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Date Topics
Text Assignments
1 1/17
Random Sampling;Lecture 1 outline
Chapter 2, 2.1.1--2.1.3, 2.1.5-2.1.6, 2.2.1
Chapter 1, 1.1, 1.2, 1.3Problems, due 1/26
2 1/19
Mendelion genetics
Population genetics modeling
Lecture 2 outlineChapter 1, 1.1, 1.2, 1.3
Chapter 3, section 2Problems,due 1/26
Solutions 3 1/24
One locus/two allele, infinite population models
Chapter 3, section 3
4 1/26
Infinite population models, continued
Chapter 3, sections 1 and 3
Problems, due 2/2
Solutions 5 1/31
Finite population models:
Moran models Chapter 3, section 3.3.7
6 2/2
Finite population models:
Markov property, Wright-Fisher Chapter 3, section 3.3.7
Problem set 3,due 2/9
Solutions 7 2/7
Nonlinear difference equations;
Models with selection
Lecture outline deriving fixation
probability in
Wright-FisherChapter 3, section 4
8 2/9
Models with selection
Chapter 3, section 4
Problems on 3.4 due 2/16
Solutions9 2/14
Continuous random variables; review
Chapter 2, sections 2.2.3, 2.3.1, 2.3.2.
10 2/16
The coverage problem
Chapter 4, section 4.1
Problems from 4.1 due 2/13
Solutions11 2/21 First Midterm
12 2/23
The coverage problem, II
Chapter 4, 4.1
Problems, due 3/2
Solutions13 2/28
Discrete models for recognition sequence locations
Chapter 4, Section 2
14 3/2
Geometric random variables; Poisson random variables.
Poisson approximation to the binomial distribution. Chapter 4, 4.3
15
3/7
Poisson process models of cut site locations
Chapter 4, 4.3
Prof. Sontag's notes on Poisson process axiomsProblems, due 3/21
Hint on 4.26 b)
Solutions
16 3/9
Markov chains
Chapter 5, section 5.1
17 3/21
Markov chains
Chapter 5
Problems, due 3/28
Hand in 4, 5, 8, 10
Solutions18 3/23
Markov chains,
Chapter 5
19 3/28
Likelihood functions and maximum likelihood
estimates
Chapter 6, 6.1-6.4
Problems, due 4/4
Solutions to Chap.
5 problems
Solutions to Chap.
6 problems 20 3/30
Hypothesis testing
Chapter 6, 6.5
21 4/4
Hypothesis testing; examples
Chapter 6, 6.5
22 4/6
Second midterm
23 4/11
Hypothesis testing;
Chapter 6, 6.5, 6.6
Problems,
due 4/13
Solutions24 4/13
Alignment of homologous protein sequences;
Scoring alignmentsChapter 6, 6.7, Chapter 7, 7.1
Extra credit problems, due 4/25
25 4/18
Optimal alignment, I
Chapter 7, pp. 1-22.
26 4/20
Optimal alignment, II
Affine gap penaltyChapter 7, to the end
Problems, due 4/28
Solutions, Part I
Solutions, Part II27 4/25
Optimal alignment, III
Repeat match alignmentChapter 7 and class notes
28 4/27
Discussion of final problem set