Publications of Steffen Klamt

Bekiaris, P. S. & Klamt, S. (2020)Automatic construction of metabolic models with enzyme constraintsBMC Bioinformatics, 21, 19doi: 10.1186/s12859-019-3329-9.

Kamp von, A. & Klamt, S. (2020)MEMO: A Method for Computing Metabolic Modules for Cell-Free Production SystemsACS Synthetic Biology, 9 (3), 556–566doi: 10.1021/acssynbio.9b00434.

Klamt, S., Mahadevan, R., & Kamp von, A. (2020)Speeding up the core algorithm for the dual calculation of minimal cut sets in large metabolic networksBMC Bioinformatics, (21), 510doi: 10.1186/s12859-020-03837-3.

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., 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. (2020)MEMOTE for standardized genome-scale metabolic model testingNature Biotechnology, 38, 272–276doi: 10.1038/s41587-020-0446-y.

Schneider, P., Kamp von, A., & Klamt, S. (2020)An extended and generalized framework for the calculation of metabolic intervention strategies based on minimal cut setsPLoS Computational Biology, 16 (7), e1008110doi: 10.1371/journal.pcbi.1008110.

Zahoor, A., Messerschmidt, K., Boecker, S., & Klamt, S. (2020)ATPase-based implementation of enforced ATP wasting in Saccharomyces cerevisiae for improved ethanol productionBiotechnology for Biofuels, (13), 185doi: 10.1186/s13068-020-01822-9.

Boecker, S., Zahoor, A., Schramm, T., Link, H., & Klamt, S. (2019)Broadening the Scope of Enforced ATP Wasting as a Tool for Metabolic Engineering in Escherichia coli.Biotechnology Journal, 14 (9), 1800438doi: 10.1002/biot.201800438.

Klamt, S., Kamp von, A., & Harder, B.-J. (2019)Computergestütztes Design mikrobieller ZellfabrikenBiospektrum, 25 (2), 156–158doi: 10.1007/s12268-019-1015-0.

Koch, S., Kohrs, F., Lahmann, P., Bissinger, T., Wendschuh, S., Benndorf, D., Reichl, U., & Klamt, S. (2019)RedCom: A strategy for reduced metabolic modeling of complex microbial communities and its application for analyzing experimental datasets from anaerobic digestionPLoS Computational Biology, 15 (2), e1006759doi: 10.1371/journal.pcbi.1006759.

Schneider, P. & Klamt, S. (2019)Characterizing and Ranking Computed Metabolic Engineering StrategiesBioinformatics, 35 (17), 3063–3072doi: 10.1093/bioinformatics/bty1065.

Thiele, S., Heise, S., Hessenkemper, W., Bongartz, H., Fensky, M., Schaper, F., & Klamt, S. (2019)Designing optimal experiments to discriminate interaction graph modelsIEEE ACM Transactions on Computational Biology and Bioinformatics, 16 (3), 925–935doi: 10.1109/TCBB.2018.2812184.

Weinrich, S., Koch, S., Bonk, F., Popp, D., Benndorf, D., Klamt, S., & Centler, F. (2019)Augmenting Biogas Process Modeling by Resolving Intracellular Metabolic ActivityFrontiers in Microbiology, 10, 1095doi: 10.3389/fmicb.2019.01095.

Bosch, J., Klamt, S., & Stoll, M. (2018)Generalizing diffuse interface methods on graphs: non-smooth potentials and hypergraphsSIAM Journal on Applied Mathematics, 78 (3), 1350–1377doi: 10.1137/17M1117835.

Hädicke, O., Kamp von, A., Aydogan, T., & Klamt, S. (2018)OptMDFpathway: Identification of metabolic pathways with maximal thermodynamic driving force and its application for analyzing the endogenous CO2 fixation potential of Escherichia coliPLoS Computational Biology, 14 (9), e1006492doi: 10.1371/journal.pcbi.1006492.

Harder, B.-J., Bettenbrock, K., & Klamt, S. (2018)Temperature-dependent dynamic control of the TCA cycle increases volumetric productivity of itaconic acid production by Escherichia coli.Biotechnology and Bioengineering, 115 (1), 156–164doi: 10.1002/bit.26446.

Klamt, S., Mahadevan, R., & Hädicke, O. (2018)When do two-stage processes outperform one-stage processes?Biotechnology Journal, 13 (2), 1700539doi: 10.1002/biot.201700539.

Klamt, S., Müller, S., Regensburger, G., & Zanghellini, J. (2018)A mathematical framework for yield (versus rate) optimization in constraint-based modeling and applications in metabolic engineeringMetabolic Engineering, 47, 153–169doi: 10.1016/j.ymben.2018.02.001.

Mahour, R., Klapproth, J., Rexer, T., Schildbach, A., Klamt, S., Pietzsch, M., Rapp, E., & Reichl, U. (2018)Establishment of a five-enzyme cell-free cascade for the synthesis of uridine diphosphate N-acetylglucosamineJournal of Biotechnology, 283, 120–129doi: 10.1016/j.jbiotec.2018.07.027.

Venayak, N., Kamp von, A., Klamt, S., & Mahadevan, R. (2018)MoVE identifies metabolic valves to switch between phenotypic statesNature Communications, 9, 5332doi: 10.1038/s41467-018-07719-4.

Hädicke, O. & Klamt, S. (2017)EColiCore2: a reference model of the central metabolism of Escherichia coli and the relationships to its genome-scale parent modelScientific Reports, 7, 39647 doi: 10.1038/srep39647.