The SBML ODE Solver Library: a native API for symbolic and fast numerical analysis of reaction networks. - Rainer Machné; Andrew Finney; Stefan Müller 009; James Lu; Stefanie Widder; Christoph Flamm (Bioinform., 2006)

Generalized Mass Action Systems: Complex Balancing Equilibria and Sign Vectors of the Stoichiometric and Kinetic-Order Subspaces. - Stefan Müller 009; Georg Regensburger (SIAM J. Appl. Math., 2012)

A Comprehensive Web-based Platform For Domain-Specific Biological Models. - Matej Klement; David Safránek; T. Ded; Ales Pejznoch; Ladislav Nedbal; Ralf Steuer; Jan Cervený; Stefan Müller 009 (CS2Bio, 2013)

Generalized Mass-Action Systems and Positive Solutions of Polynomial Equations with Real and Symbolic Exponents (Invited Talk). - Stefan Müller 009; Georg Regensburger (CASC, 2014)

Elucidating the adaptation and temporal coordination of metabolic pathways using in-silico evolution. - Willi Gottstein; Stefan Müller 009; Hanspeter Herzel; Ralf Steuer (Biosyst., 2014)

Generalized Mass-Action Systems and Positive Solutions of Polynomial Equations with Real and Symbolic Exponents. - Stefan Müller 009; Georg Regensburger (CoRR, 2014)

Biochemical Space: A Framework for Systemic Annotation of Biological Models. - Matej Klement; T. Ded; David Safránek; Jan Cervený; Stefan Müller 009; Ralf Steuer (CS2Bio, 2014)

Sign Conditions for Injectivity of Generalized Polynomial Maps with Applications to Chemical Reaction Networks and Real Algebraic Geometry. - Stefan Müller 009; Elisenda Feliu; Georg Regensburger; Carsten Conradi; Anne Shiu; Alicia Dickenstein (Found. Comput. Math., 2016)

Practical Guidelines for Incorporating Knowledge-Based and Data-Driven Strategies into the Inference of Gene Regulatory Networks. - Yu-Ting Hsiao; Wei-Po Lee; Wei Yang; Stefan Müller 009; Christoph Flamm; Ivo L. Hofacker; Philipp Kügler (IEEE ACM Trans. Comput. Biol. Bioinform., 2016)

From elementary flux modes to elementary flux vectors: Metabolic pathway analysis with arbitrary linear flux constraints. - Steffen Klamt; Georg Regensburger; Matthias P. Gerstl; Christian Jungreuthmayer; Stefan Schuster; Radhakrishnan Mahadevan; Jürgen Zanghellini; Stefan Müller 009 (PLoS Comput. Biol., 2017)

Flux tope analysis: studying the coordination of reaction directions in metabolic networks. - Matthias P. Gerstl; Stefan Müller 009; Georg Regensburger; Jürgen Zanghellini (Bioinform., 2019)

On the Bijectivity of Families of Exponential/Generalized Polynomial Maps. - Stefan Müller 009; Josef Hofbauer; Georg Regensburger (SIAM J. Appl. Algebra Geom., 2019)

What makes a reaction network "chemical"? - Stefan Müller 009; Christoph Flamm; Peter F. Stadler (J. Cheminformatics, 2022)

Elementary vectors and autocatalytic sets for resource allocation in next-generation models of cellular growth. - Stefan Müller 009; Diana Széliová; Jürgen Zanghellini (PLoS Comput. Biol., 2022)

A New Decomposition of the Graph Laplacian and the Binomial Structure of Mass-Action Systems. - Stefan Müller 009 (J. Nonlinear Sci., 2023)

A SageMath Package for Elementary and Sign Vectors with Applications to Chemical Reaction Networks. - Marcus S. Aichmayr; Stefan Müller 009; Georg Regensburger (ICMS, 2024)

Sufficient Conditions for Linear Stability of Complex-Balanced Equilibria in Generalized Mass-Action Systems. - Stefan Müller 009; Georg Regensburger (SIAM J. Appl. Dyn. Syst., 2024)