APHYS 237/BIO251: Quantitative evolutionary dynamics and genomics
The genomics revolution has fueled a renewed push to model evolutionary processes in quantitative terms. This course will provide an introduction to quantitative evolutionary modeling through the lens of statistical physics. Topics will range from the foundations of theoretical population genetics to experimental evolution of laboratory microbes. Course work will involve a mixture of pencil-and-paper math, writing basic computer simulations, and downloading and manipulating DNA sequence data from published datasets. This course is intended for upper level physics and math students with no biology background, as well as biology students who are comfortable with differential equations and probability.
Winter 2021
Course Meeting Schedule: TTh 10:30am – 11:50am (recordings will also be posted on Canvas)
Course Meeting Location: Zoom. (Link and password are available on Canvas or by request.)
Instructor: Prof. Benjamin Good, Office: Clark S231A, Email: bhgood@stanford.edu
Office Hours: Th 1pm-2pm or by appointment.
Syllabus
Mathematical Background
Problem Sets
Data files for problem sets
Problem Set 1
Problem Set 2
Problem Set 3
Problem Set 4
Virtual Whiteboards
What we actually covered in class. Recorded lectures are posted in the Slack channel.
Overview Slides (1/12/21) PDF
Lecture 01 (1/12/21) PDF
Lecture 02 (1/14/21) PDF
Lecture 03 (1/19/21) PDF
Lecture 04 (1/21/21) PDF
Lecture 05 (1/26/21) PDF
Lecture 06 (1/28/21) PDF
Lecture 07 (2/02/21) PDF
Lecture 08 (2/04/21) PDF
Lecture 09 (2/09/21) PDF
Lecture 10 (2/11/21) PDF
Lecture 11 (2/16/21) PDF
Lecture 12 (2/18/21) PDF
Lecture 13 (2/23/21) PDF
Lecture 14 (2/25/21) PDF
Lecture 15 (3/02/21) PDF
Lecture 16 (3/04/21) PDF
Lecture 17 (3/09/21) PDF
Lecture 18 (3/11/21) PDF
Lecture 19 (3/16/21) PDF
Lecture 20 (3/18/21) PDF
Summary Slide (3/18/21) PDF
Lecture Notes
(Same as last year's version of the course)
Lectures 1 & 2 (Overview slides,
Math Background,
Bio Background)
Lecture 3 (PDF)
Lecture 4 (PDF)
Lectures 5 & 6 (PDF)
Lecture 7 & 8 (PDF)
Lecture 9 (Heuristic Approach, Mutations)
Lecture 10 (PDF)
Lecture 11 (PDF)
Lecture 12 (PDF)
Lecture 13 & 14 (PDF)
Lecture 14 & 15 (PDF)
Lecture 16 (PDF)
Lecture 17 (PDF)
Lecture 18 (PDF)
Lecture 19 & 20 (PDF)
Other materials
1. BH Good (2016), Molecular evolution in rapidly evolving populations, Chapter 1
2. SF Levy, JR Blundell, et al (Nature 2015), Quantitative evolutionary dynamics using high-resolution lineage tracking, Supplementary Information
3. DS Fisher (Les Houches Course 11, 2007), Evolutionary dynamics
4. Korolev et al (Rev Mod Phys, 2010), Genetic demixing and evolution in linear stepping stone models
5. Neher and Shraiman (Rev Mod Phys, 2011), Statistical genetics and evolution of quantitative traits
Previous years
Winter 2020