The reading assignments listed below show what you should read before coming to class. You are expected to come to class prepared to discuss the assigned articles.
| SES # | TOPICS | READINGS |
|---|---|---|
| 1 | Introduction to the class and topic | |
| 2 | Simple synthetic networks |
Elowitz, M. B., and S. Leibler. "A Synthetic Oscillatory Network of Transcriptional Regulators." Nature 403 (2000): 335-8. Becskei, A., B. Seraphin, and L. Serrano. "Positive Feedback in Eukaryotic Gene Networks: Cell Differentiation by Graded to Binary Response Conversion." EMBO 20 (2001): 2528-2535. |
| 3 | Noise in gene expression I |
Elowitz, M. B., A. J. Levine, E. D. Siggia, and P. S. Swain. "Stochastic Gene Expression in a Single Cell." Science 297 (2002): 1183-86. Gillespie, D. T. "Exact Stochastic Simulation of Coupled Chemical Reactions." J Phys Chem 81 (1977): 2340-61. |
| 4 | Noise in gene expression II |
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 Res 15 (2005): 1388-92. ( 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." EMBO 9 (1990): 2835-2842. |
| 5 | Noise in gene expression III |
McAdams, H. H., and A. P. Arkin. "Stochastic Mechanisms in Gene Expression." PNAS 94 (1997): 814-19. Yu, J., J. Ciao, X. Ren, K. Lao, and X. S. Xie. "Probing Gene Expression in Live Cells, One Protein Molecule at a Time." Science 311 (2006): 1600-3. |
| 6 | Structure of biological networks |
Rosenfeld, N., M. B. Elowitz, and U. Alon. "Negative Autoregulation Speeds the Response Times of Transcription Networks." J Mol Biol 323 (2002): 785-93. 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 | Network evolution and adaptation |
Dekel, E., and U. Alon. "Optimality and Evolutionary Tuning of the Expression Level of a Protein." Nature 436 (2006): 588-592. Stern, S., T. Dror, E. Stolovicki, N. Brenner, and E. Braun. "Genome-wide Transcriptional Plasticity Underlies Cellular Adaptation to Novel Challenge." Mol Syst Biol 3 (2007): 1-9. |
| 8 | Chemotaxis I |
Purcell, E. M. "Life at Low Reynolds Number." Am J Phys 45 (1977): 3-11. ( Berg, H. C., and E. M. Purcell. "Physics of Chemoreception." Biophys J 20 (1977): 193-219. |
| 9 | Chemotaxis II |
Alon, U., M. G. Surette, N. Barkai, and S. Leibler. "Robustness in Bacterial Chemotaxis." Nature 397 (1999): 168-70. Sourjik, V., and H. C. Berg. "Receptor Sensitivity in Bacterial Chemotaxis." PNAS 99 (1997): 123-27. |
| 10 | Circadian oscillations |
Rust, M. J., J. S. Marson, W. S. Lane, D. S. Fisher, and E. K. O'Shea. "Order Phosphorylation Governs Oscillation of a Three-protein Circadian Clock." Science 318 (2007): 809-12. Nagoshi, E., C. Saini, C. Bauer, T. Laroche, F. Naef, and U. Schibler. "Circadian Gene Expression in Individual Fibroblasts Cell-autonomous and Self-sustained Oscillators Pass Time to Daughter Cells." Cell 119 (2004): 693-705. |
| 11 | Field trip | |
| 12 | Noise in development |
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. 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." Gene Dev 17 (2003): 3100-11. |
| 13 | Synthetic biology |
Levskaya, A., et al. "Genome Transplantation in Bacteria: Changing One Species to Another." Science 317 (2007): 632-8. Cohn, R. D., et al. "Angiotensin II Type 1 Receptor Blockade Attenuates TGF-beta-induced Failure of Muscle Regeneration in Multiple Myopathic States." Nat Med 13 (2007): 204-10. |
