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Items: 15

1.

Model-based identification of TNFα-induced IKKβ-mediated and IκBα-mediated regulation of NFκB signal transduction as a tool to quantify the impact of drug-induced liver injury compounds.

Oppelt A, Kaschek D, Huppelschoten S, Sison-Young R, Zhang F, Buck-Wiese M, Herrmann F, Malkusch S, Krüger CL, Meub M, Merkt B, Zimmermann L, Schofield A, Jones RP, Malik H, Schilling M, Heilemann M, van de Water B, Goldring CE, Park BK, Timmer J, Klingmüller U.

NPJ Syst Biol Appl. 2018 Jun 11;4:23. doi: 10.1038/s41540-018-0058-z. eCollection 2018.

2.

A Dynamic Mathematical Model of Bile Acid Clearance in HepaRG Cells.

Kaschek D, Sharanek A, Guillouzo A, Timmer J, Weaver RJ.

Toxicol Sci. 2018 Jan 1;161(1):48-57. doi: 10.1093/toxsci/kfx199.

3.

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.

PLoS One. 2016 Sep 2;11(9):e0162366. doi: 10.1371/journal.pone.0162366. eCollection 2016.

4.

Customized Steady-State Constraints for Parameter Estimation in Non-Linear Ordinary Differential Equation Models.

Rosenblatt M, Timmer J, Kaschek D.

Front Cell Dev Biol. 2016 May 11;4:41. doi: 10.3389/fcell.2016.00041. eCollection 2016.

5.

Fast integration-based prediction bands for ordinary differential equation models.

Hass H, Kreutz C, Timmer J, Kaschek D.

Bioinformatics. 2016 Apr 15;32(8):1204-10. doi: 10.1093/bioinformatics/btv743. Epub 2015 Dec 17.

PMID:
26685309
6.

Higher-order Lie symmetries in identifiability and predictability analysis of dynamic models.

Merkt B, Timmer J, Kaschek D.

Phys Rev E Stat Nonlin Soft Matter Phys. 2015 Jul;92(1):012920. Epub 2015 Jul 28.

PMID:
26274260
7.

RPPanalyzer toolbox: an improved R package for analysis of reverse phase protein array data.

von der Heyde S, Sonntag J, Kaschek D, Bender C, Bues J, Wachter A, Timmer J, Korf U, Beißbarth T.

Biotechniques. 2014 Sep 1;57(3):125-35. doi: 10.2144/000114205. eCollection 2014.

8.

Pre-clustering of the B cell antigen receptor demonstrated by mathematically extended electron microscopy.

Fiala GJ, Kaschek D, Blumenthal B, Reth M, Timmer J, Schamel WW.

Front Immunol. 2013 Dec 6;4:427. doi: 10.3389/fimmu.2013.00427. eCollection 2013.

9.

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.

PLoS One. 2013 Sep 30;8(9):e74335. doi: 10.1371/journal.pone.0074335. eCollection 2013. Erratum in: PLoS One. 2013;8(12). doi:10.1371/annotation/ea0193d8-1f7f-492a-b0b7-d877629fdcee. Schelke, Max [corrected to Schelker, Max].

10.

Profile likelihood in systems biology.

Kreutz C, Raue A, Kaschek D, Timmer J.

FEBS J. 2013 Jun;280(11):2564-71. doi: 10.1111/febs.12276. Epub 2013 May 9. Review.

11.

Semi-automatic determination of cell surface areas used in systems biology.

Morath V, Keuper M, Rodriguez-Franco M, Deswal S, Fiala G, Blumenthal B, Kaschek D, Timmer J, Neuhaus G, Ehl S, Ronneberger O, Schamel WW.

Front Biosci (Elite Ed). 2013 Jan 1;5:533-45.

PMID:
23277009
12.

Heterogeneous kinetics of AKT signaling in individual cells are accounted for by variable protein concentration.

Meyer R, D'Alessandro LA, Kar S, Kramer B, She B, Kaschek D, Hahn B, Wrangborg D, Karlsson J, Kvarnström M, Jirstrand M, Lehmann WD, Timmer J, Höfer T, Klingmüller U.

Front Physiol. 2012 Nov 28;3:451. doi: 10.3389/fphys.2012.00451. eCollection 2012.

13.

A variational approach to parameter estimation in ordinary differential equations.

Kaschek D, Timmer J.

BMC Syst Biol. 2012 Aug 14;6:99. doi: 10.1186/1752-0509-6-99.

14.

Division of labor by dual feedback regulators controls JAK2/STAT5 signaling over broad ligand range.

Bachmann J, Raue A, Schilling M, Böhm ME, Kreutz C, Kaschek D, Busch H, Gretz N, Lehmann WD, Timmer J, Klingmüller U.

Mol Syst Biol. 2011 Jul 19;7:516. doi: 10.1038/msb.2011.50.

15.

Model-based extension of high-throughput to high-content data.

Pfeifer AC, Kaschek D, Bachmann J, Klingmüller U, Timmer J.

BMC Syst Biol. 2010 Aug 5;4:106. doi: 10.1186/1752-0509-4-106.

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