- Biological networks components:
- Genes, RNAs, proteins
- DNA and protein sequence elements
- Types of edges
- Regulation of different types
- Physical interaction
- Interaction with small molecules (e.g., metabolism)
- Context specificity
Regulatory networks (8 lectures)
- Network characterization (2 lectures)
- Network motifs & circuits
- Modules
- Evolution (2 lectures)
- Biological data types: properties and limitations (1 lectures)
- Gene expression
- Sequence motifs
- Physical binding assays
- Reconstruction (3 lectures)
- Of cis-regulatory networks
- Of general regulatory networks
P2P networks (4 lectures)
- Network characterization (1 lecture)
- Complexes, transient interactions
- Global network characterization
- Regulation of protein interaction networks
- Evolution (1 lecture)
- Biological data types: properties and limitations (0.5 lecture)
- Protein sequences
- Protein interaction assays
- Reconstruction (1.5 lectures)
- Data integration
- Reconstructing higher level structures (complexes, linear pathways)
Metabolic networks (5 lectures)
- Network characterization (2 lectures)
- Flux balance analysis
- Regulation of network
- Network motifs
- Evolution (1 lecture)
- Data types (0.5 lecture)
- Reconstruction (1.5 lectures)
Function (2 lectures)
- Functional data
- Genetic interactions
- Phenotypes
- Function and networks
