General Info

Course Staff

Tentative Syllabus

Slides / Notes

Paper Index

Assigned Readings




Course Description

Time: TTh 11:00-12:15
Place: Braun Auditorium
Professor: Daphne Koller

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.

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.