WEEK # | TOPICS | READINGS |
---|---|---|
1 |
Introduction to the class and topic | [No Readings] |
2 |
Simple synthetic networks |
Paper 1Elowitz, M. B., and S. Leibler. "A Synthetic Oscillatory Network of Transcriptional Regulators." Nature 403 (2000): 335–38. Paper 2Becskei, 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) |
Paper 1Elowitz, 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 2Gillespie, D. T. "Exact Stochastic Simulation of Coupled Chemical Reactions." The Journal of Physical Chemistry 81 (1977): 2340–61. |
4 |
Noise in gene expression (II) |
Paper 1Ko, 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 2Bengtsson, 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) |
Paper 1McAdams, H. H., and A. P. Arkin. "Stochastic Mechanisms in Gene Expression." Proceedings of the National Academy of Sciences 94 (1997): 814–19. Paper 2Yu, 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 |
Paper 1Rosenfeld, 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 2Shen-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 |
Paper 1Purcell, E. M. "Life at Low Reynolds Number." American Journal of Physics 45 (1977): 3–11. Paper 2Berg, H. C., and E. M. Purcell. "Physics of Chemoreception." Biophysical Journal 20 (1977): 193–219. |
8 |
Field trip | [No Readings] |
9 |
Bacterial chemotaxis |
Paper 1Alon, U., M. G. Surette, N. Barkai, and S. Leibler. "Robustness in Bacterial Chemotaxis." Nature 397 (1999): 168–70. Paper 2Sourjik, 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 |
Paper 1Gregor, T., D. W. Tank, E. F. Wieschaus, and W. Bialek. "Probing the Limits to Positional Information." Cell 130 (2007): 153–64. Paper 2Ben-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 |
Paper 1Hardin, 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 2Rust, 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 |
Paper 1Wernet, 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 2Karp, 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 |
Paper 1Levskaya, 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 2Gibson, 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. |