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Items: 49


Benchmark Problems for Dynamic Modeling of Intracellular Processes.

Hass H, Loos C, Alvarez ER, Timmer J, Hasenauer J, Kreutz C.

Bioinformatics. 2019 Jan 8. doi: 10.1093/bioinformatics/btz020. [Epub ahead of print]


Increasing Neural Stem Cell Division Asymmetry and Quiescence Are Predicted to Contribute to the Age-Related Decline in Neurogenesis.

Bast L, Calzolari F, Strasser MK, Hasenauer J, Theis FJ, Ninkovic J, Marr C.

Cell Rep. 2018 Dec 18;25(12):3231-3240.e8. doi: 10.1016/j.celrep.2018.11.088.


Multi-experiment nonlinear mixed effect modeling of single-cell translation kinetics after transfection.

Fröhlich F, Reiser A, Fink L, Woschée D, Ligon T, Theis FJ, Rädler JO, Hasenauer J.

NPJ Syst Biol Appl. 2018 Dec 10;5:1. doi: 10.1038/s41540-018-0079-7. eCollection 2019.


Scalable Inference of Ordinary Differential Equation Models of Biochemical Processes.

Fröhlich F, Loos C, Hasenauer J.

Methods Mol Biol. 2019;1883:385-422. doi: 10.1007/978-1-4939-8882-2_16.


Efficient Parameter Estimation Enables the Prediction of Drug Response Using a Mechanistic Pan-Cancer Pathway Model.

Fröhlich F, Kessler T, Weindl D, Shadrin A, Schmiester L, Hache H, Muradyan A, Schütte M, Lim JH, Heinig M, Theis FJ, Lehrach H, Wierling C, Lange B, Hasenauer J.

Cell Syst. 2018 Dec 26;7(6):567-579.e6. doi: 10.1016/j.cels.2018.10.013. Epub 2018 Nov 28.


Hierarchical optimization for the efficient parametrization of ODE models.

Loos C, Krause S, Hasenauer J.

Bioinformatics. 2018 Dec 15;34(24):4266-4273. doi: 10.1093/bioinformatics/bty514.


Optimization and profile calculation of ODE models using second order adjoint sensitivity analysis.

Stapor P, Fröhlich F, Hasenauer J.

Bioinformatics. 2018 Jul 1;34(13):i151-i159. doi: 10.1093/bioinformatics/bty230.


Bayesian parameter estimation for biochemical reaction networks using region-based adaptive parallel tempering.

Ballnus B, Schaper S, Theis FJ, Hasenauer J.

Bioinformatics. 2018 Jul 1;34(13):i494-i501. doi: 10.1093/bioinformatics/bty229.


pyABC: distributed, likelihood-free inference.

Klinger E, Rickert D, Hasenauer J.

Bioinformatics. 2018 Oct 15;34(20):3591-3593. doi: 10.1093/bioinformatics/bty361.


A Hierarchical, Data-Driven Approach to Modeling Single-Cell Populations Predicts Latent Causes of Cell-To-Cell Variability.

Loos C, Moeller K, Fröhlich F, Hucho T, Hasenauer J.

Cell Syst. 2018 May 23;6(5):593-603.e13. doi: 10.1016/j.cels.2018.04.008. Epub 2018 May 2.


Community-driven roadmap for integrated disease maps.

Ostaszewski M, Gebel S, Kuperstein I, Mazein A, Zinovyev A, Dogrusoz U, Hasenauer J, Fleming RMT, Le Novère N, Gawron P, Ligon T, Niarakis A, Nickerson D, Weindl D, Balling R, Barillot E, Auffray C, Schneider R.

Brief Bioinform. 2018 Apr 23. doi: 10.1093/bib/bby024. [Epub ahead of print]


PKA-RII subunit phosphorylation precedes activation by cAMP and regulates activity termination.

Isensee J, Kaufholz M, Knape MJ, Hasenauer J, Hammerich H, Gonczarowska-Jorge H, Zahedi RP, Schwede F, Herberg FW, Hucho T.

J Cell Biol. 2018 Jun 4;217(6):2167-2184. doi: 10.1083/jcb.201708053. Epub 2018 Apr 3.


Whither systems medicine?

Apweiler R, Beissbarth T, Berthold MR, Blüthgen N, Burmeister Y, Dammann O, Deutsch A, Feuerhake F, Franke A, Hasenauer J, Hoffmann S, Höfer T, Jansen PL, Kaderali L, Klingmüller U, Koch I, Kohlbacher O, Kuepfer L, Lammert F, Maier D, Pfeifer N, Radde N, Rehm M, Roeder I, Saez-Rodriguez J, Sax U, Schmeck B, Schuppert A, Seilheimer B, Theis FJ, Vera J, Wolkenhauer O.

Exp Mol Med. 2018 Mar 2;50(3):e453. doi: 10.1038/emm.2017.290. Review.


Effects of trastuzumab and afatinib on kinase activity in gastric cancer cell lines.

Keller S, Zwingenberger G, Ebert K, Hasenauer J, Wasmuth J, Maier D, Haffner I, Schierle K, Weirich G, Luber B.

Mol Oncol. 2018 Apr;12(4):441-462. doi: 10.1002/1878-0261.12170. Epub 2018 Mar 10.


Evaluation of epidermal growth factor receptor signaling effects in gastric cancer cell lines by detailed motility-focused phenotypic characterization linked with molecular analysis.

Keller S, Kneissl J, Grabher-Meier V, Heindl S, Hasenauer J, Maier D, Mattes J, Winter P, Luber B.

BMC Cancer. 2017 Dec 13;17(1):845. doi: 10.1186/s12885-017-3822-3.


GenSSI 2.0: multi-experiment structural identifiability analysis of SBML models.

Ligon TS, Fröhlich F, Chis OT, Banga JR, Balsa-Canto E, Hasenauer J.

Bioinformatics. 2018 Apr 15;34(8):1421-1423. doi: 10.1093/bioinformatics/btx735.


PESTO: Parameter EStimation TOolbox.

Stapor P, Weindl D, Ballnus B, Hug S, Loos C, Fiedler A, Krause S, Hroß S, Fröhlich F, Hasenauer J, Wren J.

Bioinformatics. 2018 Feb 15;34(4):705-707. doi: 10.1093/bioinformatics/btx676.


A scalable moment-closure approximation for large-scale biochemical reaction networks.

Kazeroonian A, Theis FJ, Hasenauer J.

Bioinformatics. 2017 Jul 15;33(14):i293-i300. doi: 10.1093/bioinformatics/btx249.


Comprehensive benchmarking of Markov chain Monte Carlo methods for dynamical systems.

Ballnus B, Hug S, Hatz K, Görlitz L, Hasenauer J, Theis FJ.

BMC Syst Biol. 2017 Jun 24;11(1):63. doi: 10.1186/s12918-017-0433-1.


Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks.

Fröhlich F, Kaltenbacher B, Theis FJ, Hasenauer J.

PLoS Comput Biol. 2017 Jan 23;13(1):e1005331. doi: 10.1371/journal.pcbi.1005331. eCollection 2017 Jan.


Parallelization and High-Performance Computing Enables Automated Statistical Inference of Multi-scale Models.

Jagiella N, Rickert D, Theis FJ, Hasenauer J.

Cell Syst. 2017 Feb 22;4(2):194-206.e9. doi: 10.1016/j.cels.2016.12.002. Epub 2017 Jan 11.


Robust parameter estimation for dynamical systems from outlier-corrupted data.

Maier C, Loos C, Hasenauer J.

Bioinformatics. 2017 Mar 1;33(5):718-725. doi: 10.1093/bioinformatics/btw703.


Parameter estimation for dynamical systems with discrete events and logical operations.

Fröhlich F, Theis FJ, Rädler JO, Hasenauer J.

Bioinformatics. 2017 Apr 1;33(7):1049-1056. doi: 10.1093/bioinformatics/btw764.


Characterization of Rare, Dormant, and Therapy-Resistant Cells in Acute Lymphoblastic Leukemia.

Ebinger S, Özdemir EZ, Ziegenhain C, Tiedt S, Castro Alves C, Grunert M, Dworzak M, Lutz C, Turati VA, Enver T, Horny HP, Sotlar K, Parekh S, Spiekermann K, Hiddemann W, Schepers A, Polzer B, Kirsch S, Hoffmann M, Knapp B, Hasenauer J, Pfeifer H, Panzer-Grümayer R, Enard W, Gires O, Jeremias I.

Cancer Cell. 2016 Dec 12;30(6):849-862. doi: 10.1016/j.ccell.2016.11.002. Epub 2016 Dec 1.


Tailored parameter optimization methods for ordinary differential equation models with steady-state constraints.

Fiedler A, Raeth S, Theis FJ, Hausser A, Hasenauer J.

BMC Syst Biol. 2016 Aug 22;10(1):80. doi: 10.1186/s12918-016-0319-7.


Inference for Stochastic Chemical Kinetics Using Moment Equations and System Size Expansion.

Fröhlich F, Thomas P, Kazeroonian A, Theis FJ, Grima R, Hasenauer J.

PLoS Comput Biol. 2016 Jul 22;12(7):e1005030. doi: 10.1371/journal.pcbi.1005030. eCollection 2016 Jul.


MEMO: multi-experiment mixture model analysis of censored data.

Geissen EM, Hasenauer J, Heinrich S, Hauf S, Theis FJ, Radde NE.

Bioinformatics. 2016 Aug 15;32(16):2464-72. doi: 10.1093/bioinformatics/btw190. Epub 2016 Apr 19.


Analysis of CFSE time-series data using division-, age- and label-structured population models.

Hross S, Hasenauer J.

Bioinformatics. 2016 Aug 1;32(15):2321-9. doi: 10.1093/bioinformatics/btw131. Epub 2016 Mar 8.


Combinatorial Histone Acetylation Patterns Are Generated by Motif-Specific Reactions.

Blasi T, Feller C, Feigelman J, Hasenauer J, Imhof A, Theis FJ, Becker PB, Marr C.

Cell Syst. 2016 Jan 27;2(1):49-58. doi: 10.1016/j.cels.2016.01.002. Epub 2016 Jan 27.


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.


Network plasticity of pluripotency transcription factors in embryonic stem cells.

Filipczyk A, Marr C, Hastreiter S, Feigelman J, Schwarzfischer M, Hoppe PS, Loeffler D, Kokkaliaris KD, Endele M, Schauberger B, Hilsenbeck O, Skylaki S, Hasenauer J, Anastassiadis K, Theis FJ, Schroeder T.

Nat Cell Biol. 2015 Oct;17(10):1235-46. doi: 10.1038/ncb3237. Epub 2015 Sep 21.


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.


ODE constrained mixture modelling: a method for unraveling subpopulation structures and dynamics.

Hasenauer J, Hasenauer C, Hucho T, Theis FJ.

PLoS Comput Biol. 2014 Jul 3;10(7):e1003686. doi: 10.1371/journal.pcbi.1003686. eCollection 2014 Jul.


Dominant negative effects of tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL) receptor 4 on TRAIL receptor 1 signaling by formation of heteromeric complexes.

Neumann S, Hasenauer J, Pollak N, Scheurich P.

J Biol Chem. 2014 Jun 6;289(23):16576-87. doi: 10.1074/jbc.M114.559468. Epub 2014 Apr 24.


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.


Modeling of 2D diffusion processes based on microscopy data: parameter estimation and practical identifiability analysis.

Hock S, Hasenauer J, Theis FJ.

BMC Bioinformatics. 2013;14 Suppl 10:S7. doi: 10.1186/1471-2105-14-S10-S7. Epub 2013 Aug 12.


Pain modulators regulate the dynamics of PKA-RII phosphorylation in subgroups of sensory neurons.

Isensee J, Diskar M, Waldherr S, Buschow R, Hasenauer J, Prinz A, Allgöwer F, Herberg FW, Hucho T.

J Cell Sci. 2014 Jan 1;127(Pt 1):216-29. doi: 10.1242/jcs.136580. Epub 2013 Nov 4.


Determinants of robustness in spindle assembly checkpoint signalling.

Heinrich S, Geissen EM, Kamenz J, Trautmann S, Widmer C, Drewe P, Knop M, Radde N, Hasenauer J, Hauf S.

Nat Cell Biol. 2013 Nov;15(11):1328-39. doi: 10.1038/ncb2864. Epub 2013 Oct 27.


Method of conditional moments (MCM) for the Chemical Master Equation: a unified framework for the method of moments and hybrid stochastic-deterministic models.

Hasenauer J, Wolf V, Kazeroonian A, Theis FJ.

J Math Biol. 2014 Sep;69(3):687-735. doi: 10.1007/s00285-013-0711-5. Epub 2013 Aug 6.


Wound-healing growth factor, basic FGF, induces Erk1/2-dependent mechanical hyperalgesia.

Andres C, Hasenauer J, Ahn HS, Joseph EK, Isensee J, Theis FJ, Allgöwer F, Levine JD, Dib-Hajj SD, Waxman SG, Hucho T.

Pain. 2013 Oct;154(10):2216-26. doi: 10.1016/j.pain.2013.07.005. Epub 2013 Jul 16.


Sharpening of expression domains induced by transcription and microRNA regulation within a spatio-temporal model of mid-hindbrain boundary formation.

Hock S, Ng YK, Hasenauer J, Wittmann D, Lutter D, Trümbach D, Wurst W, Prakash N, Theis FJ.

BMC Syst Biol. 2013 Jun 25;7:48. doi: 10.1186/1752-0509-7-48.


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.


Analysis and simulation of division- and label-structured population models : a new tool to analyze proliferation assays.

Hasenauer J, Schittler D, Allgöwer F.

Bull Math Biol. 2012 Nov;74(11):2692-732. doi: 10.1007/s11538-012-9774-5. Epub 2012 Oct 20.


A visual analytics approach for models of heterogeneous cell populations.

Hasenauer J, Heinrich J, Doszczak M, Scheurich P, Weiskopf D, Allgöwer F.

EURASIP J Bioinform Syst Biol. 2012 May 31;2012(1):4. doi: 10.1186/1687-4153-2012-4.


Threshold-free population analysis identifies larger DRG neurons to respond stronger to NGF stimulation.

Andres C, Hasenauer J, Allgower F, Hucho T.

PLoS One. 2012;7(3):e34257. doi: 10.1371/journal.pone.0034257. Epub 2012 Mar 27.


Identification of models of heterogeneous cell populations from population snapshot data.

Hasenauer J, Waldherr S, Doszczak M, Radde N, Scheurich P, Allgöwer F.

BMC Bioinformatics. 2011 Apr 28;12:125. doi: 10.1186/1471-2105-12-125.


Cell differentiation modeled via a coupled two-switch regulatory network.

Schittler D, Hasenauer J, Allgöwer F, Waldherr S.

Chaos. 2010 Dec;20(4):045121. doi: 10.1063/1.3505000.


Parameter identification, experimental design and model falsification for biological network models using semidefinite programming.

Hasenauer J, Waldherr S, Wagner K, Allgöwer F.

IET Syst Biol. 2010 Mar;4(2):119-30. doi: 10.1049/iet-syb.2009.0030.


Allosteric regulation of the access channels to the Rb+ occlusion sites of (Na+ + K+)-ATPase.

Hasenauer J, Huang WH, Askari A.

J Biol Chem. 1993 Feb 15;268(5):3289-97.

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