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)

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)