Publications of Julio Saez-Rodriguez

Journal Article (18)

2015
Journal Article
Thiele, S., Cerone, L., Saez-Rodriguez, J., Siegel, A., Guciolowski, C., & Klamt, S. (2015)Extended notions of sign consistency to relate experimental data to signaling and regulatory network topologies.BMC Bioinformatics, 16 (1), 345doi: 10.1186/s12859-015-0733-7.
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2013
Journal Article
Chaoiya, C., Berenguier, D., Keating, S. M., Naldi, A., van Iersel, M. P., Rodriguez, N., Dräger, A., Büchel, F., Cokelaer, T., Kowal, B., 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. (2013)SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formlisms and toolsBMC Systems Biology, 7, 135doi: 10.1186/1752-0509-7-135.
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Gonçalves, E., Bucher, J., Ryll, A., Niklas, J., Mauch, K., Klamt, S., Rocha, M., & Saez-Rodriguez, J. (2013)Bridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical modelsMolecular BioSystems, 9 (7), 1576–1583doi: 10.1039/c3mb25489e.
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2009
Journal Article
Saez-Rodriguez, J., Alexopoulos, L. G., Epperlein, J., Samaga, R., Lauffenburger, D. A., Klamt, S., & Sorger, P. K. (2009)Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transductionMolecular Systems Biology, 5, 331doi: 10.1038/msb.2009.87.
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Samaga, R., Saez-Rodriguez, J., Alexopoulos, L. G., Sorger, P. K., & Klamt, S. (2009)The logic of EGFR/ErbB signaling: theoretical properties and analysis of high-throughput dataPLoS Computational Biology, 5 (8), e1000438doi: 10.1371/journal.pcbi.1000438.
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publisher-version
2008
Journal Article
Saez-Rodriguez, J., Gayer, S., Ginkel, M., & Gilles, E. D. (2008)Automatic decomposition of kinetic models of signaling networks minimizing the retroactivity among modulesBioinformatics, 24 (16), i213–i219doi: 10.1093/bioinformatics/btn289.
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Journal Article
Saez-Rodriguez, J., Hammerle-Fickinger, A., Dalal, O., Klamt, S., Gilles, E. D., & Conradi, C. (2008)Multistability of signal transduction motifsIET Systems Biology, 2 (2), 80–93doi: 10.1049/iet-syb:20070012.
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Journal Article
Wang, X. Q., Simeoni, L., Lindquist, J. A., Saez-Rodriguez, J., Ambach, A., Gilles, E. D., Kliche, S., & Schraven, B. (2008)Dynamics of proximal signaling events after TCR/CD8-mediated induction of proliferation or apoptosis in mature CD8+ T cellsJournal of Immunology, 180 (10), 6703–6712doi: 10.4049/jimmunol.180.10.6703.
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2007
Journal Article
Klamt, S., Saez-Rodriguez, J., & Gilles, E. D. (2007)Structural and functional analysis of cellular networks with CellNetAnalyzerBMC Systems Biology, 1, 2doi: 10.1186/1752-0509-1-2.
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Journal Article
Kremling, A. & Saez-Rodriguez, J. (2007)Systems biology: An engineering perspectiveJournal of Biotechnology, 129 (2), 329–351doi: 10.1016/j.jbiotec.2007.02.009.
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Journal Article
Saez-Rodriguez, J., Simeoni, L., Lindquist, J., Hemenway, R., Bommhardt, U., Arndt, B., Haus, U. U., Weismantel, R., Gilles, E. D., Klamt, S., & Schraven, B. (2007)A logical model provides insights into T cell receptor signalingPLoS Computational Biology, 3, e163doi: 10.1371/journal.pcbi.0030163.
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publisher-version
2006
Journal Article
Conzelmann, H., Saez-Rodriguez, J., Sauter, T., Kholodenko, B. N., & Gilles, E. D. (2006)A domain-oriented approach to the reduction of combinatorial complexity in signal transduction networksBMC Bioinformatics, 7, 34doi: 10.1186/1471-2105-7-34.
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Journal Article
Klamt, S., Saez-Rodriguez, J., Lindquist, J., Simeoni, L., & Gilles, E. D. (2006)A methodology for the structural and functional analysis of signaling and regulatory networksBMC Bioinformatics, 7, 56doi: 10.1186/1471-2105-7-56.
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Saez-Rodriguez, J., Mirschel, S., Hemenway, R., Klamt, S., Gilles, E. D., & Ginkel, M. (2006)Visual set-up of logical models of signaling and regulatory networks with ProMoTBMC Bioinformatics, 7, 506doi: 10.1186/1471-2105-7-506.
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2005
Journal Article
Conradi, C., Saez-Rodriguez, J., Gilles, E. D., & Raisch, J. (2005)Using Chemical Reaction Network Theory to discard a Kinetic Mechanism HypothesisIEE Proceedings Systems Biology, 152 (4), 243–248doi: 10.1049/ip-syb:20050045 .
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Journal Article
Saez-Rodriguez, J., Kremling, A., & Gilles, E. D. (2005)Dissecting the Puzzle of Life: Modularization of Signal Transduction NetworksComputers & Chemical Engineering, 29, 619–629doi: 10.1016/j.compchemeng.2004.08.035.
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2004
Journal Article
Conzelmann, H., Saez-Rodriguez, J., Sauter, T., Bullinger, E., Allgöwer, F., & Gilles, E. D. (2004)Reduction of Mathematical Models of Signal Transduction Networks: Simulation-Based Approach Applied to EGF Receptor SignallingSystems Biology, 1, 159–169doi: 10.1049/sb:20045011.
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Journal Article
Saez-Rodriguez, J., Kremling, A., Conzelmann, H., Bettenbrock, K., & Gilles, E. D. (2004)Modular Analysis of Signal Transduction NetworksIEEE Control Systems Magazine, 24 (4), 35–52doi: 10.1109/MCS.2004.1316652.
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Conference Paper (3)

2006
Conference Paper
Conradi, C., Saez-Rodriguez, J., Gilles, E. D., & Raisch, J. (2006)Chemical Reaction Network Theory: a tool for systems biologyIn: 5th MATHMOD: Full Paper CD, SP22_267_P.
MPG.PuRe
2005
Conference Paper
Conradi, C., Saez-Rodriguez, J., Gilles, E. D., & Raisch, J. (2005)Using chemical reaction network theory to discard a kinetic mechanism hypothesisIn: Foundations of Systems Biology in Engineering, FOSBE 2005, 325–328.
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