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Week
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Tue Lecture
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Tue/Thur Labs
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Thur Lecture
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Sun HW Due
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10
(3/30)
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Intro to GWAS
Slides
Videos:
GWAS Intro
GWAS Issues and eQTL
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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
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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
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11 (4/6)
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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
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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
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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
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HW5 (Epigenetics and scATAC-seq)
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12 (4/13)
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Targeted therapy, Compound screens, Drug resistance
Slides
Lecture videos:
1 2 3
Other videos:
Targeted therapy
Precision cancer medicine
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TCGA, LIMMA, Survival Analysis
Zoom recording for Lab11
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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
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13 (4/20)
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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
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Immune infiltration
MAGeCK
Link to Lab12 Recording pt.1
Link to Lab12 Recording pt.2
Other videos:
TIMER
TIDE
DepMap Tutorial
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Module III and Final Review
Slides
Lecture Videos
Module III Review
Course Review
Final Logistics
Questions to Ponder
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HW6 (Cancer Genomics)
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14 (4/27)
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Reproducible Research
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How to stay current in bioinformatics?
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Reading Period
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