In case the 2016 lecture videos are late, you can see the 2013, 2014, and 2015 lecture videos at: https://vimeo.com/stat115

Week	Tue Lecture	Wed/Thur Lab	Thur Lecture	Sun HW
1 (1/25)	Introduction to computational biology Slides Videos 1,2,3 Reading: Bioinformatics	R & BioConductor & RMA, LIMMA Slides	Microarray normalization, Expression index Slides, RMA Videos:1,2,3,4 Past videos: Microaorrays, Normalization, Expression index, Method comparison Reading: RMA
2 (2/1)	Differential expression, False discovery rate Slides Videos:1,2,3,4 Past videos: Differential expression, Multiple hypotheses testing Reading: LIMMA	Odyssey, LINUX Slides	Microarray clustering, Batch effect Slides: Videos:1,2,3,4 Past videos:Gene Ontology, Clustering, Batch effect Reading: COMBAT
3 (2/8)	Dimension reduction, Classification Slides: Videos:1,2,3,4 Past videos:Dimension reduction, Classification Reading: Statistical Learning	DAVID, Clustering, COMBAT slides	NGS, Read mapping (Wei Li) Slides Videos:1,2 Past videos: NGS, Read mapping Reading: NBT Tutorial	HW1 (Microarrays)
4 (2/15)	RNA-seq analysis (Wei Li) Slides Videos:1,2,3,4 Past videos: RNA-seq,Transcript Assembly, Differential Expression Reading: DEseq2	PCA, SVM, BWA, Python 1 Slides	RNA structure prediction (Elena Rivas) Slides Videos:1,2,3 Past videos: N/A Reading: Eddy NBT Tutorial
5 (2/22)	Motif finding Slides Videos:1,2,3 Past videos:Motif finding Reading: Gibbs Sampler	DESeq, Vienna RNA package, Python 2 RNA-seq workflow Slides	ChIP-seq Slides Videos:1,2,3,4 Past videos: ChIP-seq, Downstream Analysis, Refine Motifs Reading: BETA	HW2 (RNA-seq)
6 (2/29)	DNA methylation Slides Videos:1,2,3,4 Past videos: Epigenetics - I, II, III Reading: Epigenetics review	MACS2, UCSC, BedTools, Python 3 Slides	HMM Slides Videos:1,2,3 Past videos:Hidden Markov Model - I, II, III Reading: Rabiner tutorial
7 (3/7)	Histone modifications, Chromatin accessibility Slides Videos:1,2,3 Past videos: Histone modifications Reading: Cell review	HMM, BETA, Python 4 Slides	Feature selection and regression (Peng Jiang) Slides, Demo Code Videos:1,2,3 Past videos: N/A Reading: Introduction
8 (3/14)	Spring Recess		Spring Recess	HW3 (ChIP-seq)
9(3/21)	Evolution, Molecular clock, SNP and LD Slides Videos:1,2,3 Past videos: Evolution, Population genetics Reading:	Regression, Python 5 Slides	Haplotype inference and GWAS Slides Videos:1,2,3 Past videos:Haplotype inference, GWAS Reading:
10(3/28)	Population structures, Quantitative traits Slides Videos:1,2,3 Past videos: QTL Reading:	MAF and VCF, PLINK Slides	GWAS interpretation and application Slides Videos:1,2,3 Past videos: GWAS interpretation Reading:	HW4 (Epigenetics)
11 (4/4)	TCGA and tumor profiling Slides Videos:1,2,3,4 Past videos:Cancer genomics, TCGA Reading: Lawrence1, Lawrence2 papers	HaploReg, RegulomeDB Slides	Targeted therapy, High throughput screening Slides Videos:1,2,3 Past videos:1, 2, 3, 4, 5, 6, 7, 8 Reading: CCLE and CRISPR screen papers
12 (4/11)	Tumor Heterogeneity and evolution (Bo Li) Slides Videos:1,2,3 Past videos: Cancer heterogeneity I, II, III, IV Reading: Clonal evolution, purity and single cell papers	TCGA data access, Survival analysis Slides	Cancer immunotherapy and epigenetic therapy Slides Videos: 1,2,3 Nature1 Nature2 Past videos: Epigenetics drug and immunotherapy I , II, III Reading: Tumor response to PD-1 antibody	HW5 (GWAS)
13 (4/18)	Reproducible research Videos Reading: Peng review	Screencast videos Videos	Final review Slides Videos:1,2,3
14 (4/25)	Final Exam		Reading Period
15 (5/2)	Reading Period	HW6 (Cancer Genomics) & screencast video due	Exam Period