Journal Article (135)

2013
Journal Article
Straube, R.: Sensitivity and Robustness in Covalent Modification Cycles with a Bifunctional Converter Enzyme. Biophysical Journal 105 (8), pp. 1925 - 1933 (2013)
Journal Article
Straube, R.; Conradi, C.: Reciprocal Enzyme Regulation as a Source of Bistability in Covalent Modification Cycles. Journal of Theoretical Biology 330, pp. 56 - 74 (2013)
2012
Journal Article
Ballerstein, K.; von Kamp, A.; Klamt, S.; Haus, U.-U.: Minimal cut sets in metabolic networks are elementary modes in a dual network. Bioinformatics 28 (3), pp. 381 - 387 (2012)
Journal Article
Conradi, C.; Flockerzi, D.: Switching in mass action networks based on linear inequalities. SIAM Journal on Applied Dynamical Systems 11 (1), pp. 110 - 134 (2012)
Journal Article
Conradi, C.; Flockerzi, D.: Multistationarity in Mass Action Networks with Applications to ERK Activation. Journal of Mathematical Biology 65 (1), pp. 107 - 156 (2012)
Journal Article
Franz, A.; Rehner, R.; Kienle, A.; Grammel, H.: Rapid selection of glucose-utilizing variants of the polyhydroxyalkanoate producer Ralstonia eutropha H16 by incubation with high substrate levels. Letters in Applied Microbiology 54 (1), pp. 45 - 51 (2012)
Journal Article
Huard, J.; Mueller, S.; Gilles, E. D.; Klingmüller, U.; Klamt, S.: An integrative model links multiple inputs and signaling pathways to the onset of DNA synthesis in hepatocytes. FEBS Journal 279 (18), pp. 3290 - 3313 (2012)
Journal Article
Kolczyk, K.; Samaga, R.; Conzelmann, H.; Mirschel, S.; Conradi, C.: The Process-Interaction-Model: a common representation of rule-based and logical models allows studying signal transduction on different levels of detail. BMC Bioinformatics 13, p. 251 (2012)
Journal Article
Kremling, A.; Goehler, A.; Jahreis, K.; Nees, M.; Auerbach, B.; Schmidt-Heck, W.; Kökpinar, Ö.; Geffers, R.; Rinas, U.; Bettenbrock, K.: Analysis and Design of Stimulus Response Curves of E. coli. Metabolites 2 (4), pp. 844 - 871 (2012)
Journal Article
Marbach, A.; Bettenbrock, K.: Iac operon induction in Escherichia coli: Systematic comparison of IPTG and TMG induction and influence of the transacetylase LacA. Journal of Biotechnology 157 (1), pp. 82 - 88 (2012)
Journal Article
Pandey, R.; Flockerzi, D.; Hauser, M. J. B.; Straube, R.: An extended model for the repression of photosynthesis genes by the AppA/PpsR system in Rhodobacter sphaeroides. FEBS Journal 279 (18), pp. 3449 - 3461 (2012)
Journal Article
Pérez, M. M.; Dickenstein, A.; Shiu, A.; Conradi, C.: Chemical Reaction Systems with Toric Steady States. Bulletin of Mathematical Biology 74 (5), pp. 1027 - 1065 (2012)
Journal Article
Rudolf, C.; Grammel, H.: Fructose metabolism of the purple non-sulfur bacterium Rhodospirillum rubrum: Effect of carbon dioxide on growth, and production of bacteriochlorophyll and organic acids. Enzyme and Microbial Technology 50 (4-5), pp. 238 - 246 (2012)
Journal Article
Steinsiek, S.; Bettenbrock, K.: Glucose transport in Escherichia coli mutant strains with defects in sugar transport systems. Journal of Bacteriology 194 (21), pp. 5897 - 5908 (2012)
Journal Article
Straube, R.: Comment on "Load-induced modulation of signal transduction networks": Reconciling ultrasensitivity with bifunctionality? Science Signaling 5 (205), p. Ic1 (2012)
Journal Article
Wang, G.-S.; Grammel, H.; Abou-Aisha, K.; Sägesser, R.; Gosh, R.: High-Level Production of the Industrial Product Lycopene by the Photosynthetic Bacterium Rhodospirillum rubrum. Applied and Environmental Microbiology 78 (20), pp. 7205 - 7215 (2012)
2011
Journal Article
Carius, A. B.; Henkel, M.; Grammel, H.: Glutathione Redox Effect on Photosynthetic Membrane Expression in Rhodospirillum rubrum. Journal of Bacteriology 193 (8), pp. 1893 - 1900 (2011)
Journal Article
García Palacios, J.; Kramer, B.; Kienle, A.; Kaspereit, M.: Experimental validation of a new integrated simulated moving bed process for the production of single enantiomers. Journal of Chromatography A 2218 (16), pp. 2232 - 2239 (2011)
Journal Article
Hädicke, O.; Grammel, H.; Klamt, S.: Metabolic network modeling of redox balancing and biohydrogen production in purple nonsulfur bacteria. BMC Systems Biology 5, p. 150 (2011)
Journal Article
Hädicke, O.; Klamt, S.: Computing complex metabolic intervention strategies using constrained minimal cut sets. Metabolic Engineering 13 (2), pp. 204 - 213 (2011)
Journal Article
Klamt, S.; Kamp von, A.: An application programming interface for CellNetAnalyzer. Biosystems 105 (2), pp. 162 - 168 (2011)
Journal Article
Pandey, R.; Flockerzi, D.; Hauser, M.; Straube, R.: Modeling the Light- and Redox-Dependent Interaction of PpsR/AppA in Rhodobacter sphaeroides. Biophysical Journal 100 (10), pp. 2347 - 2355 (2011)
Journal Article
Ryll, A.; Samaga, R.; Schaper, F.; Alexopoulos, L.G.; Klamt, S.: Large-scale models of IL-1 and IL-6 signaling and their hepatocellular specification. Molecular BioSystems 7 (12), pp. 3253 - 3270 (2011)
Journal Article
Steinsiek, S.; Frixel, S.; Stagge, S.; Bettenbrock, K.: Characterization of E. coli MG1655 and frdA and sdhC mutants at various aerobiosis levels. Journal of Biotechnology 154 (1), pp. 35 - 45 (2011)
Journal Article
Wei, F.; Yang, D.; Straube, R.; Shuai, J.: Brownian diffusion of ion channels in different membrane patch geometries. Physical review E 83 (2), p. 021919 (2011)
2010
Journal Article
Franke, R.; Theis, F.J.; Klamt, S.: From Binary to Multivalued to Continuous Models: The Iac Operon as a Case Study. Journal of Integrative Bioinformatics 7 (1), p. 151 (2010)
Journal Article
Hädicke, O.; Klamt, S.: CASOP: a computational approach for strain optimization aiming at high productivity. Journal of Biotechnology 147 (2), pp. 88 - 101 (2010)
Journal Article
Klamt, S.; Flassig, R.; Sundmacher, K.: TRANSWESD: inferring cellular networks with transitive reduction. Bioinformatics 26 (17), pp. 2160 - 2168 (2010)
Journal Article
Samaga, R.; von Kamp, A.; Klamt, S.: Computing Combinatorial Intervention Strategies and Failure Modes in Signaling Networks. Journal of Computational Biology 17 (1), pp. 39 - 53 (2010)
2009
Journal Article
Klamt, S.; Haus, U.-U.; Theis, F.: Hypergraphs and cellular networks. PLoS Computational Biology 5 (5), p. e1000385 (2009)
Journal Article
Klamt, S.; von Kamp, A.: Computing Paths and Cycles in Biological Interaction Graphs. BMC Bioinformatics 10, p. 181 (2009)
Journal Article
Poltz, R.; Franke, R.; Schweitzer, K.; Klamt, S.; Gilles, E. D.; Naumann, M.: Logical network of genotoxic stress-induced NF-kB signal transduction predicts putative target structures for therapeutic intervention strategies. Advances and Applications in Bioinformatics and Chemistry 2, pp. 125 - 138 (2009)
Journal Article
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)
Journal Article
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)
Journal Article
Wittmann, D. M.; Krumsiek, J.; Saez, J.; Lauffenburger, D. A.; Klamt, S.; Theis, F.: Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling. BMC Systems Biology 3, 98 (2009)

Book Chapter (5)

2020
Book Chapter
Kalnenieks, U. Z.; Pappas, K. M.; Bettenbrock, K.: Zymomonas mobilis metabolism: Novel tools and targets for its rational engineering. In: Advances in Microbial Physiology, Vol. 77, pp. 37 - 88 (Ed. Poole, R. K.). Academic Press (2020)
2014
Book Chapter
Bettenbrock, K.; Bai, H.; Ederer, M.; Green, J.; Hellingwerf, K.J.; Holcombe, M.; Kunz, S.; Rolfe, M.D.; Sanguinetti, G.; Sawodny, O. et al.; Sharma, P.; Steinsiek, S.; Poole, R.K.: Towards a Systems Level Understanding of the Oxygen Response of Escherichia coli. In: Advances in Microbial Physiology, Vol. 64, pp. 65 - 114 (Ed. Poole, R. K.). Elsevier/Academic Press, Amsterdam (2014)
Book Chapter
Klamt, S.; Haedicke, O.; von Kamp, A.: Stoichiometric and Constraint-Based Analysis of Biochemical Reaction Networks. In: Large-Scale Networks in Engineering and Life Sciences, pp. 263 - 316. Springer International Publishing, Cham (2014)
2013
Book Chapter
Heise, S.; Flassig, R.; Klamt, S.: Benchmarking a Simple Yet Effective Approach for Inferring Gene Regulatory Networks from Systems Genetic Data. In: Gene Network Inference: Verification of Methods for Systems Genetic Data., pp. 33 - 47. Springer, Heidelberg (2013)
Book Chapter
Waddell, S. J.; Kamp von, A.; Klamt, S.; Neyrolles, O.: Host-pathogen interactions. In: Systems Biology of Tuberculosis, pp. 107 - 126. Springer, New York (2013)

Conference Paper (10)

2022
Conference Paper
Espinel-Rios, S.; Morabito , B.; Pohlodek, J.; Bettenbrock, K.; Klamt, S.; Findeisen, R.: Optimal control and dynamic modulation of the ATPase gene expression for enforced ATP wasting in batch fermentations. In: IFAC-PapersOnLine, Vol. 55, pp. 174 - 180. 13th IFAC Symposium on Dynamics and Control of Process Systems, including Biosystems, DYCOPS 2022, Busan, Korea, June 14, 2022 - June 17, 2022. (2022)
Conference Paper
Morabito, B.; Pohlodek, J.; Kranert, L.; Espinel-Rios, S.; Findeisen, R.: Efficient and Simple Gaussian Process Supported Stochastic Model Predictive Control for Bioreactors using HILO-MPC. In: IFAC-PapersOnLine, Vol. 55, pp. 922 - 927. 13th IFAC Symposium on Dynamics and Control of Process Systems, including Biosystems, DYCOPS 2022, Busan, Korea, June 14, 2022 - June 17, 2022. (2022)
2016
Conference Paper
Carneiro, T.; Bettenbrock, K.; Lorenz, H.; Seidel-Morgenstern, A.: Combination of Preferential Crystallization and Racemization – First Results. In: BIWIC 2016, 23rd International Workshop on Industrial Crystallization, pp. 173 - 178. BIWIC 2016 - 23rd International Workshop on Industrial Crystallization, Magdeburg, Germany, September 06, 2016 - September 08, 2016. Cuvillier, Göttingen (2016)
Conference Paper
Hädicke, O.; Pozzi, R.; Witt, A.; Oldiges, M.; Klamt, S.; Grammel, H.: Systembiologische Untersuchung bakterieller Stoffwechselnetzwerke und Enzyme für die technische Verwertung von CO. In: Technische Systeme für die Lebenswissenschaften, pp. 115 - 122. 18. Heiligenstädter Kolloquium, Heiligenstadt, September 19, 2016 - September 21, 2016. (2016)
2015
Conference Paper
Kramer, B.; Tüngler, R.; Bettenbrock, K.; Conradi, C.: A compact mathematical model of mandelate racemase production and chaperone overexpression in E. coli. 8th Vienna Interantional Conference on Mathematical Modelling , Vienna, Austria, February 18, 2015 - February 20, 2015. IFAC-PapersOnLine 48 (1), pp. 23 - 28 (2015)
2014
Conference Paper
Kramer, B.; Conradi, C.: Identifying network structures that can cause multistationarity. In: Proceedings of 21st International Symposium on Mathematical Theory of Networks and Systems, pp. 1548 - 1555. 21st International Symposium on Mathematical Theory of Networks and Systems, Groningen, Netherlands, July 07, 2014 - July 11, 2014. (2014)
2013
Conference Paper
Kramer, B.; Conradi, C.: On Bistability Causing Structures in Escherichia Coli’s Metabolism. In: Computational Methods in Systems Biology: 11th International Conference, CMSB 2013, pp. 276 - 277. 11th International Conference, CMSB 2013, Klosterneuburg, Österreich, September 22, 2014 - September 24, 2014. (2013)
Conference Paper
Ryll, A.; Bucher, J.; Niklas , J.; Klamt, S.: A fusion approach linking signaling logic and metabolic mass-flow kinetics in hepatocytes. In: Computational Methods in Systems Biology: 11th International Conference, CMSB 2013, pp. 255 - 256. 11th International Conference on Computational Methods in Systems Biology CMSB 13, Klosterneuburg, Austria, September 22, 2013 - September 24, 2013. (2013)
2012
Conference Paper
Franz, A.; Grammel, H.; Rehner, R.; Paetzold, P.; Kienle, A.: Multiscale Modeling of Biopolymer Production in Multicellular Systems. MATHMOD 2012 - 7th Vienna International Conference on Mathematical Modelling, Vienna, Austria, February 15, 2012 - February 17, 2012. IFAC Proceedings Volumes 45 (2), pp. 326 - 330 (2012)
2010
Conference Paper
Bohl, K.; Figueiredo, L.F.; Hädicke, O.; Klamt, S.; Kost, C.; Schuster, S.; Kaleta, C.: CASOP GS: Computing intervention strategies targeted at production improvement in genome-scale metabolic networks. In: German Conference on Bioinformatics 2010, pp. 71 - 80 (Eds. Schomburg, D.; Grote, A.). German Conference on Bioinformatics 2010, Braunschweig, Germany, September 20, 2010 - September 22, 2010. (2010)
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