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## Math 283  —  Fall 2018 Statistical Methods in Bioinformatics Calendar

### Updated 12/3/18

Note: This calendar is approximate and is subject to revision.
Chapter numbers are for the class textbook by Ewens & Grant.
Slides are posted in advance for most lectures, but are subject to revision.

 Discussion Sessions with T.A. Bokan Bao (dates TBA) Week 2 Friday October 12, 2-3:30 p.m. in AP&M 6402 Tutorial on Matlab and R. Worksheets: Matlab, R Week 5 or 6 Friday November 2, 2-3:20 p.m. in AP&M 6402 Midterm review (practice questions) (solutions) Week 7 or 8 TA review cancelled, added more linear algebra review to lecture instead Linear algebra review (worksheet) Week 10 or 11 Friday December 7, 2-3:20 p.m. in AP&M 6402 Final exam review (practice questions) Lectures: Week 1 Mon. Oct. 1 Website, syllabus, and background survey   Review of discrete random variables (slides 1-25): [slides revised again 11/23] Probability density functions (Sec. 1.2) Joint pdf (2.1, 2.2, 2.5) Conditional pdf (2.6) Combinations and permutations Mass spec Binomial (1.3.2) and multinomial (2.4.2) distributions Wed. Oct. 3 continued (slides 27-45) Expected values (1.4) and Variance (1.5) Geometric distribution (1.3.5) and Negative Binomial Distribution (1.3.6) Week 2 Mon. Oct. 8 continued (rest of slides) Mendel's Laws and Gene mapping: Note that we are finishing last week's slides, and then two additional sets of slides are posted for today's lecture. Mendel's Laws, crossovers and recombination rates, Haldane's Mapping Function (slides) Poisson distribution and crossovers (Ewens & Grant 1.3.7, 4.1-4.2) (slides 1-17) Wed. Oct. 10 Poisson distribution, continued (slides 18-22) For now, skip slides 23-31 on the Exponential and Gamma Distributions; we will cover these topics later. Lander-Waterman shotgun sequencing statistics (5.1) (slides) Week 3 Mon. Oct. 15 Maximum Likelihood Estimates (8.1-8.3) (slides) Continuous distributions (slides 1-14) Continuous distributions (1.8-1.10, 4.3) Uniform distribution Cumulative distribution function Wed. Oct. 17 Exponential and gamma distributions (1.10, 4.3) (slides 14-end) Normal distribution and Central Limit Theorem (1.10, 2.10) (slides 1-23) Normal distribution Approximating binomial distribution by normal distribution Week 4 Mon. Oct. 22 continued (rest of slides) Central Limit Theorem Hypothesis testing, intro: (slides 1-16) [revised] Distribution of the maximum of n random variables (2.11) Long repeats (5.4) and hypothesis tests (3.4) Wed. Oct. 24 continued (slides 17-20); delaying slides 23-24 Hypothesis tests for the normal distribution: (slides 1-22) [revised] z and t-tests for the mean of a normal distribution (3.5.1-3.5.2) Confidence intervals (3.3.2) Week 5 Mon. Oct. 29 continued (rest of slides) Binomial tests for p Choosing n to control Type I and Type II errors. Also the delayed slides 23-24 from the previous set of slides. Non-parametric hypothesis tests: (slides 1-12) Probability generating functions intro (1.7, 1.11, 2.3) Wilcoxon signed rank test (3.8.3) Mann-Whitney test (3.8.2) Wed. Oct. 31 Non-parametric hypothesis tests, continued (slides 13-end) Week 6 Mon. Nov. 5 Microarrays: (slides 1-33) [revised] Wed. Nov. 7 Midterm Week 7 Mon. Nov. 12 Veterans Day Wed. Nov. 14 Microarrays, continued (rest of slides) Chi-squared hypothesis tests: (slides 1-12) Chi-squared (1.10.5) and F-tests (9.5.2) for variance. Week 8 Mon. Nov. 19 Chi-squared tests for goodness-of-fit (3.5.4) and association (3.5.5) (rest of slides) Frequencies of words: Number of occurrences of a word (5.7) and a motif (5.9) allowing overlaps (slides 1-16) Wed. Nov. 21 continued (slide 24; skipping motifs) Linear Algebra Review: Diagonalizing matrices: (slides) [revised] and (writeup) with more details. Markov chains (4.5-4.9, 11.{1,2,4,6}): Markov chains (slides 1-5) [revised again 11/27] Optional FYI only: More details on Markov chains than on slides Week 9 Mon. Nov. 26 Markov chains, continued (up to slide 35) Wed. Nov. 28 Markov chains, continued (rest of slides) Principal Components Analysis (slides 1-26) [revised again 12/3] Week 10 Mon. Dec. 3 PCA, continued (rest of slides) Linear Regression (8.4.3) (slides 1-11) Linear regression applets: Demo 1, Demo 2, instructions Wed. Dec. 5 Linear regression, continued (rest of slides) Analysis of Variance (9.5-9.7, 13.3.7) (slides) This is included most years, but we probably will not have time for it. Week 11 Wed. Dec. 12 Final exam, 3-6 p.m.