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Dilan Pathirana
Dilan Pathirana
Verified email at uni-bonn.de
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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
692021
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
482021
A protocol for dynamic model calibration
AF Villaverde, D Pathirana, F Fröhlich, J Hasenauer, JR Banga
Briefings in Bioinformatics 23 (1), bbab387, 2022
462022
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
292019
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
132022
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
102023
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
62021
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
52021
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
52021
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
42017
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
32023
Predicting blood pressure in aortas treated for coarctation
D Pathirana, B Johnston, P Johnston
ANZIAM Journal 57, C32-C50, 2015
32015
Exploration of methods for computing sensitivities in ODE models at dynamic and steady states
P Lakrisenko, D Pathirana, D Weindl, J Hasenauer
arXiv preprint arXiv:2405.16524, 2024
2024
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
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Articles 1–18