Below is the lecture schedule. The lecture topics/lecturer is subject to change, but the dates and times are set. Some lectures have required readings that must be done before lecture. PDFs of the reading material is linked to in the schedule.
Scheduled office hours for the TAs to help you with your homework are 3:30-5:00 pm on Wednesdays in SPL 102.
There is a special session to help you get software installed and running for your rational design homeworks 10 am-noon on Saturday, October 8, in SFL 328.
Due dates
- Th 10/20: Homework 1 (rational design) due
- Th 11/03: Homework 2 (rational design) due
- Th 11/17: Homework 3 (directed evolution) due
- Th 12/01: Homework 4 (directed evolution) due
- Fr 12/09: Final projects due at 5 PM
Lecture Schedule
- L1: Tu 09/27: (JB) Overview of rational design
- L2: Th 09/29: (JB) Self-assembly / Thinking probabilistically: Statistical mechanics of molecular interactions
- L3: Tu 10/04: (FA) Overview of directed evolution
- L4: Th 10/06: (JB) Partition function algorithms
- L5: Tu 10/11: (JB) Kinetics of nucleic acid interactions and stochastic simulation
- L6: Th 10/13: (JB) Thermodynamics of multiple interacting strands
- L7: Tu 10/18: (JB) Design objective functions and algorithms
- L8: Th 10/20: (JB) Design paradigms
- L9: Tu 10/25: (JB) Multiobjective design
- L10: Th 10/27: (LH) Guest lecture: Rational design from start to finish, Lisa Hochrein
- L11: Tu 11/01: (JB) Rational design: From whence we came and where we are headed
- L12: Th 11/03: (FA) Evolution as a search in sequence space
- L13: Tu 11/08: (FA) Introduction to directed evolution
- L14: Th 11/10: (KY) Guest lecture: Methods of directed evolution, Kevin Yang
- L15: Tu 11/15: (FA) TBA
- L16: Th 11/17: (FA) Sex in the test tube
- L17: Tu 11/22: (FA/KY) Machine-learning guided directed evolution
- Th 11/24: Thanksgiving, no class
- L18: Tu 12/29: (DT) Guest lecture by Dave Tirrell
- L19: Th 12/01: (FA) Innovation by Evolution: Expanding the Enzyme Universe