Gao M, Veil M, Rosenblatt M, Riesle AJ, Gebhard A, Hass H, Buryanova L, Yampolsky LY, Gruening B, Ulianov VS, Timmer J, and Onichtchouk D. Pluripotency factors determine gene expression repertoire at zygotic genome activation. Nature Communications 2022;13:788.
Wieland FG, Hauber AL, Rosenblatt M, Tonsing C, and Timmer J. On structural and practical identifiability. Current Opinion in Systems Biology 2021;25:60–69.
Ochoa-Fernandez R, Abel NB, Wieland FG, Schlegel J, Koch LA, Miller JB, Engesser R, Giuriani G, Brandl SM, Timmer J, Weber W, Ott T, Simon R, and Zurbriggen MD. Optogenetic control of gene expression in plants in the presence of ambient white light. Nature Methods 2020;17:717–725.
Hauber AL, Engesser R, Vanlier J, and Timmer J. Estimating chain length for time delays in dynamical systems using profile likelihood. Bioinformatics 2019;36:1848–1854.
Lill D, Timmer J, and Kaschek D. Local Riemannian geometry of model manifolds and its implications for practical parameter identifiability. PLoS One 2019;14:e0217837.
Lucarelli P, Schilling M, Kreutz C, Vlasov A, Boehm ME, Iwamoto N, Steiert B, Lattermann S, Wäsch M, Stepath M, Matter MS, Heikenwälder M, Hoffmann K, Deharde D, Damm G, Seehofer D, Muciek M, Gretz N, Lehmann WD, Timmer J, et al. Resolving the combinatorial complexity of SMAD protein complex formation and its link to gene expression. Cell Systems 2018;6:75–89.e11.
Maiwald T, Hass H, Steiert B, Vanlier J, Engesser R, Raue A, Kipkeew F, Bock HH, Kaschek D, Kreutz C, and Timmer J. Driving the model to its limit: Profile likelihood based model reduction. PLoS One 2016;11:e0162366.
Merkle R, Steiert B, Salopiata F, Depner S, Raue A, Iwamoto N, Schelker M, Hass H, Wäsch M, Böhm ME, Mücke O, Lipka DB, Plass C, Lehmann WD, Kreutz C, Timmer J, Schilling M, and Klingmüller U. Identification of cell type-specific differences in erythropoietin receptor signaling in primary erythroid and lung cancer cells. PLoS Computational Biology 2016;12:e1005049.
Raue A, Kreutz C, Theis FJ, and Timmer J. Joining forces of Bayesian and frequentist methodology: A study for inference in the presence of non-identifiability. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 2013;371:20110544.
Rausenberger J, Tscheuschler A, Nordmeier W, Wüst F, Timmer J, Schäfer E, Fleck C, and Hiltbrunner A. Photoconversion and nuclear trafficking cycles determine phytochrome A’s response profile to far-red light. Cell 2011;146:813–825.
Institute of Medical Biometry and Statistics,
Faculty of Medicine and Medical Center –
University of Freiburg
