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## Math 283  —  Fall 2019 Statistical Methods in Bioinformatics Calendar

### Updated 12/7/19

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. George Armstrong (dates TBA) Week 2 Wednesday October 9, 4:30-5:50 p.m. in AP&M B402 Tutorial on Matlab and R. Worksheets: Matlab, R Week 5 or 6 Thursday, October 31, 3:00-3:50pm 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 6, 3-3:50 p.m. in AP&M 6402 Final exam review (practice questions) (solutions) Lectures: Week 1 Mon. Sep. 30 Website and syllabus   Review of discrete random variables: (slides 1-27) [revised 10/3] 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. 2 continued (slides 28-) Expected values (1.4) and Variance (1.5) Geometric distribution (1.3.5) and Negative Binomial Distribution (1.3.6) Week 2 Mon. Oct. 7 Mendel's Laws and Gene mapping: Note that there are two sets of slides to download 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) [revised 10/13] For now, skip slides 23-end on the Exponential and Gamma Distributions; we will cover these topics later. Wed. Oct. 9 Lander-Waterman shotgun sequencing statistics (5.1) (slides) [revised 10/13]   Conditional Probability and Bayes' Theorem (slides 4-16) Week 3 Mon. Oct. 14 Bayes' Theorem continued (review + slides 17-24) Continuous distributions: (slides 1-26) [revised again 10/14] Continuous distributions (1.8-1.10, 4.3) Uniform distribution Cumulative distribution function Exponential and gamma distributions (1.10, 4.3) Wed. Oct. 16 continued (rest of slides) Maximum Likelihood Estimates (8.1-8.3) (slides) Normal distribution and Central Limit Theorem (1.10, 2.10): (slides 1-10) [revised 10/13] Normal distribution Approximating binomial distribution by normal distribution Week 4 Mon. Oct. 21 continued (rest of slides) Central Limit Theorem Hypothesis testing, intro: (slides 1-12) Distribution of the maximum of n random variables (2.11) Long repeats (5.4) and hypothesis tests (3.4) Wed. Oct. 23 continued (review + slides 13-20; delaying slides 23-24) Hypothesis tests for the normal distribution: (slides 1-19) 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. 28 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 1-4) 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. 30 Non-parametric hypothesis tests, continued (rest of slides) Week 6 Mon. Nov. 4 Microarrays (slides 1-36) [revised 11/4] Wed. Nov. 6 Midterm Week 7 Mon. Nov. 11 Veterans Day Wed. Nov. 13 Microarrays, continued (rest of slides) Chi-squared hypothesis tests: (slides 1-17) Chi-squared (1.10.5) and F-tests (9.5.2) for variance. Week 8 Mon. Nov. 18 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) Wed. Nov. 20 Linear Algebra Review: Diagonalizing matrices: (slides) and (writeup) with more details. Markov chains (4.5-4.9, 11.{1,2,4,6}): Markov chains (slides 1-8) Optional FYI only: More details on Markov chains than on slides Week 9 Mon. Nov. 25 Markov chains, continued (8-32) Wed. Nov. 27 Markov chains, continued (rest of slides) Principal Components Analysis: (slides 1-20) Week 10 Mon. Dec. 2 PCA, continued (rest of slides) Linear Regression (8.4.3): (slides 1-5) Linear regression applets: Demo 1, Demo 2, instructions Wed. Dec. 4 Linear regression, continued (rest of slides) Analysis of Variance (9.5-9.7, 13.3.7): (slides) This is included some years, but we probably will not have time for it. Week 11 Fri. Dec. 13 Final exam, 3-6 p.m.