Lectures from SYSTEMS BIOLOGY: Constraint-based Reconstruction and Analysis

Chapter 1: Introduction

PART I: Network Reconstruction

Chapter 2: Network Reconstruction: The Concept

Chapter 3: Network Reconstruction: The Process

Chapter 4: Metabolism in Escherichia coli

Chapter 5: Prokaryotes

Chapter 6: Eukaryotes

Chapter 7: Biochemical Reaction Networks

Chapter 8: Metastructures of Genomes

PART II: Mathematical Properties of Reconsructed Networks

Chapter 9: The Stoichiometric Matrix

Chapter 10: Simple Topological Network Properties (No Lecture)

Chapter 11: Fundamental Network Properties

Chapter 12: Pathways

Chapter 13: Use of Pathway Vectors (No Lecture)

Chapter 14: Randomized Sampling

PART III: Determining the Phenotypic Potential of Reconsructed Networks

Chapter 15: Dual Causality

Chapter 16: Functional States

Chapter 17: Constraints

Chapter 18: Optimization

Chapter 19: Determining Capabilities

Chapter 20: Equivalent States (No Lecture)

Chapter 21: Distal Causation

PART IV: Basic and Applied Uses

Chapter 22: Environmental Parameters

Chapter 23: Genetic Parameters

Chapter 24: Analysis of Omic Data

Chapter 25: Model Driven Discovery

Chapter 26: Adaptive Laboratory Evolution

Chapter 27: Model Driven Design (No Lecture)

PART V: Conceptual Foundations

Chapter 28: Teaching Systems Biology (No Lecture)

Chapter 29: Epilogue (No Lecture)

Special Guest Lectures:

Constraint-based models predict metabolic and associated cellular functions

Guest Lecture by Aarash Bordbar

Growth-coupled fermentation: A strategy for automated cell design

Guest Lecture by Zachary King