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