Schedule

Week	Date	Major Topic	Computational concepts	Biological application	Slides	Reading	Lecturer
1	5-Sep	Class overview			pdf ppt		Prof. Roy
2	10-Sep	Background	Graph theory	Mol. Bio concepts	ppt pdf notes	(1)Life and its molecules (2)Topology of molecular networks	Prof. Roy
	12-Sep		Probability theory		ppt pdf		Prof. Roy
3	17-Sep	Representing and learning networks from data	Bayesian network	Gene network inference	ppt pdf	(1) Markowetz and Spang;(2)Friedman et al;(3) Segal et al	Prof. Roy
	19-Sep		Bayesian networks	Gene network inference	ppt pdf		Prof. Roy
4	24-Sep		Gaussian Graphical models	Gene network inference	ppt pdf		Prof. Roy
	26-Sep		Dependency networks	Gene network inference	ppt pdf	GENIE3	Prof. Roy
5	1-Oct		Incorporating priors in Bayesian networks	Integrative network inference	ppt pdf	(1)Werhli and Husmeier (2)Hill et al	Prof. Roy
	3-Oct		Incorporating priors in Dependency nets		ppt pdf	Greenfield et al	Prof. Roy
6	8-Oct	Context-specificity and dynamics of networks	Dynamic models & non-stationary DBNs	Representing dynamics in molecular networks/development	pptx pdf	Robinson & Hartemink	Prof. Gitter
	10-Oct		I/O Hidden Markov Models	Integrating TF-DNA interactions with time-series expression	pptx pdf	Ernst et al	Prof. Gitter
7	15-Oct		I/O Hidden Markov Models	Integrating TF-DNA interactions with time-series expression	notes		Prof. Gitter
	17-Oct		Multitask learning & GGMs	Tissue-specific networks	pptx pdf	Pierson et al	Prof. Gitter
8	22-Oct	Graph clustering and alignment	Properties of graphs: degree; motifs; modules	Finding modules/communities in graphs	pptx pdf		Prof. Roy
	24-Oct		Spectral clustering		pptx pdf	Choobdar et al	Prof. Roy
9	29-Oct		Matrix factorization based methods for graph alignment	Alignment of protein-protein interaction networks	pptx pdf	FUSE	Prof. Roy
	31-Oct		Matrix factorization based methods	Alignment/comparison of single cell datasets	pptx pdf	(1)LIGER (2)CONOS (3)SCANORAMA (4)Seurat3	Prof. Roy
10	5-Nov		Hands on session on matrix factorization	Analysis of single cell RNA-seq datasets	Code		Erika Da-Inn Lee (guest lecture)
	7-Nov	Network-based interpretation and integration of datasets	Graph diffusion and random walks	Disease gene prediction/gene prioritization	pptx pdf	GeneWanderer	Prof. Gitter
11	12-Nov		Heat kernel and subgraph identification	Data interpretation	pptx pdf	HotNet	Prof. Gitter
	14-Nov		Steiner forest/integer programs	Data integration	pptx pdf	(1)Omics Integrator (2)ILP	Prof. Gitter
12	19-Nov	Deep learning in network biology	Graph convolutional neural networks	Protein-protein and protein-ligand interactions	pptx pdf	Wu et al	Prof. Gitter
	21-Nov		Graph convolutional neural networks	Protein-protein and protein-ligand interactions	pptx pdf		Prof. Gitter
13	26-Nov		Graph generation	Synthetic biology	pptx pdf	MolGAN	Prof. Gitter
14	3-Dec	Projects
	5-Dec	Projects
15	10-Dec	Projects