Jens Timmer

Publication Activity (10 Years)

Years Active: 1992-2023
Publications (10 Years): 15

Top Topics

Biological Systems

Parameter Estimation

Estimation Problems

Dynamical Systems

Top Venues

PLoS Comput. Biol.

Appl. Math. Comput.

Publications

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) (2023)
Adrian L. Hauber, Marcus Rosenblatt, Jens Timmer
Uncovering specific mechanisms across cell types in dynamical models. PLoS Comput. Biol. 19 (9) (2023)
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)
Henrik Biermann, Franz-Georg Wieland, Jens Timmer, Daniel Memmert, Ashwin Phatak
Towards Expected Counter - Using Comprehensible Features to Predict Counterattacks. MLSA@PKDD/ECML (2022)
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 L. 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)
Adrian L. Hauber, Raphael Engesser, Joep Vanlier, Jens Timmer
Estimating chain length for time delays in dynamical systems using profile likelihood. Bioinform. 36 (6) (2020)
Helge Hass, Carolin Loos, Elba Raimúndez-Álvarez, Jens Timmer, Jan Hasenauer, Clemens Kreutz
Benchmark problems for dynamic modeling of intracellular processes. Bioinform. 35 (17) (2019)
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) (2019)
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)
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)
Bernhard Steiert, Jens Timmer, Clemens Kreutz
regularization facilitates detection of cell type-specific parameters in dynamical systems. Bioinform. 32 (17) (2016)
Helge Hass, Clemens Kreutz, Jens Timmer, Daniel Kaschek
Fast integration-based prediction bands for ordinary differential equation models. Bioinform. 32 (8) (2016)
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)
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)
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) (2015)
Andreas Raue, Johan Karlsson, Maria Pia Saccomani, Mats Jirstrand, Jens Timmer
Comparison of approaches for parameter identifiability analysis of biological systems. Bioinform. 30 (10) (2014)
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 (2014)
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 (2014)
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) (2013)
Max Schelker, Andreas Raue, Jens Timmer, Clemens Kreutz
Comprehensive estimation of input signals and dynamics in biochemical reaction networks. Bioinform. 28 (18) (2012)
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) (2012)
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 (2012)
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) (2012)
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) (2012)
Daniel Kaschek, Jens Timmer
A variational approach to parameter estimation in ordinary differential equations. BMC Syst. Biol. 6 (2012)
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) (2012)
Clemens Kreutz, Andreas Raue, Jens Timmer
Likelihood based observability analysis and confidence intervals for predictions of dynamic models. BMC Syst. Biol. 6 (2012)
Björn Schelter, Linda Sommerlade, Bettina Platt, Andrea Plano, Marco Thiel, Jens Timmer
Multivariate analysis of dynamical processes with applications to the neurosciences. EMBC (2011)
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 (2011)
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)
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) (2010)
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 (2010)
Enno Mammen, Swagata Nandi, Thomas Maiwald, Jens Timmer
Effect of Jump Discontinuity for Phase-Randomized Surrogate Data Testing. Int. J. Bifurc. Chaos 19 (1) (2009)
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) (2009)
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 (2009)
Kilian Bartholomé, Clemens Kreutz, Jens Timmer
Estimation of Gene Induction Enables a Relevance-Based Ranking of Gene Sets. J. Comput. Biol. 16 (7) (2009)
Thomas Maiwald, Jens Timmer
Dynamical modeling and multi-experiment fitting with PottersWheel. Bioinform. 24 (18) (2008)
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 (2008)
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) (2008)
Kilian Bartholomé, Jens Timmer
Regulatorische Prinzipien und Systemanalyse der bakteriellen Chemotaxis (Regulatory Principles and Systems Analysis of Bacterial Chemotaxis). Autom. 56 (5) (2008)
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 (2008)
Stefan Hengl, Clemens Kreutz, Jens Timmer, Thomas Maiwald
Data-based identifiability analysis of non-linear dynamical models. Bioinform. 23 (19) (2007)
Florian Geier, Jens Timmer, Christian Fleck
Reconstructing gene-regulatory networks from time series, knock-out data, and prior knowledge. BMC Syst. Biol. 1 (2007)
Clemens Kreutz, M. M. Bartolome Rodriguez, Thomas Maiwald, M. Seidl, H. E. Blum, L. Mohr, Jens Timmer
An error model for protein quantification. Bioinform. 23 (20) (2007)
Björn Schelter, Matthias Winterhalder, Jens Timmer, Jürgen Kurths
Phase Synchronization and Coherence Analysis: Sensitivity and specificity. Int. J. Bifurc. Chaos 17 (10) (2007)
Matthias Winterhalder, Björn Schelter, Jens Timmer
Detecting Coupling Directions in Multivariate Oscillatory Systems. Int. J. Bifurc. Chaos 17 (10) (2007)
Valko Petrov, Martin Peifer, Jens Timmer
Bistability and Self-oscillations in Cell Cycle Control. Int. J. Bifurc. Chaos 16 (4) (2006)
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) (2005)
T. G. Müller, Jens Timmer
Parameter Identification Techniques for Partial Differential Equations. Int. J. Bifurc. Chaos 14 (6) (2004)
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) (2004)
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) (2004)
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) (2004)
Marco Thiel, M. Carmen Romano, Udo Schwarz, Jürgen Kurths, Jens Timmer
Surrogate-Based Hypothesis Test without Surrogates. Int. J. Bifurc. Chaos 14 (6) (2004)
Henning U. Voss, Jens Timmer, Jürgen Kurths
Nonlinear Dynamical System Identification from Uncertain and Indirect Measurements. Int. J. Bifurc. Chaos 14 (6) (2004)
Daniel Faller, Ursula Klingmüller, Jens Timmer
Simulation Methods for Optimal Experimental Design in Systems Biology. Simul. 79 (12) (2003)
Daniel Faller, Henning U. Voss, Jens Timmer, Uwe Hobohm
Normalization of DNA-Microarray Data by Nonlinear Correlation Maximization. J. Comput. Biol. 10 (5) (2003)
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)
Werner Horbelt, Thorsten Müller, Jens Timmer, Werner Melzer, Karl Winkler
Analysis of Nonlinear Differential Equations: Parameter Estimation and Model Selection. ISMDA (2000)
Thorsten Müller, T. Ball, R. Kristeva-Feige, Thomas Mergner, Jens Timmer
Classification of Electro-encephalographic Spatial Patterns. ISMDA (2000)
Steffen Michalek, Mirko Wagner, Jens Timmer
A new approximate likelihood estimator for ARMA-filtered hidden Markov models. IEEE Trans. Signal Process. 48 (6) (2000)
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) (2000)
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) (1999)
Steffen Michalek, Jens Timmer
Estimating rate constants in hidden Markov models by the EM algorithm. IEEE Trans. Signal Process. 47 (1) (1999)
Stefan Gezeck, Jens Timmer
Detecting multimodality in saccadic reaction time distributions in gap and overlap tasks. Biol. Cybern. 78 (4) (1998)
Jens Timmer, M. Lauk, W. Pfleger, Günther Deuschl
Cross-spectral analysis of physiological tremor and muscle activity. Biol. Cybern. 78 (5) (1998)
Jens Timmer, M. Lauk, W. Pfleger, Günther Deuschl
Cross-spectral analysis of physiological tremor and muscle activity. Biol. Cybern. 78 (5) (1998)
Jens Timmer, Andreas S. Weigend
Modeling Volatility Using State Space Models. Int. J. Neural Syst. 8 (4) (1997)
Jens Timmer, C. Gantert, Günther Deuschl, Josef Honerkamp
Characteristics of hand tremor time series. Biol. Cybern. 70 (1) (1993)
C. Gantert, Josef Honerkamp, Jens Timmer
Analyzing the dynamics of hand tremor time series. Biol. Cybern. 66 (6) (1992)