Steffen Klamt

54 papers Journal 50Unranked 3
YearRankTypeTitle / Venue / Authors
2025 J jnl
Minimal cut sets in metabolic networks: from conceptual foundations to applications in metabolic engineering and biomedicine.
Briefings Bioinform.
Steffen Klamt, Jürgen Zanghellini, Axel von Kamp
2024 J jnl
Experimentally implemented dynamic optogenetic optimization of ATPase expression using knowledge-based and Gaussian-process-supported models.
CoRR
Sebastián Espinel-Ríos, Gerrich Behrendt, Jasmin Bauer, Bruno Morabito, Johannes Pohlodek, Andrea Schütze, Rolf Findeisen, Katja Bettenbrock, Steffen Klamt
2023 J jnl
Balancing biomass reaction stoichiometry and measured fluxes in flux balance analysis.
Bioinform.
Axel von Kamp, Steffen Klamt
2023 J jnl
Towards a modeling, optimization and predictive control framework for fed-batch metabolic cybergenetics.
CoRR
Sebastián Espinel-Ríos, Bruno Morabito, Johannes Pohlodek, Katja Bettenbrock, Steffen Klamt, Rolf Findeisen
2022 J jnl
CNApy: a CellNetAnalyzer GUI in Python for analyzing and designing metabolic networks.
Bioinform.
Sven Thiele, Axel von Kamp, Pavlos Stephanos Bekiaris, Philipp Schneider, Steffen Klamt
2022 J jnl
StrainDesign: a comprehensive Python package for computational design of metabolic networks.
Bioinform.
Philipp Schneider, Pavlos Stephanos Bekiaris, Axel von Kamp, Steffen Klamt
2021 J jnl
Designing microbial communities to maximize the thermodynamic driving force for the production of chemicals.
PLoS Comput. Biol.
Pavlos Stephanos Bekiaris, Steffen Klamt
2020 J jnl
An extended and generalized framework for the calculation of metabolic intervention strategies based on minimal cut sets.
PLoS Comput. Biol.
Philipp Schneider, Axel von Kamp, Steffen Klamt
2020 J jnl
Automatic construction of metabolic models with enzyme constraints.
BMC Bioinform.
Pavlos Stephanos Bekiaris, Steffen Klamt
2020 J jnl
Speeding up the core algorithm for the dual calculation of minimal cut sets in large metabolic networks.
BMC Bioinform.
Steffen Klamt, Radhakrishnan Mahadevan, Axel von Kamp
2019 J jnl
Characterizing and ranking computed metabolic engineering strategies.
Bioinform.
Philipp Schneider, Steffen Klamt
2019 J jnl
Designing Optimal Experiments to Discriminate Interaction Graph Models.
IEEE ACM Trans. Comput. Biol. Bioinform.
Sven Thiele, Sandra Heise, Wiebke Hessenkemper, Hannes Bongartz, Melissa Fensky, Fred Schaper, Steffen Klamt
2019 J jnl
RedCom: A strategy for reduced metabolic modeling of complex microbial communities and its application for analyzing experimental datasets from anaerobic digestion.
PLoS Comput. Biol.
Sabine Koch, Fabian Kohrs, Patrick Lahmann, Thomas Bissinger, Stefan Wendschuh, Dirk Benndorf, Udo Reichl, Steffen Klamt
2018 J jnl
Generalizing Diffuse Interface Methods on Graphs: Nonsmooth Potentials and Hypergraphs.
SIAM J. Appl. Math.
Jessica Bosch, Steffen Klamt, Martin Stoll
2018 J jnl
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.
Oliver Hädicke, Axel von Kamp, Timur Aydogan, Steffen Klamt
2017 J jnl
From elementary flux modes to elementary flux vectors: Metabolic pathway analysis with arbitrary linear flux constraints.
PLoS Comput. Biol.
Steffen Klamt, Georg Regensburger, Matthias P. Gerstl, Christian Jungreuthmayer, Stefan Schuster, Radhakrishnan Mahadevan, Jürgen Zanghellini, Stefan Müller
2016 J jnl
Exact quantification of cellular robustness in genome-scale metabolic networks.
Bioinform.
Matthias P. Gerstl, Steffen Klamt, Christian Jungreuthmayer, Jürgen Zanghellini
2016 J jnl
TRaCE+: Ensemble inference of gene regulatory networks from transcriptional expression profiles of gene knock-out experiments.
BMC Bioinform.
S. M. Minhaz Ud-Dean, Sandra Heise, Steffen Klamt, Rudiyanto Gunawan
2015 J jnl
An algorithm for the reduction of genome-scale metabolic network models to meaningful core models.
BMC Syst. Biol.
Philipp Erdrich, Ralf Steuer, Steffen Klamt
2015 J jnl
Disentangling the Complexity of HGF Signaling by Combining Qualitative and Quantitative Modeling.
PLoS Comput. Biol.
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
2015 J jnl
Extended notions of sign consistency to relate experimental data to signaling and regulatory network topologies.
BMC Bioinform.
Sven Thiele, Luca Cerone, Julio Saez-Rodriguez, Anne Siegel, Carito Guziolowski, Steffen Klamt
2015 J jnl
Genome-scale strain designs based on regulatory minimal cut sets.
Bioinform.
Radhakrishnan Mahadevan, Axel von Kamp, Steffen Klamt
2014 J jnl
A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models.
Biosyst.
Anke Ryll, Joachim Bucher, Anne Bonin, Sophia Bongard, Emanuel J. V. Gonçalves, Julio Saez-Rodriguez, Jens Niklas, Steffen Klamt
2014 J jnl
Enumeration of Smallest Intervention Strategies in Genome-Scale Metabolic Networks.
PLoS Comput. Biol.
Axel von Kamp, Steffen Klamt
2014 — ch.
Stoichiometric and Constraint-Based Analysis of Biochemical Reaction Networks.
Large-Scale Networks in Engineering and Life Sciences
Steffen Klamt, Oliver Hädicke, Axel von Kamp
2013 J jnl
An effective framework for reconstructing gene regulatory networks from genetical genomics data.
Bioinform.
Robert J. Flassig, Sandra Heise, Kai Sundmacher, Steffen Klamt
2013 J jnl
Comparison and improvement of algorithms for computing minimal cut sets.
BMC Bioinform.
Christian Jungreuthmayer, Govind Nair, Steffen Klamt, Jürgen Zanghellini
2013 J jnl
Detecting and Removing Inconsistencies between Experimental Data and Signaling Network Topologies Using Integer Linear Programming on Interaction Graphs.
PLoS Comput. Biol.
Ioannis N. Melas, Regina Samaga, Leonidas G. Alexopoulos, Steffen Klamt
2013 J jnl
Reconstruction of large-scale regulatory networks based on perturbation graphs and transitive reduction: improved methods and their evaluation.
BMC Syst. Biol.
Andrea Pinna, Sandra Heise, Robert J. Flassig, Alberto de la Fuente, Steffen Klamt
2013 J jnl
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools.
BMC Syst. Biol.
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
2012 J jnl
Minimal cut sets in a metabolic network are elementary modes in a dual network.
Bioinform.
Kathrin Ballerstein, Axel von Kamp, Steffen Klamt, Utz-Uwe Haus
2011 J jnl
An application programming interface for CellNetAnalyzer.
Biosyst.
Steffen Klamt, Axel von Kamp
2011 J jnl
Metabolic network modeling of redox balancing and biohydrogen production in purple nonsulfur bacteria.
BMC Syst. Biol.
Oliver Hädicke, Hartmut Grammel, Steffen Klamt
2011 J jnl
Special issue: Integration of OMICs datasets into Metabolic Pathway Analysis.
Biosyst.
Christoph Kaleta, Luis F. de Figueiredo, Ines Heiland, Steffen Klamt, Stefan Schuster
2010 — conf
CASOP GS: Computing Intervention Strategies Targeted at Production Improvement in Genome-scale Metabolic Networks.
GCB
Katrin Bohl, Luis F. de Figueiredo, Oliver Hädicke, Steffen Klamt, Christian Kost, Stefan Schuster, Christoph Kaleta
2010 J jnl
Computing Combinatorial Intervention Strategies and Failure Modes in Signaling Networks.
J. Comput. Biol.
Regina Samaga, Axel von Kamp, Steffen Klamt
2010 J jnl
From Binary to Multivalued to Continuous Models: The Lac Operon as a Case Study.
J. Integr. Bioinform.
Raimo Franke, Fabian J. Theis, Steffen Klamt
2010 J jnl
TRANSWESD: inferring cellular networks with transitive reduction.
Bioinform.
Steffen Klamt, Robert J. Flassig, Kai Sundmacher
2009 J jnl
Computing paths and cycles in biological interaction graphs.
BMC Bioinform.
Steffen Klamt, Axel von Kamp
2009 J jnl
Hypergraphs and Cellular Networks.
PLoS Comput. Biol.
Steffen Klamt, Utz-Uwe Haus, Fabian J. Theis
2009 J jnl
The Logic of EGFR/ErbB Signaling: Theoretical Properties and Analysis of High-Throughput Data.
PLoS Comput. Biol.
Regina Samaga, Julio Saez-Rodriguez, Leonidas G. Alexopoulos, Peter K. Sorger, Steffen Klamt
2009 J jnl
Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling.
BMC Syst. Biol.
Dominik M. Wittmann, Jan Krumsiek, Julio Saez-Rodriguez, Douglas A. Lauffenburger, Steffen Klamt, Fabian J. Theis
2008 J jnl
Computing Knock-Out Strategies in Metabolic Networks.
J. Comput. Biol.
Utz-Uwe Haus, Steffen Klamt, Tamon Stephen
2008 J jnl
Host-pathogen systems biology: logical modelling of hepatocyte growth factor and Helicobacter pylori induced c-Met signal transduction.
BMC Syst. Biol.
Raimo Franke, Melanie Müller, Nicole Wundrack, Ernst Dieter Gilles, Steffen Klamt, Thilo Kähne, Michael Naumann
2007 J jnl
A Logical Model Provides Insights into T Cell Receptor Signaling.
PLoS Comput. Biol.
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
2007 J jnl
Structural and functional analysis of cellular networks with CellNetAnalyzer.
BMC Syst. Biol.
Steffen Klamt, Julio Saez-Rodriguez, Ernst Dieter Gilles
2006 J jnl
A methodology for the structural and functional analysis of signaling and regulatory networks.
BMC Bioinform.
Steffen Klamt, Julio Saez-Rodriguez, Jonathan A. Lindquist, Luca Simeoni, Ernst Dieter Gilles
2006 J jnl
Visual setup of logical models of signaling and regulatory networks with ProMoT.
BMC Bioinform.
Julio Saez-Rodriguez, Sebastian Mirschel, Rebecca Hemenway, Steffen Klamt, Ernst Dieter Gilles, Martin Ginkel
2004 J jnl
Computation of elementary modes: a unifying framework and the new binary approach.
BMC Bioinform.
Julien Gagneur, Steffen Klamt
2004 J jnl
Minimal cut sets in biochemical reaction networks.
Bioinform.
Steffen Klamt, Ernst Dieter Gilles
2004 J jnl
Workbench zur Modellbildung, Simulation und Analyse zellulärer Systeme (Workbench for Model Set Up, Simulation, and Analysis of Cellular Systems).
it Inf. Technol.
Andreas Kremling, Steffen Klamt, Martin Ginkel, Ernst Dieter Gilles
2003 J jnl
FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps.
Bioinform.
Steffen Klamt, Jörg Stelling, Martin Ginkel, Ernst Dieter Gilles
2003 — conf
Making predictions about robustness and flexibility from metabolic network structure.
German Conference on Bioinformatics
Stefan Schuster, Steffen Klamt, Jörg Stelling
2001 — conf
FluxAnalyzer: A Graphical User Interface for Analyzing Structural Properties and Fluxes in Balanced Metabolic Networks.
German Conference on Bioinformatics
Steffen Klamt, Ernst Dieter Gilles