CS590G: Analysis of Biochemical Networks

Fall 07.
Tu, Th, 4:30 - 5:50 PM

Instructor: Ananth Grama, LWSN 3-154G, Office Hours: W: 1:30 - 3:00 and by appointment

Course Contents:

CS590G, Analysis of Biochemical Networks, deals with abstractions, algorithms, and statistical models, for gathering information from a broad class of rapidly emerging datasets, referred to as biochemical networks. While domain experts see great value in such data and how it can be used for phenotype characterization, knockout experiments, drug design, and, in general, understanding the biochemical processes in the cell, there is increasing realization that the computational framework needed to answer the questions needs to be developed. This course surveys developments in the past few years in techniques for generating, validating, and analyzing network data -- contributing directly to the broader systems view to biology.
The course is structured as a reading course. The first part of the course deals with introductory material, setting the scene for presentations of a variety of recent results. Students will be expected to present 1-2 papers, and undertake a semester-long project, culminating in a paper and a presentation. This will determine their grade in the class.

List of Papers

  • Kinetics of Networks
  • Gene Regulatory Networks
  • Protein Interaction Networks
  • Domain Interaction Networks
    Inferring domain-domain interactions from protein-protein interactions, domain interaction databases.
  • Topology of Biological Networks
  • Functional Annotation
  • Schedule of Presentations