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ORCIDSteffen Klamt
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2020 – today
- 2024
[i2]Sebastián Espinel-Ríos
, Gerrich Behrendt, Jasmin Bauer, Bruno Morabito, Johannes Pohlodek, Andrea Schütze, Rolf Findeisen, Katja Bettenbrock, Steffen Klamt:
Experimentally implemented dynamic optogenetic optimization of ATPase expression using knowledge-based and Gaussian-process-supported models. CoRR abs/2401.08556 (2024)- 2023
- [j47]Axel von Kamp, Steffen Klamt:
Balancing biomass reaction stoichiometry and measured fluxes in flux balance analysis. Bioinform. 39(10) (2023) - [i1]Sebastián Espinel-Ríos, Bruno Morabito, Johannes Pohlodek, Katja Bettenbrock, Steffen Klamt, Rolf Findeisen:
Towards a modeling, optimization and predictive control framework for fed-batch metabolic cybergenetics. CoRR abs/2302.02177 (2023) - 2022
- [j46]Sven Thiele, Axel von Kamp, Pavlos Stephanos Bekiaris, Philipp Schneider, Steffen Klamt:
CNApy: a CellNetAnalyzer GUI in Python for analyzing and designing metabolic networks. Bioinform. 38(5): 1467-1469 (2022) - [j45]Philipp Schneider, Pavlos Stephanos Bekiaris, Axel von Kamp, Steffen Klamt:
StrainDesign: a comprehensive Python package for computational design of metabolic networks. Bioinform. 38(21): 4981-4983 (2022) - 2021
- [j44]Pavlos Stephanos Bekiaris, Steffen Klamt:
Designing microbial communities to maximize the thermodynamic driving force for the production of chemicals. PLoS Comput. Biol. 17(6) (2021) - 2020
- [j43]Pavlos Stephanos Bekiaris, Steffen Klamt:
Automatic construction of metabolic models with enzyme constraints. BMC Bioinform. 21(1): 19 (2020) - [j42]Steffen Klamt, Radhakrishnan Mahadevan, Axel von Kamp:
Speeding up the core algorithm for the dual calculation of minimal cut sets in large metabolic networks. BMC Bioinform. 21(1): 510 (2020) - [j41]Philipp Schneider, Axel von Kamp, Steffen Klamt:
An extended and generalized framework for the calculation of metabolic intervention strategies based on minimal cut sets. PLoS Comput. Biol. 16(7) (2020)
2010 – 2019
- 2019
- [j40]Philipp Schneider, Steffen Klamt:
Characterizing and ranking computed metabolic engineering strategies. Bioinform. 35(17): 3063-3072 (2019) - [j39]Sabine Koch, Fabian Kohrs, Patrick Lahmann, Thomas Bissinger, Stefan Wendschuh, Dirk Benndorf, Udo Reichl, Steffen Klamt:
RedCom: A strategy for reduced metabolic modeling of complex microbial communities and its application for analyzing experimental datasets from anaerobic digestion. PLoS Comput. Biol. 15(2) (2019) - [j38]Sven Thiele, Sandra Heise, Wiebke Hessenkemper, Hannes Bongartz, Melissa Fensky, Fred Schaper, Steffen Klamt:
Designing Optimal Experiments to Discriminate Interaction Graph Models. IEEE ACM Trans. Comput. Biol. Bioinform. 16(3): 925-935 (2019) - 2018
- [j37]Oliver Hädicke, Axel von Kamp, Timur Aydogan, Steffen Klamt:
OptMDFpathway: Identification of metabolic pathways with maximal thermodynamic driving force and its application for analyzing the endogenous CO2 fixation potential of Escherichia coli. PLoS Comput. Biol. 14(9) (2018) - [j36]Jessica Bosch, Steffen Klamt, Martin Stoll:
Generalizing Diffuse Interface Methods on Graphs: Nonsmooth Potentials and Hypergraphs. SIAM J. Appl. Math. 78(3): 1350-1377 (2018) - 2017
- [j35]Steffen Klamt, Georg Regensburger, Matthias P. Gerstl, Christian Jungreuthmayer, Stefan Schuster, Radhakrishnan Mahadevan, Jürgen Zanghellini, Stefan Müller:
From elementary flux modes to elementary flux vectors: Metabolic pathway analysis with arbitrary linear flux constraints. PLoS Comput. Biol. 13(4) (2017) - 2016
- [j34]Matthias P. Gerstl, Steffen Klamt, Christian Jungreuthmayer, Jürgen Zanghellini:
Exact quantification of cellular robustness in genome-scale metabolic networks. Bioinform. 32(5): 730-737 (2016) - [j33]S. M. Minhaz Ud-Dean, Sandra Heise, Steffen Klamt, Rudiyanto Gunawan:
TRaCE+: Ensemble inference of gene regulatory networks from transcriptional expression profiles of gene knock-out experiments. BMC Bioinform. 17: 252 (2016) - 2015
- [j32]Radhakrishnan Mahadevan, Axel von Kamp, Steffen Klamt:
Genome-scale strain designs based on regulatory minimal cut sets. Bioinform. 31(17): 2844-2851 (2015) - [j31]Sven Thiele, Luca Cerone, Julio Saez-Rodriguez, Anne Siegel, Carito Guziolowski, Steffen Klamt:
Extended notions of sign consistency to relate experimental data to signaling and regulatory network topologies. BMC Bioinform. 16: 345:1-345:13 (2015) - [j30]Philipp Erdrich, Ralf Steuer, Steffen Klamt:
An algorithm for the reduction of genome-scale metabolic network models to meaningful core models. BMC Syst. Biol. 9: 48 (2015) - [j29]Lorenza Alice D'Alessandro, Regina Samaga, Tim Maiwald, Seong-Hwan Rho, Sandra Bonefas, Andreas Raue, Nao Iwamoto, Alexandra Kienast, Katharina Waldow, Rene Meyer, Marcel Schilling, Jens Timmer, Steffen Klamt, Ursula Klingmüller:
Disentangling the Complexity of HGF Signaling by Combining Qualitative and Quantitative Modeling. PLoS Comput. Biol. 11(4) (2015) - 2014
- [j28]Anke Ryll, Joachim Bucher, Anne Bonin, Sophia Bongard, Emanuel J. V. Gonçalves, Julio Saez-Rodriguez, Jens Niklas, Steffen Klamt:
A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models. Biosyst. 124: 26-38 (2014) - [j27]Axel von Kamp, Steffen Klamt:
Enumeration of Smallest Intervention Strategies in Genome-Scale Metabolic Networks. PLoS Comput. Biol. 10(1) (2014) - [p1]Steffen Klamt, Oliver Hädicke, Axel von Kamp:
Stoichiometric and Constraint-Based Analysis of Biochemical Reaction Networks. Large-Scale Networks in Engineering and Life Sciences 2014: 263-316 - 2013
- [j26]Robert J. Flassig, Sandra Heise, Kai Sundmacher, Steffen Klamt:
An effective framework for reconstructing gene regulatory networks from genetical genomics data. Bioinform. 29(2): 246-254 (2013) - [j25]Christian Jungreuthmayer, Govind Nair, Steffen Klamt, Jürgen Zanghellini:
Comparison and improvement of algorithms for computing minimal cut sets. BMC Bioinform. 14: 318 (2013) - [j24]Andrea Pinna, Sandra Heise, Robert J. Flassig, Alberto de la Fuente, Steffen Klamt:
Reconstruction of large-scale regulatory networks based on perturbation graphs and transitive reduction: improved methods and their evaluation. BMC Syst. Biol. 7: 73 (2013) - [j23]Claudine Chaouiya, Duncan Bérenguier, Sarah M. Keating, Aurélien Naldi, Martijn P. van Iersel, Nicolas Rodriguez, Andreas Dräger, Finja Büchel, Thomas Cokelaer, Bryan M. Kowal, Benjamin Wicks, Emanuel J. V. Gonçalves, Julien Dorier, Michel Page, Pedro T. Monteiro, Axel von Kamp, Ioannis Xenarios, Hidde de Jong, Michael Hucka, Steffen Klamt, Denis Thieffry, Nicolas Le Novère, Julio Saez-Rodriguez, Tomás Helikar:
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. BMC Syst. Biol. 7: 135 (2013) - [j22]Ioannis N. Melas, Regina Samaga, Leonidas G. Alexopoulos, Steffen Klamt:
Detecting and Removing Inconsistencies between Experimental Data and Signaling Network Topologies Using Integer Linear Programming on Interaction Graphs. PLoS Comput. Biol. 9(9) (2013) - 2012
- [j21]Kathrin Ballerstein, Axel von Kamp, Steffen Klamt, Utz-Uwe Haus:
Minimal cut sets in a metabolic network are elementary modes in a dual network. Bioinform. 28(3): 381-387 (2012) - 2011
- [j20]Christoph Kaleta, Luis F. de Figueiredo, Ines Heiland, Steffen Klamt, Stefan Schuster:
Special issue: Integration of OMICs datasets into Metabolic Pathway Analysis. Biosyst. 105(2): 107-108 (2011) - [j19]Steffen Klamt, Axel von Kamp:
An application programming interface for CellNetAnalyzer. Biosyst. 105(2): 162-168 (2011) - [j18]Oliver Hädicke, Hartmut Grammel, Steffen Klamt:
Metabolic network modeling of redox balancing and biohydrogen production in purple nonsulfur bacteria. BMC Syst. Biol. 5: 150 (2011) - 2010
- [j17]Steffen Klamt, Robert J. Flassig, Kai Sundmacher:
TRANSWESD: inferring cellular networks with transitive reduction. Bioinform. 26(17): 2160-2168 (2010) - [j16]Regina Samaga, Axel von Kamp, Steffen Klamt:
Computing Combinatorial Intervention Strategies and Failure Modes in Signaling Networks. J. Comput. Biol. 17(1): 39-53 (2010) - [j15]Raimo Franke, Fabian J. Theis, Steffen Klamt:
From Binary to Multivalued to Continuous Models: The Lac Operon as a Case Study. J. Integr. Bioinform. 7(1) (2010) - [c3]Katrin Bohl, Luis F. de Figueiredo, Oliver Hädicke, Steffen Klamt, Christian Kost, Stefan Schuster, Christoph Kaleta:
CASOP GS: Computing Intervention Strategies Targeted at Production Improvement in Genome-scale Metabolic Networks. GCB 2010: 71-80
2000 – 2009
- 2009
- [j14]Steffen Klamt, Axel von Kamp:
Computing paths and cycles in biological interaction graphs. BMC Bioinform. 10 (2009) - [j13]Dominik M. Wittmann, Jan Krumsiek, Julio Saez-Rodriguez, Douglas A. Lauffenburger, Steffen Klamt, Fabian J. Theis:
Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling. BMC Syst. Biol. 3: 98 (2009) - [j12]Steffen Klamt, Utz-Uwe Haus, Fabian J. Theis:
Hypergraphs and Cellular Networks. PLoS Comput. Biol. 5(5) (2009) - [j11]Regina Samaga, Julio Saez-Rodriguez, Leonidas G. Alexopoulos, Peter K. Sorger, Steffen Klamt:
The Logic of EGFR/ErbB Signaling: Theoretical Properties and Analysis of High-Throughput Data. PLoS Comput. Biol. 5(8) (2009) - 2008
- [j10]Raimo Franke, Melanie Müller, Nicole Wundrack, Ernst Dieter Gilles, Steffen Klamt, Thilo Kähne, Michael Naumann:
Host-pathogen systems biology: logical modelling of hepatocyte growth factor and Helicobacter pylori induced c-Met signal transduction. BMC Syst. Biol. 2: 4 (2008) - [j9]Utz-Uwe Haus, Steffen Klamt, Tamon Stephen:
Computing Knock-Out Strategies in Metabolic Networks. J. Comput. Biol. 15(3): 259-268 (2008) - 2007
- [j8]Steffen Klamt, Julio Saez-Rodriguez, Ernst Dieter Gilles:
Structural and functional analysis of cellular networks with CellNetAnalyzer. BMC Syst. Biol. 1: 2 (2007) - [j7]Julio Saez-Rodriguez, Luca Simeoni, Jonathan A. Lindquist, Rebecca Hemenway, Ursula Bommhardt, Boerge Arndt, Utz-Uwe Haus, Robert Weismantel, Ernst Dieter Gilles, Steffen Klamt, Burkhart Schraven:
A Logical Model Provides Insights into T Cell Receptor Signaling. PLoS Comput. Biol. 3(8) (2007) - 2006
- [j6]Steffen Klamt, Julio Saez-Rodriguez, Jonathan A. Lindquist, Luca Simeoni, Ernst Dieter Gilles:
A methodology for the structural and functional analysis of signaling and regulatory networks. BMC Bioinform. 7: 56 (2006) - [j5]Julio Saez-Rodriguez, Sebastian Mirschel, Rebecca Hemenway, Steffen Klamt, Ernst Dieter Gilles, Martin Ginkel:
Visual setup of logical models of signaling and regulatory networks with ProMoT. BMC Bioinform. 7: 506 (2006) - 2004
- [j4]Steffen Klamt, Ernst Dieter Gilles:
Minimal cut sets in biochemical reaction networks. Bioinform. 20(2): 226-234 (2004) - [j3]Julien Gagneur, Steffen Klamt:
Computation of elementary modes: a unifying framework and the new binary approach. BMC Bioinform. 5: 175 (2004) - [j2]Andreas Kremling, Steffen Klamt, Martin Ginkel, Ernst Dieter Gilles:
Workbench zur Modellbildung, Simulation und Analyse zellulärer Systeme (Workbench for Model Set Up, Simulation, and Analysis of Cellular Systems). it Inf. Technol. 46(1): 12-19 (2004) - 2003
- [j1]Steffen Klamt, Jörg Stelling, Martin Ginkel, Ernst Dieter Gilles:
FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps. Bioinform. 19(2): 261-269 (2003) - [c2]Stefan Schuster, Steffen Klamt, Jörg Stelling:
Making predictions about robustness and flexibility from metabolic network structure. German Conference on Bioinformatics 2003: 129-134 - 2001
- [c1]Steffen Klamt, Ernst Dieter Gilles:
FluxAnalyzer: A Graphical User Interface for Analyzing Structural Properties and Fluxes in Balanced Metabolic Networks. German Conference on Bioinformatics 2001: 194-197
Coauthor Index
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