Computational Statistics,Genetics & Microbiology.

Susan Holmes,

Schedule & Location

MW 11:00-12:15, McCullough 122. Labs F 11-12, GAtes B12.

Instructor & TAs


Susan Holmes

  • Office: Sequoia Hall #102
  • Phone: 725-1925,
  • Email: susan AT stat DOT stanford etc
  • Office hours: M, F 2:15-3:15

Teaching Assistant

Austen Head

  • Office: Sequoia Hall 208
  • Office hours: Thursday 2.30-3.30
  • Email

This course will show a series of statistical concepts in action. We will cover a series of case studies showing you how to use R and relevant tools to analyse your complex biological data sets.

Computer examples

We will be using R for most examples, and more precisely the Bioconductor suite. Both of these sites have large numbers of documents and tutorials.


Some familiarity with linear algebra and statistical methods.


  • Class participation and scribing; 20%
  • Labs/homework (5 total, best 4 count); 40%
  • midterm (project proposal); 15%
  • final project (according to Stanford calendar: due on June, 13th); 25%

Preliminary Schedule

Week Subject Lect Link Lect Link Lab Friday
April 2-6 Genomes and Sequences Lect 1 Lect2 Lab 1
April 9-13 CpG Islands Multinomials/Markov Chains/HMMs Lect3 Lect4 Lab 2
April 16-20 Multivariate Examples Lect 5 Lect 6 Lab 3
April 23-27 PCA-MDS-CA and graphs Lect 7 Lect 8 Lab 4
April 30-May 4 ML and Bayesian estimation(MCMC) Lect 9 Lect 10 None
May 7-11 Phylogenetic Trees/ Bootstrap Lect 11 Lect 12 Lab 5
May 14-18 Microarray Normalization/lowess Lect 13 Lect 14 None
May 21-25 Multivariate Analyses plots/interpretation/permutation tests Lect 15 Lect16 None
May 28-June 1 Kernel Methods Lect 17 Lect18 None
June 4-8 High Throughput sequence analyses Lect 19 Lect20 None


Lecture Materials

For relevant slides click on time table above which will lead you to the coursework repository.


I was inspired to rewrite my previous notes for this course up as a sphinx document by the wonderful work of Avril Coghlan and her little book on Bioinformatics.

Jonathan Taylor helped me through the process of getting started using sphinx, especially interfacing it with R.

All the cartoons from the website are shamelessly poached from Randall Munroe s xkcd webcomics.


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