CSE 591 - Analysis of biomolecular networks and their components

Topics

• Molecular Biology 1 (biochemistry, gene, protein, genotype, phenotype, biological processes, protein interactions, signal transduction, gene regulation, ..)
• Molecular Biology 2 (interaction detection methods, microarray, mRNA, miRNA, ..)
• Pharmacogenetics, -genomics, -kinetics, and -dynamics (drug metabolism, drug targets, The Druggable Genome, ..)
• Bioinformatics (alignment, ..)
• Information extraction from text (text mining, relation mining)
• Graph Theory (directionality, hypergraphs, adjacency matrices, graph traversal, ..)
• Network properties (scale free, random graph, power law, distance, small world, modulatiry, subgraphs)
• Network models (Erdös-Renyi, Watts-Strogatz, Barabasi-Albert)
• Network centralities (centrality, degree, shortest paths, closeness, betweenness, eccentricity, PageRank, HITS, ..)
• Network motifs (feed-forward loop, ..)
• Notations and markup languages (Kohn interaction maps; BioPAX, SMBL, GPML)
• Network and pathway visualization, browsing (tools: Cytoscape plugins, AliBaba, ..)
• Data sources (KEGG, BioPAX, interaction maps, ..)
• Biological networks (signal transduction, gene regulation, protein interaction, metabolic pathways)
• Selected, recent papers on biological network analysis

Tentative schedule

1. 8/27 -- Introduction
2. 9/01 -- Genes and proteins
3. 9/03 -- Biological processes
4. 9/08 -- Genotype and phenotype
5. 9/10 -- Reconstructing metabolic pathways (Shanshan Liang)
6. 9/15 -- Graph theory
7. 9/17 -- Global network properties
8. 9/22 -- Network centralities
9. 9/24 -- Class projects
10. 9/29 -- Network models
11. 10/1 -- Statistical testing; network motifs
12. 10/6 -- PTQL (Shanshan Liang)

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13. 10/08 -- Mid-term summary
14. 10/13 -- Mid-term exam

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15. 10/15 -- Network clustering
16. 10/20 -- Notations, markup languages
17. 10/22 -- Structure and function of the feed-forward loop motif
18. 10/27 -- Protein interaction detection methods
19. 10/29 -- Recent studies: "Human proteins interacting with pathogens"
20. 11/03 -- "Finding local communities in protein networks"
21. 11/05 -- "Automated pathway building in biological association networks" (Shanshan Liang / Chitta Baral)
22. 11/10 -- Student presentations: class projects; 3 slides each
23. 11/12 -- "Clustering to find functional modules and predict function -- when and how?"
24. 11/17 -- "Quantitative modeling and analysis of genetic regulatory networks"
25. 11/19 -- Petri nets & extensions

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26. 11/24 -- all student presentations moved to 12/03 => 2h, no class today

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27. 12/01 -- Summary

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28. 12/03 -- Student presentations: class projects; 10-15 min. each, 10 slides; starts at 4 p.m.!

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29. 12/08 -- Final exam

Thursday, Nov 26: Thanksgiving (observed). Depending on how many students are involved in the project meeting on Nov 19, there might be no class on this day.

Course material

There are some books I recommend for further reading. However, most deal with a specific topic only (covered on one or two days) or become useful only if you plan on working in this field (project, thesis, ...). I will bring all books into the class on the first day, so everybody can have a look at them. Most of the topics have nice Wikipedia entries, however, and you can start reading from there.