| 1 |
9/6/16 |
Class Overview |
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pdf |
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9/8/16 |
Background in graph theory; probability theory |
Molecular networks |
pdf ppt |
Life and its molecules |
| 2 |
9/13/16 |
Graph structure learning |
Regulatory network inference |
pdf ppt |
Markowetz & Spang |
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9/15/16 |
Bayesian networks and its variants |
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lecture 3b (pdf ppt) lecture 4 (pdf ppt) |
(1) Friedman et al (2) Segal et al |
| 3 |
9/20/16 |
Module networks |
Regulatory network inference |
lecture 4 (pdf ppt) |
Segal et al |
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9/22/16 |
Dependency networks |
Regulatory network inference |
lecture 5 (pdf ppt) |
Huynh-Thu et al. |
| 4 |
9/27/16 |
Constrained structure learning |
Integrative network inference |
lecture 6 (pdf ppt) |
Novershtern et al. |
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9/29/16 |
Class rescheduled to Oct 3rd |
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10/3/16 |
PGMs with priors |
Incorporating prior knowledge to infer networks |
lecture 7 (pdf ppt) |
Werhli et al. |
| 5 |
10/4/16 |
PGMs with priors |
Incorporating prior knowledge to infer networks |
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10/6/16 |
PGMs with priors: regularized regression |
Incorporating prior knowledge to infer networks |
lecture 8 pdf ppt |
Greenfield et al |
| 6 |
10/11/16 |
PGMs with priors |
Incorporating prior knowledge to infer networks |
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10/13/16 |
Dynamics in networks |
Context-specific and dynamic network learning |
lecture 9 pdf ppt |
Active subgraphs |
| 7 |
10/18/16 |
Dynamic Bayesian networks |
Cancer signaling networks |
lecture 10 pdf ppt |
Hill et al. |
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10/20/16 |
Graphical Gaussian models; Multi-task learning |
Tissue-specific networks |
lecture 11 pdf ppt |
Pierson et al. |
| 8 |
10/25/16 |
Hidden Markov models and I/O HMMs introduction |
Dynamic regulatory networks |
pdf ppt |
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10/27/16 |
IOHMM contd |
Dynamic regulatory network |
pdf ppt |
Ernst et al |
| 9 |
11/1/16 |
IOHMM wrap-up. Intro to Hierarchical agglomerative clustering |
Protein network module detection |
pdf ppt |
Park et al. |
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11/3/16 |
HAC and Spectral clustering |
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pdf ppt |
Park et al. |
| 10 |
11/8/16 |
Class rescheduled to Nov 14 |
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11/10/16 |
Spectral clustering |
Integrating different data types with graphs |
pdf pptx |
Wang et al |
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11/14/16 |
Seeding scoring and searching subnetworks |
Jointly activated sub networks |
pdf pptx |
Ulitsky et al |
| 11 |
11/15/16 |
Graph alignment: Pairwise pathway alignment |
Comparative analysis of networks |
pdf pptx |
Kelley et al Sharan et al |
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11/17/16 |
Global network alignment with IsoRank |
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pdf pptx |
Singh et al |
| 12 |
11/22/16 |
Global network alignment with FUSE |
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pdf pptx |
Gligorijević et al |
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11/24/16 |
Thanksgiving. No class |
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| 13 |
11/29/16 |
Random walks and graph diffusion |
Network-based gene prioritization |
pdf pptx |
Kohler et al |
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12/1/16 |
Heat diffusion kernel |
Detecting significantly mutated pathways |
pdf pptx |
Vandin et al |
| 14 |
12/6/16 |
Nested effect factor graph models |
Identifying networks from genetic perturbations |
pdf pptx |
Vaske et al |
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12/8/16 |
Project presentations |
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| 15 |
12/13/16 |
Project presentations |
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12/15/16 |
Project presentations |
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