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).


M 04/02
L1 (ME): Introduction to systems biology and genetic circuits [slides]
  • Chapter 1 of Alon
W 04/04
L2 (JB): Fast, bistable, and in control: small feedback circuits [lecture notes]
  • Chapter 2 of Alon
F 04/06
L3 (JB): *Introduction to Python for genetic circuit analysis and programming preliminaries [notebook 1, notebook 2]
M 04/09
L4 (ME): Motifs in genetic circuits [slides]
  • Chapter 6 of Alon
W 04/11
L5 (JB): The feed-forward loop (FFL) motif performs dynamic signal processing [notes]
  • Chapter 4 of Alon
F 04/13
L6 (ME): The role of robustness in genetic circuits [slides]
  • Chapter 7 of Alon
  • Sections 3.2 and 5.7 of Del Vecchio and Murray
M 04/16
L7 (JB): Multi-step amino acid incorporation provides lower error rates in translation in a process called kinetic proofreading [notes]
W 04/18
L8 (ME): The repressilator enables self-sustaining oscillations [notes, notebook, slides]
F 04/20
L9 (JB): *Delayed and combined positive-negative feedback loops enable oscillations in cells [notes, notebook]
M 04/23
L10 (JB): Gene expression is noisy! How stochastic effects lead to heterogeneity [notes]
W 04/25
L11 (JB): Bursty gene expression enables cells to regulate mean and cell-cell variability of protein levels [notes]
F 04/27
L12 (JB): *Stochastic simulation algorithms for simulating master equations [notebook]
  • Section 4.2 of Del Vecchio and Murray
M 04/30
L13 (ME): Excitable gene circuits enable probabilistic, transient differentiation [slides, notebook]
W 05/02
L14 (ME): Bet hedging and antibiotic persistence [slides]
F 05/04
L15 (ME): Time-based regulation coordinates gene expression [slides]
M 05/07
L16 (ME): Combinatorial gene regulation by relative timing of pulses [slides]
W 05/09
L17 (JB): Futile cycles in kinase systems can enable switch-like responses and linear amplification [slides]
F 05/11
L18 (JB): Paradoxical regulation enables bistable homeostatic states [slides, notebook]
M 05/14
L19 (ME): Cis interactions enable heterotypic signaling to facilitate developmental patterning [slides]
W 05/16
L20 (YA): Promiscuous receptor-ligand interactions increase the bandwidth and specificity of cell-cell communication systems (guest lecture by Yaron Antebi) [slides]
F 05/18
L21 (SN): Dynamic multiplexing enables multiple types of information to be transmitted through a single pathway (guest lecture by Sandy Nandagopal) [slides]
M 05/21
L22 (JB): Local activation and long-ranged inhibition can generate periodic spatial (Turing) patterns [notes]
W 05/23
L23 (JB): Feedbacks in morphogen patterning systems enable robust length-scale specification and scaling [notebook]
F 05/25
No class; Ditch Day
M 05/28
No class; Memorial Day
W 05/30
L24 (JB): *Example of data analysis: frequencies of nuclear localization pulses in yeast [notebook]
F 06/01
L25 (ME): Course recap and the future of understanding and programming genetic circuitry [slides]