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Items: 37

1.

Antibody-mediated targeting of TNFR2 activates CD8+ T cells in mice and promotes antitumor immunity.

Tam EM, Fulton RB, Sampson JF, Muda M, Camblin A, Richards J, Koshkaryev A, Tang J, Kurella V, Jiao Y, Xu L, Zhang K, Kohli N, Luus L, Hutto E, Kumar S, Lulo J, Paragas V, Wong C, Suchy J, Grabow S, Dugast AS, Zhang H, Depis F, Feau S, Jakubowski A, Qiao W, Craig G, Razlog M, Qiu J, Zhou Y, Marks JD, Croft M, Drummond DC, Raue A.

Sci Transl Med. 2019 Oct 2;11(512). pii: eaax0720. doi: 10.1126/scitranslmed.aax0720.

PMID:
31578241
2.

Recipes for Analysis of Molecular Networks Using the Data2Dynamics Modeling Environment.

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

Methods Mol Biol. 2019;1945:341-362. doi: 10.1007/978-1-4939-9102-0_16.

PMID:
30945255
3.

MM-131, a bispecific anti-Met/EpCAM mAb, inhibits HGF-dependent and HGF-independent Met signaling through concurrent binding to EpCAM.

Casaletto JB, Geddie ML, Abu-Yousif AO, Masson K, Fulgham A, Boudot A, Maiwald T, Kearns JD, Kohli N, Su S, Razlog M, Raue A, Kalra A, Håkansson M, Logan DT, Welin M, Chattopadhyay S, Harms BD, Nielsen UB, Schoeberl B, Lugovskoy AA, MacBeath G.

Proc Natl Acad Sci U S A. 2019 Apr 9;116(15):7533-7542. doi: 10.1073/pnas.1819085116. Epub 2019 Mar 21.

4.

Analysis of Single-Cell RNA-Seq Identifies Cell-Cell Communication Associated with Tumor Characteristics.

Kumar MP, Du J, Lagoudas G, Jiao Y, Sawyer A, Drummond DC, Lauffenburger DA, Raue A.

Cell Rep. 2018 Nov 6;25(6):1458-1468.e4. doi: 10.1016/j.celrep.2018.10.047.

5.

Modeling chemotherapy-induced stress to identify rational combination therapies in the DNA damage response pathway.

Alkan O, Schoeberl B, Shah M, Koshkaryev A, Heinemann T, Drummond DC, Yaffe MB, Raue A.

Sci Signal. 2018 Jul 24;11(540). pii: eaat0229. doi: 10.1126/scisignal.aat0229.

PMID:
30042127
6.

Estimation of immune cell content in tumour tissue using single-cell RNA-seq data.

Schelker M, Feau S, Du J, Ranu N, Klipp E, MacBeath G, Schoeberl B, Raue A.

Nat Commun. 2017 Dec 11;8(1):2032. doi: 10.1038/s41467-017-02289-3.

7.

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.

Front Physiol. 2017 Oct 9;8:775. doi: 10.3389/fphys.2017.00775. eCollection 2017.

8.

Predicting ligand-dependent tumors from multi-dimensional signaling features.

Hass H, Masson K, Wohlgemuth S, Paragas V, Allen JE, Sevecka M, Pace E, Timmer J, Stelling J, MacBeath G, Schoeberl B, Raue A.

NPJ Syst Biol Appl. 2017 Sep 20;3:27. doi: 10.1038/s41540-017-0030-3. eCollection 2017.

9.

IL-1β-induced and p38MAPK-dependent activation of the mitogen-activated protein kinase-activated protein kinase 2 (MK2) in hepatocytes: Signal transduction with robust and concentration-independent signal amplification.

Kulawik A, Engesser R, Ehlting C, Raue A, Albrecht U, Hahn B, Lehmann WD, Gaestel M, Klingmüller U, Häussinger D, Timmer J, Bode JG.

J Biol Chem. 2017 Apr 14;292(15):6291-6302. doi: 10.1074/jbc.M117.775023. Epub 2017 Feb 21.

10.

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.

11.

Identification of Cell Type-Specific Differences in Erythropoietin Receptor Signaling in Primary Erythroid and Lung Cancer Cells.

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, Klingmüller U.

PLoS Comput Biol. 2016 Aug 5;12(8):e1005049. doi: 10.1371/journal.pcbi.1005049. eCollection 2016 Aug.

12.

Model calibration and uncertainty analysis in signaling networks.

Heinemann T, Raue A.

Curr Opin Biotechnol. 2016 Jun;39:143-149. doi: 10.1016/j.copbio.2016.04.004. Epub 2016 Apr 14. Review.

PMID:
27085224
13.

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.

14.

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.

PMID:
26142188
15.

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.

16.

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.

17.

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.

18.

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.

PMID:
24728588
19.

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.

20.

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, Sauro HM, Stolovitzky G, Saez-Rodriguez J.

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

21.

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.

PMID:
24463185
22.

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].

23.

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.

PMID:
23602931
24.

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.

25.

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.

26.

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.

PMID:
23277602
27.

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.

28.

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.

29.

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.

30.

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.

31.

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.

32.

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.

33.

Addressing parameter identifiability by model-based experimentation.

Raue A, Kreutz C, Maiwald T, Klingmuller U, Timmer J.

IET Syst Biol. 2011 Mar;5(2):120-30. doi: 10.1049/iet-syb.2010.0061.

PMID:
21405200
34.

Identifiability and observability analysis for experimental design in nonlinear dynamical models.

Raue A, Becker V, Klingmüller U, Timmer J.

Chaos. 2010 Dec;20(4):045105. doi: 10.1063/1.3528102.

PMID:
21198117
35.

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.

Cancer Res. 2011 Feb 1;71(3):693-704. doi: 10.1158/0008-5472.CAN-10-2987. Epub 2010 Dec 2.

36.

Covering a broad dynamic range: information processing at the erythropoietin receptor.

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

Science. 2010 Jun 11;328(5984):1404-8. doi: 10.1126/science.1184913. Epub 2010 May 20.

37.

Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood.

Raue A, Kreutz C, Maiwald T, Bachmann J, Schilling M, Klingmüller U, Timmer J.

Bioinformatics. 2009 Aug 1;25(15):1923-9. doi: 10.1093/bioinformatics/btp358. Epub 2009 Jun 8.

PMID:
19505944

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