List of works - Steffen Klamt

A logical model provides insights into T cell receptor signaling

scientific article

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

scientific article published on 7 February 2018

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

scientific article published on 7 February 2006

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

scientific article published on 23 July 2014

ATPase-based implementation of enforced ATP wasting in Saccharomyces cerevisiae for improved ethanol production

scientific article published on 09 November 2020

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

scientific article published on December 2005

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

scientific article published on 19 August 2015

An application programming interface for CellNetAnalyzer

scientific article published on 21 February 2011

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

scientific article

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

scientific article published on 27 July 2020

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

scientific article

Automatic construction of metabolic models with enzyme constraints

scientific article published on 14 January 2020

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

scientific article published on 25 March 2013

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

scientific article published on 17 May 2019

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

scientific article published on 18 March 2010

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

scientific article published in 2021

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

scientific article published on March 2002

Calculating as many fluxes as possible in underdetermined metabolic networks

scientific article published in January 2002

Characterizing and ranking computed metabolic engineering strategies

scientific article published on 01 September 2019

Combinatorial complexity of pathway analysis in metabolic networks

scientific article published in January 2002

Comparison and improvement of algorithms for computing minimal cut sets

scientific article

Comparison of network-based pathway analysis methods

scientific article

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

scientific article

Computing combinatorial intervention strategies and failure modes in signaling networks

scientific article published in January 2010

Computing complex metabolic intervention strategies using constrained minimal cut sets

scientific article published on 13 December 2010

Computing knock-out strategies in metabolic networks

scientific article published in April 2008

Computing paths and cycles in biological interaction graphs

scientific article published on 15 June 2009

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

scientific article

Designing optimal experiments to discriminate interaction graph models

scientific article published on 15 March 2018

Detecting and removing inconsistencies between experimental data and signaling network topologies using integer linear programming on interaction graphs

scientific article

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

scientific article

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

scientific article published on 23 April 2015

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

scientific article published on 3 January 2017

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

scientific article published in 2022

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

scientific article published on 30 June 2015

Enumeration of smallest intervention strategies in genome-scale metabolic networks

scientific article (publication date: 2014)

Establishment of a five-enzyme cell-free cascade for the synthesis of uridine diphosphate N-acetylglucosamine

scientific article published on 22 July 2018

Evaluating differences of metabolic performances: statistical methods and their application to animal cell cultivations.

scientific article published on 30 April 2013

Exact quantification of cellular robustness in genome-scale metabolic networks.

scientific article

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

scientific article

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

scientific article published in January 2003

From binary to multivalued to continuous models: the lac operon as a case study

scientific article published on December 14, 2010

From elementary flux modes to elementary flux vectors: Metabolic pathway analysis with arbitrary linear flux constraints.

scientific article

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

scientific article published on January 2007

Generalized concept of minimal cut sets in biochemical networks

scientific article published on 21 November 2005

Genome-scale strain designs based on regulatory minimal cut sets

scientific article published on 25 April 2015

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

scientific article published on 22 June 2017

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

scientific article

Host–Pathogen Interactions

Hypergraphs and cellular networks

scientific article

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

scientific article published on 23 September 2013

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

scientific article published in 2021

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

scientific article

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

scientific article published on 02 March 2020

MEMOTE for standardized genome-scale metabolic model testing

scientific article published on 01 March 2020

MUFINS: multi-formalism interaction network simulator. ⬇️

scientific article

Manipulation of the ATP pool as a tool for metabolic engineering

scientific article

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

scientific article

Metabolic network structure determines key aspects of functionality and regulation

scientific article (publication date: 14 November 2002)

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

scientific article published on 21 December 2011

Minimal cut sets in biochemical reaction networks

scientific article published in January 2004

MoVE identifies metabolic valves to switch between phenotypic states

scientific article published in Nature Communications

Model-based metabolic engineering enables high yield itaconic acid production by Escherichia coli.

scientific article published on 3 June 2016

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

scientific article published on 26 June 2013

Modeling the electron transport chain of purple non-sulfur bacteria

scientific article published on 15 January 2008

Multistability of signal transduction motifs

scientific article published in March 2008

Network-Based Analysis of Nutraceuticals in Human Hepatocellular Carcinomas Reveals Mechanisms of Chemopreventive Action

scientific article published in June 2015

On the feasibility of growth-coupled product synthesis in microbial strains

scientific article published on 22 June 2015

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

scientific article published on 24 September 2018

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

scientific article

Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing

scientific article published on 01 April 2020

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

scientific article published on 8 August 2013

RedCom: A strategy for reduced metabolic modeling of complex microbial communities and its application for analyzing experimental datasets from anaerobic digestion

scientific article published on 01 February 2019

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

scientific article

Silence on the relevant literature and errors in implementation

scientific article published in April 2015

Special issue: Integration of OMICs datasets into Metabolic Pathway Analysis

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

scientific article published on 09 November 2020

Structural and functional analysis of cellular networks with CellNetAnalyzer

scientific article

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

scientific article

TRANSWESD: inferring cellular networks with transitive reduction.

scientific article published on 6 July 2010

TRaCE+: Ensemble inference of gene regulatory networks from transcriptional expression profiles of gene knock-out experiments.

scientific article

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

scientific article published on 02 September 2017

The avian cell line AGE1.CR.pIX characterized by metabolic flux analysis

scientific article

The logic of EGFR/ErbB signaling: theoretical properties and analysis of high-throughput data

scientific article

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

scientific article

Two approaches for metabolic pathway analysis?

scientific article

Use of CellNetAnalyzer in biotechnology and metabolic engineering.

scientific article

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

scientific article

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

scientific article published on 13 November 2017

List of works by Steffen Klamt

A logical model provides insights into T cell receptor signaling

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

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

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

ATPase-based implementation of enforced ATP wasting in Saccharomyces cerevisiae for improved ethanol production

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

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

An application programming interface for CellNetAnalyzer

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

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

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

Automatic construction of metabolic models with enzyme constraints

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

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

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

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

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

Calculating as many fluxes as possible in underdetermined metabolic networks

Characterizing and ranking computed metabolic engineering strategies

Combinatorial complexity of pathway analysis in metabolic networks

Comparison and improvement of algorithms for computing minimal cut sets

Comparison of network-based pathway analysis methods

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

Computing combinatorial intervention strategies and failure modes in signaling networks

Computing complex metabolic intervention strategies using constrained minimal cut sets

Computing knock-out strategies in metabolic networks

Computing paths and cycles in biological interaction graphs

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

Designing optimal experiments to discriminate interaction graph models

Detecting and removing inconsistencies between experimental data and signaling network topologies using integer linear programming on interaction graphs

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

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

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

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

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

Enumeration of smallest intervention strategies in genome-scale metabolic networks

Establishment of a five-enzyme cell-free cascade for the synthesis of uridine diphosphate N-acetylglucosamine

Evaluating differences of metabolic performances: statistical methods and their application to animal cell cultivations.

Exact quantification of cellular robustness in genome-scale metabolic networks.

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

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

From binary to multivalued to continuous models: the lac operon as a case study

From elementary flux modes to elementary flux vectors: Metabolic pathway analysis with arbitrary linear flux constraints.

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

Generalized concept of minimal cut sets in biochemical networks

Genome-scale strain designs based on regulatory minimal cut sets

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

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

Host–Pathogen Interactions

Hypergraphs and cellular networks

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

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

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

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

MEMOTE for standardized genome-scale metabolic model testing

MUFINS: multi-formalism interaction network simulator. ⬇️

Manipulation of the ATP pool as a tool for metabolic engineering

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

Metabolic network structure determines key aspects of functionality and regulation

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

Minimal cut sets in biochemical reaction networks

MoVE identifies metabolic valves to switch between phenotypic states

Model-based metabolic engineering enables high yield itaconic acid production by Escherichia coli.

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

Modeling the electron transport chain of purple non-sulfur bacteria

Multistability of signal transduction motifs

Network-Based Analysis of Nutraceuticals in Human Hepatocellular Carcinomas Reveals Mechanisms of Chemopreventive Action

On the feasibility of growth-coupled product synthesis in microbial strains

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

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

Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing

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

RedCom: A strategy for reduced metabolic modeling of complex microbial communities and its application for analyzing experimental datasets from anaerobic digestion

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

Silence on the relevant literature and errors in implementation

Special issue: Integration of OMICs datasets into Metabolic Pathway Analysis

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

Structural and functional analysis of cellular networks with CellNetAnalyzer

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