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Lessons learned from quantitative dynamical modeling in systems biology.
Raue A, Schilling M, Bachmann J, Matteson A, Schelker M, Kaschek D, Hug S, Kreutz C, Harms BD, Theis FJ, Klingmüller U, Timmer J. Raue A, et al. PLoS One. 2013 Sep 30;8(9):e74335. doi: 10.1371/journal.pone.0074335. eCollection 2013. PLoS One. 2013. PMID: 24098642 Free PMC article.
Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems.
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, Timmer J. Raue A, et al. Bioinformatics. 2015 Nov 1;31(21):3558-60. doi: 10.1093/bioinformatics/btv405. Epub 2015 Jul 3. Bioinformatics. 2015. PMID: 26142188
We present a modeling environment for MATLAB that pioneers these challenges. The numerically expensive parts of the calculations such as the solving of the differential equations and of the associated sensitivity system are parallelized and automatically compiled into effi …
We present a modeling environment for MATLAB that pioneers these challenges. The numerically expensive parts of the calculations such …
iVUN: interactive Visualization of Uncertain biochemical reaction Networks.
Vehlow C, Hasenauer J, Kramer A, Raue A, Hug S, Timmer J, Radde N, Theis FJ, Weiskopf D. Vehlow C, et al. Among authors: raue a. BMC Bioinformatics. 2013;14 Suppl 19(Suppl 19):S2. doi: 10.1186/1471-2105-14-S19-S2. Epub 2013 Nov 12. BMC Bioinformatics. 2013. PMID: 24564335 Free PMC article.
Model Based Targeting of IL-6-Induced Inflammatory Responses in Cultured Primary Hepatocytes to Improve Application of the JAK Inhibitor Ruxolitinib.
Sobotta S, Raue A, Huang X, Vanlier J, Jünger A, Bohl S, Albrecht U, Hahnel MJ, Wolf S, Mueller NS, D'Alessandro LA, Mueller-Bohl S, Boehm ME, Lucarelli P, Bonefas S, Damm G, Seehofer D, Lehmann WD, Rose-John S, van der Hoeven F, Gretz N, Theis FJ, Ehlting C, Bode JG, Timmer J, Schilling M, Klingmüller U. Sobotta S, et al. Among authors: raue a. Front Physiol. 2017 Oct 9;8:775. doi: 10.3389/fphys.2017.00775. eCollection 2017. Front Physiol. 2017. PMID: 29062282 Free PMC article.
Dynamic mathematical modeling of IL13-induced signaling in Hodgkin and primary mediastinal B-cell lymphoma allows prediction of therapeutic targets.
Raia V, Schilling M, Böhm M, Hahn B, Kowarsch A, Raue A, Sticht C, Bohl S, Saile M, Möller P, Gretz N, Timmer J, Theis F, Lehmann WD, Lichter P, Klingmüller U. Raia V, et al. Among authors: raue a. Cancer Res. 2011 Feb 1;71(3):693-704. doi: 10.1158/0008-5472.CAN-10-2987. Epub 2010 Dec 2. Cancer Res. 2011. PMID: 21127196
Driving the Model to Its Limit: Profile Likelihood Based Model Reduction.
Maiwald T, Hass H, Steiert B, Vanlier J, Engesser R, Raue A, Kipkeew F, Bock HH, Kaschek D, Kreutz C, Timmer J. Maiwald T, et al. Among authors: raue a. PLoS One. 2016 Sep 2;11(9):e0162366. doi: 10.1371/journal.pone.0162366. eCollection 2016. PLoS One. 2016. PMID: 27588423 Free PMC article.
37 results