Readings

Course readings.
WEEK #	TOPICS	READINGS
1	Introduction to the class and topic See the Lecture Summary	[No Readings]
2	Simple synthetic networks See the Lecture Summary	Paper 1 Elowitz, M. B., and S. Leibler. "A Synthetic Oscillatory Network of Transcriptional Regulators." Nature 403 (2000): 335–38. Paper 2 Becskei, A., B. Séraphin, and L. Serrano. "Positive Feedback in Eukaryotic Gene Networks: Cell Differentiation by Graded to Binary Response Conversion." The EMBO Journal 20 (2001): 2528–35.
3	Noise in gene expression (I) See the Lecture Summary	Paper 1 Elowitz, M. B., A. J. Levine, E. D. Siggia, and P. S. Swain. "Stochastic Gene Expression in a Single Cell." Science 297 (2002): 1183–6. Paper 2 Gillespie, D. T. "Exact Stochastic Simulation of Coupled Chemical Reactions." The Journal of Physical Chemistry 81 (1977): 2340–61.
4	Noise in gene expression (II) See the Lecture Summary	Paper 1 Ko, M. S., H. Nakauchi, and N. Takahashi. "The Dose Dependence of Glucocorticoid-Inducible Gene Expression Results from Changes in the Number of Transcriptionally Active Templates." The EMBO Journal 9 (1990): 2835-42. Paper 2 Bengtsson, M., A. Stahlberg, P. Rorsman, and M. Kubista. "Gene Expression Profiling in Single Cells from the Pancreatic Islets of Langerhans Reveals Lognormal Distribution of mRNA Levels." Genome Research 15 (2005): 1388–92. (PDF)
5	Noise in gene expression (III) See the Lecture Summary	Paper 1 McAdams, H. H., and A. P. Arkin. "Stochastic Mechanisms in Gene Expression." Proceedings of the National Academy of Sciences 94 (1997): 814–19. Paper 2 Yu, J., J. Xiao, X. Ren, K. Lao, and X. S. Xie. "Probing Gene Expression in Live Cells, One Protein Molecule at a Time." Science 311 (2006): 1600–1603.
6	Structure of biological networks See the Lecture Summary	Paper 1 Rosenfeld, N., M. B. Elowitz, and U. Alon. "Negative Autoregulation Speeds the Response Times of Transcription Networks." Journal of Molecular Biology 323 (2002): 785–93. Paper 2 Shen-Orr, S. S., R. Milo, S. Mangan, and U. Alon. " Network Motifs in the Transcriptional Regulation Network of Escherichia Coli." Nature Genetics 31 (2002): 64-8.
7	Physical limits of gradient and concentration sensing See the Lecture Summary	Paper 1 Purcell, E. M. "Life at Low Reynolds Number." American Journal of Physics 45 (1977): 3–11. Paper 2 Berg, H. C., and E. M. Purcell. "Physics of Chemoreception." Biophysical Journal 20 (1977): 193–219.
8	Field trip See the Lecture Summary	[No Readings]
9	Bacterial chemotaxis See the Lecture Summary	Paper 1 Alon, U., M. G. Surette, N. Barkai, and S. Leibler. "Robustness in Bacterial Chemotaxis." Nature 397 (1999): 168–70. Paper 2 Sourjik, V., and H. C. Berg. "Receptor Sensitivity in Bacterial Chemotaxis." Proceedings of the National Academy of Sciences 99 (2002): 123–7.
10	Development of multicellular organisms under noisy conditions See the Lecture Summary	Paper 1 Gregor, T., D. W. Tank, E. F. Wieschaus, and W. Bialek. "Probing the Limits to Positional Information." Cell 130 (2007): 153–64. Paper 2 Ben-Zvi, D., B. Z. Shilo, A. Fainsod, and N. Barkai. "Scaling of the BMP Activation Gradient in Xenopus Embryos." Nature 453 (2008): 1205–11.
11	Circadian oscillations See the Lecture Summary	Paper 1 Hardin, P. E., J. C. Hall, and M. Rosbash. "Feedback of the Drosophila Period Gene Product on Circadian Cycling of its Messenger RNA Levels." Nature 343 (1990): 536-40. Paper 2 Rust, M. J., J. S. Markson, W. S. Lane, D. S. Fisher, and E. K. O'Shea. "Ordered Phosphorylation Governs Oscillation of a Three-Protein Circadian Clock." Science 318 (2007): 809–12.
12	Noise in development See the Lecture Summary	Paper 1 Wernet, M. F., E. O. Mazzoni, A. Celik, D. M. Duncan, I. Duncan, and C. Desplan. "Stochastic Spineless Expression Creates the Retinal Mosaic for Colour Vision." Nature 440 (2006): 174–80. Paper 2 Karp, X., and I. Greenwald. "Post-Transcriptional Regulation of the E/Daughterless Ortholog HLH-2, Negative Feedback, and Birth Order Bias During the AC/VU Decision in C. Elegans." Genes and Development 17 (2003): 3100–3111.
13	Synthetic biology See the Lecture Summary	Paper 1 Levskaya, A., A. A. Chevalier, J. J. Tabor, Z. B. Simpson, L. A. Lavery, M. Levy, E. A. Davidson, A. Scouras, A. D. Ellington, E. M. Marcotte, and C. A. Voigt. "Synthetic Biology: Engineering E. Coli to See Light." Nature 438 (2005): 441–2. Paper 2 Gibson, D. G, J. I. Glass, C. Lartigue, V. N. Noskov, R. Y. Chuang, M. A. Algire, G. A. Benders, M. G. Montaue, L. Ma, M. M. Moodie, C. Merryman, S. Vashee, R. Krishnakumar, N. Assad-Garcia, C. Andrews-Pfannkoch, E. A. Denisova, L. Young, Z. Q. Qi, T. H. Segall-Shapiro, C. H. Calvey, P. P. Parmar, C. Hutchison III, H. O. Smith, and J. C. Venter. "Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome." Science 329 (2010): 52–6.