Steffen Klamt

发表

Automatic construction of metabolic models with enzyme constraints

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

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..

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.

Computing paths and cycles in biological interaction graphs

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

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

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

Computing Combinatorial Intervention Strategies and Failure Modes in Signaling Networks

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

FluxAnalyzer: A Graphical User Interface for Analyzing Structural Properties and Fluxes in Balanced Metabolic Networks

Steffen Klamt, Ernst Dieter Gilles, 2001, German Conference on Bioinformatics.

Designing Optimal Experiments to Discriminate Interaction Graph Models

Sandra Heise, Steffen Klamt, Sven Thiele, 2019, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Use of CellNetAnalyzer in biotechnology and metabolic engineering.

Steffen Klamt, Sven Thiele, Axel von Kamp, 2017, Journal of biotechnology.

MEMOTE for standardized genome-scale metabolic model testing

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

Exact quantification of cellular robustness in genome-scale metabolic networks

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

Two approaches for metabolic pathway analysis?

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

Making predictions about robustness and flexibility from metabolic network structure

Steffen Klamt, Stefan Schuster, Jörg Stelling, 2003, German Conference on Bioinformatics.

Generalizing Diffuse Interface Methods on Graphs: Nonsmooth Potentials and Hypergraphs

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

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

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

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

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

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

Steffen Klamt, Julio Saez-Rodriguez, Carito Guziolowski, 2015, BMC Bioinformatics.

Special issue: Integration of OMICs datasets into Metabolic Pathway Analysis

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

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

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

Genome-scale strain designs based on regulatory minimal cut sets

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

Comparison and improvement of algorithms for computing minimal cut sets

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

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

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

Silence on the relevant literature and errors in implementation

Steffen Klamt, Nils Blüthgen, Eduardo Sontag, 2015, Nature Biotechnology.

TRANSWESD: inferring cellular networks with transitive reduction

Robert J. Flassig, Steffen Klamt, Kai Sundmacher, 2010, Bioinform..

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

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

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

Steffen Klamt, Axel von Kamp, Utz-Uwe Haus, 2012, Bioinform..

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

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

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.

Minimal Cut Sets as Computational Tool in Metabolic Engineering

Steffen Klamt, 2012 .

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..

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..

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.

Hypergraphs and Cellular Networks

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

Fluxanalyzer: A Graphical Interface for Stoichiometric and Quantitative Analysis of Metabolic Networks

Steffen Klamt, Andreas Kremling, E. D. Gilles, 2001 .

A Logical Model Provides Insights into T Cell Receptor Signaling

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

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

Steffen Klamt, Leonidas G. Alexopoulos, Ioannis N. Melas, 2013, PLoS Comput. Biol..

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

Sandra Heise, Steffen Klamt, Robert Flassig, 2013 .

Computing complex metabolic intervention strategies using constrained minimal cut sets.

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

Characterizing and ranking computed metabolic engineering strategies

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

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.

Computational Systems Biology — neues Fach in den Lebenswissenschaften

Steffen Klamt, Wolfgang Wiechert, 2015, BIOspektrum.

An application programming interface for CellNetAnalyzer

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

Structural and functional analysis of cellular networks with CellNetAnalyzer

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

Workbench zur Modellbildung, Simulation und Analyse zellulärer Systeme (Workbench for Model Set Up, Simulation, and Analysis of Cellular Systems)

Steffen Klamt, Andreas Kremling, Ernst Dieter Gilles, 2004, it Inf. Technol..

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.

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

Steffen Klamt, Christian Jungreuthmayer, Stefan Schuster, 2017, PLoS Comput. Biol..

MUFINS: multi-formalism interaction network simulator

Steffen Klamt, Hiroshi Matsuno, Jacek Sroka, 2016, npj Systems Biology and Applications.

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

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

Minimal cut sets in biochemical reaction networks

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

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

Sandra Heise, Steffen Klamt, Rudiyanto Gunawan, 2016, BMC Bioinformatics.

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

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

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

Steffen Klamt, Fabian Kohrs, Dirk Benndorf, 2019, PLoS Comput. Biol..

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..

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

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

Enumeration of Smallest Intervention Strategies in Genome-Scale Metabolic Networks

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

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

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

MoVE identifies metabolic valves to switch between phenotypic states

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

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

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

Stoichiometric analysis of metabolic networks

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

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

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

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

Steffen Klamt, Udo Reichl, Ingo Jordan, 2014, BMC Biotechnology.

Applying metabolic pathway analysis to make good use of methanol

Steffen Klamt, Stefan Schuster, 2002 .

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.

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

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

Calculating as Many Fluxes as Possible in Underdetermined Metabolic Networks

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

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.

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.