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 |
A protocol for dynamic model calibration AF Villaverde, D Pathirana, F Fröhlich, J Hasenauer, JR Banga Briefings in Bioinformatics 23 (1), bbab387, 2022 | 43 | 2022 |
SerpinB2 inhibits migration and promotes a resolution phase signature in large peritoneal macrophages WA Schroder, TD Hirata, TT Le, J Gardner, GM Boyle, J Ellis, E Nakayama, ... Scientific Reports 9 (1), 12421, 2019 | 28 | 2019 |
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), 34, 2022 | 12 | 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, ... Bioinformatics 39 (11), btad711, 2023 | 6 | 2023 |
pyPESTO—Parameter EStimation TOolbox for python (0.2. 7) Y Schälte, F Fröhlich, P Stapor, J Vanhoefer, D Weindl, PJ Jost, D Wang, ... URL https://zenodo. org/record/2553546, 2021 | 6 | 2021 |
pyPESTO—Parameter EStimation TOolbox for python Y Schälte, F Fröhlich, P Stapor, J Vanhoefer, D Weindl, PJ Jost, D Wang, ... See https://github. com/ICB-DCM/pyPESTO, 2021 | 5 | 2021 |
The effects of tapering and artery wall stiffness on treatments for Coarctation of the Aorta D Pathirana, B Johnston, P Johnston Computer Methods in Biomechanics and Biomedical Engineering 20 (14), 1512-1524, 2017 | 4 | 2017 |
yaml2sbml: Human-readable and-writable specification of ODE models and their conversion to SBML J Vanhoefer, R Marta, D Pathirana, Y Schälte, J Hasenauer Journal of Open Source Software 6 (61), 3215, 2021 | 3 | 2021 |
Predicting blood pressure in aortas treated for coarctation D Pathirana, B Johnston, P Johnston ANZIAM Journal 57, C32-C50, 2015 | 3 | 2015 |
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, ... PLOS Computational Biology 19 (1), e1010783, 2023 | 2 | 2023 |
Processivity and specificity of histone acetylation by the male-specific lethal complex AE Kiss, AV Venkatasubramani, D Pathirana, S Krause, AC Sparr, ... Nucleic Acids Research, gkae123, 2024 | | 2024 |
PEtab L Schmiester, Y Schälte, FT Bergmann, T Camba, E Dudkin, J Egert, ... | | 2021 |
The effect of including increased arterial stiffness in the upper body when modelling Coarctation of the Aorta D Pathirana, B Johnston, P Johnston Computer Methods in Biomechanics and Biomedical Engineering 22 (5), 475-489, 2019 | | 2019 |
Numerical Modelling of Blood Flow for Coarctation of the Aorta: Pre-and Post-treatment Simulations D Pathirana | | 2019 |
PREDICTING THE EFFECTS OF STRAIGHT AND TAPERED STENTS ON BLOOD FLOW PROPERTIES IN THE AORTA D Pathirana, BM Johnston, PR Johnston | | |