Week Date Major Topic Computational concepts Biological application Slides Reading Lecturer
1 9-Sep Class overview ppt pdf Profs. Roy/Gitter
2 14-Sep Background Graph theory Molecular networks ppt pdf (1) Life and its molecules; (2) Topology of molecular networks Prof. Roy
16-Sep Probability theory pptx pdf Prof. Gitter
3 21-Sep Representing and learning networks from data Bayesian network Gene network inference ppt pdf (1) Markowetz and Spang (optional) (2) Friedman et al (3) Sparse candidate Prof. Roy
23-Sep Dependency networks Gene network inference ppt1 pdf1 ppt2 pdf2 (1) Module networks (2) GENIE3 Prof. Roy
4 28-Sep Incorporating priors in Bayesian networks Integrative network inference ppt pdf (1) Werhli et al (2) Cancer signaling and DBN Prof. Roy
30-Sep Incorporating priors in Dependency networks Integrative network inference ppt pdf (1) Inferelator (2) (optional) iRafNet Prof. Roy
5 5-Oct Network inference with single cell data ppt pdf (1) PIDC; (2)SCENIC Prof. Roy
7-Oct Context-specificity and dynamics of networks Dynamic models & non-stationary DBNs Representing dynamics in molecular networks/development pptx pdf nsDBN Prof. Gitter
6 12-Oct I-O Hidden Markov Models Integrating TF-DNA interactions with time-series expression pptx pdf notes DREM Prof. Gitter
14-Oct I-O Hidden Markov Models Prof. Gitter
7 19-Oct Multi-task learning & GGMs Tissue-specific networks pptx pdf GNAT Prof. Gitter
21-Oct Deep learning in network biology Network embedding and representation learning Gene function prediction pptx pdf (1) Representation learning review (2) node2vec Prof. Gitter
8 26-Oct Graph neural networks 1 Protein-protein and protein-ligand interactions pptx pdf (1) Distill intros (2) Wu et al Prof. Gitter
28-Oct Graph neural networks 2 Drug discovery pptx pdf Prof. Gitter
9 2-Nov Graph generation Synthetic biology pptx pdf MolGAN Prof. Gitter
4-Nov Topological properties of graphs Degree distribution, modularity motifs Design principles of biological networks pptx pdf (1) Barabasi and Oltvai review (2) Girvan-Newman Algorithm Prof. Roy
10 9-Nov Spectral and Louvain clustering Finding modules in networks pptx pdf (1) Louvain clustering (2) Module detection challenge Prof. Roy
11-Nov Dynamic network modules pptx pdf Prof. Roy
11 16-Nov Graph alignment Spectral methods for alignment Alignment of Protein-protein interaction networks pptx pdf (1) PathBLAST (2) IsoRank Prof. Roy
18-Nov Matrix factorization based alignment Alignment of Protein-protein interaction networks pptx pdf FUSE Prof. Roy
12 23-Nov Graph alignment for single cell datasets Integrating scOmics data pptx pdf (1) SCANORAMA (2) LIGER Prof. Roy
25-Nov Thanksgiving
13 30-Nov Network-based interpretation and integration of datasets Graph diffusion and random walks Disease gene prediction/gene prioritization pptx pdf GeneWanderer Prof. Gitter
2-Dec Graph diffusion Interpreting cancer mutations pptx pdf HotNet Prof Gitter
14 7-Dec Steiner forest/integer programs Data integration pptx pdf (1) Omics Integrator (2) ILP Prof. Gitter
9-Dec Projects
15 14-Dec Projects