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Math 283  —  Fall 2017
Statistical Methods in Bioinformatics
Calendar

Updated 12/8/17


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 13, 2-3:30 p.m. in AP&M 6402
  • Tutorial on Matlab and R. Worksheets: Matlab, R
Week 5 or 6 Monday November 6, 3:30-4:20 p.m. in AP&M 6402
Week 7 or 8 TA review cancelled, added more linear algebra review to lecture instead
Week 10 or 11 Friday December 8, 2-2:50 p.m. in AP&M 6402
Lectures: Week 1
Mon. Oct. 2 Website, syllabus, and background survey
 
Review of discrete random variables (slides 1-25):
  • 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. 4 Review of discrete random variables, continued: (slides 26-46)
  • Expected values (1.4) and Variance (1.5)
  • Geometric distribution (1.3.5) and Negative Binomial Distribution (1.3.6)
Week 2
Mon. Oct. 9
  • continued (rest of slides)

Mendel's Laws and Gene mapping:
  • Crossovers and Recombination rates (slides)
  • Poisson distribution and crossovers (Ewens & Grant 1.3.7, 4.1-4.2) (slides 1-16)
    For now, skip slides 23-31 on the Exponential and Gamma Distributions; we will cover these topics later.
  • Note that we are finishing last week's slides, and then two additional sets of slides are posted for today's lecture.
Wed. Oct. 11
  • Poisson distribution, continued (slides 17-22; skip slides 23-31, we will do those topics later)

Lander-Waterman shotgun sequencing statistics (5.1) (slides 1-28)
Week 3
Mon. Oct. 16
  • continued (rest of slides)

Continuous distributions (slides 1-19)
  • Continuous distributions (1.8-1.10, 4.3)
  • Uniform distribution
  • Cumulative distribution function
  • Exponential and gamma distributions (1.10, 4.3)
Wed. Oct. 18
  • 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)
  • Normal distribution
Week 4
Mon. Oct. 23
  • continued (rest of slides)
  • Approximating binomial distribution by normal distribution
  • Central Limit Theorem

Hypothesis testing, intro: (slides 1-7)
  • Distribution of the maximum of n random variables (2.11)
  • Long repeats (5.4) and hypothesis tests (3.4)
Wed. Oct. 25
  • continued (rest of slides)

Hypothesis tests for the normal distribution: (slides 1-15)
  • z and t-tests for the mean of a normal distribution (3.5.1-3.5.2)
Week 5
Mon. Oct. 30
  • continued (rest of slides)
  • Confidence intervals (3.3.2)
  • Binomial tests for p
  • Choosing n to control Type I and Type II errors

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. Nov. 1
  • Non-parametric hypothesis tests, continued (slides 5-28)
Week 6
Mon. Nov. 6
  • Non-parametric hypothesis tests, continued (rest of slides)

Microarrays: (slides 1-22)
Wed. Nov. 8 Midterm
Week 7
Mon. Nov. 13 Microarrays, continued (rest of slides)

Chi-squared hypothesis tests: (slides 1-6)
  • Chi-squared (1.10.5) and F-tests (9.5.2) for variance.
Wed. Nov. 15
  • Chi-squared tests for goodness-of-fit (3.5.4) and association (3.5.5) (rest of slides)

Frequencies of words:
Week 8
Mon. Nov. 20
  • continued (rest of slides)

Markov chains (4.5-4.9, 11.{1,2,4,6}):
Wed. Nov. 22
Week 9
Mon. Nov. 27
  • Markov chains, continued (rest of slides)

Wed. Nov. 29 Principal Components Analysis (slides 1-23)
Week 10
Mon. Dec. 4
  • PCA, continued (rest of slides)

Linear Regression (8.4.3) (slides 1-7)
Wed. Dec. 6
  • Demo 1 and rest of slides


Analysis of Variance (9.5-9.7, 13.3.7) (slides)
  • This is included most years, but we did not have time for it.
Week 11
Wed. Dec. 13 Final exam, 3-6 p.m.