| 1 |
6-Sep |
Class overview |
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pdf ppt |
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| 2 |
11-Sep |
Background |
Graph theory |
Molecular biology concepts |
pdf ppt notes |
(1) Life and its molecules; (2) Topology of molecular networks |
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13-Sep |
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Probability theory |
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pdf ppt prob_prac |
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| 3 |
18-Sep |
Representing and learning molecular networks from data |
Bayesian networks |
Gene network inference |
pdf ppt |
(1) Markowetz and Spang; (2) Friedman et al; (3) Segal et al |
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20-Sep |
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Bayesian networks continued |
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pdf ppt |
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| 4 |
25-Sep |
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Gaussian Graphical models |
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pdf ppt |
Graphical LASSO |
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27-Sep |
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Dependency networks |
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pdf ppt |
GENIE3 |
| 5 |
2-Oct |
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Incorporating prior into Bayesian networks |
Integrative inference of gene networks |
pdf(a) ppt(a) pdf(b) ppt(b) |
Werhli et al |
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4-Oct |
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Incorporating prior into Bayesian networks |
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pdf(b) ppt(b) |
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| 6 |
9-Oct |
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Lecture rescheduled to Oct 17th |
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11-Oct |
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Incorporating prior into Dependency networks |
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pdf ppt |
Greenfield et al. |
| 7 |
16-Oct |
Context-specificy and dynamics of networks |
Dynamical models; Skeleton network based methods |
Representing dynamics in networks |
pdf ppt |
Ideker et al |
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17-Oct |
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I/O Hidden Markov Models |
Integrating TF-DNA interactions with time-series expression |
pdf ppt video |
Ernst et al. DREM Supplement |
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18-Oct |
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I/O HMM continued |
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| 8 |
23-Oct |
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Graphical Gaussian models; Multi-task learning |
Tissue-specific networks |
pdf ppt |
Pierson et al. |
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25-Oct |
Topological properties |
Graph clustering |
Finding modules/communities in graphs |
pdf ppt |
Girvan and Newman |
| 9 |
30-Oct |
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Class rescheduled |
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1-Nov |
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Agglomerative clustering |
Hierarchical communities, link prediction |
pdf ppt |
Park et al |
| 10 |
6-Nov |
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Spectral clustering |
Finding communities on graphs |
pdf ppt |
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7-Nov |
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Spectral clustering applications |
Disease module detection, Finding TADs |
pdf ppt video |
DREAM module detection challenge |
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8-Nov |
Comparison of graphs |
Network alignment |
Conservation of subnetworks across species |
pdf ppt |
PathBLAST |
| 11 |
13-Nov |
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Spectral methods for graph alignment |
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pdf ppt |
IsoRank |
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15-Nov |
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Matrix factorization based alignment |
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pdf ppt |
FUSE |
| 12 |
20-Nov |
Network-based integration/interpretation |
Graph diffusion and walks on graphs |
Network-based gene prioritization, data imputation, smoothing of Hi-C data |
pdf ppt |
GeneWanderer |
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22-Nov |
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Thanksgiving |
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| 13 |
27-Nov |
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Heat kernel and subgraph identification |
Interpreting variants on a graph |
pdf ppt |
HOTNET |
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29-Nov |
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Information flow; matrix factorization |
Data integration and interpretation |
pdf ppt |
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| 14 |
4-Dec |
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Project presentations |
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6-Dec |
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Project presentations |
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| 15 |
11-Dec |
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Project presentations |
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