Proseminar: Einführung in die
Systembiologie
| Dozent |
C. Henneges,
A.
Schröder, A. Dräger
|
| Sprechstunde |
nach Vereinbarung
|
| Zeit |
Di., 18.00 Uhr bis 20.00 Uhr
|
| Umfang |
2 SWS |
| Beginn |
|
| Vorbesprechung |
Mi., 15.10., 14.15 Uhr, Sand 1, Raum A302
|
| Ort |
Sand 1, Raum A302
|
| Turnus |
regelmäßig |
Themen:
| Datum |
Thema |
Betreuung |
Referent(in) |
| 28.10.2008 |
1. Systembiologie - ein Überblick [1, 2, 3] |
Adrian Schröder,
Andreas Dräger,
Carsten Henneges |
Andreas Dräger |
| 04.11.2008 |
2. Modellierung und Simulation [4] |
Andreas Dräger |
Michael Ziller |
| 11.11.2008 |
3. Modellkalibrierung durch Parameteroptimierung [5, 6] |
Andreas Dräger |
Sebastian Rheinnecker |
| 18.11.2008 |
4. Standards in der Systembiologie: SBML, SBO, GO und weitere Vokabulare [9, 10] |
Andreas Dräger |
Andreas Dräger |
| 25.11.2008 |
5.Regulationsmodule: Muster in biologischen Netzwerken [19, 20] |
Carsten Henneges |
Carsten Henneges |
| 02.12.2008 |
6. Signaltransduktionsnetzwerke [21, 22] |
Adrian Schröder |
Adrian Schröder |
| 09.12.2008 |
7. Online-Datenbanken [11, 12, 13, 14, 15, 16] |
Carsten Henneges |
Andreas Schmid |
| 16.12.2008 |
8. Inferenz cis-regulatorischer Module [17] |
Adrian Schröder |
Clemens Wrzodek |
| 27.01.2008 |
9. Anwendung der Systembiologie in der Medikamentenentwicklung [23] |
Adrian Schröder |
Julian Nordt |
| 03.02.2009 |
10. Programming DNA: A 2-bit language for engineering biology,
Nachbesprechung |
Adrian Schröder,
Andreas Dräger,
Carsten Henneges |
Drew Endy |
Literaturvorschläge:
| [1] |
Lazebnik,
Y. Can a Biologist Fix a
Radio? --- or, What I Learned while Studying Apoptosis Biochemistry,
2002, 69, 1403-1406.
|
| [2] |
Systeme
des Lebens http://www.bmbf.de/pub/systembiologie.pdf, BMBF.
|
| [3] |
Kitano,
H. Systems Biology: A Brief
Overview Science, 2002, 295, 1662-1664.
|
| [4] |
Heinrich,
R. & Schuster, S. The
Regulation of Cellular Systems, Kapitel 2, Chapman and Hall, 1996.
|
| [5] |
Julio R Banga, Optimization in computational systems biology,
BMC Systems Biology, 2008
|
| [6] |
Zi, Z.
& Klipp, E. SBML-PET: a
Systems Biology Markup Language-based parameter estimation tool
Bioinformatics, 2006, 22, 2704-2705.
|
| [7] |
Chassagnole,
C.; Noisommit-Rizzi, N.;
Schmid, J. W.; Mauch, K. & Reuss, M. Dynamic Modeling of the
Central Carbon Metabolism of Escherichia coli Wiley Periodicals,
Inc., 2002, 54-73.
|
| [8] |
Gillespie,
D. T. A General Method for
Numerically Simulating the Stochastic Time Evolution of Coupled
Chemical Reactions Journal of Computational Physics, 1976, 22,
403-434.
|
| [9] |
Hucka,
M.; Finney, A.; Sauro, H. M.;
Bolouri, H.; Doyle, J. C.; Kitano, H.; Arkin, A. P.; Bornstein, B.
J.; Bray, D.; Cornish-Bowden, A.; Cuellar, A. A.; Dronov, S.; Gilles,
E. D.; Ginkel, M.; Gor, V.; Goryanin, I. I.; Hedley, W. J.; Hodgman,
T. C.; Hofmeyr, J.; Hunter, P. J.; Juty, N. S.; Kasberger, J. L.;
Kremling, A.; Kummer, U.; Le Novere, N.; Loew, L. M.; Lucio, D.;
Mendes, P.; Minch, E.; Mjolsness, E. D.; Nakayama, Y.; Nelson, M. R.;
Nielsen, P. F.; Sakurada, T.; Schaff, J. C.; Shapiro, B. E.;
Shimizu, T. S.; Spence, H. D.; Stelling, J.; Takahashi, K.; Tomita,
M.; Wagner, J. & Wang, J. The systems biology markup language
(SBML): a medium for representation and exchange of biochemical
network models Bioinformatics, 2003, 19, 524-531.
|
| [10] |
SBML.org.
|
| [11] |
Kanehisa,
M. & Goto, S. KEGG: kyoto
encyclopedia of genes and genomes. Nucleic Acids Research, 2000, 28,
27-30.
|
| [12] |
Caspi,
R.; Foerster, H.; Fulcher, C.
A.; Hopkinson, R.; Ingraham, J.; Kaipa, P.; Krummenacker, M.; Paley,
S.; Pick, J.; Rhee, S. Y.; Tissier, C.; Zhang, P. & Karp, P. D.
MetaCyc: a multiorganism database of metabolic pathways and enzymes.
Nucleic Acids Research, 2006, 34, D511-D516.
|
| [13] |
Krull,
M.; Voss, N.; Choi, C.; Pistor,
S.; Potapov, A. & Wingender, E. TRANSPATH an integrated
database
on signal transduction and a tool for array analysis Nucl. Acids
Res., 2003, 31, 97-100.
|
| [14] |
Krull,
M.; Pistor, S.; Voss, N.; Kel,
A.; Reuter, I.; Kronenberg, D.; Michael, H.; Schwarzer, K.; Potapov,
A.; Choi, C.; Kel-Margoulis, O. & Wingender, E. TRANSPATH(R):
an information resource for storing and visualizing signaling pathways
and their pathological aberrations Nucl. Acids Res., 2006, 34,
D546-551.
|
| [15] |
http://www.ingenuity.com.
|
| [16] |
http://sabio.villa-bosch.de.
|
| [17] |
Bonneau,
R.; Reiss, D. J.; Shannon, P.;
Facciotti, M.; Hood, L.; Baliga, N. S. & Thorsson, V. The
Inferelator: an algorithm for learning parsimonious regulatory
networks from systems- biology data sets de novo.
|
| [18] |
Albert,
R. Boolean Modeling of Genetic
Regulatory Networks LECTURE NOTES IN PHYSICS-NEW YORK THEN BERLIN-,
Springer, 2004, 650, 459-482.
|
| [19] |
Uri Alon,
Network motifs: theory and
experimental approaches, Nature Reviews Genetics 8, 450-461 (June
2007).
|
| [20] |
R Milo, S
Shen-Orr, S Itzkovitz, N
Kashtan, D Chklovskii & U Alon, Network Motifs: Simple Building
Blocks of Complex Networks, Science, 298:824-827 (2002).
|
| [21] |
Lauffenburger,
D. Cell signaling
pathways as control modules: Complexity for simplicity? Proceedings
of the National Academy of Sciences, 2000, 97, 5031-5033.
|
| [22] |
Sachs,
K.; Perez, O.; Pe'er, D.;
Lauffenburger, D. A. & Nolan, G. P. Causal Protein-Signaling
Networks Derived from Multiparameter Single-Cell Data Science, 2005,
308, 523-529.
|
| [23] |
Butcher,
E. C.; Berg, E. L. &
Kunkel, E. J. Systems biology in drug discovery Nat Biotech, 2004,
22, 1087-0156.
|
Stilvorlage
- Für die Erstellung der Ausarbeitung
mit
Word97/2000 gibt es hier eine Stilvorlage
(
 , 27kB).
- Wenn Sie eine andere Textverarbeitung
bevorzugen,
orientieren Sie sich bitte an diesem Muster (
 , 13kB).
- Für
 -Fans
gibt es einen Style
mit kleinem Demo.
http://www.ra.cs.uni-tuebingen.de/lehre/ws08/pro_systembio.html
© 2001-2008 University of Tübingen
|
Computer Architecture
Publications