Preface
About the Author
I: Background
Chapter 1: Probabilistic Informatics
1.1 What Is Informatics?
1.2 Bioinformatics
1.3 Probabilistic Informatics
1.4 Outline of This Book
Chapter 2: Probability Basics
2.1 Probability Basics
2.2 Random Variables
2.3 The Meaning of Probability
2.4 Random Variables in Applications
Chapter 3: Statistics Basics
3.1 Basic Concepts
3.2 Markov Chain Monte Carlo
3.3 The Normal Distribution
Chapter 4: Genetics Basics
4.1 Organisms and Cells
4.2 Genes
4.3 Mutations
II: Bayesian Networks
Chapter 5: Foundations of Bayesian Networks
5.1 What Is a Bayesian Network?
5.2 Properties of Bayesian Networks
5.3 Causal Networks as Bayesian Networks
5.4 Inference in Bayesian Networks
5.5 Networks with Continuous Variables
5.6 How Do We Obtain the Probabilities?
Chapter 6: Further Properties of Bayesian Networks
6.1 Entailed Conditional Independencies
6.2 Faithfulness
6.3 Markov Equivalence
6.4 Markov Blankets and Boundaries
Chapter 7: Learning Bayesian Network Parameters
7.1 Learning a Single Parameter
7.2 Learning Parameters in a Bayesian Network
Chapter 8: Learning Bayesian Network Structure
8.1 Model Selection
8.2 Score-Based Structure Learning
8.3 Constraint-Based Structure Learning
8.4 Causal Learning
8.5 Model Averaging
8.6 Approximate Structure Learning
8.7 Software Packages for Learning
III: Bioinformatics Applications
Chapter 9: Nonmolecular Evolutionary Genetics
9.1 No Mutations, Selection, or Genetic Drift
9.2 Natural Selection
9.3 Genetic Drift
9.4 Natural Selection and Genetic Drift
9.5 Rate of Substitution
Chapter 10: Molecular Evolutionary Genetics
10.1 Models of Nucleotide Substitution
10.2 Evolutionary Distance
10.3 Sequence Alignment
Chapter 11: Molecular Phylogenetics
11.1 Phylogenetic Trees
11.2 Distance Matrix Learning Methods
11.3 Maximum Likelihood Method
11.4 Distance Matrix Methods Using ML
Chapter 12: Analyzing Gene Expression Data
12.1 DNA Microarrays
12.2 A Bootstrap Approach
12.3 Model Averaging Approaches
12.4 Module Network Approach
Chapter 13: Genetic Linkage Analysis
13.1 Introduction to Genetic Linkage Analysis
13.2 Genetic Linkage Analysis in Humans
13.3 A Bayesian Network Model
Bibliography
Index
