Week Date Major Topic Computational concepts Biological application Slides Reading
1 3-Sep Class overview pdf ppt video
2 8-Sep Background Graph theory Molecular biology concepts pdf ppt video (1) Life and its molecules; (2) Topology of molecular networks
10-Sep Probability theory pdf ppt video
3 15-Sep Representing and learning molecular networks from data Bayesian networks Gene network inference pdf ppt video (1) Markowetz and Spang (2) Friedman et al (3) Sparse candidate
17-Sep Bayesian networks Learning modular networks pdf ppt video Module networks
4 22-Sep Dependency networks pdf ppt video GENIE3
24-Sep Incorporating priors in Bayesian networks Integrative inference of regulatory networks pdf ppt video Werhli et al
5 29-Sep Priors in Bayesian and Dependency networks Integrative inference of gene networks bnet pdf bnet ppt video1 depnet pdf depnet ppt video2 (1) Cancer signaling and DBN; (2) Greenfield et al
1-Oct Information theoretic methods Inferring networks from scRNAseq pdf ppt video (1) PIDC; (2)SCENIC
6 6-Oct Context-specificity and dynamics of networks Dynamical models Representing dynamics in molecular networks pdf ppt video Active subgraphs
8-Oct I/O Hidden Markov Models Integrating TF-DNA interactions with time-series pdf ppt video DREM
7 13-Oct Multi task learning Tissue-specific networks pdf ppt video GNAT
15-Oct Non-stationary Dynamic Bayesian networks pdf ppt video nsDBNs
8 20-Oct Topological properties of graphs Degree distribution; modularity; motifs Finding modules and communities in graphs pdf ppt video Barabasi et al; Newman Girvan modularity
22-Oct Finding modules Graph clustering pdf ppt video Louvain
9 27-Oct Applications of graph clustering pdf ppt video DREAM module detection challenge
29-Oct Comparing graphs Graph alignment Aligning protein-protein interaction networks pdf ppt video (1) PathBLAST (2) Sharan et al
10 3-Nov Spectral methods for graph alignment pdf ppt video IsoRank
5-Nov Matrix factorization based alignment pdf ppt video FUSE
11 10-Nov Graph alignment Integration of scRNA-seq datasets pdf ppt video SCANORAMA LIGER
12-Nov Graph alignment Integration of single cell omic datasets pdf ppt materials Hands on session by Erika Da-Inn Lee
12 17-Nov Network based data integration and intepretation Graph kernels for node prioritization Disease gene prediction/gene and module prioritization pdf ppt Walking the Interactome
19-Nov Heat kernel and subgraph identification Application to cancer genomics pdf ppt video HOTNET
13 24-Nov Representation learning in networks Network embedding pdf ppt video (1)OhmNet; (2) Mashup
14 1-Dec Graph neural networks pdf ppt Guest lecture by Prof. Gitter
3-Dec Projects Project presentations
15 8-Dec Project presentations
10-Dec Project presentations