Mathematical Genetics
Fall 2013
Dr. Richard Gomulkiewicz
Dr. Stephen Krone

MATHEMATICAL GENETICS COURSE Schedule, Readings, & Homework

FALL 2013

 Math Gen Course Home Page

Lecture
Date
 Location
Topics covered
Reading
Homework & Materials
-2
Aug. 19

WSU (College 135)
  • optional turorial in R programming

Aug19MathGenTutorial.R
-1
 Aug. 21 WSU (College 135)
  • optional turorial in R programming
  

Aug21MathGenTutorial.R
1
Aug. 26

Go to your home institution:

WSU (College 135)

UI (TLC 248)
  • Organizational Meeting
  

R script for deterministic spread of a new mutation
2
 Aug. 28
 UI (TLC 248) Gomulkiewicz:
  • Introduction to selection
  • Fixation probability of favored mutation
 Rice chapter 1  

Sep. 2
   Holiday (Labor Day)    
3
 Sep. 4
 UI (TLC 248) Gomulkiewicz:
  • Fixation probability of favored mutation
  

wrightfisher.R
4 Sep. 9
 WSU (College 135)

Gomulkiewicz:

  • Rice chapter 1

Rice chapter 2

Homework 1
5
 Sep. 11
 UI (TLC 248)

Gomulkiewicz:

  • Rice chapter 1
    
6
 Sep. 16
 WSU (College 135) Gomulkiewicz:
  • Rice chapter 1/2
 Rice chapter 5 FertilitySelection.R
7
 Sep. 18
 UI (TLC 248) Gomulkiewicz:
  • Rice chapter 2
   TwoLocusSelection.R
8
 Sep. 23
 WSU (College 135) Gomulkiewicz:
  • Rice chapter 2
 Rice chapter 6 Homework 1 due
9 Sep. 25
 UI (TLC 248) Gomulkiewicz:
  • Rice chapter 5
  

DlogisticCobwebPlot.R

Homework 2
10 Sep. 30
 WSU (College 135) Gomulkiewicz:
  • Rice chapter 5
  

FreqIndSelCobwebPlot.R

ProbFixExact.R
11 Oct. 2
 UI (TLC 248) Gomulkiewicz:
  • Rice chapter 6
 Coalescent Lecture Notes pp. 6-18

Homework 3

Coalescent Lecture Notes

suggested reference: Coalescent Theory, An Introduction by John Wakeley
12
 Oct. 7
 WSU (College 135)

Gomulkiewicz:

  • Rice chapter 6
  

Homework 2 due

Recent review article about Price's Theorem

Links to resources on George Price's life:
13 Oct. 9
 UI (TLC 248) Krone:
  • The Coalescent I -Basic Theory
   Homework 4
14 Oct. 14
 WSU (College 135)

Krone:

  • The Coalescent II -Statistical Inference
   Homework 3 due
15 Oct. 16
 UI (TLC 248)

class replaced by Oct. 17 Donnelly talk

   TwoLocusOptimizingSelection.R
  Oct. 17 UI College of Law Courtroom

Peter Donnelly, U Oxford

7pm, UI College of Law Courtroom

    
16 Oct. 21
 WSU (College 135)

Krone:

  • The Coalescent II -Statistical Inference
    
17 Oct. 23
 UI (TLC 248)

Krone:

  • Markov Chain Monte Carlo
  • Importance Sampling
   Homework 4 due
18 Oct. 28
 WSU (College 135)

Krone:

  • Markov Chain Monte Carlo
  • Importance Sampling
   Homework 5
19 Oct. 30
 UI (TLC 248)

Krone:

  • Markov Chain Monte Carlo
  • Importance Sampling
    
20 Nov. 4
 WSU (College 135)

Krone:

  • Aproximate Bayesian Computation and Coalescent Theory
   Homework 5 due
21 Nov. 6
 UI (TLC 248)

Krone:

  • Structured Coalescent
  • Coalescent with recombination
    
  Nov. 11
   Holiday (Veteran's Day)    
22 Nov. 13
 UI (TLC 248)

  Krone:

  • Coalescent Theory, and Inference Review
  Homework 6
23 Nov. 18
 WSU (College 135)

Student Led Discussions

  1. M Neupane, M Liu, & B Ding (30 min)
  2. H Marx & D Caetana (20 min)
  3. M France (10 min)
    
24 Nov. 20 UI (TLC 248)

Student Led Discussions

  1. B Wiedeback, M Singer, & J Asplund (30 min)
  2. D Giblin & S Payton (20 min)
  3. A MacPherson (10 min)
 

Nov. 25   Thanksgiving Break
 
  Nov. 27  

Thanksgiving Break
 
25 Dec. 2 WSU (College 135)

Student Led Discussions

  1. J Mosely, S Brooker, & J Williams (30 min)
  2. E Thornquist & M Love (20 min)
  3. I Zhbannikov (10 min)
   Homework 6 due
26 Dec. 4 UI (TLC 248)

Student Led Discussions

  1. M Rupert, N Layman, & J Madrid Thorson (30 min)
  2. F Villanea & S Krug (20 min)
  3. R Berl (10 min)