Harvard University – Introduction to Bioinformatics and Computational Biology
- Intro to Bioinfo & Comp Bio
- 1 Course information
- 2 Introduction
- 3 High throughput sequencing
- 4 RNA-seq Quantification
- 5 Differential expression, FDR, GO, and GSEA
- 6 Clustering
- 7 Dimension Reduction
- 8 Classification
- 9 Module I Review
- 10 Transcription Factor Motif Finding
- 11 ChIP-seq, Expression Integration
- 12 Epigenetics, DNA Methylation
- 13 Histone Modifications , Chromatin Accessibility
- 13.1 Nucleosome Positioning
- 13.2 Introduction to Histone Modifications
- 13.3 Infer Transcription Factor Binding from Histone Mark Dynamics
- 13.4 Using Histone Marks to Infer Gene Functions
- 13.5 Introduction to DNase-seq and ATAC-seq
- 13.6 Infer TF from Differential Genes Using LISA
- 13.7 Caution on DNase/ATAC-seq footprint analysis
- 13.8 Summary of Epigenetics and Chromatin
- 13.9 Lab 6
- 14 Hidden Markov Model
- 15 HiC
- 15.1 Introduction to Chromatin Interaction and Organization
- 15.2 Methods to Investigate 3D Genome Organization
- 15.3 Topologically Associating Domains
- 15.4 TAD Function and Loop Anchors
- 15.5 Chromatin Compartments
- 15.6 Computational Methods to Call Chromatin Loops
- 15.7 Variations of Chromatin Interaction Technologies
- 15.8 Resources for Exploring 3D Genomes
- 15.9 Lab 7
- 16 Module II Review
- 17 SNP and GWAS
- 18 GWAS and Epigenomics
- 19 Single-cell RNA-seq (1)
- 20 Single-cell RNA-seq (2)
- 21 scATAC-seq
- 22 Module III Review
- 23 Cancer Genome Sequencing , Mutation analyses
- 24 Cancer Subtyping, Survival Analyses
- 25 Targeted Therapy and Precision Medicine
- 26 Cancer Immunotherapy (1)
- 27 Cancer Immunotherapy (2)
- 28 CRISPR Screens
- 29 Module IV Review and Course Review
- Published with bookdown
Chapter 1 Course information
This is the course material for STAT115/215 BIO/BST282 at Harvard University.
All the YouTube videos in this course are organized under the 2021 STAT115 playlist.
1.1 Contributors
Xiaole Shirley Liu Harvard University and Dana-Farber Cancer Institute
Joshua Starmer StatQuest
Ting Wang Washington University
Feng Yue Northwestern University
Ming Tang Dana-Farber Cancer Institute
Martin Hemberg Wellcome Sanger Institute
Gad Getz Harvard University and Broad Institute
Yang Liu
Bo Yuan
Jack Kang
Scarlett Qian
Jiazhen Rong
Phillip Nicol
Maartin De Vries
We thank many colleagues in the community, who helped Dr. Liu in prepare the STAT115/215 BIO/BST282 course over the years. Some of the lecture slides acknowledged their contributions, but these contributors are not individually acknowledged here.
Filed under: MOOC |
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