Course Schedule

Introduction to computational biology

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Videos 1 Links to an external site.,2 Links to an external site.,3 Links to an external site.

Reading: Bioinformatics Links to an external site.

R & BioConductor & 

RMA, LIMMA

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Microarray normalization, Expression index

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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.

Past videos: Microaorrays Links to an external site., Normalization Links to an external site., Expression index Links to an external site., Method comparison Links to an external site.

Reading: RMA Links to an external site.

2 (2/1)

Differential expression, False discovery rate

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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.

Past videos: Differential expression Links to an external site., Multiple hypotheses testing Links to an external site.

Reading: LIMMA Links to an external site.

Odyssey, LINUX

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Microarray clustering, Batch effect

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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.

Past videos:Gene Ontology Links to an external site., Clustering Links to an external site., Batch effect Links to an external site.

Reading: COMBAT Links to an external site.

3 (2/8)

Dimension reduction, Classification

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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.

Past videos:Dimension reduction Links to an external site., Classification Links to an external site.

Reading: Statistical Learning Links to an external site.

DAVID, Clustering, COMBAT

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NGS, Read mapping (Wei Li)

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Videos:1 Links to an external site.,2 Links to an external site.

Past videos: NGS Links to an external site., Read mapping Links to an external site.

Reading: NBT Tutorial Links to an external site.

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RNA-seq analysis (Wei Li)

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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.

Past videos: RNA-seq Links to an external site.,Transcript Assembly Links to an external site., Differential Expression Links to an external site.

Reading: DEseq2 Links to an external site.

PCA, SVM, BWA, Python 1

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RNA structure prediction (Elena Rivas)

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Videos:1 Links to an external site.,2 Links to an external site.,3 Links to an external site.

Past videos: N/A

Reading: Eddy NBT Tutorial Links to an external site.

Motif finding

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Videos:1 Links to an external site.,2 Links to an external site.,3 Links to an external site.

Past videos:Motif finding Links to an external site.

Reading: Gibbs Sampler Links to an external site.

DESeq, Vienna RNA package, Python 2

RNA-seq workflow Links to an external site.

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ChIP-seq

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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.

Past videos: ChIP-seq Links to an external site., Downstream Analysis Links to an external site., Refine Motifs Links to an external site.

Reading: BETA Links to an external site.

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6 (2/29)

DNA methylation

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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.

Past videos: Epigenetics - I Links to an external site., II Links to an external site., III Links to an external site.

Reading: Epigenetics review Links to an external site. 

MACS2, UCSC, BedTools, Python 3

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HMM

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Videos:1 Links to an external site.,2 Links to an external site.,3 Links to an external site.

Past videos:Hidden Markov Model - I Links to an external site., II Links to an external site., III Links to an external site.

Reading: Rabiner tutorial Links to an external site.

Histone modifications, Chromatin accessibility

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Videos:1 Links to an external site.,2 Links to an external site.,3 Links to an external site.

Past videos: Histone modifications Links to an external site.

Reading: Cell review Links to an external site.

HMM, BETA, Python 4

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Feature selection and regression (Peng Jiang)

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Videos:1 Links to an external site.,2 Links to an external site.,3 Links to an external site.

Past videos: N/A

Reading: Introduction Links to an external site.

Spring Recess

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Evolution, Molecular clock, SNP and LD

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Videos:1 Links to an external site.,2 Links to an external site.,3 Links to an external site.

Past videos: Evolution, Population genetics Links to an external site.

Reading:

Regression, Python 5

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Haplotype inference and GWAS

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Videos:1 Links to an external site.,2 Links to an external site.,3 Links to an external site.

Past videos:Haplotype inference Links to an external site., GWAS Links to an external site.

Reading:

Population structures, Quantitative traits

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Videos:1 Links to an external site.,2 Links to an external site.,3 Links to an external site.

Past videos: QTL Links to an external site.

Reading:

MAF and VCF, PLINK

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GWAS interpretation and application

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Videos:1 Links to an external site.,2 Links to an external site.,3 Links to an external site.

Past videos: GWAS interpretation Links to an external site.

Reading:

11 (4/4)

TCGA and tumor profiling

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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.

Past videos:Cancer genomics, TCGA Links to an external site.

Reading: Lawrence1 Links to an external site., Lawrence2 Links to an external site. papers 

HaploReg, RegulomeDB

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Targeted therapy, High throughput screening

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Videos:1 Links to an external site.,2 Links to an external site.,3 Links to an external site.

Past 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., 6 Links to an external site., 7 Links to an external site., 8 Links to an external site.

Reading: CCLE Links to an external site. and CRISPR Links to an external site. screen papers

Tumor Heterogeneity and evolution (Bo Li)

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Videos:1 Links to an external site.,2 Links to an external site.,3 Links to an external site.

Past videos: Cancer heterogeneity I Links to an external site., II Links to an external site., III Links to an external site., IV Links to an external site.

Reading: Clonal evolution Links to an external site., purity Links to an external site. and single cell Links to an external site. papers

TCGA data access, Survival analysis

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Cancer immunotherapy and epigenetic therapy

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Videos: 1 Links to an external site.,2 Links to an external site.,3 Links to an external site.Nature1 Links to an external site.Nature2 Links to an external site.

Past videos: Epigenetics drug and immunotherapy I  Links to an external site., II Links to an external site., III Links to an external site.

Reading: Tumor response to PD-1 antibody Links to an external site.

Reproducible research

Videos Links to an external site.

Reading: Peng Links to an external site. review

Screencast videos

Videos

Final review

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Videos:1 Links to an external site.,2 Links to an external site.,3 Links to an external site.