Making predictions about robustness and flexibility from metabolic network structure. - Stefan Schuster; Steffen Klamt; Jörg Stelling (German Conference on Bioinformatics, 2003)

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. - Michael Hucka; Andrew Finney; Herbert M. Sauro; H. Bolouri; John C. Doyle 001; Hiroaki Kitano; Adam P. Arkin; Benjamin J. Bornstein; Dennis Bray; Athel Cornish-Bowden; Autumn A. Cuellar; Serge Dronov; et al. (Bioinform., 2003)

FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps. - Steffen Klamt; Jörg Stelling; Martin Ginkel; Ernst Dieter Gilles (Bioinform., 2003)

Optimal phase-tracking of the nonlinear circadian oscillator. - Neda Bagheri; Jörg Stelling; Francis J. Doyle (ACC, 2005)

Sensitivity analysis of oscillatory (bio)chemical systems. - Daniel E. Zak; Jörg Stelling; Francis J. Doyle III (Comput. Chem. Eng., 2005)

Accelerating the Computation of Elementary Modes Using Pattern Trees. - Marco Terzer; Jörg Stelling (WABI, 2006)

Quantitative performance metrics for robustness in circadian rhythms. - Neda Bagheri; Jörg Stelling; Francis J. Doyle III (Bioinform., 2007)

Elementary flux modes - state-of-the-art implementation and scope of application. - Marco Terzer; Jörg Stelling (BMC Syst. Biol., 2007)

Computational design of synthetic gene circuits with composable parts. - Mario A. Marchisio; Jörg Stelling (Bioinform., 2008)

Large-scale computation of elementary flux modes with bit pattern trees. - Marco Terzer; Jörg Stelling (Bioinform., 2008)

Circadian Phase Resetting via Single and Multiple Control Targets. - Neda Bagheri; Jörg Stelling; Francis J. Doyle III (PLoS Comput. Biol., 2008)

Synthetic Gene Network Computational Design. - Mario A. Marchisio; Jörg Stelling (ISCAS, 2009)

Parallel Extreme Ray and Pathway Computation. - Marco Terzer; Jörg Stelling (PPAM (2), 2009)

Precise Regulation of Gene Expression Dynamics Favors Complex Promoter Architectures. - Dirk Müller; Jörg Stelling (PLoS Comput. Biol., 2009)

Automatic Control in Systems Biology. - Henry Mirsky; Jörg Stelling; Rudiyanto Gunawan; Neda Bagheri; Stephanie R. Taylor; Eric Kwei; Jason E. Shoemaker; Francis J. Doyle III (Handbook of Automation, 2009)

Graph-Based Decomposition of Biochemical Reaction Networks into Monotone Subsystems. - Hans-Michael Kaltenbach; Simona Constantinescu; Justin Feigelman; Jörg Stelling (WABI, 2011)

Efficient characterization of high-dimensional parameter spaces for systems biology. - Elías Zamora-Sillero; Marc Hafner; Ariane Ibig; Jörg Stelling; Andreas Wagner (BMC Syst. Biol., 2011)

Automatic Design of Digital Synthetic Gene Circuits. - Mario A. Marchisio; Jörg Stelling (PLoS Comput. Biol., 2011)

A specialized ODE integrator for the efficient computation of parameter sensitivities. - Pedro Gonnet; Sotiris Dimopoulos; Lukas Widmer; Jörg Stelling (BMC Syst. Biol., 2012)

System-Level Insights into Yeast Metabolism by Thermodynamic Analysis of Elementary Flux Modes. - Stefan J. Jol; Anne Kümmel; Marco Terzer; Jörg Stelling; Matthias Heinemann (PLoS Comput. Biol., 2012)

Near-optimal experimental design for model selection in systems biology. - Alberto Giovanni Busetto; Alain Hauser; Gabriel Krummenacher; Mikael Sunnåker; Sotiris Dimopoulos; Cheng Soon Ong; Jörg Stelling; Joachim M. Buhmann (Bioinform., 2013)

MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks. - Mathias Ganter; Thomas Bernard; Sébastien Moretti; Jörg Stelling; Marco Pagni (Bioinform., 2013)

Modular, rule-based modeling for the design of eukaryotic synthetic gene circuits. - Mario A. Marchisio; Moreno Colaiacovo; Ellis Whitehead; Jörg Stelling (BMC Syst. Biol., 2013)

Accurate cell segmentation in microscopy images using membrane patterns. - Sotiris Dimopoulos; Christian E. Mayer; Fabian Rudolf; Jörg Stelling (Bioinform., 2014)

Topological augmentation to infer hidden processes in biological systems. - Mikael Sunnåker; Elías Zamora-Sillero; Adrián López García de Lomana; Florian Rudroff; Uwe Sauer; Jörg Stelling; Andreas Wagner (Bioinform., 2014)

A method for inverse bifurcation of biochemical switches: inferring parameters from dose response curves. - Irene Otero-Muras; Pencho Yordanov; Jörg Stelling (BMC Syst. Biol., 2014)

Efficient Characterization of Parametric Uncertainty of Complex (Bio)chemical Networks. - Claudia Schillings; Mikael Sunnåker; Jörg Stelling; Christoph Schwab (PLoS Comput. Biol., 2015)

Deterministic Description of Biochemical Networks. - Jörg Stelling; Hans-Michael Kaltenbach (Encyclopedia of Systems and Control, 2015)

Efficient Reconstruction of Predictive Consensus Metabolic Network Models. - Ruben G. A. van Heck; Mathias Ganter; Vítor A. P. Martins dos Santos; Jörg Stelling (PLoS Comput. Biol., 2016)

Modular Parameter Identification of Biomolecular Networks. - Moritz Lang; Jörg Stelling (SIAM J. Sci. Comput., 2016)

Chemical Reaction Network Theory elucidates sources of multistability in interferon signaling. - Irene Otero-Muras; Pencho Yordanov; Jörg Stelling (PLoS Comput. Biol., 2017)

BioSwitch: a tool for the detection of bistability and multi-steady state behaviour in signalling and gene regulatory networks. - Pencho Yordanov; Jörg Stelling; Irene Otero-Muras (Bioinform., 2020)

TopoFilter: a MATLAB package for mechanistic model identification in systems biology. - Mikolaj Rybinski; Simon Möller; Mikael Sunnåker; Claude Lormeau; Jörg Stelling (BMC Bioinform., 2020)

Microbial Community Decision Making Models in Batch and Chemostat Cultures. - Axel Theorell; Jörg Stelling (CMSB, 2021)

Population Design for Synthetic Gene Circuits. - Baptiste Turpin; Eline Y. Bijman; Hans-Michael Kaltenbach; Jörg Stelling (CMSB, 2021)

Probabilistic thermodynamic analysis of metabolic networks. - Mattia G. Gollub; Hans-Michael Kaltenbach; Jörg Stelling (Bioinform., 2021)

PolyRound: polytope rounding for random sampling in metabolic networks. - Axel Theorell; Johann F. Jadebeck; Katharina Nöh; Jörg Stelling (Bioinform., 2022)

Systems and Synthetic Biology. - Mustafa Hani Khammash; Jörg Stelling (Proc. IEEE, 2022)

Metabolic Networks, Microbial Consortia, and Analogies to Smart Grids. - Axel Theorell; Jörg Stelling (Proc. IEEE, 2022)

Assumptions on decision making and environment can yield multiple steady states in microbial community models. - Axel Theorell; Jörg Stelling (BMC Bioinform., 2023)

Efficient design of synthetic gene circuits under cell-to-cell variability. - Baptiste Turpin; Eline Y. Bijman; Hans-Michael Kaltenbach; Jörg Stelling (BMC Bioinform., 2023)

Minimal Metabolic Exchanges for Microbial Communities in a Chemostat at Steady State. - Alix Moawad; Jörg Stelling (CMSB, 2025)

Optimal Input Design for Model Selection in Systems with Cell-to-Cell Variability. - Andrea Stallvik; Hans-Michael Kaltenbach; Jörg Stelling (CMSB, 2025)