AMICI: high-performance sensitivity analysis for large ordinary differential equation models. - Fabian Fröhlich; Daniel Weindl; Yannik Schälte; Dilan Pathirana; Lukasz Paszkowski; Glenn Terje Lines; Paul Stapor; Jan Hasenauer (Bioinform., 2021)

yaml2sbml: Human-readable and -writable specification of ODE models and their conversion to SBML. - Jakob Vanhoefer; Marta R. A. Matos; Dilan Pathirana; Yannik Schälte; Jan Hasenauer (J. Open Source Softw., 2021)

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)

A protocol for dynamic model calibration. - Alejandro F. Villaverde; Dilan Pathirana; Fabian Fröhlich; Jan Hasenauer; Julio R. Banga (Briefings Bioinform., 2022)

Efficient computation of adjoint sensitivities at steady-state in ODE models of biochemical reaction networks. - Polina A. Lakrisenko; Paul Stapor; Stephan Grein; Lukasz Paszkowski; Dilan Pathirana; Fabian Fröhlich; Glenn Terje Lines; Daniel Weindl; Jan Hasenauer (PLoS Comput. Biol., 2023)

pyPESTO: a modular and scalable tool for parameter estimation for dynamic models. - Yannik Schälte; Fabian Fröhlich; Paul J. Jost; Jakob Vanhoefer; Dilan Pathirana; Paul Stapor; Polina A. Lakrisenko; Dantong Wang; Elba Raimúndez-Álvarez; Simon Merkt; Leonard Schmiester; Philipp Städter; et al. (Bioinform., 2023)

Non-Negative Universal Differential Equations With Applications in Systems Biology. - Maren Philipps; Antonia Körner; Jakob Vanhoefer; Dilan Pathirana; Jan Hasenauer (CoRR, 2024)