| 1 | 3-Sep | Class overview | | | pdf ppt video | |
| 2 | 8-Sep | Background | Graph theory | Molecular biology concepts | pdf ppt video | (1) Life and its molecules; (2) Topology of molecular networks |
| 10-Sep | | Probability theory | | pdf ppt video | |
| 3 | 15-Sep | Representing and learning molecular networks from data | Bayesian networks | Gene network inference | pdf ppt video | (1) Markowetz and Spang (2) Friedman et al (3) Sparse candidate |
| 17-Sep | | Bayesian networks | Learning modular networks | pdf ppt video | Module networks |
| 4 | 22-Sep | | Dependency networks | | pdf ppt video | GENIE3 |
| 24-Sep | | Incorporating priors in Bayesian networks | Integrative inference of regulatory networks | pdf ppt video | Werhli et al |
| 5 | 29-Sep | | Priors in Bayesian and Dependency networks | Integrative inference of gene networks | bnet pdf bnet ppt video1 depnet pdf depnet ppt video2 | (1) Cancer signaling and DBN; (2) Greenfield et al |
| 1-Oct | | Information theoretic methods | Inferring networks from scRNAseq | pdf ppt video | (1) PIDC; (2)SCENIC |
| 6 | 6-Oct | Context-specificity and dynamics of networks | Dynamical models | Representing dynamics in molecular networks | pdf ppt video | Active subgraphs |
| 8-Oct | | I/O Hidden Markov Models | Integrating TF-DNA interactions with time-series | pdf ppt video | DREM |
| 7 | 13-Oct | | Multi task learning | Tissue-specific networks | pdf ppt video | GNAT |
| 15-Oct | | Non-stationary Dynamic Bayesian networks | | pdf ppt video | nsDBNs |
| 8 | 20-Oct | Topological properties of graphs | Degree distribution; modularity; motifs | Finding modules and communities in graphs | pdf ppt video | Barabasi et al; Newman Girvan modularity |
| 22-Oct | | Finding modules | Graph clustering | pdf ppt video | Louvain |
| 9 | 27-Oct | | Applications of graph clustering | | pdf ppt video | DREAM module detection challenge |
| 29-Oct | Comparing graphs | Graph alignment | Aligning protein-protein interaction networks | pdf ppt video | (1) PathBLAST (2) Sharan et al |
| 10 | 3-Nov | | Spectral methods for graph alignment | | pdf ppt video | IsoRank |
| 5-Nov | | Matrix factorization based alignment | | pdf ppt video | FUSE |
| 11 | 10-Nov | | Graph alignment | Integration of scRNA-seq datasets | pdf ppt video | SCANORAMA LIGER |
| 12-Nov | | Graph alignment | Integration of single cell omic datasets | pdf ppt materials | Hands on session by Erika Da-Inn Lee |
| 12 | 17-Nov | Network based data integration and intepretation | Graph kernels for node prioritization | Disease gene prediction/gene and module prioritization | pdf ppt | Walking the Interactome |
| 19-Nov | | Heat kernel and subgraph identification | Application to cancer genomics | pdf ppt video | HOTNET |
| 13 | 24-Nov | Representation learning in networks | Network embedding | | pdf ppt video | (1)OhmNet; (2) Mashup |
| 14 | 1-Dec | | Graph neural networks | | pdf ppt | Guest lecture by Prof. Gitter |
| 3-Dec | Projects | Project presentations | | | |
| 15 | 8-Dec | | Project presentations | | | |
| 10-Dec | | Project presentations | | | |