Lecture schedule

  1. Course introduction and overview
  2. Stem cell fundamentals, cell identity, and gene expression
  3. How does scRNA-seq work?
  4. Fundamentals of scRNA-seq analysis (live analysis)
    1. HW1 assigned
  5. Data integration and cell typing
  6. Data integration and cell typing (live analysis) HW2 assigned
  7. Bio break: basics of development
  8. Pseudotime or trajectory inference
  9. Pseudotime analysis in practice (live analysis) HW3 assigned
  10. Biobreak: Mechanisms that maintain fate potency
  11. Cell potency calculators and lineage tracing
  12. Cell potency and lineage tracing analysis (live analysis) HW4 assigned
  13. Gene regulatory network inference from gene expression data
  14. ATAC-seq
  15. Regulatory network analysis (live analysis)
  16. Simulation engines and expression forecasting HW5 assigned
  17. Simulation engines and expression forecasting (live analysis) Final project distributed
  18. Cell-cell interactions inference
  19. Cell-cell interaction (live analysis) HW6 assigned
  20. Spatial transcriptomics
  21. Spatial transcriptomics (live analysis)
  22. RNA velocity
  23. RNA velocity (live analysis)
  24. Controversies and ethical considerations
  25. Final group presentations
  26. Final group presentations