Seminar: Netzwerke in der Systembiologie

Beschreibung:
In diesem Seminar werden aktuelle Forschungsthemen der Modellierung und Rekonstruktion von biologischen Netzwerken behandelt.

Teilnehmende halten ein Referat auf Deutsch oder Englisch (45min + 15min Diskussion) und erstellen eine schriftliche Ausarbeitung (ca. 15-20 Seiten entsprechend der unten angegebenen Stilvorlage).

Themen und Termine

Datum	Thema	Betreuung	Referent(in)
13.12.2007	High-throughput Screens: Microarray, Proteomics, Fluorescence Microscopy [1][2][3]	A. Schröder	Andrea Sprecher
13.12.2007	Protein-Protein-Interactions [4][5]	J. Supper	Eichner Jonas
13.12.2007	Metabolic Flux Analysis [12]	A. Schröder	Carolina Russo
13.12.2007	Pathway Databases: KEGG, BioCyc [6][7]	J. Supper	Jörg Vetter
14.12.2007	Metabolic Pathway Prediction [10][11]	A. Schröder	Jasmin Kuttner
14.12.2007	Automated Reconstruction of Signaling Networks [13]	J. Supper	Johannes Wollnik
14.12.2007	Robustness of Biological Networks [14][15][16]	A. Schröder	Marina Müller
14.12.2007	The Inferelator: an algorithm for learning parsimonious regulatory networks [19]	J. Supper	Clemens Wrzodek
14.12.2007	Synthetic Biology [21][22][23]	A. Schröder	Uszkoreit Julian

Voraussetzungen:
ab 5. Semester 

Literatur:

[1]	Pepperkok, R. and Ellenberg, J., High-throughput fluorescence microscopy for systems biology, Nat Rev Mol Cell Biol, 2006, 7, 690-696
[2]	Love, D. R., Pichler, F. B., Dodd, A., Copp, B. R., & Greenwood, D. R., Technology for high-throughput screens: the present and future using zebrafish, Current Opinion in Biotechnology, 2004, 15, 564-571
[3]	Stekel, D., Microarray Bioinformatics, Cambridge University Press, 2003
[4]	von Mering, C. and Jensen, L. J. and Snel, B. and Hooper, S. D. and Krupp, M. and Foglierini, M. and Jouffre, N. and Huynen, M. A. and Bork, P., STRING: known and predicted protein-protein associations, integrated and transferred across organisms, Nucl. Acids Res., 2005, 33, D433-437
[5]	Shayantani Mukherjee, Sampali Bal & Partha Saha, Protein interaction maps using yeast two-hybrid assay, CURRENT SCIENCE, 2001, 81, 458-464
[6]	Kanehisa, M. and Goto, S. and Hattori, M. and Aoki-Kinoshita, K. F. and Itoh, M. and Kawashima, S. and Katayama, T. and Araki, M. and Hirakawa, M., From genomics to chemical genomics: new developments in KEGG, Nucl. Acids Res., 2006, 34, D354-357
[7]	http://biocyc.org/intro.shtml
[8]	H. Kitano, A. Funahashi, Y. Matsuoka, and K. Oda. Using process diagrams for the graphical representation of biological networks. Nature Biotechnology, 23(8):961–966, August 2005.
[9]	Strömbäck, L., A method for comparison of standardized information within systems biology, WSC '06: Proceedings of the 38th conference on Winter simulation, Winter Simulation Conference, 2006, 1603-1610
[10]	Pedro Romero, Jonathan Wagg, Michelle L Green, Dale Kaiser, Markus Krummenacker & Peter D Karp, Computational prediction of human metabolic pathways from the complete human genome, Genome Biology, 2004, 6
[11]	Francke, C.; Siezen, R. J. & Teusink, B., Reconstructing the metabolic network of a bacterium from its genome, Trends in Microbiology, 2005, 13, 550-558
[12]	Sauer, U., Metabolic networks in motion: 13C-based flux analysis, Mol Syst Biol, 2006, 2
[13]	M. Steffen, A. Petti, J. Aach, P. D'haeseleer, and G. Church. Automated modelling of signal transduction networks. BMC Bioinformatics, 3:34, Nov 2002.
[14]	Kitano H, O. K., Robustness trade-offs and host-microbial symbiosis in the immune system, Mol Syst Biol, 2006, 2
[15]	Kitano, H., Biological robustness, Nature Reviews Genetics, 2004, 5, 826-837
[16]	Ma, L. and Iglesias, P. A., Quantifying robustness of biochemical network models, BMC Bioinformatics, 2002, 3:38
[17]	Oikonomou, P. & Cluzel, P., Effects of topology on network evolution, Nature Physics, 2006, 2, 532
[18]	Demetrius, L. & Manke, T., Robustness and network evolution - an entropic principle, Physica A: Statistical and Theoretical Physics, 2005, 346, 682-696
[19]	Bonneau, R. and Reiss, D. and Shannon, P. and Facciotti, M. and Hood, L. and Baliga, N. and Thorsson, V., The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo, Genome Biol, 2006, 7:5
[20]	Reiss, D. J. and Baliga, N. S. and Bonneau, R., Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks, BMC Bioinformatics, 2006, 7
[21]	Rai, A. and Boyle, J., Synthetic Biology: Caught between Property Rights, the Public Domain, and the Commons. PLoS Biol, 2007, 5
[22]	Benner, S. A. and Sismour, A. M., Synthetic biology, Nature Reviews Genetics, 2005, 533-543
[23]	Heinemann, M. and Panke, S., Synthetic biology - putting engineering into biology, Bioinformatics, 2006, 22, 2790-2799

Bemerkungen: 
Besonders geeignet für Studierende der Bioinformatik. 

Stilvorlage

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