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Model calibration and uncertainty analysis in signaling networks.

Heinemann T, Raue A.

Curr Opin Biotechnol. 2016 Apr 14;39:143-149. doi: 10.1016/j.copbio.2016.04.004. [Epub ahead of print] Review.


CERENA: ChEmical REaction Network Analyzer-A Toolbox for the Simulation and Analysis of Stochastic Chemical Kinetics.

Kazeroonian A, Fröhlich F, Raue A, Theis FJ, Hasenauer J.

PLoS One. 2016 Jan 25;11(1):e0146732. doi: 10.1371/journal.pone.0146732. eCollection 2016.


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.

Bioinformatics. 2015 Nov 1;31(21):3558-60. doi: 10.1093/bioinformatics/btv405. Epub 2015 Jul 3.


Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models.

Karr JR, Williams AH, Zucker JD, Raue A, Steiert B, Timmer J, Kreutz C; DREAM8 Parameter Estimation Challenge Consortium, Wilkinson S, Allgood BA, Bot BM, Hoff BR, Kellen MR, Covert MW, Stolovitzky GA, Meyer P.

PLoS Comput Biol. 2015 May 28;11(5):e1004096. doi: 10.1371/journal.pcbi.1004096. eCollection 2015 May.


Disentangling the Complexity of HGF Signaling by Combining Qualitative and Quantitative Modeling.

D'Alessandro LA, Samaga R, Maiwald T, Rho SH, Bonefas S, Raue A, Iwamoto N, Kienast A, Waldow K, Meyer R, Schilling M, Timmer J, Klamt S, Klingmüller U.

PLoS Comput Biol. 2015 Apr 23;11(4):e1004192. doi: 10.1371/journal.pcbi.1004192. eCollection 2015 Apr.


Deciphering the mechanism behind Fibroblast Growth Factor (FGF) induced biphasic signal-response profiles.

Kanodia J, Chai D, Vollmer J, Kim J, Raue A, Finn G, Schoeberl B.

Cell Commun Signal. 2014 May 15;12:34. doi: 10.1186/1478-811X-12-34.


Bridging the gaps in systems biology.

Cvijovic M, Almquist J, Hagmar J, Hohmann S, Kaltenbach HM, Klipp E, Krantz M, Mendes P, Nelander S, Nielsen J, Pagnani A, Przulj N, Raue A, Stelling J, Stoma S, Tobin F, Wodke JA, Zecchina R, Jirstrand M.

Mol Genet Genomics. 2014 Oct;289(5):727-34. doi: 10.1007/s00438-014-0843-3. Epub 2014 Apr 13. Review.


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.

BMC Bioinformatics. 2013;14 Suppl 19:S2. doi: 10.1186/1471-2105-14-S19-S2. Epub 2013 Nov 12.


Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach.

Meyer P, Cokelaer T, Chandran D, Kim KH, Loh PR, Tucker G, Lipson M, Berger B, Kreutz C, Raue A, Steiert B, Timmer J, Bilal E, Dream Six and Seven Parameter Estimation Consortium, Sauro HM, Stolovitzky G, Saez-Rodriguez J.

BMC Syst Biol. 2014 Feb 7;8:13. doi: 10.1186/1752-0509-8-13.


Comparison of approaches for parameter identifiability analysis of biological systems.

Raue A, Karlsson J, Saccomani MP, Jirstrand M, Timmer J.

Bioinformatics. 2014 May 15;30(10):1440-8. doi: 10.1093/bioinformatics/btu006. Epub 2014 Jan 23.


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].


High-dimensional Bayesian parameter estimation: case study for a model of JAK2/STAT5 signaling.

Hug S, Raue A, Hasenauer J, Bachmann J, Klingmüller U, Timmer J, Theis FJ.

Math Biosci. 2013 Dec;246(2):293-304. doi: 10.1016/j.mbs.2013.04.002. Epub 2013 Apr 16.


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.


A Systems Biology Study on NFκB Signaling in Primary Mouse Hepatocytes.

Pinna F, Sahle S, Beuke K, Bissinger M, Tuncay S, D'Alessandro LA, Gauges R, Raue A, Timmer J, Klingmüller U, Schirmacher P, Kummer U, Breuhahn K.

Front Physiol. 2012 Dec 31;3:466. doi: 10.3389/fphys.2012.00466. eCollection 2012.


Joining forces of Bayesian and frequentist methodology: a study for inference in the presence of non-identifiability.

Raue A, Kreutz C, Theis FJ, Timmer J.

Philos Trans A Math Phys Eng Sci. 2012 Dec 31;371(1984):20110544. doi: 10.1098/rsta.2011.0544. Print 2013 Feb 13.


Comprehensive estimation of input signals and dynamics in biochemical reaction networks.

Schelker M, Raue A, Timmer J, Kreutz C.

Bioinformatics. 2012 Sep 15;28(18):i529-i534. doi: 10.1093/bioinformatics/bts393.


Likelihood based observability analysis and confidence intervals for predictions of dynamic models.

Kreutz C, Raue A, Timmer J.

BMC Syst Biol. 2012 Sep 5;6:120. doi: 10.1186/1752-0509-6-120.


Experimental design for parameter estimation of gene regulatory networks.

Steiert B, Raue A, Timmer J, Kreutz C.

PLoS One. 2012;7(7):e40052. doi: 10.1371/journal.pone.0040052. Epub 2012 Jul 16.


In silico labeling reveals the time-dependent label half-life and transit-time in dynamical systems.

Maiwald T, Blumberg J, Raue A, Hengl S, Schilling M, Sy SK, Becker V, Klingmüller U, Timmer J.

BMC Syst Biol. 2012 Feb 27;6:13. doi: 10.1186/1752-0509-6-13.


Predictive mathematical models of cancer signalling pathways.

Bachmann J, Raue A, Schilling M, Becker V, Timmer J, Klingmüller U.

J Intern Med. 2012 Feb;271(2):155-65. doi: 10.1111/j.1365-2796.2011.02492.x. Review.

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