Schedule

Week	Date	Topic	Paper	Notes	Deliverables
1	9/3/15	Class overview		Lecture (pdf)
2	9/8/15	Introduction to Network Biology		Lecture (powerpoint)
	9/10/15	Expression-based network inference		Lecture (pdf till slide 33)
3	9/15/15			Lecture (pdf from slide 34)
	9/17/15	Integrative network reconstruction	Prior-based data integration	slides Lecture/Discussion
4	9/22/15		Physical module networks	slides Lecture/Discussion
	9/24/15		MEDUSA MouseNET/BioPixie	slides Discussion
5	9/29/15	Dynamics and context-specificity in networks	Active subgraphs	slides Discussion	Critique 1
	10/1/15		Dynamic Bayesian networks	slides Discussion
6	10/6/15		DREM/SDREM	Guest lecture by Prof. Anthony Gitter	Proposal due
	10/8/15		SMARTS	slides Discussion
7	10/13/15	Network comparisons	PathBlast	slides Discussion	Critique 2
	10/15/15		IsoRank	slides Discussion
8	10/20/15		LocalAli	slides Discussion	Final Proposal due
	10/22/15	Data integration using networks	Simultaneous clustering of multiple networks	slides Discussion	Critique 3
9	10/27/15		Similarity Network Fusion	slides Discussion
	10/29/15		Prize collecting Steiner tree	slides Discussion
10	11/3/15	Clustering/Modules in networks	MATISSE	slides Discussion	Critique 4
	11/5/15		Hierarchical Agglomerative Clustering	slides Discussion
11	11/10/15		DICER	slides Discussion
	11/12/15	Perturbations in networks	Nested Effect models	slides Lecture/Discussion	Critique 5
12	11/17/15		Dendrix	slides Discussion
	11/19/15		Dysregulated pathways	slides Discussion
13	11/24/15	Networks for gene prioritization	Random walk	slides Lecture/Discussion	Critique 6
	11/26/15		Thanksgiving	No class
14	12/1/15		Active Learning	slides Discussion
	12/3/15		GeneMania	slides Discussion
15	12/8/15		Project presentations		Critique 7
	12/10/15		Project presentations
16	12/15/15		Project presentations
	12/18/15				Final Report Due by Email