Mathematical Concepts and Methods in Modern Biology

Table of contents

1. Cover image
2. Title page
3. Table of Contents
4. Front Matter
5. Copyright
6. Contributors
7. Preface
8. Chapter 1. Mechanisms of Gene Regulation: Boolean Network Models of the Lactose Operon in Escherichia coli
   1. 1.1 Introduction
   2. 1.2 E. Coli and the LAC Operon
   3. 1.3 Boolean Network Models of the LAC Operon
   4. 1.4 Determining the Fixed Points of Boolean Networks
   5. 1.5 Conclusions and Discussion
   6. Acknowledgments
   7. 1.6 Supplementary Materials
   8. References
9. Chapter 2. Bistability in the Lactose Operon of Escherichia coli: A Comparison of Differential Equation and Boolean Network Models
   1. 2.1 Introduction
   2. 2.2 The Lactose Operon of Escherichia Coli
   3. 2.3 Modeling Biochemical Reactions with Differential Equations
   4. 2.4 The Yildirim-Mackey Differential Equation Models for the Lactose Operon
   5. 2.5 Boolean Modeling of Biochemical Interactions
   6. 2.6 Boolean Approximations of the Yildirim-Mackey Models
   7. 2.7 Conclusions and Discussion
   8. Acknowledgment
   9. 2.8 Supplementary Materials
   10. References
10. Chapter 3. Inferring the Topology of Gene Regulatory Networks: An Algebraic Approach to Reverse Engineering
    1. 3.1 Introduction
    2. 3.2 Polynomial Dynamical Systems (PDSs)
    3. 3.3 Computational Algebra Preliminaries
    4. 3.4 Construction of the Model Space: A Reverse Engineering Algorithm
    5. 3.5 Model Selection
    6. 3.6 Discretization
    7. References
11. Chapter 4. Global Dynamics Emerging from Local Interactions: Agent-Based Modeling for the Life Sciences
    1. 4.1 Introduction
    2. 4.2 Axon Guidance
    3. 4.3 An Agent-Based Model for Cholera and the Importance of Replication
    4. 4.4 Use and Description of ABM in Research: Tick-Borne Disease Agent-Based Models
    5. 4.5 Comments for Instructors
    6. Acknowledgments
    7. 4.6 Supplementary Materials
    8. References
12. Chapter 5. Agent-Based Models and Optimal Control in Biology: A Discrete Approach
    1. 5.1 Introduction
    2. 5.2 A First Example
    3. 5.3 Netlogo: An Introduction
    4. 5.4 An Introduction to Agent-Based Models
    5. 5.5 Optimization and Optimal Control
    6. 5.6 Scaling and Aggregation
    7. 5.7 A Heuristic Approach
    8. 5.8 Mathematical Framework for Representing Agent-Based Models
    9. 5.9 Translating Agent-Based Models into Polynomial Dynamical Systems
    10. 5.10 Summary
    11. 5.11 Supplementary Materials
    12. References
13. Chapter 6. Neuronal Networks: A Discrete Model
    1. 6.1 Introduction and Overview
    2. 6.2 Neuroscience in a Nutshell
    3. 6.3 The Discrete Model
    4. 6.4 Exploring the Model for Some Simple Connectivities
    5. 6.6.5 Exploring the Model for Some Random Connectivities
    6. 6.6 Another Interpretation of the Model: Disease Dynamics
    7. 6.7 More Neuroscience: Connection with ODE Models
    8. 6.8 Directions of Further Research
    9. 6.9 Supplementary Materials
    10. References
14. Chapter 7. Predicting Population Growth: Modeling with Projection Matrices
    1. 7.1 Introduction
    2. 7.2 Life Cycles and Population Growth
    3. 7.3 Determining Stages in the Life Cycle
    4. 7.4 Determining the Number of Individuals in a Stage at Time
    5. 7.5 Constructing a Projection Matrix
    6. 7.6 Predicting How a Population Changes after One Year
    7. 7.7 The Stable Distribution of Individuals across Stages
    8. 7.8 Theory Supporting the Calculation of Stable Distributions
    9. 7.9 Determining Population Growth Rate and the Stable Distribution
    10. 7.10 Further Applications of the Projection Matrix
    11. References
15. Chapter 8. Metabolic Pathways Analysis: A Linear Algebraic Approach
    1. 8.1 Introduction
    2. 8.2 Biochemical Reaction Networks, Metabolic Pathways, and the Stoichiometry Matrix
    3. 8.3 Extreme Paths and Model Improvements
    4. Acknowledgments
    5. 8.4 Supplementary Data
    6. References
16. Chapter 9. Identifying CpG Islands: Sliding Window and Hidden Markov Model Approaches
    1. 9.1 Introduction
    2. 9.2 Quantitative Characteristics of the CpG Island Regions and Sliding Windows Algorithms
    3. 9.3 Definition and Basic Properties of Markov Chains and Hidden Markov Models
    4. 9.4 Three Canonical Problems for HMMs with Applications to CGI Identification
    5. 9.5 Conclusions and Discussion
    6. Acknowledgments
    7. 9.6 Supplementary Materials
    8. References
17. Chapter 10. Phylogenetic Tree Reconstruction: Geometric Approaches
    1. 10.1 Introduction
    2. 10.2 Basics on Trees and Phylogenetic Trees
    3. 10.3 Tree Space
    4. 10.4 Neighbor-Joining and BME
    5. 10.5 Summary
    6. References
18. Index