PESTO: parameter estimation toolbox P Stapor, D Weindl, B Ballnus, S Hug, C Loos, A Fiedler, S Krause, ... Bioinformatics 34 (4), 705-707, 2018 | 102 | 2018 |
PEtab—Interoperable specification of parameter estimation problems in systems biology L Schmiester, Y Schälte, FT Bergmann, T Camba, E Dudkin, J Egert, ... PLOS Computational Biology 17 (1), e1008646, 2021 | 65 | 2021 |
AMICI: High-performance sensitivity analysis for large ordinary differential equation models F Fröhlich, D Weindl, Y Schälte, D Pathirana, Ł Paszkowski, GT Lines, ... Bioinformatics 37 (20), 3676-3677, 2021 | 45 | 2021 |
Benchmarking of numerical integration methods for ODE models of biological systems P Städter, Y Schälte, L Schmiester, J Hasenauer, PL Stapor Scientific reports 11 (1), 1-11, 2021 | 45 | 2021 |
Optimization and profile calculation of ODE models using second order adjoint sensitivity analysis P Stapor, F Fröhlich, J Hasenauer Bioinformatics 34 (13), i151-i159, 2018 | 41* | 2018 |
Challenges in the calibration of large-scale ordinary differential equation models EM Kapfer, P Stapor, J Hasenauer IFAC-PapersOnLine 52 (26), 58-64, 2019 | 17 | 2019 |
Convergence of the Gutt Star Product SW Chiara Esposito, Paul Stapor Journal of Lie theory 27, 2017 | 17* | 2017 |
Evaluation of Derivative-Free Optimizers for Parameter Estimation in Systems Biology Y Schälte, P Stapor, J Hasenauer IFAC-PapersOnLine 51 (19), 98-101, 2018 | 15 | 2018 |
Cell-to-cell variability in JAK2/STAT5 pathway components and cytoplasmic volumes defines survival threshold in erythroid progenitor cells L Adlung, P Stapor, C Tönsing, L Schmiester, LE Schwarzmüller, ... Cell Reports 36 (6), 109507, 2021 | 14 | 2021 |
Mini-batch optimization enables training of ODE models on large-scale datasets P Stapor, L Schmiester, C Wierling, S Merkt, D Pathirana, BMH Lange, ... Nature Communications 13 (1), 1-17, 2022 | 12 | 2022 |
The interplay of viral loads, clinical presentation, and serological responses in SARS-CoV-2–Results from a prospective cohort of outpatient COVID-19 cases K Puchinger, N Castelletti, R Rubio-Acero, C Geldmacher, TM Eser, ... Virology 569, 37-43, 2022 | 11 | 2022 |
pyPESTO: A modular and scalable tool for parameter estimation for dynamic models Y Schälte, F Fröhlich, PJ Jost, J Vanhoefer, D Pathirana, P Stapor, ... arXiv preprint arXiv:2305.01821, 2023 | 7 | 2023 |
Integrative modelling of reported case numbers and seroprevalence reveals time-dependent test efficiency and infection rates L Contento, N Castelletti, E Raimúndez, R Le Gleut, Y Schälte, P Stapor, ... medRxiv, 2021 | 5* | 2021 |
Efficient computation of steady states in large-scale ODE models of biochemical reaction networks GT Lines, Ł Paszkowski, L Schmiester, D Weindl, P Stapor, J Hasenauer IFAC-PapersOnLine 52 (26), 32-37, 2019 | 4 | 2019 |
Dirac mixture distributions for the approximation of mixed effects models D Wang, P Stapor, J Hasenauer IFAC-PapersOnLine 52 (26), 200-206, 2019 | 4 | 2019 |
Efficient computation of adjoint sensitivities at steady-state in ODE models of biochemical reaction networks P Lakrisenko, P Stapor, S Grein, Ł Paszkowski, D Pathirana, F Fröhlich, ... bioRxiv, 2022 | 2 | 2022 |
A more expressive spline representation for SBML models improves code generation performance in AMICI L Contento, P Stapor, D Weindl, J Hasenauer bioRxiv, 2023.06. 29.547120, 2023 | | 2023 |
Efficient computational methods for parameter estimation of ordinary differential equation and mixed-effect models in systems biology P Stapor Technische Universität München, 2021 | | 2021 |
Convergence of the Gutt Star Product: A strict Deformation Quantization P Stapor arXiv preprint arXiv:1604.05873, 2016 | | 2016 |