| Week | Date | Major Topic | Computational concepts | Biological application | Slides | Reading | Lecturer |
|---|---|---|---|---|---|---|---|
| 1 | 5-Sep | Class overview | pdf ppt | Prof. Roy | |||
| 2 | 10-Sep | Background | Graph theory | Mol. Bio concepts | ppt pdf notes | (1)Life and its molecules (2)Topology of molecular networks | Prof. Roy |
| 12-Sep | Probability theory | ppt pdf | Prof. Roy | ||||
| 3 | 17-Sep | Representing and learning networks from data | Bayesian network | Gene network inference | ppt pdf | (1) Markowetz and Spang;(2)Friedman et al;(3) Segal et al | Prof. Roy |
| 19-Sep | Bayesian networks | Gene network inference | ppt pdf | Prof. Roy | |||
| 4 | 24-Sep | Gaussian Graphical models | Gene network inference | ppt pdf | Prof. Roy | ||
| 26-Sep | Dependency networks | Gene network inference | ppt pdf | GENIE3 | Prof. Roy | ||
| 5 | 1-Oct | Incorporating priors in Bayesian networks | Integrative network inference | ppt pdf | (1)Werhli and Husmeier (2)Hill et al | Prof. Roy | |
| 3-Oct | Incorporating priors in Dependency nets | ppt pdf | Greenfield et al | Prof. Roy | |||
| 6 | 8-Oct | Context-specificity and dynamics of networks | Dynamic models & non-stationary DBNs | Representing dynamics in molecular networks/development | pptx pdf | Robinson & Hartemink | Prof. Gitter |
| 10-Oct | I/O Hidden Markov Models | Integrating TF-DNA interactions with time-series expression | pptx pdf | Ernst et al | Prof. Gitter | ||
| 7 | 15-Oct | I/O Hidden Markov Models | Integrating TF-DNA interactions with time-series expression | notes | Prof. Gitter | ||
| 17-Oct | Multitask learning & GGMs | Tissue-specific networks | pptx pdf | Pierson et al | Prof. Gitter | ||
| 8 | 22-Oct | Graph clustering and alignment | Properties of graphs: degree; motifs; modules | Finding modules/communities in graphs | pptx pdf | Prof. Roy | |
| 24-Oct | Spectral clustering | pptx pdf | Choobdar et al | Prof. Roy | |||
| 9 | 29-Oct | Matrix factorization based methods for graph alignment | Alignment of protein-protein interaction networks | pptx pdf | FUSE | Prof. Roy | |
| 31-Oct | Matrix factorization based methods | Alignment/comparison of single cell datasets | pptx pdf | (1)LIGER (2)CONOS (3)SCANORAMA (4)Seurat3 | Prof. Roy | ||
| 10 | 5-Nov | Hands on session on matrix factorization | Analysis of single cell RNA-seq datasets | Code | Erika Da-Inn Lee (guest lecture) | ||
| 7-Nov | Network-based interpretation and integration of datasets | Graph diffusion and random walks | Disease gene prediction/gene prioritization | pptx pdf | GeneWanderer | Prof. Gitter | |
| 11 | 12-Nov | Heat kernel and subgraph identification | Data interpretation | pptx pdf | HotNet | Prof. Gitter | |
| 14-Nov | Steiner forest/integer programs | Data integration | pptx pdf | (1)Omics Integrator (2)ILP | Prof. Gitter | ||
| 12 | 19-Nov | Deep learning in network biology | Graph convolutional neural networks | Protein-protein and protein-ligand interactions | pptx pdf | Wu et al | Prof. Gitter |
| 21-Nov | Graph convolutional neural networks | Protein-protein and protein-ligand interactions | pptx pdf | Prof. Gitter | |||
| 13 | 26-Nov | Graph generation | Synthetic biology | pptx pdf | MolGAN | Prof. Gitter | |
| 14 | 3-Dec | Projects | |||||
| 5-Dec | Projects | ||||||
| 15 | 10-Dec | Projects |