Biological Background and Network Construction
- 1/27/09: Lecture 1: Introduction
- 1/29/09: Lecture 2: Experimental Methods: Yeast 2-hybrid
- 2/3/09: Lecture 3: Other experimental protocols (TAP-MS, SSL, ChIP-chip)
- 2/5/09: Lecture 4: In silico prediction of edges
Function Prediction (esp. via graph partitioning)
- 2/10/09: Lecture 5: Function Prediction
(min mulitway cut, integer programming, neighborhood, majority, functional flow)
- 2/12/09: Lecture 6: Graph Summarization (guest lecture by Saket Navlakha)
- 2/17/09: Lecture 7: Notions of Node Similarity; Modularity; Kernighan-Lin
- 2/19/09: Continued slides from 2/17/09.
- 2/24/09: Lecture 8: Entropy; variation of information; VI-CUT
- 2/26/09: Lecture 9: MCODE, RNSC, started
MCL
- 3/3/09: Finished MCL (slides above), Quiz #2
Network Alignment, Comparison, Searching
- 3/5/09: Lecture 10: PathBLAST
- 3/10/09: Lecture 11: Functional Orthologs (board lecture; unedited lecture notes)
- 3/12/09: Lecture 12: Color Coding (first 9 slides)
- 3/24/09: midterm
- 3/26/09: Color Coding (Lecture 12), continued (slides above)
- 3/31/09: Lecture 13: IsoRank Alignment, Graemlin
Random Graphs, Network Motifs
- 4/2/09: Lecture 14: Random Graphs, Degree Distribution, Network Motifs
- 4/7/09: Lecture 15: Random Processes for Growing Graphs
- 4/9/09: Lecture 16: Finding motifs via symmetry breaking
Other Graph Algorithms in Computational Biology
- 4/14/09: Lecture 17: Side-chain positioning
- 4/16/09: Lecture 18: PCP Theorem & hardness of approximating SCP (board lecture)
- 4/21/09: Lecture 19: SCP via Semidefinite Programming
- 4/23/09: Lecture 20: Dynamics of Regulatory Networks
- 4/28/09: Project work day
- 4/30/09: Lecture 21: Phylogenetic trees & Reassortment Detection
- 5/5/09: Project Presentation Day #1
- 5/7/09: Project Presentation Day #2
- 5/12/09: Lecture 22: Summary, Wrap-up, etc.
