Dr. Stefan Müller

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Stefan Müller

Peer Reviewed Journal Publication
  • Müller S, Regensburger G (2016, online: 2016) Elementary vectors and conformal sums in polyhedral geometry and their relevance in metabolic pathway analysis. Frontiers in Genetics, Bd. 7:90, S. 1-11. (link)
  • Gerstl M P, Jungreuthmayer C, Müller S, Zanghellini J (2016, online: 2016) Which sets of elementary flux modes form thermodynamically feasible flux distributions?. The FEBS Journal, Bd. 283 (9), S. 1782-94. (link)
  • Müller S, Feliu E, Regensburger G, Conradi C, Shiu A, Dickenstein A (2016, online: 2015) Sign conditions for injectivity of generalized polynomial maps with applications to chemical reaction networks and real algebraic geometry. Foundations of Computational Mathematics, Bd. 16, S. 69-97. (link)
  • Müller S, Regensburger G, Steuer R (2015) Resource allocation in metabolic networks: kinetic optimization and approximations by FBA. Biochemical Society Transactions, Bd. 43 (6), S. 1195-1200. (link)
  • Müller S, Hofbauer J (2015, online: 2015) Genetic Recombination as a Chemical Reaction Network. Mathematical Modelling of Natural Phenomena, Bd. 10 (5), S. 84-99. (link)
  • Hsiao Y-T, Lee W-P, Yang W, Müller S, Flamm C, Hofacker I, Kügler P (2015, online: 2015) Practical Guidelines for Incorporating Knowledge-Based and Data-Driven Strategies into the Inference of Gene Regulatory Networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics (99), S. 1-13. (link)
  • Müller S, Regensburger G, Steuer R (2014, online: 2013) Enzyme allocation problems in kinetic metabolic networks: Optimal solutions are elementary flux modes. Journal of Theoretical Biology, Bd. 347, S. 182-190. (link)
  • Gottstein W, Müller S, Herzel H, Steuer R (2014, online: 2014) Elucidating the adaptation and temporal coordination of metabolic pathways using in-silico evolution. Biosystems, Bd. 117, S. 68-76. (link)
  • Müller S, Regensburger G (2012) Generalized mass action systems: Complex balancing equilibria and sign vectors of the stoichiometric and kinetic-order subspaces. SIAM Journal on Applied Mathematics, Bd. 72 (6), S. 1926-1947. (link)
  • Müller S, Murray DB, Machne R (2012, online: 2012) A new dynamic model for highly efficient mass transfer in aerated bioreactors and consequences for kLa identification. Biotechnology & Bioengineering, Bd. 109 (12), S. 2997-3006. (link)
  • Fonseca JP, Steffen PA, Müller S, Lu J, Sawicka A, Seiser C, Ringrose L (2012) In vivo Polycomb kinetics and mitotic chromatin binding distinguish stem cells from differentiated cells. Genes & Development, Bd. 26 (8), S. 857-71. (link)
  • Engl HW, Flamm C, Kügler P, Lu J, Müller S, Schuster P (2009) Inverse Problems in Systems Biology. Inverse Problems, Bd. 25 (12), S. 1-51. (link)
  • Philipp Kügler, Erwin Gaubitzer, Stefan Müller (2009) Parameter identification for chemical reaction systems using sparsity enforcing regularization - a case study for the Chlorite - Iodide reaction. Journal of Physical Chemistry A, Bd. 113 (12), S. 2775-85. (link)
  • Christoph Flamm, Lukas Endler, Stefan Müller, Stefanie Widder, Peter Schuster (2007) A minimal and self-consistent in silico cell model based on macromolecular interactions. Phil Trans R Soc Lond B Biol Sci, Bd. 362 (1486), S. 1831-1839. (link)
  • Müller S, Hofbauer J, Flamm C, Endler L, Schuster P (2006) A Generalized Model of the Repressilator. Journal of Mathematical Biology, Bd. 53 (6), S. 905-937. (link)
  • Machne R, Finney A, Müller S, Lu J, Flamm C (2006) The SBML ODE Solver Library: a native API for symbolic and fast numerical analysis of reaction networks. Bioinformatics, Bd. 22 (11), S. 1406-7. (link)

Conference Contribution: Publication in Proceedings
  • Müller, Stefan; Regensburger, Georg (2014) Generalized mass-action systems and positive solutions of polynomial equations with real and symbolic exponents. In: Gerdt, Vladimir P.; Koepf, Wolfram; Seiler, Werner M.; Vorozhtsov, Evgenii V. (Hrsg.), Computer Algebra in Scientific Computing. Proceedings of the 16th International Workshop (CASC 2014) (CASC 2014, Workshop on Computer Algebra in Scientific Computing) In Reihe: Lecture Notes in Computer Science (LNCS); Cham: Springer International Publishing, S. 302-323 . (link)
  • Klement M, Děd T, Šafránek D, Červený J, Müller S, Steuer R (2014, online: 2014) Biochemical Space: A Framework for Systemic Annotation of Biological Models. (Fifth International Workshop on Interactions between Computer Science and Biology, CS2Bio'14) In Reihe: Electronic Notes in Theoretical Computer Science, Volume 306, S. 31–44. (link)
  • Klement M, Šafránek D, Děd T, Pejznoch A, Nedbal L, Steuer R, Červený J, Müller S (2013, online: 2013) A comprehensive web-based platform for domain-specific biological models. (Fourth International Workshop on Interactions between Computer Science and Biology, CS2Bio'13) In Reihe: Electronic Notes in Theoretical Computer Science, Volume 299, S. 61–67. (link)
  • Lu J, Müller S, Machné R, Flamm C (2008) SBML ODE Solver Library: Extensions for Inverse Analysis., TICSP #41: Fifth International Workshop on Computational Systems Biology, WCSB 2008 (Fifth International Workshop on Computational Systems Biology, WCSB 2008, June 11-13, 2008, Leipzig, Germany) In Reihe: Tampere International Center for Signal Processing Series; Tampere: Tampere International Center for Signal Processing . (link)

Contribution in Collection
  • Jungreuthmayer C, Gerstl M P, Hanscho M, Nair G, Regensburger G, Müller S, Zanghellini J (2017) Towards Efficient Genome-Scale Metabolic Pathway Analysis. In: Wittmann C, Liao J C (Hrsg.), Industrial Biotechnology: Microorganisms: Wiley.

Research Report
  • Boros B, Hofbauer J, Müller S (2016) On global stability of the Lotka reactions with generalized mass-action kinetics. Bericht-Nr. arXiv:1611.05748 [math.DS]; Cornell University: Ithaca. (link)
  • Müller S, Regensburger G (2015) Elementary vectors and conformal sums in polyhedral geometry and applications in metabolic pathway analysis. Bericht-Nr. arXiv:1512.00267 [math.MG]; Cornell University: Ithaca. (link)
  • Müller S, Hofbauer J (2015) Genetic Recombination as a Chemical Reaction Network. Bericht-Nr. arXiv:1503.01155 [q-bio.MN]; Cornell University: Ithaca. (link)
  • Müller S, Regensburger G (2014) Generalized Mass-Action Systems and Positive Solutions of Polynomial Equations with Real and Symbolic Exponents. Bericht-Nr. arXiv:1406.6587 [math.DS]; Cornell University: Ithaca . (link)
  • Müller S, Feliu E, Regensburger G, Conradi C, Shiu A, Dickenstein A (2013) Sign conditions for injectivity of generalized polynomial maps with applications to chemical reaction networks and real algebraic geometry. Bericht-Nr. arXiv:1311.5493 [math.AG]; Cornell University: Ithaca . (link)
  • Müller S, Regensburger G, Steuer R (2013) Enzyme allocation problems in kinetic metabolic networks: Optimal solutions are elementary flux modes. Bericht-Nr. arXiv:1308.0510 [q-bio.MN]; Cornell University: Ithaca . (link)
  • Müller S, Regensburger G (2012) Generalized mass action systems: Complex balancing equilibria and sign vectors of the stoichiometric and kinetic-order subspaces. Bericht-Nr. 2012-21; Linz . (link)
  • Müller S, Lu J, Kügler P, Engl HW (2008) Parameter Identification in Systems Biology: Solving Ill-posed Inverse Problems using Regularization. Bericht-Nr. 2008-25; Linz . (link)