Mathematical Genetics
Fall 2015
Dr. Richard Gomulkiewicz
Dr. Stephen Krone

MATHEMATICAL GENETICS COURSE Schedule, Readings, & Homework

FALL 2015

 Math Gen Course Home Page

Lecture
Date
 Location
Topics covered
Reading
Homework & Materials
1
Aug. 24

Go to your home institution:

WSU (CUE 407)

UI (TLC 249)

 
  • Organizational Meeting

 
2 Aug. 26 UI (TLC 249) Gomulkiewicz:
  • Mini-intro to selection
  • Fixation probability of favored mutation
 Charlesworth2 chapter 1

 
3
Aug. 31

WSU (CUE 407)

 Gomulkiewicz:
  • Fixation probability of favored mutation
  

 
4
 Sep. 2
 UI (TLC 249)

Gomulkiewicz:

  • Charlesworth2 chapter 1
 Charlesworth2 §§2.1, 3.1  

Sep. 7
   Holiday (Labor Day)    
5
 Sep. 9 UI (TLC 249) Gomulkiewicz:
  • Charlesworth2 chapter 1/§2.1
 Charlesworth2 §§3.3, 3.4

R script: deterministic geometric population growth

R script: deterministic spread of a mutation

R script: stochastic population growth

R script: simulate Wright-Fisher model

Homework 1
  Sep. 11 WSU (Abelson 306) 2:10-3:00 Programming in R: Introduction   download R here
6 Sep. 14
 WSU (CUE 407) Gomulkiewicz:
  • Charlesworth2 §§2.1, 3.1
 Charlesworth2 §5.1

 
  Sep. 16 UI (TLC 222) 4:00-5:00 Programming in R: Introduction    
7
 Sep. 16
 UI (TLC 249) Gomulkiewicz:
  • Charlesworth2 §§3.1, 3.2
   
8 Sep. 21
 WSU (CUE 407) Krone:
  • Charlesworth2 §5.1
 Charlesworth2 §§4.1, 4.2  
9 Sep. 23
 UI (TLC 249) Krone:
  • Charlesworth2 §5.1
 Charlesworth2 §§4.3, 8.1  
10 Sep. 28
 WSU (CUE 407) Gomulkiewicz:
  • Charlesworth2 §§3.3, 3.4
Charlesworth2 §8.2i&ii

Homework 1 due

Homework 2
11 Sep. 30
 UI (TLC 249) Gomulkiewicz:
  • Charlesworth2 §§4.1, 4.2
 Charlesworth2 §8.4

 
12 Oct. 5 WSU (CUE 407) Gomulkiewicz:
  • Charlesworth2 §§8.1, 8.2i&ii
 Charlesworth2 §10.2

Coalescent Lecture Notes

suggested reference: Coalescent Theory, An Introduction by John Wakeley
13 Oct. 7
 UI (TLC 249) Gomulkiewicz:
  • Charlesworth2 §§8.2i&ii, 8.4
    
14 Oct. 12
 WSU (CUE 407) Gomulkiewicz:
  • Charlesworth2 §10.2
  

Homework 2 due

Homework 3
15 Oct. 14
 UI (TLC 249) Krone: The coalescent    
16 Oct. 19
 WSU (CUE 407) Krone:  

Partial Key for Homework 2
17 Oct. 21
 UI (TLC 249) Krone:    
18 Oct. 26
 WSU (CUE 407)

Krone:

  • Parameter estimation in the coalescent
   Homework 3 due

Homework 4
19 Oct. 28
 UI (TLC 249)

Krone:

  • Site frequency spectrum
    
20 Nov. 2
 WSU (CUE 407)

Krone:

  • Testing for neutrality, constant population size, etc.
    
21 Nov. 4 UI (TLC 249)

Krone:

  • Variations on Kingman's coalescent
    
22 Nov. 9
 WSU (CUE 407)

Krone:

  • Effective population size
   Homework 4 due
  Nov. 11
   Holiday (Veteran's Day)    
23 Nov. 16
 WSU (CUE 407)

Krone:

  • Markov chain Monte Carlo methods
  • Diffusion processes (time permitting)
   Homework 5
24 Nov. 18 UI (TLC 249)

Student Led Discussions:

  1. Ruffley/DeAguero/Streett
  2. Riazi/Wiest
  3. Linscott

Background Readings:

  1. Riazi/Wiest #1
  2. Riazi/Wiest #2
  3. Linscott
  4. Ruffley/DeAguero/Streett

Nov. 23   Thanksgiving Break
 
  Nov. 25  

Thanksgiving Break
 
25 Nov. 30 WSU (CUE 407)

Krone:

  • Markov chain Monte Carlo methods
    
26 Dec. 2 UI (TLC 249)

Student Led Discussions:

  1. Patton/Gilman/Kehinde
  2. Brown/Smithson/Jimenez Schwarzkopf
  

Background Readings:

  1. Brown/Smithson/Jimenez Schwarzkopf
  2. Patton/Gilman/Kehinde
27 Dec. 7 WSU (CUE 407)

Student Led Discussions:

  1. Hanley/Hendricks
  2. Week/Stahlke
  3. Taylor
  4. Jacobs
  

Homework 5 due

Background Readings:

  1. Jacobs
  2. Hanley/Hendricks #1
  3. Hanley/Hendricks #2
  4. Taylor
  5. Week/Stahlke #1
  6. Week/Stahlke #2
28 Dec. 9 UI (TLC 249)Full

Student Led Discussions:

  1. Fraik/Wendler/Catanese/Williams
  2. Maselko/Nunn/Kohler
  

Background Readings:

  1. Maselko/Nunn/Kohler
  2. Fraik/Wendler/Catanese/Williams