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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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1
(1/23)
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Introduction to computational biology and Microarrays
Slides
Download Slides
2017 Videos: 1
Links to an external site., 2
Links to an external site., 3
Links to an external site.
2016 Videos: 1, 2, 3
Reading: Bioinformatics
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Odyssey
Sign Up
Links to an external site. (Required)
Scott's Slides
Download Scott's Slides
Odyssey tutorial videos: 1
Links to an external site., 2
Links to an external site., 3
Links to an external site.
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Microarray normalization, Expression index
Slides
Download Slides Examples
Download Examples
2017 Videos: 1
Links to an external site., 2
Links to an external site., 3
Links to an external site.
2016 Videos:1, 2, 3, 4
Reading: RMA
Links to an external site.
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2
(1/30)
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Differential expression, False discovery rate
Slides
Download Slides
2017 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.
2016 Videos:1, 2, 3, 4
Reading: LIMMA
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R & BioConductor, Python 1, Git, LINUX, RMA, LIMMA
Git Repo
Links to an external site.
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Microarray clustering, Batch effect, Gene Ontology
Slides
Download Slides
2017 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.
2016 Videos:1, 2, 3, 4
Reading: COMBAT
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3
(2/6)
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GSEA, Dimension reduction, Unsupervised learning
Slides
Download Slides
2017 Videos: 1
Links to an external site., 2
Links to an external site., 3
Links to an external site.
2016 Videos:1, 2, 3, 4
Reading: Statistical Learning
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DAVID, Clustering, COMBAT
Git Repo
Links to an external site.
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HMM (snow day, just watch 2016 videos)
Slides
Download Slides
2016 Videos:1, 2, 3
Reading: Rabiner
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HW1
Links to an external site.
(Microarrays)
Links to an external site.
HW due date postponed to Tue 2/14
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4
(2/13)
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NGS, Read mapping (Eduardo Gusmao)
Slides
Download Slides
2017 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.
2016 Videos:1, 2
Reading: NBT Tutorial
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Classification, RNA-seq, run job on Odyssey
Lab4
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RNA-seq analysis
Slides
Download Slides
2017 Videos: 1
Links to an external site., 2
Links to an external site., 3
Links to an external site. (sorry 3rd video was incomplete)
2016 Videos:1, 2, 3, 4
Reading: DEseq2,
Difference between PTM and R/FPKM
Links to an external site.
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Quiz 1
Answer
Download Answer
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5
(2/20)
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Single-cell RNA-seq
Slides
Download Slides
2017 Videos: 1
Links to an external site., 2
Links to an external site., 3
Links to an external site.
Reading: Systematic comparison of scRNA-seq techniques
Links to an external site.
t-SNE
Links to an external site.
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RNA-seq analysis
lab5.pdf
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Motif finding
Slides
Download Slides
2017 Videos: 1
Links to an external site., 2
Links to an external site., 3
Links to an external site.
2016 Videos:1, 2, 3
Reading: Gibbs Sampler
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HW2
Links to an external site.
(RNA-seq)
Links to an external site.
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6
(2/27)
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ChIP-seq
Slides
Download Slides
2017 Videos: 1
Links to an external site., 2
Links to an external site., 3
Links to an external site.
2016 Videos:1, 2, 3, 4
Reading: BETA
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UCSC, BedTools, sc-RNAseq
Git Repo
Links to an external site.
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DNA methylation
Slides
Download Slides
2017 Videos: 1
Links to an external site., 2
Links to an external site., 3
Links to an external site.
2016 Videos:1, 2, 3 ,4
Reading: Epigenetics review
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Quiz 2
Answer
Download Answer
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7
(3/6)
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Histone modifications, Chromatin accessibility
Slides
Download Slides
2017 Videos: 1
Links to an external site., 2
Links to an external site., 3
Links to an external site.
2016 Videos:1, 2, 3
Reading: ATAC-seq
Links to an external site.
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MACS2, BETA
Git Repo
Links to an external site.
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Long range chromatin interactions; Regulatory network
(Sherlock Hu)
Slides
Download Slides
Videos: 1
Links to an external site., 2
Links to an external site., 3
Links to an external site.
Reading: Mitotic chromosome organization
Links to an external site.
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8
(3/13)
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Spring Recess
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Spring Recess
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HW3
Links to an external site.
(ChIP-Seq scRNA-Seq)
Links to an external site.
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9
(3/20)
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Feature selection and regression (Peng Jiang)
Slides
Download Slides
2017 Videos: 1
Links to an external site., 2
Links to an external site.
2016 Videos:1, 2, 3
Reading: Introduction
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Feature Selection, Epigenetics
Git Repo
Links to an external site.
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Evolution, Inheritance, Population genetics
Slides
Download Slides
2017 Videos: 1
Links to an external site., 2
Links to an external site., 3
Links to an external site.
2016 Videos:1, 2, 3
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Quiz 3
Answer
Download Answer
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10
(3/27)
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Haplotypes, GWAS
Slides
Download Slides
2017 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.
2016 Videos:1, 2, 3
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Compiling Nice R Reports
Git Repo
Links to an external site.
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Population stratification, Quantitative traits
Slides
Download Slides
2017 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.
2016 Videos:1, 2, 3
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HW4
Links to an external site.
(Epigenetics)
Links to an external site.
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11
(4/3)
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Reproducible research (no class, just watch video)
Video from Keith Baggerly
Reading: Peng review, Garraway
Links to an external site. thoughts
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GWAS
Download GWAS
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GWAS and GWAS interpretation
Slides
Download Slides
2017 videos: 1
Links to an external site., 2
Links to an external site., 3
Links to an external site.
2016 Videos:1, 2, 3
Reading: GRAIL
Links to an external site.
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Quiz4
Answer
Download Answer
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12
(4/10)
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Genome sequencing, TCGA
Slides
Download Slides
2017 videos: 1
Links to an external site., 2
Links to an external site., 3
Links to an external site.
2016 Videos:1, 2, 3, 4
Reading: Lawrence1, Lawrence2
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GRM, heritability, GCTA, SVD, association test models, Plink
Download GRM, heritability, GCTA, SVD, association test models, Plink
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Targeted therapy; High throughput screening
Slides
Download Slides
2017 videos: 1
Links to an external site., 2
Links to an external site., 3
Links to an external site.
2016 Videos:1, 2, 3
Reading: CCLE and CRISPR screen papers
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HW5
(GWAS)
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13
(4/17)
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Cancer immunotherapy
Slides
Download Slides
2017 Videos: 1
Links to an external site., 2
Links to an external site., 3
Links to an external site.
2016 Videos:1, 2, 3
Other useful Videos:Nature1Nature2
Reading: Tumor response to PD-1 antibody
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Survival, TCGA
Git Repo
Links to an external site.
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Drug Resistance,
Final review
Slides
Download Slides
2017 Videos: 1
Links to an external site., 2
Links to an external site., 3
Links to an external site.
2016 Videos: 1
Links to an external site., 2
Links to an external site., 3
Links to an external site.
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Quiz 5
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14
(4/24)
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Final Exam
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Reading Period
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HW6
(Cancer Genomics)
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15
(5/1)
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Reading Period
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Screencast video due
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Quiz 6
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