Papers in reviewed journals
Shortcuts:
in press:
M. Licheva, J. Pflaum, R. Babic, H. Mancilla, J. Elsässer, E.
Boyle, D.M. Hollenstein, J. Jimenez-Niebla, J. Pleyer, M. Heinrich,
F.G. Wieland, J. Brenneisen, C. Eickhorst, J. Brenner, S. Jiang, M Hartl,
S. Welsch, C. Hunte, J. Timmer, F. Wilfling, C. Kraft.
Phase separation
of initiation hubs on cargo is a trigger switch for selective autophagy.
Nature Cell Biology , 2024,
[365] H. Mohsenin, R. Schmachtenberg, S. Kemmer, H.J. Wagner, M.
Johnston, S. Madlener, C. Dincer, J. Timmer, W. Weber.
Signal-amplifying Biohybrid
Material Circuits for CRISPR/Cas-based
single-stranded RNA Detection. Advanced Materials Technologies.
2024, 2400981
[364] S. Pooseh, R. Kalisch, G. Köber, H. Binder, J. Timmer.
Intraindividual
time-varying dynamic network of affects: linear autoregressive mixed-effects
models for ecological momentary assessment. Frontiers in
Psychiatry 15, 2024, 1213863
[363] S.B. de Lara, S. Kemmer, I. Biermayer, S. Feiler, A. Vlasov,
L.A. D’Alessandro, B. Helm, C. Mölders, Y. Dieter, A. Ghallab, J. Hengstler,
C. Körner, M. Matz-Soja, C. Götz, G. Damm,
K. Hoffmann, D. Seehofer, T. Berg, M. Schilling, J. Timmer, U. Klingmüller.
Basal MET phosphorylation is an indicator of
hepatocyte dysregulation in liver disease. Molecular Systems Biology
20, 2024, 187-216
News & Views
[362] H. Mohsenin, H.J. Wagner, M. Rosenblatt, S. Kemmer, F. Drepper, P. Huesgen,
J. Timmer, W. Weber.
Design of a biohybrid
materials circuit with binary decoder
functionality. Advanced Materials 2024, 2308092
[361] J. Hermes, M. Rosenblatt, C. Tönsing, J. Timmer.
Non-parametric
model-based estimation of the effective reproduction
number for SARS-CoV-2. Algorithms 16, 2023, 533
[360] H. Mohsenin, J. Pacheco, S. Kemmer, H.J. Wagner, N. Höfflin,
T. Bergmann, T. Baumann, C. Jerez-Longres, A. Ripp, N. Jork,
H.J. Jessen, M. Fussenegger, M. Köhn, J. Timmer, W. Weber.
PenTag, a versatile platform for synthesizing protein-polymer
biohybrid materials. Advanced Functional Materials 2023, 2308269
[359] C. Tönsing, B. Steiert, J. Timmer, C. Kreutz.
Likelihood-ratio test statistic for the finite-sample case in
nonlinear ordinary differential equation models. PLOS
Computational Biology
19, 2023, e1011417
[358] C. Jerez-Longres, M. Gomez-Matos, J. Becker, M. Hörner,
F.-G. Wieland, J. Timmer, W. Weber.
Engineering a material-genetic
interface as safety switch for embedded therapeutic cells.
Biomaterials Advances 150, 2023, 213422
[357] A.J. Riesle, M. Gao, M. Rosenblatt, J. Hermes, H. Hass, A. Gebhard, M. Veil, B. Grüning,
J. Timmer, D. Onichtchouk.
Activator-blocker model of transcriptional regulation by pioneer-like factors.
Nature Communications 14, 2023, 5677
[356] A. Hauber, M. Rosenblatt, J. Timmer.
Uncovering specific mechanisms across cell types in dynamical models.
PLOS Computational Biology 19, 2023, e1010867
[353] S.A. Bögemann, A. Riepenhausen, L.M.C. Puhlmann, S. Bar, E.J.C. Hermsen, J. Mituniewicz,
Z.C. Reppmann, A. Uscilko, J.M.C. van Leeuwen, C. Wackerhagen, K.S.L. Yuen, M. Zerban,
J. Weermeijer, M.A. Marciniak, N. Mor, A. van Kraaij, G. Köber, S. Pooseh, P. Koval,
A. Arias-Vasquez, H. Binder, W. De Raedt, B. Kleim, I. Myin-Germeys, K. Roelofs, J. Timmer,
O. Tüscher, T. Hendler, D. Kobylinska, I. M. Veer, R. Kalisch, E. J. Hermans, H. Walter.
Investigating two mobile just-in-time adaptive
interventions to foster psychological resilience:
research protocol of the DynaM-INT study. BMC Psychology 11, 2023, 245
[352] Wackerhagen C., Veer I., van Leeuwen J., Reppmann Z., Riepenhausen A.,
Bögemann S., Mor N., Puhlmann L.,
Uscilko A., Zerban M., Mituniewicz J., Lerner A, Yuen K., Köber G.,
Marciniak M., Pooseh S., Weermeijer J., Arias-Vasquez A., Binder H.,
de Raedt W., Kleim B., Myin-Germeys I., Roelofs K., Timmer J., Tüscher O.,
Hendler T., Kobylinska D., Hermans E., Kalisch R., Walter H.
Dynamic modelling of mental resilience in young adults: Protocol for a logitudinal
observational study (DynaM-OBS). Journal of Medical Internet Research
12, 2023, e39817
[351] J. Jaiswal, J. Egert, R. Engesser, A.A. Peyroton, L. Nogay, V. Weichselberger, C.
Crucianelli, I. Grass, C. Kreutz, J. Timmer, A.-K. Classen.
Mutual repression between JNK/AP-1 and JAK/STAT stratifies cell
behaviors during tissue regeneration. PLoS Biology
21, 2023, e3001655
[350] A.L. Hauber, C. Sigloch, J. Timmer.
Detecting frequency
modulation in stochastic time-series data. Physical Review E
106, 2022, 024204
[349] S. Kemmer, S. Bang, M. Rosenblatt, J. Timmer, D. Kaschek.
BlotIt - Optimal
alignment of Western blot and qPCR experiments. PLoS ONE
17, 2022, e0264295
[348] G. Köber, S. Pooseh, H. Engen, A. Chmitorz, M. Kampa, A. Schick,
A. Sebastian, O. Tüscher, M. Wessa, K.S.L. Yuen, H. Walter, R. Kalisch,
J. Timmer, H. Binder.
Individualizing deep dynamic models for
psychological resilience data. Scientific Reports 12, 2022, 8061
[347] S. Kemmer, M. Berdiel-Acer, E. Reinz, J. Sonntag, N. Tarade,
S. Bernhardt, M. Fehling-Kaschek, M. Hasmann, U. Korf,
S. Wiemann, J. Timmer.
Disentangling ERBB signaling in breast cancer subtypes - a
model-based analysis. MDPI Cancers 14, 2022, 2379
[346] S. Hiemstra, M. Fehling-Kaschek, I. Kuijper, L. Bischoff, L. Wijaya,
M. Rosenblatt, J. Esselink, A. van Egmond, J. Mos, J. Beltman, J. Timmer,
B. van de Water, D. Kaschek.
Dynamic modeling of Nrf2
pathway activation in liver cells after toxicant exposure.
Scientific Reports 12, 2022, 7336
[345] S. Heming, P. Hansen, A. Vlasov, F. Schwörer, S. Schaumann, P.
Frolovaite, W.D. Lehmann, J. Timmer, M. Schilling, B. Helm,
U. Klingmüller.
MSPypeline: A python package for streamlined data
analysis of mass spectrometry-based proteomics. Bioinformatics Advances
2, 2022, vbac004
[344] D. Lill, A. Kümmel, V. Mitov, D. Kaschek, N. Gobeau, H. Schmidt,
J. Timmer.
Efficient simulation of clinical target response
surfaces. Pharmacometrics & Systems Pharmacology
11, 2022, 512-523
[343] T. Litwin, J. Timmer, C. Kreutz.
Optimal experimental design based on two-dimensional likelihood
profiles.
Frontiers in Molecular Biosciences 9, 2022, 800856
[342] M. Gao, M. Veil, M. Rosenblatt, A.J. Riesle, A. Gebhard, H. Hass,
L. Buryanova,
L.Y. Yampolsky, B. Grüning, J. Timmer, D. Onichtchouk.
Pluripotency factors determine gene expression repertoire at
zygotic genome activation. Nature Communications 13,
2022, 788
[341] T. Litwin, J. Timmer, M. Berger, A. Wahl-Kordon, M.J. Müller, C. Kreutz
Preventing
COVID-19 outbreaks through surveillance testing in healthcare facilities
- a modelling study. BMC Infectious Diseases 22, 2022, 105
[340] V. Akimov, M. Fehling-Kaschek, I. Barrio-Hernandez, M. Puglia,
J. Bunkenborg, M.M. Nielsen, J. Timmer, J. Dengjel, B. Blagoev.
Magnitude of ubiquitination
determines the fate of activated epidermal growth factor receptor
and downstream cellular effects. Journal of Molecular Biology
433, 2021, 167240
[339] L. Adlung, P. Stapor, C. Tönsing, L. Schmiester, L.E. Schwarzmüller,
D. Wang, J. Timmer, U. Klingmüller, J. Hasenauer, M. Schilling.
Cell-to-cell variability in JAK2/STAT5 pathway components and
cytoplasmic volumes define survival threshold in erythroid progenitor
cells. Cell Reports 36, 2021, 109507
Cover
[338] O.S. Yousefi, M. Ruggieri, V. Idstein, K.U. von Prillwitz, L.A. Herr,
J. Chalupsky, W. Weber, J. Timmer, W.W.A. Schamel.
Cross-TCR antagonism revealed by optogenetically tuning the half-life of the
TCR ligand binding. International Journal of Molecular Sciences 22, 2021, 4920
[337] F.G. Wieland, A.L. Hauber, C. Tönsing, M. Rosenblatt, J.
Timmer.
On structural and practical identifiability.
Current Opinion in Systems Biology 25, 2021, 60-69
[336] L. Schmiester, Y. Schälte, F.T. Bergmann, T. Camba, E. Dudkin, J. Egert,
F. Fröhlich, L. Fuhrmann, A.L. Hauber, S. Kemmer, P. Lakrisenko, C. Loos,
S. Merkt, W. Müller, D. Pathirana, E. Raimundez, L. Refisch,
M. Rosenblatt, P.L. Stapor, P. Städter, D. Wang, F.-G. Wieland, J. Banga,
J. Timmer, A.J. Villaverde, S. Sahle, C. Kreutz, J.
Hasenauer, D. Weindl.
PEtab - Interoperable specification of
parameter estimation problems in systems biology. PLoS Computational Biology
17, 2021, e1008646
[335] N. Schneider, F.-G. Wieland, D. Kong, A.A.M. Fischer,
M. Hörner, J. Timmer, H. Ye, W. Weber.
Liquid-liquid phase separation of light-inducible transcription
factors increases transcription activation in mammalian cells and
mice. Science Advances 7, 2021, eabd3568
[334] J.R. Donsimoni, R. Glawion, T. Hartl, B. Plachter, J. Timmer, K. Wälde,
E. Weber, C. Weiser.
Covid-19 in Deutschland - Erklärung, Prognose und Einfluss
gesundheitspolitischer Massnahmen.
Perspektiven der Wirtschaftspolitik 21, 2020, 250-262
[333] K. Robichon, T. Maiwald, M. Schilling, A. Schneider, J. Willemsen,
F. Salopiata, M. Teusel, C. Kreutz, C. Ehlting, J. Huang, S. Chakraborty, X. Huang,
G. Damm, D. Seehofer, P.H. Lang, J. Bode, M. Binder,
R. Bartenschlager, J. Timmer, U. Klingmüller.
Identification of
Interleukin 1b as an amplifier of Interferon alpha-induced
antiviral responses. PLoS Pathogens 16, 2020, e100461
[332] R. Ochoa-Fernandez, N.B. Abel, F.-G. Wieland, J. Schlegel,
L.A. Koch, B. Miller, R. Engesser, G. Giuriani, S.M. Brandl, J. Timmer,
W. Weber, T. Ott, R. Simon, M.D. Zurbriggen.
PULSE: Optogenetic
control of gene expression in plants insensitive to ambient
light. Nature Methods 17, 2020, 717-725
[331] F. Kok, M. Rosenblatt, M. Teusel, T. Nizharadze, V.G. Magalhaes,
C. Dächert, T. Maiwald, A. Vlasov, M. Wäsch, S. Tyufekchieva,
K. Hoffmann, G. Damm, D. Seehofer, T. Boettler, M. Binder, J. Timmer,
M. Schilling, U. Klingmüller.
Disentangling molecular mechanisms regulating sensitization of
interferon alpha signal transduction.
Molecular Systems Biology 16, 2020, e8955
[330] A. Hauber, R. Engesser, J. Vanlier, J. Timmer.
Estimating chain length for time delays in dynamical
systems using profile likelihood.
Bioinformatics 36 , 2020,1848-1854
[329] C. Tönsing, J. Timmer, C. Kreutz.
Optimal paths between parameter estimates in nonlinear
ODE systems using the nudged elastic band.
Frontiers in Physics 7, 2019, 149
[328] R. Kalisch, A.O.J. Cramer, H. Binder, J. Fritz, I. Leertouwer,
G. Lunansky, B. Meyer, J. Timmer, I.M. Veer, A.-L. van Harmelen.
Deconstructing and reconstructing resilience: a dynamic network
approach.
Perspectives on Psychological Science 14, 2019, 765-777
[327] H. Hass, C. Loos, E.R. Alvarez, J. Timmer, J. Hasenauer, C. Kreutz.
Benchmark Problems for Dynamic Modeling of Intracellular Processes.
Bioinformatics 35, 2019, 3073-3082
Supplement
[326] M. Fehling-Kaschek, D. Peckys, D. Kaschek, J. Timmer, N. de Jonge.
Mathematical modeling of drug-induced receptor internalization in
the HER2-positive SKBR3 breast cancer cell-line. Scientific Reports
9, 2019, 12709
Supplement
[325] P. Dolejsch, H. Hass, J. Timmer.
Extensions of L1 regularization
increase detection specificity for cell-type specific parameters
in dynamic models. BMC Bioinformatics 20 , 2019, 395
[324] D. Lill, J. Timmer, D. Kaschek.
Local Riemannian geometry of model manifolds and its
implications for practical parameter identifiability.
PLoS ONE 14, 2019, e0217837
[323] D. Lill, O.S. Rukhlenko, A.J. Mc Elwee, E. Kashdan, J. Timmer, B.N.
Kholodenko.
Mapping connections in signaling networks with ambiguous
modularity. NPJ Systems Biology and Applications 5,
2019, 19
[322] D. Kaschek, W. Mader, M. Fehling-Kaschek, M. Rosenblatt, J. Timmer.
Dynamic modeling, parameter estimation and uncertainty analysis in R.
Journal of Statistical Software 88, 2019, 1-32
Supplement 1,
Supplement 2,
Supplement 3
[321] M. Hörner, K. Raute, B. Hummel, J. Madl, G. Creusen, O.S. Thomas,
E.H. Christen, N. Hotz, R.J. Gübeli, R. Engesser, B.
Rebmann, J. Lauer, B. Rolauffs, J. Timmer, W.W.A. Schamel, J.
Pruszak, W. Römer, M.D. Zurbriggen, Ch. Friedrich, A. Walther,
S. Minguet, R. Sawarkar, W. Weber.
Phytochrome-based extracellular
matrix with reversibly tunable mechanical properties.
Advanced Materials 11, 2019, 1806727
[320] S. Bernhardt, C. Tönsing, D. Mitra, N. Erdem, K. Müller-Decker,
U. Korf, C. Kreutz, J. Timmer, S. Wiemann.
Functional proteomics
of breast cancer metabolism identifies GLUL as responder during
hypoxic adaptation. Journal of Proteome Research 18,
2019, 1352-1362
[319] H.J. Wagner, R. Engesser, K. Ermes, C. Geraths, J. Timmer, W. Weber.
Synthetic biology-inspired
design of signal-amplifying materials systems.
Materials Today 22, 2019, 25-34
[318] H.J. Wagner, S. Kemmer, R. Engesser, J. Timmer, W. Weber.
Biofunctionalized materials featuring feedforward and feedback circuits
exemplified by the
detection of Botulinum Toxin A. Advanced Science 6, 2019, 1801320
Cover page
[317] R. Seitz-Alghrouz, J.V. Hidalgo, C. Kayser, C. Kreutz, K. Technau-Hafsi, C. Diaz,
A. von Deimling, J. Timmer, M. Werner, M. Malkovsky, P. Fisch.
BRAF V600E mutations in nevi and melanocytic tumors of uncertain
malignant potential (MELTUMPs). J. Investigative Dermatology 138, 2018, 2489-2491
[316] J. Baaske, P. Gonschorek, R. Engesser, A. Dominguez-Monedero, K. Raute, P. Fischbach, K. Müller,
E. Cachat, W. Schamel, S. Minguet, J. Davies, J. Timmer,
W. Weber, M.D. Zurbriggen.
Dual-controlled optogenetic system for the rapid
down-regulation of protein levels in mammalian cells. Scientific Reports 8, 2018, 15024
[315] D. Dvornikov, M.A. Schneider, S. Ohse, M. Szczygiel, I. Titkova, M. Rosenblatt,
T. Muley, A. Warth, F.J. Herth, H. Dienemann, M. Thomas, J. Timmer, M. Schilling,
H. Busch, M. Boerries, M. Meister, U. Klingmüller.
Expression ratio of TGFb-inducible MYO10 is prognostic for overall
survival of squamous cell lung cancer patients and predicts
chemotherapy response. Scientific Reports 8, 2018, 9517
[314] A. Oppelt, D. Kaschek, S. Huppelschoten, R. Sison-Young, F. Zhang, M. Buck-Wiese,
F. Herrmann, S. Malkusch, C.L. Krüger, M. Meub, B. Merkt,
L. Zimmermann, A. Schofield, R.P. Jones, H. Malik, M. Schilling, M. Heilemann, B. van de Water,
C.E. Goldring, J. Timmer, U. Klingmüller.
Model-based identification of TNFa-induced IKKb- and IkBa-mediated
regulation of NFkB signal transduction as a tool to quantify the impact of
Drug-Induced Liver Injury compounds.
NPG Systems Biology and Application 4, 2018, 23
[313] H.J. Wagner, R. Engesser, K. Ermes, C. Geraths, J. Timmer, W. Weber.
Characterization of the synthetic biology-inspired implementation
of a materials-based positive feedback loop.
Data in Brief 19, 2018, 665-677
[312] C. Chatelle, R. Ochoa-Fernandez, R. Engesser, N. Schneider, H.M. Beyer, A.R. Jones,
J. Timmer, M.D. Zurbriggen, W. Weber.
A green light-responsive system for the
control of transgene expression in mammalian and plant cells.
ACS Synthetic Biology 8, 2018, 1349-1358
[311] C. Tönsing, J. Timmer, C. Kreutz.
Profile likelihood based analyses of infectious disease
models. Statistical Methods in Medical Research 27, 2018, 1979-1998
[310] H.M. Beyer, R. Engesser, M. Hörner, J. Koschmieder, P. Beyer, J. Timmer,
M.D. Zurbriggen, W. Weber.
Synthetic Biology makes Polymer Materials count. Advanced Materials, 2018, 1800472
Supplement
[309] P. Lucarelli, M. Schilling, C. Kreutz, A. Vlasov, M.E. Böhm,
N. Iwamoto, B. Steiert, S. Lattermann, M. Wäsch, M. Stepath,
M.S. Matter, M. Heikenwälder, K. Hoffmann,
D. Deharde, G. Damm, D. Seehofer, M. Muciek, N. Gretz, W.D. Lehmann,
J. Timmer, U. Klingmüller.
Resolving the combinatorial complexity of Smad protein complex
formation and the link to gene expression. Cell Systems
6, 2018, 75-89
[308] D. Kaschek, A. Sharanek, A. Guillouzo, J. Timmer, R.J. Weaver.
A dynamic mathematical model of bile acid clearance in
HepaRG cells. Toxicological Sciences 161, 2018, 48-57
[307] J. Koschmieder, M. Fehling-Kaschek, P. Schaub, S. Ghisla, A. Brausemann,
J. Timmer, P. Beyer.
Plant-type phytoene desaturase: Functional evaluation of structural
implications. PLoS ONE 12, 2017, e0187628
[306] C. Kreutz, S. MacNelly, M. Follo, A. Wäldin, P. Binninger-Lacour, J. Timmer,
M.M.B. Rodriguez.
Hepatocyte ploidy is a diverstiy factor for liver homeostatis.
Frontiers in Physiology 8, 2017, 862
[305] H. Hass, F. Kipkeew, A. Gauhar, E. Bouche, P. May, J. Timmer, H.H.
Bock.
Mathematical model of early Reelin-induced Src family
kinase-mediated signaling. PLoS ONE 12, 2017, e0186927
[304] S. Sobotta, A. Raue, X. Huang, J. Vanlier, A. Jünger, S. Bohl, U. Albrecht,
M.J. Hahnel, S. Wolf, N.S. Müller, L.A. D'Alessandro, S. Mueller-Bohl,
M.E. Böhm, P. Lucarelli, S. Bonefas, G. Damm, D. Seehofer, W.D. Lehmann,
S. Rose-John, F. van der Hoeven, N. Gretz, F.J. Theis, J.G. Bode, J. Timmer,
M. Schilling, U. Klingmüller.
Model based targeting of IL-6-induced inflammatory responses in cultured
primary hepatocytes to improve application of the JAK inhibitor
ruxolitinib. Frontiers in Physiology 8, 2017, 775
[303] H. Hass, K. Masson, S. Wohlgemuth, V. Paragas, J.E. Allen, M. Sevecka,
E. Pace, J. Timmer, J. Stelling, G. MacBeath, B. Schoeberl, A. Raue.
Predicting ligand-dependent tumors from simulated signaling features.
NPJ Systems Biology and Applications 3, 2017, 27
[302] D. Kurzhunov, R. Borowiak, H. Hass, P. Wagner, A. Krafft, J. Timmer
M. Bock.
Quantification of oxygen metabolic rates in
Human brain with dynamic O-17 MRI: Profile likelihood analysis.
Magnetic Resonance in Medicine 78, 2017, 1157-1167
[301] 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 52, 2017, 1144-1155
[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
Corrigendum
[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
