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Handbook of Research on Computational and Systems Biology

Book Description

Handbook of Research on Computational and Systems Biology: Interdisciplinary Applications summarizes some of the most recent research carried out in computational biology and systems biology to encourage and guide future study. Submissions to this comprehensive text present methods, tools, and applications developed and considered by many leading experts around the globe.

Table of Contents

  1. Cover
  2. Title Page
  3. Copyright Page
  4. Editorial Advisory Board and List of Reviewers
    1. Editorial Advisory Board
    2. List of Reviewers
  5. Preface
    1. ORGANIZATION OF THE BOOK
  6. Acknowledgment
  7. Section 1: Drug Development and Medicine
    1. Chapter 1: Ethics and Privacy Considerations for Systems Biology Applications in Predictive and Personalized Medicine
      1. Abstract
      2. INTRODUCTION
      3. PERSONALIZED MEDICINE: THE HISTORY
      4. SYSTEMS BIOLOGY AND PERSONALIZED MEDICINE
      5. PRIVACY AND ETHICAL DILEMMAS: A PROBLEM STATEMENT
      6. ETHICS ISSUES IN THE ERA OF PERSONALIZED MEDICINE
      7. PRIVACY CONSIDERATIONS IN THE ERA OF PERSONALIZED MEDICINE
      8. CONCLUSION
    2. Chapter 2: Virtual Screening
      1. ABSTRACT
      2. INTRODUCTION
      3. STRUCTURE-BASED VIRTUAL SCREENING (SBVS)
      4. CASE STUDIES FOR SBVS
      5. LIGAND BASED VIRTUAL SCREENING (LBVS)
      6. CONCLUSION
    3. Chapter 3: Systems Biology-Based Approaches Applied to Vaccine Development
      1. ABSTRACT
      2. INTRODUCTION
      3. REVERSE VACCINOLOGY AND BEYOND, ACCELERATING VACCINE DISCOVERY
      4. BIOINFORMATICS AND THE EMERGENT ROLE OF IMMUNOINFORMATICS
      5. VACCINOMICS: IMPROVING VACCINE DESIGN BY STUDYING HOST GENETIC VARIATION
      6. A PROMISING TREND: SYNTHETIC WHOLE ORGANISM VACCINES
      7. CONCLUSION
    4. Chapter 4: Current Omics Technologies in Biomarker Discovery
      1. ABSTRACT
      2. INTRODUCTION
      3. GENETIC BIOMARKER
      4. TRANSCRIPTOMIC BIOMARKER
      5. MASS SPECTROMETRY-BASED QUANTITATIVE PROTEOMICS FOR BIOMARKER DISCOVERY
      6. METABONOMICS IN BIOMARKER DISCOVERY
      7. CONCLUSION
  8. Section 2: Method Development in Bioinformatics
    1. Chapter 5: Single Nucleotide Polymorphism and its Application in Mapping Loci Involved in Developing Human Diseases and Traits
      1. Abstract
      2. INTRODUCTION
      3. THE POWER OF GENOME-WIDE ASSOCAITION STUDIES
      4. STAGES OF A GENOME-WIDE ASSOCIATION STUDY
      5. UNEXPLAINED HERITABILITY
      6. RARE ALLELES AND COMMON DISEASES AND TRAITS
      7. STRUCTURAL VARIANTS AND COMMON DISEASES AND TRAITS
      8. THE UTILITY OF EXPRESSION QTLS
      9. IDENTIFICATION OF CAUSAL ALLELES
      10. CONCLUSION
    2. Chapter 6: Addressing the Challenges of Detecting Epistasis in Genome-Wide Association Studies of Common Human Diseases Using Biological Expert Knowledge
      1. Abstract
      2. INTRODUCTION
      3. GENOME-WIDE ASSOCIATION STUDIES (GWAS)
      4. CHALLENGES OF DETECTING EPISTASIS IN GWAS
      5. BIOLOGICAL EXPERT KNOWLEDGE
      6. OUTLOOK/ CONCLUDING REMARKS
    3. Chapter 7: Biclustering of DNA Microarray Data
      1. Abstract
      2. INTRODUCTION
      3. BICLUSTERING OF DNA MICROARRAY DATA
      4. BICLUSTER MODELS, INTERPRETATIONS, AND EVALUATIONS
      5. ALGORITHMS FOR BICLUSTERS IDENTIFICATION
      6. BIOLOGICAL APPLICATIONS OF BICLUSTERING ALGORITHMS
      7. CONCLUSION, DISCUSSION AND FUTURE RESEARCH DIRECTIONS
      8. ADDITIONAL READING
    4. Chapter 8: Prediction of Epigenetic Target Sites by Using Genomic DNA Sequence
      1. Abstract
      2. INTRODUCTION
      3. METHODS TO PREDICT EPIGENETIC TARGETS
      4. DISCUSSION
    5. Chapter 9: A New Approach for Sequence Analysis
      1. ABSTRACT
      2. INTRODUCTION
      3. COMPUTATIONAL ANALYSIS: INPUT
      4. COMPUTATIONAL ANALYSIS: METHOD
      5. COMPUTATIONAL ANALYSIS: OUTPUT
      6. CONCLUSION
  9. Section 3: Biological Networks and Pathways
    1. Chapter 10: Knowledge-Driven, Data-Assisted Integrative Pathway Analytics
      1. Abstract
      2. INTRODUCTION
      3. PATHWAY AND NETWORK ANALYSIS TOOLS
      4. INTEGRATIVE ANALYSIS AND EXAMPLES OF ITS APPLICATION
      5. FUTURE DIRECTIONS
    2. Chapter 11: Modules in Biological Networks
      1. ABSTRACT
      2. INTRODUCTION
      3. COMPUTATIONAL METHODS FOR MODULE IDENTIFICATION
      4. MODULE-BASED APPLICATIONS IN BIOLOGICAL STUDIES
      5. CONCLUSION
    3. Chapter 12: Using Functional Linkage Gene Networks to Study Human Diseases
      1. Abstract
      2. INTRODUCTION AND BACKGROUND
      3. MAIN FOCUS OF THE CHAPTER
      4. FUTURE RESEARCH DIRECTIONS
      5. CONCLUSION
    4. Chapter 13: Network-Driven Analysis Methods and their Application to Drug Discovery
      1. ABSTRACT
      2. INTRODUCTION
      3. APPLICATIONS IN DRUG DISCOVERY
      4. METHODS AND RESOURCES
      5. CURRENT GAPS
      6. PERSPECTIVES AND CONCLUSION
    5. Chapter 14: Pathway Resources at the Rat Genome Database
      1. ABSTRACT
      2. INTRODUCTION
      3. BACKGROUND
      4. MAIN FOCUS OF THE CHAPTER
      5. NEW DEVELOPMENTS
      6. CONCLUSIONS AND FUTURE DIRECTIONS
      7. Author’s Note
    6. Chapter 15: Unsupervised Methods to Identify Cellular Signaling Networks from Perturbation Data
      1. Abstract
      2. INTRODUCTION
      3. COMBINING MULTI-VARIATE MEASUREMENT DATA INTO QUANTITATIVE ESTIMATES OF SIGNAL TRANSDUCTION
      4. FUTURE RESEARCH DIRECTIONS
      5. CONCLUSION
      6. Appendix
    7. Chapter 16: Complexity and Modularity of MAPK Signaling Networks
      1. Abstract
      2. INTRODUCTION
      3. BACKGROUND
      4. MAIN FOCUS OF THE CHAPTER
      5. DISCUSSION
      6. CONCLUSION
    8. Chapter 17: Cancer and Signaling Pathway Deregulation
      1. Abstract
      2. INTRODUCTION
      3. BACKGROUND
      4. MAIN FOCUS OF THE CHAPTER
      5. IMPLICATIONS AND FUNTURE DIRECTIONS
    9. Chapter 18: Computational Methods for Identification of Novel Secondary Metabolite Biosynthetic Pathways by Genome Analysis
      1. ABSTRACT
      2. INTRODUCTION
      3. BACKGROUND INFORMATION ON VARIOUS DIFFERENT PARADIGMS FOR BIOSYNTHESIS OF POLYKETIDES AND NONRIBOSOMAL PEPTIDES
      4. DECIPHERING THE SECONDARY METABOLITE BIOSYNTHETIC CODE BY IN SILICO ANALYSIS
      5. PREDICTION OF DOMAIN ORGANIZATION IN PKS/NRPS GENE CLUSTERS
      6. PREDICTION OF SUBSTRATE SPECIFICITY OF VARIOUS CATALYTIC DOMAINS
      7. PREDICTION OF NUMBER OF ITERATIONS CATALYZED BY TYPE I ITERATIVE PKSs
      8. PREDICTION OF THE ORDER OF SUBSTRATE CHANNELING IN MODULAR PKS CLUSTERS
      9. PREDICTION OF SPECIFICITY OF THIOESTERASE DOMAINS AND TAILORING ENZYMES
      10. APPLICATION OF IN SILICO PREDICTIONS IN EXPERIMENTAL STUDIES INVOLVING DISCOVERY OF NEW SECONDARY METABOLITES & REPROGRAMMING OF KNOWN BIOSYNTHETIC PATHWAYS
      11. FUTURE DIRECTIONS
      12. CONCLUSION
    10. Chapter 19: Linking Interactome to Disease
      1. Abstract
      2. INTRODUCTION
      3. BACKGROUND
      4. INTERACTOME-TRANSCRIPTOME INTEGRATION
      5. RESULTS
      6. CONCLUSION AND FUTURE RESEARCH DIRECTIONS
    11. Chapter 20: Using Systems Biology Approaches to Predict New Players in the Innate Immune System
      1. Abstract
      2. INTRODUCTION
      3. METHODS
      4. RESULTS
      5. DISCUSSION
      6. CONCLUSION
      7. FUTURE WORK
      8. APPENDIX
    12. Chapter 21: Dynamic Modeling and Parameter Identification for Biological Networks
      1. Abstract
      2. INTRODUCTION
      3. BACKGROUND
      4. INTRODUCTION TO MODELING GENE EXPRESSION
      5. SENSITIVITY AND IDENTIFIABILITY ANALYSIS
      6. PARAMETER ESTIMATION
      7. RESULTS
      8. FUTURE RESEARCH DIRECTIONS
      9. CONCLUSION
      10. APPENDIX BASIC BIOLOGY
    13. Chapter 22: Granger Causality
      1. ABSTRACT
      2. INTRODUCTION
      3. GENE CIRCUIT OF ARABIDOPSIS LEAF
      4. UNIFIED CAUSAL MODEL
      5. CONCLUSION
    14. Chapter 23: Connecting Microbial Population Genetics with Microbial Pathogenesis Engineering Microfluidic Cell Arrays for High-throughput Interrogation of Host-Pathogen Interaction
      1. ABSTRACT
      2. INTRODUCTION
      3. FUTURE DIRECTIONS AND DEVELOPMENTAL PROSPECTS
  10. Section 4: Structural and Mathematical Modeling
    1. Chapter 24: Structural Alignment of RNAs with Pseudoknots
      1. Abstract
      2. INTRODUCTION
      3. PSEUDOKNOT DEFINITIONS
      4. DEFINITION OF STRUCTURAL ALIGNMENT
      5. ALGORITHM FOR REGULAR STRUCTURE
      6. ALGORITHM FOR STANDARD PSEUDOKNOTS
      7. ALGORITHM FOR SIMPLE NON-STANDARD PSEUDOKNOTS
      8. ALGORITHM FOR 2-LEVEL RECURSIVE PSEUDOKNOTS
      9. EXPERIMENTAL RESULTS
      10. CONCLUSION
    2. Chapter 25: Finding Attractors on a Folding Energy Landscape
      1. ABSTRACT
      2. INTRODUCTION
      3. RNA FOLDING MODEL
      4. RESULTS AND DISCUSSION
      5. CONCLUSION
    3. Chapter 26: Visualization of Protein 3D Structures in ‘Double-Centroid’ Reduced Representation
      1. ABSTRACT
      2. INTRODUCTION
      3. METHODS
      4. RESULTS AND DISCUSSION
      5. CONCLUSION AND FUTURE DIRECTIONS
    4. Chapter 27: Mechanical Models of Cell Adhesion Incorporating Nonlinear Behavior and Stochastic Rupture of the Bonds
      1. Abstract
      2. INTRODUCTION
      3. LITERATURE SURVEY OF DETERMINISTIC AND PROBABILISTIC CELL ADHESION MODELS
      4. SKETCH OF THE CELL-WALL INTERACTIONS
      5. ADHESION OF MOLECULAR CONNECTIONS
      6. CELL PROTRUSION DUE TO CYTOSKELETON POLYMERIZATION
      7. SIMULATION RESULTS
      8. FUTURE RESEARCH DIRECTIONS
    5. Chapter 28: A Multiscale Computational Model of Chemotactic Axon Guidance
      1. Abstract
      2. INTRODUCTION
      3. BIOLOGICAL BACKGROUND
      4. MATHEMATICAL BACKGROUND
      5. METHOD: THE MATHEMATICAL MODEL
      6. RESULTS
      7. DISCUSSION AND CONCLUSION
  11. Compilation of References
  12. About the Contributors
  13. Index