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Ernst Dieter Gilles
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Research Profile (preview)
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Network (preview)
12
Kremling, Andreas
10
Klamt, Steffen
9
Saez-Rodriguez, Julio
7
Sauter, Thomas
7
Bettenbrock, Katja
5
Conzelmann, Holger
5
Jahreis, Knut
5
Stelling, Jörg
4
Ginkel, Martin
4
Lengeler, Joseph
3
Lindquist, Jonathan
3
Nutsch, Torsten
3
Grammel, Hartmut
3
Bullinger, Eric
3
Allgöwer, Frank
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Publications
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Geonetwork of Ernst Dieter Gilles (preview)
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All Publications
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2009: Mirschel Sebastian; Steinmetz Katrin; Rempel Michael; Ginkel Martin; Gilles Ernst Dieter
PROMOT: modular modeling for systems biology.
Bioinformatics (Oxford, England) 2009;25(5):687-9.
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2008: Saez-Rodriguez Julio; Gayer Stefan; Ginkel Martin; Gilles Ernst Dieter
Automatic decomposition of kinetic models of signaling networks minimizing the retroactivity among modules.
Bioinformatics (Oxford, England) 2008;24(16):i213-9.
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2008: Wang Xiaoqian; Simeoni Luca; Lindquist Jonathan A; Saez-Rodriguez Julio; Ambach Andreas; Gilles Ernst D; Kliche Stefanie; Schraven Burkhart
Dynamics of proximal signaling events after TCR/CD8-mediated induction of proliferation or apoptosis in mature CD8+ T cells.
Journal of immunology (Baltimore, Md. : 1950) 2008;180(10):6703-12.
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2008: Kremling A; Bettenbrock K; Gilles E D
A feed-forward loop guarantees robust behavior in Escherichia coli carbohydrate uptake.
Bioinformatics (Oxford, England) 2008;24(5):704-10.
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2008: Koschorreck Markus; Gilles Ernst Dieter
ALC: automated reduction of rule-based models.
BMC systems biology 2008;2():91.
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2008: Conzelmann Holger; Fey Dirk; Gilles Ernst D
Exact model reduction of combinatorial reaction networks.
BMC systems biology 2008;2():78.
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2008: Conzelmann Holger; Gilles Ernst-Dieter
Dynamic pathway modeling of signal transduction networks: a domain-oriented approach.
Methods in molecular biology (Clifton, N.J.) 2008;484():559-78.
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2008: Koschorreck Markus; Gilles Ernst Dieter
Mathematical modeling and analysis of insulin clearance in vivo.
BMC systems biology 2008;2():43.
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2008: Klamt Steffen; Grammel Hartmut; Straube Ronny; Ghosh Robin; Gilles Ernst Dieter
Modeling the electron transport chain of purple non-sulfur bacteria.
Molecular systems biology 2008;4():156.
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2008: Franke Raimo; Müller Melanie; Wundrack Nicole; Gilles Ernst-Dieter; Klamt Steffen; Kähne Thilo; Naumann Michael
Host-pathogen systems biology: logical modelling of hepatocyte growth factor and Helicobacter pylori induced c-Met signal transduction.
BMC systems biology 2008;2():4.
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2007: Bettenbrock Katja; Sauter Thomas; Jahreis Knut; Kremling Andreas; Lengeler Joseph W; Gilles Ernst-Dieter
Correlation between growth rates, EIIACrr phosphorylation, and intracellular cyclic AMP levels in Escherichia coli K-12.
Journal of bacteriology 2007;189(19):6891-900.
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2007: Saez-Rodriguez Julio; Simeoni Luca; Lindquist Jonathan A; Hemenway Rebecca; Bommhardt Ursula; Arndt Boerge; Haus Utz-Uwe; Weismantel Robert; Gilles Ernst D; Klamt Steffen; Schraven Burkhart
A logical model provides insights into T cell receptor signaling.
PLoS computational biology 2007;3(8):e163.
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2007: Ederer Michael; Gilles Ernst Dieter
Thermodynamically feasible kinetic models of reaction networks.
Biophysical journal 2007;92(6):1846-57.
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2007: Koschorreck Markus; Conzelmann Holger; Ebert Sybille; Ederer Michael; Gilles Ernst Dieter
Reduced modeling of signal transduction - a modular approach.
BMC bioinformatics 2007;8():336.
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2007: Kremling Andreas; Bettenbrock Katja; Gilles Ernst Dieter
Analysis of global control of Escherichia coli carbohydrate uptake.
BMC systems biology 2007;1():42.
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2007: Klamt Steffen; Saez-Rodriguez Julio; Gilles Ernst D
Structural and functional analysis of cellular networks with CellNetAnalyzer.
BMC systems biology 2007;1():2.
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2006: Anders Alexander; Lilie Hauke; Franke Kathlen; Kapp Lutz; Stelling Jörg; Gilles Ernst D; Breunig Karin D
The galactose switch in Kluyveromyces lactis depends on nuclear competition between Gal4 and Gal1 for Gal80 binding.
The Journal of biological chemistry 2006;281(39):29337-48.
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2006: Bettenbrock Katja; Fischer Sophia; Kremling Andreas; Jahreis Knut; Sauter Thomas; Gilles Ernst-Dieter
A quantitative approach to catabolite repression in Escherichia coli.
The Journal of biological chemistry 2006;281(5):2578-84.
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2006: Saez-Rodriguez Julio; Mirschel Sebastian; Hemenway Rebecca; Klamt Steffen; Gilles Ernst Dieter; Ginkel Martin
Visual setup of logical models of signaling and regulatory networks with ProMoT.
BMC bioinformatics 2006;7():506.
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2006: Klamt Steffen; Saez-Rodriguez Julio; Lindquist Jonathan A; Simeoni Luca; Gilles Ernst D
A methodology for the structural and functional analysis of signaling and regulatory networks.
BMC bioinformatics 2006;7():56.
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2006: Conzelmann Holger; Saez-Rodriguez Julio; Sauter Thomas; Kholodenko Boris N; Gilles Ernst D
A domain-oriented approach to the reduction of combinatorial complexity in signal transduction networks.
BMC bioinformatics 2006;7():34.
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2005: Conradi C; Saez-Rodriguez J; Gilles E D; Raisch J
Using chemical reaction network theory to discard a kinetic mechanism hypothesis.
Systems biology 2005;152(4):243-8.
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2005: Nutsch Torsten; Oesterhelt Dieter; Gilles Ernst Dieter; Marwan Wolfgang
A quantitative model of the switch cycle of an archaeal flagellar motor and its sensory control.
Biophysical journal 2005;89(4):2307-23.
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2004: Kremling A; Heermann R; Centler F; Jung K; Gilles E D
Analysis of two-component signal transduction by mathematical modeling using the KdpD/KdpE system of Escherichia coli.
Bio Systems 2004;78(1-3):23-37.
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2004: Schmid Joachim W; Mauch Klaus; Reuss Matthias; Gilles Ernst D; Kremling Andreas
Metabolic design based on a coupled gene expression-metabolic network model of tryptophan production in Escherichia coli.
Metabolic engineering 2004;6(4):364-77.
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2004: Stelling Jörg; Gilles Ernst Dieter
Mathematical modeling of complex regulatory networks.
IEEE transactions on nanobioscience 2004;3(3):172-9.
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2004: Kremling Andreas; Fischer Sophia; Gadkar Kapil; Doyle Francis J; Sauter Thomas; Bullinger Eric; Allgöwer Frank; Gilles Ernst D
A benchmark for methods in reverse engineering and model discrimination: problem formulation and solutions.
Genome research 2004;14(9):1773-85.
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2004: Stelling Jörg; Gilles Ernst Dieter; Doyle Francis J
Robustness properties of circadian clock architectures.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(36):13210-5.
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2004: Eissing Thomas; Conzelmann Holger; Gilles Ernst D; Allgöwer Frank; Bullinger Eric; Scheurich Peter
Bistability analyses of a caspase activation model for receptor-induced apoptosis.
The Journal of biological chemistry 2004;279(35):36892-7.
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2004: 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 2004;1(1):159-69.
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2004: Sauter T; Gilles E D
Modeling and experimental validation of the signal transduction via the Escherichia coli sucrose phospho transferase system.
Journal of biotechnology 2004;110(2):181-99.
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2004: Klamt Steffen; Gilles Ernst Dieter
Minimal cut sets in biochemical reaction networks.
Bioinformatics (Oxford, England) 2004;20(2):226-34.
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2004: Kremling A; Fischer S; Sauter T; Bettenbrock K; Gilles E D
Time hierarchies in the Escherichia coli carbohydrate uptake and metabolism.
Bio Systems 2004;73(1):57-71.
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2003: Grammel Hartmut; Gilles Ernst-Dieter; Ghosh Robin
Microaerophilic cooperation of reductive and oxidative pathways allows maximal photosynthetic membrane biosynthesis in Rhodospirillum rubrum.
Applied and environmental microbiology 2003;69(11):6577-86.
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2003: Nutsch Torsten; Marwan Wolfgang; Oesterhelt Dieter; Gilles Ernst Dieter
Signal processing and flagellar motor switching during phototaxis of Halobacterium salinarum.
Genome research 2003;13(11):2406-12.
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2003: Ginkel M; Kremling A; Nutsch T; Rehner R; Gilles E D
Modular modeling of cellular systems with ProMoT/Diva.
Bioinformatics (Oxford, England) 2003;19(9):1169-76.
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2003: Klamt Steffen; Stelling Jörg; Ginkel Martin; Gilles Ernst Dieter
FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps.
Bioinformatics (Oxford, England) 2003;19(2):261-9.
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2002: Stelling Jörg; Klamt Steffen; Bettenbrock Katja; Schuster Stefan; Gilles Ernst Dieter
Metabolic network structure determines key aspects of functionality and regulation.
Nature 2002;420(6912):190-3.
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2002: Schoeberl Birgit; Eichler-Jonsson Claudia; Gilles Ernst Dieter; Müller Gertraud
Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors.
Nature biotechnology 2002;20(4):370-5.
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2002: Klamt Steffen; Schuster Stefan; Gilles Ernst Dieter
Calculability analysis in underdetermined metabolic networks illustrated by a model of the central metabolism in purple nonsulfur bacteria.
Biotechnology and bioengineering 2002;77(7):734-51.
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2001: Wang J; Gilles E D; Lengeler J W; Jahreis K
Modeling of inducer exclusion and catabolite repression based on a PTS-dependent sucrose and non-PTS-dependent glycerol transport systems in Escherichia coli K-12 and its experimental verification.
Journal of biotechnology 2001;92(2):133-58.
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2001: Kremling A; Bettenbrock K; Laube B; Jahreis K; Lengeler J W; Gilles E D
The organization of metabolic reaction networks. III. Application for diauxic growth on glucose and lactose.
Metabolic engineering 2001;3(4):362-79.
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2001: Kremling A; Gilles E D
The organization of metabolic reaction networks. II. Signal processing in hierarchical structured functional units.
Metabolic engineering 2001;3(2):138-50.
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2000: Kremling A; Jahreis K; Lengeler J W; Gilles E D
The organization of metabolic reaction networks: a signal-oriented approach to cellular models.
Metabolic engineering 2000;2(3):190-200.
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1998: Grammel H; Wolf H; Gilles E D; Huth F; Laatsch H
Carbazole antibiotics synthesis in a Streptomyces tendae bald mutant, created by acriflavine treatment.
Zeitschrift für Naturforschung. C, Journal of biosciences 1998;53(5-6):325-30.
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1997: Treskatis S K; Orgeldinger V; Wolf H; Gilles E D
Morphological characterization of filamentous microorganisms in submerged cultures by on-line digital image analysis and pattern recognition.
Biotechnology and bioengineering 1997;53(2):191-201.
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