Fröhlich K, Brombacher E, Fahrner M, Vogele D, Kook L, Pinter N, Bronsert P, Timme-Bronsert S, Schmidt A, Bärenfaller K, Kreutz C, and Schilling O. Benchmarking of analysis strategies for data-independent acquisition proteomics using a large-scale dataset comprising inter-patient heterogeneity. Nature Communications 2022;13:2622.
Schmiester L, Schälte Y, Bergmann FT, […], Kreutz C, et al. PEtab-Interoperable specification of parameter estimation problems in systems biology. PLoS Computational Biology 2021;17:e1008646.
Kreutz C, Can NS, Bruening RS, Meyberg R, Mérai Z, Fernandez-Pozo N, and Rensing SA. A blind and independent benchmark study for detecting differentially methylated regions in plants. Bioinformatics 2020;36:3314–3321.
Hass H, Loos C, Raimúndez-Álvarez E, Timmer J, Hasenauer J, and Kreutz C. Benchmark problems for dynamic modeling of intracellular processes. Bioinformatics 2019;35:3073–3082.
Kreutz C. Guidelines for benchmarking of optimization-based approaches for fitting mathematical models. Genome Biology 2019;20:281.
Becker K, Bluhm A, Casas-Vila N, Dinges N, Dejung M, Sayols S, Kreutz C, Roignant JY, Butter F, and Legewie S. Quantifying post-transcriptional regulation in the development of Drosophila melanogaster. Nature communications 2018;9:1–14.
Kreutz C. An easy and efficient approach for testing identifiability. Bioinformatics 2018;34:1913–1921.
Steiert B, Timmer J, and Kreutz C. L1 regularization facilitates detection of cell type-specific parameters in dynamical systems. Bioinformatics 2016;32:i718–i726.
Raue A, Steiert B, Schelker M, Kreutz C, Maiwald T, Hass H, Vanlier J, Tönsing C, Adlung L, Engesser R, Mader W, Heinemann T, Hasenauer J, Schilling M, Höfer T, Klipp E, Theis F, Klingmüller U, Schöberl B, and Timmer J. Data2Dynamics: A modeling environment tailored to parameter estimation in dynamical systems. Bioinformatics 2015;31:3558–3560.
Kreutz C, Raue A, and Timmer J. Likelihood based observability analysis and confidence intervals for predictions of dynamic models. BMC Systems Biology 2012;6:120.
Institute of Medical Biometry and Statistics,
Faculty of Medicine and Medical Center –
University of Freiburg
