Steffen Klamt
Orcid: 0000-0003-2563-7561
According to our database1,
Steffen Klamt
authored at least 53 papers
between 2001 and 2024.
Collaborative distances:
Collaborative distances:
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Bibliography
2024
Experimentally implemented dynamic optogenetic optimization of ATPase expression using knowledge-based and Gaussian-process-supported models.
CoRR, 2024
2023
Balancing biomass reaction stoichiometry and measured fluxes in flux balance analysis.
Bioinform., October, 2023
Towards a modeling, optimization and predictive control framework for fed-batch metabolic cybergenetics.
CoRR, 2023
2022
StrainDesign: a comprehensive Python package for computational design of metabolic networks.
Bioinform., October, 2022
CNApy: a CellNetAnalyzer GUI in Python for analyzing and designing metabolic networks.
Bioinform., 2022
2021
Designing microbial communities to maximize the thermodynamic driving force for the production of chemicals.
PLoS Comput. Biol., 2021
2020
An extended and generalized framework for the calculation of metabolic intervention strategies based on minimal cut sets.
PLoS Comput. Biol., 2020
Speeding up the core algorithm for the dual calculation of minimal cut sets in large metabolic networks.
BMC Bioinform., 2020
BMC Bioinform., 2020
2019
IEEE ACM Trans. Comput. Biol. Bioinform., 2019
RedCom: A strategy for reduced metabolic modeling of complex microbial communities and its application for analyzing experimental datasets from anaerobic digestion.
PLoS Comput. Biol., 2019
Bioinform., 2019
2018
Generalizing Diffuse Interface Methods on Graphs: Nonsmooth Potentials and Hypergraphs.
SIAM J. Appl. Math., 2018
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., 2018
2017
From elementary flux modes to elementary flux vectors: Metabolic pathway analysis with arbitrary linear flux constraints.
PLoS Comput. Biol., 2017
2016
TRaCE+: Ensemble inference of gene regulatory networks from transcriptional expression profiles of gene knock-out experiments.
BMC Bioinform., 2016
Bioinform., 2016
2015
Disentangling the Complexity of HGF Signaling by Combining Qualitative and Quantitative Modeling.
PLoS Comput. Biol., 2015
An algorithm for the reduction of genome-scale metabolic network models to meaningful core models.
BMC Syst. Biol., 2015
Extended notions of sign consistency to relate experimental data to signaling and regulatory network topologies.
BMC Bioinform., 2015
2014
PLoS Comput. Biol., 2014
A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models.
Biosyst., 2014
Proceedings of the Large-Scale Networks in Engineering and Life Sciences, 2014
2013
Detecting and Removing Inconsistencies between Experimental Data and Signaling Network Topologies Using Integer Linear Programming on Interaction Graphs.
PLoS Comput. Biol., 2013
Reconstruction of large-scale regulatory networks based on perturbation graphs and transitive reduction: improved methods and their evaluation.
BMC Syst. Biol., 2013
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools.
BMC Syst. Biol., 2013
BMC Bioinform., 2013
An effective framework for reconstructing gene regulatory networks from genetical genomics data.
Bioinform., 2013
2012
Bioinform., 2012
2011
Metabolic network modeling of redox balancing and biohydrogen production in purple nonsulfur bacteria.
BMC Syst. Biol., 2011
Biosyst., 2011
2010
J. Integr. Bioinform., 2010
Computing Combinatorial Intervention Strategies and Failure Modes in Signaling Networks.
J. Comput. Biol., 2010
CASOP GS: Computing Intervention Strategies Targeted at Production Improvement in Genome-scale Metabolic Networks.
Proceedings of the German Conference on Bioinformatics 2010, 2010
2009
The Logic of EGFR/ErbB Signaling: Theoretical Properties and Analysis of High-Throughput Data.
PLoS Comput. Biol., 2009
Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling.
BMC Syst. Biol., 2009
2008
Host-pathogen systems biology: logical modelling of hepatocyte growth factor and Helicobacter pylori induced c-Met signal transduction.
BMC Syst. Biol., 2008
2007
PLoS Comput. Biol., 2007
BMC Syst. Biol., 2007
2006
BMC Bioinform., 2006
A methodology for the structural and functional analysis of signaling and regulatory networks.
BMC Bioinform., 2006
2004
Workbench zur Modellbildung, Simulation und Analyse zellulärer Systeme (Workbench for Model Set Up, Simulation, and Analysis of Cellular Systems).
it Inf. Technol., 2004
BMC Bioinform., 2004
2003
FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps.
Bioinform., 2003
Making predictions about robustness and flexibility from metabolic network structure.
Proceedings of the German Conference on Bioinformatics, 2003
2001
FluxAnalyzer: A Graphical User Interface for Analyzing Structural Properties and Fluxes in Balanced Metabolic Networks.
Proceedings of the Computer science and biology: Proceedings of the German Conference on Bioinformatics, 2001