Course Schedule

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