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Stefan Schuster
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Publications
- 2021
- [j45]Jan Ewald, Flora Rivieccio, Lukás Radosa, Stefan Schuster, Axel A. Brakhage, Christoph Kaleta:
Dynamic optimization reveals alveolar epithelial cells as key mediators of host defense in invasive aspergillosis. PLoS Comput. Biol. 17(12) (2021) - 2017
- [j39]Steffen Klamt, Georg Regensburger, Matthias P. Gerstl, Christian Jungreuthmayer, Stefan Schuster, Radhakrishnan Mahadevan, Jürgen Zanghellini, Stefan Müller:
From elementary flux modes to elementary flux vectors: Metabolic pathway analysis with arbitrary linear flux constraints. PLoS Comput. Biol. 13(4) (2017) - 2016
- [j38]Sebastian Germerodt, Katrin Bohl, Anja Lück, Samay Pande, Anja Schröter, Christoph Kaleta, Stefan Schuster, Christian Kost:
Pervasive Selection for Cooperative Cross-Feeding in Bacterial Communities. PLoS Comput. Biol. 12(6) (2016) - [p1]Stefan Schuster, Björn H. Junker:
Topological Analysis of Metabolic and Regulatory Networks. Modeling in Systems Biology, The Petri Net Approach 2016: 209-224 - 2015
- [i2]Stefan Schuster, Daniel Boley, Philip Möller, Christoph Kaleta:
A minimal model for explaining the higher ATP production in the Warburg effect. PeerJ Prepr. 3: e1309 (2015) - 2013
- [j34]Alberto Rezola, Jon Pey, Luis F. de Figueiredo, Adam Podhorski, Stefan Schuster, Angel Rubio, Francisco J. Planes:
Selection of human tissue-specific elementary flux modes using gene expression data. Bioinform. 29(16): 2009-2016 (2013) - [j33]Martin Pohl, Ralf H. Bortfeldt, Konrad Grützmann, Stefan Schuster:
Alternative splicing of mutually exclusive exons - A review. Biosyst. 114(1): 31-38 (2013) - 2012
- [j30]Christian Bodenstein, Marko Gosak, Stefan Schuster, Marko Marhl, Matjaz Perc:
Modeling the Seasonal Adaptation of Circadian Clocks by Changes in the Network Structure of the Suprachiasmatic Nucleus. PLoS Comput. Biol. 8(9) (2012) - [e1]Sebastian Böcker, Franziska Hufsky, Kerstin Scheubert, Jana Schleicher, Stefan Schuster:
German Conference on Bioinformatics 2012, GCB 2012, Jena, Germany, September 20-22, 2012. OASIcs 26, Schloss Dagstuhl - Leibniz-Zentrum für Informatik 2012, ISBN 978-3-939897-44-6 [contents] - 2011
- [j29]Alberto Rezola, Luis F. de Figueiredo, Matthias Brock, Jon Pey, Adam Podhorski, Christoph Wittmann, Stefan Schuster, Alexander Bockmayr, Francisco J. Planes:
Exploring metabolic pathways in genome-scale networks via generating flux modes. Bioinform. 27(4): 534-540 (2011) - [j28]Christoph Kaleta, Luis F. de Figueiredo, Ines Heiland, Steffen Klamt, Stefan Schuster:
Special issue: Integration of OMICs datasets into Metabolic Pathway Analysis. Biosyst. 105(2): 107-108 (2011) - [j27]Stefan Schuster, Luis F. de Figueiredo, Anja Schröter, Christoph Kaleta:
Combining Metabolic Pathway Analysis with Evolutionary Game Theory. Explaining the occurrence of low-yield pathways by an analytic optimization approach. Biosyst. 105(2): 147-153 (2011) - [j26]Anna-Katharina Göhler, Öznur Kökpinar, Wolfgang Schmidt-Heck, Robert Geffers, Reinhard Guthke, Ursula Rinas, Stefan Schuster, Knut Jahreis, Christoph Kaleta:
More than just a metabolic regulator - elucidation and validation of new targets of PdhR in Escherichia coli. BMC Syst. Biol. 5: 197 (2011) - [j25]Thomas Hinze, Mathias Schumann, Christian Bodenstein, Ines Heiland, Stefan Schuster:
Biochemical Frequency Control by Synchronisation of Coupled Repressilators: An In Silico Study of Modules for Circadian Clock Systems. Comput. Intell. Neurosci. 2011: 262189:1-262189:9 (2011) - [j24]Christoph Kaleta, Luis F. de Figueiredo, Sarah Werner, Reinhard Guthke, Michael Ristow, Stefan Schuster:
In Silico Evidence for Gluconeogenesis from Fatty Acids in Humans. PLoS Comput. Biol. 7(7) (2011) - [c29]Thomas Hinze, Mathias Schumann, Stefan Schuster:
Synchronisation of Biological Clock Signals - Capturing Coupled Repressilators from a Control Systems Perspective. BIOSIGNALS 2011: 101-106 - [c27]Thomas Hinze, Christian Bodenstein, Benedict Schau, Ines Heiland, Stefan Schuster:
Chemical Analog Computers for Clock Frequency Control Based on P Modules. Int. Conf. on Membrane Computing 2011: 182-202 - [i1]Thomas Hinze, Christian Bodenstein, Ines Heiland, Stefan Schuster:
Capturing Biological Frequency Control of Circadian Clocks by Reaction System Modularization. ERCIM News 2011(85): 27-28 (2011) - 2010
- [j23]Martin Bartl, Pu Li, Stefan Schuster:
Modelling the optimal timing in metabolic pathway activation - Use of Pontryagin's Maximum Principle and role of the Golden section. Biosyst. 101(1): 67-77 (2010) - [j22]Rileen Sinha, Thorsten Lenser, Niels Jahn, Ulrike Gausmann, Swetlana Friedel, Karol Szafranski, Klaus Huse, Philip Rosenstiel, Jochen Hampe, Stefan Schuster, Michael Hiller, Rolf Backofen, Matthias Platzer:
TassDB2 - A comprehensive database of subtle alternative splicing events. BMC Bioinform. 11: 216 (2010) - [j21]Christoph Kaleta, Anna-Katharina Göhler, Stefan Schuster, Knut Jahreis, Reinhard Guthke, Swetlana Nikolajewa:
Integrative inference of gene-regulatory networks in Escherichia coli using information theoretic concepts and sequence analysis. BMC Syst. Biol. 4: 116 (2010) - [j20]Ralf H. Bortfeldt, Stefan Schuster, Ina Koch:
Exhaustive Analysis of the Modular Structure of the Spliceosomal Assembly Network: A Petri Net Approach. Silico Biol. 10(1-2): 89-123 (2010) - [j19]Beate Knoke, Christian Bodenstein, Marko Marhl, Matjaz Perc, Stefan Schuster:
Jensen's inequality as a tool for explaining the effect of oscillations on the average cytosolic calcium concentration. Theory Biosci. 129(1): 25-38 (2010) - [c26]Gabi Escuela, Thomas Hinze, Peter Dittrich, Stefan Schuster, Mario Moreno-Álvarez:
Modelling Modified Atmosphere Packaging for Fruits and Vegetables using Membrane Systems. BIOSIGNALS 2010: 306-311 - [c24]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 - 2009
- [j18]Luis F. de Figueiredo, Stefan Schuster, Christoph Kaleta, David A. Fell:
Can sugars be produced from fatty acids? A test case for pathway analysis tools. Bioinform. 25(1): 152-158 (2009) - [j17]Luis F. de Figueiredo, Adam Podhorski, Angel Rubio, Christoph Kaleta, John E. Beasley, Stefan Schuster, Francisco J. Planes:
Computing the shortest elementary flux modes in genome-scale metabolic networks. Bioinform. 25(23): 3158-3165 (2009) - [j16]Luis F. de Figueiredo, Stefan Schuster, Christoph Kaleta, David A. Fell:
Response to comment on 'Can sugars be produced from fatty acids? A test case for pathway analysis tools'. Bioinform. 25(24): 3330-3331 (2009) - [j15]Jeanice Kielbassa, Ralf H. Bortfeldt, Stefan Schuster, Ina Koch:
Modeling of the U1 snRNP assembly pathway in alternative splicing in human cells using Petri nets. Comput. Biol. Chem. 33(1): 46-61 (2009) - [j14]Jörn Behre, Stefan Schuster:
Modeling Signal Transduction in Enzyme Cascades with the Concept of Elementary Flux Modes. J. Comput. Biol. 16(6): 829-844 (2009) - [c23]Christoph Kaleta, Luis F. de Figueiredo, Jörn Behre, Stefan Schuster:
Computing Elementary Flux Modes in Genome-scale Metabolic Networks. GCB 2009: 179-189 - [c22]Thomas Hinze, Thorsten Lenser, Gabi Escuela, Ines Heiland, Stefan Schuster:
Modelling Signalling Networks with Incomplete Information about Protein Activation States: A P System Framework of the KaiABC Oscillator. Workshop on Membrane Computing 2009: 316-334 - 2008
- [j12]Luis F. de Figueiredo, Stefan Schuster, Christoph Kaleta, David A. Fell:
Can sugars be produced from fatty acids? A test case for pathway analysis tools. Bioinform. 24(22): 2615-2621 (2008) - [j10]Beate Knoke, Marko Marhl, Matjaz Perc, Stefan Schuster:
Equality of average and steady-state levels in some nonlinear models of biological oscillations. Theory Biosci. 127(1): 1-14 (2008) - 2007
- [j9]Roland Schwarz, Chunguang Liang, Christoph Kaleta, Mark Kühnel, Eik Hoffmann, Sergei Kuznetsov, Michael Hecker, Gareth Griffiths, Stefan Schuster, Thomas Dandekar:
Integrated network reconstruction, visualization and analysis using YANAsquare. BMC Bioinform. 8 (2007) - [j8]Michael Hiller, Swetlana Nikolajewa, Klaus Huse, Karol Szafranski, Philip Rosenstiel, Stefan Schuster, Rolf Backofen, Matthias Platzer:
TassDB: a database of alternative tandem splice sites. Nucleic Acids Res. 35(Database-Issue): 188-192 (2007) - 2006
- [j7]Axel von Kamp, Stefan Schuster:
Metatool 5.0: fast and flexible elementary modes analysis. Bioinform. 22(15): 1930-1931 (2006) - 2005
- [j6]Roland Schwarz, Patrick Musch, Axel von Kamp, Bernd Engels, R. Heiner Schirmer, Stefan Schuster, Thomas Dandekar:
YANA - a software tool for analyzing flux modes, gene-expression and enzyme activities. BMC Bioinform. 6: 135 (2005) - [j5]Ionela Zevedei-Oancea, Stefan Schuster:
A theoretical framework for detecting signal transfer routes in signalling networks. Comput. Chem. Eng. 29(3): 597-617 (2005) - 2003
- [j4]Ionela Zevedei-Oancea, Stefan Schuster:
Topological analysis of metabolic networks based on Petri net theory. Silico Biol. 3(3): 323-345 (2003) - [c10]Stefan Schuster, Steffen Klamt, Jörg Stelling:
Making predictions about robustness and flexibility from metabolic network structure. German Conference on Bioinformatics 2003: 129-134 - 2002
- [j3]Stefan Schuster, Thomas Pfeiffer, Ferdinand Moldenhauer, Ina Koch, Thomas Dandekar:
Exploring the pathway structure of metabolism: decomposition into subnetworks and application to Mycoplasma pneumoniae. Bioinform. 18(2): 351-361 (2002) - 2001
- [c9]Ferdinand Moldenhauer, Ionela Zevedei-Oancea, Stefan Schuster:
Pathway Analysis of Metabolic Networks: New version of METATOOL and convenient classification of metabolites. German Conference on Bioinformatics 2001: 210 - [c8]Ionela Zevedei-Oancea, Stefan Schuster:
Treatment of multifunctional enzymesin metabolic pathway analysis. German Conference on Bioinformatics 2001: 241-242 - 2000
- [c7]Stefan Schuster, Thomas Pfeiffer, Ferdinand Moldenhauer, Ina Koch, Thomas Dandekar:
Structural Analysis of Metabolic Networks: Elementary Flux Modes, Analogy to Petri Nets, and Application to Mycoplasma Pneumoniae. German Conference on Bioinformatics 2000: 115-120 - 1999
- [j2]Thomas Pfeiffer, Ignacio Sánchez-Valdenebro, Juan Carlos Nuño, Francisco Montero, Stefan Schuster:
METATOOL: for studying metabolic networks. Bioinform. 15(3): 251-257 (1999) - [c6]Ina Koch, Stefan Schuster, Monika Heiner:
Simulation and analysis of metabolic networks by time-dependent Petri nets. German Conference on Bioinformatics 1999: 208-209 - [c5]Thomas Pfeiffer, Juan Carlos Nuño, Francisco Montero, Stefan Schuster:
Analyzing Large enzymatic reaction networks. German Conference on Bioinformatics 1999: 221-223 - 1998
- [c4]Thomas Dandekar, Stefan Schuster, Martijn A. Huynen, Peer Bork:
Pathway alignment: Application in the comparative analysis of glycolysis. German Conference on Bioinformatics 1998 - [c3]Ignacio Sánchez-Valdenebro, Thomas Pfeiffer, Juan Carlos Nuño, Francisco Montero, Stefan Schuster:
A structural approach to the analysis of metabolic networks illustrated with erythrocyte metabolism. German Conference on Bioinformatics 1998
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