Efficient exact inference for dynamical systems with noisy measurements using sequential approximate Bayesian computation. - Yannik Schälte; Jan Hasenauer (Bioinform., 2020)

Efficient parameterization of large-scale dynamic models based on relative measurements. - Leonard Schmiester; Yannik Schälte; Fabian Fröhlich; Jan Hasenauer; Daniel Weindl (Bioinform., 2020)

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)

pyABC: Efficient and robust easy-to-use approximate Bayesian computation. - Yannik Schälte; Emmanuel Klinger; Emad Alamoudi; Jan Hasenauer (J. Open Source Softw., 2022)

BayesFlow: Amortized Bayesian Workflows With Neural Networks. - Stefan T. Radev; Marvin Schmitt; Lukas Schumacher; Lasse Elsemüller; Valentin Pratz; Yannik Schälte; Ullrich Köthe; Paul-Christian Bürkner (J. Open Source Softw., 2023)

FitMultiCell: simulating and parameterizing computational models of multi-scale and multi-cellular processes. - Emad Alamoudi; Yannik Schälte; Robert Müller; Jörn Starruß; Nils Bundgaard; Frederik Graw; Lutz Brusch; Jan Hasenauer (Bioinform., 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)

An amortized approach to non-linear mixed-effects modeling based on neural posterior estimation. - Jonas Arruda; Yannik Schälte; Clemens Peiter; Olga Teplytska; Ulrich Jaehde; Jan Hasenauer (ICML, 2024)

Missing data in amortized simulation-based neural posterior estimation. - Zijian Wang; Jan Hasenauer; Yannik Schälte (PLoS Comput. Biol., 2024)