Papers in reviewed journals


in press:

C. Tönsing, J. Timmer, C. Kreutz.
Profile likelihood based analyses of infectious disease models. Statistical Methods in Medical Research , 2017,

P. Fisch, S. Rathmann, C. Keck, C. Kreutz, N. Weit, M. Mueller, J. Timmer, S. Glatzel, M. Follo, M. Malkovsky, J. Finke, R. Handgretinger, M. Werner.
Partial break in tolerance of NKG2A-/LIR-1- single KIR+ NK cells early in the course of HLA matched, KIR mismatched hematopoietic cell transplantation. Bone Marrow Transplantation , 2017,

D. Kurzhunov, R. Borowiak, H. Hass, P. Wagner, A. Krafft, J. Timmer M. Bock.
In vivo quantification of oxygen metabolic rates in the human brain with dynamic 17 O MRI: profile likelihood analysis. Magnetic Resonance in Medicine , 2017,


[300] A. Kulawik, R. Engesser, C. Ehtling, A. Raue, U. Albrecht, B. Hahn, W.D. Lehmann, M. Gästel, U. Klingmüller, D. Häussinger, J. Timmer, J.G. Bode
IL-1beta induced and p38MAPK-dependent activation of the mitogen-activated protein kinase (MAPK)-activated protein kinase (MK) 2 in hepatocytes: signal transduction with robust and concentration-independent signal amplification. J. Biological Chemistry 292, 2017, 6291-6302

[299] L. Adlung, S. Kar, M.-C. Wagner, B. She, S. Chakraborty, J. Bao, S. Lattermann, M. Boerries, H. Busch, P. Wuchter, A.D. Ho, J. Timmer, M. Schilling, T. Höfer, U. Klingmüller.
Protein abundance pattern of AKT and ERK pathway components governs cell-type-specific regulation of proliferation. Molecular Systems Biology 13 , 2017, 904


[298] D. Kaschek, F. Henjes, M. Hasmann, U. Korf, J. Timmer.
Testing the pattern of AKT activation by variational parameter estimation. IEEE Life Science Letters 2, 2016, 13-16
Supplementary Information

[297] M. Bruno, J. Koschmieder, F. Wuest, P. Schaub, M. Fehling-Kaschek, J. Timmer, P. Beyer, S. Al-Babili.
Enzymatic study on AtCCD4 and AtCCD7 and their potential in forming acyclic regulatory metabolites. J. Experimental Biology 67, 2016, 5993-6005

[296] O. Ucar, K. Li, D. Dvornikov, C. Kreutz, J. Timmer, S. Matt, L. Brenner, C. Smedley, M.A. Travis, T.G. Hofmann, U. Klingmüller B. Kyewski.
A thymic epithelial stem cell pool persists throughout ontogeny and is modulated by TGF-beta. Cell Reports 17, 2016, 448-457

[295] T. Maiwald, H. Hass, B. Steiert, J. Vanlier, R. Engesser, A. Raue, F. Kipkeew, H.H. Bock, D. Kaschek, C. Kreutz, J. Timmer.
Driving the model to its limit: profile likelihood based model reduction. PLoS ONE 11, 2016, e0162366.

[294] B. Steiert, J. Timmer, C. Kreutz.
L1 regularization facilitates detection of cell type-specific parameters in dynamical systems. Bioinformatics 32, 2016, i718-i726

[293] R. Merkle, B. Steiert, F. Salopiata, S. Depner, A. Raue, N. Iwamoto, M. Schelker, H. Hass, M. Wäsch, M. Böhm, O. Mücke, D.B. Lipka, C. Plass, W.D. Lehmann, C. Kreutz, J. Timmer, M. Schilling, U. Klingmüller.
Identification of cell type-specific differences in erythropoietin receptor signaling in primary erythroid and lung cancer cells. PLoS Comp. Biology 12, 2016, 1005049

[292] H. Binder, T. Kurz, S. Teschner, C. Kreutz, M. Geyer, J. Donauer, A. Kraemer-Guth, J. Timmer, M. Schumacher, G. Walz.
Dealing with prognostic signature instability: a strategy illustrated for cardiovascular events in patients with end-stage renal disease. BMC Medical Genetics 9, 2016, 43

[291] M. Schirrmann, M. Joschko, D. Barkusky, R. Gebbers, E. Kramer, M. Zörner, J. Timmer.
Proximal soil sensing - a contribution for species habitat distribution modelling of earthworms in agricultural soils? PLoS ONE 11, 2016, e0158271

[290] M. Rosenblatt, J. Timmer, D. Kaschek.
Customized steady-state constraints for parameter estimation in non-linear ordinary differential equation models. Frontiers in Cell and Developmental Biology 4, 2016, 41

[289] H. Hass, D. Kaschek, J. Timmer, C. Kreutz.
Fast integration-based prediction bands for ordinary differential equation models. Bioinformatics 32, 2016, 1204-1210
Supplementary Information

[288] S. Gholami, E. Sayad, R. Gebbers, M. Joschko, J. Timmer.
Spatial analysis of riparian forest soil macrofauna and its relation to abiotic soil properties. Pedobiologia 59, 2016, 27-36


[287] A. Raue, B. Steiert, M. Schelker, C. Kreutz, T. Maiwald, H. Hass, J. Vanlier, C. Tönsing, L. Adlung, R. Engesser, W. Mader, T. Heinemann, J. Hasenauer, M. Schilling, T. Höfer, E. Klipp, F. Theis, U. Klingmüller, B. Schöberl, J. Timmer.
Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems. Bioinformatics 31, 2015, 3558-3560
Supplementary Information I
Supplementary Information II
Supplementary Information III

[286] W.B. Buchenberg, W. Mader, G. Hoppe, R. Lorenz, M. Menza, M. Büchert, J. Timmer, B. Jung.
An in vitro study to simulate the intracardiac magnetohydrodynamic effect. Magnetic Resonance in Medicine 74, 2015, 850-857

[285] B. Merkt, J. Timmer, D. Kaschek.
Higher-order Lie-symmetries in identifiability and predictability analysis of dynamic models. Phys. Rev. E 92, 2015, 012920

[284] L.O. Schwen, A. Schenk, C. Kreutz, J. Timmer, M.M. Bartolome Rodriguez, L. Küpfer, T. Preusser.
Representative sinusoids for hepatic four-scale pharmacokinetics simulations. PLoS ONE 10, 2015, e0133653

[283] T. Goldmann, N. Zeller, J. Raasch, K. Kierdorf, K. Frenzel, L. Ketscher, A. Basters, O. Staszewski, S.M. Brendecke, A. Spiess, T.L. Tay, C. Kreutz, J. Timmer, G.M. Mancini, T. Blank, G. Fritz, K. Biber, R. Lang, D. Malo, D. Merkler, M. Heikenwälder, K.P. Knobeloch, M. Prinz.
USP18 lack in microglia causes destructive interferonopathy of the mouse brain. EMBO Journal 34, 2015, 1612-1629
See also here

[282] W. Mader, M. Mader, J. Timmer, M. Thiel, B. Schelter.
Networks: On the relation of bi- and multivariate measures. Scientific Reports 5, 2015, 10805

[281] J.R. Karr, A.H. Williams, J.D. Zucker, A. Raue, B. Steiert, J. Timmer, C. Kreutz, DREAM8 Parameter Estimation Challenge Consortium, S. Wilkinson, B.A. Allgood, B.M. Bot, B.R. Hoff, M.R. Kellen, M.W. Covert, G.A. Stolovitzky, P. Meyer.
Summary of the DREAM8 parameter estimation challenge: Toward parameter identification for whole-cell models. PLoS Comp. Biol. 11, 2015, e1004096

[280] L.A. D'Alessandro, R. Samaga, T. Maiwald, S.-H. Rho, S. Bonefas, A. Raue, N. Iwamoto, A. Kienast, K. Waldow, R. Meyer, M. Schilling, J. Timmer, S. Klamt, U. Klingmüller.
Disentangling the complexity of HGF signaling by combining qualitative and quantitative modeling. PLoS Computational Biology 11, 2015, e1004192

[279] C. Arand, E. Scheller, B. Seeber, J. Timmer, S. Klöppel, B. Schelter.
Assessing parameter identifiability for Dynamic Causal Modelling of fMRI data. Frontiers in Neuroscience 9, 2015, 43

[278] H. Klett, M. Rodriguez-Fernandez, S. Dineen, L.R. Leon, J. Timmer, F.J. Doyle III.
Modeling the inflammatory response in the hypothalamus ensuing heat stroke: Iterative cycle of model calibration, identifiability analysis, experimental design and data collection. Mathematical Biosciences 260, 2015, 35-46

[277] L. Sommerlade, M. Thiel, M. Mader, W. Mader, J. Timmer, B. Platt, B. Schelter.
Assessing the strength of directed influences among neural signals: An approach to noisy data. J. Neuroscience Methods 239, 2015, 47-64


[276] D. Drasdo, J. Bode, U. Dahmen, O. Dirsch, S. Dooley, R. Gebhardt, A. Ghallab, P. Godoy, D. Häussinger, S. Hammad, S. Hoehme, H.-G. Holzhütter, U. Klingmüller, L. Kuepfer, J. Timmer, M. Zerial, J.G. Hengstler.
The virtual liver: state of the art and future perspectives. Arch. Toxicol. 88, 2014, 2071-2075

[275] K. Müller, R. Engesser, J. Timmer, M.D. Zurbriggen, W. Weber.
Orthogonal optogenetic triple-gene control in mammalian cells. ACS Synthetic Biology 3, 2014, 796-801
Supplementary Information

[274] M. Mader, J. Klatt, F. Amtage, B. Hellwig, W. Mader, L. Sommerlade, J. Timmer, B. Schelter.
Spectral and higher-order-spectral analysis of tremor time series. Clinical & Experimental Pharmacology 4, 2014, 149

[273] F. Cordoba-Valdes, R. Castaneda-Priego, J. Timmer, C. Fleck.
The ratio of the lateral correlation length and particle radius determines the density profile of spherical molecules near a fluctuating membrane. Soft Matter 10, 2014, 8475-8481

[272] M. Reinhard, K. Schumacher, S. Rutsch, M. Oeinck, J. Timmer, I. Mader, B. Schelter, C. Weiller, C.P. Kaller.
Spatial mapping of dynamic cerebral autoregulation with multichannel near-infrared spectroscopy in high-grade carotid artery disease. Journal of Biomedical Optics 19, 2014, 097005

[271] M. Mischnik, S. Gambaryan, H. Subramanian, J. Geiger, C. Schütz, J. Timmer, T. Dandekar.
A comparative analysis of the bistability switch for platelet aggregation by logic ODE based dynamical modeling. Molecular Biosystems 10, 2014, 2082-2089

[270] M. Mader, W. Mader, B.J. Gluckman, J. Timmer, B. Schelter.
Statistical evaluation of forecasts. Phys. Rev. E 90, 2014, 022133

[269] S. von der Heyde, J. Sonntag, D. Kaschek, C. Bender, J. Timmer, U. Korf, T. Beissbarth.
RPPanalyzer Toolbox: An improved R package for the analysis of reverse phase protein array data. BioTechniques 57, 2014, 125-135

[268] C. Tönsing, J. Timmer, C. Kreutz.
Cause and cure of sloppiness in ordinary differential equation models. Phys. Rev. E 90, 2014, 023303

[267] S.D. Wahane, M.T. Prentzell, S.C. Weise, N. Hellbach, R. Vezzali, C. Kreuz, J. Timmer, K. Krieglstein, K. Thedieck, T. Vogel.
PI3K-p110-alpha-subtype-signalling mediates survival, proliferation and neurogenesis of cortical progenitor cells via activation of mTORC2. J. of Neurochemistry 130, 2014, 255-267

[266] K. Hubertus, M. Mischnik, J. Timmer, S. Herterich, R. Mark, M. Moulard, U. Walter, J. Geiger.
Reciprocal regulation of human platelet function by endogenous prostanoids and through multiple prostanoid receptors. European Journal of Pharmacology 740, 2014, 15-27

[265] W. Mader, Y. Linke, M. Mader, J. Timmer, B. Schelter.
A numerically efficient implementation of the Expectation Maximization algorithm for state space models. Applied Mathematics and Computation 241, 2014, 222-232
The software

[265] A. Raue, J. Karlsson, M.P. Saccomani, M. Jirstrand, J. Timmer.
Comparison of approaches for parameter identifiability analysis of biological systems. Bioinformatics 30, 2014, 1440-1448

[264] L. Sommerlade, M. Mader, W. Mader, J. Timmer, M. Thiel, C. Grebogi, B. Schelter.
Optimized spectral estimation for nonlinear synchronizing systems. Phys. Rev. E 89, 2014, 032912

[263] P. Meyer, T. Cokelaer, D. Chandran, K.H. Kim, P.-R. Loh, G. Tucker, M. Lipson, B. Berger, C. Kreutz, A. Raue, B. Steiert, J. Timmer, E. Bilal, H. Sauro, G. Stolovitzky, J. Saez-Rodriguez.
Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach. BMC Systems Biology 8, 2014, 13


[262] G.J. Fiala, D. Kaschek, B. Blumenthal, M. Reth, J. Timmer, W.W.A Schamel.
Pre-clustering of the B cell antigen receptor demonstrated by mathematically extended electron microscopy. Frontiers in Immunology 4, 2013, 427

[261] S. Hug, A. Raue, J. Bachmann, U. Klingmüller, J. Timmer, F.J. Theis.
High-Dimensional Bayesian Parameter Estimation: Case Study for a Model of JAK2/STAT5 Signaling. Mathematical Biocsiences 246, 2013, 293-304

[260] C. Vehlow, J. Hasenauer, A. Kramer, A. Raue, S. Hug, J. Timmer, N. Radde, F.J. Theis, D. Weiskopf.
iVUN: interactive Visualization of Uncertain biochemical reaction Networks. BMC Bioinformatics 14, 2013, S2

[259] A. Schad, J. Timmer, M. Roth.
Global helioseismic evidence for a deeply penetrating solar meridional flow consisting of multiple flow cells. Astrophysical J. 778 , 2013, L38

[258] A. Raue, M. Schilling, J. Bachmann, A. Matteson, M. Schelker, D. Kaschek, S. Hug, C. Kreutz, B.D. Harms, F.J. Theis, U. Klingmuller, J. Timmer.
Lessons learned from quantitative dynamical modeling in systems biology. PLoS ONE 8, 2013, e74335

[257] K. Müller, R. Engesser, J. Timmer, F. Nagy, M.D. Zurbriggen, W. Weber.
Synthesis of phycocyanobilin in mammalian cells. ChemComm 49, 2013, 8970-8972

[256] M. Mader, W. Mader, L. Sommerlade, J. Timmer, B. Schelter.
Block-bootstrapping for noisy data. J. Neuroscience Methods 219, 2013, 285-291

[255] M. Mischnik, K. Hubertus, J. Geiger, T. Dandekar, J. Timmer.
Dynamical modeling of prostaglandin signalling in platelets reveals individual receptor contributions and feedback properties. Molecular Biosystems 9, 2013, 2520-2529

[254] K. Aumann, A. Frey, A.M. May, D. Hauschke, C. Kreutz, J. Marx, J. Timmer, M. Werner, H. L. Pahl.
Subcellular mislocalization of the transcription factor NF-E2 in erythroid cells discriminates pre-fibrotic primary myelofibrosis from essential thrombocythemia. Blood 122, 2013, 93-99

[253] R. Ramb, M. Eichler, A. Ing, M. Thiel, C. Weiller, C. Grebogi, C. Schwarzbauer, J. Timmer, B. Schelter.
The impact of latent confounders in directed network analysis in neuroscience. Phil. Trans. A 137, 2013, 20110612

[252] P. Thomas, A.V. Straube, J. Timmer, C. Fleck, R. Grima.
Signatures of nonlinearity in single cell noise-induced oscillations. J. Theo. Biol. 335, 2013, 222-234

[251] K. Müller, R. Engesser, S. Schulz, T. Steinberg, P. Tomakidi, C.C. Weber, R. Ulm, J. Timmer, M.D. Zurbriggen, W. Weber.
Multi-chromatic control of mammalian gene expression and signaling. Nucleic Acids Research 41, 2013, e124

[250] C. Kreutz, A. Raue, D. Kaschek, J. Timmer.
Profile likelihood in systems biology. FEBS Journal 280, 2013, 2564-2571

[249] M. Mischnik, D. Boyanova, K. Hubertus, J. Geiger, M. Dittrich, G. Wangorsch, J. Timmer, T. Dandekar.
A Boolean view separates platelet activatory and inhibitory signalling as verified by phosphorylation monitoring including threshold behaviour and integrin modulation. Molecular Biosystems 9, 2013, 1326-1339

[248] K. Müller, R. Engesser, S. Metzger, S. Schulz, M.M. Kämpf, M. Busacker, T. Steinberg, P. Tomakidi, M. Ehrbar, F. Nagy, J. Timmer, M.D. Zurbriggen, W. Weber.
A red/far-red light-responsive bi-stable toggle switch to control gene expression in mammalian cells. Nucleic Acids Research 41, 2013, e77

[247] V. Morath, M. Keuper, M. Rodriguez-Franco, S. Deswal, G. Fiala, B. Blumenthal, D. Kaschek, J. Timmer, G. Neuhaus, O. Ronneberger, W. Schamel.
Semi-automatic procedure for the determination of the cell surface area used in systems immunology. Frontiers in Bioscience E5, 2013, 533-545

[246] A. Yalcin, C. Kreutz, D. Pfeifer, M. Abdelkarim, G. Klaus, J. Timmer, M. Lübbert, B. Hackanson.
MeDIP coupled with a promoter tiling array as a platform to investigate global DNA methylation pattern in AML cells. Leukemia Research 37, 2013, 102-111

[245] A. Raue, C. Kreutz, F. Theis, J. Timmer.
Joining forces of Bayesian and frequentist methodology: A study for inference in the presence of non-identifiability. Phil. Trans. Roy. Soc. A 371, 2013, 20110544


[244] A. Schad, J. Timmer, and M. Roth
Measuring the solar meridional flow from perturbations of eigenfunctions of global oscillations Astronomische Nachrichten 333, 2013, 991-994

[243] F. Pinna, S. Sahle, K. Beuke, M. Bissinger, S. Tuncay, L.A. D`Alessandro, R. Gauges, A. Raue, J. Timmer, U. Klingmüller, P. Schirmacher, U. Kummer, K. Breuhahn.
A systems biology study on NF-kB signalling in primary mouse hepatocytes. Frontiers in Physiology 3, 2012, 466

[242] R. Meyer, L.A. D`Alessandro, S. Kar, B. Kramer, B. She, D. Kaschek, B. Hahn, D. Wrangborg, J. Karlsson, M. Kvarnstrom, M. Jirstrand, W.D. Lehmann, J. Timmer, T. Höfer, U. Klingmüller.
Heterogeneous kinetics of AKT signaling in individual cells are accounted for by variable protein concentration. Frontiers in Systems Biology 3, 2012, 451

[241] B. Greese, K. Wester, R. Bensch, O. Ronneberger, J. Timmer, M. Hülskamp, C. Fleck.
Influence of cell-to-cell variability onto spatial pattern formation. IET Systems Biology 6, 2012, 143-153

[240] J. Klatt, H. Feldwisch-Drentrup, M. Ihle, V. Navarro, M. Neufang, C. Teixeira, C. Adam, M. Valderrama, C. Alvarado-Rojas, A. Witon, M. Le Van Quyen, F. Sales, A. Dourado, J. Timmer, A. Schulze-Bonhage, B. Schelter.
The EPILEPSIAE database: An extensive EEG database of epilepsy patients. Epilepsia 9, 2012, 1669-1676

[239] M. Schelker, A. Raue, J. Timmer, C. Kreutz.
Comprehensive estimation of input signals and dynamics in biochemical reaction networks. Bioinformatics 28, 2012, i529-i534

[238] C. Kreutz, A. Raue, J. Timmer.
Likelihood based observability analysis and confidence intervals for predictions of dynamic network models. BMC Systems Biology 6, 2012, 120

[237] D. Kaschek, J. Timmer.
A variational approach to parameter estimation in ordinary differential equations. BMC Systems Biology 6, 2012, 99

[236] L. Sommerlade, B. Schelter, J. Timmer, M. Reinhard.
Grading of dynamic cerebral autoregulation without blood pressure recordings: a simple Doppler-based method.Ultrasound in Medicine and Biology 38, 2012, 1546-1551

[235] B. Steiert, A. Raue, J. Timmer, C. Kreutz.
Experimental design for parameter estimation of gene regulatory networks. PLoS ONE 7, 2012, e40052

[234] M.M. Kämpf, R. Engesser, M. Busacker, M Hörner, M. Karlsson, M.D. Zurbriggen, M. Fussenegger, J. Timmer, W. Weber.
Rewiring and dosing of systems modules as a design approach for synthetic mammalian signaling networks. Molecular BioSystems 8, 2012, 1824-1832

[233] R. Schlatter, N. Philippi, G. Wangorsch, R. Pick, O. Sawodny, C. Borner, J. Timmer, M. Ederer, T. Dandekar.
Integration of Boolean models exemplified on hepatocyte signal transduction. Briefings in Bioinformatics 13, 2012, 365-376

[232] C. Kreutz, J. Gehring, D. Lang, R. Reski, J. Timmer, S.A. Rensing.
TSSi - An R package for transcription start site identification from 5' mRNA tag data. Bioinformatics 28, 2012, 1641-1642

[231] K. Sa Ferreira, C. Kreuz, S. MacNelly, K. Neubert, A. Haber, M. Bogyo, J. Timmer, C. Borner.
Caspase-3 feeds back on caspase-8, Bid and XIAP in type I Fas signaling in primary mouse hepatocytes. Apoptosis 17, 2012, 503-515

[230] M. Ihle, H. Feldwisch-Drentrup, C.A. Teixeira, A. Witon, B. Schelter, J. Timmer, A. Schulze-Bonhage.
EPILEPSIAE - A European epilepsy database. Computer Methods and Programs in Biomedicine 106, 2012, 127-138

[229] T. Maiwald, J. Blumberg, A. Raue, S. Hengl, M. Schilling, S.K.B. Sy, V. Becker, U. Klingmüller, J. Timmer.
In silico labeling reveals the time-dependent label half-life and transit-time in dynamical systems. BMC Systems Biology 9, 2012, 13

[228] J. Bachmann, A. Raue, M. Schilling, V. Becker, J. Timmer, U. Klingmüller.
Predictive mathematical models of cancer signaling pathways. J. Internal Medicine 271, 2012, 155-165

[227] V. Becker, J. Timmer, U. Klingmuller.
Receptor dynamics in signaling. Adv. Exp. Med. Biol. 736, 2012, 313-323

[226] L. Sommerlade, M. Thiel, B. Platt, A. Plano, G. Riedel, C. Grebogi, J. Timmer, B. Schelter.
Inference of Granger causal time-dependent influences in noisy multivariate time series. J. Neuroscience Methods 203, 2012, 173-185

[225] D.B. Den Ouden, D. Saur, W. Mader, B. Schelter, S. Lukic, E. Wali, J. Timmer, C.K. Thompson.
Network modulation during complex syntactic processing. NeuroImage 59, 2012, 815-823


[224] M. Reinhard, M. Roth, B. Guschlbauer, M. Czosnyka, J. Timmer, C. Weiller, A. Hetzel.
The course of dynamic cerebral autoregulation during cervical internal carotid artery occlusion. Neurological Research 33, 2011, 921-926

[223] H. Feldwisch-Drentrup, M. Ihle, M. Le Van Quyen, C. Teixeira, A. Dourado, J. Timmer, F. Sales, V. Navarro, A. Schulze-Bonhage, B. Schelter.
Anticipating the unobserved: Prediction of subclinical seizures. Epilepsy & Behavior 11, 2011, S119-S126

[222] M. Lenz, M. Musso, Y. Linke, O. Tüscher, J. Timmer, C. Weiller, B. Schelter.
Joint EEG/fMRI state space model for the detection of directed interactions in human brains. Physiological Measurements 32, 2011, 1725-1736

[221] C.A. Teixeira, B. Direito, H. Feldwisch-Drentrup, M. Valderrama, R.P. Costa, C. Alvarado-Rojas, S. Nikolopoulos, M. Le Van Quyen, J. Timmer, B. Schelter, A. Dourado.
EPILAB: A software package for studies on the prediction of epileptic seizures. J. Neurosciences Methods 200, 2011, 257-271

[220] J. Rausenberger, A. Tscheuschler, W. Nordmeier, F. Wüst, J. Timmer, E. Schäfer, Ch. Fleck, A. Hiltbrunner.
Photoconversion and nuclear trafficking cycles determine phytochrome A's response profile to far-red light. Cell 146, 2011, 813-825
Supplementary Information

[219] J. Bachmann, A. Raue, M. Schilling, M. Böhm, A.C. Pfeifer, C. Kreutz, D. Kaschek, H. Busch, N. Gretz, W.D. Lehmann, J. Timmer, U. Klingmüller.
Division of labor by dual feedback regulators controls JAK2/STAT5 signaling over broad ligand range. Mol. Sys. Bio. 7, 2011, 516
Supplementary Information
SBML model file

[218] H. Feldwisch-Drentrup, M. Staniek, A. Schulze-Bonhage, J. Timmer, H. Dickten, C.E. Elger, B. Schelter, K. Lehnertz.
Identification of preseizure states in epilepsy: A data-driven approach for multichannel EEG recordings. Frontiers in Computational Neuroscience 5, 2011, 32

[217] H. Feldwisch-Drentrup, A. Schulze-Bonhage, J. Timmer, B. Schelter.
Statistical validation of event predictors: A comparative study based on the field of seizure prediction. Phys. Rev. E 83, 2011, 066704. See also Erratum

[216] Maiwald T., Blumberg J., Timmer J., Schulze-Bonhage A.
Are prodromes preictal events? A prospective PDA-based study. Epilepsy & Behavior 21, 2011, 184-188

[215] A. Schad, J. Timmer, M. Roth.
A unified approach to the helioseismic inversion problem of the solar meridional flow from global oscillations. Astrophys. J. 734, 2011, 97

[214] P. Christopoulos, D. Pfeifer, K. Bartholome, M. Follo, J. Timmer, P. Fisch, H. Veelken.
Definition and characterization of the systemic T-cell dysregulation in untreated indolent B cell lymphoma and very early CLL. Blood 117, 2011, 3836-3846

[213] A. Raue, C. Kreutz, T. Maiwald, U. Klingmüller, J. Timmer.
Addressing Parameter identifiability by model-based experimentation. IET Systems Biology 5, 2011, 120-130

[212] M. Warncke, M. Buchner, G. Thaller, A. Dodero, A. Bulashevska, D. Pfeifer, J. Timmer, H. Veelken.
Control of the specificity of T cell-mediated anti-idiotype immunity by natural regulatory T cells. Cancer Immunology Immunotherapy 60, 2011, 49-60

[211] L. Sommerlade, F. Amtage, O. Lapp, B. Hellwig, C.-H. LÜcking, J. Timmer, B. Schelter.
On the estimation of the direction of information flow in networks of dynamical systems. J. Neurosci. Meth. 196, 2011, 182-189

[210] V. Raia, M. Schilling, M. Böhm, B. Hahn, A. Kowarsch, A. Raue, C. Sticht, S. Bohl, M. Saile, P. Möller, N. Gretz, J. Timmer, F. Theis, W.-D. Lehmann, P. Lichter, U. Klingmüller.
Dynamic mathematical modeling of IL13-induced signaling in Hodgkin and primary mediastinal B-cell lymphoma allows prediction of therapeutic targets. Cancer Research 71, 2011, 693-704
Supplementary Information


[209] A. Raue, V. Becker, U. Klingmüller, J. Timmer.
Identifiability and observability analysis for experimental design in non-linear dynamical models. Chaos 20, 2010, 045105
Also published in the Virtual Journal of Biological Physics Research - January 1, 2011

[208] S. Zellmer, W. Schmidt-Heck, A. Bauer, C. Meyer, T. Lehmann, T. Sparna, P. Godoy, J. Amin, W. Schormann, E. Bedawy, S. Hammad, C. Kern, C. Kreutz, J. Timmer, G. Walz, F. von Weizsäcker, P.A. Thürmann, S. Dooley, I. Merfort, R. Guthke, J.G. Hengstler, R. Gebhardt.
The transcription factors ETF, E2F and SP-1 are involved in cytokine-independent proliferation of murine hepatocytes. Hepatology 52, 2010, 2127-2136

[207] H. Feldwisch, B.Schelter, M. Jachan, J. Nawrath, J. Timmer J., A. Schulze-Bonhage.
Joining the benefits: Combining epileptic seizures prediction methods. Epilepsia 51, 2010, 1598-1606

[206] M. Joschko, R. Gebbers, D. Barkusky, J. Timmer.
The apparent electrical conductivity as surrogate variable for predicting earthworm abundances in tilled soil. J. Plant Nutrition Soil Science 173, 2010, 584-590

[205] A.C. Pfeifer, D. Kaschek, J. Bachmann, U. Klingmüller, J. Timmer.
Model-based extension of high-throughput to high-content techniques. BMC Systems Biology 4, 2010, 106

[204] V. Becker, M. Schilling, J. Bachmann, U. Baumann, A. Raue, T. Maiwald, J. Timmer, U. Klingmüller.
Covering a broad dynamic range: Information processing at the erythropoietin receptor. Science 328, 2010, 1404-1408
Supplementary Information
Data and models of the paper

[203] J. Rausenberger, A. Hussong, D. Kirchenbauer, S. Kircher, J. Timmer, F. Nagy, E. Schäfer, C. Fleck.
An integrative model for phytochrome B mediated photomorphogenesis: From protein dynamics to physiology. PLoS ONE 5, 2010, e10721

[202] D. Onichtchouk, F. Geier, B. Polok, D. Messerschmidt, R. Mössner, B. Wendik, S. Song, V. Taylor, J. Timmer, W. Driever.
Zebrafish Pou5f1-dependent transcriptional networks in temporal control of early development. Molecular Systems Biology 6, 2010, 354
Supplementary Information

[201] B. Schelter, H. Feldwisch-Drentrup, J. Timmer, J. Gotman, A. Schulze-Bonhage.
A common strategy and database to compare the performance of seizure prediction algorithms. Epilepsy & Behavior 17, 2010, 154-156

[200] D. Saur, B. Schelter, S. Schnell, D. Kratochvil, H. Küpper, P. Kellmeyer, D. Kümmerer, S. Klöppel, V. Glauche, R. Lange, W. Mader, D. Feess, J. Timmer, C. Weiller.
Combining functional and anatomical connectivity reveals brain networks for auditory language comprehension. Neuroimage 49, 2010, 3187-3197

[199] M. Reinhard, F. Neunhoeffer, T.A. Gerds, W.-D. Niesen, K.-J. Buttler, J. Timmer, B. Schmidt, M. Czosnyka, C. Weiller, A. Hetzel.
Secondary decline of cerebral autoregulation associates with worse outcome after intracerebral hemorrhage. Intensive Care Medicine 36, 2010, 264-271

[198] J. Nawrath, M.C. Romano, M. Thiel, I.Z. Kiss, M. Wickramasinghe, J. Timmer, J. Kurths, B. Schelter.
Distinguishing direct and indirect interactions in oscillatory networks with multiple time scales. Phys. Rev. Lett. 104, 2010, 038701


[197] M. Schilling, T. Maiwald, S. Hengl, D. Winter, C. Kreutz, W. Kolch, W.D. Lehmann, J. Timmer, U. Klingmüller
Theoretical and experimental analysis links isoform-specific ERK signalling to cell fate decisions. Molecular Systems Biology 5, 2009, 334
Supplementary Information
Data analyzed in the paper
SBML-file of the model

[196] L. Sommerlade, M. Eichler, M. Jachan, K. Henschel, J. Timmer, B. Schelter.
Estimating causal dependencies in networks of nonlinear stochastic dynamical systems. Phys. Rev. E 80, 2009, 051128

[195] L. Sommerlade, K. Henschel, J. Wohlmuth, M. Jachan, F. Amtage, B. Hellwig, C.H. Lücking, J. Timmer, B. Schelter.
Time-variant estimation of directed influence during Parkinsonian tremor. J. Physiol.103, 2009, 348-352

[194] J. Rausenberger, C. Fleck, J. Timmer, M. Kollmann.
Signature of gene expression noise in cellular systems. Progress Biophysics Molecular Biology 100, 2009, 57-66

[193] V. Petrov, J. Timmer.
One-dimensional model of somitic cells polarization in a bistability window of embryonic mesoderm. Mechanics in Medicine and Biology 9, 2009, 259-272

[192] F. Amtage, K. Henschel, B. Schelter, J. Vesper, J. Timmer, C.H. Lücking, B. Hellwig.
High functional connectivity of tremor related subthalamic neurons in Parkinson's disease. Clinical Neurophys. 120, 2009, 1755-1761

[191] N. Philippi, D. Walter, R. Schlatter, K.S. Ferreira, M. Ederer, O. Sawodny, J. Timmer, C. Borner, T. Dandekar.
Modeling system states in liver cells: Survival, apoptosis and their modifications in response to viral infection. BMC Systems Biology 3, 2009, 97

[190] M. Jachan, K. Henschel, J. Nawrath, A. Schad, J. Timmer, B. Schelter.
Inferring direct directed information flow from multivariate non-linear time series. Phys. Rev. E 80, 2009, 011138

[189] A. Raue, C. Kreutz, T. Maiwald, J. Bachmann, M. Schilling, U. Klingmüller, J. Timmer.
Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood. Bioinformatics 25, 2009, 1923-1929
Supplementary Information

[188] M. Jachan, M. Reinhard, L. Spindeler, A. Hetzel, B. Schelter, J. Timmer.
Parametric versus nonparametric transfer function estimation of cerebral autoregulation from spontaneous blood-pressure oscillations. Cardiovascular Engineering 9, 2009, 72-82

[187] M. Buchner, S. Fuchs, G. Prinz, D. Pfeifer, K. Bartholome, M. Burger, N. Chevalier, L. Vallat, J. Timmer, J.G. Gribben, H. Jumaa, H. Veelken, C. Dierks, K. Zirlik.
Spleen Tyrosine Kinase (SYK) is overexpressed and represents a potential therapeutic target in chronic lymphocytic leukemia. Cancer Research 69, 2009, 5424-5432

[186] Bartholome K., Kreutz C., Timmer J.
Estimating of gene induction enables a relevance-based ranking of genes sets. J. Comp. Biol. 16, 2009, 959-967

[185] B. Rumberger, C. Kreutz, C. Nickel, M. Klein, S. Lagoutte, S. Teschner, J. Timmer, G. Walz.
Combination of immunosuppressive drugs leaves specific ''fingerprint'' on gene expression in vitro. Immunopharmacology Immunotoxicology 31, 2009, 283-292

[184] K. Wester, S. Digiuni, F. Geier, J. Timmer, C. Fleck, M. Hülskamp.
Functional diversity of R3 single-repeat genes in trichome development. Development 136, 2009, 1487-1496

[183] N. Borisov, E. Aksamitiene, A. Kiyatkin, S. Legewie, J. Berkhout, T. Maiwald, N.P. Kaimachnikov, J. Timmer, J.B. Hoek, B.N. Kholodenko.
Systems-level interactions between insulin-EGF networks amplify mitogenic signaling. Mol. Sys. Bio. 5, 2009, 256

[182] T. Wiech, E. Nikolopoulos, R. Weis, R. Langer, K. Bartholome, J. Timmer, A. Walch, H. Höfler, M. Werner.
Genome-wide analysis of genetic alterations in Barrett's adenocarcinoma using single nucleotide polymorphism arrays. Laboratory Investigation 89, 2009, 385-397

[181] Mammen E., Nandi S., Maiwald T., Timmer J.
Effect of jump discontinuity for phase-randomized surrogate data testing. Int. J. Bif. Chaos 19, 2009, 403-408

[180] B. Schelter, J. Timmer, M. Eichler.
Assessing the strength of directed influences among neural signals using renormalized partial directed coherence. J. Neuroscience Methods 179, 2009, 121-130

[179] S. Lassmann, C. Kreutz, A. Schoepflin, U. Hopt, J. Timmer, M. Werner.
A novel approach for reliable microarray analysis of microdissected tumour cells from formalin-fixed and paraffin-embedded colorectal cancer resection specimens. J. Molecular Medicine 87, 2009, 211-224

[178] Hellwig B., Mund P., Schelter B. Guschlbauer B., Timmer J., Lücking C.H.
A longitudinal study of tremor frequencies in Parkinson's disease and essential tremor. Clinical Neurophysiology 120, 2009, 431-435

[177] M. Gerstung, J. Timmer, C. Fleck.
Noisy signalling through promoter logic gates. Phys. Rev. E 79, 2009, 11923

[176] Kreutz C., Timmer J.
Systems biology: experimental design. FEBS Journal 276, 2009, 923-942

[175] M. Joschko, R. Gebbers, D. Barkusky, J. Rogasik, W. Höhn, W. Hierold, C.A. Fox, J. Timmer.
Location-dependency of earthworm response to reduced tillage on sandy soil. Soil & Tillage Research 102, 2009, 55-66


[174] W. Mader, D. Feess, R. Lange, D. Saur, V. Glauche, C. Weiller, J. Timmer, B. Schelter.
On the detection of direct directed information flow in fMRI. IEEE J. Sel. Topics in Signal Processing 2, 2008, 965-974

[173] K. Henschel, B. Hellwig, F. Amtage, M. Jachan, C.H. Lücking, J. Timmer, B. Schelter.
Multivariate Analyis of dynamical processes: Point processes and time series. Europ. Phys. J. 165, 2008, 25-34

[172] F. Geier, J.U. Lohmann, M. Gerstung, A.T. Maier, J. Timmer, C. Fleck.
A quantitative and dynamic model for plant stem cell regulation. PLoS One 3, 2008, e3553

[171] M. Reinhard, T.A. Gerds, D. Grabiak, P. Zimmermann, M. Roth, B. Guschlbauer, J. Timmer, M. Czosnyka, C. Weiller, A. Hetzel.
Cerebral dysautoregulation and the risk of ischemic events in occlusive carotid artery disease. J. Neurology 255, 2008, 195-199

[170] M. Reinhard, Z. Waldkircher, B. Guschlbaur, J. Timmer, C. Weiller, A. Hetzel.
Cerebellar autoregulation dynamics in humans. J. Cerebral Blood Flow Metabolism 28, 2008, 1605-1612

[169] S. Digiuni, S. Schellmann, F. Geier, B. Greese, M. Pesch. K. Wester, B. Dartan, V. Mach, B. P. Srinivas, J. Timmer, C. Fleck, M. Hülskamp.
A competitive complex formation mechanism underlies trichome patterning on Arabidopsis leaves. Mol. Sys. Bio. 4, 2008, 217
Supplementary Information

[168] T. Maiwald, J. Timmer
Dynamical modeling and multi-experiment fitting with PottersWheel. Bioinformatics 24, 2008, 2037-2043
Supplementary Information

[167] F. Amtage, K. Henschel, B. Schelter, J. Vesper, J. Timmer, C. Weiller, C.H. Lücking, B. Hellwig.
Tremor-correlated neuronal activity in the subthalamic nucleus of Parkinsonian patients. Neuroscience Lett. 442, 2008, 195-199

[166] M. Joschko, J. Oehley, R. Gebbers, M. Wiemer, J. Timmer, C.A. Fox.
A spatial approach to soil-ecological experimentation at landscape scale. J. Plant Nutr. Soil Science 171, 2008, 339-343

[165] M. Reinhard, C. Wihler, M. Roth, A. Harloff, W.-D. Niesen, J. Timmer, C. Weiller, A. Hetzel.
Cerebral autoregulation dynamics in acute ischemic stroke after rtPA thrombolysis. Cerebrovascular Diseases 26, 2008, 147-155

[164] Bartholome K, Timmer J.
Regulatory principles and systems analysis of bacterial chemotaxis. AT Automatisierungstechnik 56, 2008, 241-249

[163] D. Bouyer, F. Geier, F. Kragler, A. Schnittger, M. Pesch, K. Wester, R. Balkunde, J. Timmer, C. Fleck, M. Hülskamp.
Two-dimensional patterning by a trapping/depletion mechanism: The role of TTG1 and GL3 in Arabidopsis trichome formation. PloS Biology 6, 2008, e141

[162] J. Vera , J. Bachmann, A.C. Pfeifer, V. Becker, J.A. Hormiga, N.V. Torres Darias, J. Timmer, U. Klingmüller, O. Wolkenhauer.
A systems biology approach to analyse amplification in the JAK2-STAT5 signalling pathway. BMC Systems Biology 2, 2008, 38
Supplementary Information

[161] E. Balsa-Canto, M. Peifer, J.R. Banga, J. Timmer, C. Fleck.
Hybrid optimization method with general switching strategy for parameter estimation. BMC Systems Biology 2, 2008, 26

[160] A. Schad, K. Schindler, M. Winterhalder, B. Schelter, T. Maiwald, A. Brandt, J. Timmer, A. Schulze-Bonhage.
Application of a multivariate seizure detection and prediction method to non-invasive and intracranial long-term EEG recordings. Clinical Neurophysiology 119, 2008, 197-211


[159] T. Maiwald, C. Kreutz, A. Pfeifer, S. Bohl, U. Klingmüller, J. Timmer.
Dynamic pathway modeling - Feasibility analysis and optimal experimental design. Annals New York Acad. Sci. 1115, 2007, 212-220

[158] Winterhalder M., Schelter B., Timmer J.
Detecting coupling directions in multivariate oscillatory systems. Int. J. Bif. Chaos 17, 2007, 3735-3739

[157] Schelter B., Winterhalder M., Kurths J., Timmer J.
Phase synchronization and coherence analysis: sensitivity and specificity. Int. J. Bif. Chaos 17, 2007, 3551-3556

[156] E. Anastasiou, S. Kenz, M. Gerstung, D. MacLean, J. Timmer, C. Fleck, M. Lenhard.
Control of plant organ size by KLUH/CYP78A5-dependent intracellular signalling. Developmental Cell 13, 2007, 843-856

[155] C. Kreutz, M.M. Bartholome Rodriguez, T. Maiwald, M. Seidl, H.E. Blum, L. Mohr, J. Timmer.
An error model for protein quantification. Bioinformatics 23, 2007, 2747-2753
Supplementary Information

[154] Hengl S., Kreutz C., Timmer J. Maiwald T.
Data-based identifiability analysis of nonlinear dynamical models. Bioinformatics 23, 2007, 2612-2618
Supplementary Information

[153] Rumberger B., Vonend O., Kreutz C., Wilpert J., Donauer J., Amann K., Rohrbach R., Timmer J., Walz G., Gerke P.
cDNA mircoarray analysis of adaptive changes after renal ablation in a sclerosis-resistant mouse strain. Kidney Blood Pressure Res. 30, 2007, 377-378

[152] Bartholome K., Rius M., Letschert K., Keller D. Timmer J., Keppler D.
Data-based mathematical modeling of vectorial transport across double-transfected polarized cells. Drug Metabolism and Disposition 35, 2007, 1476-1481
Supplementary Information

[151] Reinhard M., Wehrle-Wieland E., Roth M., Niesen W.D., Timmer, J. Weiller C., Hetzel A.
Preserved dynamic cerebral autoregulation in the middle cerebral artery among persons with migraine. Exp. Brain Res. 180, 2007, 517-523

[150] Schelter B., Peifer M., Winterhalder M., Timmer J.
Testing for phase synchronization. Phys. Lett. A 366, 2007, 382-390

[149] Peifer M., Timmer J.
Parameter estimation in ordinary differential equations for biochemical processes using the method of multiple shooting. IET Systems Biology 1, 2007, 78-88.
Please find here the code of the multiple shooting implementation used in the manuscript. Please note that we do not provide any support or warranties of the results generated.

[148] Lindenmeyer M.T., Kern C., Sparna T. Donauer J., Wilpert J., Schwager J., Porath D. Kreutz C., Timmer J., Merfort I.
Microarray analysis reveals influence of the sesquiterpene lactone parthenolide on gene transcription profiles in human epithelial cells. Life Sciences 80, 2007, 1608-1618

[147] Geier F., Timmer J., Fleck C.
Reconstructing gene-regulatory networks from time series, knock-out data, and prior knowledge. BMC Systems Biology 1, 2007, 11

[146] Schelter B., Winterhalder M., Feldwisch H., Wohlmuth J., Nawrath J., Brandt A., Schulze-Bonhage A., Timmer J.
Seizure prediction: The impact of long prediction horizons. Epilepsy Research 73, 2007, 213-217

[145] Smirnov D., Schelter B., Winterhalder M., Timmer J.
Revealing direction of coupling between neuronal oscillators from time series: Phase dynamics modeling versus partial directed coherence. Chaos 17, 2007, 013111

[144] Pfeifer D., Pantic M., Skatulla I., Rawluk J., Kreutz C., Martens U., Fisch P., Timmer J., Veelken H.
Genome-wide analysis of DNA copy number changes in CLL using high-density SNP arrays. Blood 109, 2007, 1202-1210


[143] Sick S., Reinker S., Timmer J., Schlake T.
WNT and DKK determine hair follicle spacing through a reaction-diffusion mechanism. Science 314, 2006, 1447-1450
Supplementary Information
Science Perspective
Preview in Cell

[142] Schelter B., Winterhalder M., Maiwald T., Brandt A., Schad A., Timmer J., Schulze-Bonhage A.
Do false predictions of seizure depend on the state of vigilance? A report from two seizure prediction methods and proposed remedies. Epilepsia 47, 2006, 2058-2070

[141] Klingmüller U., Bauer A., Bohl S., Nickel P., Breitkopf K., Dooley S., Zellmer S., Kern C., Merfort I, Sparna T., Donauer J., Walz G., Geyer M., Kreutz C., Hermes M., Götschel F., Hecht A., Walter D., Egger L., Neubert K., Borner C., Brulport M., Schormann W., Sauer C., Baumann F., Preiss R., MacNelly S., Godoy P., Wiercinska E., Ciuclan L., Edelmann J., Kleemann W.J., Zeilinger K., Heinrich M., Zanger U.M., Reuss M., Bader A., Gebhardt R., Maiwald T., Timmer J., von Weizsäcker F., Hengstler J.G.
Primary mouse hepatocytes for systems biology approaches: a standardized in vitro system for modelling of signal transduction pathways. IEE Proc. Systems Biology 153, 2006, 433-447

[140] Winterhalder M., Schelter B., Hesse W., Schwab K., Leistritz L., Timmer J. and Witte H.
Detection of directed information flow in multidimensional biosignals. Biomed. Tech. 51, 2006, 281-287

[139] Warnke P.C., Kopitzki K., Timmer J., Ostertag C.B.
Capillary physiology of human medulloblastoma - Impact on chemotherapy. Cancer 107, 2006, 2223-2227

[138] Reinhard M., Wehrle-Wieland E., Grabiak D., Roth M., Guschlbauer B., Timmer J., Weiller C., Hetzel A.
Oscillatory cerebral hemodynamics - the macro- vs. microvascular level. J. Neurol. Sci. 250, 2006, 103-109

[137] Winterhalder M., Schelter B., Schulze-Bonhage A., Timmer J.
Comment on: "Performance of a seizure warning algorithm based on the dynamics of intracranial EEG". Epilepsy Res. 72, 2006, 80-81

[136] Winterhalder M., Schelter B., Maiwald T., Brandt A., Schad A., Schulze-Bonhage A., Timmer J.
Spatio-temporal patient-individual assessment of synchronization changes for epileptic seizure prediction. Clin. Neurophys. 117, 2006, 2399-2413

[135] Schieren G., Rumberger B., Klein M., Kreutz C., Wilpert J., Geyer M., Faller D., Timmer J., Quack I., Rump L.C., Walz G., Donauer J.
Gene profiling of polycystic kidneys. Nephrol. Dial. Transplant. 21, 2006, 1816-1824

[134] Reinker S., Altman R.M., Timmer J.
Parameter estimation in stochastic biochemical reactions. IEE Trans. Syst. Biol. 153, 2006, 168-178

[133] Winterhalder M., Schelter B., Kurths J., Schulze-Bonhage A., Timmer J.
Sensitivity and specificity of coherence and phase synchronization analysis. Phys. Lett. A 356, 2006, 26-34

[132] Petrov V., Peifer M., Timmer J.
Bistability and self-oscillations in cell cycle control. Int. J. Bif. Chaos 16, 2006, 1057-1066

[131] Fang X., Zeisel M.B., Wilpert J., Gissler B., Thimme R., Kreutz C., Maiwald T., Timmer J., Kern W.V., Donauer J., Geyer M., Walz G., Delpa E., von Weizsäcker F., Blum H.E., Baumert T.F.
Host cell responses induced by Hepatitis C virus binding. Hepatology 43, 2006, 1326-1336

[130] Schelter B., Winterhalder M. Kurths J., Dahlhaus R., Timmer J.
Partial-phase synchronization for multivariate synchronizing systems. Phys. Rev. Lett. 96, 2006, 208103

[129] The Y.-K., Fernandez J., Popa M.O., Alekov A.K., Timmer J., Lerche H.
Modeling of single non-inactivating Na channels: evidence for two open and several fast inactivated states. Biophys. J. 90, 2006, 3511-3522

[128] Schelter B., Winterhalder M., Eichler M., Peifer M., Hellwig B., Guschlbauer B., Lücking C.H., Dahlhaus R., Timmer J.
Testing for directed influences among neural signals using partial directed coherence. Journal of Neuroscience Methods 152, 2006, 210-219

[127] The Y.-K., Timmer J.
Analysis of single ion channel data incorporating time interval omission and sampling. J. Roy. Soc. Interface 3, 2006, 87-97

[126] Schelter, B., Winterhalder M., Maiwald T., Brandt A., Schad A., Schulze-Bonhage A., Timmer J.
Testing statistical significance of multivariate time series methods for epileptic seizure prediction. Chaos 16, 2006, 013108

[125] Joschko M., Fox,C., Lentzsch P., Kiesel J., Hierold W., Krück S., Timmer J.
Spatial analysis of earthworm biodiversity at the regional scale. Agriculture, Ecosystems & Environment 112, 2006, 367-380

[124] Schelter B., Winterhalder M., Hellwig B., Guschlbauer B., Lücking C.H., Timmer J.
Direct or Indirect ? Graphical models for neural oscillators. J. Physiol. 99, 2006, 37-46


[123] Kollmann M., Bartholome K., Lovdok L., Timmer J., Sourjik V.
Design principles of a bacterial signalling network. Nature 438, 2005, 504-507
Supplementary Information

[122] Schilling M,. Maiwald T., Bohl S., Kollmann M., Kreutz C., Timmer J., Klingmüller U.
Quantitative data generation for systems biology - the impact of randomisation, calibrators and normalisers. IEE Proc. Systems Biology 152, 2005, 193-200

[121] Schilling M., Maiwald T., Bohl S., Kollmann M., Kreutz C., Timmer J., Klingmüller U.
Computational processing and error reduction strategies for standardized quantitative data in biological networks. FEBS Journal 272, 2005, 6400-6411
Supplementary Information

[120] Winterhalder M., Schelter B., Hesse W., Schwab K., Leistritz L., Klan D., Bauer R., Timmer J., Witte H.
Comparison of linear signal processing techniques to infer directed interactions in multivariate neural systems. Signal Processing 85, 2005, 2137-2160

[119] Peifer M., Schelter B., Winterhalder M., Timmer J.
Mixing properties of the Rossler system and consequences for coherence and synchronization analysis. Phys. Rev. E 72, 2005, 026213

[118] Reinhard M., Roth M., Guschlbauer B., Harloff A., Timmer J., Czosnyka M., Hetzel A.
Dynamic cerebral autoregulation in acute ischemic stroke assessed from spontaneous blood pressure fluctuations. Stroke 36, 2005, 1684-1689

[117] Peifer M., Schelter B., Guschlbauer B., Hellwig B., Luecking C.H., Timmer J.
On studentising and blocklength selection for the bootstrap on time series. Biometrical Journal 47, 2005, 346-357

[116] Petrov V., Peifer M., Timmer J.
Structural stability analysis of a cell cycle control model. Comptes rendus de l'Acad. Bulg. Sci. 58, 2005, 19-24

[115] The Y.-K., Fernandez J., Popa O., Lerche H., Timmer J.
Estimating rate constants from single ion channel currents when the initial distribution is known. Eur. Biophys. J. 34, 2005, 306-313

[114] Goerttler P.S., Kreutz C., Donauer J., Faller D., Maiwald T., Klein M., März E., Rumberger B. Sparna T., Schmitt-Gräff A., Wilpert J., Timmer J., Walz G., Pahl H.
Gene Expression Profiling in Polycythemia vera: Overexpression of transcription factor NF-E2. British Journal of Haematology 129, 2005, 138-150

[113] Warnke P.C., Timmer J., Ostertag C.B., Kopitzki K.
Capillary physiology and drug delivery in central nervous system lymphomas. Annals Neurology 57, 2005, 136-139


[112] von Gruenberg H.H., Peifer M., Timmer J., Kollmann M.
Variations in substitution rate in human and mouse genomes. Phys. Rev. Lett. 93, 2004, 208102

[111] Rossberg A., Bartholome K., Voss H.U., Timmer J.
Phase synchronization from noisy univariate signals. Phys. Rev. Lett. 93, 2004, 154103

[110] Petrov V., Timmer J.
Bifurcation Analysis of a Cell Mitosis Control Model. J. Theor. Appl. Mech. 34, 2004, 87-100

[109] Petrov V., Nikolova E., Timmer J.
Dynamical Analysis of Cell Function Models. A Review. J. Theor. Appl. Mech. 34, 2004, 55-78

[108] Petrov V., Peifer M., Timmer J.
Constructing Dynamical Model of Cell Cycle Control. Comptes Rendus de l'Acad. Bulg. Sci. 57, 2004, 15-22

[107] Maraun D., Rust H., and Timmer, J.
Tempting long-memory - on the interpretation of DFA results. Nonlinear Processes in Geophysics 11, 2004, 495-503

[106] Steltner H., Vogel A., Sprung E., Timmer J., Guttmann J., Sorichter S.
Incomplete forced expiration - estimating vital capacity by a mathematical method. Respiration 71, 2004, 353-359

[105] Raethjen J., Lauk M., Pawlas F., Koster B., Fietzek U., Friege L., Timmer J., Lucking C.H., Deuschl G.
Tremor analysis in two normal cohorts. Clin. Neurophys. 115, 2004, 2151-2156

[104] Müller T.G., Faller D., Timmer J., Swameye I., Sandra O., Klingmüller U.
Tests for cycling in a signalling pathway. J. Roy. Stat. Soc. C: Applied Stat. 53, 2004, 557 - 568

[103] Thiel M., Romano, M.C., Schwarz U., Kurths J., Timmer J.
Surrogate based hypothesis test without surrogates. Int. J. Bif. Chaos 14, 2004, 2107-2114

[102] Maraun D., Horbelt W., Rust H., Timmer J., Happersberger H.P., Drepper F.
Identificaton of rate constants and non-observable absorption spectra in nonlinear biochemical reaction dynamics. Int. J. Bif. Chaos 14, 2004, 2081-2092

[101] Müller T.G., Timmer J.
Parameter identification techniques for partial differential equations. Int. J. Bif. Chaos 14, 2004, 2053-2060

[100] Timmer J., Müller T.G., Swameye I., Sandra O., Klingmüller U.
Modelling the nonlinear dynamics of cellular signal transduction. Int. J. Bif. Chaos 14, 2004, 2069-2079

[99] Voss H.U., Timmer J., Kurths J.
Nonlinear dynamical system identification from uncertain and incomplete measurements. Int. J. Bif. Chaos 14, 2004, 1905-1933

[98] Maiwald T., Winterhalder M., Aschenbrenner-Scheibe R., Voss H.U., Schulze-Bonhage A., Timmer J.
Comparison of three nonlinear seizure prediction methods by means of the seizure prediction characteristic. Physica D 194, 2004, 357-368

[97] Reinhard M., Roth M., Muller T, Guschlbauer B., Czosnyka M., Timmer J, Hetzel A.
Effect of carotid endarterectomy or stenting on impairment of dynamic cerebral autoregulation. Stroke 35, 2004, 1381-1387

[96] Raethjen J., Lindemann M., Morsnowski A., Dümpelmann M., Wenzelburger R., Stolze H., Fietzek U., Pfister G., Elgar C.E., Timmer J., Deuschl G.
Is the rhythm of physiological tremor involved in cortico-cortical interactions ? Movement Disorders 19, 2004, 458-465

[95] Faller D., Reinheckel T., Wenzler D., Hagemann S., Xiao K., Honerkamp J., Peters Ch., Dandekar T., Timmer J.
An open source protein gel documentation system for proteome analyses, J. Chem. Inf. Comp. Sci. 44, 2004, 168-169

[94] Bertram C.D., Timmer J., Muller T.G., Maiwald T., Winterhalder M., Voss H.U.
Aperiodic flow-induced oscillations of collapsible tubes: a critical reappraisal. Medical Engineering & Physics 26, 2004, 201-214

[93] Rossberg A.G., Bartholome K., Timmer J.
Data driven optimal filtering for phase and frequency of noisy oscillations application to vortex flowmetering. Phys. Rev. E 69, 2004, 016216

[92] Rossberg A.G., Riegler P., Buhl F., Herwig J., Timmer J.
Detection of improper installation from the sensor signal of vortex flowmeters. Flow Measurement and Instrumentation 15, 2004, 29-35


[91] Faller D., Klingmüller U., Timmer J.
Simulation methods for optimal experimental design in systems biology. Simulation: Trans. Soc. Modeling Computer Simulation 79, 2003, 717-725

[90] Müller T., Lauk M., Reinhardt M., Hetzel A., Lücking C.H., Timmer J.
Estimation of time-delays in biological systems, Annals Biomed. Eng. 31, 2003, 1423-1439

[89] Reinhard M., Müller T., Roth M., Guschlbauer B., Timmer J., Hetzel A.
Bilateral severe carotid artery stenosis or occlusion - cerebral autoregulation dynamics and collateral flow patterns Acta Neurochirurgica 145, 2003, 1053-1060

[88] Peifer M., Timmer J., Voss H.U.
Non-parametric identification of non-linear oscillating systems. J. Sound Vib. 267, 2003, 1157-1167

[87] Aschenbrenner-Schiebe R., Maiwald T., Winterhalder M., Voss H.U., Timmer J., Schulze-Bonhage A.
How well can epileptic seizures be predicted? An evaluation of a nonlinear method. Brain 216, 2003, 2616-2626

[86] Donauer J., Rumberger B.G., Klein M., Faller D., Wilpert J., Sparna T., Schieren G., Rohrbach R., Dern P., Timmer J., Pisarski P., Kirste G., Walz G.
Expression profiling on chronically rejected transplant kidneys. Transplantation 76, 2003, 539-547.

[85] Reinhard, M., Roth, M., Müller, T., Czosnyka, M., Timmer, J., Hetzel, A.
Cerebral autoregulation in carotid artery occlusive disease assessed from spontaneous blood pressure fluctuations by the correlation coefficient index. Stroke 34, 2003, 2138-2244

[84] Kappler B., Tuchbreiter A., Faller D., Liebetraut P., Horbelt W., Timmer J., Honerkamp J., Mülhaupt R.
Real-time monitoring of ethene/1-hexene copolymerizations: Determination of catalyst activity, copolymer composition and copolymerization parameters. Polymer 44, 2003, 6179-6186

[83] Faller D., Voss H.U., Timmer J., Hobohm U.
Normalization of DNA-mircoarray data by nonlinear correlation maximization. J. Comp. Biol. 10, 2003, 751-761

[82] Reinhard M., Roth M., Müller T., Guschlbauer B., Timmer J., Hetzel A.
Dynamic cerebral autoregulation and collateral flow patterns in patients with severe carotid stenosis or occlusion. Ultrasound Med. Biol. 29, 2003, 1105-1113

[81] Hellwig B., Schelter B., Guschlbauer B., Timmer J., Lücking C.H.
Dynamic synchronisation of central oscillators in essential tremor. Clinical Neurophysiology 114, 2003, 1462-1467

[80] Voss H.U., Rust H., Horbelt W., Timmer J.
A combined approach for the identification of continuous nonlinear systems. Int. J. Adaptive Control 17, 2003, 335-352

[79] Winterhalder M., Maiwald T., Aschenbrenner-Schiebe R., Voss H.U., Timmer J., Schulze-Bonhage A.
The seizure prediction characteristic: A general framework to assess and compare seizure prediction methods. Epilepsy and Behavior 4, 2003, 318-325

[78] Horbelt W., Timmer J.
Asymptotic scaling laws for precision of parameter estimates in dynamical systems. Phys. Lett. A 310, 2003, 269-280

[77] Müller T., Reinhard M., Oehm E., Hetzel A., Timmer J.
Detection of very low frequency oscillations of cerebral hemodyamics is influenced by data detrending. Med. & Biol. Eng. & Comp. 41, 2003, 69-74

[76] Swameye I., Müller T.G., Timmer J., Sandra O., Klingmüller U.
Identification of nucleocytoplasmic cycling as a remote sensor in cellular signaling by data-based modeling. Proc. Natl. Acad. Sci. 100, 2003, 1028-1033.
Supplementary Information
Data analyzed in the paper

[75] Reinhard M., Müller T., Guschlbauer B., Timmer J., Hetzel A.
Transfer function analysis for clinical evaluation of dynamic of cerebral autoregulation - a comparison between spontaneous and respiratory-induced oscillations. Physiological Measurement 24, 2003, 27-45.

[74] Horbelt W., Timmer J., Bünner M., Meucci R., Ciofini M.
Dynamical modelling of measured time series from a Q-switched CO_2 laser. Chaos, Solitons & Fractals 17, 2003, 397-404


[73] Kopitzki K., Saparin P., Kurths J., Warnke P., Timmer J.
Comment on ''Kullback-Leibler and renormalized entropies: Application to electroencephalograms of epileptic patients'' Phys. Rev. E 66, 2002, 043902

[72] Horbelt W., Voss H.U., Timmer J.
Parameter estimation in nonlinear delayed feedback systems from noisy data. Phys. Lett. A 299, 2002, 513-521

[71] Müller T.G., Timmer J.
Fitting parameters in partial differential equations from partially observed noisy data. Physica D 171, 2002, 1-7

[70] Altenburger R., Heitz C., Timmer J.
Analysis of phase resolved partial discharge patterns of voids based on a stochastic process approach. J. Physics D: Applied Physics 35, 2002, 1149-1163

[69] Köster B., Deuschl G., Lauk M., Timmer J., Guschlbauer B., Lücking C.H.
Essential tremor and cerebellar dysfunction: Abnormal ballistic movements. J. Neurology, Neurosurgery, Psychiatry 73 , 2002, 400-405

[68] Walkenhorst O., Luther J., Reinhart Ch., Timmer J.
Dynamic annual indoor illuminance simulations based on one-hour and one-minute means of irradiance data. Solar Energy 72, 2002, 385-395

[67] Steltner H., Staats R., Timmer J., Vogel M., Guttmann J., Matthys H., Virchow J.C.
Diagnosis of sleep apnea based on automatic analysis of nasal pressure and forced oscillation impedance. Am. J. Resp. Crit. Care Med. 165, 2002, 940-944. Supplement

[66] Kristeva-Feige R., Fritsch Ch., Timmer J., Lücking C.H.
Influence of distraction of attention and precision level of exerted force on beta range EEG-EMG synchronization during maintainted motor contraction task. Clin. Neurophys. 113, 2002, 124-131

[65] The Y.-K., Wagner M., Timmer J.
Method Independent Effects in Testing for Detailed Balance in Ion Channels Gating. Biophys. J. 82, 2002, 2275-2276

[64] Müller T., Noykova N., Gyllenberg M., Timmer J.
Parameter identification in a dynamical model of anaerobic waste water treatment processes. Math. Biosciences 177-178, 2002, 147-160

[63] Noykova N., Müller T., Gyllenberg M., Timmer J.
Quantitative analysis of anaerobic wastewater treatment processes: identifiability and parameter estimation. Biotech. & Bioeng. 78, 2002, 89-103

[62] Raethjen J., Lindemann M., Dümpelmann M., Wenzelburger R., Stolze H., Pfister G., Elgar C., Timmer J., Deuschl G.
Corticomuscular coherence in the 6-15 Hz band. Does the central component of physiological tremor originate from the cortex? Exp. Brain. Res. 142, 2002, 32-40


[61] Michalek S., Wagner M., Vach W., Timmer J.
Finite size properties of maximum likelihood estimators and likelihood ratio tests in Hidden Markov Models. Biometrical J. 43, 2001, 863-879

[60] Lindemann M., Raethjen J., Timmer J., Deuschl G., Pfister G.
Delay estimation for cortico-peripheral relations. J. Neuroscience Methods 111, 2001, 127-139

[59] Lauk M., Timmer J., B. Guschlbauer, Hellwig B. Lücking C.H.
Variability of frequency and phase between antagonistic muscle pairs in pathological human tremors. Muscle & Nerve 24, 2001, 1365-1370

[58] Horbelt W., Timmer J., Bünner M.J., Meucci R., Ciofini M.
Identifying physical properties of a C02 laser by dynamical modeling of measured time series. Phys. Rev. E 64, 2001, 016222

[57] Steltner H., Vogel A., Sorichter S., Guttmann J., Matthys H., Timmer J.
Analysis of forced expired volume signals using multiexponential functions. Med. & Biol. Eng. & Comp. 39, 2001, 190-194

[56] Hellwig B., Häußler S., Schelter B., Lauk M., Guschlbauer B., Timmer J., Lücking C.H.
Tremor-correlated cortical activity in essential tremor. The Lancet 357, 2001, 519-523

[55] Wagner M., Timmer J.
Model selection in non-nested Markov models for ion channel gating J. Theo. Biol. 208, 2001, 439-450


[54] Timmer J., Rust H., Horbelt W., Voss H.U.
Parametric, nonparametric and parametric modeling of a chaotic circuit time series. Phys. Lett. A 274, 2000, 123-134

[53] Wagner M., Timmer J.
The effects of non-identifiability on testing for detailed balance in aggregated Markov models of ion-channel gating. Biophys. J. 79, 2000, 2918-2924

[52] Timmer J.
What can be inferred from surrogate data testing? Phys. Rev. Lett. 85, 2000, 2647

[51] Reisch S., Timmer J., Steltner H., Rühle K.H., Ficker J.H., Guttmann J.
Detection of obstructive sleep apnea by analysis of phase angle signal using the forced oscillation signal. Respiration Physiology 123, 2000, 87-99

[50] Reisch S., Daniuk J., Steltner H., Timmer J., Rühle K.H., Geiger K., Guttmann J.
Detection of different disordered breathing pattern with the forced oscillation technique compared to 3 polysomnographic signals. Respiration 67, 2000, 518-525

[49] J. Timmer, M. Lauk, S. Häußler, V. Radt, B. Köster, B. Hellwig, B. Guschlbauer, C.H. Lücking, M. Eichler, G. Deuschl
Cross-spectral analysis of tremor time series. Int J Bif Chaos 10, 2000, 2595-2610

[48] Timmer J.
Parameter estimation in nonlinear stochastic differential equations. Chaos, Solitons & Fractals 11, 2000, 2571-2578

[47] S. Michalek, M. Wagner, and J. Timmer.
Maximum approximate likelihood estimator for MA-filtered hidden Markov models. IEEE Trans Signal Proc 48, 2000, 1537-1547

[46] B. Hellwig, S. Häussler, M. Lauk, B. Köster, B. Guschlbauer, R. Kristeva-Feige, J. Timmer, and C.H. Lücking.
Tremor-correlated cortical activity detected by electroencephalography. Electroencephalography and Clinical Neurophysiology 111 2000, 806-809

[45] Timmer J., Häußler S., Lauk M., Lücking C.H.
Pathological tremors: Deterministic chaos or nonlinear stochastic oscillators ? Chaos 10, 2000, 278-288
Data analyzed in this paper

[44] Müller T., Ball T., Kristeva-Feige R., Mergner T., Timmer J.
Selecting relevant electrode positions for classification tasks based on the electro-encephalogram. Medical & Biological Engineering & Computing 38, 2000, 62-67

[43] Timmer J., Schwarz U., Voss H.U., Wardinski I., Belloni T., Hasinger G., van der Klis M., Kurths J.
Linear and nonlinear time series analysis of the black hole candidate Cygnus X-1. Phys. Rev. E 61, 2000, 1342-1352


[42] Michalek S., Timmer J.
Estimating rate constants in Hidden Markov Models by the EM algorithm. IEEE Trans. Signal Proc. 47, 1999, 226-228

[41] König M., Paunzen E., Timmer J.
On the irregular behaviour of the variable star R Scuti. Monthly Notices Royal Astronomical Society 303, 1999, 297-300

[40] Timmer J., Lauk M., Vach W., Lücking C.H.
A test for a difference between spectral peak frequencies. Comp Stat Data Analysis 30, 1999, 45-55

[39] Köster B., Lauk M., Timmer J., Poersch M., Guschlbauer B., Glocker F.X., Deuschl G., Lücking C.H.
Involvement of cranial muscles in orthostatic tremor. Ann. Neur. 45, 1999, 384-388

[38] Lücking C.-H., Köster B., Guschlbauer B., Lauk M., Timmer J.
Parkinsonian and essential tremor: Different entities or different manifestations of the same disorder ? Advances in Neurology 80, 1999, 335-339

[37] Lauk M., Timmer J., Lücking C.H., Honerkamp J., Deuschl G.
A software for recording and analysis of human tremor. Computer Methods and Programs in Biomedicine 60, 1999, 65-77

[36] Reisch S., Steltner H. Renotte C., Timmer J., Guttmann J.
Early detection of upper airway obstruction by analysis of acoustical respiratory input impedance. Biolog. Cybern. 81, 1999, 25-37

[35] Glocker F.X., Lauk M., Föll D., Köster B., Guschlbauer B., Timmer J., Deuschl G., Lücking C.H.
Classical conditioning of the electrically elicited blink reflex in humans: A new method of data analysis. J. Neuroscience Methods 89, 1999, 133-140

[34] S. Michalek, H. Lerche, M. Wagner, N. Mitrovic, M. Schiebe, F. Lehmann-Horn and J. Timmer.
On identification of sodium channel gating schemes using moving-average filtered hidden Markov models. Europ. Biophys. J. 28, 1999, 605-609

[33] M. Wagner, S. Michalek, and J. Timmer.
Estimating rate constants in aggregated Markov models of ion channel gating with loops and with with nearly equal dwell times. Proc. Roy. Soc. B 266, 1999, 1919-1926

[32] Lauk M., Köster B., Timmer J., Guschlbauer B., Deuschl G. and Lücking C.H.
Side-to-side correlation of muscle activity in physiological and pathological human tremors. Electroencephalography and Clinical Neurophysiology 110, 1999, 1774-1783


[31] Köster B., Lauk M., Timmer J., Winter T., Guschlbauer B. Glocker F.X., Danek A., Deuschl G., Lücking C.H.
Central mechanisms in human enhanced physiological tremor. Neuroscience Letters 241, 1998, 135-138

[30] Gezeck S., Timmer J.
Detecting multimodality in Saccadic reaction time distributions in gap and overlap tasks., Biolog. Cybern. 78, 1998, 293-305

[29] Timmer J., Lauk M., Pfleger W., Deuschl G.
Cross-spectral analysis of physiological tremor and muscle activity. I: Theory and application to unsynchronized EMG. Biolog. Cybern. 78, 1998, 349-357

[28] Timmer J., Lauk M., Pfleger W., Deuschl G.:
Cross-spectral analysis of physiological tremor and muscle activity. II: Application to synchronized EMG. Biolog. Cybern. 78, 1998, 359-368

[27] Timmer J., Müller T., Melzer W.
Numerical methods for the determination of calcium release from calcium transients in muscle data. Biophys. J. 74, 1998, 1694-1706

[26] Timmer J.
The power of surrogate data testing with respect to non-stationarity. PRE 58, 1998, 5153-5156

[25] Kopitzki K., Warnke P., Timmer J.
Quantitative analysis by renormalized entropy of invasive electroencephalograph recordings in focal epilepsy. PRE 58, 1998, 4859-4864

[24] Timmer J.
Modeling noisy time series: Physiological tremor. Int. J. Bif. Chaos 8, 1998, 1505-1516

[23] Reisch S., Schneider M., Timmer J., Geiger K., Guttmann J.
Evaluation of forced oscillation technique for early detection of airway obstruction in sleep apnea: a model study . Tech. Health Care 6, 1998, 245-257


[22] Klein S., Timmer J., Honerkamp J.
Analysis of multichannel patch clamp recordings by Hidden Markov Models. Biometrics 53, 1997, 870-884

[21] Timmer J., Klein S.
Testing the Markov condition in ion channel recordings. Phys. Rev. E 55, 1997, 3306-3310

[20] König M., Friedrich S., Staubert R., Timmer J.
The Seyfert Galaxy NGC 6814 -- a highly variable X-ray source, Astronomy and Astrophysics 322. 1997, 747-750

[19] Gezeck S., Fischer B., Timmer J.
Saccadic reaction times: a statistical analysis of multimodal distributions. Vision Research 37, 1997, 2119-2131

[18] König M., Timmer J.
Analyzing X-ray variability by Linear State Space Models. Astronomy and Astrophysics, SS 124, 1997, 589-596

[17] Timmer J., Lauk M., Lücking C.H.
Confidence regions for spectral peak frequencies. Biometrical J. 39, 1997, 849-861

[16] Timmer J., Weigend A.
Modeling volatility using state space models. Int. J. Neur. Syst. 8, 1997, 385-398

[15] Heitz C., Timmer J.
Using Optimized Time-Frequency Representations for Acoustic Quality Control of Motors. Acta Acoustica 83, 1997, 1053-1064

[14] S. Lauer, J. Timmer, D. van Calker, D. Maier, J. Honerkamp
Optimal weighed Bayesian design applied to dose-response-curve analysis. Communications in Statistics - Theory and Methods 26, 1997, 2879-2903


[13] G. Deuschl, P. Krack, M. Lauk, J. Timmer
Clinical neurophysiology of tremor. Journal of Clinical Neurophysiology 13, 1996, 110-121

[12] Gebicke-Härter P., Christoffel F., Timmer, J., Norhoff H., Berger M., van Calker D.
Both Adenosine A1- and A2-receptors are required to stimulate microglial proliferation, Neurochemistry International 29, 1996, 37-42

[11] Weyerbrock A., Timmer J., Hohagen F., Berger M., Bauer J.
Effects of light and chronotherapie on human circadian rhythm in delayed sleep phase syndrom (DSPS): cytokines, cortisol, growth hormone and the sleep-wake cycle, Biological Psychiatry 40, 1996, 794-797

[10] J. Timmer, M. Lauk, G. Deuschl
Quantitative analysis of tremor time series, Electroencephalography and Clinical Neurophysiology 101, 1996, 461-468

[9] M. Bohus, U. Förstner, C. Kiefer, P. Gebicke-Härter, J. Timmer, G. Spraul, H. Wark, H. Hecht, M. Berger, D. van Calker
Increased sensitivity of the inositol-phospholipid system in neutrophils from patients with acute Major Depressive episodes, Psychiatry Research 65, 1996, 45-61


[8] Krieger S., Timmer J., Lis S., Olbrich H.M.
Some considerations on the Interpretation of Event-Related-Potentials, Journal of Neural Transmission 99, 1995, 103-129

[7] Deuschl G., Lauk M., Timmer J.
Tremor Classification and Tremor Time Series Analysis, Chaos 5, 1995, 48-52

[6] Timmer J., König, M.
On generating power law noise, Astronomy and Astrophysics, 300, 1995, 707-710


[5] Bauer J., Hohagen F., Elbert T., Timmer J., Ganter U., Krieger S., Lis S., Postler E., Voderholzer U., Berger M.
Interleukin-6 Serum Levels in Healthy Persons correspond to the Sleep-Wake-Cycle, Clinical Investigator 72, 1994, 312

[4] Jedynak A., Bach M., Timmer J.
Failure of Dimension Analysis in a simple Five-Dimensional System, Phys. Rev. E 50, 1994, 1770-1780


[3] Timmer, J., Gantert, C., Deuschl, G., Honerkamp, J.
Characteristics of Hand Tremor Time Series, Biol. Cybern. 70, 1993, 75-80

[2] Hohagen F., Timmer J., Weyerbrock A., Fritsch-Monero R., Ganter U., Krieger S., Berger M., Bauer J.:
Cytokine Production during Sleep and Wakefulness and its Relationship to Cortisol in Healthy Humans, Neuropsychobiology 28, 1993, 9-16


[1] Gantert C., Honerkamp J., Timmer J.:
Analysing the dynamics of hand tremor time series, Biol. Cybern. 66, 1992, 479-484

Book and conference contributions, abstracts, complete until 2000


N. Noykova, T. Müller, M. Gyllenberg, J. Timmer: Identifiability problems in a mathematical model of anaerobic digestion, Int. Conf. Automatics and Informatics, A-37-40, 2001

Steltner H., Staats R., Timmer J., Virchow J. C., Matthys H., Guttmann J.: Diagnosis of sleep-disordered breathing based on automatic analysis of nasal pressure and forced oscillation impedance, Proceedings of the International Federation for Medical & Biological Engineering, IX Mediterranean Conference on Medical and Biological Engineering and Computing, 390-393, 2001

Steltner H., Staats R., Timmer J., Virchow J. C., Matthys H., Guttmann J.: Automatische Diagnose schlafbezogener Atmungsstörungen durch Analyse von Resistooszillometrie und Maskendruck, Somnologie 5, 52, 2001

Timmer J., Wagner M.: Modelling ion channel time series by Hidden Markov Models, in: Trends in Statistical Modelling (Eds.: B. Klein, L. Korsholm), 2001, 67-78

Timmer J., Rust H., Horbelt W., Voss H.U.: Identification of a nonlinear circuit, GAMM Conference 2001, in press


Lauk M., Timmer J., Lücking C.H., Deuschl G., Honerkamp J.: An application for the analysis of human tremor time-series, in ''Mathematik - Schlüsseltechnologie für die Zukunft'', Springer, Heidelberg, 2000

Walkenhorst O., Reinhart C. Timmer J.: Jahressimulation des Tageslichtangebotes in Gebäuden auf der Basis von minütlichen und stündlichen Strahlungsdaten, 7. Symposium Innovative Lichttechnik in Gebäuden, Staffelstein, 2000

Steltner H, Vogel M, Timmer J, Sorichter S, Guttmann J: "Modeling of forced expired volume signals using multiexponential functions", Proceedings of the World Congress on Medical Physics and Biomedical Engineering in Chicago, 2000 (On CD-ROM)

Staats R, Steltner H, Sorichter S, Timmer J, Matthys H, Guttmann J, Virchow JC: Apnoeanalyse mittels kardiogener Oszillationen und Resistooszillometrie, Somnologie 4, 25-26, 2000

Steltner H, Staats R, Timmer J, Virchow JC, Matthys H, Guttmann J: Automatische Klassifikation von Schlafapnoen durch Analyse von Atemwegsimpedanz und Maskendruck, Somnologie 4, 60, 2000

Steltner H, Staats R, Vogel M, Timmer J, Virchow C, Matthys H, Guttmann J: Klassifizierung von Schlafapnoen auf der Basis von nasalem Druck und Atemwegsimpedanz, Biomedizinische Technik 45, 440-441, 2000

Steltner H, Vogel M, Timmer J, Sorichter S, Guttmann J, Matthys H: Analysis of forced expired volume signals using multiexponential functions, European Respiratory Journal (Suppl), 2000

Steltner H, Staats R, Vogel M, Timmer J, Virchow C, Matthys H, Guttmann J: Automatic detection and classification of sleep-disordered breathing using nasal pressure and forced oscillation impedance, European Respiratory Journal 16, 453s, 2000

Müller T., Ball T., Kristeva-Feige R., T. Mergner, Timmer J.: Classification of electro-encephalographic spatial patterns, ISMDA-Proceeding, Lecture Notes in Computer Science 1933, Springer, 2000, 55-60

H. Steltner, R. Staats, M. Vogel, J. Guttmann, Timmer J: Detection and classification of sleep-disordered breathing using acoustic respiratory input impedance and nasal pressure, ISMDA-Proceeding, Lecture Notes in Computer Science 1933, Springer, 2000, 61-66

W. Horbelt, T. Müller, J. Timmer, W. Melzer, and K. Winkler: Analysis of Nonlinear Differential Equations: Parameter Estimation and Model Selection, ISMDA-Proceeding, Lecture Notes in Computer Science 1933, Springer, 2000, 152-158

Rust H., Timmer J., Horbelt W. Voss H.: Parametric, nonparametric and parametric modelling of a chaotic circuit time series, NOLTA-Proceedings Vol.2, 713-716, 2000

M. Lindemann, J. Raethjen, J. Timmer, G. Deuschl, G. Pfister: Robust Delay Estimation applied to Cortical and Peripheral Signals. Brain Topography, 2000

Swameye I., Mueller T., Timmer J., Sandra O., Klingmueller U.: Properties of a signalling pathway revealed by dynamical modelling. BLOOD 96, 2000, 4306

Timmer J., Horbelt W., Rust H.:
Estimating parameters in ODEs with application to the first example of the Y2k Benchmarks of Predictability. EGS 2000

Timmer J., Horbelt W., Rust H., Voss H.:
Parametric and non-parametric modeling of time series with application to the second example of the Y2k Benchmarks of Predictability. EGS 2000

Timmer J., Häußler S., Lauk M., Lücking C.-H.
Pathological tremors: Deterministic chaos or nonlinear stochastic oscillators? in D.S. Broomhead, E.A. Luchinskaya, P.V.E. Clintock and T. Mullin, ed., Stochaos: Stochastic and Chaotic Dynamics in the Lakes , American Institute of Physics, Melville, NY, USA, 2000, 197-202

Timmer J., Horbelt W., Bünner M., Ciofini M., Meucci R.
Estimating Parameters in Differential Equations with Application to Laser Data. in D.S. Broomhead, E.A. Luchinskaya, P.V.E. McClintock and T. Mullin, ed., Stochaos: Stochastic and Chaotic Dynamics in the Lakes , American Institute of Physics, Melvilley, NY, USA, 2000, 617-623


Timmer J.
Denoising time series by the Kalman filter. Geophysical Research Abstracts 1, 788, 1999

Hellwig B., Häußler S., Lauk M., Guschlbauer B., Köster B., Kristeva-Feige R., Timmer J., Luecking C.H.
Tremor-correlated cortical activity in essential tremor detected by electroencephalography Clinical Neurophysiology 110, 180, 1999

Wagner M., Michalek S., Timmer J.
Testing for the number of states in Hidden Markov models with application to ion channel data in: Studies in classification, data analysis and knowledge organization, W. Gaul, H. Locarek-Junge (Eds.) GfKL-Proceedings, Dresden, Springer, 1999, 260-267

Wagner M., Lauk M., Timmer J.
Doppelblattkontrolle -- Steigerung der Zuverlässigkeit von Kuvertiermaschinen In: VDI Statusseminar ''Technische Anwendungen von Erkenntnissen der Nichtlinearen Dynamik'', 1999, 251-254

Horbelt W., Timmer J., Honerkamp J., Bünner M.
Estimating parameters in nonlinear differential equations with application to Q-switched lasers In: VDI Statusseminar ''Technische Anwendungen von Erkenntnissen der Nichtlinearen Dynamik'', 1999, 311-314

Michalek S., Wagner M., Timmer J.
New maximum approximate likelihood estimators for moving-average filtered hidden Markov models In: Prague Stochastics, Eds. M. Huskova, P. Lachout, J.A. Visek. 1999

Wagner M., Michalek S., Timmer J.
Hidden Markov Models applied to single ion channel recordings Proc. of 52nd Session of the International Statistical Institute, 1999

Müller T., Horbelt W., Timmer J.:
Analysis of non-linear dynamical systems: estimating parameters and model selection, Theory and Mathematics in Biology and Medicine, Amsterdam, 1999, 355

Müller T., Winkler K., Timmer J.:
Parameter estimation and model selection in ODEs, Equadiff 99, Berlin, 269-270

Steltner H., Timmer J., Guttmann J.:
Acoustical respiratory input impedance with compliant upper airway walls and pharyngeal obstruction: a mathematical model study, Medical and Biological Engineering & Computing 37, 1198-1199, 1999

Steltner H., Timmer J., Guttmann J.:
Acoustical imput impedance, an early indicator of obstructive sleep apneas: a theoretical study, Sleep Research Online 2, 447, 1999


Timmer J., Wardinsky I., Schwarz U., Hasinger G., Kurths J.:
Linear and non-linear time series analysis of Cyg X-1, Annales of Geophysics, Suppl IV 16, 1998, C1098

Horbelt W., Timmer J., Melzer W.:
Estimating parameters in nonlinear differential equations with application to physiological data
Proc. 2nd Int. Conf. Differential Equations and Applications, St. Petersburg, Ed. G. Osipenko, 1998, p.23-33 Timmer J., Weigend A.:
Modeling volatilities using the state space model In: Decision Technologies for Computational Finance, edited by A.-P. N. Refenes, A. N. Burgess, and J. E. Moody (Proceedings of the Fifth International Conference Computational Finance, London, December 1997), p. 233-246. Dordrecht: Kluwer, 1998

Michalek S., Lerche H, Mitrovic N., Schiebe M., Lehmann-Horn F., Timmer J.:
Generalized Hidden Markov Models considering correlated noise and filtering for analyzing sodium channel recordings
Biophys. J. 74, A321, 1998

Michalek S., Lerche H, Mitrovic N., Schiebe M., Lehmann-Horn F., Timmer J.:
Generalized Hidden Markov Models considering correlated noise and filtering for analyzing sodium channel recordings
Deutsche und Skandinavische Physiologische Gesellschaft, Hamburg, 1998

Köster B., Lauk M., Timmer J., Guschlbauer B., Glocker, F.X., Lücking CH.:
Involvement of a transcortical pathway in Parkinsonian postural and resting tremor: a study in a Parkinsonian patient with congenital mirror movements , Electroencephalography and Clinical Neurophysiology 107, 1998, 66

Reisch S., Steltner H., Renotte C., Timmer J., Geiger K., Guttmann J.:
Verlauf der akustischen Atemwegsimpedanz bei simulierter Obstruktion der oberen Atemwege, Biomedizinische Technik
Biomedizinische Technik, 43 (Suppl 1), 306-307, 1998

Hellwig B. Häussler S. Lauk M., Guschlbauer B., Köster B., Kristeva-Feige R., Timmer J., Lücking C.H.:
Tremor-related EEG activity in patients with Parkinsonian disease. Electroenceph. clin. Neurophys. 107, 46P, 1998

Kopitzki K., Timmer J., Warnke P.C.:
Spatial Measurement of blood-brain-barrier permeability. Acta Neurochir 140, 871-872, 1998


König M., Staubert R., Timmer J.:
Analyzing X-ray variability by State Space Models, in: D.Maoz et al (eds.), Astronomical Time Series, 265-268, 1997, Kluwer Academic Publishers

Michalek S., Lerche H, Mitrovic N., Schiebe M., Lehmann-Horn F., Timmer J.:
Identification of gating schemes of wild type and mutant sodium channels from single channel recordings using Hidden Markov models, Pflug. Arch. 433, 1997, 505

Köster B., Lauk M., Timmer J., Lücking CH.:
Side-to-side correlation of pathological tremors, Electroencephalography and Clinical Neurophysiology 103, 1997, 211

Haan H., Timmer J., Mathar R., Krüger J.:
Multidimensional scaling: Analyzing multineural spike patterns. R.Klar, O.Opitz (Eds.): Classification and Knowledge Organisation, 15-19, Springer, 1997

Michalek S., Lerche H, Mitrovic N., Schiebe M., Lehmann-Horn F., Timmer J.:
Identification of gating schemes of wild type and mutant sodium channels from single channel recordings using Hidden Markov models, Biophys. J. 72, 1997, A117

Reisch S., Timmer J., Rühle K-H., Geiger K., Guttmann J.:
Detektion von obstruktiven Schlafapnoen durch statistische Analyse der Phasenwinkelveränderungen der Atemwegsimpedanz, Biomedizinische Technik 42, Ergänzungsband 2, 295-296, 1997

Vibe-Rheymer K., Timmer J., Vesin J.M.:
On a method for investigating long-range correlations, 1997 IEEE Workshop on Nonlinear Signal and Image Processing, Michigan

Timmer J., Heitz, C.: Akustische Qualitätskontrolle von Elektromotoren mit Zeitfrequenzverteilungen , Workshop Zeitreihenanalyse, 51-54, VDI, 1997


Michalek S., Timmer J., Lerche H., Schiebe M.:
A new method for an automatic leak current removal during voltage jump experiments on patch-clamped voltage gated ion channels. Pflügers Arch 431, 1996, R91

Köster, B., M. Lauk, M. Poersch, J. Timmer, B. Guschlbauer, F.X. Glocker, G. Deuschl, C.H. Lücking:
Primary Orthostatic Tremor: Subclinical Involvement of cranial Muscles, Electroencephalography and Clinical Neurophysiology 99, 1996, 372

H. Haan, J.Timmer, J. Krüger. Explorative data analysis by Multidimensional Scaling. in N. Elsner and H.-U. Schnitzler, Göttingen Neurobiology Report. Thieme Verlag, 1996

H. Haan, J. Timmer, I. Bondar, J. Krüger Local field potentials (LFPs) and spikes in monkey striate cortex. in N. Elsner and H.-U. Schnitzler, Göttingen Neurobiology Report. Thieme Verlag, 1996

Köster, B., M. Lauk, J. Timmer, T. Winter, B. Guschlbauer, F.X. Glocker, G. Deuschl, C.H. Lücking:
Involvement of Central Pathways in Enhanced Physiological Tremor, Electroencephalography and Clinical Neurophysiology 99, 1996, 371

König M., Timmer J.:
Analyzing X-ray variability by Linear State Space Models, in: Babu J.G., Feigelson E.D. (eds.) Statistical challenges in modern astronomy II, 1996, 393-394

Michalek S., Lerche H., Mitrovic N., Schiebe M., Lehmann-Horn F., Timmer J.:
Identifizierung von Gating-Schemata aus Patch-Clamp Messungen von Na Kanälen mit Hilfe von Hidden-Markov-Modellen. Biomedizinische Technik 41, Ergänzungsband 1, 336-337, 1996

Huber W., Kopitzki K., Timmer J. Warnke P.:
Ortsaufgelöste Messung und Modellierung der Permeabilität der Blut-Hirn-Schranke. Biomedizinische Technik 41, Ergänzungsband 1, 160-161, 1996

Reisch S., Kulstrunk M., Timmer J., Schneider M., Rühle K.H., Geiger K., Gutmann J.:
Physikalisches Modell zur Simulation von Zeitverläufen der Atemwegsimpedanz bei obstruktiver Schlafapnoe. Biomedizinische Technik 41, Ergänzungsband 1, 84-85, 1996

Reisch S., Renotte C., Timmer J., Honerkamp J., Geiger K., Gutmann J.:
Theoretische Evaluierung der Resisto-Oszillometrie bei obstruktiver Schlafapnoe. Biomedizinische Technik 41, Ergänzungsband 1, 108-109, 1996

Michalek S., Lerche H, Mitrovic N., Schiebe M., Lehmann-Horn F., Timmer J.: Identification of gating schemes of wild type and mutant sodium channels from using Hidden Markov models, 3rd European Conference on Mathematics Applied to Biology and Medicine, 1996, p.212


Deuschl G., Timmer J., Genger H., Gantert C., Lücking C.H., Honerkamp J.:
Frequency, amplitude and waveform characteristics of physiologic and pathologic tremors, In: Quantitative methods and scoring in extrapyramidal disorders. H. Przuntek, P. H. Kraus, P. Klotz, A.D. Korczyn (Hrsg.) Springer, Heidelberg 1995, p. 93-100

Timmer J.:
Vorverarbeitung, Modellierung und Klassifikation von Zeitreihen, Verlag Harri Deutsch, 1995

Haan H., Timmer J., Krüger J.:
Multineuronal Spike Patterns: Visualization of relationships by Multidimensional Scaling, in N. Elsner, R. Menzel (Ed.): Learning and Memory. Georg Thieme Verlag, 1995, 475

Deuschl G., Lauk M., Timmer J.:
Tremor Classification and Tremor Time Series Analysis, In: Belair J, Glass L, an der Heiden U, Milton J(eds). Dynamical Disease. Mathematical Analysis of Human Illness. AIP Press, (1995).

Gezeck S., Timmer J.:
Detecting Multimodality in Saccadic Reaction Time Distributions, Proceedings of the 8. European Conference on Eye Movements, 1995, pp. 66-67

Timmer J.:
Hidden Markov Models of ion channels, Neuromuscular Disorders, ENMC, 1995


Krieger S., Tritschler B., Lis S., Timmer J., Hohagen F. Berger M.:
Cholinerge Modulation von REM - Schlaf: Entwicklung eines spektralanalytischen Untersuchungsverfahrens, In: Schlafmedizin, Gustav Fischer Verlag, 1993

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