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