BE 150/Bi 250b Winter 2012
BE 150: Quantitative studies of cellular and developmental systems in biology, including the architecture of specific genetic circuits controlling microbial behaviors and multicellular development in model organisms. Specific topics include chemotaxis, multistability and differentiation, biological oscillations, stochastic effects in circuit operation, as well as higher-level circuit properties such as robustness. Organization of transcriptional and protein-protein interaction networks at the genomic scale. Topics are approached from experimental, theoretical and computational perspectives.
Bi 250b: 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.
- 11 Dec 2011: updated syllabus (should be final now)
- 19 Nov 2011: added TAs; updated schedule
- 2 Oct 2011: 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:
|[FBS]||K. J. Astrom and R. M. Murray, Feedback Systems. Available online at http://www.cds.caltech.edu/~murray/amwiki.|
|[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.|
|[Strogatz]||Steven Strogatz, Nonlinear Dynamics And Chaos: With Applications To Physics, Biology, Chemistry, And Engineering. Westview Press, 2001.|
The ﬁnal grade will be based on biweekly homework sets. The homework will be due in class one week after they are assigned. Late homework will not be accepted without prior permission from the instructor. The lowest homework score you receive will be dropped in computing your homework average.
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 in should reﬂect your understanding of the subject matter at the time of writing.
There will be two 1-hour lectures each week, as well as a 1-hour recitation section.
|1|| 4 Jan
| Course overview
|2|| 9 Jan
| Gene circuit dynamics
| Circuit motifs
|4|| 23 Jan
| Biological clocks: how to produce oscillations in cells
Background slides on modeling and stability
|5|| 30 Jan
|6|| 6 Feb*
|7|| 13 Feb+
| Burstiness in gene expression and signalling
|9|| 27 Feb
| Fine grain patterns
|10|| 5 Mar
|Modeling of complex biological networks (MBK)|