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Computer Science Dept.
University of Tübingen
 
 

Seminar: Netzwerke in der Systembiologie

Dozent Jochen Supper, Adrian Schröder
Sprechstunde n.V. (vorher anrufen oder per E-Mail)
Zeit
Umfang 2 SWS
Beginn 13.12.2008, 9:00 Uhr
Vorbesprechung Dienstag 23.10.2007, 14:15
Ort Wird noch bekannt gegeben
Turnus unregelmäßig

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

  • Für die Erstellung der Ausarbeitung mit Word97/2000 gibt es hier eine Stilvorlage (Word97-Format, 27kB).
  • Wenn Sie eine andere Textverarbeitung bevorzugen, orientieren Sie sich bitte an diesem Muster (PDF-Format, 13kB).
  • Für Latex-Fans gibt es einen Style mit kleiner Demo.


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