
Week	Tue Lecture	Tue/Thur Labs	Thur Lecture	Sun HW Due
1 (1/28)	Introduction Slides Lecture videos: 1 2 3 4 Other Videos: Dynamic programming Reading: Difference between Bioinformatics and Computational Biology Levels of Bioinformatics Research	Odyssey, LINUX R Markdown Lab Video Other videos: Unix Shell Python Tutorial	Microarrays (RMA) Slides RMA demo Lecture videos: 1 2 3 4 Other videos: Microarrays Normalization Background correction Expression index	Sign up for the Odyssey
2 (2/4)	Differential expression Slides No class today. Just watch videos. Lecture videos: 1 2 3 4 Other videos: Heatmaps QQ plot Differential expression Design Matrix P values False discovery rate	RMA, LIMMA, Python Lab Video	Clustering Slides Lecture videos: 1 2 3 4 5 Other videos: Hierarchical clustering K-means clustering Batch effect removal Gene Ontology DAVID Gene Set Enrichment Analyses	HW1 (Basics)
3 (2/11)	Classification Slides Lecture videos: 1 2 3 4 Other videos: Overview of machine learning K nearest neighbors MDS PCA Cross Validation Multiple regression Logistic regression Regularization Decision trees Random forest Support vector machine	Batch Effect, Clustering, PCA, BWA, STAR, Odyssey Video 1: Limma with Contrasts and Kmeans Video 2: Batch Effect, hclust, ComBat Video 3: PCA Video 4: BWA, STAR, Odyssey, Command Line	NGS Slides Lecture videos: 1 2 3 4 5 Other videos: Illumina sequencing FASTQ files FASTQC Smith-Waterman algorithm BLAST BWT FM Index Suffix trees Suffix arrays BAM files
4 (2/18)	RNA-Seq analysis Slides Lecture Videos: 1 2 3 4 Other Videos: RNA-Seq STAR Salmon RPKM, FPKM, TPM DESeq2 Pt1 DESeq2 Pt2	KNN, SVM, DAVID, GSEA Lab 4 Video	Single-cell RNA-seq (Chenfei) Slides Lecture Videos 1 2 3 4 Other Videos DropSeq 10X Genomics t-SNE Course on scRNA-seq analyses	HW2 (Microarrays)
5 (2/25)	Module I Review Slides Lecture Videos 1 2 3 Other videos: Overview CITE-seq	Salmon, DESeq2, Cluster Computing Lab 5 Video	Motif finding Slides Lecture videos: 1 2 3 4 5 Other videos: Transcription regulation Post-transcriptional regulation Gibbs sampling Expectation Maximization Motif discovery
6 (3/4)	ChIP-seq Slides Lecture Videos 1 2 3 4 Other Videos ChIP-seq MACS Cistrome AP Cistrome DB	Seurat, Odyssey Lab 6 Video Part I Lab 6 Video Part II	Epigenetics Slides Lecture Videos: 1 2 3 4 Other Videos Basic intro1 Basic intro2 CpG islands and DNA methylation DNA methylation and cancer DNA methylation analyses	HW3 (RNA-seq, scRNA-seq)
7 (3/11)	Histone modifications, Chromatin accessibility No class today. Just watch videos. Slides Lecture videos (from last year) 1 2 3 Other videos: Histone modifications DNase-seq ATAC-seq	MACS2, Genome Browser, BedTools, Odyssey Lab 7 Video	Long range chromatin interactions Slides Lecture videos 1 2 3 4 Other videos HiC (start at 4:30) Chromosome organization Loop extrusion model
8 (3/18)	Spring Recess		Spring Recess
9 (3/25)	GWAS and eQTL Slides Lecture Videos: 1 2 3 4 Other Videos: Epidemiology studies Odds ratio and risk ratio QTL mapping GWAS	BETA, VCF, ChIP-seq Motif Lab 8 Video Linear regression in R Multiple regression in R Logistic regression in R Ridge, LASSO, Elastic-Net in R	Module II Reivew Slides Lecture Videos 1 2 3 Other videos: RegulomeDB and HaploReg Enhancer Target Gene Prediction	HW4 (ChIP-seq)
10 (4/1)	Hidden Markov Model Slides Lecture videos 1 2 3 4 Other videos: HMM Intro HMM Applications Forward-backward algorithm Viterbi algorithm	HMM, TCGA Lab 9 Video (Part I): Concepts of HMM Lab 9 Video (Part II): Examples of HMM, TCGA	Cancer genome sequencing, TCGA Slides Lecture videos 1 2 3 4 Other videos: DNA Repair Defects and Cancer TCGA & Cancer Research
11 (4/8)	Cancer subtyping from RNA-seq and DNA methylation Slides Lecture Videos 1 2 3 4 Other Videos: Survival Data Hazard Ratios LogRank Test Cox Regression	GWAS(Including HaploReg, RegulomeDB, MAF), Regression and Feature Selection Lab 10 Video	Targeted therapy and drug resistance Slides Lecture videos: 1 2 3 4 Other videos: Targeted therapy Precision cancer medicine	HW5 (Epigenetics)
12 (4/15)	Cancer immunotherapy Slides Lecture Videos: 1 2 3 4 Other Videos: Cancer Immunology Cancer immunotherapy Antigen presentation VDJ recombination CAR-T cell therapy Cancer vaccines	TCGA, Survival analysis, MAGeCK Lab 11 Video	Cancer Immunotherapy 2 and CRISPR Screens Slides Lecture Videos 1 2 3 Other Videos: CRISPR CRISPR PAM CRISPR screens CRISPR Crash Course
13 (4/22)	Epigenetic Therapy, Combination Therapy Slides Lecture Videos 1 2 3 4 5 Other Videos IDH1 Mutations in Cancers Epigenetic Mechanisms of Cancer 5AZA in Cancer	HW6 Help	Final Review Slides Lecture Videos 1 2 3	HW6 (Cancer Genomics)
14 (4/29)	No class today. Just watch the video Reproducible research		Reading Period
15 (4/30)	Reading Period