Math 338, Spring 2010: Syllabus

This is a tentative syllabus. It will be updated and modified and assignments will be added as the semester progresses.
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The chapter and section numbers listed under "text" refer to the on-line text.

INFORMATION ABOUT SUMMER REU's (Research Experiences for Undergraduates).

Date Topics TextAssignments
1 1/19 Random sampling
Intro. to Population Genetics
Chapter 1, especially 1.1-1.3
Chapter 2, Section 1
Lecture 1 slides
Assignment 1
Solutions
2 1/21 Populations, genotype and allele frequencies random mating, infinite populations Chapter 3, section 3.2  
3 1/26 One locus/two allele, infinite population model
Hardy-Weinberg 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 Wright-Fisher Models
Chapter 4, 4.1 and 4.2  
8 2/11 Wright-Fisher 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 MidtermOpen 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: log-likelihood tests, p-values,
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 
234/13 Second Midterm Information on second midterm  
244/15 Optimal alignment; linear gap penalty case Chapter 7
254/20 Optimal alignments Chapter 7 Assignment 11, due 4/22
Solutions to Assignment 11
264/22 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
274/27 Hidden Markov models; forward and Viterbi algorithms Chapter 8  
284/29 HMM problem solutions; Final Exam Review    
295/12FINAL EXAM4-7PM, SEC-208 Information on final