Steffen Klamt

Publication Activity (10 Years)

Years Active: 2001-2024
Publications (10 Years): 17

Top Topics

Metabolic Networks

Escherichia Coli

Experimental Data

Top Venues

PLoS Comput. Biol.

Publications

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 (2024)
Axel von Kamp, Steffen Klamt
Balancing biomass reaction stoichiometry and measured fluxes in flux balance analysis. Bioinform. 39 (10) (2023)
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 (2023)
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) (2022)
Philipp Schneider, Pavlos Stephanos Bekiaris, Axel von Kamp, Steffen Klamt
StrainDesign: a comprehensive Python package for computational design of metabolic networks. Bioinform. 38 (21) (2022)
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)
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)
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) (2020)
Pavlos Stephanos Bekiaris, Steffen Klamt
Automatic construction of metabolic models with enzyme constraints. BMC Bioinform. 21 (1) (2020)
Philipp Schneider, Steffen Klamt
Characterizing and ranking computed metabolic engineering strategies. Bioinform. 35 (17) (2019)
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)
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) (2019)
Jessica Bosch, Steffen Klamt, Martin Stoll
Generalizing Diffuse Interface Methods on Graphs: Nonsmooth Potentials and Hypergraphs. SIAM J. Appl. Math. 78 (3) (2018)
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)
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)
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 (2016)
Matthias P. Gerstl, Steffen Klamt, Christian Jungreuthmayer, Jürgen Zanghellini
Exact quantification of cellular robustness in genome-scale metabolic networks. Bioinform. 32 (5) (2016)
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 (2015)
Radhakrishnan Mahadevan, Axel von Kamp, Steffen Klamt
Genome-scale strain designs based on regulatory minimal cut sets. Bioinform. 31 (17) (2015)
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)
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 (2015)
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 (2014)
Axel von Kamp, Steffen Klamt
Enumeration of Smallest Intervention Strategies in Genome-Scale Metabolic Networks. PLoS Comput. Biol. 10 (1) (2014)
Robert J. Flassig, Sandra Heise, Kai Sundmacher, Steffen Klamt
An effective framework for reconstructing gene regulatory networks from genetical genomics data. Bioinform. 29 (2) (2013)
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 (2013)
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)
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 (2013)
Christian Jungreuthmayer, Govind Nair, Steffen Klamt, Jürgen Zanghellini
Comparison and improvement of algorithms for computing minimal cut sets. BMC Bioinform. 14 (2013)
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) (2012)
Steffen Klamt, Axel von Kamp
An application programming interface for CellNetAnalyzer. Biosyst. 105 (2) (2011)
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) (2011)
Oliver Hädicke, Hartmut Grammel, Steffen Klamt
Metabolic network modeling of redox balancing and biohydrogen production in purple nonsulfur bacteria. BMC Syst. Biol. 5 (2011)
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)
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)
Regina Samaga, Axel von Kamp, Steffen Klamt
Computing Combinatorial Intervention Strategies and Failure Modes in Signaling Networks. J. Comput. Biol. 17 (1) (2010)
Steffen Klamt, Robert J. Flassig, Kai Sundmacher
TRANSWESD: inferring cellular networks with transitive reduction. Bioinform. 26 (17) (2010)
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)
Steffen Klamt, Utz-Uwe Haus, Fabian J. Theis
Hypergraphs and Cellular Networks. PLoS Comput. Biol. 5 (5) (2009)
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 (2009)
Steffen Klamt, Axel von Kamp
Computing paths and cycles in biological interaction graphs. BMC Bioinform. 10 (2009)
Utz-Uwe Haus, Steffen Klamt, Tamon Stephen
Computing Knock-Out Strategies in Metabolic Networks. J. Comput. Biol. 15 (3) (2008)
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 (2008)
Steffen Klamt, Julio Saez-Rodriguez, Ernst Dieter Gilles
Structural and functional analysis of cellular networks with CellNetAnalyzer. BMC Syst. Biol. 1 (2007)
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)
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 (2006)
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 (2006)
Julien Gagneur, Steffen Klamt
Computation of elementary modes: a unifying framework and the new binary approach. BMC Bioinform. 5 (2004)
Steffen Klamt, Ernst Dieter Gilles
Minimal cut sets in biochemical reaction networks. Bioinform. 20 (2) (2004)
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) (2004)
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) (2003)
Stefan Schuster, Steffen Klamt, Jörg Stelling
Making predictions about robustness and flexibility from metabolic network structure. German Conference on Bioinformatics (2003)
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)