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)

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)

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)

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)

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)

Espinel-Rios, S.; Bettenbrock, K.; Klamt, S.; Avalos, J. L.; Findeisen, R.: Machine learning-supported cybergenetic modeling, optimization and control for synthetic microbial communities. In: 33rd European Symposium on Computer Aided Chemical Engineering, pp. 2601 - 2606 (Eds. Kokossis, A.; Georgiadis, M. C.; Pistikopoulos, E.). 33rd European Symposium on Computer Aided Process Engineering, Athen, Greece, June 18, 2023 - June 21, 2023. Elsevier, Amsterdam, Netherlands (2023)

Espinel-Rios, S.; Kok, R.; Klamt, S.; Avalos, J. L.; Findeisen, R.: Batch-to-Batch Optimization with Model Adaptation Leveraging Gaussian Processes: The Case of Optogenetically Assisted Microbial Consortia. In: International Conference on Control, Automation and Systems, pp. 1292 - 1297. 23rd International Conference on Control, Automation and Systems, ICCAS 2023, Yeosu, Korea, October 17, 2023 - October 20, 2023. IEEE, Boca Raton (2023)

Espinel-Rios, S.; Slaviero, G.; Bettenbrock, K.; Klamt, S.; Findeisen, R.: Monitoring intracellular metabolite concentrations by moving horizon estimation based on kinetic modeling. IFAC-PapersOnLine 56 (2), pp. 4608 - 4613 (2023)

Espinel-Rios, S.; Huber, N.; Alcalá Orozco, E. A.; Morabito, B.; Rexer, T.; Reichl, U.; Klamt, S.; Findeisen, R.: Cell-free biosynthesis meets dynamic optimization and control: a fed-batch framework. 9th IFAC Conference on Foundations of Systems Biology in Engineering (FOSBE), Cambridge, MA, August 28, 2022 - August 31, 2022. IFAC-PapersOnLine 55 (23), pp. 92 - 97 (2022)

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)

Espinel-Rios, S.; Morabito, B.; Bettenbrock, K.; Findeisen, R.: Soft sensor for monitoring dyamic changes in cell composition. 9th IFAC Conference on Foundations of Systems Biology in Engineering (FOSBE), Cambridge, MA, August 28, 2022 - August 31, 2022. IFAC-PapersOnLine 55 (23), pp. 98 - 103 (2022)

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)

Slaviero, G.; Steuer, R.; Klamt, S.: Using parameter sampling to explore key properties of E. coli's anaerobic metabolism. 9th IFAC Conference on Foundations of Systems Biology in Engineering (FOSBE), Cambridge, MA, August 28, 2022 - August 31, 2022. IFAC-PapersOnLine 55 (23), pp. 109 - 114 (2022)

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)

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)

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)

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)

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)

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)

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)

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)

Bekiaris, P. S.: Entwicklung neuer Methoden zur Integration thermodynamischer und enzymatischer Nebenbedingungen in der constraint-basierten metabolischen Modellierung. Dissertation, Otto-von-Guericke-Universität, Magdeburg (2024)

Espinel-Rios, S.: Modeling, optimization, and predictive control for metabolic cybergenetics. Dissertation, Otto-von-Guericke-Universität, Magdeburg (2023)

Schneider, P.: Advances in Computational Strain Design with Minimal Cut Sets. Dissertation, Shaker Verlag (2021)

Koch, S.: Stöchiometrische Modellierung von mikrobiellen Gemeinschaften in Biogasanlagen. Dissertation, Otto-von-Guericke-Universität, Magdeburg (2020)

Harder, B.-J.: Modellbasiertes Metabolic Engineering zur Optimierung der Itaconatproduktion in Escherichia coli. Dissertation, 144 pp., Shaker Verlag, Aachen (2018)

Samaga, R.: Qualitative and Semi-Quantitative Analysis of Signal Transduction Networks. Dissertation, 288 pp., Shaker Verlag, Aachen (2018)

Erdrich, P.: Modellbasierte Bestimmung von Interventionsstrategien zur Optimierung der Produktion von Biokraftstoffen in Cyanobakterien. Dissertation, Otto-von-Guericke-Universität, Magdeburg (2016)

Hädicke, O.: Modellbasierte Identifizierung von Interventionsstrategien für Stoffwechselnetzwerke. Dissertation, Shaker Verlag, Aachen (2014)

Marbach, A.: Zellheterogenität am Beispiel der Expression des Escherichia coli lac Operona. Dissertation, Otto-von-Guericke-Universität, Magdeburg (2013)

Carius, A. B.: Untersuchungen zur Redoxregulation der Photosynthesemembranexpression in dem fakultativ phototrophen Bakterium Rhodospirillum rubrum. Dissertation, Otto-von-Guericke-Universität, Magdeburg, Germany (2012)

Jahn, S.: Das Stickstoff-PTS und seine regulatorische Funktion im Metabolismus von Escherichia coli LJ110. Dissertation, Universität, Osnabrück (2012)

Mirschel, S.: Interactive Visualization of Complex Structures in Modular Models for Systems Biology. Dissertation, Shaker, Aachen (2012)

Pandey, R.: Modeling the AppA / PpsR Signal Transduction System of Rhodobacter sphaeroides. Dissertation, Otto-von-Guericke-Universität, Magdeburg (2012)

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

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 ) (2011)

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)