Steffen Klamt
Zeitschriftenartikel (103)
1.
Zeitschriftenartikel
11 (11), S. 3855 - 3864 (2022)
Zymo-Parts: A Golden Gate Modular Cloning Toolbox for Heterologous Gene Expression in Zymomonas mobilis. ACS Synthetic Biology 2.
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73, S. 50 - 57 (2022)
Enabling anaerobic growth of Escherichia coli on glycerol in defined minimal medium using acetate as redox sink. Metabolic Engineering 3.
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68 (4), e17555 (2022)
Maximizing batch fermentation efficiency by constrained model-based optimization and predictive control of adenosine triphosphate turnover. AIChE-Journal 4.
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12 (7), 585 (2022)
Analyzing and Resolving Infeasibility in Flux Balance Analysis of Metabolic Networks. Metabolites 5.
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23 (2), e202100361 (2022)
Cell‐free multi‐enzyme synthesis and purification of uridine diphosphate galactose. ChemBioChem 6.
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38 (21), S. 4981 - 4983 (2022)
StrainDesign: a Comprehensive Python Package for Computational Design of Metabolic Networks. Bioinformatics 7.
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38 (5), S. 1467 - 1469 (2022)
CNApy: a CellNetAnalyzer GUI in Python for Analyzing and Designing Metabolic Networks. Bioinformatics 8.
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17 (6), e1009093 (2021)
Designing microbial communities to maximize the thermodynamic driving force for the production of chemicals. PLoS Computational Biology 9.
Zeitschriftenartikel
20, 63 (2021)
Increasing ATP turnover boosts productivity of 2,3-butanediol synthesis in Escherichia coli. Microbial Cell Factories 10.
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17, e10504 (2021)
Deciphering the physiological response of Escherichia coli under high ATP demand. Molecular Systems Biology 11.
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323, 124573 (2021)
Blending industrial blast furnace gas with H 2 enables Acetobacterium woodii to efficiently co-utilize CO, CO2 and H2. Bioresource Technology 12.
Zeitschriftenartikel
16, 2100236 (2021)
Systematizing the different notions of growth-coupled product synthesis and a single framework for computing corresponding strain designs. Biotechnology Journal 13.
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21, 19 (2020)
Automatic construction of metabolic models with enzyme constraints. BMC Bioinformatics 14.
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9 (3), S. 556 - 566 (2020)
MEMO: A Method for Computing Metabolic Modules for Cell-Free Production Systems. ACS Synthetic Biology 15.
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Speeding up the core algorithm for the dual calculation of minimal cut sets in large metabolic networks. BMC Bioinformatics (21), 510 (2020)
16.
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38, S. 272 - 276 (2020)
MEMOTE for standardized genome-scale metabolic model testing. Nature Biotechnology 17.
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16 (7), e1008110 (2020)
An extended and generalized framework for the calculation of metabolic intervention strategies based on minimal cut sets. PLoS Computational Biology 18.
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ATPase-based implementation of enforced ATP wasting in Saccharomyces cerevisiae for improved ethanol production. Biotechnology for Biofuels (13), 185 (2020)
19.
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14 (9), 1800438 (2019)
Broadening the Scope of Enforced ATP Wasting as a Tool for Metabolic Engineering in Escherichia coli. Biotechnology Journal 20.
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25 (2), S. 156 - 158 (2019)
Computergestütztes Design mikrobieller Zellfabriken. Biospektrum 21.
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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 22.
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35 (17), S. 3063 - 3072 (2019)
Characterizing and Ranking Computed Metabolic Engineering Strategies. Bioinformatics 23.
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16 (3), S. 925 - 935 (2019)
Designing optimal experiments to discriminate interaction graph models. IEEE ACM Transactions on Computational Biology and Bioinformatics 24.
Zeitschriftenartikel
10, 1095 (2019)
Augmenting Biogas Process Modeling by Resolving Intracellular Metabolic Activity. Frontiers in Microbiology 25.
Zeitschriftenartikel
78 (3), S. 1350 - 1377 (2018)
Generalizing diffuse interface methods on graphs: non-smooth potentials and hypergraphs. SIAM Journal on Applied Mathematics 26.
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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 27.
Zeitschriftenartikel
115 (1), S. 156 - 164 (2018)
Temperature-dependent dynamic control of the TCA cycle increases volumetric productivity of itaconic acid production by Escherichia coli. Biotechnology and Bioengineering 28.
Zeitschriftenartikel
13 (2), 1700539 (2018)
When do two-stage processes outperform one-stage processes? Biotechnology Journal 29.
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47, S. 153 - 169 (2018)
A mathematical framework for yield (versus rate) optimization in constraint-based modeling and applications in metabolic engineering. Metabolic Engineering 30.
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283, S. 120 - 129 (2018)
Establishment of a five-enzyme cell-free cascade for the synthesis of uridine diphosphate N-acetylglucosamine. Journal of Biotechnology 31.
Zeitschriftenartikel
9, 5332 (2018)
MoVE identifies metabolic valves to switch between phenotypic states. Nature Communications 32.
Zeitschriftenartikel
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 33.
Zeitschriftenartikel
8, 15926 (2017)
Growth-coupled overproduction is feasible for almost all metabolites in five major production organisms. Nature Communications 34.
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261, S. 221 - 228 (2017)
Use of CellNetAnalyzer in biotechnology and metabolic engineering. Journal of Biotechnology 35.
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13 (4), e1005409 (2017)
From elementary flux modes to elementary flux vectors: Metabolic pathway analysis with arbitrary linear flux constraints. PLoS Computational Biology 36.
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32 (5), S. 730 - 737 (2016)
Exact quantification of cellular robustness in genome-scale metabolic networks. Bioinformatics 37.
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38, S. 29 - 37 (2016)
Model-Based metabolic engineering enables high yield itaconic acid production by Escherichia coli. Metabolic Engineering 38.
Zeitschriftenartikel
9, 17 (2016)
Predicting compositions of microbial communities from stoichiometric models with applications for the biogas process. Biotechnology for Biofuels 39.
Zeitschriftenartikel
17 (17), 252 (2016)
TRaCE+: Ensemble inference of gene regulatory networks from transcriptional expression profiles of gene knock-out experiments. BMC Bioinformatics 40.
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2, 16032 (2016)
MUFINS: multi-formalism interaction network simulator. npj Systems Biology and Applications 41.
Zeitschriftenartikel
33 (4), S. 336 - 339 (2015)
Silence on the relevant literature and errors in implementation. Nature Biotechnology 42.
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11 (4), e1004192 (2015)
Disentangling the Complexity of HGF Signaling by Combining Qualitative and Quantitative Modeling. PLoS Computational Biology 43.
Zeitschriftenartikel
9, 48 (2015)
An algorithm for the reduction of genome-scale metabolic network models to meaningful core models. BMC Systems Biology 44.
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112 (10), S. 2195 - 2199 (2015)
Enforced ATP futile cycling increases specific productivity and yield of anaerobic lactate production in Escherichia coli. Biotechnology and Bioengineering 45.
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43 (6), S. 1140 - 1145 (2015)
Manipulation of the ATP pool as a tool for metabolic engineering. Biochemical Society Transactions (London) 46.
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30, S. 166 - 178 (2015)
On the feasibility of growth-coupled product synthesis in microbial strains. Metabolic Engineering 47.
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31 (17), S. 2844 - 2851 (2015)
Genome-scale strain designs based on regulatory minimal cut sets. Bioinformatics 48.
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4 (6), S. 350 - 361 (2015)
Network-Based Analysis of Nutraceuticals in Human Hepatocellular Carcinomas Reveals Mechanisms of Chemopreventive Action. CPT: Pharmacometrics & Systems Pharmacology 49.
Zeitschriftenartikel
11, 795 (2015)
T160‐phosphorylated CDK2 defines threshold for HGF‐dependent proliferation in primary hepatocytes. Molecular Systems Biology 50.
Zeitschriftenartikel
16 (1), 345 (2015)
Extended notions of sign consistency to relate experimental data to signaling and regulatory network topologies. BMC Bioinformatics 51.
Zeitschriftenartikel
21 (1), S. 46 - 48 (2015)
Computational Systems Biology — neues Fach in den Lebenswissenschaften. Biospektrum 52.
Zeitschriftenartikel
13, S. 128 - 128 (2014)
Cyanobacterial biofuels: new insights and strain design strategies revealed by computational modeling. Microbial Cell Factories 53.
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10 (1), e1003378 (2014)
Enumeration of Smallest Intervention Strategies in Genome-Scale Metabolic Networks. PLoS Computational Biology 54.
Zeitschriftenartikel
14, S. 72 (2014)
The avian cell line AGE1.CR.pIX characterized by metabolic flux analysis. BMC Biotechnology 55.
Zeitschriftenartikel
124, S. 26 - 38 (2014)
A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models. Biosystems 56.
Zeitschriftenartikel
7, S. 135 (2013)
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formlisms and tools. BMC Systems Biology 57.
Zeitschriftenartikel
29 (2), S. 246 - 254 (2013)
An effective framework for reconstructing gene regulatory networks from genetical genomics data. Bioinformatics 58.
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9 (7), S. 1576 - 1583 (2013)
Bridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical models. Molecular BioSystems 59.
Zeitschriftenartikel
12, 84 (2013)
In silico profiling of Escherichia coli and Saccharomyces cerevisiae as terpenoid factories. Microbial Cell Factories 60.
Zeitschriftenartikel
110 (10), S. 2633 - 2642 (2013)
Evaluating differences of metabolic performances: Statistical methods and their application to animal cell cultivations. Biotechnology and Bioengineering 61.
Zeitschriftenartikel
14 (1), S. 318 (2013)
Comparison and improvement of algorithms for computing minimal cut sets. BMC Bioinformatics 62.
Zeitschriftenartikel
9 (9), S. e1003204 (2013)
Detecting and Removing Inconsistencies between Experimental Data and Signaling Network Topologies Using Integer Linear Programming on Interaction Graphs. PLoS Computational Biology 63.
Zeitschriftenartikel
7, S. 73 (2013)
Reconstruction of large-scale regulatory networks based on perturbation graphs and transitive reduction: improved methods and their evaluation. BMC Systems Biology 64.
Zeitschriftenartikel
11 (1), S. 43 (2013)
Modeling approaches for qualitative and semi-quantitative analysis of cellular signaling networks. Cell Communication and Signaling 65.
Zeitschriftenartikel
28 (3), S. 381 - 387 (2012)
Minimal cut sets in metabolic networks are elementary modes in a dual network. Bioinformatics 66.
Zeitschriftenartikel
279 (18), S. 3290 - 3313 (2012)
An integrative model links multiple inputs and signaling pathways to the onset of DNA synthesis in hepatocytes. FEBS Journal 67.
Zeitschriftenartikel
5, S. 150 (2011)
Metabolic network modeling of redox balancing and biohydrogen production in purple nonsulfur bacteria. BMC Systems Biology 68.
Zeitschriftenartikel
13 (2), S. 204 - 213 (2011)
Computing complex metabolic intervention strategies using constrained minimal cut sets. Metabolic Engineering 69.
Zeitschriftenartikel
105 (2), S. 162 - 168 (2011)
An application programming interface for CellNetAnalyzer. Biosystems 70.
Zeitschriftenartikel
7 (12), S. 3253 - 3270 (2011)
Large-scale models of IL-1 and IL-6 signaling and their hepatocellular specification. Molecular BioSystems 71.
Zeitschriftenartikel
7 (1), S. 151 (2010)
From Binary to Multivalued to Continuous Models: The Iac Operon as a Case Study. Journal of Integrative Bioinformatics 72.
Zeitschriftenartikel
147 (2), S. 88 - 101 (2010)
CASOP: a computational approach for strain optimization aiming at high productivity. Journal of Biotechnology 73.
Zeitschriftenartikel
26 (17), S. 2160 - 2168 (2010)
TRANSWESD: inferring cellular networks with transitive reduction. Bioinformatics 74.
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17 (1), S. 39 - 53 (2010)
Computing Combinatorial Intervention Strategies and Failure Modes in Signaling Networks. Journal of Computational Biology 75.
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5 (5), S. e1000385 (2009)
Hypergraphs and cellular networks. PLoS Computational Biology 76.
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10, S. 181 (2009)
Computing Paths and Cycles in Biological Interaction Graphs. BMC Bioinformatics 77.
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2, S. 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 78.
Zeitschriftenartikel
5, S. 331 (2009)
Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction. Molecular Systems Biology 79.
Zeitschriftenartikel
5 (8), e1000438 (2009)
The logic of EGFR/ErbB signaling: theoretical properties and analysis of high-throughput data. PLoS Computational Biology 80.
Zeitschriftenartikel
3, 98 (2009)
Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling. BMC Systems Biology 81.
Zeitschriftenartikel
2, 4 (2008)
Host-pathogen systems biology: Logical modelling of hepatocyte growth factor and Helicobacter pylori induced c-Met signal transduction. BMC Systems Biology 82.
Zeitschriftenartikel
15 (3), S. 259 - 268 (2008)
Computing knock-out strategies in metabolic networks. Journal of Computational Biology 83.
Zeitschriftenartikel
4, 156 (2008)
Modeling the electron transport chain of purple non-sulfur bacteria. Molecular Systems Biology 84.
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2 (2), S. 80 - 93 (2008)
Multistability of signal transduction motifs. IET Systems Biology 85.
Zeitschriftenartikel
8, R89 (2007)
GSMN-TB: a web-based genome-scale network model of Mycobacterium tuberculosis metabolism. Genome Biology 86.
Zeitschriftenartikel
1, 2 (2007)
Structural and functional analysis of cellular networks with CellNetAnalyzer. BMC Systems Biology 87.
Zeitschriftenartikel
3, e163 (2007)
A logical model provides insights into T cell receptor signaling. PLoS Computational Biology 88.
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83 (2-3 ), S. 233 - 247 (2006)
Generalized concept of minimal cut sets in biochmical networks. Biosystems 89.
Zeitschriftenartikel
7, S. 56 (2006)
A methodology for the structural and functional analysis of signaling and regulatory networks. BMC Bioinformatics 90.
Zeitschriftenartikel
7, 506 (2006)
Visual set-up of logical models of signaling and regulatory networks with ProMoT. BMC Bioinformatics 91.
Zeitschriftenartikel
152 (4), S. 249 - 255 (2005)
Algorithmic approaches for computing elementary modes in large biochemical reaction networks. IEE Proceedings - Systems Biology 92.
Zeitschriftenartikel
5, 175 (2004)
Computation of elementary modes: a unifying framework and the new binary approach. BMC Bioinformatics 93.
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20, S. 226 - 234 (2004)
Minimal cut sets in biochemical reaction networks. Bioinformatics 94.
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46, S. 12 - 19 (2004)
Workbench zur Modellbildung, Simulation und Analyse zellulärer Systeme. it - Information Technology 95.
Zeitschriftenartikel
22 (8), S. 400 - 405 (2004)
Comparison of network-based pathway analysis methods. Trends in Biotechnology 96.
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21 (2), S. 64 - 69 (2003)
Two approaches for metabolic pathway analysis? Trends in Biotechnology 97.
Zeitschriftenartikel
19 (2), S. 261 - 269 (2003)
FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps. Bioinformatics 98.
Zeitschriftenartikel
29 (1-2), S. 243 - 248 (2002)
Calculating as many fluxes as possible in underdetermined metabolic networks. Molecular Biology Reports 99.
Zeitschriftenartikel
77 (7), S. 734 - 751 (2002)
Calculability analysis in underdetermined metabolic networks illustrated by a model of the central metabolism in purple nonsulfur bacteria. Biotechnology and Bioengineering