Schedule
There are four chapters, or broad themes, that we will cover in this course:
- single cell genomics
- cell identity
- trajectory inference and fate potential
- regulatory networks
Access to videos and slides listed here is available to current students
The lecture videos and slides can only be accessed after authenticating via Hopkin's SSO
| What | Date | Chapter | Topic | video | slides | other |
|---|---|---|---|---|---|---|
| Lecture 1 | 01-20-26 | 1 | Course introduction | intro to course | slides | |
| Lecture 2 | 01-22-26 | 1 | scRNAseq data generation | dropseq | slides | |
| Lecture 3 | 01-27-26 | 1 | Hematopoiesis; scRNAseq analysis I | tutorial | notebook | Colab setup |
| Lecture 4 | 01-29-26 | 1 | scRNAseq analysis II | scRNAseq analysis II | notebook | |
| HW 1 due | 01-30-26 11:59pm | 1 | HW1: scRNAseq analysis I | HW 1 | ||
| Lecture 5 | 02-03-26 | 1 | scRNAseq analysis III; cell cycle | scRNAseq analysis III | - | |
| Lecture 6 | 02-05-26 | 1 | end scRNAseq; pluripotency | pluripotency | slides | |
| HW 2 due | 02-13-26 11:59pm | 1 | HW2: more scRNAseq analysis | HW 2 | ||
| Test 1 | 02-10-26 | 1 | sc omics | |||
| Lecture 7 | 02-12-26 | 2 | Cell identity | part I part II | slides | |
| Lecture 8 | 02-17-26 | 2 | Cell typing and data integration theory | video | slides | |
| HW 3 posted | 02-17-26 | 2 | HW3: cell identity | HW 3 | ||
| Lecture 9 | 02-19-26 | 2 | Cell typing and data integration practice | video | notebook | |
| Off | 02-24-26 | 2 | - | - | ||
| Lecture 10 | 02-26-26 | 2 | Cell typing metrics | video | notes | |
| Lecture 11 | 03-03-26 | 2 | Epigenetics | video | slides | |
| Test 2 | 03-05-26 | 2 | cell identity | |||
| HW 3 due | 03-06-26 | 2 | HW3: cell identity | |||
| Lecture 12 | 03-10-26 | 3 | Intro to Trajectory Inference (TI) | pre-recorded video | slides | |
| Lecture 13 | 03-12-26 | 3 | scFates tutorial | prerecorded video | notebook | |
| Spring Break | 03-17-26 | NA | - | - | ||
| Spring Break | 03-19-26 | NA | - | - | ||
| Lecture 14 | 03-24-26 | 3 | Dev bio fundamentals | video | slides & notes | |
| Lecture 15 | 03-26-26 | 3 | 'Stemness' | video | slides | |
| Lecture 16 | 03-31-26 | 3 | Optimal transport & RNA velocity | RNA velocity video OT explained by Dr. Schiebinger | RV slides | |
| Test 3 | 04-02-26 | 3 | Trajectories and fate potential | |||
| HW 4 due | 04-08-26 | 3 | HW4: trajectories and fate potential | - | ||
| Lecture 17 | 04-07-26 | 4 | Gene regulatory networks (GRNs) | video | slides | |
| Lecture 18 | 04-09-26 | 4 | GRNs from single cell omics data | pre-recorded video | slides | |
| Lecture 19 | 04-14-26 | 4 | Computational approaches to cell fate engineering | video | slides | |
| Lecture 20 | 04-16-26 | 4 | Simulating single cell trajectories | video | slides | oneSC documentation |
| Lecture 21 | 04-21-26 | 4 | Spatial transcriptomics and cell-cell communications | video | slides | |
| Test 4 | 04-23-26 | 4 | Regulatory networks | |||
| HW 5 due | 04-27-26 | 4 | HW5: Regulatory networks | HW 5 |