Publications of S. Klamt

Klamt, S. & Gilles, E. D. (2004)Minimal cut sets in biochemical reaction networksBioinformatics, 20, 226–234doi: 10.1093/bioinformatics/btg395.

Kremling, A., Ginkel, M., Klamt, S., & Gilles, E. D. (2004)Workbench zur Modellbildung, Simulation und Analyse zellulärer Systemeit - Information Technology, 46, 12–19doi: 10.1524/itit.46.1.12.26503 .

Papin, J. A., Stelling, J., Price, N. D., Klamt, S., Schuster, S., & Palsson, B. O. (2004)Comparison of network-based pathway analysis methodsTrends in Biotechnology, 22 (8), 400–405doi: 10.1016/j.tibtech.2004.06.010.

Klamt, S. & Stelling, J. (2003)Two approaches for metabolic pathway analysis?Trends in Biotechnology, 21 (2), 64–69doi: 10.1016/S0167-7799(02)00034-3.

Klamt, S., Stelling, J., Ginkel, M., & Gilles, E. D. (2003)FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux mapsBioinformatics, 19 (2), 261–269doi: 10.1093/bioinformatics/19.2.261.

Klamt, S. & Schuster, S. (2002)Calculating as many fluxes as possible in underdetermined metabolic networksMolecular Biology Reports, 29 (1-2), 243–248doi: 10.1023/A:1020394300385.

Klamt, S., Schuster, S., & Gilles, E. D. (2002)Calculability analysis in underdetermined metabolic networks illustrated by a model of the central metabolism in purple nonsulfur bacteriaBiotechnology and Bioengineering, 77 (7), 734–751doi: 10.1002/bit.10153.

Klamt, S. & Stelling, J. (2002)Combinatorial complexity of pathway analysis in metabolic networksMolecular Biology Reports, 29 (1-2), 233–236doi: 10.1023/A:1020390132244.

Schuster, S. & Klamt, S. (2002)Applying metabolic pathway analysis to make good use of methanolTrends in Biotechnology, 20 (8), 322doi: 10.1016/S0167-7799(02)02026-7.

Schuster, S., Klamt, S., Weckwerth, W., Moldenhauer, F., & Pfeiffer, T. (2002)Use of network analysis of metabolic systems in bioengineeringBioprocess and Biosystems Engineering, 24 (6), 363–372doi: 10.1007/s004490100253.

Stelling, J., Klamt, S., Bettenbrock, K., Schuster, S., & Gilles, E. D. (2002)Metabolic network structure determines key aspects of functionality and regulationNature, 420 (6912), 190–193doi: 10.1038/nature01166.

Klamt, S., Haedicke, O., & von Kamp, A. (2014)Stoichiometric and Constraint-Based Analysis of Biochemical Reaction NetworksLarge-Scale Networks in Engineering and Life Sciences263–316Cham: Springer International Publishingdoi: 10.1007/978-3-319-08437-4_5.

Heise, S., Flassig, R., & Klamt, S. (2013)Benchmarking a Simple Yet Effective Approach for Inferring Gene Regulatory Networks from Systems Genetic DataIn: de la Fuente, A. (Eds.) Gene Network Inference: Verification of Methods for Systems Genetic Data.33–47Heidelberg: Springerdoi: 10.1007/978-3-642-45161-4_3.

Waddell, S. J., Kamp von, A., Klamt, S., & Neyrolles, O. (2013)Host-pathogen interactionsSystems Biology of Tuberculosis107–126New York: Springerdoi: 10.1007/978-1-4614-4966-9_6.

Espinel-Rios, S., Bettenbrock, K., Klamt, S., Avalos, J. L., & Findeisen, R. (2023)Machine learning-supported cybergenetic modeling, optimization and control for synthetic microbial communitiesIn: 33rd European Symposium on Computer Aided Chemical Engineering, 2601–2606doi: 10.1016/B978-0-443-15274-0.50413-3.

Espinel-Rios, S., Kok, R., Klamt, S., Avalos, J. L., & Findeisen, R. (2023)Batch-to-Batch Optimization with Model Adaptation Leveraging Gaussian Processes: The Case of Optogenetically Assisted Microbial ConsortiaIn: International Conference on Control, Automation and Systems, 1292–1297doi: 10.23919/ICCAS59377.2023.10316811.

Espinel-Rios, S., Slaviero, G., Bettenbrock, K., Klamt, S., & Findeisen, R. (2023)Monitoring intracellular metabolite concentrations by moving horizon estimation based on kinetic modelingIn: IFAC-PapersOnLine, 4608–4613doi: 10.1016/j.ifacol.2023.10.968.

Espinel-Rios, S., Huber, N., Alcalá Orozco, E. A., Morabito, B., Rexer, T., Reichl, U., Klamt, S., & Findeisen, R. (2022)Cell-free biosynthesis meets dynamic optimization and control: a fed-batch frameworkIn: IFAC-PapersOnLine, 92–97doi: 10.1016/j.ifacol.2023.01.021.

Espinel-Rios, S., Morabito , B., Pohlodek, J., Bettenbrock, K., Klamt, S., & Findeisen, R. (2022)Optimal control and dynamic modulation of the ATPase gene expression for enforced ATP wasting in batch fermentationsIn: IFAC-PapersOnLine, 174–180doi: 10.1016/j.ifacol.2022.07.440.

Slaviero, G., Steuer, R., & Klamt, S. (2022)Using parameter sampling to explore key properties of E. coli's anaerobic metabolismIn: IFAC-PapersOnLine, 109–114doi: 10.1016/j.ifacol.2023.01.024.