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ORCIDJens Timmer
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- affiliation: University of Freiburg, Germany
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2020 – today
- 2023
[j62]Jacques Hermes
, Marcus Rosenblatt, Christian Tönsing, Jens Timmer:
Non-Parametric Model-Based Estimation of the Effective Reproduction Number for SARS-CoV-2. Algorithms 16(12): 533 (2023)- [j61]Adrian L. Hauber, Marcus Rosenblatt, Jens Timmer:
Uncovering specific mechanisms across cell types in dynamical models. PLoS Comput. Biol. 19(9) (2023) - [j60]Christian Tönsing, Bernhard Steiert, Jens Timmer, Clemens Kreutz:
Likelihood-ratio test statistic for the finite-sample case in nonlinear ordinary differential equation models. PLoS Comput. Biol. 19(9) (2023) - 2022
- [c7]Henrik Biermann, Franz-Georg Wieland, Jens Timmer, Daniel Memmert, Ashwin Phatak:
Towards Expected Counter - Using Comprehensible Features to Predict Counterattacks. MLSA@PKDD/ECML 2022: 3-13 - 2021
- [j59]Leonard Schmiester, Yannik Schälte, Frank T. Bergmann, Tacio Camba, Erika Dudkin, Janine Egert, Fabian Fröhlich, Lara Fuhrmann, Adrian L. Hauber, Svenja Kemmer, Polina A. Lakrisenko, Carolin Loos, Simon Merkt, Wolfgang Müller, Dilan Pathirana, Elba Raimúndez-Álvarez, Lukas Refisch, Marcus Rosenblatt, Paul Stapor, Philipp Städter, Dantong Wang, Franz-Georg Wieland, Julio R. Banga, Jens Timmer, Alejandro F. Villaverde, Sven Sahle, Clemens Kreutz, Jan Hasenauer, Daniel Weindl:
PEtab - Interoperable specification of parameter estimation problems in systems biology. PLoS Comput. Biol. 17(1) (2021) - 2020
- [j58]Adrian L. Hauber, Raphael Engesser, Joep Vanlier, Jens Timmer:
Estimating chain length for time delays in dynamical systems using profile likelihood. Bioinform. 36(6): 1848-1854 (2020)
2010 – 2019
- 2019
- [j57]Helge Hass, Carolin Loos, Elba Raimúndez-Álvarez, Jens Timmer, Jan Hasenauer, Clemens Kreutz:
Benchmark problems for dynamic modeling of intracellular processes. Bioinform. 35(17): 3073-3082 (2019) - [j56]Pascal Dolejsch, Helge Hass, Jens Timmer:
Extensions of ℓ 1 regularization increase detection specificity for cell-type specific parameters in dynamic models. BMC Bioinform. 20(1): 395:1-395:13 (2019) - 2018
- [c6]Benjamin Winkelmann, Callum M. Zgierski-Johnston, Eike Moritz Wülfers, Jens Timmer, Gunnar Seemann:
Computational Mechanistic Investigation of Chronotropic Effects on Murine Sinus Node Cells. CinC 2018: 1-4 - 2016
- [j55]Helge Hass, Clemens Kreutz, Jens Timmer, Daniel Kaschek:
Fast integration-based prediction bands for ordinary differential equation models. Bioinform. 32(8): 1204-1210 (2016) - [j54]Bernhard Steiert, Jens Timmer, Clemens Kreutz:
L1 regularization facilitates detection of cell type-specific parameters in dynamical systems. Bioinform. 32(17): 718-726 (2016) - [j53]Ruth Merkle, Bernhard Steiert, Florian Salopiata, Sofia Depner, Andreas Raue, Nao Iwamoto, Max Schelker, Helge Hass, Marvin Wäsch, Martin E. Böhm, Oliver Mücke, Daniel B. Lipka, Christoph Plass, Wolf D. Lehmann, Clemens Kreutz, Jens Timmer, Marcel Schilling, Ursula Klingmüller:
Identification of Cell Type-Specific Differences in Erythropoietin Receptor Signaling in Primary Erythroid and Lung Cancer Cells. PLoS Comput. Biol. 12(8) (2016) - 2015
- [j52]Andreas Raue, Bernhard Steiert, Max Schelker, Clemens Kreutz, Tim Maiwald, Helge Hass, Joep Vanlier, Christian Tönsing, Lorenz Adlung, Raphael Engesser, Wolfgang Mader, Tim Heinemann, Jan Hasenauer, Marcel Schilling, Thomas Höfer, Edda Klipp, Fabian J. Theis, Ursula Klingmüller, Birgit Schoeberl, Jens Timmer:
Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems. Bioinform. 31(21): 3558-3560 (2015) - [j51]Lorenza Alice D'Alessandro, Regina Samaga, Tim Maiwald, Seong-Hwan Rho, Sandra Bonefas, Andreas Raue, Nao Iwamoto, Alexandra Kienast, Katharina Waldow, Rene Meyer, Marcel Schilling, Jens Timmer, Steffen Klamt, Ursula Klingmüller:
Disentangling the Complexity of HGF Signaling by Combining Qualitative and Quantitative Modeling. PLoS Comput. Biol. 11(4) (2015) - [j50]Jonathan R. Karr, Alex H. Williams, Jeremy D. Zucker, Andreas Raue, Bernhard Steiert, Jens Timmer, Clemens Kreutz, Simon Wilkinson, Brandon A. Allgood, Brian M. Bot, Bruce R. Hoff, Michael R. Kellen, Markus W. Covert, Gustavo A. Stolovitzky, Pablo Meyer:
Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models. PLoS Comput. Biol. 11(5) (2015) - 2014
- [j49]Wolfgang Mader, Yannick Linke, Malenka Mader, Linda Sommerlade, Jens Timmer, Björn Schelter:
A numerically efficient implementation of the expectation maximization algorithm for state space models. Appl. Math. Comput. 241: 222-232 (2014) - [j48]Andreas Raue, Johan Karlsson, Maria Pia Saccomani, Mats Jirstrand, Jens Timmer:
Comparison of approaches for parameter identifiability analysis of biological systems. Bioinform. 30(10): 1440-1448 (2014) - [j47]Pablo Meyer, Thomas Cokelaer, Deepak Chandran, Kyung Hyuk Kim, Po-Ru Loh, George Tucker, Mark Lipson, Bonnie Berger, Clemens Kreutz, Andreas Raue, Bernhard Steiert, Jens Timmer, Erhan Bilal, Herbert M. Sauro, Gustavo Stolovitzky, Julio Saez-Rodriguez:
Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach. BMC Syst. Biol. 8: 13 (2014) - 2013
- [j46]Corinna Vehlow, Jan Hasenauer, Andrei Kramer, Andreas Raue, Sabine Hug, Jens Timmer, Nicole Radde, Fabian J. Theis, Daniel Weiskopf:
iVUN: interactive Visualization of Uncertain biochemical reaction Networks. BMC Bioinform. 14(S-19): S2 (2013) - 2012
- [j45]Rebekka Schlatter, Nicole Philippi, Gaby Wangorsch, Robert Pick, Oliver Sawodny, Christoph Borner, Jens Timmer, Michael Ederer, Thomas Dandekar:
Integration of Boolean models exemplified on hepatocyte signal transduction. Briefings Bioinform. 13(3): 365-376 (2012) - [j44]Clemens Kreutz, J. S. Gehring, Daniel Lang, Ralf Reski, Jens Timmer, Stefan A. Rensing:
TSSi - an R package for transcription start site identification from 5′ mRNA tag data. Bioinform. 28(12): 1641-1642 (2012) - [j43]Max Schelker, Andreas Raue, Jens Timmer, Clemens Kreutz:
Comprehensive estimation of input signals and dynamics in biochemical reaction networks. Bioinform. 28(18): 529-534 (2012) - [j42]Thomas Maiwald, Julie Blumberg, Andreas Raue, Stefan Hengl, Marcel Schilling, Sherwin K. B. Sy, Verena Becker, Ursula Klingmüller, Jens Timmer:
In silico labeling reveals the time-dependent label half-life and transit-time in dynamical systems. BMC Syst. Biol. 6: 13 (2012) - [j41]Daniel Kaschek, Jens Timmer:
A variational approach to parameter estimation in ordinary differential equations. BMC Syst. Biol. 6: 99 (2012) - [j40]Clemens Kreutz, Andreas Raue, Jens Timmer:
Likelihood based observability analysis and confidence intervals for predictions of dynamic models. BMC Syst. Biol. 6: 120 (2012) - [j39]Matthias Ihle, Hinnerk Feldwisch-Drentrup, César Alexandre Teixeira, Adrien Witon, Björn Schelter, Jens Timmer, Andreas Schulze-Bonhage:
EPILEPSIAE - A European epilepsy database. Comput. Methods Programs Biomed. 106(3): 127-138 (2012) - [j38]Dirk-Bart den Ouden, Dorothee Saur, Wolfgang Mader, Björn Schelter, Sladjana Lukic, Eisha Wali, Jens Timmer, Cynthia K. Thompson:
Network modulation during complex syntactic processing. NeuroImage 59(1): 815-823 (2012) - 2011
- [j37]Hinnerk Feldwisch-Drentrup, Matthäus Staniek, Andreas Schulze-Bonhage, Jens Timmer, Henning Dickten, Christian Erich Elger, Björn Schelter, Klaus Lehnertz:
Identification of Preseizure States in Epilepsy: A Data-Driven Approach for Multichannel EEG Recordings. Frontiers Comput. Neurosci. 5: 32 (2011) - [c5]Björn Schelter, Hinnerk Feldwisch-Drentrup, Matthias Ihle, Andreas Schulze-Bonhage, Jens Timmer:
Seizure prediction in epilepsy: From circadian concepts via probabilistic forecasting to statistical evaluation. EMBC 2011: 1624-1627 - [c4]Björn Schelter, Linda Sommerlade, Bettina Platt, Andrea Plano, Marco Thiel, Jens Timmer:
Multivariate analysis of dynamical processes with applications to the neurosciences. EMBC 2011: 5931-5934 - 2010
- [j36]Andrea C. Pfeifer, Daniel Kaschek, Julie Bachmann, Ursula Klingmüller, Jens Timmer:
Model-based extension of high-throughput to high-content data. BMC Syst. Biol. 4: 106 (2010) - [j35]Dorothee Saur, Björn Schelter, Susanne Schnell, David Kratochvil, Hanna Küpper, Philipp Kellmeyer, Dorothee Kümmerer, Stefan Klöppel, Volkmar Glauche, Rüdiger Lange, Wolfgang Mader, David Feess, Jens Timmer, Cornelius Weiller:
Combining functional and anatomical connectivity reveals brain networks for auditory language comprehension. NeuroImage 49(4): 3187-3197 (2010)
2000 – 2009
- 2009
- [j34]Andreas Raue, Clemens Kreutz, Thomas Maiwald, Julie Bachmann, Marcel Schilling, Ursula Klingmüller, Jens Timmer:
Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood. Bioinform. 25(15): 1923-1929 (2009) - [j33]Nicole Philippi, Dorothee Walter, Rebekka Schlatter, Karine Ferreira, Michael Ederer, Oliver Sawodny, Jens Timmer, Christoph Borner, Thomas Dandekar:
Modeling system states in liver cells: Survival, apoptosis and their modifications in response to viral infection. BMC Syst. Biol. 3: 97 (2009) - [j32]Enno Mammen, Swagata Nandi, Thomas Maiwald, Jens Timmer:
Effect of Jump Discontinuity for Phase-Randomized Surrogate Data Testing. Int. J. Bifurc. Chaos 19(1): 403-408 (2009) - [j31]Kilian Bartholomé, Clemens Kreutz, Jens Timmer:
Estimation of Gene Induction Enables a Relevance-Based Ranking of Gene Sets. J. Comput. Biol. 16(7): 959-967 (2009) - 2008
- [j30]Kilian Bartholomé, Jens Timmer:
Regulatorische Prinzipien und Systemanalyse der bakteriellen Chemotaxis (Regulatory Principles and Systems Analysis of Bacterial Chemotaxis). Autom. 56(5): 241-249 (2008) - [j29]Thomas Maiwald, Jens Timmer:
Dynamical modeling and multi-experiment fitting with PottersWheel. Bioinform. 24(18): 2037-2043 (2008) - [j28]Eva Balsa-Canto, Martin Peifer, Julio R. Banga, Jens Timmer, Christian Fleck:
Hybrid optimization method with general switching strategy for parameter estimation. BMC Syst. Biol. 2: 26 (2008) - [j27]Julio Vera, Julie Bachmann, Andrea C. Pfeifer, Verena Becker, Jose A. Hormiga, Néstor Torres Darias, Jens Timmer, Ursula Klingmüller, Olaf Wolkenhauer:
A systems biology approach to analyse amplification in the JAK2-STAT5 signalling pathway. BMC Syst. Biol. 2: 38 (2008) - [j26]Wolfgang Mader, David Feess, Rüdiger Lange, Dorothee Saur, Volkmar Glauche, Cornelius Weiller, Jens Timmer, Björn Schelter:
On the Detection of Direct Directed Information Flow in fMRI. IEEE J. Sel. Top. Signal Process. 2(6): 965-974 (2008) - 2007
- [j25]Stefan Hengl, Clemens Kreutz, Jens Timmer, Thomas Maiwald:
Data-based identifiability analysis of non-linear dynamical models. Bioinform. 23(19): 2612-2618 (2007) - [j24]Clemens Kreutz, M. M. Bartolome Rodriguez, Thomas Maiwald, Maxmilian Seidl, H. E. Blum, L. Mohr, Jens Timmer:
An error model for protein quantification. Bioinform. 23(20): 2747-2753 (2007) - [j23]Florian Geier, Jens Timmer, Christian Fleck:
Reconstructing gene-regulatory networks from time series, knock-out data, and prior knowledge. BMC Syst. Biol. 1: 11 (2007) - [j22]Björn Schelter, Matthias Winterhalder, Jens Timmer, Jürgen Kurths:
Phase Synchronization and Coherence Analysis: Sensitivity and specificity. Int. J. Bifurc. Chaos 17(10): 3551-3556 (2007) - [j21]Matthias Winterhalder, Björn Schelter, Jens Timmer:
Detecting Coupling Directions in Multivariate Oscillatory Systems. Int. J. Bifurc. Chaos 17(10): 3735-3739 (2007) - 2006
- [j20]Valko Petrov, Martin Peifer, Jens Timmer:
Bistability and Self-oscillations in Cell Cycle Control. Int. J. Bifurc. Chaos 16(4): 1057-1066 (2006) - 2005
- [j19]Matthias Winterhalder, Björn Schelter, Wolfram Hesse, Karin Schwab, Lutz Leistritz, Daniel Klan, Reinhard Bauer, Jens Timmer, Herbert Witte:
Comparison of linear signal processing techniques to infer directed interactions in multivariate neural systems. Signal Process. 85(11): 2137-2160 (2005) - 2004
- [j18]Henning U. Voss, Jens Timmer, Jürgen Kurths:
Nonlinear Dynamical System Identification from Uncertain and Indirect Measurements. Int. J. Bifurc. Chaos 14(6): 1905-1933 (2004) - [j17]T. G. Müller, Jens Timmer:
Parameter Identification Techniques for Partial Differential Equations. Int. J. Bifurc. Chaos 14(6): 2053-2060 (2004) - [j16]Jens Timmer, T. G. Müller, I. Swameye, O. Sandra, Ursula Klingmüller:
Modeling the Nonlinear Dynamics of Cellular Signal Transduction. Int. J. Bifurc. Chaos 14(6): 2069-2079 (2004) - [j15]Douglas Maraun, Werner Horbelt, Henning W. Rust, Jens Timmer, H. P. Happersberger, F. Drepper:
Identification of Rate Constants and nonobservable Absorption Spectra in Nonlinear Biochemical Reaction Dynamics. Int. J. Bifurc. Chaos 14(6): 2081-2092 (2004) - [j14]Marco Thiel, M. Carmen Romano, Udo Schwarz, Jürgen Kurths, Jens Timmer:
Surrogate-Based Hypothesis Test without Surrogates. Int. J. Bifurc. Chaos 14(6): 2107-2114 (2004) - [j13]Daniel Faller, Thomas Reinheckel, Daniel Wenzler, Sascha Hagemann, Ke Xiao, Josef Honerkamp, Christoph Peters, Thomas Dandekar, Jens Timmer:
An Open Source Protein Gel Documentation System for Proteome Analyses. J. Chem. Inf. Model. 44(1): 168-169 (2004) - 2003
- [j12]Daniel Faller, Henning U. Voss, Jens Timmer, Uwe Hobohm:
Normalization of DNA-Microarray Data by Nonlinear Correlation Maximization. J. Comput. Biol. 10(5): 751-762 (2003) - [j11]Daniel Faller, Ursula Klingmüller, Jens Timmer:
Simulation Methods for Optimal Experimental Design in Systems Biology. Simul. 79(12): 717-725 (2003) - 2000
- [j10]Jens Timmer, Michael Lauk, S. Häußler, V. Radt, B. Köster, B. Hellwig, B. Guschlbauer, C. H. Lücking, M. Eichler, Günther Deuschl:
Cross-spectral Analysis of tremor Time Series. Int. J. Bifurc. Chaos 10(11): 2595-2610 (2000) - [j9]Steffen Michalek, Mirko Wagner, Jens Timmer:
A new approximate likelihood estimator for ARMA-filtered hidden Markov models. IEEE Trans. Signal Process. 48(6): 1537-1547 (2000) - [c3]Thorsten Müller, T. Ball, R. Kristeva-Feige, Thomas Mergner, Jens Timmer:
Classification of Electro-encephalographic Spatial Patterns. ISMDA 2000: 55-60 - [c2]Holger Steltner, Richard Staats, Michael Vogel, Christian Virchow, Heinrich Matthys, Josef Guttmann, Jens Timmer:
Detection and Classification of Sleep-Disordered Breathing Using Acoustic Respiratory Input Impedance and Nasal Pressure. ISMDA 2000: 61-66 - [c1]Werner Horbelt, Thorsten Müller, Jens Timmer, Werner Melzer, Karl Winkler:
Analysis of Nonlinear Differential Equations: Parameter Estimation and Model Selection. ISMDA 2000: 152-158
1990 – 1999
- 1999
- [j8]S. Reisch, Holger Steltner, Jens Timmer, Christine Renotte, Josef Guttmann:
Early detection of upper airway obstructions by analysis of acoustical respiratory input impedance. Biol. Cybern. 81(1): 25-37 (1999) - [j7]Steffen Michalek, Jens Timmer:
Estimating rate constants in hidden Markov models by the EM algorithm. IEEE Trans. Signal Process. 47(1): 226-228 (1999) - 1998
- [j6]Stefan Gezeck, Jens Timmer:
Detecting multimodality in saccadic reaction time distributions in gap and overlap tasks. Biol. Cybern. 78(4): 293-305 (1998) - [j5]Jens Timmer, M. Lauk, W. Pfleger, Günther Deuschl:
Cross-spectral analysis of physiological tremor and muscle activity. Biol. Cybern. 78(5): 349-357 (1998) - [j4]Jens Timmer, M. Lauk, W. Pfleger, Günther Deuschl:
Cross-spectral analysis of physiological tremor and muscle activity. Biol. Cybern. 78(5): 359-368 (1998) - 1997
- [j3]Jens Timmer, Andreas S. Weigend:
Modeling Volatility Using State Space Models. Int. J. Neural Syst. 8(4): 385-398 (1997) - 1993
- [j2]Jens Timmer, C. Gantert, Günther Deuschl, Josef Honerkamp:
Characteristics of hand tremor time series. Biol. Cybern. 70(1): 75-80 (1993) - 1992
- [j1]C. Gantert, Josef Honerkamp, Jens Timmer:
Analyzing the dynamics of hand tremor time series. Biol. Cybern. 66(6): 479-484 (1992)
Coauthor Index
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