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Emerging Research in the Analysis and Modeling of Gene Regulatory Networks

Book Description

While technological advancements have been critical in allowing researchers to obtain more and better quality data about cellular processes and signals, the design and practical application of computational models of genomic regulation continues to be a challenge. Emerging Research in the Analysis and Modeling of Gene Regulatory Networks presents a compilation of recent and emerging research topics addressing the design and use of technology in the study and simulation of genomic regulation. Exploring both theoretical and practical topics, this publication is an essential reference source for students, professionals, and researchers working in the fields of genomics, molecular biology, bioinformatics, and drug development.

Table of Contents

  1. Cover
  2. Title Page
  3. Copyright Page
  4. Book Series
    1. Mission
    2. Coverage
  5. External Advisory Board
    1. External Advisory Board
    2. List of Reviewers
  6. Preface
    1. REFERENCES
  7. Chapter 1: Inference of Gene Regulatory Networks by Topological Prior Information and Data Integration
    1. ABSTRACT
    2. 1. INTRODUCTION
    3. 2. BACKGROUND
    4. 3. GRN INFERENCE BY INCORPORATING TOPOLOGICAL INFORMATION
    5. 4. FUNCTIONAL DATA SOURCES USED IN GRN INFERENCE
    6. 5. DATA SOURCE INTEGRATION IN GRN INFERENCE
    7. 6. CONCLUSION
    8. REFERENCES
    9. ENDNOTE
  8. Chapter 2: Relationships between Models of Genetic Regulatory Networks with Emphasis on Discrete State Stochastic Models
    1. ABSTRACT
    2. INTRODUCTION
    3. MODEL APPROXIMATIONS
    4. DISCUSSIONS
    5. REFERENCES
  9. Chapter 3: Modeling Stochastic Gene Regulatory Networks Using Direct Solutions of Chemical Master Equation and Rare Event Sampling
    1. ABSTRACT
    2. 1. INTRODUCTION
    3. 2. DISCRETE CHEMICAL MASTER EQUATION FRAMEWORK FOR MODELING STOCHASTIC NETWORKS
    4. 3. DIRECT SOLUTIONS TO THE dCME
    5. 4. EXAMPLES OF REALISTIC GENE REGULATORY NETWORKS
    6. 5. DISCUSSIONS
    7. REFERENCES
  10. Chapter 4: Structural Intervention and External Control for Markovian Regulatory Network Models
    1. ABSTRACT
    2. 1. INTRODUCTION
    3. 2. BACKGROUNDS
    4. 3. STRUCTURAL INTERVENTION
    5. 4. EXTERNAL CONTROL OF PBNs
    6. 5. PHENOTYPICALLY CONSTRAINED INTERVENTION
    7. 6. ROBUST AND ADAPTIVE CONTROL OF PBNs
    8. 7. DISCUSSION
    9. REFERENCES
  11. Chapter 5: Optimal Intervention Methods for Markovian Gene Regulatory Networks
    1. ABSTRACT
    2. INTRODUCTION
    3. MARKOVIAN GENE REGULATORY NETWORKS
    4. CONCLUSION
    5. REFERENCES
  12. Chapter 6: Why Are Multiple Regulators Required for Transcription of Each Gene?
    1. ABSTRACT
    2. INTRODUCTION
    3. COMPUTER SIMULAION ANALYSIS OF CONSENSUS SEQUENCES
    4. PHYSIOLOGICAL FUNCTIONS OF CONSENSUS SEQUENCES
    5. BENEFITS OF GENE REGULATION BY MULTIPLE REGULATORS
    6. COMPUTER ANALYSIS SUPPORTS COMPLEXITY OF SINGAL PATHWAYS
    7. CONCLUSION
    8. REFERENCES
    9. KEY TERMS AND DEFINITIONS
    10. APPENDIX 1: GENERATION OF RANDOM SEQUENCES
    11. APPENDIX 2: SEARCH FOR HOMOLOGOUS SEQUENCES
    12. APPENDIX 3: THE SOURCE CODE OF THE PROGRAM USED IN THE SIMULATIONS
  13. Chapter 7: Computational Inference of Gene Regulation from Whole-Transcriptome Analysis of Early Embryos
    1. ABSTRACT
    2. INTRODUCTION
    3. BACKGROUND
    4. PREIMPLANTATION EMBRYONIC DEVELOPMENT
    5. COMPUTATIONAL INFERENCE OF GENE REGULATION
    6. INFERENCE OF TRANSCRIPTIONAL REGULATION IN ZGA
    7. FUTURE RESEARCH DIRECTIONS
    8. CONCLUSION
    9. REFERENCES
    10. KEY TERMS AND DEFINITIONS
  14. Chapter 8: Prioritize Transcription Factor Binding Sites for Multiple Co-Expressed Gene Sets Based on Lasso Multinomial Regression Models
    1. ABSTRACT
    2. INTRODUCTION
    3. EXPERIMENTAL IDENTIFICATION OF TRANSCRIPTION FACTOR BINDING SITES
    4. THE APPROACH PROPOSED IN THIS CHAPTER
    5. RESULTS
    6. DISCUSSION
    7. FURTHER DEVELOPMENT
    8. REFERENCES
    9. KEY TERMS AND DEFINITIONS
  15. Chapter 9: Dynamical Analysis of Drug Efficacy and Mechanism of Action Using GFP Reporters
    1. ABSTRACT
    2. INTRODUCTION
    3. EXPERIMENTAL APPARATUS
    4. RESULTS
    5. CONCLUSION
    6. REFERENCES
    7. KEY TERMS AND DEFINITIONS
  16. Compilation of References
  17. About the Contributors