Jens Timmer

Orcid: 0000-0003-4517-1383

  • University of Freiburg, Germany

According to our database1, Jens Timmer authored at least 68 papers between 1992 and 2023.

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PhD thesis 


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Likelihood-ratio test statistic for the finite-sample case in nonlinear ordinary differential equation models.
PLoS Comput. Biol., 2023

Uncovering specific mechanisms across cell types in dynamical models.
PLoS Comput. Biol., 2023

Non-Parametric Model-Based Estimation of the Effective Reproduction Number for SARS-CoV-2.
Algorithms, 2023

Towards Expected Counter - Using Comprehensible Features to Predict Counterattacks.
Proceedings of the Machine Learning and Data Mining for Sports Analytics, 2022

PEtab - Interoperable specification of parameter estimation problems in systems biology.
PLoS Comput. Biol., 2021

Estimating chain length for time delays in dynamical systems using profile likelihood.
Bioinform., 2020

Extensions of ℓ 1 regularization increase detection specificity for cell-type specific parameters in dynamic models.
BMC Bioinform., 2019

Benchmark problems for dynamic modeling of intracellular processes.
Bioinform., 2019

Computational Mechanistic Investigation of Chronotropic Effects on Murine Sinus Node Cells.
Proceedings of the Computing in Cardiology, 2018

Identification of Cell Type-Specific Differences in Erythropoietin Receptor Signaling in Primary Erythroid and Lung Cancer Cells.
PLoS Comput. Biol., 2016

<i>L</i><sub>1</sub> regularization facilitates detection of cell type-specific parameters in dynamical systems.
Bioinform., 2016

Fast integration-based prediction bands for ordinary differential equation models.
Bioinform., 2016

Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models.
PLoS Comput. Biol., 2015

Disentangling the Complexity of HGF Signaling by Combining Qualitative and Quantitative Modeling.
PLoS Comput. Biol., 2015

Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems.
Bioinform., 2015

Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach.
BMC Syst. Biol., 2014

Comparison of approaches for parameter identifiability analysis of biological systems.
Bioinform., 2014

A numerically efficient implementation of the expectation maximization algorithm for state space models.
Appl. Math. Comput., 2014

iVUN: interactive Visualization of Uncertain biochemical reaction Networks.
BMC Bioinform., 2013

Network modulation during complex syntactic processing.
NeuroImage, 2012

EPILEPSIAE - A European epilepsy database.
Comput. Methods Programs Biomed., 2012

In silico labeling reveals the time-dependent label half-life and transit-time in dynamical systems.
BMC Syst. Biol., 2012

Likelihood based observability analysis and confidence intervals for predictions of dynamic models.
BMC Syst. Biol., 2012

A variational approach to parameter estimation in ordinary differential equations.
BMC Syst. Biol., 2012

Comprehensive estimation of input signals and dynamics in biochemical reaction networks.
Bioinform., 2012

TSSi - an R package for transcription start site identification from 5′ mRNA tag data.
Bioinform., 2012

Integration of Boolean models exemplified on hepatocyte signal transduction.
Briefings Bioinform., 2012

Identification of Preseizure States in Epilepsy: A Data-Driven Approach for Multichannel EEG Recordings.
Frontiers Comput. Neurosci., 2011

Multivariate analysis of dynamical processes with applications to the neurosciences.
Proceedings of the 33rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 2011

Seizure prediction in epilepsy: From circadian concepts via probabilistic forecasting to statistical evaluation.
Proceedings of the 33rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 2011

Combining functional and anatomical connectivity reveals brain networks for auditory language comprehension.
NeuroImage, 2010

Model-based extension of high-throughput to high-content data.
BMC Syst. Biol., 2010

Estimation of Gene Induction Enables a Relevance-Based Ranking of Gene Sets.
J. Comput. Biol., 2009

Effect of Jump Discontinuity for Phase-Randomized Surrogate Data Testing.
Int. J. Bifurc. Chaos, 2009

Modeling system states in liver cells: Survival, apoptosis and their modifications in response to viral infection.
BMC Syst. Biol., 2009

Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood.
Bioinform., 2009

On the Detection of Direct Directed Information Flow in fMRI.
IEEE J. Sel. Top. Signal Process., 2008

A systems biology approach to analyse amplification in the JAK2-STAT5 signalling pathway.
BMC Syst. Biol., 2008

Hybrid optimization method with general switching strategy for parameter estimation.
BMC Syst. Biol., 2008

Dynamical modeling and multi-experiment fitting with PottersWheel.
Bioinform., 2008

Regulatorische Prinzipien und Systemanalyse der bakteriellen Chemotaxis (Regulatory Principles and Systems Analysis of Bacterial Chemotaxis).
Autom., 2008

Detecting Coupling Directions in Multivariate Oscillatory Systems.
Int. J. Bifurc. Chaos, 2007

Phase Synchronization and Coherence Analysis: Sensitivity and specificity.
Int. J. Bifurc. Chaos, 2007

Reconstructing gene-regulatory networks from time series, knock-out data, and prior knowledge.
BMC Syst. Biol., 2007

An error model for protein quantification.
Bioinform., 2007

Data-based identifiability analysis of non-linear dynamical models.
Bioinform., 2007

Bistability and Self-oscillations in Cell Cycle Control.
Int. J. Bifurc. Chaos, 2006

Comparison of linear signal processing techniques to infer directed interactions in multivariate neural systems.
Signal Process., 2005

An Open Source Protein Gel Documentation System for Proteome Analyses.
J. Chem. Inf. Model., 2004

Nonlinear Dynamical System Identification from Uncertain and Indirect Measurements.
Int. J. Bifurc. Chaos, 2004

Modeling the Nonlinear Dynamics of Cellular Signal Transduction.
Int. J. Bifurc. Chaos, 2004

Surrogate-Based Hypothesis Test without Surrogates.
Int. J. Bifurc. Chaos, 2004

Parameter Identification Techniques for Partial Differential Equations.
Int. J. Bifurc. Chaos, 2004

Identification of Rate Constants and nonobservable Absorption Spectra in Nonlinear Biochemical Reaction Dynamics.
Int. J. Bifurc. Chaos, 2004

Simulation Methods for Optimal Experimental Design in Systems Biology.
Simul., 2003

Normalization of DNA-Microarray Data by Nonlinear Correlation Maximization.
J. Comput. Biol., 2003

A new approximate likelihood estimator for ARMA-filtered hidden Markov models.
IEEE Trans. Signal Process., 2000

Cross-spectral Analysis of tremor Time Series.
Int. J. Bifurc. Chaos, 2000

Detection and Classification of Sleep-Disordered Breathing Using Acoustic Respiratory Input Impedance and Nasal Pressure.
Proceedings of the Medical Data Analysis, First International Symposium, 2000

Classification of Electro-encephalographic Spatial Patterns.
Proceedings of the Medical Data Analysis, First International Symposium, 2000

Analysis of Nonlinear Differential Equations: Parameter Estimation and Model Selection.
Proceedings of the Medical Data Analysis, First International Symposium, 2000

Estimating rate constants in hidden Markov models by the EM algorithm.
IEEE Trans. Signal Process., 1999

Early detection of upper airway obstructions by analysis of acoustical respiratory input impedance.
Biol. Cybern., 1999

Cross-spectral analysis of physiological tremor and muscle activity.
Biol. Cybern., 1998

Detecting multimodality in saccadic reaction time distributions in gap and overlap tasks.
Biol. Cybern., 1998

Modeling Volatility Using State Space Models.
Int. J. Neural Syst., 1997

Characteristics of hand tremor time series.
Biol. Cybern., 1993

Analyzing the dynamics of hand tremor time series.
Biol. Cybern., 1992