Algorithmen in der Systembiologie SS 2011

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
11. April	Vorlesung	Martin Vingron	Gene expression (Skript Pape)
11. April	Seminar	Daniel Pommer Jörn Bethune	Genexpression

15. April	Vorlesung	Martin Vingron	Information theory and networks
18. April	Vorlesung	Roland Krause	Protein protein interactions
18. April	Seminar	Franzi Metge Jan Josten	Protein-Protein Interaktionen
29. April	Übungen	Roland Krause	U1
2. Mai	Vorlesung	Julia Lasserre	Unsupervised learning
2. Mai	Seminar	Aileen Chefai Anke Penzlin	Clustering
6. Mai	Vorlesung	Julia Lasserre	Supervised learning
9. Mai	Vorlesung	Julia Lasserre	Graphical models
13. Mai	Übungen	Julia Lasserre	U2 Solution

Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell. 9(12):3273-97. (1998)
de Lichtenberg U, Jensen LJ, Fausbøll A, Jensen TS, Bork P, Brunak S. Comparison of computational methods for the identification of cell cycle-regulated genes.Bioinformatics. 21(7):1164-71. (2005)

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).

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)
Frey, B.J., Dueck, D. Clustering by Passing Messages Between Data Points. Science Vol. 315 no. 5814 pp. 972-976

Last update 2011-02-03