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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

Overview 

  • 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