Schedule

Week Date Topic Paper Notes Deliverables
1 9/3/15 Class overview  Lecture (pdf)
2 9/8/15 Introduction to Network Biology Lecture (powerpoint)
9/10/15  Expression-based network inference Lecture (pdf till slide 33)
3 9/15/15 Lecture (pdf from slide 34)
9/17/15 Integrative network reconstruction Prior-based data integration  slides Lecture/Discussion
4 9/22/15 Physical module networks  slides Lecture/Discussion
9/24/15 MEDUSA MouseNET/BioPixie slides Discussion
5 9/29/15 Dynamics and context-specificity in networks Active subgraphs slides Discussion  Critique 1
10/1/15 Dynamic Bayesian networks slides Discussion
6 10/6/15 DREM/SDREM Guest lecture by Prof. Anthony Gitter Proposal due
10/8/15 SMARTS slides Discussion
7 10/13/15 Network comparisons PathBlast slides Discussion Critique 2
10/15/15 IsoRank  slides Discussion
8 10/20/15 LocalAli slides Discussion   Final Proposal due
10/22/15 Data integration using networks Simultaneous clustering of multiple networks  slides Discussion  Critique 3
9 10/27/15 Similarity Network Fusion slides Discussion
10/29/15 Prize collecting Steiner tree slides Discussion
10 11/3/15 Clustering/Modules in networks MATISSE slides Discussion  Critique 4
11/5/15 Hierarchical Agglomerative Clustering slides Discussion
11 11/10/15 DICER slides Discussion
11/12/15 Perturbations in networks Nested Effect models slides Lecture/Discussion  Critique 5
12 11/17/15 Dendrix slides Discussion
11/19/15 Dysregulated pathways slides Discussion
13 11/24/15 Networks for gene prioritization Random walk slides Lecture/Discussion  Critique 6
11/26/15 Thanksgiving  No class
14 12/1/15 Active Learning slides Discussion
12/3/15 GeneMania slides Discussion
15 12/8/15 Project presentations  Critique 7
12/10/15 Project presentations
16 12/15/15 Project presentations
12/18/15 Final Report Due by Email