### MCB112: Biological Data Analysis (Fall 2017)

Lectures: week 00 | 01 | 02 | 03 | 04 | 05 | 06 | 07 | 08 | 09 | 10 | 11 | 12 | 13

Sections: week 00 | 01a | 01b | 01c | 02 | 03 | 04 | 05 | 06 | 07 | 08 | 09 | 10 | 11 |

Homeworks: week 01 | 02 | 03 | 04 | 05 | 06 | 07 | 08 | 09 | 10 | 11 |

Answers: week 01 | 02 | 03 | 04 | 05 | 06 | 07 | 08 | 09 | 10 | 11 |

**week 00: Thurs 31 Aug**- welcome and preview
- [Lecture notes] [Example Jupyter notebook page] [Section notes]

**week 01: Tues/Thurs 5/7 Sept**- molecular biology of genes, gene expression, and RNA-seq
- [Lecture notes] [Section notes (molbio)] [Section notes (jupyter] [Section notes (python]
- [Homework] [Answers]

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

**week 03: Tues/Thurs 19/21 Sept**- data exploration and visualization – subsampling data – tidy data
- [Lecture notes] [Section notes]
- [Homework] [Answers]

**week 04: Tues/Thurs 26/28 Sept**- probability, likelihood, and inference – Laplace and Bayes
- [Lecture notes] [Section notes]
- [Homework] [Answers]

**week 05: Tues/Thurs 3/5 Oct**- P-values and statistical significance
- [Lecture notes] [Section notes]
- [Homework] [Answers]

**week 06: Tues/Thurs 10/12 Oct**- mixture models – K-means – expectation maximization
- [Lecture notes] [Section notes]
- [Homework] [Answers]

**week 07: Tues/Thurs 17/19 Oct**- regression – regression as probabilistic inference
- [Lecture notes] [Section notes]
- [Homework] [Answers]

**week 08: Tues/Thurs 24/26 Oct**- inference and hypothesis testing – differential expression analysis
- [Lecture notes] [Section notes]
- [Homework] [Answers]

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

**week 10: Tues/Thurs 7/9 Nov**- cluster analysis – non-negative matrix factorization
- [Lecture notes] [Section notes]
- [Homework] [Answers]

**week 11: Tues/Thurs 14/16 Nov**- dimensionality reduction – principal component analysis
- [Lecture notes] [Section notes]
- [Homework] [Answers]

**week 12: Tues 21 Nov (Thanksgiving week)**- work patterns in computational research
- [Lecture notes] (no section)
- (no homework)

**week 13: Tues/Thurs 28/30 Nov**- t-SNE
- [Lecture notes] [Section notes]
- [Homework] [Answers]

5/7 Dec |
Fini! Harvard reading period – no further assignments |

12/14 Dec |
Finals week – no further assignments |