Restrictions: The course is restricted to students in COE programs, but the instructor is happy to request an override to allow non-COE students to register. Please reach out to Stephen Ramsey by email.

				# pages	plan for notebooks
class01	Part 1: network fundamentals	Course organization and policies; using JupyterHub	syllabus		notebook 2
class02		Graph fundamentals and data structures	Newman 6.intro, 6.1, 6.2, 6.3, 6.4, 6.7, 9.intro, 9.1, 9.2, 9.3, 9.4, 9.5, 9.6	39	notebooks 3-5
class03		Degree & degree distribution; scalefree networks; attack tolerance	Newman 6.9, 7.intro, 7.1, 8.3, 8.4, 10.intro, 10.1, 5.1.2, Jeong et al. Nature v411 pp41-42 (2001).	20	notebook 6
class04		Clustering coefficients, density	Newman 7.9, 8.6, 10.2, 5.1.3, Potapov et al. Genome Inform. v16(2) pp 270-274 (2005).	20	notebook 7
class05		Paths, geodesic paths, diameter, components, depthfirst	Newman 6.10, 6.11, 8.intro, 8.1, 5.intro, 5.1.1	20	notebook 8
class06		Single-vertex shortestpaths (Breadth-First); Dijkstras algorithm	Newman 8.2, 10.3, Jeong et al., Nature v407 pp651-654 (2000).	17	notebook 9
class07		Centralities	Newman 7.2, 7.3, 7.4, 7.6, 8.5,	17	notebooks 10, 12
class08		Betweenness centrality	Newman 7.7, 10.3.6, Poulo Joy et al., J Biomed Biotechnol v2 pp96-103 (2005).	19	notebook 11
class09		similarity, topological overlap, assortative mixing, degree correlations (without GO)	Newman 7.12, 7.13, 8.7	21	notebook 13
class10		graph partitioning for community detection; date hubs, party hubs	Newman 11.2, 11.11, Raval 8.2.2, Han et al. Nature v430 pp88-93 (2004)	19	notebook 17
class11	Part 2: network inference	Predicting protein-protein interactions	Raval 3.5, 3.6	17
class12		Inferring PPI, naïve bayes	Raval 5.6; Rhodes et al. PLOS Comp Biol v23, n8 2005.	14
class13		correlation networks	Junker & Schreiber Chapter 13 (2008).	17	notebook 19
class14		partial correlation	de la Fuente et al., Bioinformatics v20, n18, pp3565-3574 (2004)	10	notebook 20
class15		mutual information	Raval 3.1, 3.2, 3.3, 3.4; Basso et al. Nat Genet v37 n4 pp382-390 (2005)	24	notebook 21
class16		bayesian network, MCMC	Sachs et al., Science v308 pp523-529 plus supplement (2005).	14
class17		Dynamic Bayesian network	Raval 3.4; Rangel et al., Bioinformatics v20, n9, pp1361-1372 (2004).	22	notebook 26
class18	Part 3: network analysis	markov clustering	Raval 5.4; Krogan et al. Nature v440 pp637-643 (2006).	24	notebook 14
class19		cliques/cores, MCODE	Newman 7.8, Bader & Hogue BMC Bioinform. v4 pp1-27 (2003).	15	notebook 15
class20		boolean network, attractors, dynamical simulation	Raval 6.4; Li et al. PNAS v101 n14 pp4781-4786 (2004)	17	notebook 27

CS446/546, Networks in Computational Biology, Winter 2023