Publications ARB group

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)

MPG.PuRe

Journal Article

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

MPG.PuRe

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)

MPG.PuRe

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)

MPG.PuRe

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)

MPG.PuRe

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)

MPG.PuRe

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)

MPG.PuRe

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)

MPG.PuRe

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)

MPG.PuRe

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)

MPG.PuRe

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)

MPG.PuRe

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)

MPG.PuRe

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)

MPG.PuRe

2020

Journal Article

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

MPG.PuRe

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)

MPG.PuRe

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)

MPG.PuRe

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)

MPG.PuRe

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)

MPG.PuRe

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)

MPG.PuRe

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)

MPG.PuRe

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)

MPG.PuRe

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 (13), 185 (2020)

MPG.PuRe

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)

MPG.PuRe

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)

MPG.PuRe

Journal Article

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

MPG.PuRe

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)

MPG.PuRe

Journal Article

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

MPG.PuRe

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)

MPG.PuRe

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)

MPG.PuRe

Journal Article

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)

MPG.PuRe

Journal Article

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)

MPG.PuRe

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)

MPG.PuRe

Journal Article

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)

MPG.PuRe

Journal Article

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)

MPG.PuRe

Journal Article

Klamt, S.; Mahadevan, R.; Hädicke, O.: When do two-stage processes outperform one-stage processes? Biotechnology Journal 13 (2), 1700539 (2018)

MPG.PuRe

Journal Article

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)

MPG.PuRe

Journal Article

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)

MPG.PuRe

Journal Article

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)

MPG.PuRe

Journal Article

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)

MPG.PuRe

Journal Article

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)

MPG.PuRe

Journal Article

Venayak, N.; Kamp von, A.; Klamt, S.; Mahadevan, R.: MoVE identifies metabolic valves to switch between phenotypic states. Nature Communications 9, 5332 (2018)

MPG.PuRe

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)

MPG.PuRe

Journal Article

Kamp von, A.; Klamt, S.: Growth-coupled overproduction is feasible for almost all metabolites in five major production organisms. Nature Communications 8, 15926 (2017)

MPG.PuRe

Journal Article

Kamp von, A.; Thiele, S.; Hädicke, O.; Klamt, S.: Use of CellNetAnalyzer in biotechnology and metabolic engineering. Journal of Biotechnology 261, pp. 221 - 228 (2017)

MPG.PuRe

Journal Article

Klamt, S.; Regensburger, G.; Gerstl, P.M.; Jungreuthmayer, C.; Schuster, S.; Mahadevan, R.; Zanghellini, J.; Müller, S.: From elementary flux modes to elementary flux vectors: Metabolic pathway analysis with arbitrary linear flux constraints. PLoS Computational Biology 13 (4), e1005409 (2017)

MPG.PuRe

Journal Article

Prigent, S.; Frioux, C.; Dittami, S. M.; Thiele, S.; Larhlimi, A.; Collet, G.; Gutknecht, F.; Got, J.; Eveillard, D.; Bourdon, J. et al.; Plewniak, F.; Tonon, T.; Siegel, A.: Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks. PLoS Computational Biology 13, e1005276 (2017)

MPG.PuRe

Journal Article

Straube, R.: Analysis of network motifs in cellular regulation: Structural similarities, input–output relations and signal integration. Biosystems 162, pp. 2015 - 232 (2017)

MPG.PuRe

Journal Article

Straube, R.; Shah, M.; Flockerzi, D.; Wolf, D.A.: Trade-off and flexibility in the dynamic regulation of the cullin-RING ubiquitin ligase repertoire. PLoS Computational Biology 13 (11), e1005869 (2017)

MPG.PuRe

Journal Article

Zander, D.; Samaga, D.; Straube, R.; Bettenbrock, K.: Bistability and Nonmonotonic Induction of the lac Operon in the Natural Lactose Uptake System. Biophysical Journal 112 (9), pp. 1984 - 1996 (2017)

MPG.PuRe