Steffen Klamt
Zeitschriftenartikel (80)
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1.ZeitschriftenartikelDesigning optimal experiments to discriminate interaction graph models. IEEE ACM Transactions on Computational Biology and Bioinformatics (angenommen)
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2.ZeitschriftenartikelGeneralizing diffuse interface methods on graphs: non-smooth potentials and hypergraphs. SIAM Journal on Applied Mathematics 78 (3), S. 1350 - 1377 (2018)
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3.ZeitschriftenartikelOptMDFpathway: 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)
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4.ZeitschriftenartikelTemperature-dependent dynamic control of the TCA cycle increases volumetric productivity of itaconic acid production by Escherichia coli. Biotechnology and Bioengineering 115 (1), S. 156 - 164 (2018)
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5.ZeitschriftenartikelWhen do two-stage processes outperform one-stage processes? Biotechnology Journal 13 (2), 1700539 (2018)
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6.ZeitschriftenartikelA mathematical framework for yield (versus rate) optimization in constraint-based modeling and applications in metabolic engineering. Metabolic Engineering 47, S. 153 - 169 (2018)
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7.ZeitschriftenartikelEstablishment of a five-enzyme cell-free cascade for the synthesis of uridine diphosphate N-acetylglucosamine. Journal of Biotechnology 283, S. 120 - 129 (2018)
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8.ZeitschriftenartikelMoVE identifies metabolic valves to switch between phenotypic states. Nature Communications 9, 5332 (2018)
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9.ZeitschriftenartikelEColiCore2: a reference model of the central metabolism of Escherichia coli and the relationships to its genome-scale parent model. Scientific Reports 7, 39647 (2017)
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10.ZeitschriftenartikelGrowth-coupled overproduction is feasible for almost all metabolites in five major production organisms. Nature Communications 8, 15926 (2017)
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11.ZeitschriftenartikelUse of CellNetAnalyzer in biotechnology and metabolic engineering. Journal of Biotechnology 261, S. 221 - 228 (2017)
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12.ZeitschriftenartikelFrom elementary flux modes to elementary flux vectors: Metabolic pathway analysis with arbitrary linear flux constraints. PLoS Computational Biology 13 (4), e1005409 (2017)
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13.ZeitschriftenartikelExact quantification of cellular robustness in genome-scale metabolic networks. Bioinformatics 32 (5), S. 730 - 737 (2016)
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14.ZeitschriftenartikelModel-Based metabolic engineering enables high yield itaconic acid production by Escherichia coli. Metabolic Engineering 38, S. 29 - 37 (2016)
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15.ZeitschriftenartikelPredicting compositions of microbial communities from stoichiometric models with applications for the biogas process. Biotechnology for Biofuels 9, 17 (2016)
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16.ZeitschriftenartikelTRaCE+: Ensemble inference of gene regulatory networks from transcriptional expression profiles of gene knock-out experiments. BMC Bioinformatics 17 (17), 252 (2016)
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17.ZeitschriftenartikelMUFINS: multi-formalism interaction network simulator. npj Systems Biology and Applications 2, 16032 (2016)
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18.ZeitschriftenartikelSilence on the relevant literature and errors in implementation. Nature Biotechnology 33 (4), S. 336 - 339 (2015)
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19.ZeitschriftenartikelDisentangling the Complexity of HGF Signaling by Combining Qualitative and Quantitative Modeling. PLoS Computational Biology 11 (4), e1004192 (2015)
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20.ZeitschriftenartikelAn algorithm for the reduction of genome-scale metabolic network models to meaningful core models. BMC Systems Biology 9, 48 (2015)
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21.ZeitschriftenartikelManipulation of the ATP pool as a tool for metabolic engineering. Biochemical Society Transactions (London) 43 (6), S. 1140 - 1145 (2015)
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22.ZeitschriftenartikelEnforced ATP futile cycling increases specific productivity and yield of anaerobic lactate production in Escherichia coli. Biotechnology and Bioengineering 112 (10), S. 2195 - 2199 (2015)
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23.ZeitschriftenartikelOn the feasibility of growth-coupled product synthesis in microbial strains. Metabolic Engineering 30, S. 166 - 178 (2015)
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24.ZeitschriftenartikelGenome-scale strain designs based on regulatory minimal cut sets. Bioinformatics 31 (17), S. 2844 - 2851 (2015)
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25.ZeitschriftenartikelNetwork-Based Analysis of Nutraceuticals in Human Hepatocellular Carcinomas Reveals Mechanisms of Chemopreventive Action. CPT: Pharmacometrics & Systems Pharmacology 4 (6), S. 350 - 361 (2015)
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26.ZeitschriftenartikelT160‐phosphorylated CDK2 defines threshold for HGF‐dependent proliferation in primary hepatocytes. Molecular Systems Biology 11, 795 (2015)
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27.ZeitschriftenartikelExtended notions of sign consistency to relate experimental data to signaling and regulatory network topologies. BMC Bioinformatics 16 (1), 345 (2015)
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28.ZeitschriftenartikelComputational Systems Biology — neues Fach in den Lebenswissenschaften. Biospektrum 21 (1), S. 46 - 48 (2015)
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29.ZeitschriftenartikelCyanobacterial biofuels: new insights and strain design strategies revealed by computational modeling. Microbial Cell Factories 13, S. 128 - 128 (2014)
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30.ZeitschriftenartikelEnumeration of Smallest Intervention Strategies in Genome-Scale Metabolic Networks. PLoS Computational Biology 10 (1), e1003378 (2014)
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31.ZeitschriftenartikelThe avian cell line AGE1.CR.pIX characterized by metabolic flux analysis. BMC Biotechnology 14, S. 72 (2014)
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32.ZeitschriftenartikelA model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models. Biosystems 124, S. 26 - 38 (2014)
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33.ZeitschriftenartikelSBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formlisms and tools. BMC Systems Biology 7, S. 135 (2013)
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34.ZeitschriftenartikelAn effective framework for reconstructing gene regulatory networks from genetical genomics data. Bioinformatics 29 (2), S. 246 - 254 (2013)
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35.ZeitschriftenartikelBridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical models. Molecular BioSystems 9 (7), S. 1576 - 1583 (2013)
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36.ZeitschriftenartikelIn silico profiling of Escherichia coli and Saccharomyces cerevisiae as terpenoid factories. Microbial Cell Factories 12, 84 (2013)
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37.ZeitschriftenartikelEvaluating differences of metabolic performances: Statistical methods and their application to animal cell cultivations. Biotechnology and Bioengineering 110 (10), S. 2633 - 2642 (2013)
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38.ZeitschriftenartikelComparison and improvement of algorithms for computing minimal cut sets. BMC Bioinformatics 14 (1), S. 318 (2013)
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39.ZeitschriftenartikelDetecting and Removing Inconsistencies between Experimental Data and Signaling Network Topologies Using Integer Linear Programming on Interaction Graphs. PLoS Computational Biology 9 (9), S. e1003204 (2013)
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40.ZeitschriftenartikelReconstruction of large-scale regulatory networks based on perturbation graphs and transitive reduction: improved methods and their evaluation. BMC Systems Biology 7, S. 73 (2013)
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41.ZeitschriftenartikelModeling approaches for qualitative and semi-quantitative analysis of cellular signaling networks. Cell Communication and Signaling 11 (1), S. 43 (2013)
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42.ZeitschriftenartikelMinimal cut sets in metabolic networks are elementary modes in a dual network. Bioinformatics 28 (3), S. 381 - 387 (2012)
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43.ZeitschriftenartikelAn integrative model links multiple inputs and signaling pathways to the onset of DNA synthesis in hepatocytes. FEBS Journal 279 (18), S. 3290 - 3313 (2012)
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44.ZeitschriftenartikelComputing complex metabolic intervention strategies using constrained minimal cut sets. Metabolic Engineering 13 (2), S. 204 - 213 (2011)
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45.ZeitschriftenartikelMetabolic network modeling of redox balancing and biohydrogen production in purple nonsulfur bacteria. BMC Systems Biology 5, S. 150 (2011)
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46.ZeitschriftenartikelAn application programming interface for CellNetAnalyzer. Biosystems 105 (2), S. 162 - 168 (2011)
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47.ZeitschriftenartikelLarge-scale models of IL-1 and IL-6 signaling and their hepatocellular specification. Molecular BioSystems 7 (12), S. 3253 - 3270 (2011)
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48.ZeitschriftenartikelFrom Binary to Multivalued to Continuous Models: The Iac Operon as a Case Study. Journal of Integrative Bioinformatics 7 (1), S. 151 (2010)
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49.ZeitschriftenartikelCASOP: a computational approach for strain optimization aiming at high productivity. Journal of Biotechnology 147 (2), S. 88 - 101 (2010)
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50.ZeitschriftenartikelTRANSWESD: inferring cellular networks with transitive reduction. Bioinformatics 26 (17), S. 2160 - 2168 (2010)
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51.ZeitschriftenartikelComputing Combinatorial Intervention Strategies and Failure Modes in Signaling Networks. Journal of Computational Biology 17 (1), S. 39 - 53 (2010)
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52.ZeitschriftenartikelComputing Paths and Cycles in Biological Interaction Graphs. BMC Bioinformatics 10, S. 181 (2009)
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53.ZeitschriftenartikelHypergraphs and cellular networks. PLoS Computational Biology 5 (5), S. e1000385 (2009)
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54.ZeitschriftenartikelLogical network of genotoxic stress-induced NF-kB signal transduction predicts putative target structures for therapeutic intervention strategies. Advances and Applications in Bioinformatics and Chemistry 2, S. 125 - 138 (2009)
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55.ZeitschriftenartikelDiscrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction. Molecular Systems Biology 5, S. 331 (2009)
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56.ZeitschriftenartikelThe logic of EGFR/ErbB signaling: theoretical properties and analysis of high-throughput data. PLoS Computational Biology 5 (8), e1000438 (2009)
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57.ZeitschriftenartikelTransforming Boolean models to continuous models: methodology and application to T-cell receptor signaling. BMC Systems Biology 3, 98 (2009)
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58.ZeitschriftenartikelHost-pathogen systems biology: Logical modelling of hepatocyte growth factor and Helicobacter pylori induced c-Met signal transduction. BMC Systems Biology 2, 4 (2008)
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59.ZeitschriftenartikelComputing knock-out strategies in metabolic networks. Journal of Computational Biology 15 (3), S. 259 - 268 (2008)
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60.ZeitschriftenartikelModeling the electron transport chain of purple non-sulfur bacteria. Molecular Systems Biology 4, 156 (2008)
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61.ZeitschriftenartikelMultistability of signal transduction motifs. IET Systems Biology 2 (2), S. 80 - 93 (2008)
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62.ZeitschriftenartikelGSMN-TB: a web-based genome-scale network model of Mycobacterium tuberculosis metabolism. Genome Biology 8, R89 (2007)
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63.ZeitschriftenartikelStructural and functional analysis of cellular networks with CellNetAnalyzer. BMC Systems Biology 1, 2 (2007)
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64.ZeitschriftenartikelA logical model provides insights into T cell receptor signaling. PLoS Computational Biology 3, e163 (2007)
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65.ZeitschriftenartikelGeneralized concept of minimal cut sets in biochmical networks. Biosystems 83 (2-3 ), S. 233 - 247 (2006)
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66.ZeitschriftenartikelA methodology for the structural and functional analysis of signaling and regulatory networks. BMC Bioinformatics 7, S. 56 (2006)
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67.ZeitschriftenartikelVisual set-up of logical models of signaling and regulatory networks with ProMoT. BMC Bioinformatics 7, 506 (2006)
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68.ZeitschriftenartikelAlgorithmic approaches for computing elementary modes in large biochemical reaction networks. IEE Proceedings - Systems Biology 152 (4), S. 249 - 255 (2005)
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69.ZeitschriftenartikelComputation of elementary modes: a unifying framework and the new binary approach. BMC Bioinformatics 5, 175 (2004)
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70.ZeitschriftenartikelMinimal cut sets in biochemical reaction networks. Bioinformatics 20, S. 226 - 234 (2004)
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71.ZeitschriftenartikelWorkbench zur Modellbildung, Simulation und Analyse zellulärer Systeme. it - Information Technology 46, S. 12 - 19 (2004)
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72.ZeitschriftenartikelComparison of network-based pathway analysis methods. Trends in Biotechnology 22 (8), S. 400 - 405 (2004)
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73.ZeitschriftenartikelTwo approaches for metabolic pathway analysis? Trends in Biotechnology 21 (2), S. 64 - 69 (2003)
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74.ZeitschriftenartikelFluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps. Bioinformatics 19 (2), S. 261 - 269 (2003)
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75.ZeitschriftenartikelCalculability analysis in underdetermined metabolic networks illustrated by a model of the central metabolism in purple nonsulfur bacteria. Biotechnology and Bioengineering 77 (7), S. 734 - 751 (2002)
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76.ZeitschriftenartikelCombinatorial complexity of pathway analysis in metabolic networks. Molecular Biology Reports 29 (1-2), S. 233 - 236 (2002)
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77.ZeitschriftenartikelCalculating as many fluxes as possible in underdetermined metabolic networks. Molecular Biology Reports 29 (1-2), S. 243 - 248 (2002)
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78.ZeitschriftenartikelUse of network analysis of metabolic systems in bioengineering. Bioprocess and Biosystems Engineering 24 (6), S. 363 - 372 (2002)
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79.ZeitschriftenartikelApplying metabolic pathway analysis to make good use of methanol. Trends in Biotechnology 20 (8), S. 322 (2002)
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80.ZeitschriftenartikelMetabolic network structure determines key aspects of functionality and regulation. Nature 420 (6912), S. 190 - 193 (2002)
Buchkapitel (3)
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81.BuchkapitelStoichiometric and Constraint-Based Analysis of Biochemical Reaction Networks. In: Large-Scale Networks in Engineering and Life Sciences, S. 263 - 316. Springer International Publishing, Cham (2014)
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82.BuchkapitelBenchmarking a Simple Yet Effective Approach for Inferring Gene Regulatory Networks from Systems Genetic Data. In: Gene Network Inference: Verification of Methods for Systems Genetic Data., S. 33 - 47. Springer, Heidelberg (2013)
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83.BuchkapitelHost-pathogen interactions. In: Systems Biology of Tuberculosis, S. 107 - 126. Springer, New York (2013)
Konferenzbeitrag (3)
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84.KonferenzbeitragA fusion approach linking signaling logic and metabolic mass-flow kinetics in hepatocytes. In: Computational Methods in Systems Biology: 11th International Conference, CMSB 2013, S. 255 - 256. 11th International Conference on Computational Methods in Systems Biology CMSB 13, Klosterneuburg, Austria, 22. September 2013 - 24. September 2013. (2013)
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85.KonferenzbeitragCASOP GS: Computing intervention strategies targeted at production improvement in genome-scale metabolic networks. In: German Conference on Bioinformatics 2010, S. 71 - 80 (Hg. Schomburg, D.; Grote, A.). German Conference on Bioinformatics 2010, Braunschweig, Germany, 20. September 2010 - 22. September 2010. (2010)
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86.KonferenzbeitragFluxAnalyzer: a graphical user interface for stoichiometric and quantitative analysis of metabolic networks. 8th IFAC Internationall Conference on Computer Applications in Biotechnology, Québec, 24. Juni 2001 - 27. Juni 2001. IFAC Proceedings Volumes, S. 119 - 124 (2001)
Vortrag (4)
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87.VortragModel-based Metabolic Engineering of Escherichia coli for high yield itaconic acid production. Himmelfahrtstagung "Models for Developing and Optimising Biotech Production", Neu-Ulm, Germany (2017)
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88.VortragModel-based Metabolic Engineering of Escherichia coli for high yield itaconic acid production. Systems Biology meets Synthetic Biology, Frankfurt am Main, Germany (2017)
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89.VortragModel-based Metabolic Engineering of Escherichia coli for high yield itaconic acid production. Annual Conference 2016 of the Association for General and Applied Microbiology (VAAM), Jena, Germany (2016)
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90.VortragPredicting compositions of microbial communities from stoichiometric models with applications for the biogas process. Annual Conference 2016 of the Association for General and Applied Microbiology (VAAM), Jena, Germany (2016)
Poster (6)
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91.PosterStrategies for Modeling of Large-Scale Metabolic Models of Microbial Communities. Metabolic Pathway Analysis 2017, Bozeman, Montana, USA (2017)
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92.PosterModel-Based Metabolic Engineering of Escherichia Coli for High Yield Itaconic Acid Production. 6th International Conference on Foundations of Systems Biology in Engineering, Magdeburg, Germany (2016)
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93.PosterModel-Based Metabolic Engineering of Escherichia coli for High Yield Itaconic Acid Production. Metabolic Engineering 11, Kobe, Japan (2016)
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94.PosterNew Methods for Modeling of Microbial Communities with Stoichiometric Metabolic Models. 6th International Conference on Foundations of Systems Biology in Engineering, Magdeburg, Germany (2016)
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95.PosterPrediction of Community Compositions in Stoichiometric Community Models. 4th Conference on Constraint-Based Reconstruction and Analysis, Heidelberg, Germany (2015)
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96.PosterAn effective Framework for Gene RegulatoryNetwork Reconstruction from Genetical Genomics Data. GCB 2012, Jena, Germany (2012)
Hochschulschrift - Doktorarbeit (1)
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97.Hochschulschrift - DoktorarbeitStrukturelle Analyse von Stoffwechselnetzen illustriert am bakteriellen Redox- und Zentralstoffwechsel. Dissertation, 194 S., Shaker, Aachen (2005)
Heft (1)
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98.HeftProceedings of the workshop "Integration of OMICs datasets into metabolic pathway analysis" Edingburgh, U.K., 15 October 2010 IOMPA 2010 (Sonderheft). (2011)
Editorial (1)
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99.EditorialSpecial Issue: Integration of OMICs datasets into Metabolic Pathway Analysis. Biosystems 105 (2), S. 107 - 108 (2011)