Characterizing and utilizing oxygen-dependent promoters for efficient dynamic metabolic engineering
- Julian Wichmann, Gerrich Behrendt, Simon Boecker, …, Gerrich Behrendt, Simon Boecker, Steffen Klamt
- Metab Eng, 10.1016/j.ymben.2023.04.006
Zymo-Parts: A Golden Gate Modular Cloning Toolbox for Heterologous Gene Expression in Zymomonas mobilis
- Gerrich Behrendt, Jonas Frohwitter, Maria Vlachonikolou, …, Maria Vlachonikolou, Steffen Klamt, Katja Bettenbrock
- ACS Synth Biol, 10.1021/acssynbio.2c00428
StrainDesign: a comprehensive Python package for computational design of metabolic networks
- Philipp Schneider, Pavlos Stephanos Bekiaris, Axel von Kamp, Steffen Klamt
- Bioinformatics, 10.1093/bioinformatics/btac632
Analyzing and Resolving Infeasibility in Flux Balance Analysis of Metabolic Networks
- Steffen Klamt, Axel von Kamp
- None, 10.3390/metabo12070585
Enabling anaerobic growth of Escherichia coli on glycerol in defined minimal medium using acetate as redox sink
- Simon Boecker, Sebastián Espinel-RÃos, Katja Bettenbrock, Steffen Klamt
- Metab Eng, 10.1016/j.ymben.2022.05.006
Deciphering the physiological response of Escherichia coli under high ATP demand
- Simon Boecker, Giulia Slaviero, Thorben Schramm, …, Ralf Steuer, Hannes Link, Steffen Klamt
- Mol Syst Biol, 10.15252/msb.202110504
CNApy: a CellNetAnalyzer GUI in Python for analyzing and designing metabolic networks
- Sven Thiele, Axel von Kamp, Pavlos Stephanos Bekiaris, …, Pavlos Stephanos Bekiaris, Philipp Schneider, Steffen Klamt
- Bioinformatics, 10.1093/bioinformatics/btab828
Designing microbial communities to maximize the thermodynamic driving force for the production of chemicals
- Pavlos Stephanos Bekiaris, Steffen Klamt
- PLoS Comput Biol, 10.1371/journal.pcbi.1009093
Increasing ATP turnover boosts productivity of 2,3-butanediol synthesis in Escherichia coli
- Simon Boecker, Björn-Johannes Harder, Regina Kutscha, Stefan Pflügl, Steffen Klamt
- Microb Cell Fact, 10.1186/s12934-021-01554-x
Blending industrial blast furnace gas with H 2 enables Acetobacterium woodii to efficiently co-utilize CO, CO 2 and H 2
- Katharina Novak, Christian Simon Neuendorf, Irmela Kofler, Nina Kieberger, Steffen Klamt, Stefan Pflügl
- Bioresour Technol, 10.1016/j.biortech.2020.124573
ATPase-based implementation of enforced ATP wasting in Saccharomyces cerevisiae for improved ethanol production
- Ahmed Zahoor, Katrin Messerschmidt, Simon Boecker, Steffen Klamt
- None, 10.1186/s13068-020-01822-9
Speeding up the core algorithm for the dual calculation of minimal cut sets in large metabolic networks
- Steffen Klamt, Radhakrishnan Mahadevan, Axel von Kamp
- BMC Bioinformatics, 10.1186/s12859-020-03837-3
SBML Level 3: an extensible format for the exchange and reuse of biological models
- Sarah M Keating, Dagmar Waltemath, Matthias König, …, Henning Hermjakob, John C Doyle, Michael Hucka
- Mol Syst Biol, 10.15252/msb.20199110
An extended and generalized framework for the calculation of metabolic intervention strategies based on minimal cut sets
- Philipp Schneider, Axel von Kamp, Steffen Klamt
- PLoS Comput Biol, 10.1371/journal.pcbi.1008110
MEMO: A Method for Computing Metabolic Modules for Cell-Free Production Systems
- Axel von Kamp, Steffen Klamt
- ACS Synth Biol, 10.1021/acssynbio.9b00434
Automatic construction of metabolic models with enzyme constraints
- Pavlos Stephanos Bekiaris, Steffen Klamt
- BMC Bioinformatics, 10.1186/s12859-019-3329-9
Optimization of a reduced enzymatic reaction cascade for the production of L-alanine
- Tobias J Gmelch, Josef M Sperl, Volker Sieber
- Sci Rep, 10.1038/s41598-019-48151-y
Augmenting Biogas Process Modeling by Resolving Intracellular Metabolic Activity
- Sören Weinrich, Sabine Koch, Fabian Bonk, …, Dirk Benndorf, Steffen Klamt, Florian Centler
- None, 10.3389/fmicb.2019.01095
Broadening the Scope of Enforced ATP Wasting as a Tool for Metabolic Engineering in Escherichia coli
- Simon Boecker, Ahmed Zahoor, Thorben Schramm, Hannes Link, Steffen Klamt
- Biotechnol J, 10.1002/biot.201800438
RedCom: A strategy for reduced metabolic modeling of complex microbial communities and its application for analyzing experimental datasets from anaerobic digestion
- Sabine Koch, Fabian Kohrs, Patrick Lahmann, …, Dirk Benndorf, Udo Reichl, Steffen Klamt
- PLoS Comput Biol, 10.1371/journal.pcbi.1006759
Characterizing and ranking computed metabolic engineering strategies
- Philipp Schneider, Steffen Klamt
- Bioinformatics, 10.1093/bioinformatics/bty1065
MoVE identifies metabolic valves to switch between phenotypic states
- Naveen Venayak, Axel von Kamp, Steffen Klamt, Radhakrishnan Mahadevan
- Nat Commun, 10.1038/s41467-018-07719-4
Establishment of a five-enzyme cell-free cascade for the synthesis of uridine diphosphate N-acetylglucosamine
- Reza Mahour, Jan Klapproth, Thomas F T Rexer, …, Markus Pietzsch, Erdmann Rapp, Udo Reichl
- J Biotechnol, 10.1016/j.jbiotec.2018.07.027
A mathematical framework for yield (vs. rate) optimization in constraint-based modeling and applications in metabolic engineering
- Steffen Klamt, Stefan Müller, Georg Regensburger, Jürgen Zanghellini
- Metab Eng, 10.1016/j.ymben.2018.02.001
Growth-coupled overproduction is feasible for almost all metabolites in five major production organisms
- Axel von Kamp, Steffen Klamt
- Nat Commun, 10.1038/ncomms15956
Use of CellNetAnalyzer in biotechnology and metabolic engineering
- Axel von Kamp, Sven Thiele, Oliver Hädicke, Steffen Klamt
- J Biotechnol, 10.1016/j.jbiotec.2017.05.001
From elementary flux modes to elementary flux vectors: Metabolic pathway analysis with arbitrary linear flux constraints
- Steffen Klamt, Georg Regensburger, Matthias P Gerstl, …, Radhakrishnan Mahadevan, Jürgen Zanghellini, Stefan Müller
- PLoS Comput Biol, 10.1371/journal.pcbi.1005409