This year, the course material has been modified and reorganized from last year, so some of the videos from 2017 may not match up exactly to this year's course.

Week	Tues Lecture	Tues/Thurs Labs	Thurs Lecture	Sun HW Due
1 (1/22)	Intro to computational biology and microarrays Slides Videos: 1, 2, 3, 4 Reading: Bioinformatics	Odyssey, R, Bioconductor, Odyssey sign up (required) Git repo	Microarray normalization, Expression index Slides, Example Videos: 1, 2, 3, 4, 5 Reading: RMA
2 (1/29)	Differential expression, False discovery rate Slides Videos: 1, 2, 3, 4 Reading: LIMMA	Python, RMA, LIMMA Github Repo	Microarray clustering, Batch effect, Gene ontology Slides Videos: 1, 2, 3, 4 Reading: COMBAT	HW1 (Basics)
3 (2/5)	Dimension reduction, Unsupervised learning Slides Videos: 1, 2, 3, 4 Reading: Statistical Learning	DAVID, Clustering, COMBAT Github Repo	NGS, Read mapping Slides Videos: 1, 2, 3, 4 Reading: Read mapping Tutorial
4 (2/12)	RNA-seq analysis Slides Videos: 1, 2, 3, 4, 5 Readings: DESeq2, Difference between PTM and R/FPKM	PCA, SVM, BWA Github Repo	Alternative Splicing Slides Videos: 1, 2, 3 Readings: Systematic comparison of scRNA-seq techniques scRNA-seq Overview	HW2 (Microarrays)
5 (2/19)	scRNA-seq + TF motifs Slides Videos: 1, 2, 3 References: t-SNE, Seurat and SCDE	Salmon, DESeq2, Python 2	Motif finding Slides Videos: 1, 2, 3, 4 Readings: Gibbs sampler
6 (2/26)	ChIP-seq Slides Videos: 1, 2, 3, 4 Reading: MACS	scRNA-seq	Integrating ChIP-seq with gene expression Slides Videos: 1, 2, 3 Reading: BETA	HW3 (RNA-seq)
7 (3/5)	Epigenetics, DNA Methylation Slides 1, 2, 3, 4 Readings: Epigenetics review	MACS2, SAMTools	Hidden Markov Model Slides Snow Day. Please watch 2016 Videos: 1, 2, 3 Readings: Rabiner
8 (3/12)	Spring Recess		Spring Recess
9 (3/19)	Histone modifications, Chromatin accessibility Slides Videos: 1, 2, 3 Reading: ATAC-seq	BETA	Long range chromatin interactions Slides Videos: 1, 2, 3, 4 Reading: Mitotic chromatin organization	HW4 (scRNA-seq)
10 (3/26)	SNP and GWAS Videos: 1, 2, 3	HMM, regression, LASSO	GWAS Interpretation Slides Videos: 1, 2, 3, 4 Readings: EWAS
11 (4/2)	Genome Sequencing, TCGA Slides Videos: 1, 2, 3, 4 Reading: Lawrence1, Lawrence2	Data manipulation	Targeted therapy, drug resistance Slides Videos: 1, 2, 3, 4 Reading: CCLE, CRISPR Screens	HW5 (Epigenetics and Integration)
12 (4/9)	Cancer Immunotherapy Slides Videos: 1, 2, 3, 4 Reading: Tumor response to PD-1 antibody Other useful videos: Nature1 Nature2	TCGA, tumor subtype, survival	Cancer Epigenetics Slides Videos: 1, 2, 3 Reading: Cancer Epigenetics Review
13 (4/16)	Reproducible research Shirley at AACR, no lecture Just watch Video by Keith Baggerly Reading: Peng review, Garraway thoughts	MAGeCK	Deep learning (Matt Ploenzke) Slides Videos: 1, 2	HW6 (Cancer Genomics)
14 (4/23)	Final exam review Slides Videos: 1, 2, 3, 4		Reading period
15 (4/30)	Reading period		Screencast videos: Jumanah Alshenaifi: BWA Jiaqi Xie: HMM Rebecca Carlson: ScanPy Yushi Tang: Salmon
16 (5/7)