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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, 1.3 |
Problems, due 1/26 |
2 | 1/19 | Mendelion genetics Population genetics modeling Lecture 2 outline |
Chapter 1, 1.1, 1.2, 1.3 Chapter 3, section 2 |
Problems,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-Fisher |
Chapter 3, section 4 | |
8 | 2/9 | Models with selection | Chapter 3, section 4 | Problems on 3.4 due 2/16
Solutions |
9 | 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 Solutions |
11 | 2/21 | First Midterm | ||
12 | 2/23 | The coverage problem, II | Chapter 4, 4.1 | Problems, due 3/2 Solutions |
13 | 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 axioms |
Problems, 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 Solutions |
18 | 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 Solutions |
24 | 4/13 | Alignment of homologous protein sequences; Scoring alignments |
Chapter 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 penalty |
Chapter 7, to the end | Problems, due 4/28 Solutions, Part I Solutions, Part II |
27 | 4/25 | Optimal alignment, III Repeat match alignment |
Chapter 7 and class notes | |
28 | 4/27 | Discussion of final problem set |