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.

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. (This resource may not render correctly in a screen reader.PDF)

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. (This resource may not render correctly in a screen reader.PDF)

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.