Publications ARB group

Journal Article (141)

2024
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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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 (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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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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Klamt, S.; Kamp von, A.; Harder, B.-J.: Computergestütztes Design mikrobieller Zellfabriken. Biospektrum 25 (2), pp. 156 - 158 (2019)
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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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Schneider, P.; Klamt, S.: Characterizing and Ranking Computed Metabolic Engineering Strategies. Bioinformatics 35 (17), pp. 3063 - 3072 (2019)
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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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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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Witt, A.; Pozzi, R.; Diesch, S.; Hädicke, O.; Grammel, H.: New light on ancient enzymes – in vitro CO2 Fixation by Pyruvate Synthase of Desulfovibrio africanus and Sulfolobus acidocaldarius. The FEBS Journal 286 (22), pp. 4494 - 4508 (2019)
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Zahoor, A.; Küttner, F. T. F.; Blank , L. M.; Ebert , B. E.: Evaluation of pyruvate decarboxylase‐negative Saccharomyces cerevisiae strains for the production of succinic acid. Engineering in Life Sciences 19 (10), pp. 711 - 720 (2019)
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2018
Journal Article
Bosch, J.; Klamt, S.; Stoll, M.: Generalizing diffuse interface methods on graphs: non-smooth potentials and hypergraphs. SIAM Journal on Applied Mathematics 78 (3), pp. 1350 - 1377 (2018)
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Hädicke, O.; Kamp von, A.; Aydogan, T.; Klamt, S.: OptMDFpathway: Identification of metabolic pathways with maximal thermodynamic driving force and its application for analyzing the endogenous CO2 fixation potential of Escherichia coli. PLoS Computational Biology 14 (9), e1006492 (2018)
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Harder, B.-J.; Bettenbrock, K.; Klamt, S.: Temperature-dependent dynamic control of the TCA cycle increases volumetric productivity of itaconic acid production by Escherichia coli. Biotechnology and Bioengineering 115 (1), pp. 156 - 164 (2018)
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Klamt, S.; Mahadevan, R.; Hädicke, O.: When do two-stage processes outperform one-stage processes? Biotechnology Journal 13 (2), 1700539 (2018)
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Klamt, S.; Müller, S.; Regensburger, G.; Zanghellini, J.: A mathematical framework for yield (versus rate) optimization in constraint-based modeling and applications in metabolic engineering. Metabolic Engineering 47, pp. 153 - 169 (2018)
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Kyselova, L.; Kreitmayer, D.; Kremling, A.; Bettenbrock, K.: Type and capacity of glucose transport influences succinate yield in two-stage cultivations. Microbial Cell Factories 17, 132 (2018)
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Liu, X.; Reitsma, J. M.; Mamrosh, J. L.; Zhang, Y.; Straube, R.; Deshaies, R. J.: Cand1-Mediated Adaptive Exchange Mechanism Enables Variation in F-Box Protein Expression. Molecular Cell 69 (5), pp. 773 - 786 (2018)
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Mahour, R.; Klapproth, J.; Rexer, T.; Schildbach, A.; Klamt, S.; Pietzsch, M.; Rapp, E.; Reichl, U.: Establishment of a five-enzyme cell-free cascade for the synthesis of uridine diphosphate N-acetylglucosamine. Journal of Biotechnology 283, pp. 120 - 129 (2018)
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Nitzschke, A.; Bettenbrock, K.: All three quinone species play distinct roles in ensuring optimal growth under aerobic and fermentative conditions in E. coli K 12. PLoS One 13 (4), 20194699 (2018)
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Venayak, N.; Kamp von, A.; Klamt, S.; Mahadevan, R.: MoVE identifies metabolic valves to switch between phenotypic states. Nature Communications 9, 5332 (2018)
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2017
Journal Article
Hädicke, O.; Klamt, S.: EColiCore2: a reference model of the central metabolism of Escherichia coli and the relationships to its genome-scale parent model. Scientific Reports 7, 39647 (2017)
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