The exhaustive list of topics in Computational methods for analysis and reconstruction of biological networks in which we provide Help with Homework Assignment and Help with Project is as follows:
P2P networks
- Network characterization
- Regulation of protein interaction networks
- Evolution
- Biological data types: properties and limitations
- Protein sequences
- Protein interaction assays
- Reconstruction
- Data integration
- Reconstructing higher level structures (complexes, linear pathways)
Metabolic networks
- Evolution
- Data types
- Reconstruction
- Network characterization
- Flux balance analysis
- Regulation of network
- Network motifs
Regulatory networks
- Network characterization
- Network motifs & circuits
- Modules
- Evolution
- Biological data types: properties and limitations
- Gene expression
- Sequence motifs
- Physical binding assays
- Reconstruction
- Of cis-regulatory networks
- Of general regulatory networks
- 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
Function
- Functional data
- Genetic interactions
- Phenotypes
- Function and networks