MCB112 schedule

As we progress through the course, links to lecture and section notes, psets, and pset answers get added here, and also in the sidebar of the mcb112 web site.

(Dates here are accurate, but the schedule of topics might be updated before the course starts in fall.)

week 00: Wed 31 Aug welcome and preview
[Lecture notes]
[Section notes]
(no pset)


week 01: Wed 7 Sept (Monday is Labor Day)
molecular biology of genes, gene expression, and RNA-seq
[Lecture notes]
[Section notes - Python]
[Section notes - Molecular biology]
[Homework]
[Answers]


week 02: Mon/Wed 12/14 Sept RNA-seq read mapping -- doing controls on new programs -- kallisto -- unix command line
[Lecture notes]
[Section notes]
[Homework]
[Answers]


week 03: Mon/Wed 19/21 Sept
data exploration and visualization -- subsampling data -- tidy data
[Lecture notes]
[Section notes]
[Homework]
[Answers]


week 04: Mon/Wed 26/28 Sept
probability, likelihood, and inference -- Laplace and Bayes
[Lecture notes]
[Section notes]
[Homework]
[Answers]


week 05: Mon/Wed 3/5 Oct
mixture models -- K-means -- expectation maximization
[Lecture notes]
[Section notes]
[Homework]
[Answers]


week 06: Wed 12 Oct (Mon is Indigenous People's Day)
P-values and statistical significance
[Lecture notes]
[Section notes]
[Homework]
[Answers]


week 07: Mon/Wed 17/19 Oct
inference and hypothesis testing -- differential expression analysis
[Lecture notes]
[Section notes]
[Homework]
[Answers]


week 08: Mon/Wed 24/26 Oct
regression -- regression as probabilistic inference
[Lecture notes]
[Section notes]
[Homework]
[Answers]


week 09: Mon 31 Oct/Wed 2 Nov
inferring hidden variables -- multimapped reads and mRNA isoform expression estimation -- expectation maximization again
[Lecture notes]
[Section notes]
[Homework]
[Answers]


week 10: Mon/Wed 7/9 Nov
cluster analysis -- non-negative matrix factorization
[Lecture notes]
[Section notes]
[Homework]
[Answers]


week 11: Mon/Wed 14/16 Nov
principal component analysis -- dimensionality reduction
[Lecture notes]
[Section notes]
[Homework]
[Answers]


week 12: Mon 21 Nov (Wednesday-Sunday are Thanksgiving holidays)
work patterns in computational research
no pset - Thanksgiving weekend
[Lecture notes]


week 13: Mon/Weds 28/30 Nov t-SNE
[Lecture notes]
[Section notes]
[Homework]
[Answers]

(Harvard classes end Thursday 1 Dec. Friday section optional.)


Fini! Harvard reading period begins -- no further assignments. Last assignment due after reading period, in finals week, on Mon 12 Dec. No final exam.