Algorithmen in der Systembiologie SS 2010

Max Planck Institute for Molecular Genetics - Ihnestraße 63-73 - 14195 Berlin - Germany -
Phone: (+49 30) 8413 1150 - Fax: (+49 30) 8413 1394

Algorithmen in der Systembiologie (P3)

In Zusammenarbeit mit Prof. Bockmayr.

Overview of topics for exam preparation

Datum	Veranstaltung	Vortragende	Themen
19. April	Vorlesung	Roland Krause	Protein-Protein Interaktionen
19. April	Seminar	Kersten Döring Christian Hoppe	Protein-Protein Interaktionen
10. Mai	Vorlesung	Martin Vingron	Genexpression I
10. Mai	Seminar	Corinna Blasse Sebastian Thieme	Genexpression
14. Mai	Vorlesung	Martin Vingron	Genexpression II (Skript Pape)
17. Mai	Vorlesung	Martin Vingron	Regulatorische Netze I
17. Mai	Seminar	Max Homilius John Wiedenhoeft	Vergleich von Netzen
21. Mai	Übungen	Roland Krause	Exercise . Solution FDR and MCMC.
24. Mai	Pfingstmontag
28. Mai	Vorlesung	Ina Koch	Petrinetze Materialien zur VL
31. Mai	Vorlesung	Martin Vingron	Regulatorische Netze II
31. Mai	Seminar	(Bockmayr)	Constraint-based modeling
4. Juni	Übung	Roland Krause	Exercise
7. Juni	Vorlesung	Matteo Pardo	Clustering
7. Juni	Seminar	Svenja Specovius Sabrina Krakau	Clustering
11. Juni	Vorlesung	Matteo Pardo	Classification and Feature Selection
14. Juni	Seminar	Christoph Standfuß Nicolas Balcazar	Bi-clustering

Tusher, V. G., Tibshirani, R. & Chu, G. Significance analysis of microarrays applied to the ionizing radiation response. PNAS 98, 5116-5121 (2001) >
Noble, W. S. How does multiple testing correction work? Nature biotechnology 27, 1135-1137 (2009)

Date hubs and party hubs - phenomenon or artifact

Han, J.-D. D. et al. Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature 430, 88-93 (2004).
Batada, N. N. et al. Stratus not altocumulus: a new view of the yeast protein interaction network. PLoS biology 4, e317+ (2006). (A "different view" on hubs)

2 publications plus discussion

Markov Chain Clustering (MCL)
Enright, A. J., Van Dongen, S. & Ouzounis, C. A. An efficient algorithm for large-scale detection of protein families. NAR 30, 1575-1584 (2002)
Slonim, N., Atwal, G. S. S., Tkacik, G. & Bialek, W. Information-based clustering. PNAS. 102, 18297-18302 (2005).

Tanay, A., Sharan, R., Kupiec, M. & Shamir, R. Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data. PNAS 101, 2981-2986 (2004).
Ihmels, J., Bergmann, S. & Barkai, N. Defining transcription modules using large-scale gene expression data. Bioinformatics 20, 1993-2003 (2004).

Scott, J., Ideker, T., Karp, R. M. & Sharan, R. Efficient algorithms for detecting signaling pathways in protein interaction networks. Journal of computational biology 13, 133-144 (2006).
Berg, J. & Lässig, M. Cross-species analysis of biological networks by bayesian alignment. PNAS 103, 10967-10972 (2006).

Last update 2010-02-09