PeriNAA

^{Dorešić, D., S. Grein, and J. Hasenauer (2024). "Efficient parameter estimation for ODE models of cellular processes using semi-quantitative data." Bioinformatics 40(Supplement_1): i558–i566. doi.org/10.1093/bioinformatics/btae210.}

^{Krause, N., and A. Wegner (2024). "N-acetyl-aspartate metabolism at the interface of cancer, immunity, and neurodegeneration." Current Opinion Biotechnology 85. doi.org/10.1016/j.copbio.2023.103051.}

^{Lakrisenko, P., D. Pathirana, D. Weindl, and J. Hasenauer (2024). "Benchmarking methods for computing local sensitivities in ordinary differential equation models at dynamic and steady states." PLoS One 19(10). doi.org/10.1371/journal.pone.0312148}

Lakrisenko, P., P. Stapor, S. Grein, Ł. Paszkowski, D. Pathirana, F. Fröhlich, G. T. Lines, D. Weindl, and J. Hasenauer (2023). "Efficient computation of adjoint sensitivities at steady-state in ODE models of biochemical reaction networks." PLoS Comput Biol 19(1): e1010783. PeriNAA  doi.org/10.1371/journal.pcbi.1010783.

Schälte, Y., F. Fröhlich, P. J. Jost, J. Vanhoefer, D. Pathirana, P. Stapor, P. Lakrisenko, D. Wang, E. Raimúndez, S. Merkt, L. Schmiester, P. Städter, S. Grein, E. Dudkin, D. Doresic, D. Weindl, and J. Hasenauer (2023). "pyPESTO: a modular and scalable tool for parameter estimation for dynamic models." Bioinformatics 39(11): btad711. doi.org/10.1093/bioinformatics/btad711.

Zerbato, B., M. Gobbi, T. Ludwig, V. Brancato, A. Pessina, L. Brambilla, A. Wegner, and F. Chiaradonna (2023). "PGM3 inhibition shows cooperative effects with erastin inducing pancreatic cancer cell death via activation of the unfolded protein response." Front Oncol 13: 1125855. PeriNAA  doi.org/10.3389/fonc.2023.1125855.

Starke, C. and A. Wegner (2022). "MetAMDB: Metabolic Atom Mapping Database." Metabolites 12(2): 122. PeriNAA doi.org/10.3390/metabo12020122.

Fröhlich, F., D. Weindl, Y. Schälte, D. Pathirana, Ł. Paszkowski, G. T. Lines, P. Stapor and J. Hasenauer (2021). "AMICI: high-performance sensitivity analysis for large ordinary differential equation models." Bioinformatics 37(20): 3676. PeriNAA & INCOME doi.org/10.1093/bioinformatics/btab227.

Lakrisenko, P. and D. Weindl (2021). "Dynamic models for metabolomics data integration." Curr Opin Syst Biol 28: 100358. PeriNAA doi.org/10.1016/j.coisb.2021.100358.

Schmiester, L., Y. Schälte, F. T. Bergmann, T. Camba, E. Dudkin, J. Egert, F. Fröhlich, L. Fuhrmann, A. L. Hauber, S. Kemmer, P. Lakrisenko, C. Loos, S. Merkt, W. Müller, D. Pathirana, E. Raimúndez, L. Refisch, M. Rosenblatt, P. L. Stapor, P. Städter, D. Wang, F.-G. Wieland, J. R. Banga, J. Timmer, A. F. Villaverde, S. Sahle, C. Kreutz, J. Hasenauer and D. Weindl (2021). "PEtab—Interoperable specification of parameter estimation problems in systems biology." PLoS Comput. Biol. 17(1). PeriNAA, INCOME, SYS-Stomach, doi.org/10.1371/journal.pcbi.1008646.

Krause, N., and A. Wegner (2020). "Fructose Metabolism in Cancer." Cells 9(12): 2635. doi.org/10.3390/cells9122635.