CSE529/599C: Computational Genomics

Week 1
- Lecture 1 - introduction and motivation here
- Lecture 2 - review, ML, stats, genomics here
- Reading & videos:
  - Short videos describing central dogma of biology here and here
  - Intro to Mol Biology for Computer Scientists (Hunter) here
Week 2
- Lecture 3 - GWAS here
- Lecture 4 - GWAS and confounding here
- Reading & videos:
  - GWAS review paper here
  - Videos by StatQuest: P-values here, Bonferroni correction here , and FDR here.
Week 3
- Lecture 5 - GWAS and confounding here
- Lecture 6 - Guest lecture: population diversity and GWAS here
- Suggested reading & videos:
  - Videos on statistical power here and power analysis here.
  - Population structure in genetics review article here
  - PCA videos: 20min video from StatQuest
Week 4
- Lecture 7 - Gene regulation Intro here
- Lecture 8 - Explainable AI Intro here
- Suggested reading & videos:
  - Video on gene expression process here.
  - Video on regulation of gene transcription here.
  - Review on regulatory elements here.
  - Short videos on regularized regression Part 1, Part 2, Part 3, and Part 4
  - First TWAS paper here
Week 5
- Lecture 9 - Gene regulation con'd here
- Lecture 10 - Confounding and causality con'd here
- Suggested reading & videos:
  - Historically important paper by Jeff Leek and co-authors, studies batch effect issues in gene expression datasets here.
  - Causality, "an introduction" blog post here.
Week 6
- Lecture 11 - Regulatory Genomics - Epigenomics here
- Lecture 12 - Regulatory Genomics - CNNs here
- Suggested reading & videos:
  - Review of xAI in regulatory genomics here
Week 8
- Lecture 15 - Single cell RNA-seq intro here
- Lecture 16 - Single cell data integration here
- Suggested reading:
  - Nature Reviews Genetics (NRG) intro here
  - Best practices NRG here

Week 9
- Lecture 17 - single cell data integration II here
- Suggested reading:
  - Integrative single cell analysis NRG here

- - Connecting single cell genomics and human genetics NRG here