Lectures
The topics that we cover can be broadly split into three categories: stem cell biology, single cell data generation platforms, and computational methods for analyses of these data.
Access to lecture videos is available to current students
The lecture videos below can only be viewed after authenticating via Hopkin's SSO
| Lecture | Date | Topic | link to video | lecture slides |
|---|---|---|---|---|
| 1 | 01-21-25 | Course introduction | intro to course | slides |
| 2 | 01-23-25 | Stem cell biology | stem cell basics | slides |
| 2 | 01-23-25 | Single cell biology | game show video | NA |
| 3 | 01-28-25 | scRNAseq data generation | dropseq | slides |
| 4 | 01-30-25 | Scanpy tutorial | scanpy analysis | notebook |
| 5 | 02-04-25 | Data integration and cell typing | hcl,scmap,bbknn,scn | slides |
| 6 | 02-06-25 | Integration & typing tutorial | cell typing and integration | notebook |
| 7 | 02-11-25 | Trajectory inference and pseudotime | theory | TI slides |
| 8 | 02-13-25 | TI tutorial | video | notebook |
| 9 | 02-18-25 | Fate potency and stemness (pre-recorded) | video | slides |
| 10 | 02-20-25 | How-to infer fate potency (pre-recorded) | video | notebook |
| 11 | 02-25-25 | Gene regulatory networks | video | slides |
| 12 | 02-27-25 | scGRN | video | slides |
| 13 | 03-04-25 | Computational approaches to cell fate engineering | video | slides |
| 14 | 03-06-25 | Simulating single cell trajectories | video | slides |
| 15 | 03-11-25 | Intro to ST and Cell-to-cell communications | video | slides |
| 16 | 03-13-25 | Machine Learning for Spatial and Network Biology (In Malone 228; Uhtsav Chitra) | - | - |
| -- | 03-18-25 | Spring break | - | - |
| -- | 03-20-25 | Spring break | - | - |
| 17 | 03-25-25 | Early development and signaling | video | slides |
| 18 | 03-27-25 | Till and McCulloch | video | slides |
| 19 | 04-01-25 | Final project overview | video | slides |
| 20 | 04-03-25 | Epigenomics | video | slides |
| 21 | 04-08-25 | Multiomics | video | slides |
| 22 | 04-15-25 | Chromatin accessibility & ChIP-seq analysis | video | slides |
| 23A | 04-17-25 | RNA Velocity | video | slides |
| 23B | 04-17-25 | Cell modeling | video | slides |
| 24 | 04-22-25 | Controversies in the stem cell world | - | - |
| 25 | 04-24-25 | Clinical trials with stem cells | - | - |