Schedule

Below is the tentative class schedule, which is subject to change. All meetings are in 100 Broad. Suggested readings are listed below each lecture topic. Specific citations to original literature is contained within the posted lecture slides and notes. For lecture topics beginning with an asterisk (*), you should bring your laptop (otherwise don't).


< 04/01
L0 (JB): Setting up a Python distribution
M 04/01
L1 (ME): Introduction to biological circuit design
  • Chapter 1 of Alon
W 04/03
L2 (JB): *Introduction to Python for genetic circuit analysis and programming preliminaries
F 04/05
L3 (ME): Fast, bistable, and in control: small feedback circuits
  • Chapter 2 of Alon
M 04/08
L4 (ME): Motifs in genetic circuits
  • Chapter 6 of Alon
W 04/10
L5 (JB): The feed-forward loop (FFL) performs dynamic signal processing
  • Chapter 4 of Alon
F 04/12
L6 (JB): The role of robustness in genetic circuits
  • Chapter 7 of Alon
  • Sections 3.2 and 5.7 of Del Vecchio and Murray
M 04/15
L7 (JB): Multi-step amino acid incorporation provides lower error rates in translation in a process called kinetic proofreading
W 04/17
L8 (ME): The repressilator enables self-sustaining oscillations
F 04/19
L9 (JB): Delayed and combined positive-negative feedback loops enable oscillations in cells
M 04/22
L10 (JB): Gene expression is noisy! How stochastic effects lead to heterogeneity
W 04/24
L11 (JB): Bursty gene expression enables cells to regulate mean and cell-cell variability of protein levels
F 04/26
L12 (JB): *Stochastic simulation algorithms for simulating master equations
  • Section 4.2 of Del Vecchio and Murray
M 04/29
L13 (JB): Excitable gene circuits enable probabilistic, transient differentiation
W 05/01
L14 (ME): Bet hedging and antibiotic persistence
F 05/03
LG1 (RK): Predicting and preventing the evolution of antibiotic resistance
M 05/06
L15 (ME): Time-based regulation coordinates gene expression
W 05/08
L16 (JB): Futile cycles in kinase systems can enable switch-like responses and linear amplification
F 05/10
L17 (JB): Paradoxical regulation enables bistable homeostatic states
M 05/13
L18 (ME): Cis interactions enable heterotypic signaling to facilitate developmental patterning
W 05/15
L19 (ME): Promiscuous receptor-ligand interactions increase the bandwidth and specificity of cell-cell communication systems
F 05/17
L20 (ME): Dynamic multiplexing enables multiple types of information to be transmitted through a single pathway
M 05/20
L21 (JB): Local activation and long-ranged inhibition can generate periodic spatial (Turing) patterns
W 05/22
L22 (JB): Feedbacks in morphogen patterning systems enable robust length-scale specification and scaling
F 05/24
L23 (JB): *Example of data analysis: frequencies of nuclear localization pulses in yeast
M 05/27
No class; Memorial Day
W 05/29
L23 (JB): Example of data analysis: Bayesian generative modeling of noise (temporarily unavailable)
W 05/29
L24 (JB): Logarithmic sensors
F 05/31
L25 (ME): Course recap and the future of understanding and programming genetic circuitry