Schedule

Week	Date	Computational concepts	Biological application	Slides	Reading
1	9/6/16	Class Overview		pdf
	9/8/16	Background in graph theory; probability theory	Molecular networks	pdf ppt	Life and its molecules
2	9/13/16	Graph structure learning	Regulatory network inference	pdf ppt	Markowetz & Spang
	9/15/16	Bayesian networks and its variants		lecture 3b (pdf ppt) lecture 4 (pdf ppt)	(1) Friedman et al (2) Segal et al
3	9/20/16	Module networks	Regulatory network inference	lecture 4 (pdf ppt)	Segal et al
	9/22/16	Dependency networks	Regulatory network inference	lecture 5 (pdf ppt)	Huynh-Thu et al.
4	9/27/16	Constrained structure learning	Integrative network inference	lecture 6 (pdf ppt)	Novershtern et al.
	9/29/16	Class rescheduled to Oct 3rd
	10/3/16	PGMs with priors	Incorporating prior knowledge to infer networks	lecture 7 (pdf ppt)	Werhli et al.
5	10/4/16	PGMs with priors	Incorporating prior knowledge to infer networks
	10/6/16	PGMs with priors: regularized regression	Incorporating prior knowledge to infer networks	lecture 8 pdf ppt	Greenfield et al
6	10/11/16	PGMs with priors	Incorporating prior knowledge to infer networks
	10/13/16	Dynamics in networks	Context-specific and dynamic network learning	lecture 9 pdf ppt	Active subgraphs
7	10/18/16	Dynamic Bayesian networks	Cancer signaling networks	lecture 10 pdf ppt	Hill et al.
	10/20/16	Graphical Gaussian models; Multi-task learning	Tissue-specific networks	lecture 11 pdf ppt	Pierson et al.
8	10/25/16	Hidden Markov models and I/O HMMs introduction	Dynamic regulatory networks	pdf ppt
	10/27/16	IOHMM contd	Dynamic regulatory network	pdf ppt	Ernst et al
9	11/1/16	IOHMM wrap-up. Intro to Hierarchical agglomerative clustering	Protein network module detection	pdf ppt	Park et al.
	11/3/16	HAC and Spectral clustering		pdf ppt	Park et al.
10	11/8/16	Class rescheduled to Nov 14
	11/10/16	Spectral clustering	Integrating different data types with graphs	pdf pptx	Wang et al
	11/14/16	Seeding scoring and searching subnetworks	Jointly activated sub networks	pdf pptx	Ulitsky et al
11	11/15/16	Graph alignment: Pairwise pathway alignment	Comparative analysis of networks	pdf pptx	Kelley et al Sharan et al
	11/17/16	Global network alignment with IsoRank		pdf pptx	Singh et al
12	11/22/16	Global network alignment with FUSE		pdf pptx	Gligorijević et al
	11/24/16	Thanksgiving. No class
13	11/29/16	Random walks and graph diffusion	Network-based gene prioritization	pdf pptx	Kohler et al
	12/1/16	Heat diffusion kernel	Detecting significantly mutated pathways	pdf pptx	Vandin et al
14	12/6/16	Nested effect factor graph models	Identifying networks from genetic perturbations	pdf pptx	Vaske et al
	12/8/16	Project presentations
15	12/13/16	Project presentations
	12/15/16	Project presentations