# Math 338, Spring 2006: Syllabus and Assignments

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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 geneticsPopulation 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