Search returns 310 hits.
2018

Patricia Sieber, Kerstin Voigt, Philipp Kämmer, Sascha Brunke, Stefan Schuster, Jörg Linde
Comparative study on alternative splicing in human fungal pathogens suggests its involvement during host invasion
Frontiers in Microbiology XX, 2018, XX, accepted
bibtex ]

Stefan N. Lang, Sebastian Germerodt, Christina Glock, Christine Skerka, Peter F. Zipfel, Stefan Schuster
Molecular crypsis by pathogenic fungi using human factor H. A numerical model
bioRxiv, 2018, 250662, preprint
bibtex | abstract |  doi  |  url  ]

S. Hummert, C. Glock, S. N. Lang, C. Hummert, C. Skerka, P.F. Zipfel, S. Germerodt, S. Schuster
Playing ’hide-and-seek’ with factor H: Game-theoretical analysis of a single nucleotide polymorphism
Journal of the Royal Society Interface 15, 2018, 20170963
bibtex | abstract ]

S. Peres, S. Schuster, P. Dague
Thermodynamic constraints for identifying the elementary flux modes
Biochemical Society Transactions 46(3), 2018, 641-647
bibtex | abstract |  doi  ]

Anja LĂĽck, Lukas Klimmasch, Peter GroĂźmann, Sebastian Germerodt, Christoph Kaleta
Computational Investigation of Environment-Noise Interaction in Single-Celled Organisms: The Merit of Expression Stochasticity Depends on the Quality of Environmental Fluctuations
Scientific Reports 8, 2018, 333
bibtex | abstract |  doi  ]

P.Aramillo Irizar, S.Schäuble, D.Esser, M.Groth, C.Frahm, S.Priebe, M.Baumgart, N.Hartmann, S.Marthandan, U.Menzel, J.Müller, S.Schmidt, V.Ast, A.Caliebe, R.König, M.Krawczak, M.Ristow, S.Schuster, A.Cellerino, S.Diekmann, C.Englert, P.Hemmerich, J.Sühnel, R.Guthke, O.W.Witte, M.Platzer, E.Ruppin, C.Kaleta
Transcriptomic alterations during ageing reflect the shift from cancer to degenerative diseases in the elderly
Nature Communications 9, 2018, 327
bibtex | abstract |  doi  ]

P. Möller, X. Liu, S. Schuster, D. Boley
Linear programming model can explain respiration of fermentation products.
PloS one 13, 2018, e0191803
bibtex |  doi  |  PudMed-ID: 29415045 ]

S. Vlaic, T. Conrad, C. Tokarski-Schnelle, M. Gustafsson, U. Dahmen, R. Guthke, S. Schuster
ModuleDiscoverer: Identification of regulatory modules in protein-protein interaction networks
Scientific Reports 8, 2018, 433
bibtex ]

P. Sieber, M. Platzer, S. Schuster
The definition of open reading frame revisited
Trends in Genetics 34, 2018, 167-170
bibtex | abstract |  doi  ]

Thomas Hinze, Benjamin Förster
Event-based Life in a Nutshell: How Evaluation of Individual Life Cycles Can Reveal Statistical Inferences using Action-accumulating P Systems
Lecture Notes in Computer Science 10725, 2018, 129-150, In: M. Gheorghe, G. Rozenberg, A. Salomaa, C. Zandron (Eds.), Membrane Computing. 18th International Conference. ISBN 978-3-319-73358-6, Springer Verlag
bibtex | abstract ]

D. Ward, J. Trinogga, K. Wiegand, J. Du Toit, D. Okubamichael, S. Reinsch, J. Schleicher
Large shrubs increase soil nutrients in a semi-arid savanna.
Geoderma 310, 2018, 153-162
bibtex |  url  ]

2017

H. Stark, M. Fichtner, P. Arnold, B. Hesse, I. Mischewski, M. S. Fischer
Methoden zur Quantifizierung kollagenhaltiger Strukturen
In: Kongressband 23. Erfurter Tage “Prävention von arbeitsbedingten Gesundheitsgefahren und Erkrankungen”. (eds. I. Dienstbühl, M. Stadler, H.-C. Scholle), Verlag Bussert & Stadeler, 2017, 299-304
bibtex ]

P. GroĂźmann, A. LĂĽck, C. Kaleta
Model-based genome-wide determination of RNA chain elongation rates in Escherichia coli.
Scientific reports 7, 2017, 17213
bibtex | abstract |  doi  |  PudMed-ID: 29222445 ]

T. Hinze
Interview with Gheorghe Paun
Bulletin of the International Membrane Computing Society, 2017, to appear in issue December 2017
bibtex ]

B. Christ, U. Dahmen, K.l-H. Herrmann, M. König, J. R. Reichenbach, T. Ricken, J. Schleicher, L. O. Schwen, S. Vlaic, N. Waschinsky
Computational Modeling in Liver Surgery
Frontiers in Physiology - Gastrointestinal Sciences 8, 2017, 906
bibtex | abstract |  doi  ]

J. Schleicher, U. Dahmen, R. Guthke, S. Schuster
Zonation of hepatic fat accumulation: insights from mathematical modelling of nutrient gradients and fatty acid uptake.
Journal of the Royal Society Interface 14, 2017, pii: 20170443
bibtex | abstract |  doi  |  PudMed-ID: 28835543 ]

J. Ewald, M. Bartl, C. Kaleta
Deciphering the regulation of metabolism with dynamic optimization: an overview of recent advances
Biochemical Society Transactions 45 (4), 2017, 1-9
bibtex | abstract |  doi  ]

S. DĂĽhring, J. Ewald, S. Germerodt, C. Kaleta, T. Dandekar and S. Schuster
Modelling the host–pathogen interactions of macrophages and Candida albicans using Game Theory and dynamic optimization
Journal of The Royal Society Interface 14 (132), 2017, 20170095
bibtex | abstract |  doi  ]

S. Schuster
A new solution concept for the ultimatum game leading to the Golden Ratio
Scientific Reports 7, 2017, 5642
bibtex | abstract |  doi  ]

S. Klamt, G. Regensburger, M.P. Gerstl, C. Jungreuthmayer, S. Schuster, R. Mahadevan, J. Zanghellini, S. MĂĽller
From Elementary Flux Modes to Elementary Flux Vectors: Metabolic Pathway Analysis with Arbitrary Linear Flux Constraints
PLOS Computational Biology 13 (4), 2017, e1005409
bibtex | abstract |  doi  ]

J. Ewald, M. Bartl, T. Dandekar, C. Kaleta
Optimality principles reveal a complex interplay of intermediate toxicity and kinetic efficiency in the regulation of prokaryotic metabolism
PLOS Computational Biology 13, 2017, e1005371
bibtex |  doi  ]

S. Peres, M. Jolicoeur, C. Moulin, P. Dague, S. Schuster
How important is thermodynamics for identifying elementary flux modes?
PLOS One 12, 2017, e0171440
bibtex | abstract |  doi  ]

S. Schuster, M. Fichtner, S. Sasso
Use of Fibonacci numbers in lipidomics - Enumerating various classes of fatty acids
Scientific Reports 7, 2017, 39821
bibtex | abstract |  doi  ]

K. Czakai, M. Dittrich, M. Kaltdorf, T. Müller, S. Krappmann, A. Schedler, M. Bonin, S. Dühring, S. Schuster, C. Speth, G. Rambach, H. Einsele, T. Dandekar, J. Löffler
Influence of platelet-rich plasma on the immune response of human monocyte-derived dendritic cells and macrophages simulated with Aspergillus fumigatus
International Journal of Medical Microbiology 307 (2), 2017, 95–107
bibtex ]

T. Hinze
Coping with Dynamical Structures for Interdisciplinary Applications of Membrane Computing
Springer Series Lecture Notes in Computer Science 10105, 2017, 16-27
bibtex | abstract |  doi  ]

S. Ellenberger, A. Burmester, S. Schuster, J. Wöstemeyer
Post-translational regulation by structural changes of 4-dihydromethyltrisporate dehydrogenase, a key enzyme in sexual and parasitic communication mediated by the trisporic acid pheromone system, of the fungal fusion parasite Parasitella parasitica
Journal of theoretical Biology 413, 2017, 50-57
bibtex | abstract |  doi  ]

M. Fichtner, K. Voigt, S. Schuster
The tip and hidden part of the iceberg: Proteinogenic and non-proteinogenic aliphatic amino acids
Biochimica and Biophysica Acta - General Subjects 1861 ( 1, Part A), 2017, 3258-3269
bibtex | abstract |  doi  ]

T. Hinze, L. Weber, U. Hatnik
Walking Membranes: Grid-exploring P Systems with Artificial Evolution for Multi-purpose Topological Optimisation of Cascaded Processes
Lecture Notes in Computer Science 10105 , 2017, 251-271
bibtex | abstract |  doi  ]

2016

A. J. Heidel, C. Kiefer, G. Coupland, L. E. Rose
Pinpointing genes underlying annual/perennial transitions with comparative genomics.
BMC genomics 17, 2016, 921
bibtex | abstract |  doi  |  PudMed-ID: 27846808 ]

M. Hölzer, V. Krähling ,F. Amman, E. Barth, S.H. Bernhart, V.A. Carmelo, M. Collatz, G. Doose , F. Eggenhofer, J. Ewald, J. Fallmann, L.M. Feldhahn , M. Fricke, J. Gebauer, A.J. Gruber, F. Hufsky, H. Indrischek, S. Kanton, J. Linde, N. Mostajo, R. Ochsenreiter, K. Riege, L. Rivarola-Duarte, A.H. Sahyoun, S.J. Saunders, S.E. Seemann, A. Tanzer, B. Vogel, S. Wehner, M.T. Wolfinger, R. Backofen, J. Gorodkin, I. Grosse, I. Hofacker, S. Hoffmann, C. Kaleta, P.F. Stadler, S. Becker, M. Marz
Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells
Scientific Reports 6: 34589, 2016,
bibtex | abstract |  PudMed-ID: 27713552 ]

Hebecker B, S. Vlaic, Conrad T, Bauer M, Brunke S, Kapitan M, Linde J, Hube B, Jacobsen ID
Dual-species transcriptional profiling during systemic candidiasis reveals organ-specific host-pathogen interactions.
Scientific Reports 6, 2016, 36055
bibtex |  PudMed-ID: 27808111 ]

A. Dix, S. Vlaic, R. Guthke, J. Linde
Use of systems biology to decipher host-pathogen interaction networks and predict biomarkers.
Clinical Microbiology and Infection 22 (7), 2016, 600-606
bibtex |  PudMed-ID: 27113568 ]

S. Germerodt, K. Bohl, A. Lück, S. Pande, A. Schröter, C. Kaleta, S. Schuster, C. Kost
Pervasive Selection for Cooperative Cross-Feeding in Bacterial Communities
PLOS Computational Biology 12 (6), 2016, e1004986
bibtex ]

J. Pollmächer, S. Timme, S. Schuster, A.A. Brakhage, P.F. Zipfel, M.T. Figge
Deciphering the counterplay of Aspergillus fumigatus infection and host inflammation by evolutionary games on graphs
Scientific Reports 6, 2016, Article number: 278072016
bibtex |  doi  ]

J. Gebauer , C. Gentsch , J. Mansfeld , K. Schmeißer , S. Waschina , S.Brandes , L. Klimmasch , N. Zamboni , K. Zarse , S. Schuster , M. Ristow , S. Schäuble , C. Kaleta
A Genome-Scale Database and Reconstruction of Caenorhabditis elegans Metabolism
Cell Systems 2 (5), 2016, 312-322
bibtex |  doi  |  url  ]

T. Weise, S. Schuster, M. Pfaff
Bestimmung algenbiotechnologisch relevanter Parameter im kontinuierlichen Bioprozessregime: Ertrags- und Maintenance-Koeffizient
In: Tagungsband 17. NW-Konferenz der mittel- und ostdeutschen Hochschulen fĂĽr angewandte Wissenschaften (eds. T. Seul), 2016, 30-35
bibtex ]

S. Ellenberger, L. Siegmund, S. Schuster, J. Wöstemeyer
Horizontal gene transfer between bacteria and protozoa: Gene-specific detection by combining different approaches in a new score-based algorithm
Endocytobiosis and Cell Research 27 (2), 2016, 36-46
bibtex ]

S. Widder, R. J. Allen, T. Pfeiffer, ..., S. Schuster, ...,O. S. Soyer
Challenges in microbial ecology: building predictive understanding of community function and dynamics
ISME Journal 10, 2016, 2557-2568
bibtex |  doi  ]

T. Hinze, J. Behre, K. Kirkici, Pa. Sauer, Pe. Sauer, S. Hayat
Passion to P for Polymorphic Processes in Practice
In: Multidisciplinary Creativity. Homage to Gheorghe Paun on His 65th Birthday (eds. M. Gheorghe, I. Petre, M.J. Perez-Jimenez, G. Rozenberg, A. Salomaa), ISBN 978-606-8401-63-8, Spandugino, 2016, ch. 7, 77-88
bibtex | abstract ]

T. Hinze, K. Kirkici, Pa. Sauer, Pe. Sauer, J. Behre
Membrane Computing Meets Temperature: A Thermoreceptor Model as Molecular Slide Rule with Evolutionary Potential
Springer Lecture Notes in Computer Science 9504, 2016, 215-235
bibtex | abstract |  doi  |  url  ]

S. Pande, F. Kaftan, S. Lang, A. Svatos, S. Germerodt, C. Kost
Privatization of cooperative benefits stabilizes mutualistic cross-feeding interactions in spatially structured environments
ISME Journal 10, 2016, 1413-1423
bibtex | abstract |  doi  ]

M. T. Prauße, S. Schäuble, R. Guthke, S. Schuster
Computing the various pathways of penicillin synthesis and their molar yields.
Biotechnology and bioengineering 113 (1), 2016, 173-181
bibtex |  doi  |  PudMed-ID: 26134880 ]

2015

A. Lopez Garcia de Lomana, S. Schäuble, J. Valenzuela, S. Imam, W. Carter, D. D. Bilgin, C. B. Yohn, S. Turkarslan, D. J. Reiss, M. V. Orellana, N. D. Price, N. S. Baliga
Transcriptional program for nitrogen starvation-induced lipid accumulation in Chlamydomonas reinhardtii.
Biotechnology for biofuels 8, 2015, 207
bibtex | abstract |  doi  |  PudMed-ID: 26633994 ]

J.Mansfeld, N.Urban, S.Priebe, M.Groth, C.Frahm, N.Hartmann, J.Gebauer, M.Ravichandran, A.Dommaschk, S.Schmeisser, D.Kuhlow, S.Monajembashi, S.Bremer-Streck, P.Hemmerich, M.Kiehntopf, N.Zamboni, C.Englert, R.Guthke, C.Kaleta, M.Platzer, J.SĂĽhnel, O.W.Witte, K.Zarse, M.Ristow
Branched-chain amino acid catabolism is a conserved regulator of physiological ageing
Nature Communications 6, 2015, 10043
bibtex |  doi  ]

S. Imam, S. Schäuble, J. Valenzuela, A. Lopez Garcia de Lomana, W. Carter, N. D. Price, N. S. Baliga
A refined genome-scale reconstruction of Chlamydomonas metabolism provides a platform for systems-level analyses.
The Plant journal : for cell and molecular biology 84 (6), 2015, 1239–1256
bibtex | abstract |  doi  |  PudMed-ID: 26485611 ]

S. K. Ludwig, C. Tokarski, S. N. Lang, L. A. van Ginkel, H. Zhu, A. Ozcan, M. W. Nielen
Calling biomarkers in milk using a protein microarray on your smartphone
PloS one 10, 2015, e0134360
bibtex | abstract |  doi  |  PudMed-ID: 26308444 ]

S. Schuster, D. Boley, P. Möller, H. Stark, C. Kaleta
Mathematical models for explaining the Warburg effect: A review focussed on ATP and biomass production
Biochemical Society Transactions 43 (6), 2015, 1187-1194
bibtex |  doi  ]

H. Stark, M. Fichtner, R. König, S. Lorkowski, S. Schuster
Causes of upregulation of glycolysis in lymphocytes upon stimulation. A comparison with other cell types
Biochimie 118, 2015, 185-194
bibtex |  doi  ]

M. Bartl, M. Pfaff, A. Ghallab, D. Driesch, S. G. Henkel, J. G. Hengstler, S. Schuster, C. Kaleta, R. Gebhardt, S. Zellmer P. Li
Optimality in the zonation of ammonia detoxification in rodent liver
Archives of Toxicology 89 (11), 2015, 2069-2078
bibtex | abstract |  doi  ]

S. Schuster, D. Boley, P. Möller, C. Kaleta
A minimal model for explaining the higher ATP production in the Warburg effect
Proceed. GCB 2015, PeerJ PrePrints 3, 2015, e1609
bibtex |  doi  |  url  ]

K. Kupczik, H. Stark, R. Mundry, F.T. Neininger, T. Heidlauf, O. Röhrle
Reconstruction of muscle fascicle architecture from iodine-enhanced microCT images: A combined texture mapping and streamline approach
Journal of Theoretical Biology 382, 2015, 34-43
bibtex |  doi  ]

P. Sauer, T. Hinze, P. Hofstedt
Dynamic Ad-hoc Topologies for Mobile Robot Navigation Based on Non-Uniform Grid Maps
International Journal of Mechanical and Mechatronics Engineering 2(6), 2015, 92-101
bibtex | abstract ]

S. DĂĽhring, S. Germerodt, C. Skerka, P. F. Zipfel, T. Dandekar, S. Schuster
Host-pathogen interactions between the human innate immune system and Candida albicans - Understanding and modeling defense and evasion strategies
Frontiers in Microbiology 6 (625), 2015,
bibtex | abstract |  doi  ]

G.M.de Hijas-Liste, E.Balsa-Canto, J. Ewald, M. Bartl, P.Li, J.R.Banga, C. Kaleta
Optimal programs of pathway control: dissecting the influence of pathway topology and feedback inhibition on pathway regulation
BMC Bioinformatics 16, 2015, 163
bibtex |  doi  ]

T. Weise, S. Schuster, M. Pfaff
Mikroalgen- Kultivierung im tubulären Photobioreaktor: Biomasse-Produktivität von Nannochloropsis salina im dis- und semikontinuierlichen Bioprozessregime
In: Tagungsband 16. Nachwuchswissenschaftlerkonferenz der mittel- und ostdeutschen Hochschulen fĂĽr angewandte Wissenschaften (eds. M. Knaut), 2015, 257-262
bibtex |  pdf  ]

J. Ewald, M. Kötzing, M. Bartl, C. Kaleta
Footprints of Optimal Protein Assembly Strategies in the Operonic Structure of Prokaryotes
Metabolites 5 (2), 2015, 252-269
bibtex |  doi  ]

J.A. Nyakatura, H. Stark
Aberrant back muscle function correlates with intramuscular architecture of dorsovertebral muscles in two-toed sloths
Mammalian Biology - Zeitschrift für Säugetierkunde 80, 2015, 114-121
bibtex |  doi  ]

S. Schuster
The Golden Ratio as a proposed solution of the Ultimatum Game: An explanation by continued fractions
arXiv:1502.02552, 2015,
bibtex | abstract ]

J. Schleicher; C. Tokarski; E. Marbach; M. Matz-Soja; S. Zellmer; R. Gebhardt; S. Schuster
Zonation of hepatic fatty acid metabolism - the diversity of its regulation and the benefit of modeling
BBA - Molecular and Cell Biology of Lipids 1851, 2015, 641-656
bibtex |  doi  |  PudMed-ID: 25677822 ]

J. Linde, S. Duggan, M. Weber, F. Horn, P. Sieber, D. Hellwig, K. Riege, M. Marz, R. Martin, R. Guthke, O. Kurzai
Defining the transcriptomic landscape of Candida glabrata by RNA-Seq.
Nucleic acids research 43, 2015, 1392-1406
bibtex | abstract |  doi  |  PudMed-ID: 25586221 ]

T. Hinze, K. Grützmann, B. Höckner, P. Sauer, S. Hayat
Categorised Counting Mediated by Blotting Membrane Systems for Particle-Based Data Mining and Numerical Algorithms
Lecture Notes in Computer Science 8961, 2015, 241-257
bibtex | abstract |  doi  |  url  ]

2014

G. D'Souza, S. Waschina, S. Pande, K. Bohl, C. Kaleta, C. Kost
Less is more: selective advantages can explain the prevalent loss of biosynthetic genes in bacteria.
Evolution 68, 2014, 2559-2570
bibtex | abstract |  doi  |  PudMed-ID: 24910088 ]

D. Siegismund, A. Schröter, C. Lüdecke, A. Undisz, K. D. Jandt, M. Roth, M. Rettenmayr, S. Schuster, S. Germerodt
Discrimination between random and non-random processes in early bacterial colonization on biomaterial surfaces: application of point pattern analysis
Biofouling 30, 2014, 9
bibtex |  doi  |  url  ]

K. Bohl, S. Hummert, S. Werner, D. Basanta, A. Deutsch, S. Schuster, G. TheiĂźen, A. Schroeter
Evolutionary game theory: molecules as players
Molecular Biosystems 10 (12), 2014, 3066 - 3074
bibtex |  doi  ]

S. Hummert, K. Bohl, D. Basanta, A. Deutsch, S. Werner, G. TheiĂźen, A. Schroeter, S. Schuster
Evolutionary game theory: cells as players
Molecular Biosystems 10 (12), 2014, 3044 - 3065
bibtex |  doi  ]

S. Schuster
Zur Rolle von Computersimulationen, speziell des Stoffwechsels, in der Synthetischen Biologie
In: Lebensformen - Leben formen. Ethik und Synthetische Biologie. Kritisches Jahrbuch der Philosophie (eds. J. Achatz & N. Knoepffler), Verlag Königshausen & Neumann, Würzburg, 2014, ch. -, 13-25, ISBN: 978-3-8260-5578-2
bibtex ]

C. LĂĽdecke, K. D. Jandt , D. Siegismund, M. J. Kujau, E. Zang, M. Rettenmayr, J. Bossert, M. Roth
Reproducible Biofilm Cultivation of Chemostat-Grown Escherichia coli and Investigation of Bacterial Adhesion on Biomaterials Using a Non-Constant-Depth Film Fermenter.
Plos One 9 (1), 2014, e84837
bibtex |  doi  ]

U. Deichmann; S. Schuster; J.-P. Mazat, A. Cornish-Bowden
Commemorating the 1913 Michaelis-Menten paper Die Kinetik der Invertinwirkung: three perspectives
FEBS Journal 281, 2014, 435-463
bibtex | abstract ]

S. Pande, H. Merker, K. Bohl, M. Reichelt, S. Schuster, L.F. de Figueiredo, C. Kaleta , C. Kost
Fitness and stability of obligate cross-feeding interactions that emerge upon gene loss in bacteria
ISME Journal 8, 2014, 953–962
bibtex |  doi  ]

S. Schuster, H. Stark
What can we learn from Einstein and Arrhenius about the optimal flow of our blood?
Biochimica et Biophysica Acta - General Subjects 1840 (1), 2014, 271–276
bibtex | abstract |  doi  ]

K. GrĂĽtzmann , K. Szafranski, M. Pohl , K. Voigt , A. Petzold , S. Schuster
Fungal alternative splicing is associated with multicellular complexity and virulence - A genome-wide multi-species study
DNA Research 21, 2014, 37-39
bibtex |  doi  |  pdf  |  url  |  PudMed-ID: 24122896 ]

D. Siegismund, A. Undisz, S. Germerodt, S. Schuster, M. Rettenmayr
Quantification of the interaction between biomaterial surfaces and bacteria by 3-D modeling.
Acta Biomaterialia 10(1), 2014, 267-275
bibtex | abstract |  doi  |  PudMed-ID: 24071002 ]

J. Schleicher, R. Guthke, U. Dahmen, O. Dirsch, H.G. HolzhĂĽtter, S. Schuster
A theoretical study of lipid accumulation in the liver - Implications for nonalcoholic fatty liver disease
Biochimica et Biophysica Acta - Molecular and Cell Biology of Lipids 1841 (1), 2014, 62-69
bibtex | abstract |  doi  ]

T. Hinze, J. Behre, C. Bodenstein, G. Escuela, G. GrĂĽnert, P. Hofstedt, P. Sauer, S. Hayat, P. Dittrich
Membrane Systems and Tools Combining Dynamical Structures with Reaction Kinetics for Applications in Chronobiology
In: Applications of Membrane Computing in Systems and Synthetic Biology (eds. P. Frisco, M. Gheorghe, M.J. Perez-Jimenez), Springer Series Emergence, Complexity, and Computation, 2014, ch. 5, 133-173
bibtex |  doi  |  url  ]

2013

H. Stark, N. Schilling, M. S. Fischer, A. Gussew, P. Hiepe, R. Rzanny, J. R. Reichenbach, B. Ullrich, G. O.Hofmann, F. Taut, K. Wohlfarth, P. Schenk, C. Anders, H.-C. Scholle
Probandenspezifische Modellanpassungen für die Simulation ausgewählter Maßnahmen einer Wirbelsäulenstabilisierung
In: Kongressband 19. Erfurter Tage “Prävention von arbeitsbedingten Gesundheitsgefahren und Erkrankungen (eds. C. -J. Kirchner, M. Stadler, H.-C. Scholle), Verlag Bussert & Stadeler, 2013, 335-339
bibtex ]

G. Fuellen, M. Boerries, H. Busch, A.D. de Grey, U. Hahn, T. Hiller, A. Hoeflich, L. Jansen, G.E. Janssens, C. Kaleta, A.C. Meinema, S. Schäuble, P.N. Schofield, B. Smith, J. Sühnel, J. Vera, W. Wagner, E.C. Wönne, D. Wuttke, A. Simm A.
In silico approaches and the role of ontologies in aging research
Rejuvenation Research 16 (6), 2013, 540-546
bibtex | abstract |  doi  ]

S. Schuster
The combinatorial multitude of fatty acids can be described by Fibonacci numbers
arXiv:1303.7189, 2013,
bibtex | abstract ]

T. Hinze
Unraveling Oscillating Structures by Means of P Systems
International Journal of Foundations of Computer Science 24(5), 2013, 605-607
bibtex |  doi  ]

A. K. Stavrum, I. Heiland, S. Schuster, P. Puntervoll, M. Ziegler
Model of Tryptophan Metabolism, Readily Scalable using Tissue-Specific Gene Expression Data.
Journal of Biological Chemistry 288, 2013, 34555-34566
bibtex | abstract |  doi  |  PudMed-ID: 24129579 ]

M. Bartl, M. Kötzing, S. Schuster, P. Li, C. Kaleta
Dynamic optimization identifies optimal programmes for pathway regulation in prokaryotes.
Nature Communications 4, 2013, 2243
bibtex | abstract |  doi  |  PudMed-ID: 23979724 ]

K. Schmeisser, J. Mansfeld, D. Kuhlow, S. Weimer, K. Zarse, S. Priebe, I. Heiland, M. Birringer, M. Groth, A Segref, C. Werner, S. Schmeisser, S. Schuster, A. Pfeiffer, R. Guthke, M. Platzer, T. Hoppe, H. Cohen, D. Sinclair, M. Ristow
Role of sirtuins in lifespan regulation is linked to methylation of nicotinamide
Nature Chemical Biology 9, 2013, 693-700
bibtex |  doi  ]

T. Hinze
Computer der Natur
T. Hinze, Verlag bookboon.com, ISBN 978-87-403-0378-0, 2013, eBook
bibtex |  url  ]

M. Pohl, R. H. Bortfeldt, K. GrĂĽtzmann, S. Schuster
Alternative splicing of mutually exclusive exons - a review
BioSystems 114, 2013, 31-38
bibtex | abstract |  doi  |  url  |  PudMed-ID: 23850531 ]

G. G. Zampar, A. KĂĽmmel, J. Ewald, S. Jol, B. Niebel, P. Picotti, R. Aebersold, U. Sauer, N. Zamboni, M. Heinemann
Temporal system-level organization of the switch from glycolytic to gluconeogenic operation in yeast.
Molecular Systems Biology 9, 2013, 651
bibtex | abstract |  doi  |  PudMed-ID: 23549479 ]

S. Schäuble, A. K. Stavrum, P. Puntervoll, S. Schuster, I. Heiland
E ffect of substrate competition in kinetic models of metabolic networks
FEBS Letters 587, 2013, 2818-2824
bibtex | abstract |  doi  ]

A. Rezola, J. Pey, L.F. de Figueiredo, A. Podhorski, S. Schuster, A. Rubio, F.J. Planes
Selection of human tissue-specific elementary flux modes using gene expression data
Bioinformatics 29 (16), 2013, 2009-2016
bibtex |  doi  ]

C. Kaleta, S. Schäuble, U. Rinas, S. Schuster
Metabolic costs of amino acid and protein production in Escherichia coli
Biotechnology Journal 8, 2013, 1105-1114
bibtex | abstract |  doi  |  PudMed-ID: 23744758 ]

D. Siegismund, A. Schröter, S. Schuster, M.Rettenmayr
Quantitative Modeling of Fibrinogen Adsorption on Different Biomaterials
Cellular and Molecular Bioengineering 6 (2), 2013, 210-219
bibtex |  doi  ]

T. Hinze, B. Schell, M. Schumann, C. Bodenstein
Maintenance of Chronobiological Information by P System Mediated Assembly of Control Units for Oscillatory Waveforms and Frequency
In: Membrane Computing. 13th International Conference (eds. E. Csuhaj-Varju, M. Gheorghe, G. Paun, G. Rozenberg, A. Salomaa, G. Vaszil), Vol. 7762, Springer Verlag, 2013, 208-227
bibtex |  doi  ]

S. Ellenberger; S. Schuster; J. Wöstemeyer
Correlation between sequence, structure and function for trisporoid processing proteins in the model zygomycete Mucor mucedo
Journal of theoretical Biology 320, 2013, 66-75
bibtex | abstract |  doi  |  PudMed-ID: 23261395 ]

H. Stark, R. Fröber, N. Schilling
Intramuscular architecture of the autochthonous back muscles in humans.
Journal of Anatomy 222 (2), 2013, 214–222
bibtex | abstract |  doi  |  PudMed-ID: 23121477 ]

S. A. Shabalovskaya, D. Siegismund, E. Heurich, M. Rettenmayr
Evaluation of wettability and surface energy of native Nitinol surfaces in relation to hemocompatibility
Materials Science & Engineering C-Materials for Biological Applications 33 (1), 2013, 127–132
bibtex |  doi  ]

2012

B. Krüger, C. Liang, Florian Prell, A. Fieselmann, A. Moya, S. Schuster, U. Völker T. Dandekar
Metabolic adaptation and protein complexes in prokaryotes
Metabolites 2, 2012, 940-958
bibtex ]

F. Wessely, M. Bartl, R. Guthke, P. Li, C. Kaleta
Out of (transcriptional) control? Design principles of the regulatory network controlling metabolic pathways in Escherichia coli
Proceedings of the German Conference on Bioinformatics 2012 , 2012,
bibtex ]

C. Kaleta und I. Heiland
Stoffwechselanalyse: Neue Wege im Labyrinth entdecken
Laborwelt 4, 2012, 30-32
bibtex ]

N. Kottenhagen, L. Gramzow, F. Horn, M. Pohl and G. TheiĂźen
Polyglutamine and polyalanine tracts are enriched in transcription factors of plants
In: Proceedings of the German Conference on Bioinformatics 2012 (eds. S. Böcker, F. Hufsky, K. Scheubert, J. Schleicher, S. Schuster), OASICS, 2012, 93-107
bibtex |  pdf  ]

H. Stark, S. Schuster
Reply to Böning, Maassen, and Pries.
Journal of Applied Physiology 113, 2012, 1169
bibtex |  doi  |  PudMed-ID: 23027829 ]

M. Pohl, G. Theissen, S. Schuster
GC content dependency of Open Reading Frame prediction via stop codon frequencies
Gene 511, 2012, 441-446
bibtex |  doi  |  pdf  |  url  ]

T. I. Gossmann, M. Ziegler, P. Puntervoll, L. F. de Figueiredo, S. Schuster, I. Heiland
Two new perspectives on NAD metabolism
In: Proceedings of the German Conference on Bioinformatics 2012 (eds. ), 2012, 5-8
bibtex |  pdf  |  url  ]

C. Bodenstein, M. Gosak, S. Schuster, M. Marhl, M. Perc
Modeling the Seasonal Adaptation of Circadian Clocks by Changes in the Network Structure of the Suprachiasmatic Nucleus
PLoS Computational Biology 8(9), 2012, e1002697
bibtex |  doi  |  pdf  |  url  |  PudMed-ID: 23028293 ]

J. Behre, R. Voigt, I. Althöfer, S. Schuster
On the evolutionary significance of the size and planarity of the proline ring
Naturwissenschaften 99, 2012, 789-799
bibtex ]

H. Stark, R. Fröber, C. Anders, N. Schilling
Intramuskuläre Architektur der menschlichen Rückenmuskulatur – Rekonstruktion, Modellierung & Simulation.
In: Kongressband 18. Erfurter Tage “Prävention von arbeitsbedingten Gesundheitsgefahren und Erkrankungen”. (eds. Grieshaber, R.; Stadler, M.; Scholle, H.-Ch.), Verlag Bussert & Stadeler, 2012,
bibtex ]

J. Gebauer, S. Schuster, L. F. de Figueiredo, C. Kaleta
Detecting and investigating substrate cycles in a genome-scale human metabolic network
FEBS Journal 279, September, 2012, 3192–3202
bibtex |  doi  |  url  ]

S. Schäuble, K. Klement, S. Marthandan, S. Münch, I. Heiland, S. Schuster, P. Hemmerich, S. Diekmann
Quantitative model of cell cycle arrest and cellular senescence in primary human fibroblasts.
PLoS ONE 7, 2012, e42150
bibtex | abstract |  doi  |  PudMed-ID: 22879912 ]

S. Werner, A. Schroeter, C. Schimek, S. Vlaic, J. Wöstemeyer, S. Schuster
Model of the synthesis of trisporic acid in Mucorales showing bistability
IET Systems Biology 6, 2012, 207-214
bibtex ]

H. Stark, S. Schuster
Comparison of various approaches to calculating the optimal hematocrit in vertebrates.
Journal of Applied Physiology 113, 2012, 355-367
bibtex | abstract |  doi  |  PudMed-ID: 22604890 ]

C. Bodenstein, I. Heiland, S. Schuster
Temperature compensation and entrainment in circadian rhythms.
Physical Biology 9, 2012, 036011
bibtex | abstract |  doi  |  pdf  |  url  |  PudMed-ID: 22683844 ]

T. Hinze
Unraveling Oscillating Structures by Means of P Systems
In: Research Topics in Membrane Computing (eds. M. Gheorghe, G. Paun, M.J. Perez-Jimenez), University of Sevilla, 2012, 39-42
bibtex |  pdf  |  url  ]

C. Tokarski, S. Hummert, F. Mech, M.T. Figge, S. Germerodt, A. Schroeter, S. Schuster
Agent-based modeling approach of immune defense against spores of opportunistic human pathogenic fungi
Frontiers in Microbial Immunology 3, 2012, 129
bibtex | abstract |  doi  |  pdf  |  url  ]

C. Kaleta, L.F. de Figueiredo, S. Schuster
Against the stream: Relevance of gluconeogenesis from fatty acids for natives of the arctic regions
International Journal of Circumpolar Health 71, 2012, 18436
bibtex ]

T. I. Gossmann, M. Ziegler, P. Puntervoll, L. F. de Figueiredo, S. Schuster, I. Heiland
NAD biosynthesis and salvage - a phylogenetic perspective.
FEBS Journal 279 (18), September, 2012, 3355-3363
bibtex | abstract |  doi  |  PudMed-ID: 22404877 ]

I. Heiland, C. Bodenstein, T. Hinze, O. Weisheit, O. Ebenhoeh, M. Mittag and S. Schuster
Modelling temperature entrainment of circadian clocks using the Arrhenius equation and a reconstructed model from Chlamydomonas reinhardtii
Journal of Biological Physics 38 (3), 2012, 449-464
bibtex | abstract |  doi  ]

T. Hinze, C. Bodenstein, B. Schau, I. Heiland, S. Schuster
Chemical Analog Computers for Clock Frequency Control Based on P Modules
In: Membrane Computing. Proceedings of the 12th International Conference (CMC12) (eds. M. Gheorghe, G. Paun, R. Rozenberg, A. Salomaa, S. Verlan), Springer Verlag, Vol. 7184, 2012, 182-202
bibtex | abstract |  doi  ]

G. Gruenert, G. Escuela, P. Dittrich, T. Hinze
Morphological Algorithms: Membrane Receptor-ligand Interactions and Rule-based Molecule Graph Evolution for Exact Set Cover Problems
In: Membrane Computing. Proceedings of the 12th International Conference (CMC12) (eds. M. Gheorghe, G. Paun, R. Rozenberg, A. Salomaa, S. Verlan), Springer Verlag, Vol. 7184, 2012, 160-181
bibtex | abstract |  doi  ]

J. Behre, L. F. de Figueiredo, S. Schuster, C. Kaleta
Detecting structural invariants in biological reaction networks.
Methods in Molecular Biology 804, 2012, 377-407
bibtex | abstract |  doi  |  PudMed-ID: 22144164 ]

2011

I. Zevedei-Oancea, S. Schuster
Topological analysis of metabolic networks based on petri net theory.
Studies in health technology and informatics 162, 2011, 17-37
bibtex | abstract |  PudMed-ID: 21685562 ]

M. Böl, N. Schilling, H. Stark
Erratum to: Micromechanical modelling of skeletal muscles: from the single fibre to the whole muscle
Archive of Applied Mechanics 81, 2011, 1757-1757
bibtex |  doi  ]

M. Böl, H. Stark, N. Schilling
On a phenomenological model for fatigue effects in skeletal muscles.
J. Theor. Biol. 281, 2011, 122-132
bibtex | abstract |  doi  |  PudMed-ID: 20211632 ]

A. Göhler, Ö, Kökpinar, W. Schmidt-Heck, R. Geffers, R. Guthke, U. Rinas, S. Schuster, K. Jahreis, C. Kaleta
More than just a metabolic regulator – elucidation and validation of new targets of PdhR in Escherichia coli
BMC Systems Biology 5 (197), 2011,
bibtex | abstract |  doi  ]

S. Schäuble, S. Schuster, C. Kaleta
Hands-on Metabolism Analysis of Complex Biochemical Networks Using Elementary Flux Modes.
Methods in Enzymology 500, 2011, 437-456
bibtex | abstract |  doi  |  PudMed-ID: 21943910 ]

F. Wessely, M. Bartl, R. Guthke, P. Li, S. Schuster, C. Kaleta
Optimal regulatory strategies for metabolic pathways in Escherichia coli depending on protein costs.
Molecular Systems Biology 7, 2011, 515
bibtex | abstract |  doi  |  url  |  PudMed-ID: 21772263 ]

C. Bodenstein, I. Heiland and S. Schuster
Calculating activation energies for temperature compensation in circadian rhythms
Physical Biology 8 (5), 2011, 056007
bibtex | abstract |  doi  |  pdf  |  url  |  PudMed-ID: 21891835 ]

S. Schäuble, I. Heiland, O. Voytsekh, M. Mittag, S. Schuster.
Predicting the Physiological Role of Circadian Metabolic Regulation in the Green Alga Chlamydomonas reinhardtii
Plos ONE 6 (8), 2011, e23026
bibtex |  doi  |  url  |  PudMed-ID: 21887226 ]

T. Hinze, M. Schumann, C. Bodenstein, I. Heiland, S. Schuster
Biochemical Frequency Control by Synchronisation of Coupled Repressilators: An In-silico Study of Modules for Circadian Clock Systems.
Computational Intelligence and Neuroscience, vol. 2011, 2011, ID 262189
bibtex | abstract |  doi  |  url  |  PudMed-ID: 22046179 ]

L.F. de Figueiredo, T.I. Gossmann, M. Ziegler, S. Schuster
Pathway Analysis of NAD+ metabolism
Biochemical Journal 439 , 2011, 341–348
bibtex |  doi  |  PudMed-ID: 21729004 ]

C. Kaleta, L.F. de Figueiredo, S. Werner, R. Guthke, M. Ristow, S. Schuster
In silico evidence for gluconeogenesis from fatty acids in humans
PLoS Computational Biology 7, 2011, e1002116
bibtex ]

C. Kaleta, L. F. de Figueiredo, I. Heiland, S. Klamt, S. Schuster
Special issue: Integration of OMICs datasets into metabolic pathway analysis.
BioSystems 105, 2011, 107-108
bibtex |  doi  |  PudMed-ID: 21619911 ]

S. Schuster, L. de Figueiredo, A. Schroeter, C. Kaleta
Combining Metabolic Pathway Analysis with Evolutionary Game Theory. Explaining the occurrence of low-yield pathways by an analytic optimization approach
BioSystems 105, 2011, 147-153
bibtex |  PudMed-ID: 21620931 ]

G. Beuster, K. Zarse, C. Kaleta, R. Thierbach, M. Kiehntopf, P. Steinberg, S. Schuster, M. Ristow
Inhibition of alanine aminotransferase (ALAT) in silico and in vivo promotes mitochondrial metabolism to impair malignant growth
Journal of Biological Chemistry 286 (25), 2011, 22323-22330, Highlighted in Pädiatrix 6/2011 in the article "Stoffwechsel und Krebs – Krebs und Stoffwechsel" by Dr. Corinna Volz-Zang
bibtex | abstract |  doi  |  PudMed-ID: 21540181 ]

Y. Elhanati, S. Schuster, N. Brenner
Dynamic modeling of cooperative protein secretion in microorganism populations
Theoretical Population Biology 80 (1), 2011, 49-63
bibtex |  doi  |  PudMed-ID: 21510966 ]

R.H. Bortfeldt, S. Schuster, I. Koch
Exhaustive analysis of the modular structure of the spliceosomal assembly network – a Petri net approach.
Studies in Health Technology and Informatics 162, 2011, 244-278, Reprint of an article published in In Silico Biol. 10 (2010) 0007
bibtex ]

T. Hinze, C. Bodenstein, I. Heiland, S. Schuster
Capturing Biological Frequency Control of Circadian Clocks by Reaction System Modularization
ERCIM News 85, 2011, 27-29
bibtex | abstract ]

A. Rezola, L. F. de Figueiredo, M. Brock, J. Pey, A. Podhorski, C. Wittmann, S. Schuster, A. Bockmayr, F.J. Planes
Exploring metabolic pathways in genome-scale networks via generating flux modes.
Bioinformatics 27 (4), Feb, 2011, 534-540
bibtex | abstract |  doi  |  PudMed-ID: 21149278 ]

S. Schuster, B. Junker
Topological Analysis of Metabolic and Regulatory Networks.
In: Modeling in Systems Biology – the Petri Net Approach (eds. I. Koch, W. Reisig, F. Schreiber), Springer-Verlag, 2011, ch. 10, 209-224
bibtex ]

K. Grützmann, S. Böcker, S. Schuster
Combinatorics of aliphatic amino acids
Naturwissenschaften 98 (1), 2011, 79-86
bibtex |  doi  ]

T. Hinze, M. Schumann, S. Schuster
Synchronisation of Biological Clock Signals: Capturing Coupled Repressilators from a Control Systems Perspective
In: Proceedings of the Fourth International Conference on Bio-Inspired Systems and Signal Processing (BIOSIGNALS2011) (eds. F. Babiloni, A. Fred, J. Filipe, H. Gamboa), IEEE Engineering in Medicine and Biology Society, Institute for Systems and Technologies of Information Control and Communication, SciTePress, ISBN 978-989-8425-35-5, 2011, 101-106
bibtex | abstract ]

2010

H. Stark, N. Schilling
A novel method of studying fascicle architecture in relaxed and contracted muscles.
Journal of Biomechanics 43, 2010, 2897-2903
bibtex |  doi  |  PudMed-ID: 20800841 ]

Membrane Computing. Eleventh International Conference, CMC 2010, Jena, Germany, August 24-27, 2010. Revised Selected Papers.
M. Gheorghe, T. Hinze, G. Paun, G. Rozenberg, A. Salomaa (Eds.), Series: Lecture Notes in Computer Science (Vol. 6501), Subseries: Theoretical Computer Science and General Issues , Springer Verlag, Heidelberg 2010, 393, ISBN: 978-3642181221
bibtex | abstract ]

Proceedings Compendium of the Fourth Workshop on Membrane Computing and Biologically Inspired Process Calculi (MeCBIC2010) and of the First Workshop on Applications of Membrane Computing, Concurrency, and Agent-based Modelling in Population Biology (AMCA-POP2010)
J. Behre, G. Escuela, T. Hinze (Eds.), ProBusiness Verlag, Berlin 2010, 238, ISBN: 978-3-86805-767-6
bibtex ]

G. Escuela, T. Hinze, P. Dittrich, S. Schuster, M. Moreno
Modelling Modified Atmosphere Packaging for Fruits and Vegetables using Membrane Systems
In: Proceedings of the Third International Conference on Bio-inspired Systems and Signal Processing (BIOSIGNALS2010) (eds. ), IEEE Engineering in Medicine and Biology Society, Institute for Systems and Technologies of Information Control and Communication, INSTICC press, 2010, 306-311, ISBN: 978-989-674-018-4
bibtex ]

R. H. Bortfeldt, S. Schuster, I. Koch
Exhaustive analysis of the modular structure of the spliceosomal assembly network - a Petri net approach
In Silico Biology 10, 2010, 0007
bibtex | abstract |  url  ]

B. Knoke, C. Bodenstein, M. Marhl, M. Perc, S. Schuster
Jensen's Inequality as a Tool for Explaining the Effect of Oscillations on the Average Cytosolic Calcium Concentration
Theory in Biosciences 129 (1), 2010, 25–38
bibtex | abstract |  PudMed-ID: 20157853 ]

F. Centler, C. Kaleta, P. Speroni di Fenizio, P. Dittrich
A parallel algorithm to compute chemical organizations in biological networks
Bioinformatics 26 (14), 2010, 1788-1789
bibtex | abstract |  doi  |  PudMed-ID: 20501552 ]

G. GrĂĽnert, B. Ibrahim, T. Lenser, M. Lohel, T. Hinze, P. Dittrich
Rule-based spatial modeling with diffusing, geometrically constrained molecules
BMC Bioinformatics 11, 2010, 307
bibtex | abstract |  doi  |  PudMed-ID: 20529264 ]

J. Decraene, T. Hinze
A Multidisciplinary Survey of Computational Techniques for the Modelling, Simulation and Analysis of Biochemical Networks
Journal of Universal Computer Science 16 (9), 2010, 1152-1175
bibtex | abstract |  url  ]

M. Sturm, T. Hinze
Verfahren zur AusfĂĽhrung von mathematischen Operationen mittels eines DNA-Computers und DNA-Computer hierzu
Deutsches Patent, DE 101 59 886 B4, IPC G06N 3/00 patent, Deutsches Patentamt MĂĽnchen, 2010, granted 2010
bibtex ]

G. Escuela, T. Hinze, P. Dittrich, S. Schuster, M. Moreno-Alvarez
Applying Membrane Systems in Food Engineering
In: Eight Brainstorming Week on Membrane Computing (eds. M.A. Martinez-del-Amor, G. Paun, I. Perez-Hurtado, A. Riscos-Nunez), Fenix Editora, Sevilla 2010, 109-121, ISBN: 978-84-614-2357-6
bibtex ]

H. Bordihn, R. Freund, T. Hinze, M. Holzer, M. Kutrib, F. Otto
Proceedings of the Second Workshop on Non-Classical Models for Automata and Applications - Vol. 263 (NCMA2)
Austrian Computer Society 2010, ISBN: 978-3-85403-263-2
bibtex ]

M. Gheorghe T. Hinze, G. Paun
Proceedings of the Eleventh International Conference on Membrane Computing (CMC11)
ProBusiness Verlag, Berlin 2010, ISBN: 978-3-86805-721-8
bibtex ]

M. Bartl, M. Pfaff,S. Toepfer, S. Zellmer, R. Gebhardt, S. Schuster, P. Li
Model-based Optimization to Explain Liver Zonation in Nitrogen Metabolism
In: Proceedings of the 55th International Scientific Colloquium (eds. ), Ilmenau, Germany 2010, 235-240
bibtex ]

M. Bartl, M. Kötzing, C. Kaleta, S. Schuster, P. Li
Just-in-time activation of a glycolysis inspired metabolic network - solution with a dynamic optimization approach
In: Proceedings of the 55th International Scientific Colloquium (eds. ), Ilmenau, Germany 2010, 217-222
bibtex ]

K. Bohl, L. F. de Figueiredo, O. Hädicke, S. Klamt, C. Kost, S. Schuster and C. Kaleta
CASOP GS: Computing intervention strategies targeted at production improvement in genome-scale metabolic networks
In: Proceedings of the 25th German Conference on Bioinformatics (eds. D. Schomburg, A. Grote), Gesellschaft f. Informatik, Bonn, 2010, 71-80, ISBN 978-3-88579-267-3
bibtex ]

C. Kaleta, A. Göhler, S. Schuster, K. Jahreis, R. Guthke, S. Nikolajewa
Integrative inference of gene-regulatory networks in Escherichia coli using information theoretic concepts and sequence analysis
BMC Systems Biology 4, 2010, 116
bibtex | abstract |  doi  |  pdf  |  PudMed-ID: 20718955 ]

G. Gruenert, B. Ibrahim, T. Lenser, M. Lohel, T. Hinze, P. Dittrich
Rule-based spatial modeling with diffusing, geometrically constrained molecules.
BMC Bioinformatics 11, 2010, 307
bibtex |  PudMed-ID: 20529264 ]

T. Hinze, J. Decraene, G.G. Mitchell, J. Behre, S. Schuster
Towards a Unified Approach for the Modelling, Analysis, and Simulation of Cell Signalling Networks.
In: Sequence and Genome Analysis: Methods and Applications (eds. Z. Zhao), iConcept Press, 2010, ch. 13, 227-257
bibtex |  pdf  ]

S. Werner, G. Diekert, S. Schuster
Revisiting the thermodynamic theory of optimal ATP stoichiometries by analysis of various ATP-producing metabolic pathways
The Journal of Molecular Evolution 71, 2010, 346-355
bibtex | abstract |  doi  |  PudMed-ID: 20922363 ]

D. Siegismund, T.F. Keller, K.D. Jandt, M. Rettenmayr
Fibrinogen adsorption on biomaterials - a numerical study
Macromol Biosci 10, 2010, 1216-1233
bibtex | abstract |  PudMed-ID: 20602495 ]

S. Schuster, L. F. de Figueiredo, C. Kaleta
Predicting novel pathways in genome-scale metabolic networks
Biochemical Society Transactions 38, 2010, 1202-1205
bibtex | abstract |  PudMed-ID: 20863284 ]

S. Hummert, S. Schuster, C. Hummert
Batman – The Dark Knight: A Game Theoretical Approach
In: Proceedings of the 6th International Conference on Foundations of Computer Science (FCS) (eds. ), 2010, 29-34
bibtex | abstract ]

S. Hummert, C. Hummert, A. Schröter, B. Hube, S. Schuster
Game theoretical modelling of survival strategies of Candida albicans inside macrophages
J Theor Biol 264, 2010, 312-318
bibtex | abstract |  PudMed-ID: 20100495 ]

C. Bodenstein, B. Knoke, M. Marhl, M. Perc, S. Schuster
Using Jensen's inequality to explain the role of regular calcium oscillations in protein activation
Physical Biology 7, 2010, 036009
bibtex | abstract |  doi  |  pdf  |  url  |  PudMed-ID: 20834115 ]

E. Ruppin, J.A. Papin, L. F. de Figueiredo, S. Schuster
Metabolic reconstruction, constraint-based analysis and game theory to probe genome-scale metabolic networks
Current Opinion in Biotechnology 21, 2010, 502-510
bibtex | abstract |  PudMed-ID: 20692823 ]

C. Gille, C. Bölling, A. Hoppe, S. Bulik, S. Hoffmann, K. Hübner, A. Karlstädt, R. Ganeshan, M. König, K. Rother, M. Weidlich, J. Behre, H.G. Holzhütter
HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology.
Molecular Systems Biology 6, 2010, 411
bibtex | abstract |  doi  |  PudMed-ID: 20823849 ]

D. Kenanov, C. Kaleta, A. Petzold, C. Hoischen, S. Diekmann, R.A. Siddiqui, S. Schuster
Theoretical study of lipid biosynthesis in wild-type Escherichia coli and in a protoplast-type L-form using elementary flux mode analysis
FEBS J 277, 2010, 1023-1034
bibtex | abstract |  PudMed-ID: 20088879 ]

S. Schuster, J.U. Kreft, N. Brenner, F. Wessely, G. Theißen, E. Ruppin, A. Schröter
Cooperation and cheating in microbial exoenzyme production - Theoretical analysis for biotechnological applications
Biotechnology Journal 5, 2010, 751-758
bibtex | abstract |  doi  |  PudMed-ID: 20540107 ]

M. Bartl, P. Li, S. Schuster
Modelling the optimal timing in metabolic pathway activation-Use of Pontryagin's Maximum Principle and role of the Golden section
Biosystems 101, 2010, 67-77
bibtex | abstract |  PudMed-ID: 20420882 ]

R. Sinha, T. Lenser, N. Jahn, U. Gausmann, S. Friedel, K. Szafranski, K. Huse, P. Rosenstiel, J. Hampe, S. Schuster, M. Hiller, R. Backofen, M. Platzer
TassDB2 - A comprehensive database of subtle alternative splicing events
BMC Bioinformatics 11, 2010, 216
bibtex | abstract |  PudMed-ID: 20429909 ]

T. Hinze, T. Lenser, G. Escuela, I. Heiland, S. Schuster
Modelling Signalling Networks with Incomplete Information about Protein Activation States: A P System Framework of the KaiABC Oscillator
In: Proceedings of the 10th International Workshop on Membrane Computing (WMC) (eds. G. Paun, M.J. Perez-Jimenez, A. Riscos-Nunez, A. Salomaa), Springer Verlag, 2010, 316-334
bibtex ]

2009

R. Haberland, T. Hinze
Prolog-based XML processing for compact representation and deductive evaluation of biological reaction networks
In: Abstract Booklet, International Conference Biosystems Analysis and Engineering (BioSys) (eds. G. Antranikian, D. Chiu, F. Keil, A. Liese, T.Scheper, A.-P. Zeng), University of Technology Hamburg, 2009, 27
bibtex ]

C. Kaleta, L. F. de Figueiredo, S. Schuster
Detecting Metabolic Conversions in Genome-Scale Metabolic Networks on the Basis of Elementary Flux Patterns in Subnetworks
In: Proceedings of the Vienna Conference on Mathematical Modelling 2009 - Vol. 2 of ARGESIM Reports (eds. I. Troch, F. Breitenecker), MathMod, Vienna 2009, 748-759
bibtex ]

L. F. de Figueiredo, A. Podhorski, A. Rubio, J.E. Beasley, S. Schuster, F.J. Planes
Calculating the K-shortest elementary flux modes in metabolic networks
In: Proceedings of the Vienna Conference on Mathematical Modelling 2009 - Vol. 2 of ARGESIM Reports (eds. I. Troch, F.Breitenecker), MathMod, Vienna 2009, 736-747
bibtex ]

T. Hinze, R. FaĂźler, G. Escuela, B. Ibrahim, S. Schuster
Computation by Synthetic Cell Signaling and Oscillating Processes Modelled using Mass-Action Kinetics
In: Proceedings Booklet Fifth Conference on Computability in Europe (CiE) (eds. K. Ambos-Spies, B. Löwe, W. Merkle), University of Heidelberg 2009, 186-195
bibtex ]

A. Schröter, S. Hummert, J.U. Kreft, S. Schuster
Modelling host-pathogen and pathogen-pathogen interactions of opportunistic fungal infections in humans: evolutionary game theory and individual-based modelling
Mycoses 52 (5), 2009, 425-425
bibtex ]

C. Kaleta
From Artificial Chemistry to Systems Biology: Software for Chemical Organization Theory
In: Artificial Life Models in Software - Vol. II (eds. A. Adamatzky, M. Komosinski), Springer, London, 2009, 319-342
bibtex ]

N. Matsumaru, T. Hinze, P. Dittrich
Organization-Oriented Chemical Programming of Distributed Artifacts
International Journal of Nanotechnology and Molecular Computation 1 (4), 2009, 54-70
bibtex ]

C. Kaleta, L. F. de Figueiredo, J. Behre, S. Schuster
EFMEvolver: Computing elementary flux modes in genome-scale metabolic networks
In: Proceedings of the 14th German Conference on Bioinformatics (GCB) (eds. I. Grosse, S. Neumann, S. Posch, F. Schreiber, P. Stadler), Gesellschaft f. Informatik e.V., Bonn 2009, 180-190
bibtex ]

L. F. de Figueiredo, A. Podhorski, A. Rubio, C. Kaleta, J.E. Beasley, S. Schuster, F.J. Planes
Computing the shortest elementary flux modes in genome-scale metabolic networks
Bioinformatics 25, 2009, 3158-3165
bibtex | abstract |  PudMed-ID: 19793869 ]

L. F. de Figueiredo, S. Schuster, C. Kaleta, D.A. Fell
Response to comment on 'Can sugars be produced from fatty acids? A test case for pathway analysis tools'
Bioinformatics 25, 2009, 3330-3331
bibtex |  doi  |  PudMed-ID: 19825797 ]

C. Kaleta, L. F. de Figueiredo, S. Schuster
Can the whole be less than the sum of its parts? Pathway analysis in genome-scale metabolic networks using elementary flux patterns
Genome Research 19, 2009, 1872-1883
bibtex | abstract |  PudMed-ID: 19541909 ]

C. Kaleta, S. Richter, P. Dittrich
Using chemical organization theory for model checking
Bioinformatics 25, 2009, 1915-1922
bibtex | abstract |  doi  |  PudMed-ID: 19468053 ]

T. Hinze, R. Fassler, T. Lenser, P. Dittrich
Register Machine Computations on Binary Numbers by Oscillating and Catalytic Chemical Reactions Modelled using Mass-Action Kinetics
International Journal of Foundations of Computer Science 20, 2009, 411-426
bibtex ]

T. Hinze, R. Fassler, T. Lenser, N. Matsumaru, P. Dittrich
Event-Driven Metamorphoses of P Systems
Lecture Notes in Computer Science 5391, 2009, 231-245
bibtex ]

J. Behre, S. Schuster
Modeling signal transduction in enzyme cascades with the concept of elementary flux modes
J Comput Biol 16, 2009, 829-844
bibtex |  PudMed-ID: 19522666 ]

L. F. de Figueiredo, S. Schuster, C. Kaleta, D.A. Fell
Can sugars be produced from fatty acids? A test case for pathway analysis tools (Erratum)
Bioinformatics 25, 2009, 152-158
bibtex | abstract |  doi  |  PudMed-ID: 19117076 ]

J. Kielbassa, R. Bortfeldt, S. Schuster, I. Koch
Modeling of the U1 snRNP assembly pathway in alternative splicing in human cells using Petri nets
Computational Biology and Chemistry 33, 2009, 46-61
bibtex | abstract |  PudMed-ID: 18775676 ]

B. Knoke, S. Textor, J. Gershenzon, S. Schuster
Mathematical modelling of aliphatic glucosinolate chain length distribution in Arabidopsis thaliana leaves
Phytochemistry Reviews 8, 2009, 39-51
bibtex |  doi  ]

2008

S. Schuster, J. U. Kreft, A. Schroeter, T. Pfeiffer
Use of game-theoretical methods in biochemistry and biophysics.
Journal of Biological Physics 34, 2008, 1-17
bibtex | abstract |  doi  |  PudMed-ID: 19669489 ]

T. Hinze, S. Hayat, T. Lenser, N. Matsumaru, P. Dittrich
Biosignal-Based Computing by AHL Induced Synthetic Gene Regulatory Networks
In: Proceedings of the First International Conference on Bio-Inspired Systems and Signal Processing (BIOSIGNALS) (eds. ), IEEE Engineering in Medicine and Biology Society, Institute for Systems and Technologies of Information Control and Communication, 2008, 162-169
bibtex ]

T. Lenser, N. Matsumaru, T. Hinze, P. Dittrich
Tracking the Evolution of Chemical Computing Networks
In: Proceedings of Artificial Life XI (eds. ), 2008, 343-350
bibtex ]

F. Centler, C. Kaleta, Fenizio. PS. di, P. Dittrich
Computing chemical organizations in biological networks.
Bioinformatics 24, 2008, 1611-1618
bibtex |  PudMed-ID: 18480100 ]

S. Hayat, T. Hinze
Toward integration of in vivo molecular computing devices: successes and challenges
HFSP Journal 2, 2008, 239-243
bibtex ]

K.S. Hilden, R. Bortfeldt, M. Hofrichter, A. Hatakka, T.K. Lundell
Molecular characterization of the basidiomycete isolate Nematoloma frowardii b19 and its manganese peroxidase places the fungus in the corticioid genus Phlebia
Microbiology 154, 2008, 2371-2379
bibtex | abstract |  PudMed-ID: 18667569 ]

L. F. de Figueiredo, S. Schuster, C. Kaleta, DA. Fell
Can sugars be produced from fatty acids? A test case for pathway analysis tools.
Bioinformatics 24, 2008, 2615-2621
bibtex |  PudMed-ID: 18806269 ]

D. Deutscher, I. Meilijson, S. Schuster, E. Ruppin
Can single knockouts accurately single out gene functions?
BMC Systems Biology 2, 2008, 50
bibtex | abstract |  pdf  |  PudMed-ID: 18564419 ]

C. Kaleta, F. Centler, Fenizio. PS. di, P. Dittrich
Phenotype prediction in regulated metabolic networks.
BMC Systems Biology 2, 2008, 1-15
bibtex |  PudMed-ID: 18439260 ]

R. Bortfeldt, S. Schindler, K. Szafranski, S. Schuster, D. Holste
Comparative analysis of sequence features involved in the recognition of tandem splice sites
BMC Genomics 9, 2008, 202
bibtex | abstract |  pdf  |  PudMed-ID: 18447903 ]

S. Schuster, T. Pfeiffer, D.A. Fell
Is maximization of molar yield in metabolic networks favoured by evolution?
Journal of Theoretical Biology 252, 2008, 497-504
bibtex | abstract |  PudMed-ID: 18249414 ]

J. Behre, T. Wilhelm, A. von Kamp, E. Ruppin, S. Schuster
Structural robustness of metabolic networks with respect to multiple knockouts
Journal of Theoretical Biology 252, 2008, 433-441
bibtex | abstract |  doi  |  PudMed-ID: 18023456 ]

B. Knoke, M. Marhl, M. Perc, S. Schuster
Equality of average and steady-state levels in some nonlinear models of biological oscillations
Theory in Biosciences 127, 2008, 1-14
bibtex | abstract |  PudMed-ID: 18197448 ]

2007

R. Bortfeldt, A. Herrmann, H. Pospisil, S. Schuster
Validation of human alternative splice forms using the EASED platform and multiple splice site discriminating features
In: Mathematical Modeling of Biological Systems - Vol. I (eds. A. Deutsch, L. Brusch, H. Byrne, G. de Vries,, H.-P. Herzel), Birkhäuser, Boston, 2007, 337-349
bibtex ]

B. Knoke, M. Marhl, S. Schuster
Selective Regulation of Protein Activity by Complex Ca2+Oscillations: A Theoretical Study
In: Mathematical Modeling of Biological Systems - Vol. I (eds. A. Deutsch, L. Brusch, H. Byrne, G. de Vries, H.-P. Herzel), Birkhäuser, Boston, 2007, 11-24
bibtex ]

S. Schuster, D.A. Fell
Modelling and simulating metabolic networks
In: Bioinformatics: From Genomes to Therapies (eds. T.Lengauer), Wiley-VCH, Weinheim, 2007, ch. 20, 755-805
bibtex ]

T. Hinze, S. Hayat, T. Lenser, N. Matsumaru, P. Dittrich
Hill Kinetics Meets P Systems: A Case Study on Gene Regulatory Networks as Computing Agents in silico and in vivo
Series Lecture Notes in Computer Science 4860, 2007, 320-335
bibtex ]

S. Schuster, A. von Kamp, M. Pachkov
Understanding the roadmap of metabolism by pathway analysis.
Methods in Molecular Biology 358, 2007, 199-226
bibtex |  PudMed-ID: 17035688 ]

R. Schwarz, C. Liang, C. Kaleta, M. Kuhnel, E. Hoffmann, S. Kuznetsov, M. Hecker, G. Griffiths, S. Schuster, T. Dandekar
Integrated network reconstruction, visualization and analysis using YANAsquare
BMC Bioinformatics 8, 2007, 313
bibtex | abstract |  pdf  |  PudMed-ID: 17725829 ]

G. Neumann, S. Schuster
Continuous model for the rock-scissors-paper game between bacteriocin producing bacteria
J of Mathematical Biology 54, 2007, 815-846
bibtex | abstract |  PudMed-ID: 17457587 ]

M. Hiller, S. Nikolajewa, K. Huse, K. Szafranski, P. Rosenstiel, S. Schuster, R. Backofen, M. Platzer
TassDB: a database of alternative tandem splice sites
Nucleic Acids Research 35, 2007, D188-D192
bibtex | abstract |  pdf  |  PudMed-ID: 17142241 ]

M. Pachkov, T. Dandekar, J. Korbel, P. Bork, S. Schuster
Use of pathway analysis and genome context methods for functional genomics of Mycoplasma pneumoniae nucleotide metabolism
Gene 396, 2007, 215-225
bibtex | abstract |  PudMed-ID: 17467928 ]

G. Neumann, S. Schuster
Modeling the rock - scissors - paper game between bacteriocin producing bacteria by Lotka-Volterra equations
Discrete and Continuous Dynamical Systems 8, 2007, 207-228
bibtex ]

2006

S. Schuster, E. Klipp, M. Marhl
The predictive power of molecular network modelling - case studies of predictions with subsequent experimental verification
In: Discovering Biomolecular Mechanisms with Computational Biology (eds. F. Eisenhaber), Landes Bioscience, Georgetown 2006, 95-103
bibtex |  pdf  ]

T. Aho, T. Wilhelm, A. Beyer, S. Schuster, O. Yli-Harja
Finding infeasible reactions in metabolic networks: comparison of methods
In: Proceedings of the 4th TICSP Workshop on Computational Systems Biology (eds. P. Ruusuvuori et al.), WCSB 2006, Tampere 2006, 23-26
bibtex ]

S. Schuster, E. Klipp, M. Marhl
The Predictive Power of Molecular Network Modelling. Case Studies of Predictions with Subsequent Experimental Verification.
In: Discovering Biomolecular Mechanisms with Computational Biology (F. Eisenhaber, ed.) Landes Bioscience, 2006, 95-103
bibtex ]

C. Kaleta, F. Centler, P. Dittrich
Analyzing molecular reaction networks: from pathways to chemical organizations.
Molecular Biotechnology 34, 2006, 117-123
bibtex |  PudMed-ID: 17172657 ]

A. von Kamp, S. Schuster
Metatool 5.0: fast and flexible elementary modes analysis
Bioinformatics 22, 2006, 1930-1931
bibtex | abstract |  pdf  |  PudMed-ID: 16731697 ]

S. Schuster, R. Eils, K. Prank
5th International Conference on Systems Biology (ICSB 2004), Heidelberg, October 9-13, 2004.
Biosystems 83, 2006, 71-74
bibtex |  PudMed-ID: 16242837 ]

M. Marhl, M. Perc, S. Schuster
A minimal model for decoding of time-limited Ca2+ oscillations
Biophys Chem 120, 2006, 161-167
bibtex | abstract |  PudMed-ID: 16338050 ]

2005

A. Fajmut, M. Brumen, S. Schuster
Theoretical model of the interactions between Ca2+, calmodulin and myosin light chain kinase
FEBS Letters 579 (20), 2005, 4361-4366
bibtex | abstract |  PudMed-ID: 16051224 ]

M. Marhl, M. Perc, S. Schuster
Selective regulation of cellular processes via protein cascades acting as band-pass filters for time-limited oscillations
FEBS Letters 579, 2005, 5461-5465
bibtex | abstract |  PudMed-ID: 16213486 ]

I. Zevedei-Oancea, S. Schuster
A theoretical framework for detecting signal transfer routes in signalling networks
Computers and Chemical Enginering 29, 2005, 597-617
bibtex ]

R. Schwarz, P. Musch, A. von Kamp, B. Engels, H. Schirmer, S. Schuster, T. Dandekar
YANA - a software tool for analyzing flux modes, gene-expression and enzyme activities
BMC Bioinformatics 6, 2005, 135
bibtex | abstract |  pdf  |  PudMed-ID: 15929789 ]

S. Schuster, D. Kenanov
Adenine and adenosine salvage pathways in erythrocytes and the role of S-adenosylhomocysteine hydrolase. A theoretical study using elementary flux modes
FEBS Journal 272, 2005, 5278-5290
bibtex | abstract |  PudMed-ID: 16218958 ]

S. Schuster, B. Knoke, M. Marhl
Differential regulation of proteins by bursting calcium oscillations - a theoretical study
Biosystems 81, 2005, 49-63
bibtex | abstract |  pdf  |  PudMed-ID: 15917128 ]

T. Pfeiffer, S. Schuster
Game-theoretical approaches to studying the evolution of biochemical systems
Trends in Biochemical Sciences 30, 2005, 20-25
bibtex | abstract |  PudMed-ID: 15653322 ]

S. Klamt, J. Gagneur, A. von Kamp
Algorithmic approaches for computing elementary modes in large biochemical reaction networks
Systems Biology (Stevenage) 152, 2005, 249-255
bibtex | abstract |  PudMed-ID: 16986267 ]

2004

S. Schuster, I. Zevedei-Oancea
Multifunctional enzymes and pathway modelling
In: Experimental Standard Conditions of Enzyme Characterizations (eds. M. G. Hicks, C. Kettner), Logos-Verlag, Berlin, 2004, 115-127
bibtex | abstract |  pdf  ]

T. Wilhelm, J. Behre, S. Schuster
Analysis of structural robustness of metabolic networks
Systems Biology (Stevenage) 1, 2004, 114-120
bibtex | abstract |  pdf  |  PudMed-ID: 17052121 ]

J.A. Papin, J. Stelling, N.D. Price, S. Klamt, S. Schuster, B.O. Palsson
Comparison of network-based pathway analysis methods.
Trends in Biotechnology 22, 2004, 400-405
bibtex | abstract |  PudMed-ID: 15283984 ]

W. Liebermeister, E. Klipp, S. Schuster, R. Heinrich
A theory of optimal differential gene expression
Biosystems 76, 2004, 261-278
bibtex | abstract |  pdf  |  PudMed-ID: 15351149 ]

2003

T. Frick, S. Schuster
An example of the prisoner's dilemma in biochemistry
Naturwissenschaften 90 (7), 2003, 327-331
bibtex | abstract |  PudMed-ID: 12883777 ]

S. Schuster, S. Klamt, J. Stelling
Making predictions about robustness and flexibility from metabolic network structure
In: Proceedings of German Conference on Bioinformatics 2003 (eds. H.-W. Mewes, V. Heun, D. Frishman, S. Kramer), Belleville Verlag, MĂĽnchen 2003, 129-134
bibtex ]

S. Schuster
Metabolic pathway analysis in biotechnology
In: Metabolic Engineering in the Post Genomic Era (eds. B.N. Kholodenko, H.V. Westerhoff), Horizon Scientific, Wymondham, 2003, 181-208
bibtex ]

I. Zevedei-Oancea, S. Schuster
Topological analysis of metabolic networks based on Petri net theory
In Silico Biology 3 (3), 2003, 323-345
bibtex |  PudMed-ID: 12954094 ]

M. Marhl, S. Schuster
Under what conditions signal transduction pathways are highly flexible in response to external forcing? A case study on calcium oscillations.
Journal of Theoretical Biology 224 (4), 2003, 491-500
bibtex |  PudMed-ID: 12957122 ]

T. Dandekar, F. Moldenhauer, S. Bulik, H. Bertram, S. Schuster
A method for classifying metabolites in topological pathway analyses based on minimization of pathway number.
Biosystems 70, 2003, 255-270
bibtex | abstract |  pdf  |  PudMed-ID: 12941488 ]

2002

S. Schuster, S. Klamt
Applying Metabolic Pathway Analysis to make good use of methanol (Commentary)
Trends in Biotechnology 20 (8), 2002, 322
bibtex ]

S. Schuster
Mapping the combinatorial regulation by transcription factors (Commentary)
Trends in Biotechnology 20 (1), 2002, 5-6
bibtex ]

S. Schuster, M. Marhl, T. Höfer
Modelling of Simple and Complex Calcium Oscillations. From Single-cell Responses to Intercellular Signalling (Review)
European Journal of Biochemistry 269, 2002, 1333-1355
bibtex ]

S. Klamt, S. Schuster
Calculating as many fluxes as possible in under determined metabolic networks
Molecular Biology Reports 29 (1-2), 2002, 243-248
bibtex ]

S. Schuster, S. Klamt, W. Weckwerth, F. Moldenhauer, T. Pfeiffer
Use of network analysis of metabolic systems in bioengineering
Bioproc. Biosyst. Eng. 24, 2002, 363-372
bibtex ]

J. Stelling, S. Klamt, K. Bettenbrock, S. Schuster, ED. Gilles
Metabolic network structure determines key aspects of functionality and regulation.
Nature 420 (6912), 2002, 190-193
bibtex |  PudMed-ID: 12432396 ]

S. Schuster, C. Hilgetag, J.H. Woods, D.A. Fell
Reaction routes in biochemical reaction systems: algebraic properties, validated calculation procedure and example from nucleotide metabolism
Journal of Mathematical Biology 45, 2002, 153-181
bibtex | abstract |  doi  |  PudMed-ID: 12181603 ]

S. Schuster, I. Zevedei-Oancea
Treatment of multifunctional enzymes in metabolic pathway analysis
Biophysical Chemistry 99, 2002, 63-75
bibtex | abstract |  doi  |  PudMed-ID: 12223240 ]

S. Schuster, M. Marhl, T. Höfer
Modelling of simple and complex calcium oscillations. From single-cell responses to intercellular signalling.
European Journal of Biochemistry 269, 2002, 1333-1355
bibtex |  doi  |  PudMed-ID: 11874447 ]

S. Schuster, S. Klamt, W. Weckwerth, F. Moldenhauer and T. Pfeiffer
Use of network analysis of metabolic systems in bioengineering.
Bioprocess and Biosystems Engineering 24, 2002, 363-372
bibtex ]

S. Schuster, T. Pfeiffer, F. Moldenhauer, I. Koch, T. Dandekar
Exploring the pathway structure of metabolism: decomposition into subnetworks and application to Mycoplasma pneumoniae
Bioinformatics 18, 2002, 351-361
bibtex | abstract |  PudMed-ID: 11847093 ]

S. Klamt, S. Schuster
Calculating as many fluxes as possible in underdetermined metabolic networks.
Molecular Biology Reports 29 (1-2), 2002, 243-248
bibtex |  PudMed-ID: 12241065 ]

S. Klamt, S. Schuster, E.D. Gilles
Calculability analysis in underdetermined metabolic networks illustrated by a model of the central metabolism in purple nonsulfur bacteria
Biotechnology and Bioengineering 77, 2002, 734-751
bibtex | abstract |  PudMed-ID: 11835134 ]

2001

S. Schuster
Protons and sodium ions acting as intracellular carrier pigeons? (Commentary)
Trends in Biotechnology 19, 2001, 330
bibtex ]

T. Dandekar, S. Schuster
The Large-scale Organization of Metabolic Networks (Commentary)
Chemtracts 14, 2001, 137-141
bibtex ]

S. Schuster
What can Silent Mutations Tell us? (Commentary)
Trends in Biotechnology 19, 2001, 242
bibtex ]

S. Schuster, M. Marhl
Bifurcation analysis of calcium oscillations: time-scale separation, canards, and frequency lowering.
Journal of Biological Systems 9, 2001, 291-314
bibtex |  doi  ]

T. Pfeiffer, S. Schuster, S. Bonhoeffer
Cooperation and competition in the evolution of ATP-producing pathway
Science 292, 2001, 504-507
bibtex | abstract |  PudMed-ID: 11283355 ]

2000

S. Schuster
Flux determination by isotopomer balancing - a successful application of theory to experiment (Commentary)
Trends in Biotechnology 19, 2000, 85
bibtex ]

S. Schuster, T. Pfeiffer, F. Moldenhauer, I. Koch, T. Dandekar
Structural Analysis of Metabolic Networks: Elementary Flux Modes, Analogy to Petri Nets, and Application to Mycoplasma pneumoniae
In: Proceedings of the German Conference on Bioinformatics 2000 (eds. E. Bornberg-Bauer, U. Rost, J. Stoye, M. Vingron), Logos Verlag, Berlin 2000, 115-120
bibtex ]

S. Schuster
Breeding of Escherichia coli Based on Colour (Commentary)
Trends in Biotechnology 8 (11), 2000, 442
bibtex ]

S. Schuster
Biotechnology in silico. Metabolic Proteomics of Haemophilus influenzae (Commentary)
Trends in Biotechnology 18, 2000, 328
bibtex ]

T. Pfeiffer, T. Dandekar, F. Moldenhauer, S. Schuster
Topological Analysis of Metabolic Networks. Application to the Metabolism of Mycoplasma pneumoniae
In: BioThermoKinetics 2000, Animating the Cellular Map (eds. J.-H.S. Hofmeyr, J.M. Rohwer, J.L. Snoep), Stellenbosch University Press, Stellenbosch, 2000, 229-234
bibtex ]

S. Schuster, T. Dandekar, K. Mauch, M. Reuss, D.A. Fell
Recent Developments in Metabolic Pathway Analysis and Their Potential Implications for Biotechnology and Medicine
In: Technological and Medical Implications of Metabolic Control Analysis (eds. A. Cornish-Bowden, M.L. Cárdenas), Kluwer, Dordrecht, 2000, 57-66
bibtex ]

S. Schuster, B. N. Kholodenko, H. V. Westerhoff
Cellular information transfer regarded from a stoichiometry and control analysis perspective
Biosystems 55 (1-3), 2000, 73-81
bibtex ]

S. Schuster, DA. Fell, T. Dandekar
A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks
Nat Biotechnol 18, 2000, 326-332
bibtex | abstract |  PudMed-ID: 10700151 ]

1999

S. Schuster
Pathway Analysis of Biochemical Reaction Networks
In: Proceedings of Workshop on Computation of Biochemical Pathways and Genetic Networks (eds. E. Bornberg-Bauer, A. de Beuckelaer, U. Kummer, U. Rost), Logos Verlag, Berlin, 1999, 117-121
bibtex ]

S. Schuster
Studies on the Stoichiometric Structure of Enzymatic Reaction Systems
Theory in Biosciences 118 (2), 1999, 125-139
bibtex | abstract ]

S. Schuster
Use and limitations of modular metabolic control analysis in medicine and biotechnology
Metabolic Engineering 1, 1999, 232-242
bibtex | abstract |  PudMed-ID: 10937938 ]

S. Schuster, H.V. Westerhoff
Modular control analysis of slipping enzymes
Biosystems 49, 1999, 1-15
bibtex | abstract |  pdf  |  PudMed-ID: 10091969 ]

S. Schuster, T. Dandekar, D.A. Fell
Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering
Trends in Biotechnology 17, 1999, 53-60
bibtex | abstract |  doi  |  PudMed-ID: 10087604 ]

C.H. Schilling, S. Schuster, B.O. Palsson, R. Heinrich
Metabolic pathway analysis: basic concepts and scientific applications in the post-genomic era
Biotechnology Progress 15, 1999, 296-303
bibtex | abstract |  doi  |  PudMed-ID: 10356246 ]

T. Pfeiffer, I. Sánchez-Valdenebro, J.C. Nuño, F. Montero, S. Schuster
METATOOL: for studying metabolic networks
Bioinformatics 15, 1999, 251-257
bibtex | abstract |  PudMed-ID: 10222413 ]

T. Dandekar, S. Schuster, B. Snel, M. Huynen, P. Bork
Pathway alignment: application to the comparative analysis of glycolytic enzymes.
Biochemical Journal 343, 1999, 115-124
bibtex | abstract |  doi  |  PudMed-ID: 10493919 ]

1998

M. Marhl, S. Schuster, M. Brumen, R. Heinrich
Modelling Oscillations of Calcium and Endoplasmic Reticulum Transmembrane Potential. Role of the Signalling and Buffering Proteins and of the Size of the Ca2+ Sequestering ER Subcompartments
Bioelectrochemistry and Bioenergetics 46 (1), 1998, 79-90
bibtex | abstract ]

S. Schuster, R. Ouhabi, M. Rigoulet, J.-P. Mazat
Modelling the Interrelations between the Transmembrane Potential and pH Difference across Membranes with Electrogenic Proton Transport upon Build-up of the Proton-motive Force
Bioelectrochemistry and Bioenergetics 45 (2), 1998, 181-192
bibtex | abstract ]

R. Heinrich, S. Schuster
The Modelling of Metabolic Systems. Structure, Control and Optimality
Biosystems 47 (1-2), 1998, 61-77
bibtex | abstract |  pdf  |  PudMed-ID: 9715751 ]

S. Schuster, D.A. Fell, T. Pfeiffer, T. Dandekar, P. Bork
Elementary Modes Analysis Illustrated with Human Red Cell Metabolism
In: BioThermoKinetics in the Post Genomic Era (eds. C. Larsson, I.-L. Pahlman, L. Gustafsson), Chalmers, Göteborg, 1998, 332-339
bibtex |  url  ]

S. Schuster, M. Marhl, M. Brumen, R. Heinrich
Influence of Calcium Binding to Proteins on Calcium Oscillations and ER Membrane Potential Oscillations. A Mathematical Model
In: Information Processing in Cells and Tissues (eds. R. Paton, M. Holcombe), Plenum Press, New York, 1998, 137-150
bibtex ]

R. Heinrich, S. Schuster
The modelling of metabolic systems. Structure, control and optimality
Biosystems 47, 1998, 61-77
bibtex ]

S. Schuster, R. Ouhabi, M. Rigoulet, J.-P. Mazat
Modelling the interrelation between the transmembrane potential and pH difference across membranes with electrogenic proton transport upon build-up of the proton-motive force
Bioelectrochemistry and Bioenergetics 45, 1998, 181-192
bibtex |  doi  ]

B. N. Kholodenko, S. Schuster, J. Garcia, H. V. Westerhoff, M. Cascante
Control analysis of metabolic systems involving quasi-equilibrium reactions
Biochimica et Biophysica Acta 1379 (3), 1998, 337-352
bibtex |  doi  |  PudMed-ID: 9545597 ]

M. Marhl, S. Schuster, M. Brumen
Mitochondria as an important factor in the maintenance of constant amplitudes of cytosolic calcium oscillations
Biophysical Chemistry 71, 1998, 125-132
bibtex | abstract |  doi  |  PudMed-ID: 17029696 ]

M. Marhl, S. Schuster, M. Brumen, R. Heinrich
Modelling oscillations of calcium and endoplasmic reticulum transmembrane potential: Role of the signalling and buffering proteins and of the size of the Ca2+ sequestering ER subcompartments.
Bioelectrochemistry and Bioenergetics 46 (1), 1998, 79-90
bibtex |  doi  ]

1997

T. Wilhelm, S. Schuster, R. Heinrich
Kinetic and Thermodynamic Analyses of the Reversible Version of the Smallest Chemical Reaction System with Hopf Bifurcation
Nonlinear World 4, 1997, 295-321
bibtex | abstract ]

M. Marhl, S. Schuster, M. Brumen, R. Heinrich
Modeling the interrelations between the calcium oscillations and ER membrane potential oscillations.
Biophysical Chemistry 63 (2-3), 1997, 221-239
bibtex |  doi  |  PudMed-ID: 12362939 ]

1996

The Regulation of Cellular Systems
R. Heinrich, S. Schuster, Chapman & Hall, New York (Springer; 1st edition, 1996), 1996, ISBN-10: 0412032619; ISBN-13: 978-0412032615
bibtex | abstract ]

S. Schuster, C. Hilgetag, J.H. Woods, D.A. Fell
Elementary Modes of Functioning in Biochemical Networks
In: Computation in Cellular and Molecular Biological Systems (eds. R. Cuthbertson, M. Holcombe, R. Paton), World Scientific, Singapore, 1996, 151-165
bibtex ]

S. Schuster, C. Hilgetag, R. Schuster
Determining Elementary Modes of Functioning in Biochemical Reaction Networks at Steady State
In: Biomedical and Life Physics (eds. D.N. Ghista), Vieweg, Wiesbaden, 1996, 101-114
bibtex ]

S. Schuster
Control Analysis in Terms of Generalized Variables Characterizing Metabolic Systems
Journal of Theoretical Biology 182 (3), 1996, 259-268
bibtex |  doi  |  PudMed-ID: 8944157 ]

J. M. Rohwer, S. Schuster, H. V. Westerhoff
How to Recognize Monofunctional Units in a Metabolic System
Journal of Theoretical Biology 179 (3), 1996, 213-228
bibtex |  doi  |  PudMed-ID: 8762334 ]

1995

S. Schuster, R. Heinrich
Use of the Theories of Multi-criteria Optimization and of Linear Inequality Systems for the Steady-state Modelling of Biochemical Systems
In: Mathematical Population Dynamics: Analysis of Heterogeneity - Vol. 2 (eds. O. Arino et al.), Wuerz, Winnipeg, 1995, 35-48
bibtex ]

S. Schuster, C. Hilgetag
What Information about the Conserved-Moiety Structure of Chemical Reaction Systems Can be Derived from Their Stoichiometry?
Journal of Physical Chemistry 99 (20), 1995, 8017-8023
bibtex | abstract ]

B. N. Kholodenko, S. Schuster, J. M. Rohwer, M. Cascante, H. V. Westerhoff
Composite control of cell function: metabolic pathways behaving as single control units
FEBS Letters 368 (1), 1995, 1-4
bibtex |  doi  |  PudMed-ID: 7615057 ]

B. N. Kholodenko, D. Molenaar, S. Schuster, R. Heinrich, H. V. Westerhoff
Defining control coefficients in non-ideal metabolic pathways
Biophysical Chemistry 56, 1995, 215-226
bibtex |  doi  |  PudMed-ID: 17023325 ]

1994

S. Schuster, C. Hilgetag
On Elementary Flux Modes in Biochemical Reaction Systems at Steady State
Journal of Biological Systems 2, 1994, 165-182
bibtex | abstract ]

S. Schuster, T. Höfer, C. Hilgetag, R. Schuster
Use of Convex Analysis for the Modelling of Biochemical Reaction Systems
In: Lecture Notes in Control and Information Sciences (eds. J. Henry, J.-P. Yvon), Springer, London, 1994, 365-374
bibtex ]

S. Schuster, C. Hilgetag, D.A. Fell
Detecting Elementary Modes of Functioning in Metabolic Networks
In: What is Controlling Life? (eds. E. Gnaiger, F.N. Gellerich, M. Wyss), Innsbruck University Press, Innsbruck, 1994, 103-105
bibtex ]

J.M. Rohwer, S. Schuster, H.V. Westerhoff
An Invariance Property of Coresponse Coefficients in Modular Metabolic Control and Regulation Analysis
In: What is Controlling Life? (eds. E. Gnaiger, F.N. Gellerich, M. Wyss), Innsbruck University Press, Innsbruck, 1994, 109-110
bibtex ]

1993

S. Schuster, J.-P. Mazat
A Model Study on the Interrelation between the Transmembrane Potential and pH Difference Across the Mitochondrial Inner Membrane
In: Modern Trends in Biothermokinetics (eds. S. Schuster, M. Rigoulet, R. Ouhabi, J.-P. Mazat), Plenum Press, New York and London, 1993, 39-44
bibtex ]

S. Schuster, D. Kahn, H.V. Westerhoff
Modular analysis of the control of complex metabolic pathways
Biophysical Chemistry 48, 1993, 1-17
bibtex | abstract |  PudMed-ID: 8257764 ]

R. Schuster, S. Schuster
Refined algorithm and computer program for calculating all non-negative fluxes admissible in steady states of biochemical reaction systems with or without some flux rates fixed
Computer applications in the biosciences 9, 1993, 79-85
bibtex |  PudMed-ID: 8435772 ]

1992

S. Schuster, R. Schuster
Decomposition of biochemical reaction systems according to flux control insusceptibility
Journal De Chimie Physique Et De Physico-Chimie Biologique 89 (9), 1992, 1887-1910
bibtex ]

S. Schuster, R. Heinrich
The definitions of metabolic control analysis revisited
Biosystems 27, 1992, 1-15
bibtex ]

R. Schuster, S. Schuster, H.-G. HolzhĂĽtter
Simplification of Complex Kinetic Models used for the Quantitative Analysis of Nuclear Magnetic Resonance or Radioactive Tracer Studies
Journal of the Chemical Society-Faraday Transactions 88 (19), 1992, 2837-2844
bibtex |  doi  ]

1991

R. Schuster, S. Schuster
Relationships between modal analysis andrapid-equilibrium approximation in the modeling of biochemicalnetworks
Systems Analysis Modelling Simulation 8 (8), 1991, 623-633
bibtex ]

S. Schuster, T. Höfer
Determining all extreme semi-positive conservation relations in chemical reaction systems: A test criterion for conservativity.
Journal of the Chemical Society-Faraday Transactions 87 (16), 1991, 2561-2566
bibtex |  doi  ]

S. Schuster, R. Schuster, R. Heinrich
Minimization of intermediate concentrations as a suggested optimality principle for biochemical networks. II. Time hierarchy, enzymatic rate laws, and erythrocyte metabolism.
Journal of Mathematical Biology 29, 1991, 443-455
bibtex | abstract |  PudMed-ID: 1875162 ]

S. Schuster, R. Heinrich
Minimization of intermediate concentrations as a suggested optimality principle for biochemical networks - I. Theoretical analysis
Journal of Mathematical Biology 29, 1991, 425-442
bibtex |  doi  ]

R. Heinrich, S. Schuster, H.-G. Holzhuetter
Mathematical analysis of enzymic reaction systems using optimization principles
Eur J Biochem 201, 1991, 1-21
bibtex ]

R. Heinrich, S. Schuster
Is metabolic channelling the complicated solution to the easy problem of reducing transient times?
Journal of Theoretical Biology 152, 1991, 57-61
bibtex |  doi  |  PudMed-ID: 1753768 ]

S. Schuster, R. Schuster
Detecting strictly detailed balanced subnetworks in open chemical reaction networks.
Journal of Mathematical Chemistry 6 (1), 1991, 17-40
bibtex |  doi  ]

1990

S. Schuster, R. Schuster
A necessary and sufficient condition for open chemically reacting systems endowed with a generalized mass action kinetics to be detailed balanced
Z. phys. Chem. 271, 1990, 337-345
bibtex ]

1989

S. Schuster, R. Schuster
A generalization of Wegschneiders condition. Implications for properties of steady states and for quasi-steady-state approximation
Journal of Mathematical Chemistry 3, 1989, 25-42
bibtex ]

1987

S. Schuster, R. Heinrich
Time Hierarchy in Enzymatic Reaction Chains Resulting from Optimality Principles
Journal of Theoretical Biology 129, 1987, 189-209
bibtex |  PudMed-ID: 3455462 ]

R. Heinrich, H.-G. Holzhuetter, S. Schuster
A theoretical approach to the evolution and structural design of enzymatic networks; linear enzymatic chains, branched pathways and glycolysis of erythrocytes
Bulletin of Mathematical Biology 49 (5), 1987, 539-595
bibtex |  doi  |  PudMed-ID: 3435799 ]