Schedule overview¶
The weekly schedule is below. All sessions are accessed via the course Zoom link.
Lecture: Mondays, Wednesdays, Fridays 11–11:50 am PDT
TA homework help sessions
John: Mondays 7–8 pm PDT
Ankita: Tuesdays 3:30-4:30 pm PDT
TA-led discussion: Thursdays, 11 am-noon PDT
Instructor office hours
Justin: Fridays 2:30-3:30 PDT
Michael: By appointment
Lectures are recorded and posted on Google Drive.
Homework due dates¶
Below are tentative homework due dates.
Homework 1: due 11 am PDT, April 7
Homework 2: due 11 am PDT, April 14
Homework 3: due 11 am PDT, April 21
Homework 4: due 11 am PDT, April 28
Homework 5: due 11 am PDT, May 5
Homework 6: due 11 am PDT, May 12
Homework 7: due 11 am PDT, May 19
Homework 8: due 11 am PDT, May 26
Homework 9: due 11 am PDT, June 2
Homework 10: due 11 am PDT, June 3
Lecture schedule¶
Lectures will roughly cover one chapter in the posted materials and will proceed in order. The schedule is subject to change. Under some lectures are suggested readings.
Before class - Chapter 0: Configuring your computer to use Python for scientific computing
M 03/29 - Chapter 1: Introduction to biological circuit design (ME)
Chapter 1 of Alon
W 03/31 - Chapter 2: Introduction to Python for biological circuits (JB)
F 04/02 - Chapter 3: Big functions from small circuits (ME)
Chapter 2 of Alon
M 04/05 - Chapter 4: Motifs in biological circuits (ME)
Chapter 4 of Alon
W 04/07 - Chapter 5: A coherent feed-forward loop can perform dynamic signal processing (JB)
Chapter 3 of Alon
F 04/09 - Chapter 6: Incoherent feed-forward loops perform pulse generation and dosage compensation (ME)
M 04/12 - Chapter 7: Molecular titration generates ultrasensitive responses (ME)
W 04/14 - Guest lecture 1: Ronghui Zhu presents MultiFate: A scalable architecture for multistability in mammalian cells
F 04/16 - Chapter 8: Robustness in sensory circuits (JB)
Chapters 8 and 9 of Alon
Sections 3.2 and 5.7 of Del Vecchio and Murray
M 04/19 - Chapter 9: Kinetic proofreading: Multi-step processes reduce error rates in molecular recognition (JB)
Chapter 7 of Alon
W 04/21 - Chapter 10: Blinking bacteria: delayed negative feedback circuits generate periodic oscillations (ME)
F 04/23 - Chapter 11: Oscillators II: Applications and alternative architectures (ME)
M 04/26 - Chapter 12: The noise inside the cell: How stochastic gene expression produces cellular heterogeneity (JB)
Appendix D of Alon
W 04/28 - Chapter 13: Bursty gene expression enables regulation of protein variability (JB)
Section 4.1 of Del Vecchio and Murray
F 04/30 - Chapter 14: Simulating stochastic circuit dynamics (JB)
Section 4.2 of Del Vecchio and Murray
M 05/03 - Chapter 15: Excitable circuit dynamics enable probabilistic, transient differentiation (JB)
W 05/05 - Chapter 16: Bacterial bet-hedging and antibiotic persistence (ME)
F 05/07 - Chapter 17: Time-based regulation coordinates gene expression (ME)
M 05/10 - Chapter 18: Paradoxical circuits enable switch-like responses and linear amplification (JB)
W 05/12: Special guest lecture 2: Lacromioara Bintu presents Principles of chromatin-based regulation
F 05/14 - Chapter 19: Cis-interactions enable unidirectional signaling (ME)
M 05/17 - Chapter 20: Promiscuous ligand-receptor interactions allow combinatorial signal processing (ME)
W 05/19 - Chapter 21: Local activation and long-ranged inhibition can generate periodic spatial (Turing) patterns (JB)
F 05/21 - No class; Ditch Day!
M 05/24 - Special guest lecture 3: Uri Alon presents a special lecture and song on systems medicine
W 05/26 - Chapter 22: Feedbacks and scaling in morphogenetic patterning (JB)
F 05/28 - Course recap and the future of understanding and programming genetic circuitry (ME)