Below is the lecture schedule. All lectures are in 100 CNRB at 1:00 pm. The lecture topics and lecturer are subject to change, but the dates and times are set. Readings listed under each lecture should be read before lecture. Some readings are marked as optional, though you are encouraged to read all of the posted materials. The readings will be updated as the term progresses.
Scheduled office hours for the TAs to help you with your homework will be decided during the first week of class.
Assignment/due dates
- Homework 1 assigned Th 10/06, due Th 10/20
- Homework 2 assigned Th 10/20, due Th 11/03
- Homework 3 assigned Th 11/03, due Th 11/17
- Homework 4 assigned Th 11/17, due Fr 12/02
- News and Views assigned Tues 09/27, due at 11:59 PM, Fri 12/09
All problem sets are submitted as Jupyter notebooks, and the News & Views article is submitted as a PDF. All are submitted via Canvas.
Lecture Schedule
- L1: Tu 09/27: (NAP)
- Borges, 1941
- Cameron, Bashor, Collins, 2014 (optional)
- Huang, Boyken, Baker, 2016 (optional)
- Pinheiro, et al., 2011 (optional)
- Zhang and Seelig, 2011 (optional)
- L2: Th 09/29: Intro to Protein Engineering (SLM)
- L3: Tu 10/04: (NAP)
- L4: Th 10/06: (NAP)
- L5: Tu 10/11: (NAP)
- L6: Th 10/13: (NAP)
- L7: Tu 10/18: (NAP)
- L8: Th 10/20: (NAP)
- L9: Tu 10/25: (NAP)
- L10: Th 10/27: (NAP)
- L11: Tu 11/01: Sequence Evolution and notes (SLM)
- L12: Th 11/03: Directed Evolution and notes (SLM)
- L13: Tu 11/08: epPCR and SSM and notes (SLM)
- L14: Th 11/10: Recombination and notes (SLM)
- L15: Tu 11/15: Bioscience Industry Day 12-3pm
- L16: Th 11/17: Selection and Screening and notes (SLM)
- Packer and Liu, 2015 (optional)
- Kan et al., 2016 (optional)
- Meta et al., 2006 (optional)
- Roberts and Szostak, 1997 (optional)
- Tabata et al., 2009 (optional)
- Seelig and Szostak, 2007 (optional)
- Hanes and Pluckthun, 1997 (optional)
- Smith, 2019 (optional)
- Smeal et al., 2017 (optional)
- Jaroszewicz et al., 2021 (optional)
- Cherf and Cochran, 2015 (optional)
- Boder and Wittrup, 1997 (optional)
- L17: Tu 11/22: Protein Stability and notes (SLM)
- L18: Tu 11/29: MM and MD and recording (SLM)
- L19: Th 12/01: CPD, notes, and recording (SLM)
- Pabo, 1983 (optional)
- Alvizo and Mayo, 2008 (optional)
- Marshall and Mayo, 2001 (optional)
- Dunbrack and Karplus, 1993 (optional)
- Metropolis et al., 1953 (optional)
- Dahiyat and Mayo, PNAS, 1997 (optional)
- Malakauskas and Mayo, 1998 (optional)
- Dahiyat and Mayo, Science, 1997 (optional)
- Kuhlman et al., 2003 (optional)
- Bolon and Mayo, 2001 (optional)
Sequences and Structures from lecture that you can play around with on NUPACK.