Steffen Klamt

发表

Modeling approaches for qualitative and semi-quantitative analysis of cellular signaling networks

S. Klamt, Regina Samaga, Steffen Klamt, 2013, Cell Communication and Signaling.

Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction

D. Lauffenburger, P. Sorger, J. Sáez-Rodríguez, 2009, Molecular systems biology.

Computing paths and cycles in biological interaction graphs

Steffen Klamt, Axel von Kamp, S. Klamt, 2009, BMC Bioinformatics.

Stoichiometric and Constraint-Based Analysis of Biochemical Reaction Networks

Steffen Klamt, O. Haedicke, A. von Kamp, 2014, Large-Scale Networks in Engineering and Life Sciences.

T160‐phosphorylated CDK2 defines threshold for HGF‐dependent proliferation in primary hepatocytes

S. Klamt, M. Schilling, U. Klingmüller, 2015, Molecular systems biology.

T160-phosphorylated CDK2 defines threshold for HGF-dependent proliferation in primary hepatocytes

S. Klamt, M. Schilling, U. Klingmüller, 2015, Molecular systems biology.

Host-pathogen interactions

S. Klamt, A. V. Kamp, S. Waddell, 2013 .

Large-scale network models of IL-1 and IL-6 signalling and their hepatocellular specification.

S. Klamt, L. Alexopoulos, R. Samaga, 2011, Molecular bioSystems.

StrainDesign: a comprehensive Python package for computational design of metabolic networks

Pavlos Stephanos Bekiaris, S. Klamt, A. V. Kamp, 2022, Bioinform..

MEMOTE for standardized genome-scale metabolic model testing

Steffen Klamt, Anne Richelle, Hyun Uk Kim, 2020, Nature Biotechnology.

Automatic construction of metabolic models with enzyme constraints

Steffen Klamt, Pavlos Stephanos Bekiaris, S. Klamt, 2020, BMC Bioinformatics.

Balancing biomass reaction stoichiometry and measured fluxes in flux balance analysis

Steffen Klamt, Axel von Kamp, 2023, Bioinformatics.

Maximizing batch fermentation efficiency by constrained model‐based optimization and predictive control of ATP turnover

R. Findeisen, K. Bettenbrock, S. Espinel‐Ríos, 2021, AIChE Journal.

MoVE identifies metabolic valves to switch between phenotypic states

Steffen Klamt, Radhakrishnan Mahadevan, Naveen Venayak, 2018, Nature Communications.

When Do Two-Stage Processes Outperform One-Stage Processes?

S. Klamt, R. Mahadevan, O. Hädicke, 2018, Biotechnology journal.

EColiCore2: a reference network model of the central metabolism of Escherichia coli and relationships to its genome-scale parent model

S. Klamt, O. Hädicke, Steffen Klamt, 2017, Scientific Reports.

Enforced ATP futile cycling increases specific productivity and yield of anaerobic lactate production in Escherichia coli.

S. Klamt, K. Bettenbrock, O. Hädicke, 2015, Biotechnology and bioengineering.

Genome-scale strain designs based on regulatory minimal cut sets

Steffen Klamt, Radhakrishnan Mahadevan, Axel von Kamp, 2015, Bioinform..

An algorithm for the reduction of genome-scale metabolic network models to meaningful core models

Steffen Klamt, Ralf Steuer, Philipp Erdrich, 2015, BMC Systems Biology.

Enumeration of Smallest Intervention Strategies in Genome-Scale Metabolic Networks

Steffen Klamt, Axel von Kamp, S. Klamt, 2014, PLoS Comput. Biol..

ATP futile cycling increases specific productivity and yield of anaerobic lactate production in Escherichia coli

S. Klamt, K. Bettenbrock, O. Hädicke, 2016 .

CASOP GS: Computing Intervention Strategies Targeted at Production Improvement in Genome-scale Metabolic Networks

Steffen Klamt, Christoph Kaleta, Stefan Schuster, 2010, GCB.

Blending industrial blast furnace gas with H2 enables Acetobacterium woodii to efficiently co-utilize CO, CO2 and H2.

S. Klamt, Katharina Novak, C. Neuendorf, 2020, Bioresource technology.

OptMDFpathway: Identification of metabolic pathways with maximal thermodynamic driving force and its application for analyzing the endogenous CO2 fixation potential of Escherichia coli

Steffen Klamt, Axel von Kamp, Oliver Hädicke, 2018, PLoS Comput. Biol..

Modeling the electron transport chain of purple non-sulfur bacteria

E. Gilles, S. Klamt, R. Ghosh, 2008, Molecular systems biology.

Cyanobacterial biofuels: new insights and strain design strategies revealed by computational modeling

S. Klamt, R. Steuer, Henning Knoop, 2014, Microbial Cell Factories.

FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps

Steffen Klamt, Jörg Stelling, Ernst Dieter Gilles, 2003, Bioinform..

Hypergraphs and Cellular Networks

Steffen Klamt, Fabian J. Theis, Fabian J Theis, 2009, PLoS Comput. Biol..

Broadening the Scope of Enforced ATP Wasting as a Tool for Metabolic Engineering in Escherichia coli.

S. Klamt, H. Link, Thorben Schramm, 2019, Biotechnology journal.

Host-pathogen systems biology: logical modelling of hepatocyte growth factor and Helicobacter pylori induced c-Met signal transduction

Steffen Klamt, Ernst Dieter Gilles, Michael Naumann, 2008, BMC Systems Biology.

Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling

Steffen Klamt, Fabian J. Theis, Julio Saez-Rodriguez, 2009, BMC Systems Biology.

The Logic of EGFR/ErbB Signaling: Theoretical Properties and Analysis of High-Throughput Data

Steffen Klamt, Julio Saez-Rodriguez, Peter K. Sorger, 2009, PLoS Comput. Biol..

GSMN-TB: a web-based genome-scale network model of Mycobacterium tuberculosis metabolism

S. Klamt, A. Kierzek, B. Bonde, 2007, Genome Biology.

Reconstruction of large-scale regulatory networks based on perturbation graphs and transitive reduction: improved methods and their evaluation

S. Klamt, A. Fuente, R. Flassig, 2013, BMC Systems Biology.

Computation of elementary modes: a unifying framework and the new binary approach

Steffen Klamt, Julien Gagneur, J. Gagneur, 2004, BMC Bioinformatics.

Metabolic network structure determines key aspects of functionality and regulation

S. Schuster, J. Stelling, E. Gilles, 2002, Nature.

Generalizing Diffuse Interface Methods on Graphs: Nonsmooth Potentials and Hypergraphs

Steffen Klamt, Martin Stoll, Jessica Bosch, 2016, SIAM J. Appl. Math..

A Logical Model Provides Insights into T Cell Receptor Signaling

Steffen Klamt, Julio Saez-Rodriguez, Ernst Dieter Gilles, 2007, PLoS Comput. Biol..

Two approaches for metabolic pathway analysis?

Steffen Klamt, Jörg Stelling, J. Stelling, 2003, Trends in biotechnology.

Designing microbial communities to maximize the thermodynamic driving force for the production of chemicals

Pavlos Stephanos Bekiaris, S. Klamt, Steffen Klamt, 2021, PLoS Comput. Biol..

A mathematical framework for yield (vs. rate) optimization in constraint-based modeling and applications in metabolic engineering

Steffen Klamt, Georg Regensburger, Stefan Müller, 2018, Metabolic engineering.

Computing complex metabolic intervention strategies using constrained minimal cut sets.

Steffen Klamt, Oliver Hädicke, S. Klamt, 2011, Metabolic engineering.

CASOP: a computational approach for strain optimization aiming at high productivity.

Steffen Klamt, Oliver Hädicke, 2010, Journal of biotechnology.

Calculability analysis in underdetermined metabolic networks illustrated by a model of the central metabolism in purple nonsulfur bacteria.

Steffen Klamt, Stefan Schuster, Ernst Dieter Gilles, 2002, Biotechnology and bioengineering.

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools

Steffen Klamt, Aurélien Naldi, Denis Thieffry, 2013, BMC Systems Biology.

Modeling approaches for qualitative and semi-quantitative analysis of cellular signaling networks

S. Klamt, R. Samaga, Regina Samaga, 2013, Cell Communication and Signaling.

An effective framework for reconstructing gene regulatory networks from genetical genomics data

Sandra Heise, Robert J. Flassig, Steffen Klamt, 2013, Bioinform..

Benchmarking a Simple Yet Effective Approach for Inferring Gene Regulatory Networks from Systems Genetic Data

Sandra Heise, Steffen Klamt, Robert Flassig, 2013 .

Growth-coupled anaerobic production of isobutanol from glucose in minimal medium with Escherichia coli

Simon Boecker, Steffen Klamt, Peter Schulze, 2023, Biotechnology for Biofuels and Bioproducts.

Characterizing and utilizing oxygen-dependent promoters for efficient dynamic metabolic engineering

S. Klamt, Simon Boecker, G. Behrendt, 2023, Metabolic engineering.

Enabling anaerobic growth of Escherichia coli on glycerol in defined minimal medium using acetate as redox sink.

S. Klamt, K. Bettenbrock, Simon Boecker, 2022, Metabolic engineering.

Deciphering the physiological response of Escherichia coli under high ATP demand

S. Klamt, R. Steuer, H. Link, 2021, Molecular systems biology.

Increasing ATP turnover boosts productivity of 2,3-butanediol synthesis in Escherichia coli

S. Klamt, S. Pflügl, Björn-Johannes Harder, 2021, Microbial Cell Factories.

Temperature‐dependent dynamic control of the TCA cycle increases volumetric productivity of itaconic acid production by Escherichia coli

S. Klamt, K. Bettenbrock, Björn-Johannes Harder, 2017, Biotechnology and bioengineering.

Predicting compositions of microbial communities from stoichiometric models with applications for the biogas process

S. Klamt, D. Benndorf, U. Reichl, 2016, Biotechnology for Biofuels.

A methodology for the structural and functional analysis of signaling and regulatory networks

Steffen Klamt, Julio Saez-Rodriguez, Ernst Dieter Gilles, 2006, BMC Bioinformatics.

From Binary to Multivalued to Continuous Models: The lac Operon as a Case Study

Fabian J Theis, S. Klamt, Raimo Franke, 2010, J. Integr. Bioinform..

Advances and Applications in Bioinformatics and Chemistry Dovepress Open Access to Scientific and Medical Research Open Access Full Text Article Logical Network of Genotoxic Stress-induced Nf-κb Signal Transduction Predicts Putative Target Structures for Therapeutic Intervention Strategies

M. Naumann, Raimo Franke, Rainer Poltz, 2022 .

Minimal cut sets in a metabolic network are elementary modes in a dual network

A. V. Kamp, U. Haus, Kathrin Ballerstein, 2012, Bioinform..

Computing Knock-Out Strategies in Metabolic Networks

Steffen Klamt, Tamon Stephen, Utz-Uwe Haus, 2007, J. Comput. Biol..

Speeding up the core algorithm for the dual calculation of minimal cut sets in large metabolic networks

Steffen Klamt, Radhakrishnan Mahadevan, Axel von Kamp, 2020, BMC Bioinformatics.

An extended and generalized framework for the calculation of metabolic intervention strategies based on minimal cut sets

Steffen Klamt, Axel von Kamp, Philipp Schneider, 2020, PLoS Comput. Biol..

Exact quantification of cellular robustness in genome-scale metabolic networks

Steffen Klamt, Christian Jungreuthmayer, Matthias P. Gerstl, 2015, Bioinform..

An application programming interface for CellNetAnalyzer

Steffen Klamt, Axel von Kamp, S. Klamt, 2011, Biosyst..

Generalized concept of minimal cut sets in biochemical networks.

S. Klamt, Steffen Klamt, 2006, Bio Systems.

Algorithmic approaches for computing elementary modes in large biochemical reaction networks.

S Klamt, J Gagneur, A von Kamp, 2005, Systems biology.

Minimal cut sets in biochemical reaction networks

Steffen Klamt, Ernst Dieter Gilles, E. Gilles, 2004, Bioinform..

Computing Combinatorial Intervention Strategies and Failure Modes in Signaling Networks

Steffen Klamt, Axel von Kamp, Regina Samaga, 2010, J. Comput. Biol..

GSMN-TB: a web-based genome-scale network model of Mycobacterium tuberculosis metabolism

A. Kierzek, B. Bonde, P. Wheeler, 2007, Genome Biology.

Comparison of network-based pathway analysis methods.

Jason A. Papin, S. Schuster, B. Palsson, 2004, Trends in biotechnology.

Growth-coupled overproduction is feasible for almost all metabolites in five major production organisms

Steffen Klamt, Axel von Kamp, S. Klamt, 2017, Nature Communications.

EColiCore2: a reference network model of the central metabolism of Escherichia coli and relationships to its genome-scale parent model

S. Klamt, O. Hädicke, Steffen Klamt, 2017, Scientific Reports.

CNApy: a CellNetAnalyzer GUI in Python for analyzing and designing metabolic networks

Pavlos Stephanos Bekiaris, S. Klamt, A. V. Kamp, 2021, Bioinform..

Memote: A community driven effort towards a standardized genome-scale metabolic model test suite

Steffen Klamt, Anne Richelle, Hyun Uk Kim, 2018, bioRxiv.

Stoichiometric analysis of metabolic networks

Steffen Klamt, Jörg Stelling, J. Stelling, 2003 .

Bridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical models.

Steffen Klamt, Miguel Rocha, Julio Saez-Rodriguez, 2013, Molecular bioSystems.

Comparison and improvement of algorithms for computing minimal cut sets

Steffen Klamt, Christian Jungreuthmayer, Govind Nair, 2013, BMC Bioinformatics.

Metabolic network modeling of redox balancing and biohydrogen production in purple nonsulfur bacteria

Steffen Klamt, Oliver Hädicke, Hartmut Grammel, 2011, BMC Systems Biology.

MEMO: A Method for Computing Metabolic Modules for Cell-Free Production Systems

Steffen Klamt, Axel von Kamp, A. V. Kamp, 2020, ACS synthetic biology.

An integrative model links multiple inputs and signaling pathways to the onset of DNA synthesis in hepatocytes

Steffen Klamt, Ursula Klingmüller, E. Gilles, 2012, The FEBS journal.

Manipulation of the ATP pool as a tool for metabolic engineering.

S. Klamt, O. Hädicke, Steffen Klamt, 2015, Biochemical Society transactions.

Disentangling the Complexity of HGF Signaling by Combining Qualitative and Quantitative Modeling

Steffen Klamt, Ursula Klingmüller, Jens Timmer, 2015, PLoS Comput. Biol..

Calculating as Many Fluxes as Possible in Underdetermined Metabolic Networks

Steffen Klamt, Stefan Schuster, S. Schuster, 2004, Molecular Biology Reports.

Extended notions of sign consistency to relate experimental data to signaling and regulatory network topologies

J. Sáez-Rodríguez, A. Siegel, Carito Guziolowski, 2015, BMC Bioinformatics.

Detecting and Removing Inconsistencies between Experimental Data and Signaling Network Topologies Using Integer Linear Programming on Interaction Graphs

Ioannis N. Melas, L. Alexopoulos, Regina Samaga, 2013, PLoS Comput. Biol..

Visual setup of logical models of signaling and regulatory networks with ProMoT

E. Gilles, J. Sáez-Rodríguez, Martin Ginkel, 2006, BMC Bioinformatics.

Characterizing and ranking computed metabolic engineering strategies

Steffen Klamt, Philipp Schneider, S. Klamt, 2019, Bioinform..

Special issue: Integration of OMICs datasets into Metabolic Pathway Analysis

Steffen Klamt, Christoph Kaleta, Stefan Schuster, 2011, Biosyst..

In silico profiling of Escherichia coli and Saccharomyces cerevisiae as terpenoid factories

Steffen Klamt, Oliver Hädicke, Oliver Kayser, 2013, Microbial Cell Factories.

Analyzing and Resolving Infeasibility in Flux Balance Analysis of Metabolic Networks

S. Klamt, A. von Kamp, Steffen Klamt, 2022, Metabolites.

A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models

Steffen Klamt, Julio Saez-Rodriguez, Emanuel J. V. Gonçalves, 2014, Biosyst..