Publications of Julio Saez-Rodriguez

Thiele, S.; Cerone, L.; Saez-Rodriguez, J.; Siegel, A.; Guciolowski, C.; Klamt, S.: Extended notions of sign consistency to relate experimental data to signaling and regulatory network topologies. BMC Bioinformatics 16 (1), 345 (2015)

Chaoiya, C.; Berenguier, D.; Keating, S. M.; Naldi, A.; van Iersel, M. P.; Rodriguez, N.; Dräger, A.; Büchel, F.; Cokelaer, T.; Kowal, B. et al.; Wicks, B.; Gonçalves, E.; Dorier, J.; Page, M.; Monteiro, P. T.; Kamp von, A.; Xenarius , I.; de Jong, H.; Hucka, M.; Klamt, S.; Thieffrey, D.; Le Novère, N.; Saez-Rodriguez, J.; Helikar, T.: SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formlisms and tools. BMC Systems Biology 7, 135 (2013)

Gonçalves, E.; Bucher, J.; Ryll, A.; Niklas, J.; Mauch, K.; Klamt, S.; Rocha, M.; Saez-Rodriguez, J.: Bridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical models. Molecular BioSystems 9 (7), pp. 1576 - 1583 (2013)

Saez-Rodriguez, J.; Alexopoulos, L. G.; Epperlein, J.; Samaga, R.; Lauffenburger, D. A.; Klamt, S.; Sorger, P. K.: Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction. Molecular Systems Biology 5, p. 331 (2009)

Samaga, R.; Saez-Rodriguez, J.; Alexopoulos, L. G.; Sorger, P. K.; Klamt, S.: The logic of EGFR/ErbB signaling: theoretical properties and analysis of high-throughput data. PLoS Computational Biology 5 (8), e1000438 (2009)

Saez-Rodriguez, J.; Gayer, S.; Ginkel, M.; Gilles, E. D.: Automatic decomposition of kinetic models of signaling networks minimizing the retroactivity among modules. Bioinformatics 24 (16), pp. i213 - i219 (2008)

Saez-Rodriguez, J.; Hammerle-Fickinger, A.; Dalal, O.; Klamt, S.; Gilles, E. D.; Conradi, C.: Multistability of signal transduction motifs. IET Systems Biology 2 (2), pp. 80 - 93 (2008)

Wang, X. Q.; Simeoni, L.; Lindquist, J. A.; Saez-Rodriguez, J.; Ambach, A.; Gilles, E. D.; Kliche, S.; Schraven, B.: Dynamics of proximal signaling events after TCR/CD8-mediated induction of proliferation or apoptosis in mature CD8⁺ T cells. Journal of Immunology 180 (10), pp. 6703 - 6712 (2008)

Klamt, S.; Saez-Rodriguez, J.; Gilles, E. D.: Structural and functional analysis of cellular networks with CellNetAnalyzer. BMC Systems Biology 1, 2 (2007)

Kremling, A.; Saez-Rodriguez, J.: Systems biology: An engineering perspective. Journal of Biotechnology 129 (2), pp. 329 - 351 (2007)

Saez-Rodriguez, J.; Simeoni, L.; Lindquist, J.; Hemenway, R.; Bommhardt, U.; Arndt, B.; Haus, U. U.; Weismantel, R.; Gilles, E. D.; Klamt, S. et al.; Schraven, B.: A logical model provides insights into T cell receptor signaling. PLoS Computational Biology 3, e163 (2007)

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

Klamt, S.; Saez-Rodriguez, J.; Lindquist, J.; Simeoni, L.; Gilles, E. D.: A methodology for the structural and functional analysis of signaling and regulatory networks. BMC Bioinformatics 7, p. 56 (2006)

Saez-Rodriguez, J.; Mirschel, S.; Hemenway, R.; Klamt, S.; Gilles, E. D.; Ginkel, M.: Visual set-up of logical models of signaling and regulatory networks with ProMoT. BMC Bioinformatics 7, 506 (2006)

Conradi, C.; Saez-Rodriguez, J.; Gilles, E. D.; Raisch, J.: Using Chemical Reaction Network Theory to discard a Kinetic Mechanism Hypothesis. IEE Proceedings Systems Biology 152 (4), pp. 243 - 248 (2005)

Saez-Rodriguez, J.; Kremling, A.; Gilles, E. D.: Dissecting the Puzzle of Life: Modularization of Signal Transduction Networks. Computers & Chemical Engineering 29, pp. 619 - 629 (2005)

Conzelmann, H.; Saez-Rodriguez, J.; Sauter, T.; Bullinger, E.; Allgöwer, F.; Gilles, E. D.: Reduction of Mathematical Models of Signal Transduction Networks: Simulation-Based Approach Applied to EGF Receptor Signalling. Systems Biology 1, pp. 159 - 169 (2004)

Saez-Rodriguez, J.; Kremling, A.; Conzelmann, H.; Bettenbrock, K.; Gilles, E. D.: Modular Analysis of Signal Transduction Networks. IEEE Control Systems Magazine 24 (4), pp. 35 - 52 (2004)

Conradi, C.; Saez-Rodriguez, J.; Gilles, E. D.; Raisch, J.: Chemical Reaction Network Theory: a tool for systems biology. In: 5th MATHMOD: Full Paper CD, p. SP22_267_P. 5th MATHMOD, Vienna, Austria, February 08, 2006 - February 10, 2006. (2006)

Conradi, C.; Saez-Rodriguez, J.; Gilles, E. D.; Raisch, J.: Using chemical reaction network theory to discard a kinetic mechanism hypothesis. In: Foundations of Systems Biology in Engineering, FOSBE 2005, pp. 325 - 328. Foundations of Systems Biology in Engineering, Santa Barbara, August 07, 2005 - August 10, 2005. (2005)