BE 150/Bi 250b Winter 2012: Difference between revisions
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* Review: differential equations | * Review: differential equations | ||
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* {{be250c pdf|wi11|caltech/bfs-class-coreproc_01Jan11.pdf|BFS, Ch 2}}: Modeling of Core Processes | * {{be250c pdf|wi11|caltech/bfs-class-coreproc_01Jan11.pdf|BFS, Ch 2}}: Modeling of Core Processes | ||
* Alon, Ch 3: Autoregulation : a network motif | * Alon, Ch 3: Autoregulation : a network motif | ||
| HW #1 | | HW #1 | ||
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| 3 | | 3 | ||
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* Alon, Ch 5: Temporal programs and the global structure of transcription networks | * Alon, Ch 5: Temporal programs and the global structure of transcription networks | ||
* Alon, Ch 6: Network motifs in developmental, signal transduction, and neuronal networks | * Alon, Ch 6: Network motifs in developmental, signal transduction, and neuronal networks | ||
| | | HW #2 | ||
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| 4 | | 4 | ||
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* [http://www.nature.com/nature/journal/v456/n7221/full/nature07389.html A fast, robust and tunable synthetic gene oscillator], Stricker, ''et al.''. ''Nature'', 456:516-519, 2008. | * [http://www.nature.com/nature/journal/v456/n7221/full/nature07389.html A fast, robust and tunable synthetic gene oscillator], Stricker, ''et al.''. ''Nature'', 456:516-519, 2008. | ||
* [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855407/ Cyanobacterial clock, a stable phase oscillator with negligible intercellular coupling], M. Amdaoud, M. Vallade, C. Weiss-Schaber, and I. Mihalcescu. ''Proc Natl Acad Sci'', 104(17):7051–7056, 2007. | * [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855407/ Cyanobacterial clock, a stable phase oscillator with negligible intercellular coupling], M. Amdaoud, M. Vallade, C. Weiss-Schaber, and I. Mihalcescu. ''Proc Natl Acad Sci'', 104(17):7051–7056, 2007. | ||
| | | HW #3 | ||
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| 5 | | 5 | ||
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* BFS, Sec 5.4: Bacterial chemotaxis | * BFS, Sec 5.4: Bacterial chemotaxis | ||
* [http://www.pnas.org/content/97/9/4649.full Robust perfect adaptation in bacterial chemotaxis through integral feedback control], Tau-Mu Yi, Yun Huang, Melvin I. Simon and John Doyle. ''PNAS'', 97(9):4649-4653, 2000. | * [http://www.pnas.org/content/97/9/4649.full Robust perfect adaptation in bacterial chemotaxis through integral feedback control], Tau-Mu Yi, Yun Huang, Melvin I. Simon and John Doyle. ''PNAS'', 97(9):4649-4653, 2000. | ||
| | | HW #4 | ||
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| 6 | | 6 | ||
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* Intrinsic and extrinsic noise | * Intrinsic and extrinsic noise | ||
* Stochastic modeling | * Stochastic modeling | ||
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* BFS, Ch 4 and App C | * BFS, Ch 4 and App C | ||
* [http://www.sciencemag.org/content/297/5584/1183 Stochastic Gene Expression in a Single Cell], Michael B. Elowitz, Arnold J. Levine, Eric D. Siggia and Peter S. Swain. ''Science'', 297(5584):1183-1186, 2002. | * [http://www.sciencemag.org/content/297/5584/1183 Stochastic Gene Expression in a Single Cell], Michael B. Elowitz, Arnold J. Levine, Eric D. Siggia and Peter S. Swain. ''Science'', 297(5584):1183-1186, 2002. | ||
* [http://www.nature.com/nature/journal/v440/n7082/full/nature04599.html Stochastic protein expression in individual cells at the single molecule level], Long Cai, Nir Friedman and X. Sunney Xie. ''Nature'', 440:358-362, 2006. | * [http://www.nature.com/nature/journal/v440/n7082/full/nature04599.html Stochastic protein expression in individual cells at the single molecule level], Long Cai, Nir Friedman and X. Sunney Xie. ''Nature'', 440:358-362, 2006. | ||
| | | HW #5 | ||
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| 7 | | 7 | ||
| 13 Feb+ <br> 15 Feb <br><br> | | 13 Feb+ <br> 15 Feb <br><br> MBE | ||
| | | Burstiness in gene expression and signalling | ||
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* [http://www.nature.com/ng/journal/v36/n2/full/ng1293.html Dynamics of the p53-Mdm2 feedback loop in individual cells], Galit Lahav ''et al''. ''Nature Genetics'', 36:147-150, 2004. | * [http://www.nature.com/ng/journal/v36/n2/full/ng1293.html Dynamics of the p53-Mdm2 feedback loop in individual cells], Galit Lahav ''et al''. ''Nature Genetics'', 36:147-150, 2004. | ||
* [http://www.nature.com/nature/journal/v455/n7212/full/nature07292.html Frequency-modulated nuclear localization bursts coordinate gene regulation], Long Cai, Chiraj K. Dalal and Michael B. Elowitz. Nature 455:485-490, 2008. | * [http://www.nature.com/nature/journal/v455/n7212/full/nature07292.html Frequency-modulated nuclear localization bursts coordinate gene regulation], Long Cai, Chiraj K. Dalal and Michael B. Elowitz. Nature 455:485-490, 2008. | ||
* [http://www.nature.com/nature/journal/v466/n7303/full/nature09145.html Single-cell NF-kB dynamics reveal digital activation and analogue information processing], S. Tay ''et al''. ''Nature'', 466(7303):267-271, 2010 | * [http://www.nature.com/nature/journal/v466/n7303/full/nature09145.html Single-cell NF-kB dynamics reveal digital activation and analogue information processing], S. Tay ''et al''. ''Nature'', 466(7303):267-271, 2010 | ||
| | | HW #6 | ||
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| 8 | | 8 | ||
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* [http://linkinghub.elsevier.com/retrieve/pii/S0959437X04000887 Elucidating mechanisms underlying robustness of morphogen gradients], Avigdor Eldar, Ben-Zion Shilo and Naama Barkai. ''Curr Opin Genet Dev.'', 14(4):435-439, 2004. | * [http://linkinghub.elsevier.com/retrieve/pii/S0959437X04000887 Elucidating mechanisms underlying robustness of morphogen gradients], Avigdor Eldar, Ben-Zion Shilo and Naama Barkai. ''Curr Opin Genet Dev.'', 14(4):435-439, 2004. | ||
* [http://www.pnas.org/content/107/15/6924.short Scaling of morphogen gradients by an expansion-repression integral feedback control], Danny Ben-Zvia and Naama Barkai. ''PNAS'', 107(15):6924-6929, 2010. | * [http://www.pnas.org/content/107/15/6924.short Scaling of morphogen gradients by an expansion-repression integral feedback control], Danny Ben-Zvia and Naama Barkai. ''PNAS'', 107(15):6924-6929, 2010. | ||
| | | HW #7 | ||
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| 9 | | 9 | ||
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* [http://www.ncbi.nlm.nih.gov/pubmed/9015458 Pattern formation by lateral inhibition with feedback: a mathematical model of delta-notch intercellular signalling], Collier et al. Journal of theoretical biology (1996) vol. 183 (4) pp. 429-46. | * [http://www.ncbi.nlm.nih.gov/pubmed/9015458 Pattern formation by lateral inhibition with feedback: a mathematical model of delta-notch intercellular signalling], Collier et al. Journal of theoretical biology (1996) vol. 183 (4) pp. 429-46. | ||
* [http://www.ncbi.nlm.nih.gov/pubmed/20418862 Cis-interactions between Notch and Delta generate mutually exclusive signalling states], Sprinzak et al. Nature (2010) vol. 465 (7294) pp. 86-90 | * [http://www.ncbi.nlm.nih.gov/pubmed/20418862 Cis-interactions between Notch and Delta generate mutually exclusive signalling states], Sprinzak et al. Nature (2010) vol. 465 (7294) pp. 86-90 | ||
| | | HW #8 | ||
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| 10 | | 10 | ||
| 5 Mar <br> 7 Mar <br> | | 5 Mar <br> 7 Mar <br> MBK | ||
| | | Modeling of complex biological networks (MBK) | ||
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| <!-- Homework --> | | <!-- Homework --> | ||
Revision as of 18:42, 19 November 2011
Systems Biology | |
Instructors
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Teaching Assistants
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Course Description
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.
Announcements
- 19 Nov 2011: added TAs; updated schedule
- 2 Oct 2011: web page creation
Textbook
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. |
Grading
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 Policy
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.
Lecture Schedule
There will be two 1-hour lectures each week, as well as a 1-hour recitation section.
Week | Date | Topic | Reading | Homework |
1 | 4 Jan 6 Jan MBE/RMM |
Course overview
Recitation section:
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2 | 9 Jan 11 Jan+ MBE |
Gene circuit dynamics
Recitation sections:
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HW #1 |
3 | 18 Jan* 20 Jan* RMM |
Circuit motifs
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HW #2 |
4 | 23 Jan 25 Jan RMM |
Biological clocks: how to produce oscillations in cells
Background slides on modeling and stability |
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HW #3 |
5 | 30 Jan 1 Feb RMM |
Robustness
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HW #4 |
6 | 6 Feb* 8 Feb MBE |
Noise
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HW #5 |
7 | 13 Feb+ 15 Feb MBE |
Burstiness in gene expression and signalling |
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HW #6 |
8 | 22 Feb 24 Feb RMM |
Patterning
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HW #7 |
9 | 27 Feb 29 Feb*+ MBE/RMM |
Fine grain patterns
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HW #8 |
10 | 5 Mar 7 Mar MBK |
Modeling of complex biological networks (MBK) |