Publications ARB group

Journal Article

Kamp von, A.: LumbriCyc: towards metabolic modelling of earthworms. npj Systems biology and applications 12, 37 (2026)

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Journal Article

Kostanjšek, M.; Raynal, A.; Dimopoulos, G.; Behrendt, G.; Martins Dos Santos, V. A. P.; Beekwilder, J.; Batianis, C.; Weusthuis, R. A.; Asin-García, E.; Bisschops, M. M. M.: Rhodo-Box: A Synthetic Biology Toolbox to Facilitate Metabolic Engineering of Rhodobacter sphaeroides. ACS Synthetic Biology (2026)

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2025

Journal Article

Klamt, S.; Zanghellini, J.; Kamp von, A.: Minimal cut sets in metabolic networks: from conceptual foundations to applications in metabolic engineering and biomedicine. Briefings in Bioinformatics 26 (2), bbaf188 (2025)

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2024

Journal Article

Bauer, J.; Klamt, S.: OptMSP: A Toolbox for Designing Optimal Multi-Stage (Bio)Processes. Journal of Biotechnology 383, pp. 94 - 102 (2024)

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Journal Article

Behrendt, G.; Vlachonikolou, M.; Tietgens, H.; Bettenbrock, K.: Construction and comparison of different vehicles for heterologous gene expression in Zymomonas mobilis. Microbial Biotechnology 17 (1), e14381 (2024)

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Journal Article

Dietz, K.; Sagstetter, C.; Speck, M.; Roth, A.; Klamt, S.; Fabarius, J. T.: A novel engineered strain of Methylorubrum extorquens for methylotrophic production of glycolic acid. Microbial Cell Factories 23, 344 (2024)

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Journal Article

Espinel-Rios, S.; Behrendt, G.; Bauer, J.; Morabito, B.; Pohlodek, J.; Schütze, A.; Findeisen, R.; Bettenbrock, K.; Klamt, S.: Experimentally implemented dynamic optogenetic optimization of ATPase expression using knowledge-based and Gaussian-process-supported models. Process Biochemistry (143), pp. 174 - 185 (2024)

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Journal Article

Espinel-Rios, S.; Morabito, B.; Pohlodek, J.; Bettenbrock, K.; Klamt, S.; Findeisen, R.: Toward a modeling, optimization, and predictive control framework for fed-batch metabolic cybergenetics. Biotechnology and Bioengineering 121 (1), pp. 366 - 379 (2024)

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Journal Article

Frohwitter, J.; Behrendt, G.; Klamt, S.; Bettenbrock, K.: A new Zymomonas mobilis platform strain for the efficient production of chemicals. Microbial Cell Factories 23, 143 (2024)

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Journal Article

Huber, N.; Alcalá Orozco, E. A.; Rexer, T.; Reichl, U.; Klamt, S.: Model-based optimization of cell-free enzyme cascades exemplified for the production of GDP-fucose. Metabolic Engineering 81, pp. 10 - 25 (2024)

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Journal Article

Kutscha, R.; Tomin, T.; Birner-Gruenberger, R.; Bekiaris, P. S.; Klamt, S.; Pflügl, S.: Efficiency of acetate-based isopropanol synthesis in Escherichia coli W is controlled by ATP demand. Biotechnology for Biofuels and Bioproducts 17, 110 (2024)

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Journal Article

Schulz-Mirbach, H.; Krüsemann, J. L.; Andreadaki, T.; Nerlich, J. N.; Mavrothalassiti, E.; Boecker, S.; Schneider, P.; Weresow, M.; Abdelwahab, O.; Paczia, N. et al.; Dronsella, B.; Erb, T. J.; Bar-Even, A.; Klamt, S.; Lindner, S. N.: Engineering new-to-nature biochemical conversions by combining fermentative metabolism with respiratory modules. Nature Communications 15 (1), 6725 (2024)

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2023

Journal Article

Alcalá Orozco, E. A.; Grote, V.; Fiebig, T.; Klamt, S.; Reichl, U.; Rexer, T.: A Cell‐Free Multi‐enzyme Cascade Reaction for the Synthesis of CDP‐Glycerol. ChemBioChem: A European Journal of Chemical Biology 24 (21), e202300463 (2023)

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Journal Article

Bekiaris, P. S.; Klamt, S.: Network-wide thermodynamic constraints shape NAD(P)H cofactor specificity of biochemical reactions. Nature Communications 14, 4660 (2023)

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Journal Article

Boecker, S.; Schulze, P.; Klamt, S.: Growth-coupled anaerobic production of isobutanol from glucose in minimal medium with Escherichia coli. Biotechnology for Biofuels and Bioproducts 16, 148 (2023)

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Journal Article

Hülsmann, J.; Fraune, T.; Dodawatta, B.; Reuter, F.; Beutner, M.; Beck, V.; Hackert-Oschätzchen, M.; Ohl , C. D.; Bettenbrock, K.; Janiga, G. et al.; Wippermann, J.; Wacker, M.: Integrated biophysical matching of bacterial nanocellulose coronary artery bypass grafts towards bioinspired artery typical functions. Scientific Reports 13 (1), 18274 (2023)

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Journal Article

Kamp von, A.; Klamt, S.: Balancing biomass reaction stoichiometry and measured fluxes in flux balance analysis. Bioinformatics 39 (10), btad600 (2023)

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Journal Article

Wichmann, J.; Behrendt, G.; Boecker, S.; Klamt, S.: Characterizing and utilizing oxygen-dependent promoters for efficient dynamic metabolic engineering. Metabolic Engineering 77, pp. 199 - 207 (2023)

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2022

Journal Article

Behrendt, G.; Frohwitter, J.; Vlachonikolou, M.; Klamt, S.; Bettenbrock, K.: Zymo-Parts: A Golden Gate Modular Cloning Toolbox for Heterologous Gene Expression in Zymomonas mobilis. ACS Synthetic Biology 11 (11), pp. 3855 - 3864 (2022)

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Journal Article

Boecker, S.; Espinel-Rios, S.; Bettenbrock, K.; Klamt, S.: Enabling anaerobic growth of Escherichia coli on glycerol in defined minimal medium using acetate as redox sink. Metabolic Engineering 73, pp. 50 - 57 (2022)

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Journal Article

Espinel-Rios, S.; Bettenbrock, K.; Klamt, S.; Findeisen, R.: Maximizing batch fermentation efficiency by constrained model-based optimization and predictive control of adenosine triphosphate turnover. AIChE-Journal 68 (4), e17555 (2022)

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Journal Article

Klamt, S.; Kamp von, A.: Analyzing and Resolving Infeasibility in Flux Balance Analysis of Metabolic Networks. Metabolites 12 (7), 585 (2022)

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Journal Article

Mahour, R.; Lee, J. W.; Grimpe, P.; Boecker, S.; Grote, V.; Klamt, S.; Seidel-Morgenstern, A.; Rexer, T.; Reichl, U.: Cell‐free multi‐enzyme synthesis and purification of uridine diphosphate galactose. ChemBioChem 23 (2), e202100361 (2022)

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Journal Article

Petras, D.; Phelan, V. V.; Acharya, D.; Allen, A. E.; Aron, A. T.; Bandeira, N.; Bowen, B. P.; Belle-Oudry, D.; Boecker, S.; Cummings, D. A. et al.; Deutsch, J. M.; Fahy, E.; Garg, N.; Gregor, R.; Handelsman, J.; Navarro-Hoyos, M.; Jarmusch, A. K.; Jarmusch, S. A.; Louie, K.; Maloney, K. N.; Marty, M. T.; Meijler, M. M.; Mizrahi, I.; Neve, R. L.; Northen, T. R.; Molina-Santiago, C.; Panitchpakdi, M.; Pullman, B.; Puri, A. W.; Schmid, R.; Subramaniam, S.; Thukral, M.; Vasquez-Castro, F.; Dorrestein, P. C.; Wang, M.: GNPS Dashboard: collaborative exploration of mass spectrometry data in the web browser. Nature Methods 19, pp. 134 - 136 (2022)

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Journal Article

Schneider, P.; Bekiaris, P. S.; Kamp von, A.; Klamt, S.: StrainDesign: a Comprehensive Python Package for Computational Design of Metabolic Networks. Bioinformatics 38 (21), pp. 4981 - 4983 (2022)

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Journal Article

Thiele, S.; Kamp von, A.; Bekiaris, P. S.; Schneider, P.; Klamt, S.: CNApy: a CellNetAnalyzer GUI in Python for Analyzing and Designing Metabolic Networks. Bioinformatics 38 (5), pp. 1467 - 1469 (2022)

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Journal Article

Zhaopeng, L.; Nees, M.; Bettenbrock, K.; Rinas, U.: Is energy excess the initial trigger of carbon overflow metabolism? Transcriptional network response of carbon-limited Escherichia coli to transient carbon excess. Microbial Cell Factories 21, 67 (2022)

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2021

Journal Article

Bekiaris, P. S.; Klamt, S.: Designing microbial communities to maximize the thermodynamic driving force for the production of chemicals. PLoS Computational Biology 17 (6), e1009093 (2021)

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Journal Article

Boecker, S.; Harder, B.-J.; Kutscha, R.; Pflügl, S.; Klamt, S.: Increasing ATP turnover boosts productivity of 2,3-butanediol synthesis in Escherichia coli. Microbial Cell Factories 20, 63 (2021)

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Journal Article

Boecker, S.; Slaviero, G.; Schramm, T.; Szymanski, W.; Steuer , R.; Link, H.; Klamt, S.: Deciphering the physiological response of Escherichia coli under high ATP demand. Molecular Systems Biology 17, e10504 (2021)

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Journal Article

Harriehausen, I.; Bollmann, J.; Carneiro, T.; Bettenbrock, K.; Seidel-Morgenstern, A.: Characterization of an Immobilized Amino Acid Racemase for Potential Application in Enantioselective Chromatographic Resolution Processes. Catalysts 11 (6), 726 (2021)

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Journal Article

Novak, K.; Neuendorf, C. S.; Kofler, I.; Kieberger, N.; Klamt, S.; Pflügl, S.: Blending industrial blast furnace gas with H 2 enables Acetobacterium woodii to efficiently co-utilize CO, CO2 and H2. Bioresource Technology 323, 124573 (2021)

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Journal Article

Schneider, P.; Radhakrishnan, M.; Klamt, S.: Systematizing the different notions of growth-coupled product synthesis and a single framework for computing corresponding strain designs. Biotechnology Journal 16, 2100236 (2021)

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2020

Journal Article

Bekiaris, P. S.; Klamt, S.: Automatic construction of metabolic models with enzyme constraints. BMC Bioinformatics 21, 19 (2020)

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Journal Article

Carneiro, T.; Wrzosek, K.; Bettenbrock, K.; Lorenz, H.; Seidel-Morgenstern, A.: Immobilization of an amino acid racemase for application in crystallization‐based chiral resolutions of asparagine monohydrate. Engineering in Life Sciences 20 (12), pp. 550 - 561 (2020)

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Journal Article

Kamp von, A.; Klamt, S.: MEMO: A Method for Computing Metabolic Modules for Cell-Free Production Systems. ACS Synthetic Biology 9 (3), pp. 556 - 566 (2020)

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Journal Article

Klamt, S.; Mahadevan, R.; Kamp von, A.: Speeding up the core algorithm for the dual calculation of minimal cut sets in large metabolic networks. BMC Bioinformatics (21), 510 (2020)

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Journal Article

Lieven, C.; Beber, M. E.; Olivier, B. G.; Bergmann, F. T.; Ataman, M.; Babaei, P.; Bartell, J. A.; Blank, L. M.; Chauhan, S.; Correia, K. et al.; Diener, C.; Dräger, A.; Ebert, B. E.; Edirisinghe, J. N.; Faria, J. P.; Feist, A. M.; Fengos, G.; Fleming, R. M. T.; García-Jiménez, B.; Hatzimanikatis, V.; van Helvoirt, W.; Henry, C. S.; Hermjakob, H.; Herrgård, M. J.; Kaafarani, A.; Kim, H. U.; King, Z.; Klamt, S.; Klipp, E.; Koehorst, J. J.; König, M.; Lakshmanan, M.; Lee, D.-Y.; Lee, S. Y.; Lee, S.; Lewis, N. E.; Liu, F.; Ma, H.; Machado, D.; Mahadevan, R.; Maia, P.; Mardinoglu, A.; Medlock, G. L.; Monk, J. M.; Nielsen, J.; Nielsen, L. K.; Nogales, J.; Nookaew, I.; Palsson, B. O.; Papin, J. A.; Patil, K. R.; Poolman, M.; Price, N. D.; Resendis-Antonio, O.; Richelle, A.; Rocha, I.; Sánchez, B. J.; Schaap, P. J.; Malik Sheriff, R. S.; Shoaie, S.; Sonnenschein, N.; Teusink, B.; Vilaça, P.; Vik, J. O.; Wodke, J. A. H.; Xavier, J. C.; Yuan, Q.; Zakhartsev, M.; Zhang, C.: MEMOTE for standardized genome-scale metabolic model testing. Nature Biotechnology 38, pp. 272 - 276 (2020)

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supplementary-material

Journal Article

Rexer, T.; Wenzel, L.; Hoffmann, M.; Tischlik, S.; Bergmann, C.; Grote, V.; Boecker, S.; Bettenbrock, K.; Schildbach, A.; Kottler, R. et al.; Mahour, R.; Rapp, E.; Pietzsch, M.; Reichl, U.: Synthesis of lipid-linked oligosaccharides by a compartmentalized multi-enzyme cascade for the in vitro N-glycosylation of peptides. Journal of Biotechnology 322 (10), pp. 54 - 65 (2020)

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Journal Article

Schneider, P.; Kamp von, A.; Klamt, S.: An extended and generalized framework for the calculation of metabolic intervention strategies based on minimal cut sets. PLoS Computational Biology 16 (7), e1008110 (2020)

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Journal Article

Schütze, A.; Benndorf, D.; Püttker, S.; Kohrs, F.; Bettenbrock, K.: The Impact of ackA, pta, and ackA-pta Mutations on Growth, Gene Expression and Protein Acetylation in Escherichia coli K-12. Frontiers in Microbiology 11, 233 (2020)

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Journal Article

Zahoor, A.; Messerschmidt, K.; Boecker, S.; Klamt, S.: ATPase-based implementation of enforced ATP wasting in Saccharomyces cerevisiae for improved ethanol production. Biotechnology for Biofuels and Bioproducts (13), 185 (2020)

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2019

Journal Article

Boecker, S.; Zahoor, A.; Schramm, T.; Link, H.; Klamt, S.: Broadening the Scope of Enforced ATP Wasting as a Tool for Metabolic Engineering in Escherichia coli. Biotechnology Journal 14 (9), 1800438 (2019)

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Journal Article

Kalnenieks, U.; Balodite, E.; Strähler, S.; Strazdina, I.; Rex, J.; Pentjuss, A.; Fuchino, K.; Bruheim, P.; Rutkis, R.; Pappas, K. M. et al.; Poole, R. K.; Sawodny, O.; Bettenbrock, K.: Improvement of Acetaldehyde Production in Zymomonas mobilis by Engineering of Its Aerobic Metabolism. Frontiers in Microbiology 10, 2533 (2019)

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Journal Article

Klamt, S.; Kamp von, A.; Harder, B.-J.: Computergestütztes Design mikrobieller Zellfabriken. Biospektrum 25 (2), pp. 156 - 158 (2019)

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Journal Article

Koch, S.; Kohrs, F.; Lahmann, P.; Bissinger, T.; Wendschuh, S.; Benndorf, D.; Reichl, U.; Klamt, S.: RedCom: A strategy for reduced metabolic modeling of complex microbial communities and its application for analyzing experimental datasets from anaerobic digestion. PLoS Computational Biology 15 (2), e1006759 (2019)

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Journal Article

Schneider, P.; Klamt, S.: Characterizing and Ranking Computed Metabolic Engineering Strategies. Bioinformatics 35 (17), pp. 3063 - 3072 (2019)

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Journal Article

Thiele, S.; Heise, S.; Hessenkemper, W.; Bongartz, H.; Fensky, M.; Schaper, F.; Klamt, S.: Designing optimal experiments to discriminate interaction graph models. IEEE ACM Transactions on Computational Biology and Bioinformatics 16 (3), pp. 925 - 935 (2019)

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Journal Article

Weinrich, S.; Koch, S.; Bonk, F.; Popp, D.; Benndorf, D.; Klamt, S.; Centler, F.: Augmenting Biogas Process Modeling by Resolving Intracellular Metabolic Activity. Frontiers in Microbiology 10, 1095 (2019)

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