| 1 |
5-Sep |
Class overview |
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pdf ppt |
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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 |
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12-Sep |
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Probability theory |
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ppt pdf |
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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 |
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19-Sep |
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Bayesian networks |
Gene network inference |
ppt pdf |
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Prof. Roy |
| 4 |
24-Sep |
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Gaussian Graphical models |
Gene network inference |
ppt pdf |
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Prof. Roy |
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26-Sep |
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Dependency networks |
Gene network inference |
ppt pdf |
GENIE3 |
Prof. Roy |
| 5 |
1-Oct |
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Incorporating priors in Bayesian networks |
Integrative network inference |
ppt pdf |
(1)Werhli and Husmeier (2)Hill et al |
Prof. Roy |
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3-Oct |
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Incorporating priors in Dependency nets |
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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 |
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10-Oct |
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I/O Hidden Markov Models |
Integrating TF-DNA interactions with time-series expression |
pptx pdf |
Ernst et al |
Prof. Gitter |
| 7 |
15-Oct |
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I/O Hidden Markov Models |
Integrating TF-DNA interactions with time-series expression |
notes |
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Prof. Gitter |
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17-Oct |
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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 |
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Prof. Roy |
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24-Oct |
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Spectral clustering |
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pptx pdf |
Choobdar et al |
Prof. Roy |
| 9 |
29-Oct |
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Matrix factorization based methods for graph alignment |
Alignment of protein-protein interaction networks |
pptx pdf |
FUSE |
Prof. Roy |
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31-Oct |
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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 |
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Hands on session on matrix factorization |
Analysis of single cell RNA-seq datasets |
Code |
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Erika Da-Inn Lee (guest lecture) |
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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 |
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Heat kernel and subgraph identification |
Data interpretation |
pptx pdf |
HotNet |
Prof. Gitter |
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14-Nov |
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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 |
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21-Nov |
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Graph convolutional neural networks |
Protein-protein and protein-ligand interactions |
pptx pdf |
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Prof. Gitter |
| 13 |
26-Nov |
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Graph generation |
Synthetic biology |
pptx pdf |
MolGAN |
Prof. Gitter |
| 14 |
3-Dec |
Projects |
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5-Dec |
Projects |
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| 15 |
10-Dec |
Projects |
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