| 1 | 6-Sep | Class overview | | | pdf ppt | |
| 2 | 11-Sep | Background | Graph theory | Molecular biology concepts | pdf ppt notes | (1) Life and its molecules; (2) Topology of molecular networks |
| 13-Sep | | Probability theory | | pdf ppt prob_prac | |
| 3 | 18-Sep | Representing and learning molecular networks from data | Bayesian networks | Gene network inference | pdf ppt | (1) Markowetz and Spang; (2) Friedman et al; (3) Segal et al |
| 20-Sep | | Bayesian networks continued | | pdf ppt | |
| 4 | 25-Sep | | Gaussian Graphical models | | pdf ppt | Graphical LASSO |
| 27-Sep | | Dependency networks | | pdf ppt | GENIE3 |
| 5 | 2-Oct | | Incorporating prior into Bayesian networks | Integrative inference of gene networks | pdf(a) ppt(a) pdf(b) ppt(b) | Werhli et al |
| 4-Oct | | Incorporating prior into Bayesian networks | | pdf(b) ppt(b) | |
| 6 | 9-Oct | | Lecture rescheduled to Oct 17th | | | |
| 11-Oct | | Incorporating prior into Dependency networks | | pdf ppt | Greenfield et al. |
| 7 | 16-Oct | Context-specificy and dynamics of networks | Dynamical models; Skeleton network based methods | Representing dynamics in networks | pdf ppt | Ideker et al |
| 17-Oct | | I/O Hidden Markov Models | Integrating TF-DNA interactions with time-series expression | pdf ppt video | Ernst et al. DREM Supplement |
| 18-Oct | | I/O HMM continued | | | |
| 8 | 23-Oct | | Graphical Gaussian models; Multi-task learning | Tissue-specific networks | pdf ppt | Pierson et al. |
| 25-Oct | Topological properties | Graph clustering | Finding modules/communities in graphs | pdf ppt | Girvan and Newman |
| 9 | 30-Oct | | Class rescheduled | | | |
| 1-Nov | | Agglomerative clustering | Hierarchical communities, link prediction | pdf ppt | Park et al |
| 10 | 6-Nov | | Spectral clustering | Finding communities on graphs | pdf ppt | |
| 7-Nov | | Spectral clustering applications | Disease module detection, Finding TADs | pdf ppt video | DREAM module detection challenge |
| 8-Nov | Comparison of graphs | Network alignment | Conservation of subnetworks across species | pdf ppt | PathBLAST |
| 11 | 13-Nov | | Spectral methods for graph alignment | | pdf ppt | IsoRank |
| 15-Nov | | Matrix factorization based alignment | | pdf ppt | FUSE |
| 12 | 20-Nov | Network-based integration/interpretation | Graph diffusion and walks on graphs | Network-based gene prioritization, data imputation, smoothing of Hi-C data | pdf ppt | GeneWanderer |
| 22-Nov | | Thanksgiving | | | |
| 13 | 27-Nov | | Heat kernel and subgraph identification | Interpreting variants on a graph | pdf ppt | HOTNET |
| 29-Nov | | Information flow; matrix factorization | Data integration and interpretation | pdf ppt | |
| 14 | 4-Dec | | Project presentations | | | |
| 6-Dec | | Project presentations | | | |
| 15 | 11-Dec | | Project presentations | | | |