Week Date Major Topic Computational concepts Biological application Slides Reading Lecturer
1 8-Sep Class overview What is Network Biology pptx pdf molbio_graphtheory_background probability_background 1. Molecules of life 2. Topology of molecular networks Profs. Roy/Gitter
2 13-Sep Representing and learning networks from data Introductory concepts of graphs and PGMs Representing gene regulatory networks pptx pdf (1) Friedman et al (2) Sparse candidate (3) Markowetz and Spang (optional) Prof. Roy
15-Sep Learning directed PGMs from data Gene network inference with and without priors pptx pdf (1) Werhli et al (2) Cancer signaling and DBN Prof. Roy
3 20-Sep Learning directed PGMs from data and priors pptx pdf Prof. Roy
22-Sep Learning dependency networks from data Linear and tree models for GRNs pptx pdf (1) GENIE3 (2) Inferelator Prof. Roy
4 27-Sep GGMs and multi-task learning Prof. Roy
29-Sep Recent advances in graph learning single cell GRNs and causality Prof. Roy
5 4-Oct Deep learning in network biology Network embedding/Representation learning Prof. Gitter
6-Oct Graph convolutional networks Prof. Gitter
6 11-Oct Graph convolutional networks Predicting protein interfaces Prof. Gitter
13-Oct Perturbations and GNNs Prof. Gitter
7 18-Oct GANs and graph generative models Prof. Gitter
20-Oct GANs and graph generative models Representing molecules Prof. Gitter
8 25-Oct Graph topology and modules Degree distributions and modules Organizational properties of networks Prof. Roy
27-Oct Spectral and Louvain clustering Modules on graphs Prof. Roy
9 1-Nov GNN methods for module finding Prof. Roy/Gitter
3-Nov Dynamic modules Prof. Roy
10 8-Nov Network-based data integration and interpretation Graph kernels for node prioritization Finding important genes of process/disease Prof. Gitter
10-Nov Graph diffusion Finding patient/disease pathways in cancer Prof. Gitter
11 15-Nov Data integration using networks: Steiner forests Integrating data from small samples Prof. Gitter
17-Nov Data integration using networks Integrating data from large samples Prof. Gitter
12 22-Nov Graph alignment Spectal and matrix factorization based alignment Aligning protein-protein interaction networks Prof. Roy
24-Nov Thanksgiving
13 29-Nov Graph alignment of single cell datasets Aligning and integrating single cell omic datasets Prof. Roy
1-Dec Dana Pe'er seminar
14 6-Dec Projects
8-Dec Projects
15 13-Dec Projects