Bibliography

1

J. Saez-Rodriguez, A. Hammerle-Fickinger, O. Dalal, S. Klamt, E. D. Gilles, C. Conradi
On the Multistability of Signal Transduction Motifs.
IET Systems Biology., in press.

2

J. Saez-Rodriguez, L. Simeoni, J. Lindquist, R. Hemenway, U. Bommhardt, B. Arndt, U. U. Haus, R. Weismantel, E. D. Gilles, S. Klamt, and B. Schraven.
A logical model provides insights into T-cell Receptor signaling.
PloS Comp. Biol., 3:8,163, 2007.
doi:10.1371/journal.pcbi.0030163

3

A. Kremling and J. Saez-Rodriguez.
Systems biology - an engineering perspective.
J. Biotechnology 129, 2:329-351, 2007.
doi:10.1186//j.jbiotec.2007.02.009.

4

J. Saez-Rodriguez*, S. Mirschel*, R. Hemenway, S. Klamt, E. D. Gilles, and M. Ginkel.
Visual set-up of logical models of signaling and regulatory networks with ProMoT.
BMC Bioinformatics, 7:506, 2006.
[*both authors contributed equally to this work].
doi:10.1186/1471-2105-7-506.

5

S. Klamt, J. Saez-Rodriguez, and E. D. Gilles.
Structural and functional analysis of cellular networks with CellNetAnalyzer.
BMC Systems Biology, 1:2, 2007.
doi:10.1186/1752-0509-1-2.

6

S. Klamt*, J. Saez-Rodriguez*, J. Lindquist, L. Simeoni, and E. D. Gilles.
A methodology for the structural and functional analysis of signaling and regulatory networks.
BMC Bioinformatics, 7:56, 2006
[*both authors contributed equally to this work].
doi:10.1186/1471-2105-7-56.

7

H. Conzelmann, J. Saez-Rodriguez, T. Sauter, B.N. Kholodenko, and E. D. Gilles.
A domain-oriented approach to the reduction of combinatorial complexity in signal transduction networks.
BMC Bioinformatics, 7:34, 2006.
doi:10.1186/1471-2105-7-34.

8

C. Conradi*, J. Saez-Rodriguez*, E.D. Gilles, and J. Raisch.
Using chemical reaction network theory to discard a kinetic mechanism hypothesis.
IEE Proc. Systems Biology, 152(4):243-248, 2005
[*both authors contributed equally to this work].
doi:10.1049/ip-syb:20050045.

9

J. Saez-Rodriguez, A. Kremling, and E. D. Gilles.
Dissecting the puzzle of life: Modularization of signal transduction networks.
Comput. Chem. Eng., 29(3):619-629, 2005.
doi:10.1016/j.compchemeng.2004.08.035.

10

H. Conzelmann, J. Saez-Rodriguez, T. Sauter, E. Bullinger, F. Allgöwer, and E. D. Gilles.
Reduction of mathematical models of signal transduction networks: Simulation-based approach applied to EGF receptor signaling.
Systems Biology, 1(1):159-169, 2004.
doi:10.1049/sb:20045011.

11

J. Saez-Rodriguez, A. Kremling, H. Conzelmann, K. Bettenbrock, and E. D. Gilles.
Modular analysis of signal transduction networks.
IEEE Contr. Syst. Mag., 24(4):35-52, 2004.
doi:10.1109/MCS.2004.1316652.
There are some minor corrections to this article ( click here)

Conference proceedings

12

C. Conradi, J. Saez-Rodriguez, E.D. Gilles, and J. Raisch.
Chemical reaction network theory- a tool for systems biology.
In F. Breitenecker I. Troch, editor, Proceedings of the 5th MATHMOD Conference, pages 2-1,2-9, Vienna, Austria, February 2006.

13

J. Saez-Rodriguez*, H. Conzelmann*, T. Sauter, B.N. Kholodenko, and E. D. Gilles.
Domain-oriented and modular approaches to the reduction of mathematical models of signaling networks.
In U. Kummer, J. Pahle, I. Surovtsova, and J. Zobeley, editors, 4th Workshop on Computation of Biochemical Pathways and Genetic Networks,
pages 13-20. Logos-Verlag Berlin, September 2005
[*both authors contributed equally to this work].

14

C. Conradi*, J. Saez-Rodriguez*, E.D. Gilles, and J. Raisch.
Using chemical reaction network theory to discard a kinetic mechanism hypothesis.
In Proceedings of Foundations of Systems Biology and Engineering, pages 325-328, University of California Santa Barbara, USA, August 2005
[*both authors contributed equally to this work].

Talks

15

J. Saez-Rodriguez.
Structural analysis of signal transduction networks.
Contributed talk at the Conference on Systems Biology of Mammalian Cells, Heidelberg, Germany, July 2006.

16

S. Klamt and J. Saez-Rodriguez.
Structural and functional analysis of signaling networks:t-cell signaling as an example.
Invited talk at the Spring Academy of Systems Biology of the German Genetics Society, Magdeburg, Germany, April 2006.

17

J. Saez-Rodriguez.
Structural and modular analysis of RTKs signaling pathways.
Invited talk at the workshop of the Receptor Tyrosine Kinase Consortium at the 6th International Conference on Systems Biology, Boston, U.S.A., October 2005.

18

J. Saez-Rodriguez.
Structural and dynamical mathematical analysis of T-cell signaling.
Talk at Merrimack Pharmaceuticals, Boston, U.S.A., October 2005.

19

J. Saez-Rodriguez, H. Conzelmann, T. Sauter, B.N. Kholodenko, and E. D. Gilles.
Domain-oriented and modular approaches to the reduction of mathematical models of signaling networks.
Contributed talk at the 4th Workshop on Computation of Biochemical Pathways and Genetic Networks, Heidelberg, Germany, September 2005.

20

J. Saez-Rodriguez.
Quantitative and qualitative analysis of tcr-mediated signaling.
Talk at the Inaugural Workshop of the Research Center Immunobiology, Magdeburg, Germany, July 2005.

Poster presentation at conferences

21

J. Saez-Rodriguez, L. Simeoni, J. Lindquist, R. Hemenway, U. Bommhardt, U. U. Haus, R.t Weismantel, E. D. Gilles, S. Klamt, and B. Schraven.
Structural analysis of the t-cell-receptor-induced signaling network.
Poster at the 7th International Conference on Systems Biology, Yokohama, Japan, October 2006.
http://www.icsb-2006.org/.

22

J. Saez-Rodriguez, R. Hemenway, J. Lindquist, L. Simeoni, S. Klamt, U.U. Haus, S. Mirschel, M. Ginkel, R. Weismantel, B. Schraven, and E. D. Gilles.
Structural analysis of the signaling network governing T-cell activation.
Poster at the 6th International Conference on Systems Biology, Boston, USA, October 2005.
http://www.icsb-2005.org/.

23

J. Saez-Rodriguez, X. Wang, S. Kliche, B. Schoeberl, B. Schraven, and E. D. Gilles.
Analysis of the dynamics of TCR-induced MAPK cascade.
Poster at the 6th International Conference on Systems Biology, Boston, USA, October 2005.
http://www.icsb-2005.org/.

24

J. Saez-Rodriguez, S. Klamt, B. Schraven, and E. D. Gilles.
Structural analysis of T-cell signaling.
Poster at the European Conference on Mathematical and Theoretical Biology, Dresden, Germany, July 2005.

25

J. Saez-Rodriguez, X. Wang, B. Schoeberl, S. Klamt, J. Lindquist, S. Kliche, B. Schraven, and E. D. Gilles.
Analysis of the signaling network involved in the activation of T-lymphocytes.
Poster at the 1st FEBS Advanced Course on Systems Biology, Gosau, Austria, March 2005.

26

J. Saez-Rodriguez, X. Wang, B. Schoeberl, B. Schraven, and E. D. Gilles.
Analysis of the regulation of the MAP kinase cascade in T-lymphocytes.
Poster at the 5th International Conference on Systems Biology, Heidelberg, Germany, October 2004.
http://www.icsb2004.org/.

27

J. Saez-Rodriguez, A. Kremling, M. Ginkel, and E. D. Gilles.
Modular analysis of signal transduction networks.
Poster at the 5th International Conference on Systems Biology, Heidelberg, Germany, October 2004.
http://www.icsb2004.org/.

28

J. Saez-Rodriguez and E.D. Gilles.
Modular analysis of the EGF-induced mapk cascade.
Poster at the 3rd International Conference on Systems Biology, Stockholm, Sweden, December 2002.

Miscellaneous

30

J. Saez-Rodriguez.
Modular Analisys of Signaling Networks
Ph.D. Thesis, University of Magdeburg and Max-Planck-Institute for the dynamics of complex technical systems, 2007.

31

J. Saez-Rodriguez.
Computer aided set-up and analysis of dynamic signalling networks: The TGF-beta signal transduction in eukaryotic systems.
Master's thesis, University of Stuttgart, 2001.

Supervised Thesis

32

Stefan Gayer.
System-theoretical decomposition of kinetic models of signal transduction networks
Master thesis, University of Stuttgart, 2007.

33

Stefan Gayer.
Analysis of dynamic properties of signal transduction modules.
Student thesis, University of Stuttgart, 2006.

34

Andrea Hammerle.
Analysis of multistability of signal trasduction modules.
Master thesis, University of Magdeburg, 2005.

35

Holger Conzelmann.
Modelling and analysis of the egf signaling pathway and caspase activation.
Master thesis, University of Stuttgart, 2003.