Course Schedule


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