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Steffen 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
Towards a modeling, optimization and predictive control framework for fed-batch metabolic cybergenetics. CoRR abs/2302.02177 (2023) - 2022
- [j46]Sven Thiele
CNApy: a CellNetAnalyzer GUI in Python for analyzing and designing metabolic networks. Bioinform. 38(5): 1467-1469 (2022) - [j45]Philipp Schneider
StrainDesign: a comprehensive Python package for computational design of metabolic networks. Bioinform. 38(21): 4981-4983 (2022) - 2021
- [j44]Pavlos Stephanos Bekiaris
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
Automatic construction of metabolic models with enzyme constraints. BMC Bioinform. 21(1): 19 (2020) - [j42]Steffen Klamt
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
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
Characterizing and ranking computed metabolic engineering strategies. Bioinform. 35(17): 3063-3072 (2019) - [j39]Sabine Koch
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
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
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
Generalizing Diffuse Interface Methods on Graphs: Nonsmooth Potentials and Hypergraphs. SIAM J. Appl. Math. 78(3): 1350-1377 (2018) - 2017
- [j35]Steffen Klamt
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
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
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
Genome-scale strain designs based on regulatory minimal cut sets. Bioinform. 31(17): 2844-2851 (2015) - [j31]Sven Thiele
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
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
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
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
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
An effective framework for reconstructing gene regulatory networks from genetical genomics data. Bioinform. 29(2): 246-254 (2013) - [j25]Christian Jungreuthmayer, Govind Nair
Comparison and improvement of algorithms for computing minimal cut sets. BMC Bioinform. 14: 318 (2013) - [j24]Andrea Pinna, Sandra Heise, Robert J. Flassig
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
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
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
Minimal cut sets in a metabolic network are elementary modes in a dual network. Bioinform. 28(3): 381-387 (2012) - 2011
- [j20]Christoph Kaleta
Special issue: Integration of OMICs datasets into Metabolic Pathway Analysis. Biosyst. 105(2): 107-108 (2011) - [j19]Steffen Klamt
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
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
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
Computing paths and cycles in biological interaction graphs. BMC Bioinform. 10 (2009) - [j13]Dominik M. Wittmann, Jan Krumsiek, Julio Saez-Rodriguez
Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling. BMC Syst. Biol. 3: 98 (2009) - [j12]Steffen Klamt
Hypergraphs and Cellular Networks. PLoS Comput. Biol. 5(5) (2009) - [j11]Regina Samaga, Julio Saez-Rodriguez
The Logic of EGFR/ErbB Signaling: Theoretical Properties and Analysis of High-Throughput Data. PLoS Comput. Biol. 5(8) (2009) - 2008
- [j10]Raimo Franke
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
Computing Knock-Out Strategies in Metabolic Networks. J. Comput. Biol. 15(3): 259-268 (2008) - 2007
- [j8]Steffen Klamt
Structural and functional analysis of cellular networks with CellNetAnalyzer. BMC Syst. Biol. 1: 2 (2007) - [j7]Julio Saez-Rodriguez
A Logical Model Provides Insights into T Cell Receptor Signaling. PLoS Comput. Biol. 3(8) (2007) - 2006
- [j6]Steffen Klamt
A methodology for the structural and functional analysis of signaling and regulatory networks. BMC Bioinform. 7: 56 (2006) - [j5]Julio Saez-Rodriguez
Visual setup of logical models of signaling and regulatory networks with ProMoT. BMC Bioinform. 7: 506 (2006) - 2004
- [j4]Steffen Klamt
Minimal cut sets in biochemical reaction networks. Bioinform. 20(2): 226-234 (2004) - [j3]Julien Gagneur
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
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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