Simulation of biochemical networks using COPASI: a complex pathway simulator. - Sven Sahle; Ralph Gauges; Jürgen Pahle; Natalia Simus; Ursula Kummer; Stefan Hoops; Christine Lee; Mudita Singhal; Liang Xu; Pedro Mendes 001 (WSC, 2006)

Approaches to complexity reduction in a systems biology research environment (SYCAMORE). - Irina Surovtsova; Sven Sahle; Jürgen Pahle; Ursula Kummer (WSC, 2006)

A model diagram layout extension for SBML. - Ralph Gauges; Ursula Rost; Sven Sahle; Katja Wegner (Bioinform., 2006)

COPASI - a COmplex PAthway SImulator. - Stefan Hoops; Sven Sahle; Ralph Gauges; Christine Lee; Jürgen Pahle; Natalia Simus; Mudita Singhal; Liang Xu; Pedro Mendes 001; Ursula Kummer (Bioinform., 2006)

SYCAMORE - a systems biology computational analysis and modeling research environment. - Andreas Weidemann; Stefan Richter 002; Matthias Stein; Sven Sahle; Ralph Gauges; Razif R. Gabdoulline; Irina Surovtsova; Nils Semmelrock; Bruno Besson; Isabel Rojas; Rebecca C. Wade; Ursula Kummer (Bioinform., 2008)

Accessible methods for the dynamic time-scale decomposition of biochemical systems. - Irina Surovtsova; Natalia Simus; Thomas Lorenz; Artjom König; Sven Sahle; Ursula Kummer (Bioinform., 2009)

Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language. - Dagmar Waltemath; Richard R. Adams; Frank T. Bergmann; Michael Hucka; Fedor A. Kolpakov; Andrew K. Miller; Ion I. Moraru; David P. Nickerson; Sven Sahle; Jacky L. Snoep; Nicolas Le Novère (BMC Syst. Biol., 2011)

Minimum Information About a Simulation Experiment (MIASE). - Dagmar Waltemath; Richard R. Adams; Daniel A. Beard; Frank T. Bergmann; Upinder S. Bhalla; Randall Britten; Vijayalakshmi Chelliah; Mike T. Cooling; Jonathan Cooper; Edmund J. Crampin; Alan Garny; Stefan Hoops; et al. (PLoS Comput. Biol., 2011)

Simplification of biochemical models: a general approach based on the analysis of the impact of individual species and reactions on the systems dynamics. - Irina Surovtsova; Natalia Simus; Katrin Hübner; Sven Sahle; Ursula Kummer (BMC Syst. Biol., 2012)

A termination criterion for parameter estimation in stochastic models in systems biology. - Christoph Zimmer; Sven Sahle (Biosyst., 2015)

The Systems Biology Markup Language (SBML) Level 3 Package: Layout, Version 1 Core. - Ralph Gauges; Ursula Rost; Sven Sahle; Katja Wengler; Frank Thomas Bergmann (J. Integr. Bioinform., 2015)

Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions. - Michael Hucka; Frank T. Bergmann; Andreas Dräger; Stefan Hoops; Sarah M. Keating; Nicolas Le Novère; Chris J. Myers; Brett G. Olivier; Sven Sahle; James C. Schaff; Lucian P. Smith; Dagmar Waltemath; et al. (J. Integr. Bioinform., 2015)

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core. - Michael Hucka; Frank T. Bergmann; Stefan Hoops; Sarah M. Keating; Sven Sahle; James C. Schaff; Lucian P. Smith; Darren J. Wilkinson (J. Integr. Bioinform., 2015)

Piecewise parameter estimation for stochastic models in COPASI. - Frank T. Bergmann; Sven Sahle; Christoph Zimmer (Bioinform., 2016)

Comparison of approaches for parameter estimation on stochastic models: Generic least squares versus specialized approaches. - Christoph Zimmer; Sven Sahle (Comput. Biol. Chem., 2016)

Reducing local minima in fitness landscapes of parameter estimation by using piecewise evaluation and state estimation. - Christoph Zimmer; Frank T. Bergmann; Sven Sahle (CoRR, 2016)

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3). - Frank T. Bergmann; Jonathan Cooper; Matthias König 003; Ion I. Moraru; David P. Nickerson; Nicolas Le Novère; Brett G. Olivier; Sven Sahle; Lucian P. Smith; Dagmar Waltemath (J. Integr. Bioinform., 2018)

SBML Level 3 package: Render, Version 1, Release 1. - Frank T. Bergmann; Sarah M. Keating; Ralph Gauges; Sven Sahle; Katja Wengler (J. Integr. Bioinform., 2018)

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core. - Michael Hucka; Frank T. Bergmann; Andreas Dräger; Stefan Hoops; Sarah M. Keating; Nicolas Le Novère; Chris J. Myers; Brett G. Olivier; Sven Sahle; James C. Schaff; Lucian P. Smith; Dagmar Waltemath; et al. (J. Integr. Bioinform., 2018)

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core. - Michael Hucka; Frank T. Bergmann; Andreas Dräger; Stefan Hoops; Sarah M. Keating; Nicolas Le Novère; Chris J. Myers; Brett G. Olivier; Sven Sahle; James C. Schaff; Lucian P. Smith; Dagmar Waltemath; et al. (J. Integr. Bioinform., 2018)

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2. - Michael Hucka; Frank T. Bergmann; Claudine Chaouiya; Andreas Dräger; Stefan Hoops; Sarah M. Keating; Matthias König 003; Nicolas Le Novère; Chris J. Myers; Brett G. Olivier; Sven Sahle; James C. Schaff; et al. (J. Integr. Bioinform., 2019)

PEtab - Interoperable specification of parameter estimation problems in systems biology. - Leonard Schmiester; Yannik Schälte; Frank T. Bergmann; Tacio Camba; Erika Dudkin; Janine Egert; Fabian Fröhlich; Lara Fuhrmann; Adrian L. Hauber; Svenja Kemmer; Polina A. Lakrisenko; Carolin Loos; et al. (PLoS Comput. Biol., 2021)

Stochastic dynamics of Type-I interferon responses. - Benjamin D. Maier; Luis U. Aguilera; Sven Sahle; Pascal Mutz; Priyata Kalra; Christopher Dächert; Ralf Bartenschlager; Marco Binder; Ursula Kummer (PLoS Comput. Biol., 2022)

DuneCopasi: A multi-compartment reaction-diffusion simulator for systems biology. - Santiago Ospina De Los Ríos; Peter Bastian; Liam Keegan; Sven Sahle; Dylan Vermoortele; Lilija Wehling (J. Open Source Softw., 2024)