MCB112: Biological Data Analysis (Fall 2018)


week 00: Wed 5 Sept
welcome and preview

week 01: Mon/Wed 10/12 Sept
molecular biology of genes, gene expression, and RNA-seq

week 02: Mon/Wed 17/19 Sept
RNA-seq read mapping – doing controls on new programs – kallisto – the unix command line

week 03: Mon/Wed 24/26 Sept
data exploration and visualization – subsampling data – tidy data

week 04: Mon/Wed 1/3 Oct
probability, likelihood, and inference – Laplace and Bayes

week 05: Wed 10 Oct
P-values and statistical significance

week 06: Mon/Wed 15/17 Oct
mixture models – K-means – expectation maximization

week 07: Mon/Wed 22/24 Oct
regression – regression as probabilistic inference

week 08: Mon/Wed 29/31 Oct
inferring hidden variables – multimapped reads and mRNA isoform expression estimation – expectation maximization again

week 09: Mon/Wed 5/7 Nov
cluster analysis – non-negative matrix factorization

week 10: Wed 14 Nov
inference and hypothesis testing – differential expression analysis

week 11: Mon/Wed 19/21 Nov
work patterns in computational research – artifacts, batch effect
no pset - Thanksgiving weekend

week 12: Mon/Wed 26/28 Nov
dimensionality reduction – principle component analysis

week 13: Mon/Wed 3/5 Dec
t-SNE

Fini! Harvard reading period, finals begin – no further assignments