Steffen Klamt
Journal Article (111)
1.
Journal Article
383, pp. 94 - 102 (2024)
OptMSP: A Toolbox for Designing Optimal Multi-Stage (Bio)Processes. Journal of Biotechnology 2.
Journal Article
121 (1), pp. 366 - 379 (2024)
Toward a modeling, optimization, and predictive control framework for fed-batch metabolic cybergenetics. Biotechnology and Bioengineering 3.
Journal Article
81, pp. 10 - 25 (2024)
Model-based optimization of cell-free enzyme cascades exemplified for the production of GDP-fucose. Metabolic Engineering 4.
Journal Article
24 (21), e202300463 (2023)
A Cell‐Free Multi‐enzyme Cascade Reaction for the Synthesis of CDP‐Glycerol. ChemBioChem: A European Journal of Chemical Biology 5.
Journal Article
14, 4660 (2023)
Network-wide thermodynamic constraints shape NAD(P)H cofactor specificity of biochemical reactions. Nature Communications 6.
Journal Article
16, 148 (2023)
Growth-coupled anaerobic production of isobutanol from glucose in minimal medium with Escherichia coli. Biotechnology for Biofuels and Bioproducts 7.
Journal Article
39 (10), btad600 (2023)
Balancing biomass reaction stoichiometry and measured fluxes in flux balance analysis. Bioinformatics 8.
Journal Article
77, pp. 199 - 207 (2023)
Characterizing and utilizing oxygen-dependent promoters for efficient dynamic metabolic engineering. Metabolic Engineering 9.
Journal Article
11 (11), pp. 3855 - 3864 (2022)
Zymo-Parts: A Golden Gate Modular Cloning Toolbox for Heterologous Gene Expression in Zymomonas mobilis. ACS Synthetic Biology 10.
Journal Article
73, pp. 50 - 57 (2022)
Enabling anaerobic growth of Escherichia coli on glycerol in defined minimal medium using acetate as redox sink. Metabolic Engineering 11.
Journal Article
68 (4), e17555 (2022)
Maximizing batch fermentation efficiency by constrained model-based optimization and predictive control of adenosine triphosphate turnover. AIChE-Journal 12.
Journal Article
12 (7), 585 (2022)
Analyzing and Resolving Infeasibility in Flux Balance Analysis of Metabolic Networks. Metabolites 13.
Journal Article
23 (2), e202100361 (2022)
Cell‐free multi‐enzyme synthesis and purification of uridine diphosphate galactose. ChemBioChem 14.
Journal Article
38 (21), pp. 4981 - 4983 (2022)
StrainDesign: a Comprehensive Python Package for Computational Design of Metabolic Networks. Bioinformatics 15.
Journal Article
38 (5), pp. 1467 - 1469 (2022)
CNApy: a CellNetAnalyzer GUI in Python for Analyzing and Designing Metabolic Networks. Bioinformatics 16.
Journal Article
17 (6), e1009093 (2021)
Designing microbial communities to maximize the thermodynamic driving force for the production of chemicals. PLoS Computational Biology 17.
Journal Article
20, 63 (2021)
Increasing ATP turnover boosts productivity of 2,3-butanediol synthesis in Escherichia coli. Microbial Cell Factories 18.
Journal Article
17, e10504 (2021)
Deciphering the physiological response of Escherichia coli under high ATP demand. Molecular Systems Biology 19.
Journal Article
323, 124573 (2021)
Blending industrial blast furnace gas with H 2 enables Acetobacterium woodii to efficiently co-utilize CO, CO2 and H2. Bioresource Technology 20.
Journal Article
16, 2100236 (2021)
Systematizing the different notions of growth-coupled product synthesis and a single framework for computing corresponding strain designs. Biotechnology Journal 21.
Journal Article
21, 19 (2020)
Automatic construction of metabolic models with enzyme constraints. BMC Bioinformatics 22.
Journal Article
9 (3), pp. 556 - 566 (2020)
MEMO: A Method for Computing Metabolic Modules for Cell-Free Production Systems. ACS Synthetic Biology 23.
Journal Article
Speeding up the core algorithm for the dual calculation of minimal cut sets in large metabolic networks. BMC Bioinformatics (21), 510 (2020)
24.
Journal Article
38, pp. 272 - 276 (2020)
MEMOTE for standardized genome-scale metabolic model testing. Nature Biotechnology 25.
Journal Article
16 (7), e1008110 (2020)
An extended and generalized framework for the calculation of metabolic intervention strategies based on minimal cut sets. PLoS Computational Biology 26.
Journal Article
ATPase-based implementation of enforced ATP wasting in Saccharomyces cerevisiae for improved ethanol production. Biotechnology for Biofuels (13), 185 (2020)
27.
Journal Article
14 (9), 1800438 (2019)
Broadening the Scope of Enforced ATP Wasting as a Tool for Metabolic Engineering in Escherichia coli. Biotechnology Journal 28.
Journal Article
25 (2), pp. 156 - 158 (2019)
Computergestütztes Design mikrobieller Zellfabriken. Biospektrum 29.
Journal Article
15 (2), e1006759 (2019)
RedCom: A strategy for reduced metabolic modeling of complex microbial communities and its application for analyzing experimental datasets from anaerobic digestion. PLoS Computational Biology 30.
Journal Article
35 (17), pp. 3063 - 3072 (2019)
Characterizing and Ranking Computed Metabolic Engineering Strategies. Bioinformatics 31.
Journal Article
16 (3), pp. 925 - 935 (2019)
Designing optimal experiments to discriminate interaction graph models. IEEE ACM Transactions on Computational Biology and Bioinformatics 32.
Journal Article
10, 1095 (2019)
Augmenting Biogas Process Modeling by Resolving Intracellular Metabolic Activity. Frontiers in Microbiology 33.
Journal Article
78 (3), pp. 1350 - 1377 (2018)
Generalizing diffuse interface methods on graphs: non-smooth potentials and hypergraphs. SIAM Journal on Applied Mathematics 34.
Journal Article
14 (9), e1006492 (2018)
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 35.
Journal Article
115 (1), pp. 156 - 164 (2018)
Temperature-dependent dynamic control of the TCA cycle increases volumetric productivity of itaconic acid production by Escherichia coli. Biotechnology and Bioengineering 36.
Journal Article
13 (2), 1700539 (2018)
When do two-stage processes outperform one-stage processes? Biotechnology Journal 37.
Journal Article
47, pp. 153 - 169 (2018)
A mathematical framework for yield (versus rate) optimization in constraint-based modeling and applications in metabolic engineering. Metabolic Engineering 38.
Journal Article
283, pp. 120 - 129 (2018)
Establishment of a five-enzyme cell-free cascade for the synthesis of uridine diphosphate N-acetylglucosamine. Journal of Biotechnology 39.
Journal Article
9, 5332 (2018)
MoVE identifies metabolic valves to switch between phenotypic states. Nature Communications 40.
Journal Article
7, 39647 (2017)
EColiCore2: a reference model of the central metabolism of Escherichia coli and the relationships to its genome-scale parent model. Scientific Reports 41.
Journal Article
8, 15926 (2017)
Growth-coupled overproduction is feasible for almost all metabolites in five major production organisms. Nature Communications 42.
Journal Article
261, pp. 221 - 228 (2017)
Use of CellNetAnalyzer in biotechnology and metabolic engineering. Journal of Biotechnology 43.
Journal Article
13 (4), e1005409 (2017)
From elementary flux modes to elementary flux vectors: Metabolic pathway analysis with arbitrary linear flux constraints. PLoS Computational Biology 44.
Journal Article
32 (5), pp. 730 - 737 (2016)
Exact quantification of cellular robustness in genome-scale metabolic networks. Bioinformatics 45.
Journal Article
38, pp. 29 - 37 (2016)
Model-Based metabolic engineering enables high yield itaconic acid production by Escherichia coli. Metabolic Engineering 46.
Journal Article
9, 17 (2016)
Predicting compositions of microbial communities from stoichiometric models with applications for the biogas process. Biotechnology for Biofuels 47.
Journal Article
17 (17), 252 (2016)
TRaCE+: Ensemble inference of gene regulatory networks from transcriptional expression profiles of gene knock-out experiments. BMC Bioinformatics 48.
Journal Article
2, 16032 (2016)
MUFINS: multi-formalism interaction network simulator. npj Systems Biology and Applications 49.
Journal Article
33 (4), pp. 336 - 339 (2015)
Silence on the relevant literature and errors in implementation. Nature Biotechnology 50.
Journal Article
11 (4), e1004192 (2015)
Disentangling the Complexity of HGF Signaling by Combining Qualitative and Quantitative Modeling. PLoS Computational Biology 51.
Journal Article
9, 48 (2015)
An algorithm for the reduction of genome-scale metabolic network models to meaningful core models. BMC Systems Biology 52.
Journal Article
112 (10), pp. 2195 - 2199 (2015)
Enforced ATP futile cycling increases specific productivity and yield of anaerobic lactate production in Escherichia coli. Biotechnology and Bioengineering 53.
Journal Article
43 (6), pp. 1140 - 1145 (2015)
Manipulation of the ATP pool as a tool for metabolic engineering. Biochemical Society Transactions (London) 54.
Journal Article
30, pp. 166 - 178 (2015)
On the feasibility of growth-coupled product synthesis in microbial strains. Metabolic Engineering 55.
Journal Article
31 (17), pp. 2844 - 2851 (2015)
Genome-scale strain designs based on regulatory minimal cut sets. Bioinformatics 56.
Journal Article
4 (6), pp. 350 - 361 (2015)
Network-Based Analysis of Nutraceuticals in Human Hepatocellular Carcinomas Reveals Mechanisms of Chemopreventive Action. CPT: Pharmacometrics & Systems Pharmacology 57.
Journal Article
11, 795 (2015)
T160‐phosphorylated CDK2 defines threshold for HGF‐dependent proliferation in primary hepatocytes. Molecular Systems Biology 58.
Journal Article
16 (1), 345 (2015)
Extended notions of sign consistency to relate experimental data to signaling and regulatory network topologies. BMC Bioinformatics 59.
Journal Article
21 (1), pp. 46 - 48 (2015)
Computational Systems Biology — neues Fach in den Lebenswissenschaften. Biospektrum 60.
Journal Article
13, p. 128 - 128 (2014)
Cyanobacterial biofuels: new insights and strain design strategies revealed by computational modeling. Microbial Cell Factories 61.
Journal Article
10 (1), e1003378 (2014)
Enumeration of Smallest Intervention Strategies in Genome-Scale Metabolic Networks. PLoS Computational Biology 62.
Journal Article
14, p. 72 (2014)
The avian cell line AGE1.CR.pIX characterized by metabolic flux analysis. BMC Biotechnology 63.
Journal Article
124, pp. 26 - 38 (2014)
A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models. Biosystems 64.
Journal Article
7, p. 135 (2013)
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formlisms and tools. BMC Systems Biology 65.
Journal Article
29 (2), pp. 246 - 254 (2013)
An effective framework for reconstructing gene regulatory networks from genetical genomics data. Bioinformatics 66.
Journal Article
9 (7), pp. 1576 - 1583 (2013)
Bridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical models. Molecular BioSystems 67.
Journal Article
12, 84 (2013)
In silico profiling of Escherichia coli and Saccharomyces cerevisiae as terpenoid factories. Microbial Cell Factories 68.
Journal Article
110 (10), pp. 2633 - 2642 (2013)
Evaluating differences of metabolic performances: Statistical methods and their application to animal cell cultivations. Biotechnology and Bioengineering 69.
Journal Article
14 (1), p. 318 (2013)
Comparison and improvement of algorithms for computing minimal cut sets. BMC Bioinformatics 70.
Journal Article
9 (9), p. e1003204 (2013)
Detecting and Removing Inconsistencies between Experimental Data and Signaling Network Topologies Using Integer Linear Programming on Interaction Graphs. PLoS Computational Biology 71.
Journal Article
7, p. 73 (2013)
Reconstruction of large-scale regulatory networks based on perturbation graphs and transitive reduction: improved methods and their evaluation. BMC Systems Biology 72.
Journal Article
11 (1), p. 43 (2013)
Modeling approaches for qualitative and semi-quantitative analysis of cellular signaling networks. Cell Communication and Signaling 73.
Journal Article
28 (3), pp. 381 - 387 (2012)
Minimal cut sets in metabolic networks are elementary modes in a dual network. Bioinformatics 74.
Journal Article
279 (18), pp. 3290 - 3313 (2012)
An integrative model links multiple inputs and signaling pathways to the onset of DNA synthesis in hepatocytes. FEBS Journal 75.
Journal Article
5, p. 150 (2011)
Metabolic network modeling of redox balancing and biohydrogen production in purple nonsulfur bacteria. BMC Systems Biology 76.
Journal Article
13 (2), pp. 204 - 213 (2011)
Computing complex metabolic intervention strategies using constrained minimal cut sets. Metabolic Engineering 77.
Journal Article
105 (2), pp. 162 - 168 (2011)
An application programming interface for CellNetAnalyzer. Biosystems 78.
Journal Article
7 (12), pp. 3253 - 3270 (2011)
Large-scale models of IL-1 and IL-6 signaling and their hepatocellular specification. Molecular BioSystems 79.
Journal Article
7 (1), p. 151 (2010)
From Binary to Multivalued to Continuous Models: The Iac Operon as a Case Study. Journal of Integrative Bioinformatics 80.
Journal Article
147 (2), pp. 88 - 101 (2010)
CASOP: a computational approach for strain optimization aiming at high productivity. Journal of Biotechnology 81.
Journal Article
26 (17), pp. 2160 - 2168 (2010)
TRANSWESD: inferring cellular networks with transitive reduction. Bioinformatics 82.
Journal Article
17 (1), pp. 39 - 53 (2010)
Computing Combinatorial Intervention Strategies and Failure Modes in Signaling Networks. Journal of Computational Biology 83.
Journal Article
5 (5), p. e1000385 (2009)
Hypergraphs and cellular networks. PLoS Computational Biology 84.
Journal Article
10, p. 181 (2009)
Computing Paths and Cycles in Biological Interaction Graphs. BMC Bioinformatics 85.
Journal Article
2, pp. 125 - 138 (2009)
Logical network of genotoxic stress-induced NF-kB signal transduction predicts putative target structures for therapeutic intervention strategies. Advances and Applications in Bioinformatics and Chemistry 86.
Journal Article
5, p. 331 (2009)
Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction. Molecular Systems Biology 87.
Journal Article
5 (8), e1000438 (2009)
The logic of EGFR/ErbB signaling: theoretical properties and analysis of high-throughput data. PLoS Computational Biology 88.
Journal Article
3, 98 (2009)
Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling. BMC Systems Biology 89.
Journal Article
2, 4 (2008)
Host-pathogen systems biology: Logical modelling of hepatocyte growth factor and Helicobacter pylori induced c-Met signal transduction. BMC Systems Biology 90.
Journal Article
15 (3), pp. 259 - 268 (2008)
Computing knock-out strategies in metabolic networks. Journal of Computational Biology 91.
Journal Article
4, 156 (2008)
Modeling the electron transport chain of purple non-sulfur bacteria. Molecular Systems Biology 92.
Journal Article
2 (2), pp. 80 - 93 (2008)
Multistability of signal transduction motifs. IET Systems Biology 93.
Journal Article
8, R89 (2007)
GSMN-TB: a web-based genome-scale network model of Mycobacterium tuberculosis metabolism. Genome Biology 94.
Journal Article
1, 2 (2007)
Structural and functional analysis of cellular networks with CellNetAnalyzer. BMC Systems Biology 95.
Journal Article
3, e163 (2007)
A logical model provides insights into T cell receptor signaling. PLoS Computational Biology 96.
Journal Article
83 (2-3 ), pp. 233 - 247 (2006)
Generalized concept of minimal cut sets in biochmical networks. Biosystems 97.
Journal Article
7, p. 56 (2006)
A methodology for the structural and functional analysis of signaling and regulatory networks. BMC Bioinformatics 98.
Journal Article
7, 506 (2006)
Visual set-up of logical models of signaling and regulatory networks with ProMoT. BMC Bioinformatics 99.
Journal Article
152 (4), pp. 249 - 255 (2005)
Algorithmic approaches for computing elementary modes in large biochemical reaction networks. IEE Proceedings - Systems Biology