Below is the course schedule (which is subject to change), with links to readings and videos. Before class starts, you should watch the welcome video, which contains information about how the course is structured and run.
Zoom links
- Monday 1-2 pm homework help (RW)
- Tuesday 7:30-8:30 pm homework help (JM)
- Wednesday 3-4 pm discussion (RW)
- Thursday 4-5 pm discussion (ME)
- Friday 10-11 am discussion (JM)
- Friday 3-4 pm discussion (JB)
Lecture schedule
- < 04/06
- L0 (JB): Setting up a Python distribution
- M 04/06
- L1 (ME): Introduction to biological circuit design [video]
- Chapter 1 of Alon
- W 04/08
- L2 (JB): Introduction to Python for genetic circuit analysis and programming preliminaries [video]
- F 04/10
- L3 (ME): Big functions from small circuits [video]
- Chapter 2 of Alon
- M 04/13
- L4 (ME): Motifs in genetic circuits [video]
- Chapter 4 of Alon
- W 04/15
- L5 (JB): The feed-forward loop (FFL) performs dynamic signal processing [video]
- Chapter 3 of Alon
- Alon, 2007
- F 04/17
- L6 (JB): Robustness in sensory circuits [video]
- Chapters 8 and 9 of Alon
- Sections 3.2 and 5.7 of Del Vecchio and Murray
- M 04/20
- L7 (JB): Kinetic proofreading: Multi-step processes reduce error rates in molecular recognition [video]
- Ch. 7 of Alon
- Chakraborty and Weiss, 2014
- W 04/22
- L8 (ME): The repressilator: delayed negative feedback generates self-sustaining oscillations [video]
- F 04/24
- L9 (ME): Using, simplifying, and elaborating delayed negative feedback oscillators [video]
- M 04/27
- L10 (JB): Gene expression is noisy! How stochastic effects lead to heterogeneity [video]
- Appendix D of Alon
- Elowitz, et el., 2002
- W 04/29
- L11 (JB): Bursty gene expression
enables cells to regulate mean and cell-cell variability of
protein levels [video]
- Section 4.1 of Del Vecchio and Murray
- Cai, et al., 2006
- Singer, et al., 2014
- F 05/01
- L12 (JB): Stochastic simulation
algorithms for simulating master equations [video]
- Section 4.2 of Del Vecchio and Murray
- M 05/04
- L13 (JB): Excitable gene circuits enable probabilistic, transient differentiation [video]
- W 05/06
- L14 (ME): Bet hedging and antibiotic persistence [video]
- F 05/08
- L15 (ME): Time-based regulation coordinates gene expression [video]
- M 05/11
- L16 (JB): Paradoxical regulation can enable switch-like responses and linear amplification [video]
- W 05/13
- L17 (ME): Molecular titration generates ultrasensitive responses [video]
- F 05/15
- L18 (ME): Cis interactions enable heterotypic signaling to facilitate developmental patterning [video only]
- M 05/18
- L19 (ME): Promiscuous receptor-ligand interactions increase the bandwidth and specificity of cell-cell communication systems [video only]
- W 05/20
- GL1 (RZ): Guest lecture by Ron Zhu [video]
- F 05/22
- L20 (JB): Local activation and long-ranged inhibition can generate periodic spatial (Turing) patterns [video]
- M 05/25
- Memorial Day
- W 05/27
- L21 (JB): Feedbacks in morphogen patterning systems enable robust length-scale specification and scaling [video]
- F 05/29
- L22 (ME): Course recap and the future of understanding and programming genetic circuitry [video]