| 1 |
5-Sep |
Class overview |
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What is Network Biology |
pptx pdf |
1. Molecules of life 2. Topology of molecular networks 3. Current and Future Directions in Network Biology |
Profs. Roy/Gitter |
| 2 |
10-Sep |
Representing and learning networks from data |
Introductory concepts of graphs and PGMs |
Representing gene regulatory networks |
pptx pdf |
(1) Friedman et al (2) Sparse candidate (3) Markowetz and Spang (optional) |
Prof. Roy |
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12-Sep |
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Learning directed PGMs from data |
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pdf pptx |
DBN and Cancer signaling |
Prof. Roy |
| 3 |
17-Sep |
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Extensions to directed PGMs |
Modeling cycles; time; TF activities and prior knowledge |
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Prof. Roy |
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19-Sep |
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Prof. Roy |
| 4 |
24-Sep |
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Causal graph learning |
Causal GRNs |
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Prof. Roy |
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26-Sep |
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Prof. Roy |
| 5 |
1-Oct |
Deep learning in network biology |
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Prof. Gitter |
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3-Oct |
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Prof. Gitter |
| 6 |
8-Oct |
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Prof. Gitter |
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10-Oct |
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Prof. Gitter |
| 7 |
15-Oct |
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Prof. Gitter |
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17-Oct |
Analysis of graphs |
Degree distribution; clusters/modules and motifs |
Design principles of biological networks |
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Spencer Halberg & Erika Lee |
| 8 |
22-Oct |
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Graph clustering |
Finding modules in graphs |
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Prof. Roy |
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24-Oct |
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Unsupervised Representation learning |
Task agnostic graph analysis |
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Prof. Roy |
| 9 |
29-Oct |
Graph alignment |
Spectral and matrix factorization alignment |
Aligning protein-protein interactions |
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Prof. Roy |
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31-Oct |
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Aligning single cell omic datasets |
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Prof. Roy |
| 10 |
5-Nov |
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Alignment continued |
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Prof. Roy |
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7-Nov |
Network-based integration and interpretation |
Graph kernels for node prioritization |
Finding important genes of a process/disease |
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Prof. Gitter |
| 11 |
12-Nov |
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Graph diffusion |
Finding patient/disease pathways associated with cancer |
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Prof. Gitter |
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14-Nov |
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Graph diffusion |
More interpretation |
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Prof. Gitter |
| 12 |
19-Nov |
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Data integration using networks: Steiner forests |
Integrating data from small samples |
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Prof. Gitter |
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21-Nov |
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Data integration using networks: SNF |
Integrating data from large samples |
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Prof. Gitter |
| 13 |
26-Nov |
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More integration |
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Prof. Gitter |
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28-Nov |
Thanksgiving |
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| 14 |
3-Dec |
Projects |
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5-Dec |
Projects |
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| 15 |
10-Dec |
Projects |
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