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Week

Tue Lecture

Tue/Thur Labs

Thur Lecture

Sun HW Due

1

(1/23)

Introduction to computational biology and Microarrays

Slides

2017 Videos: 1, 2, 3

2016 Videos: 1, 2, 3

Reading: Bioinformatics

Odyssey

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Scott's Slides

Odyssey tutorial videos: 1, 2, 3

Microarray normalization, Expression index

Slides Examples

2017 Videos: 1, 2, 3

2016 Videos:1, 2, 3, 4

Reading: RMA

2

(1/30)

Differential expression, False discovery rate

Slides

2017 Videos: 1, 2, 3, 4

2016 Videos:1, 2, 3, 4

Reading: LIMMA

R & BioConductor, Python 1, Git, LINUX, RMA, LIMMA

Git Repo

Microarray clustering, Batch effect, Gene Ontology

Slides

2017 Videos: 1, 2, 3, 4

2016 Videos:1, 2, 3, 4

Reading: COMBAT

3

(2/6)

GSEA, Dimension reduction, Unsupervised learning

Slides

2017 Videos: 1, 2, 3

2016 Videos:1, 2, 3, 4

Reading: Statistical Learning

DAVID, Clustering, COMBAT

Git Repo

HMM (snow day, just watch 2016 videos)

Slides

2016 Videos:1, 2, 3

Reading: Rabiner

HW1

(Microarrays)

HW due date postponed to Tue 2/14

4

(2/13)

NGS, Read mapping (Eduardo Gusmao)

Slides

2017 Videos: 1, 2, 3, 4

2016 Videos:1, 2

Reading: NBT Tutorial

Classification, RNA-seq, run job on Odyssey

Lab4

RNA-seq analysis

Slides

2017 Videos: 1, 2, 3 (sorry 3rd video was incomplete)

2016 Videos:1, 2, 3, 4

Reading: DEseq2,

Difference between PTM and R/FPKM

Quiz 1

Answer

5

(2/20)

Single-cell RNA-seq

Slides

2017 Videos: 1, 2, 3

Reading: Systematic comparison of scRNA-seq techniques

t-SNE

RNA-seq analysis

lab5.pdf

Motif finding

Slides

2017 Videos: 1, 2, 3

2016 Videos:1, 2, 3

Reading: Gibbs Sampler

HW2

(RNA-seq)

6

(2/27)

ChIP-seq

Slides

2017 Videos: 1, 2, 3

2016 Videos:1, 2, 3, 4

Reading: BETA

UCSC, BedTools, sc-RNAseq

Git Repo

DNA methylation

Slides

2017 Videos: 1, 2, 3

2016 Videos:1, 2, 3 ,4

Reading: Epigenetics review

Quiz 2

Answer

7

(3/6)

Histone modifications, Chromatin accessibility

Slides

2017 Videos: 1, 2, 3

2016 Videos:1, 2, 3

Reading: ATAC-seq

MACS2, BETA
Git Repo

Long range chromatin interactions; Regulatory network
(Sherlock Hu)

Slides

Videos: 1, 2, 3

Reading: Mitotic chromosome organization

8

(3/13)

Spring Recess

Spring Recess

HW3

(ChIP-Seq scRNA-Seq)

9

(3/20)

Feature selection and regression (Peng Jiang)

Slides

2017 Videos: 1, 2

2016 Videos:1, 2, 3

Reading: Introduction

Feature Selection, Epigenetics

Git Repo

Evolution, Inheritance, Population genetics

Slides

2017 Videos: 1, 2, 3

2016 Videos:1, 2, 3

Quiz 3

Answer

10

(3/27)

Haplotypes, GWAS

Slides

2017 Videos: 1, 2, 3, 4

2016 Videos:1, 2, 3

Compiling Nice R Reports

Git Repo

Population stratification, Quantitative traits

Slides

2017 Videos: 1, 2, 3, 4

2016 Videos:1, 2, 3

HW4

(Epigenetics)

11

(4/3)

Reproducible research (no class, just watch video)

Video from Keith Baggerly

Reading: Peng review, Garraway thoughts

GWAS

GWAS and GWAS interpretation

Slides

2017 videos: 1, 2, 3

2016 Videos:1, 2, 3

Reading: GRAIL

Quiz4

Answer

12

(4/10)

Genome sequencing, TCGA

Slides

2017 videos: 1, 2, 3

2016 Videos:1, 2, 3, 4

Reading: Lawrence1, Lawrence2

GRM, heritability, GCTA, SVD, association test models, Plink

Targeted therapy; High throughput screening

Slides

2017 videos: 1, 2, 3

2016 Videos:1, 2, 3

Reading: CCLE and CRISPR screen papers

HW5

(GWAS)

13

(4/17)

Cancer immunotherapy

Slides

2017 Videos: 1, 2, 3

2016 Videos:1, 2, 3

Other useful Videos:Nature1 Nature2

Reading: Tumor response to PD-1 antibody

Survival, TCGA

Git Repo

Drug Resistance,

Final review

Slides

2017 Videos: 1, 2, 3

2016 Videos: 1, 2, 3

Quiz 5

14

(4/24)

Final Exam

Reading Period

HW6

(Cancer Genomics)

15

(5/1)

Reading Period

Screencast video due

Quiz 6