Jens Timmer

69 papers Journal 62Unranked 7
YearRankTypeTitle / Venue / Authors
2025 J jnl
A linear pathway for inositol pyrophosphate metabolism revealed by 18O labeling and model reduction.
PLoS Comput. Biol.
Jacques Hermes, Geun-Don Kim, Guizhen Liu, Maria Giovanna De Leo, Andreas Mayer, Henning J. Jessen, Jens Timmer
2023 J jnl
Likelihood-ratio test statistic for the finite-sample case in nonlinear ordinary differential equation models.
PLoS Comput. Biol.
Christian Tönsing, Bernhard Steiert, Jens Timmer, Clemens Kreutz
2023 J jnl
Non-Parametric Model-Based Estimation of the Effective Reproduction Number for SARS-CoV-2.
Algorithms
Jacques Hermes, Marcus Rosenblatt, Christian Tönsing, Jens Timmer
2023 J jnl
Uncovering specific mechanisms across cell types in dynamical models.
PLoS Comput. Biol.
Adrian L. Hauber, Marcus Rosenblatt, Jens Timmer
2022 — conf
Towards Expected Counter - Using Comprehensible Features to Predict Counterattacks.
MLSA@PKDD/ECML
Henrik Biermann, Franz-Georg Wieland, Jens Timmer, Daniel Memmert, Ashwin Phatak
2021 J jnl
PEtab - Interoperable specification of parameter estimation problems in systems biology.
PLoS Comput. Biol.
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
2020 J jnl
Estimating chain length for time delays in dynamical systems using profile likelihood.
Bioinform.
Adrian L. Hauber, Raphael Engesser, Joep Vanlier, Jens Timmer
2019 J jnl
Benchmark problems for dynamic modeling of intracellular processes.
Bioinform.
Helge Hass, Carolin Loos, Elba Raimúndez-Álvarez, Jens Timmer, Jan Hasenauer, Clemens Kreutz
2019 J jnl
Extensions of ℓ 1 regularization increase detection specificity for cell-type specific parameters in dynamic models.
BMC Bioinform.
Pascal Dolejsch, Helge Hass, Jens Timmer
2018 — conf
Computational Mechanistic Investigation of Chronotropic Effects on Murine Sinus Node Cells.
CinC
Benjamin Winkelmann, Callum M. Zgierski-Johnston, Eike Moritz Wülfers, Jens Timmer, Gunnar Seemann
2016 J jnl
Fast integration-based prediction bands for ordinary differential equation models.
Bioinform.
Helge Hass, Clemens Kreutz, Jens Timmer, Daniel Kaschek
2016 J jnl
Identification of Cell Type-Specific Differences in Erythropoietin Receptor Signaling in Primary Erythroid and Lung Cancer Cells.
PLoS Comput. Biol.
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
2015 J jnl
Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems.
Bioinform.
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
2015 J jnl
Disentangling the Complexity of HGF Signaling by Combining Qualitative and Quantitative Modeling.
PLoS Comput. Biol.
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
2015 J jnl
Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models.
PLoS Comput. Biol.
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
2014 J jnl
A numerically efficient implementation of the expectation maximization algorithm for state space models.
Appl. Math. Comput.
Wolfgang Mader, Yannick Linke, Malenka Mader, Linda Sommerlade, Jens Timmer, Björn Schelter
2014 J jnl
Comparison of approaches for parameter identifiability analysis of biological systems.
Bioinform.
Andreas Raue, Johan Karlsson, Maria Pia Saccomani, Mats Jirstrand, Jens Timmer
2014 J jnl
Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach.
BMC Syst. Biol.
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
2013 J jnl
iVUN: interactive Visualization of Uncertain biochemical reaction Networks.
BMC Bioinform.
Corinna Vehlow, Jan Hasenauer, Andrei Kramer, Andreas Raue, Sabine Hug, Jens Timmer, Nicole Radde, Fabian J. Theis, Daniel Weiskopf
2012 J jnl
A variational approach to parameter estimation in ordinary differential equations.
BMC Syst. Biol.
Daniel Kaschek, Jens Timmer
2012 J jnl
Comprehensive estimation of input signals and dynamics in biochemical reaction networks.
Bioinform.
Max Schelker, Andreas Raue, Jens Timmer, Clemens Kreutz
2012 J jnl
EPILEPSIAE - A European epilepsy database.
Comput. Methods Programs Biomed.
Matthias Ihle, Hinnerk Feldwisch-Drentrup, César Alexandre Teixeira, Adrien Witon, Björn Schelter, Jens Timmer, Andreas Schulze-Bonhage
2012 J jnl
In silico labeling reveals the time-dependent label half-life and transit-time in dynamical systems.
BMC Syst. Biol.
Thomas Maiwald, Julie Blumberg, Andreas Raue, Stefan Hengl, Marcel Schilling, Sherwin K. B. Sy, Verena Becker, Ursula Klingmüller, Jens Timmer
2012 J jnl
Integration of Boolean models exemplified on hepatocyte signal transduction.
Briefings Bioinform.
Rebekka Schlatter, Nicole Philippi, Gaby Wangorsch, Robert Pick, Oliver Sawodny, Christoph Borner, Jens Timmer, Michael Ederer, Thomas Dandekar
2012 J jnl
Likelihood based observability analysis and confidence intervals for predictions of dynamic models.
BMC Syst. Biol.
Clemens Kreutz, Andreas Raue, Jens Timmer
2012 J jnl
Network modulation during complex syntactic processing.
NeuroImage
Dirk-Bart den Ouden, Dorothee Saur, Wolfgang Mader, Björn Schelter, Sladjana Lukic, Eisha Wali, Jens Timmer, Cynthia K. Thompson
2012 J jnl
TSSi - an R package for transcription start site identification from 5′ mRNA tag data.
Bioinform.
Clemens Kreutz, J. S. Gehring, Daniel Lang, Ralf Reski, Jens Timmer, Stefan A. Rensing
2011 J jnl
Identification of Preseizure States in Epilepsy: A Data-Driven Approach for Multichannel EEG Recordings.
Frontiers Comput. Neurosci.
Hinnerk Feldwisch-Drentrup, Matthäus Staniek, Andreas Schulze-Bonhage, Jens Timmer, Henning Dickten, Christian Erich Elger, Björn Schelter, Klaus Lehnertz
2011 — conf
Multivariate analysis of dynamical processes with applications to the neurosciences.
EMBC
Björn Schelter, Linda Sommerlade, Bettina Platt, Andrea Plano, Marco Thiel, Jens Timmer
2011 — conf
Seizure prediction in epilepsy: From circadian concepts via probabilistic forecasting to statistical evaluation.
EMBC
Björn Schelter, Hinnerk Feldwisch-Drentrup, Matthias Ihle, Andreas Schulze-Bonhage, Jens Timmer
2010 J jnl
Combining functional and anatomical connectivity reveals brain networks for auditory language comprehension.
NeuroImage
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
2010 J jnl
Model-based extension of high-throughput to high-content data.
BMC Syst. Biol.
Andrea C. Pfeifer, Daniel Kaschek, Julie Bachmann, Ursula Klingmüller, Jens Timmer
2009 J jnl
Effect of Jump Discontinuity for Phase-Randomized Surrogate Data Testing.
Int. J. Bifurc. Chaos
Enno Mammen, Swagata Nandi, Thomas Maiwald, Jens Timmer
2009 J jnl
Estimation of Gene Induction Enables a Relevance-Based Ranking of Gene Sets.
J. Comput. Biol.
Kilian Bartholomé, Clemens Kreutz, Jens Timmer
2009 J jnl
Modeling system states in liver cells: Survival, apoptosis and their modifications in response to viral infection.
BMC Syst. Biol.
Nicole Philippi, Dorothee Walter, Rebekka Schlatter, Karine Ferreira, Michael Ederer, Oliver Sawodny, Jens Timmer, Christoph Borner, Thomas Dandekar
2009 J jnl
Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood.
Bioinform.
Andreas Raue, Clemens Kreutz, Thomas Maiwald, Julie Bachmann, Marcel Schilling, Ursula Klingmüller, Jens Timmer
2008 J jnl
A systems biology approach to analyse amplification in the JAK2-STAT5 signalling pathway.
BMC Syst. Biol.
Julio Vera, Julie Bachmann, Andrea C. Pfeifer, Verena Becker, Jose A. Hormiga, Néstor Torres Darias, Jens Timmer, Ursula Klingmüller, Olaf Wolkenhauer
2008 J jnl
Dynamical modeling and multi-experiment fitting with PottersWheel.
Bioinform.
Thomas Maiwald, Jens Timmer
2008 J jnl
Hybrid optimization method with general switching strategy for parameter estimation.
BMC Syst. Biol.
Eva Balsa-Canto, Martin Peifer, Julio R. Banga, Jens Timmer, Christian Fleck
2008 J jnl
On the Detection of Direct Directed Information Flow in fMRI.
IEEE J. Sel. Top. Signal Process.
Wolfgang Mader, David Feess, Rüdiger Lange, Dorothee Saur, Volkmar Glauche, Cornelius Weiller, Jens Timmer, Björn Schelter
2008 J jnl
Regulatorische Prinzipien und Systemanalyse der bakteriellen Chemotaxis (Regulatory Principles and Systems Analysis of Bacterial Chemotaxis).
Autom.
Kilian Bartholomé, Jens Timmer
2007 J jnl
An error model for protein quantification.
Bioinform.
Clemens Kreutz, M. M. Bartolome Rodriguez, Thomas Maiwald, Maxmilian Seidl, H. E. Blum, L. Mohr, Jens Timmer
2007 J jnl
Data-based identifiability analysis of non-linear dynamical models.
Bioinform.
Stefan Hengl, Clemens Kreutz, Jens Timmer, Thomas Maiwald
2007 J jnl
Detecting Coupling Directions in Multivariate Oscillatory Systems.
Int. J. Bifurc. Chaos
Matthias Winterhalder, Björn Schelter, Jens Timmer
2007 J jnl
Phase Synchronization and Coherence Analysis: Sensitivity and specificity.
Int. J. Bifurc. Chaos
Björn Schelter, Matthias Winterhalder, Jens Timmer, Jürgen Kurths
2007 J jnl
Reconstructing gene-regulatory networks from time series, knock-out data, and prior knowledge.
BMC Syst. Biol.
Florian Geier, Jens Timmer, Christian Fleck
2006 J jnl
Bistability and Self-oscillations in Cell Cycle Control.
Int. J. Bifurc. Chaos
Valko Petrov, Martin Peifer, Jens Timmer
2005 J jnl
Comparison of linear signal processing techniques to infer directed interactions in multivariate neural systems.
Signal Process.
Matthias Winterhalder, Björn Schelter, Wolfram Hesse, Karin Schwab, Lutz Leistritz, Daniel Klan, Reinhard Bauer, Jens Timmer, Herbert Witte
2004 J jnl
An Open Source Protein Gel Documentation System for Proteome Analyses.
J. Chem. Inf. Model.
Daniel Faller, Thomas Reinheckel, Daniel Wenzler, Sascha Hagemann, Ke Xiao, Josef Honerkamp, Christoph Peters, Thomas Dandekar, Jens Timmer
2004 J jnl
Identification of Rate Constants and nonobservable Absorption Spectra in Nonlinear Biochemical Reaction Dynamics.
Int. J. Bifurc. Chaos
Douglas Maraun, Werner Horbelt, Henning W. Rust, Jens Timmer, H. P. Happersberger, F. Drepper
2004 J jnl
Modeling the Nonlinear Dynamics of Cellular Signal Transduction.
Int. J. Bifurc. Chaos
Jens Timmer, T. G. Müller, I. Swameye, O. Sandra, Ursula Klingmüller
2004 J jnl
Nonlinear Dynamical System Identification from Uncertain and Indirect Measurements.
Int. J. Bifurc. Chaos
Henning U. Voss, Jens Timmer, Jürgen Kurths
2004 J jnl
Parameter Identification Techniques for Partial Differential Equations.
Int. J. Bifurc. Chaos
T. G. Müller, Jens Timmer
2004 J jnl
Surrogate-Based Hypothesis Test without Surrogates.
Int. J. Bifurc. Chaos
Marco Thiel, M. Carmen Romano, Udo Schwarz, Jürgen Kurths, Jens Timmer
2003 J jnl
Normalization of DNA-Microarray Data by Nonlinear Correlation Maximization.
J. Comput. Biol.
Daniel Faller, Henning U. Voss, Jens Timmer, Uwe Hobohm
2003 J jnl
Simulation Methods for Optimal Experimental Design in Systems Biology.
Simul.
Daniel Faller, Ursula Klingmüller, Jens Timmer
2000 J jnl
A new approximate likelihood estimator for ARMA-filtered hidden Markov models.
IEEE Trans. Signal Process.
Steffen Michalek, Mirko Wagner, Jens Timmer
2000 — conf
Analysis of Nonlinear Differential Equations: Parameter Estimation and Model Selection.
ISMDA
Werner Horbelt, Thorsten Müller, Jens Timmer, Werner Melzer, Karl Winkler
2000 — conf
Classification of Electro-encephalographic Spatial Patterns.
ISMDA
Thorsten Müller, T. Ball, R. Kristeva-Feige, Thomas Mergner, Jens Timmer
2000 J jnl
Cross-spectral Analysis of tremor Time Series.
Int. J. Bifurc. Chaos
Jens Timmer, Michael Lauk, S. Häußler, V. Radt, B. Köster, B. Hellwig, B. Guschlbauer, C. H. Lücking, M. Eichler, Günther Deuschl
2000 — conf
Detection and Classification of Sleep-Disordered Breathing Using Acoustic Respiratory Input Impedance and Nasal Pressure.
ISMDA
Holger Steltner, Richard Staats, Michael Vogel, Christian Virchow, Heinrich Matthys, Josef Guttmann, Jens Timmer
1999 J jnl
Early detection of upper airway obstructions by analysis of acoustical respiratory input impedance.
Biol. Cybern.
S. Reisch, Holger Steltner, Jens Timmer, Christine Renotte, Josef Guttmann
1999 J jnl
Estimating rate constants in hidden Markov models by the EM algorithm.
IEEE Trans. Signal Process.
Steffen Michalek, Jens Timmer
1998 J jnl
Cross-spectral analysis of physiological tremor and muscle activity.
Biol. Cybern.
Jens Timmer, M. Lauk, W. Pfleger, Günther Deuschl
1998 J jnl
Cross-spectral analysis of physiological tremor and muscle activity.
Biol. Cybern.
Jens Timmer, M. Lauk, W. Pfleger, Günther Deuschl
1998 J jnl
Detecting multimodality in saccadic reaction time distributions in gap and overlap tasks.
Biol. Cybern.
Stefan Gezeck, Jens Timmer
1997 J jnl
Modeling Volatility Using State Space Models.
Int. J. Neural Syst.
Jens Timmer, Andreas S. Weigend
1993 J jnl
Characteristics of hand tremor time series.
Biol. Cybern.
Jens Timmer, C. Gantert, Günther Deuschl, Josef Honerkamp
1992 J jnl
Analyzing the dynamics of hand tremor time series.
Biol. Cybern.
C. Gantert, Josef Honerkamp, Jens Timmer