| 1 |
3-Sep |
Class overview |
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pdf ppt video |
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| 2 |
8-Sep |
Background |
Graph theory |
Molecular biology concepts |
pdf ppt video |
(1) Life and its molecules; (2) Topology of molecular networks |
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10-Sep |
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Probability theory |
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pdf ppt video |
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| 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 |
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17-Sep |
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Bayesian networks |
Learning modular networks |
pdf ppt video |
Module networks |
| 4 |
22-Sep |
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Dependency networks |
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pdf ppt video |
GENIE3 |
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24-Sep |
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Incorporating priors in Bayesian networks |
Integrative inference of regulatory networks |
pdf ppt video |
Werhli et al |
| 5 |
29-Sep |
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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 |
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1-Oct |
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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 |
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8-Oct |
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I/O Hidden Markov Models |
Integrating TF-DNA interactions with time-series |
pdf ppt video |
DREM |
| 7 |
13-Oct |
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Multi task learning |
Tissue-specific networks |
pdf ppt video |
GNAT |
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15-Oct |
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Non-stationary Dynamic Bayesian networks |
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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 |
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22-Oct |
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Finding modules |
Graph clustering |
pdf ppt video |
Louvain |
| 9 |
27-Oct |
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Applications of graph clustering |
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pdf ppt video |
DREAM module detection challenge |
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29-Oct |
Comparing graphs |
Graph alignment |
Aligning protein-protein interaction networks |
pdf ppt video |
(1) PathBLAST (2) Sharan et al |
| 10 |
3-Nov |
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Spectral methods for graph alignment |
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pdf ppt video |
IsoRank |
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5-Nov |
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Matrix factorization based alignment |
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pdf ppt video |
FUSE |
| 11 |
10-Nov |
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Graph alignment |
Integration of scRNA-seq datasets |
pdf ppt video |
SCANORAMA LIGER |
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12-Nov |
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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 |
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19-Nov |
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Heat kernel and subgraph identification |
Application to cancer genomics |
pdf ppt video |
HOTNET |
| 13 |
24-Nov |
Representation learning in networks |
Network embedding |
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pdf ppt video |
(1)OhmNet; (2) Mashup |
| 14 |
1-Dec |
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Graph neural networks |
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pdf ppt |
Guest lecture by Prof. Gitter |
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3-Dec |
Projects |
Project presentations |
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| 15 |
8-Dec |
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Project presentations |
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10-Dec |
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Project presentations |
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