Employing NeuGen 2.0 to Automatically Generate Realistic Morphologies of Hippocampal Neurons and Neural Networks in 3D. - Susanne Wolf; Stephan Grein; Gillian Queisser (Neuroinformatics, 2013)

1D-3D hybrid modeling - from multi-compartment models to full resolution models in space and time. - Stephan Grein; Martin Stepniewski; Sebastian Reiter 002; Markus M. Knodel; Gillian Queisser (Frontiers Neuroinformatics, 2014)

Density Visualization Pipeline: A Tool for Cellular and Network Density Visualization and Analysis. - Stephan Grein; Guanxiao Qi; Gillian Queisser (Frontiers Comput. Neurosci., 2020)

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)

IntestLine: a shiny-based application to map the rolled intestinal tissue onto a line. - Altay Yuzeir; David Alejandro Bejarano; Stephan Grein; Jan Hasenauer; Andreas Schlitzer; Jiangyan Yu (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)

Efficient parameter estimation for ODE models of cellular processes using semi-quantitative data. - Domagoj Doresic; Stephan Grein; Jan Hasenauer (Bioinform., 2024)