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