Computational Statistics,Genetics & Microbiology.¶
Schedule & Location¶
MW 11:00-12:15, McCullough 122. Labs F 11-12, GAtes B12.
Instructor & TAs¶
- Office: Sequoia Hall #102
- Phone: 725-1925,
- Email: susan AT stat DOT stanford etc
- Office hours: M, F 2:15-3:15
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%
|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|
- Crash Course in Genomics
- Seeing the structure and the surprises
- Sequence Data are Strings
- Markov Chains
- Hidden Markov Models - the Unfair Casino
- Hidden Markov Model for CpG islands
- Underlying Algorithms
- PCA : Interpretation Examples
- PCA, SVD and MDS
- Binary Table/Contingency Table representation
- Binary Data and Graphs
- Modelling Mixtures: the Dirichlet distribution
- Gibbs Sampler Examples
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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