CS279: Computational Methods for Analysis and Reconstruction of Biological Networks

Course Description

A living cell performs its activity via multiple complex networks of interacting entities, which include genes, RNAs, proteins, and small molecules. These inter-related networks include: regulatory networks, spanning both direct transcriptional regulation and other regulatory mechanisms (such as signaling, RNA degradation or chromatin structure modification); networks of protein-protein interactions; and networks of metabolic reactions where compounds are processed to produce other compounds. This new course, which lies at the intersection of systems biology and computational biology, covers computational methods for understanding and reconstructing these networks. For each type of network, the course will discuss: characterization of network structure in terms of high-level structure and basic building blocks; understanding the effect of these structural characteristics on network function; available biological data that can help reveal aspects of the network; and algorithms for reconstructing the network from biological data. The course will discuss the interactions between the different types of network, and the connection between networks and cellular functions.

Prerequisites

The course is intended to be accessible to both biologically- and computationally-oriented students, with some amount of background in both disciplines:

Basic biological concepts at the level of Bio41.
Basic computer science and data structures at the level of CS103.
Programming skills in some scientific programming language (C, C++, Java, or Matlab).
Probability and statistics at the level of Stats 116.

Workload

The course will be project-based, with the primary workload consisting of a two-part project, performed in small inter-disciplinary teams combining both biologists and computer-scientists. In the first part of the project, the team will read, summarize, and critique 3-4 papers relating to a particular topic within the scope of the course. Continuing on the same topic, in the second part, each team will design and implement a new computational experiment and analyze the results.

Three small problem sets, 5% of the grade each, no programming required.
Project deliverable:
- Review and Critique - 30% of the grade (Friday, 10/27).
- A poster - 15% of the grade (Friday, 12/8)
- A written report - 40% of the grade (Monday, 12/11).
Note: Some extra credit will be assigned based on class participation.

Textbook

The optional textbook (covers about 2 weeks of material) is:

An Introduction to Systems Biology: Design Principles of Biological Circuits by Uri Alon
CRC Press, 2006

Communication

We strongly recommend asking questions on the newsgroup (su.class.cs279). This forum enables students to discuss problems that they encounter. It is also an excellent place to find a group for the project. For information on how to access and use class newsgroups see A Stanford Intro to Usenet .

There is also a homework question queue at cs279-qa@cs.stanford.edu, which is monitored by the course staff. Please include the homework number and question number in the subject line, for example, “HW1 Q2”.