCBS SLOTS
      5. A NOVEL BENEFICIATION FLOWSHEET
      6. CONCLUSION
  13. Compilation of References
  14. About the Contributors