| Slides Set # | Topic | Slides |
Additional material |
| 0 |
Staff, grading, and schedule |
|
Syllabus (rough; subject to change) |
| 1 |
The Emergence of Systems Biology |
PDF |
[Executable Cell Biology] |
| 2 |
Molecular Cell Biology: A Brief Review |
PDF |
|
| 3 |
Biological Sequence Analysis: A Brief Overview |
PDF |
|
| 4 |
Computational Techniques: A Brief Review |
PDF |
|
| 5 |
Graphical Models: Linear networks, Boolean networks, Bayesian
networks |
PDF |
[Dana Pe'er's
Dissertation],
[Primer on Bayesian Networks],
[The REVEAL Algorithm] |
| 6 |
Graphical Models: Petri Nets |
PDF |
[Petri Nets for Biology] |
| 7 |
Graph-theoretic properties and models of networks |
PDF |
[Survey 1], [Survey 2] |
| 8 |
Graph-theoretic properties and models of biological networks |
PDF |
[1], [2], [3] |
| 9 |
Network motifs |
PDF |
|
| 10 |
A (very) quick tutorial on Python and NetworkX |
PDF |
|
| 11 |
Network modularity and community detection |
PDF |
|
| 12 |
Graph-theoretic approaches for clustering gene expression data |
PDF |
|
| 13 |
Comparative network analysis |
PDF |
[1] , [2] , [3] , [4] , [5] , [6] , [7] , [8] , [9] , [10] , [11], [12] |
| 14 |
Modeling and analysis of metabolic networks |
PDF |
Survey |
| 15 |
Bayesian network analysis of signaling networks |
PDF |
A Primer by D. Pe'er |