| Date |
Lecture Topic |
Instructor |
| 1/15 |
Introduction
Genome assembly (Part 1) |
Kingsford
Compeau |
| 1/17 |
Genome assembly (Complete) |
Compeau |
| 1/18 |
Recitation on Genome Assembly |
TAs |
| 1/22 |
Sequence alignment (Part 1)
Alignment Demo |
Kingsford |
| 1/24 |
Sequence alignment (Part 2) |
Kingsford |
| 1/25 |
Recitation on Dynamic Programming |
TAs |
| 1/29 |
Read mapping (Part 1)
Suffix Tree Math |
Compeau |
| 1/31 |
No Class (cancelled due to cold) |
Polar Vortex |
| 2/1 |
Recitation on Read Mapping (Part 1) |
TAs |
| 2/5 |
Read mapping (Part 2) |
Compeau |
| 2/7 |
Multiple sequence alignment |
Kingsford |
| 2/8 |
Recitation on Read Mapping (Part 2) |
TAs |
| 2/12 |
Mini-lecture day 1 |
| 2/14 |
Midterm 1 |
|
| 2/19 |
Hidden Markov models |
Kingsford |
| 2/21 |
Metagenomics |
Compeau |
| 2/22 |
Recitation on HMMs |
TAs |
| 2/26 |
Phylogenetics (in progress) |
Compeau |
| 2/28 |
Phylogenetics (complete) and some necessary mathematics |
Compeau |
| 3/1 |
MCMC for Phylogenetics |
TAs |
| 3/5 |
Motif Finding, Gibbs Sampling, EM |
Kingsford |
| 3/7 |
RNA sequencing, gene expression |
Kingsford |
| S P R I N G B R E A K |
| 3/19 |
Network biology: intro & function prediction |
Kingsford |
| 3/21 |
Network biology: evolution of modularity |
Kingsford |
| 3/26 |
Population Genetics |
Compeau |
| 3/28 |
Mini-lecture day 2 |
|
| 3/29 |
Recitation on Soft Clustering |
TAs |
| 4/2 |
Midterm 2 |
|
| Note: All topics after Midterm 2 are tentative and subject to change. |
| 4/4 |
Evolutionary Game Theory
Animated GIF |
Kingsford |
| 4/9 |
Neural Modeling |
Kingsford |
| S P R I N G C A R N I V A L |
| 4/16 |
Universality of Neural Networks and Deep Learning (incomplete) |
Compeau |
| 4/18 |
Protein Structure Prediction |
Kingsford |
| 4/19 |
Recitation on Neural Nets |
TAs |
| 4/23 |
Finishing up Neural Nets |
Compeau |
| 4/25 |
Three Mini-"Great Ideas": Turing Patterns, Fragile Genomes, and DNA Computing |
Compeau |
| 4/26 |
Drop-in Project Office Hours During Recitation |
TAs |
| 4/30 |
Project Presentations |
Students |
| 5/2 |
Project Presentations |
Students |