This is a tentative syllabus. It will be updated and
modified
and assignments will be added as the semester progresses.
Be sure to ``refresh'' this page every time you visit;
otherwise, you may be viewing an outofdate cached copy!
The chapter and section numbers listed under "text" refer to the online text.
INFORMATION ABOUT SUMMER REU's (Research Experiences for Undergraduates).
Date  Topics  Text  Assignments  
1  1/19  Random sampling Intro. to Population Genetics 
Chapter 1, especially 1.11.3 Chapter 2, Section 1 Lecture 1 slides 
Assignment 1 Solutions 

2  1/21  Populations, genotype and allele frequencies  Chapter 3, section 3.2  
3  1/26 
One locus/two allele, infinite population model HardyWeinberg equilibrium 
Chapter 3, section 3.3  
4  1/28 
Difference Equations Other infinite population models 
Chapter 3, Sections 3.1 and 3.3  Assignment 2, due
Feb. 4 Solutions to Assignment 2 

5  2/2  Nonlinear difference equations; Model with selection 
Chapter 3, section 3.4  
6  2/4  Model with selection; derivation and analysis  Chapter 3, section 3.4 Some corrections to Chapter 3 More corrections 
Assignment 3, due
Feb. 11 Solutions to Assignment 3 Solution to problem B, Assignment 3 

7  2/9  Markov chains; The Moran and WrightFisher Models  Chapter 4, 4.1 and 4.2  
8  2/11  WrightFisher Model Calculating distributions of Markov chains 
Chapter 4 with 4.3  Assignment 4, due Feb. 18 Solutions to Assignment 4 

9  2/16  Markov chains with absorbtion; Invariant measures 
Chapter 4, 4.3  
10  2/18  Markov chains with recurrent states  Chapter 4, section 4.4(link to entire chapter)  Assignment 5, due Feb. 25 Solutions to Assignment 5 

11  2/23  Ergodic theory of Markov chains;  Chapter 4 Maple worksheet with example 

12  2/25  Class Cancelled 
Homework due March 2 Solutions to Assignment 6 

13  3/2  First Midterm  Open book and notes, FIRST MIDTERM IS MOVED TO March 4 

14  3/4  Restriction Enzyme digests Poisson processes; introduction 
Chapter 5, section 5.2 up to page 22, section 5.3  
15  3/9  Coverage for shotgun sequencing Poisson processeds 
Chapter 5, 5.1, 5.3  Assignment 7, due March
11 Solutions to Assignment 7 

16  3/11  Poisson processes; current and residual life, gamma distribution Restriction enzyme library coverage 
Chapter 5, sections 5.3 and 5.4  
17  3/23  Poisson processes; current and residual life, gamma distribution Restriction enzyme library coverage 
Chapter 5, 6.3  Assignment 8, due March 25
Solutions to Assignment 8 

18  3/25  Hypothesis testing  Chapter 6, 6.3, 6.4  Assignment 9, due 4/1 Solutions to Assignment 9 

19  3/30  Hypothesis testing: loglikelihood tests, pvalues, Testing the Markov chain hypothesis 
Chapter 6, 6.4 and 6.5  
20  4/1  Testing IID sites versus Markov models; Introduction to the alignment problem 
Chapter 6, sections 6.6, 6.7  
21  4/6  Scoring alignments Introduction to dynamic programming  Chapter 6, 6.7; Chapter 7, 7.1  Assignment 10, due 4/8 Solutions, Assignment 10 

22  4/8  Test review; BLOSUM substitution matrices  Chapter 6, 6.7  
23  4/13  Second Midterm  Information on second midterm  
24  4/15  Optimal alignment; linear gap penalty case  Chapter 7  
25  4/20  Optimal alignments  Chapter 7  Assignment 11, due 4/22 Solutions to Assignment 11 

26  4/22  Repeat Match Alignment Hidden Markov models; introduction 
Chapter 7;Example of repeat match algorithm  Assignment 12, due April
30
Solutions, Assignment 12 Solution to 1 b) Solution to 5 

27  4/27  Hidden Markov models; forward and Viterbi algorithms  Chapter 8  
28  4/29  HMM problem solutions; Final Exam Review  
29  5/12  FINAL EXAM  47PM, SEC208  Information on final 