Bi/BE 250c Winter 2011
The class will focus on quantitative studies of cellular and developmental systems in biology. It will examine the architecture of specific genetic circuits controlling microbial behaviors and multicellular development in model organisms. The course will approach most topics from both experimental and theoretical/computational perspectives. Specific topics include chemotaxis, multistability and differentiation, biological oscillations, stochastic effects in circuit operation, as well as higher-level circuit properties such as robustness. The course will also consider the organization of transcriptional and protein-protein interaction networks at the genomic scale.
- 24 Oct 2010: web page creation
The primary text for the course (available via the online bookstore) is
|[Alon]||U. Alon, An Introduction to Systems Biology: Design Principles of Biological Circuits, CRC Press, 2006.|
The following additional texts and notes may be useful for some students:
|[BFS]||D. Del Vecchio and R. M. Murray, Biomolecular Feedback Systems. Available online at http://www.cds.caltech.edu/~murray/amwiki/BFS.|
|[Klipp]||Edda Klipp, Wolfram Liebermeister, Christoph Wierling, Axel Kowald, Hans Lehrach, Ralf Herwig, Systems biology: a textbook. Wiley, 2009.|
|Course overview; gene circuit dynamics
||Alon, Ch 1-3|
||Alon, Ch 3-5|
|Dynamic signal modeling
|Fine grain patterns
|Epistasis and modulatory (Keasling) - ???|
The ﬁnal grade will be based on homework and a ﬁnal exam:
- Homework (75%) - There will be 9 one-week problem sets, due in class one week after they are assigned. Late homework will not be accepted without prior permission from the instructor.
- Final exam (25%) - The ﬁnal will be handed out the last day of class and is due back at the end of ﬁnals week. Open book, time limit to be decided (likely N hours over a 4-8N hour period).
The lowest homework score you receive will be dropped in computing your homework average. In addition, if your score on the ﬁnal is higher than the weighted average of your homework and ﬁnal, your ﬁnal will be used to determine your course grade.
Collaboration on homework assignments is encouraged. You may consult outside reference materials, other students, the TA, or the instructor. Use of solutions from previous years in the course is not allowed. All solutions that are handed should reﬂect your understanding of the subject matter at the time of writing.
No collaboration is allowed on the ﬁnal exam.