Journal Article (115)

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 (4)

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 (8)

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)

Thesis - PhD (9)

2018
Thesis - PhD
Harder, B.-J.: Modellbasiertes Metabolic Engineering zur Optimierung der Itaconatproduktion in Escherichia coli. Dissertation, 144 pp., Shaker Verlag, Aachen (2018)
Thesis - PhD
Samaga, R.: Qualitative and Semi-Quantitative Analysis of Signal Transduction Networks. Dissertation, 288 pp., Shaker Verlag, Aachen (2018)
2016
Thesis - PhD
Erdrich, P.: Modellbasierte Bestimmung von Interventionsstrategien zur Optimierung der Produktion von Biokraftstoffen in Cyanobakterien. Dissertation, Otto-von-Guericke-Universität, Magdeburg (2016)
2014
Thesis - PhD
Hädicke, O.: Modellbasierte Identifizierung von Interventionsstrategien für Stoffwechselnetzwerke. Dissertation, Shaker, Aachen (2014)
2013
Thesis - PhD
Marbach, A.: Zellheterogenität am Beispiel der Expression des Escherichia coli lac Operona. Dissertation, Otto-von-Guericke-Universität, Magdeburg (2013)
2012
Thesis - PhD
Carius, A. B.: Untersuchungen zur Redoxregulation der Photosynthesemembranexpression in dem fakultativ phototrophen Bakterium Rhodospirillum rubrum. Dissertation, Otto-von-Guericke-Universität, Magdeburg, Germany (2012)
Thesis - PhD
Jahn, S.: Das Stickstoff-PTS und seine regulatorische Funktion im Metabolismus von Escherichia coli LJ110. Dissertation, Universität, Osnabrück (2012)
Thesis - PhD
Mirschel, S.: Interactive Visualization of Complex Structures in Modular Models for Systems Biology. Dissertation, Shaker, Aachen (2012)
Thesis - PhD
Pandey, R.: Modeling the AppA / PpsR Signal Transduction System of Rhodobacter sphaeroides. Dissertation, Otto-von-Guericke-Universität, Magdeburg (2012)

Thesis - Habilitation (1)

2011
Thesis - Habilitation
Straube, R.: Räumliche Aspekte intrazellulärer Signalübertragung und Musterbildung in der Glykolyse. Habilitation, Otto von Guericke Universität, Magdeburg (2011)

Issue (1)

2011
Issue
Schuster, S.; Kaleta, C.; Klamt, S.; Figueiredo de, L.F. (Eds.): Proceedings of the workshop "Integration of OMICs datasets into metabolic pathway analysis" Edingburgh, U.K., 15 October 2010 IOMPA 2010 (Special issue). Biosystems 105, (2 ) (2 ) (2011)

Editorial (1)

2011
Editorial
Kaleta, C.; de Figueiredo, L. F.; Heiland, I.; Klamt, S.; Schuster, S.: Special Issue: Integration of OMICs datasets into Metabolic Pathway Analysis. Biosystems 105 (2), pp. 107 - 108 (2011)
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