Week

Tue Lecture

Tue/Thur Labs

Thur Lecture

Sun HW Due

10

(3/30)

Intro to GWAS 

Slides

Videos:

GWAS Intro

GWAS Issues and eQTL

See Part I and Part II from this YouTube playlist

https://www.youtube.com/playlist?list=PLvLWaa3SS8qUnxF_FfEZtundapXOWCIum

 

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Other Videos

GWAS Catalogue

LD Link

HaploReg

GWAS interpretation using epigenetics

Guest lecturer: Omer Weissbrod

Slides

Lecture Videos: 

Intro to GWAS Annotation

GWAS Functional Enrichment

Find Causal SNPs

Predict Disease Risks

Other Videos:

Epidemiology studies

Odds ratio and risk ratio

QTL mapping

GWAS

RegulomeDB and HaploReg

 

11 (4/6)

Cancer genome sequencing (TCGA), Mutation analyses

Slides

Lecture videos:

Introduction

Mutation Characterization

Cancer Mutation Patterns

Purity and Clonality

Mutation Interpretation

Find Cancer Genes

Summary and Future

Other videos:

DNA Repair Defects and Cancer

TCGA & Cancer Research

See Part III and Part IV from this YouTube playlist

https://www.youtube.com/playlist?list=PLvLWaa3SS8qUnxF_FfEZtundapXOWCIum

 

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Other videos:

TCGA and cBioPortal

OpenCRAVAT

Cancer subtyping, Survival analyses

Slides

Lecture Videos

Cancer Subtypes

Survival Analysis

Oncogenes and Tumor Suppressors

Tumor Epigenetics

Hallmarks of Cancer

Other Videos:

Survival Data

Hazard Ratios

LogRank Test

Cox Regression

 

HW5 (Epigenetics and scATAC-seq)

12 (4/13)

Targeted therapy, Compound screens, Drug resistance

Slides

Lecture videos: 

1 2 3

Other videos:

Targeted therapy

Precision cancer medicine



 

 

 

 

 

 

 

 

TCGA, LIMMA, Survival Analysis

Zoom recording for Lab11

 

Cancer immunology

Slides

Lecture Videos:

Intro to Cancer Immunotherapy

Neoantigen Presentation

Immune Deconvolution

Immune Receptor Repertoires

Other Videos:

Cancer Immunology

Cancer immunotherapy

Antigen presentation

VDJ recombination

CAR-T cell therapy

Cancer vaccines

 

 

 

 

 

13 (4/20)

Cancer immunotherapy, CRISPR screens

Slides

Lecture Videos

Immune Signaling

Immunotherapy Biomarkers

CRISPR Screens

CRISPR Screen Computational Analysis

Other Videos:

Shirley's seminar at DFCI

CRISPR

CRISPR PAM

CRISPR screens

CRISPR Crash Course

 

Immune infiltration

MAGeCK

Link to Lab12 Recording pt.1

Link to Lab12 Recording pt.2

Other videos: 

TIMER

TIDE

DepMap Tutorial

 

 

Module III and Final Review

Slides

Lecture Videos

Module III Review

Course Review

Final Logistics

Questions to Ponder

 

HW6 (Cancer Genomics)

14 (4/27)

Reproducible Research

 

How to stay current in bioinformatics?

Reading Period