Quantitative Biology: Theory, Computational Methods, and Models (Hardcover)

1 Introduction to Quantitative Biology
2 Fostering Collaborations between Experimentalists and Modelers
I DEFINING AND SIMULATING MODELS
3 Modeling with Ordinary Differential Equations
4 Modeling with Partial Differential Equations
5 Stochasticity or Noise in Biochemical Reactions
6 The Linear-Noise Approximation and Moment Closure Approximations for Stochastic Chemical Kinetics
7 Kinetic Monte Carlo Analyses of Discrete Biomolecular Events
8 The Extra Reaction Algorithm for Stochastic Simulation of Biochemical Reaction Systems in Fluctuating Environments
9 Spatial-Stochastic Simulation of Reaction-Diffusion Systems
10 Introduction to Molecular Simulation
II MODEL DEVELOPMENT AND ANALYSIS TOOLS
11 Reverse-Engineering Biological Networks from Large Data Sets
12 Mathematically Controlled Comparisons for Elucidation of Biological Design Principles
13 Parameter Estimation, Sloppiness, and Model Identifiability
14 Sensitivity Analysis
15 Experimental Design
16 Bayesian Parameter Estimation and Markov Chain Monte Carlo
17 Uses of Bifurcation Analysis in Understanding Cellular Decision-Making
18 Performance Measures for Stochastic Processes and the Matrix-Analytic Approach
III MODELING IN PRACTICE
19 Setting Up and Simulating ODE Models
20 Accelerating Stochastic Simulations Using Graphics Processing Units
21 Rule-Based Modeling Using Virtual Cell (VCELL)
21 Rule-Based Modeling Using Virtual Cell (VCELL)
23 Stochastic Simulation of Well-Mixed and Spatially Inhomogeneous Biochemical Systems
24 Spatial Stochastic Modeling with MCELL and CELLBLENDER
IV EXAMPLE MODELS AND SPECIALIZED METHODS
25 The Use of Linear Analysis and Sensitivity Functions in Exploring Trade-Offs in Biology: Applications to Glycolytic Oscillations
26 Models of Bacterial Chemotaxis
27 Modeling Viral Dynamics
28 Stochastic Modeling of Gene Expression, Protein Modification, and Polymerization
29 Modeling Cell-Fate Decisions in Biological Systems: Bacteriophage, Hematopoietic Stem Cells, Epithelial-to-Mesenchymal Transition, and Beyond
30 Tutorial on the Identification of Gene Regulation Models from Single-Cell Data