J. Timmer

C. Weiller, J. Timmer, M. Reinhard, 2008, Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism.

Bilateral severe carotid artery stenosis or occlusion – cerebral autoregulation dynamics and collateral flow patterns

B. Guschlbauer, J. Timmer, J. Timmer, 2003, Acta Neurochirurgica.

Cerebral autoregulation in carotid artery occlusive disease assessed from spontaneous blood pressure fluctuations by the correlation coefficient index.

M Czosnyka, J Timmer, J. Timmer, 2003, Stroke.

Transfer function analysis for clinical evaluation of dynamic cerebral autoregulation—a comparison between spontaneous and respiratory-induced oscillations

J Timmer, J. Timmer, T. Müller, 2003, Physiological measurement.

Host cell responses induced by hepatitis C virus binding

T. Maiwald, J. Timmer, C. Kreutz, 2006, Hepatology.

Networks: On the relation of bi- and multivariate measures

Jens Timmer, Wolfgang Mader, Björn Schelter, 2015, Scientific Reports.

Mathematical model of early Reelin-induced Src family kinase-mediated signaling

Jens Timmer, Helge Hass, Hans H Bock, 2017, PloS one.

Cell-to-cell variability in JAK2/STAT5 pathway components and cytoplasmic volumes defines survival threshold in erythroid progenitor cells.

J. Hasenauer, J. Timmer, M. Schilling, 2021, Cell reports.

Spleen tyrosine kinase is overexpressed and represents a potential therapeutic target in chronic lymphocytic leukemia.

Jens Timmer, Hendrik Veelken, Kilian Bartholomé, 2009, Cancer research.

Dealing with prognostic signature instability: a strategy illustrated for cardiovascular events in patients with end-stage renal disease

T. Kurz, J. Timmer, H. Binder, 2016, BMC Medical Genomics.

Genome-wide analysis of genetic alterations in Barrett's adenocarcinoma using single nucleotide polymorphism arrays

Jens Timmer, Martin Werner, Kilian Bartholomé, 2009, Laboratory Investigation.

Variations in substitution rate in human and mouse genomes.

J Timmer, J. Timmer, M. Peifer, 2004, Physical review letters.

Protein abundance of AKT and ERK pathway components governs cell type‐specific regulation of proliferation

Melanie Boerries, Ursula Klingmüller, Jens Timmer, 2017, Molecular systems biology.

Zebrafish Pou 5 f 1-dependent transcriptional networks control temporal regulation of early differentiation programs

W. Driever, J. Timmer, V. Taylor, 2009 .

Pou 5 f 3 and Sox 19 b select gene expression repertoire at Zygotic Genome Activation

J. Timmer, L. Yampolsky, B. Grüning, 2022 .

Combination of immunosuppressive drugs leaves specific “fingerprint” on gene expression in vitro

J. Timmer, C. Kreutz, S. Teschner, 2009, Immunopharmacology and immunotoxicology.

Transcription factors ETF, E2F, and SP‐1 are involved in cytokine‐independent proliferation of murine hepatocytes

Jens Timmer, Reinhard Guthke, Clemens Kreutz, 2010, Hepatology.

A Systems Biology Study on NFκB Signaling in Primary Mouse Hepatocytes

J. Timmer, P. Schirmacher, A. Raue, 2012, Front. Physio..

MeDIP coupled with a promoter tiling array as a platform to investigate global DNA methylation patterns in AML cells.

J. Timmer, C. Kreutz, M. Lübbert, 2013, Leukemia research.

Higher-order Lie symmetries in identifiability and predictability analysis of dynamic models.

Jens Timmer, Daniel Kaschek, Benjamin Merkt, 2015, Physical review. E, Statistical, nonlinear, and soft matter physics.

Model-based extension of high-throughput to high-content data

Ursula Klingmüller, Jens Timmer, Daniel Kaschek, 2010, BMC Systems Biology.

Magnitude of ubiquitination determines the fate of epidermal growth factor receptor upon ligand stimulation.

J. Timmer, B. Blagoev, M. Fehling-Kaschek, 2021, Journal of molecular biology.

Disentangling the Complexity of HGF Signaling by Combining Qualitative and Quantitative Modeling

Steffen Klamt, Ursula Klingmüller, Jens Timmer, 2015, PLoS Comput. Biol..

Normalization of DNA-Microarray Data by Nonlinear Correlation Maximization

Jens Timmer, Henning U. Voss, Uwe Hobohm, 2003, J. Comput. Biol..

Control of the specificity of T cell-mediated anti-idiotype immunity by natural regulatory T cells

J. Timmer, A. Bulashevska, H. Veelken, 2010, Cancer Immunology, Immunotherapy.

Functional Proteomics of Breast Cancer Metabolism Identifies GLUL as Responder during Hypoxic Adaptation.

S. Wiemann, J. Timmer, C. Kreutz, 2019, Journal of proteome research.

Control of plant organ size by KLUH/CYP78A5-dependent intercellular signaling.

Jens Timmer, Moritz Gerstung, Daniel MacLean, 2007, Developmental cell.

Dual-controlled optogenetic system for the rapid down-regulation of protein levels in mammalian cells

Jens Timmer, Raphael Engesser, Matias D Zurbriggen, 2018, Scientific Reports.

Quantitative data generation for systems biology: the impact of randomisation, calibrators and normalisers.

J Timmer, U Klingmüller, M Schilling, 2005, Systems biology.

Simulation Methods for Optimal Experimental Design in Systems Biology

Ursula Klingmüller, Jens Timmer, Daniel Faller, 2003, Simul..

Identification of Cell Type-Specific Differences in Erythropoietin Receptor Signaling in Primary Erythroid and Lung Cancer Cells

Ursula Klingmüller, Jens Timmer, Marcel Schilling, 2016, PLoS Comput. Biol..

Gene expression profiling in polycythaemia vera: overexpression of transcription factor NF‐E2

T. Maiwald, J. Timmer, C. Kreutz, 2005, British journal of haematology.

A red/far-red light-responsive bi-stable toggle switch to control gene expression in mammalian cells

Jens Timmer, Simon Schulz, Wilfried Weber, 2013, Nucleic acids research.

Photoconversion and Nuclear Trafficking Cycles Determine Phytochrome A's Response Profile to Far-Red Light

J. Timmer, E. Schäfer, C. Fleck, 2011, Cell.

Estimating rate constants in hidden Markov models by the EM algorithm

Jens Timmer, Steffen Michalek, J. Timmer, 1999, IEEE Trans. Signal Process..

Dynamical modeling and multi-experiment fitting with PottersWheel

Jens Timmer, Thomas Maiwald, T. Maiwald, 2008, Bioinform..

Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems

Fabian J. Theis, Edda Klipp, Ursula Klingmüller, 2015, Bioinform..

USP18 lack in microglia causes destructive interferonopathy of the mouse brain

Tuan Leng Tay, J. Timmer, K. Knobeloch, 2015, The EMBO journal.

Two-Dimensional Patterning by a Trapping/Depletion Mechanism: The Role of TTG1 and GL3 in Arabidopsis Trichome Formation

Jens Timmer, Arp Schnittger, Florian Geier, 2008, PLoS biology.

Resolving the Combinatorial Complexity of Smad Protein Complex Formation and Its Link to Gene Expression.

Ursula Klingmüller, Jens Timmer, Marcel Schilling, 2017, Cell systems.

Gene profiling of polycystic kidneys.

J. Timmer, C. Kreutz, J. Donauer, 2006, Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association.

Expression ratio of the TGFβ-inducible gene MYO10 is prognostic for overall survival of squamous cell lung cancer patients and predicts chemotherapy response

J. Timmer, A. Warth, H. Dienemann, 2018, Scientific Reports.

RPPanalyzer toolbox: an improved R package for analysis of reverse phase protein array data.

Jens Timmer, Daniel Kaschek, Tim Beißbarth, 2014, BioTechniques.

untreated indolent B-cell lymphoma and very early CLL Definition and characterization of the systemic T-cell dysregulation in

J. Timmer, K. Bartholomé, H. Veelken, 2011 .

Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models

Jens Timmer, Pablo Meyer, Bernhard Steiert, 2015, PLoS Comput. Biol..

A systems biology approach to analyse amplification in the JAK2-STAT5 signalling pathway

Olaf Wolkenhauer, Ursula Klingmüller, Jens Timmer, 2008, BMC Systems Biology.

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

Jens Timmer, Kilian Bartholomé, J. Timmer, 2008, Autom..

Design principles of signal transduction pathways to compensate intracellular perturbations

Jens Timmer, Kilian Bartholome, Markus Kollmann, 2006, 2006 IEEE Conference on Computer Aided Control System Design, 2006 IEEE International Conference on Control Applications, 2006 IEEE International Symposium on Intelligent Control.

An error model for protein quantification

Jens Timmer, Clemens Kreutz, Thomas Maiwald, 2007, Bioinform..

Aperiodic flow-induced oscillations of collapsible tubes: a critical reappraisal.

T. Maiwald, M. Winterhalder, H. Voss, 2004, Medical engineering & physics.

Pathological tremors: Deterministic chaos or nonlinear stochastic oscillators?

M. Lauk, J. Timmer, C. Lucking, 2000, Chaos.

Modeling system states in liver cells: Survival, apoptosis and their modifications in response to viral infection

Oliver Sawodny, Jens Timmer, Michael Ederer, 2009, BMC Systems Biology.

Hepatocyte Ploidy Is a Diversity Factor for Liver Homeostasis

J. Timmer, C. Kreutz, S. MacNelly, 2017, Front. Physiol..

Identification of Rate Constants and nonobservable Absorption Spectra in Nonlinear Biochemical Reaction Dynamics

Jens Timmer, F. Drepper, Werner Horbelt, 2004, Int. J. Bifurc. Chaos.

Computational processing and error reduction strategies for standardized quantitative data in biological networks

Sebastian Bohl, Ursula Klingmüller, Jens Timmer, 2005, The FEBS journal.

The ratio of the lateral correlation length and particle radius determines the density profile of spherical molecules near a fluctuating membrane.

J. Timmer, C. Fleck, R. Castañeda-Priego, 2014, Soft matter.

BRAF V600E Mutations in Nevi and Melanocytic Tumors of Uncertain Malignant Potential.

J. Timmer, C. Kreutz, A. von Deimling, 2018, The Journal of investigative dermatology.

Identification of Gene Regulatory Networks, Machine Learning

Jens Timmer, Andreas Raue, Zhong-Yuan Zhang, 2013 .

untreated indolent B-cell lymphoma and very early CLL Definition and characterization of the systemic T-cell dysregulation in

J. Timmer, K. Bartholomé, H. Veelken, 2011 .

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

Jens Timmer, Daniel Lang, Ralf Reski, 2012, Bioinform..

Caspase-3 feeds back on caspase-8, Bid and XIAP in type I Fas signaling in primary mouse hepatocytes

C. Borner, J. Timmer, M. Bogyo, 2012, Apoptosis.

Expression profiling on chronically rejected transplant kidneys1

J. Timmer, J. Donauer, B. Rumberger, 2003 .

Expression profiling on chronically rejected transplant kidneys.

J. Timmer, J. Donauer, B. Rumberger, 2003, Transplantation.

PEtab—Interoperable specification of parameter estimation problems in systems biology

Cambridge, Adrian L Hauber, Frank T. Bergmann, 2020, PLoS Comput. Biol..

Non-parametric identification of non-linear oscillating systems

Jens Timmer, Martin Peifer, Henning U. Voss, 2003 .

Testing for phase synchronization

Jens Timmer, Martin Peifer, Bjoern Schelter, 2007 .

Continuous Nonlinear Delayed‐Feedback Dynamics from Noisy Observations

H. Voss, J. Timmer, W. Horbelt, 2002 .

Synthesis of phycocyanobilin in mammalian cells.

Matias D. Zurbriggen, J. Timmer, F. Nagy, 2013, Chemical communications.

Mathematical modeling of drug-induced receptor internalization in the HER2-positive SKBR3 breast cancer cell-line

D. Peckys, J. Timmer, Daniel Kaschek, 2019, Scientific Reports.

A variational approach to parameter estimation in ordinary differential equations

Jens Timmer, Daniel Kaschek, J. Timmer, 2011, BMC Systems Biology.

The apparent electrical conductivity as a surrogate variable for predicting earthworm abundances in tilled soils.

J. Timmer, R. Gebbers, M. Joschko, 2010 .

Multivariate Time Series Analysis

Rainer Dahlhaus, Jürgen Kurths, Jens Timmer, 2008 .

Systems biology of JAK/STAT signalling.

Ursula Klingmüller, Jens Timmer, Andrea C Pfeifer, 2008, Essays in biochemistry.

Bistability and Self-oscillations in Cell Cycle Control

Jens Timmer, Martin Peifer, Valko Petrov, 2006, Int. J. Bifurc. Chaos.

Diagnosis of sleep apnea by automatic analysis of nasal pressure and forced oscillation impedance.

Jens Timmer, Josef Guttmann, Heinrich Matthys, 2002, American journal of respiratory and critical care medicine.

A novel approach for reliable microarray analysis of microdissected tumor cells from formalin-fixed and paraffin-embedded colorectal cancer resection specimens

J. Timmer, C. Kreutz, M. Werner, 2009, Journal of Molecular Medicine.

Integration of Boolean models exemplified on hepatocyte signal transduction

Oliver Sawodny, Jens Timmer, Michael Ederer, 2012, Briefings Bioinform..

Surrogate Data — A Qualitative and Quantitative Analysis

E. Mammen, T. Maiwald, J. Timmer, 2008 .

Receptor dynamics in signaling.

Ursula Klingmüller, Jens Timmer, Verena Becker, 2012, Advances in experimental medicine and biology.

Quantitative analysis by renormalized entropy of invasive electroencephalograph recordings in focal epilepsy

K. Kopitzki, J. Timmer, J. Timmer, 1998, physics/9808008.

A longitudinal study of tremor frequencies in Parkinson’s disease and essential tremor

B. Guschlbauer, J. Timmer, J. Timmer, 2009, Clinical Neurophysiology.

Handbook of Time Series Analysis

Jens Timmer, Matthias Winterhalder, Bjeorn Schelter, 2006 .

Optimal Paths Between Parameter Estimates in Non-linear ODE Systems Using the Nudged Elastic Band Method

Jens Timmer, Clemens Kreutz, Christian Tönsing, 2019, Front. Phys..

Benchmark problems for dynamic modeling of intracellular processes

Jens Timmer, Jan Hasenauer, Clemens Kreutz, 2018, bioRxiv.

Preserved dynamic cerebral autoregulation in the middle cerebral artery among persons with migraine

C. Weiller, J. Timmer, M. Reinhard, 2007, Experimental Brain Research.

Secondary decline of cerebral autoregulation is associated with worse outcome after intracerebral hemorrhage

C. Weiller, J. Timmer, M. Czosnyka, 2010, Intensive Care Medicine.

An Integrative Model for Phytochrome B Mediated Photomorphogenesis: From Protein Dynamics to Physiology

J. Timmer, E. Schäfer, F. Nagy, 2010, PloS one.

On structural and practical identifiability

Jens Timmer, Marcus Rosenblatt, Adrian L Hauber, 2021, 2102.05100.

Profile likelihood in systems biology

Jens Timmer, Daniel Kaschek, Clemens Kreutz, 2013, The FEBS journal.

Network modulation during complex syntactic processing

Jens Timmer, Wolfgang Mader, Dorothee Saur, 2012, NeuroImage.

Identification of Preseizure States in Epilepsy: A Data-Driven Approach for Multichannel EEG Recordings

Andreas Schulze-Bonhage, Matthäus Staniek, Klaus Lehnertz, 2011, Front. Comput. Neurosci..

Spatial mapping of dynamic cerebral autoregulation by multichannel near-infrared spectroscopy in high-grade carotid artery disease

Cornelius Weiller, Jens Timmer, Björn Schelter, 2014, Journal of biomedical optics.

Abstract Journal of Neuroscience Methods xxx (2005) xxx–xxx Testing for directed influences among neural signals using partial directed coherence

Michael Eichler, Jens Timmer, Björn Schelter, 2005 .

In silico labeling reveals the time-dependent label half-life and transit-time in dynamical systems

Ursula Klingmüller, Jens Timmer, Marcel Schilling, 2012, BMC Systems Biology.

The EPILEPSIAE database: An extensive electroencephalography database of epilepsy patients

Jens Timmer, Matthias Ihle, Bjoern Schelter, 2012, Epilepsia.

EPILEPSIAE - A European epilepsy database

Andreas Schulze-Bonhage, Jens Timmer, César Alexandre Teixeira, 2012, Comput. Methods Programs Biomed..

Modeling Volatility Using State Space Models

Jens Timmer, Andreas S. Weigend, A. Weigend, 1997, Int. J. Neural Syst..

Comparison of approaches for parameter identifiability analysis of biological systems

Johan Karlsson, Jens Timmer, Mats Jirstrand, 2014, Bioinform..

Functional diversity of R3 single-repeat genes in trichome development

J. Timmer, C. Fleck, M. Hülskamp, 2009, Development.

Joining forces of Bayesian and frequentist methodology: a study for inference in the presence of non-identifiability

Jens Timmer, Clemens Kreutz, Andreas Raue, 2012, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences.

ONE-DIMENSIONAL MODEL OF SOMITIC CELLS POLARIZATION IN A BISTABILITY WINDOW OF EMBRYONIC MESODERM

J. Timmer, V. Petrov, 2009 .

Optimal weighted bayesian design applied to dose-response-curve analysis

Jens Timmer, Josef Honerkamp, D. Maier, 1997 .

Cross-spectral analysis of physiological tremor and muscle activity

Jens Timmer, Günther Deuschl, M. Lauk, 1998, Biological Cybernetics.

Correction: An Integrative Model for Phytochrome B Mediated Photomorphogenesis: From Protein Dynamics to Physiology

J. Timmer, E. Schäfer, F. Nagy, 2010, PLoS ONE.

Seizure prediction methods: assessment and comparison of three methods by means of the seizure prediction characteristic

Andreas Schulze-Bonhage, Jens Timmer, Henning U. Voss, 2004 .

Profile likelihood-based analyses of infectious disease models

Jens Timmer, Clemens Kreutz, Christian Tönsing, 2018, Statistical methods in medical research.

Driving the Model to Its Limit: Profile Likelihood Based Model Reduction

Jens Timmer, Daniel Kaschek, Bernhard Steiert, 2016, PloS one.

Identifiability and observability analysis for experimental design in nonlinear dynamical models.

A Raue, V Becker, U Klingmüller, 2010, Chaos.

Analysis of Nonlinear Differential Equations: Parameter Estimation and Model Selection

Jens Timmer, Karl Winkler, Werner Melzer, 2000, ISMDA.

Some considerations on estimating event-related brain signals

J. Timmer, J. Timmer, S. Krieger, 2005, Journal of Neural Transmission / General Section JNT.

Seizure prediction in epilepsy: From circadian concepts via probabilistic forecasting to statistical evaluation

Andreas Schulze-Bonhage, Jens Timmer, Matthias Ihle, 2011, 2011 Annual International Conference of the IEEE Engineering in Medicine and Biology Society.

The seizure prediction characteristic: a new terminology and assessment criterion for epileptic seizure prediction methods

Andreas Schulze-Bonhage, Jens Timmer, Henning U. Voss, 2004 .

Likelihood based observability analysis and confidence intervals for predictions of dynamic models

Jens Timmer, Andreas Raue, Clemens Kreutz, 2011, BMC Systems Biology.

Characteristics of hand tremor time series

Jens Timmer, Günther Deuschl, Josef Honerkamp, 1993, Biological Cybernetics.

Distinguishing direct from indirect interactions in oscillatory networks with multiple time scales.

Jürgen Kurths, Jens Timmer, Björn Schelter, 2010, Physical review letters.

Effects of light and chronotherapy on human circadian rhythms in delayed sleep phase syndrome: Cytokines, cortisol, growth hormone, and the sleep-wake cycle

J. Timmer, J. Bauer, F. Hohagen, 1996, Biological Psychiatry.

Synthetic biology-inspired design of signal-amplifying materials systems

Jens Timmer, Raphael Engesser, Wilfried Weber, 2019, Materials Today.

Early detection of upper airway obstructions by analysis of acoustical respiratory input impedance

Jens Timmer, Josef Guttmann, S. Reisch, 1999, Biological Cybernetics.

Estimating causal dependencies in networks of nonlinear stochastic dynamical systems.

Michael Eichler, Jens Timmer, Björn Schelter, 2009, Physical review. E, Statistical, nonlinear, and soft matter physics.

Inferring direct directed-information flow from multivariate nonlinear time series.

Jens Timmer, Björn Schelter, Michael Jachan, 2009, Physical review. E, Statistical, nonlinear, and soft matter physics.

Direct or indirect? Graphical models for neural oscillators

Jens Timmer, Björn Schelter, Matthias Winterhalder, 2004, Journal of Physiology-Paris.

Statistical validation of event predictors: a comparative study based on the field of seizure prediction.

Jens Timmer, Björn Schelter, Hinnerk Feldwisch-Drentrup, 2011, Physical review. E, Statistical, nonlinear, and soft matter physics.

Are prodromes preictal events? A prospective PDA-based study

A. Schulze-Bonhage, T. Maiwald, J. Timmer, 2011, Epilepsy & Behavior.

Time-variant estimation of directed influences during Parkinsonian tremor

Björn Schelter, Linda Sommerlade, Michael Jachan, 2009, Journal of Physiology-Paris.

Optimized spectral estimation for nonlinear synchronizing systems.

Jens Timmer, Celso Grebogi, Wolfgang Mader, 2014, Physical review. E, Statistical, nonlinear, and soft matter physics.

Multi-chromatic control of mammalian gene expression and signaling

Jens Timmer, Simon Schulz, Wilfried Weber, 2013, Nucleic acids research.

Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach

Julio Saez-Rodriguez, Jens Timmer, Erhan Bilal, 2014, BMC Systems Biology.

Rewiring and dosing of systems modules as a design approach for synthetic mammalian signaling networks.

Martin Fussenegger, Jens Timmer, Matias D Zurbriggen, 2012, Molecular bioSystems.

Handbook of time series analysis : recent theoretical developments and applications

Jens Timmer, Björn Schelter, Matthias Winterhalder, 2006 .

The impact of latent confounders in directed network analysis in neuroscience

Cornelius Weiller, Jens Timmer, Celso Grebogi, 2013, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences.

Synthetic Biology Makes Polymer Materials Count

Matias D. Zurbriggen, Hannes M. Beyer, J. Timmer, 2018, Advanced materials.

Detection of directed information flow in biosignals

Jens Timmer, Herbert Witte, Lutz Leistritz, 2006, Biomedizinische Technik. Biomedical engineering.

Power of surrogate data testing with respect to nonstationarity

Jens Timmer, J. Timmer, 1998, chao-dyn/9807039.

Customized Steady-State Constraints for Parameter Estimation in Non-Linear Ordinary Differential Equation Models

Jens Timmer, Daniel Kaschek, Marcus Rosenblatt, 2016, Front. Cell Dev. Biol..

Numerical methods to determine calcium release flux from calcium transients in muscle cells.

J Timmer, J. Timmer, T. Müller, 1998, Biophysical journal.

A software for recording and analysis of human tremor.

M Lauk, J Timmer, C H Lücking, 1999, Computer methods and programs in biomedicine.

A test for a difference between spectral peak frequencies

Jens Timmer, C. H. Lücking, W. Vach, 1999 .

Individualizing deep dynamic models for psychological resilience data

Haakon G. Engen, G. KoÌber, S. Pooseh, 2020, Scientific Reports.

Dynamical modelling of prostaglandin signalling in platelets reveals individual receptor contributions and feedback properties.

J. Timmer, T. Dandekar, J. Geiger, 2013, Molecular bioSystems.

On Studentising and Blocklength Selection for the Bootstrap on Time Series

B Hellwig, J Timmer, J. Timmer, 2005, Biometrical journal. Biometrische Zeitschrift.

A two-dimensional bootstrap approach to model discrimination

Jens Timmer, Rickard Johansson, Gunnar Cedersund, 2013 .

Reconstructing gene-regulatory networks from time series, knock-out data, and prior knowledge

Jens Timmer, Christian Fleck, Florian Geier, 2007, BMC Systems Biology.

Analysis of multichannel patch clamp recordings by hidden Markov models.

J Honerkamp, S Klein, J Timmer, 1997, Biometrics.

L1 regularization facilitates detection of cell type-specific parameters in dynamical systems

Jens Timmer, Bernhard Steiert, Clemens Kreutz, 2016, Bioinform..

GLOBAL HELIOSEISMIC EVIDENCE FOR A DEEPLY PENETRATING SOLAR MERIDIONAL FLOW CONSISTING OF MULTIPLE FLOW CELLS

J. Timmer, A. Schad, M. Roth, 2013, 1311.7623.

Measuring the solar meridional flow from perturbations of eigenfunctions of global oscillations

J. Timmer, A. Schad, M. Roth, 2012 .

Mapping connections in signaling networks with ambiguous modularity

Oleksii S. Rukhlenko, Anthony James Mc Elwee, B. Kholodenko, 2019, npj Systems Biology and Applications.

Influence of cell-to-cell variability on spatial pattern formation.

J Timmer, O. Ronneberger, J. Timmer, 2012, IET systems biology.

Analysis of forced expired volume signals using multi-exponential functions

H. Matthys, J. Guttmann, J. Timmer, 2001, Medical and Biological Engineering and Computing.

BlotIt—Optimal alignment of Western blot and qPCR experiments

J. Timmer, Daniel Kaschek, Marcus Rosenblatt, 2022, bioRxiv.

Systems biology of mammalian cells: a report from the Freiburg conference.

Jens Timmer, Adriano Henney, Andrew Moore, 2010, BioEssays : news and reviews in molecular, cellular and developmental biology.

Optogenetic control of gene expression in plants in the presence of ambient white light

Matias D. Zurbriggen, J. Timmer, R. Simon, 2020, Nature Methods.

BIOINFORMATICS ORIGINAL PAPER doi:10.1093/bioinformatics/btm382 Systems biology Data-based identifiability analysis of non-linear dynamical models

T. Maiwald, J. Timmer, C. Kreutz, 2022 .

Analyzing effective models: An example from JAK/STAT5 signaling

Jens Timmer, Martin Peifer, Christian Fleck, 2014, 1410.6341.

Mathematical methods in signal processing and digital image analysis

Rainer Dahlhaus, Jürgen Kurths, Jens Timmer, 2008 .

Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood

T. Maiwald, J. Timmer, J. Bachmann, 2009, Bioinform..

Estimating chain length for time delays in dynamical systems using profile likelihood

Jens Timmer, Adrian L Hauber, Raphael Engesser, 2019, Bioinform..

Extensions of ℓ1 regularization increase detection specificity for cell-type specific parameters in dynamic models

Helge Hass, Jens Timmer, Pascal Dolejsch, 2019, BMC Bioinformatics.

Comprehensive estimation of input signals and dynamics in biochemical reaction networks

Jens Timmer, Andreas Raue, Clemens Kreutz, 2012, Bioinform..

Correction: Lessons Learned from Quantitative Dynamical Modeling in Systems Biology

Fabian J. Theis, Ursula Klingmüller, Jens Timmer, 2013, PLoS ONE.

Classification of grass pollen through the quantitative analysis of surface ornamentation and texture

Charless C. Fowlkes, Fabian J Theis, J. Timmer, 2013 .

Likelihood based observability analysis and confidence intervals for predictions of dynamic models

J. Timmer, A. Raue, C. Kreutz, 2011, BMC Systems Biology.

Modeling and identification of nonlinear systems

Jürgen Kurths, Jens Timmer, Henning U. Voss, 2004 .

Surrogate-Based Hypothesis Test without Surrogates

Jürgen Kurths, Jens Timmer, Udo Schwarz, 2004, Int. J. Bifurc. Chaos.

Effect of Jump Discontinuity for Phase-Randomized Surrogate Data Testing

Jens Timmer, Swagata Nandi, Thomas Maiwald, 2009, Int. J. Bifurc. Chaos.

A comparative analysis of the bistability switch for platelet aggregation by logic ODE based dynamical modeling.

Jens Timmer, Thomas Dandekar, Hariharan Subramanian, 2014, Molecular bioSystems.

Mathematical modeling of drug-induced receptor internalization in the HER2-positive SKBR3 breast cancer cell-line

D. Peckys, J. Timmer, Daniel Kaschek, 2019, Scientific Reports.

Influence of cell-to-cell variability on spatial pattern formation

O. Ronneberger, J. Timmer, Christian Fleck, 2012 .

Hybrid optimization method with general switching strategy for parameter estimation

J. Timmer, J. Banga, E. Balsa-Canto, 2008 .

Partial phase synchronization for multivariate synchronizing systems.

Rainer Dahlhaus, Jürgen Kurths, Jens Timmer, 2006, Physical review letters.

Molecular Systems Biology 5; Article number 256; doi:10.1038/msb.2009.19 Citation: Molecular Systems Biology 5:256

B. Kholodenko, N. Borisov, T. Maiwald, 2022 .

USP18 lack in microglia causes destructive interferonopathy of the mouse brain

Tuan Leng Tay, J. Timmer, K. Knobeloch, 2015, The EMBO journal.

Computational Mechanistic Investigation of Chronotropic Effects on Murine Sinus Node Cells

Gunnar Seemann, Jens Timmer, Callum M. Zgierski-Johnston, 2018, 2018 Computing in Cardiology Conference (CinC).

The virtual liver: state of the art and future perspectives

Ursula Klingmüller, Jens Timmer, Jan G. Hengstler, 2014, Archives of Toxicology.

Systems-level interactions between insulin–EGF networks amplify mitogenic signaling

B. Kholodenko, N. Borisov, T. Maiwald, 2009, Molecular systems biology.

Detecting multimodality in saccadic reaction time distributions in gap and overlap tasks

Jens Timmer, Stefan Gezeck, J. Timmer, 1998, Biological Cybernetics.

Assessing parameter identifiability for dynamic causal modeling of fMRI data

Stefan Klöppel, Jens Timmer, Björn Schelter, 2015, Front. Neurosci..

Modeling the inflammatory response in the hypothalamus ensuing heat stroke: iterative cycle of model calibration, identifiability analysis, experimental design and data collection.

F. Doyle, L. Leon, J. Timmer, 2015, Mathematical biosciences.

Combining functional and anatomical connectivity reveals brain networks for auditory language comprehension

C. Weiller, J. Timmer, B. Schelter, 2010, NeuroImage.

Epilepsy as a Disease of the Dynamics of Neuronal Networks – Models and Predictions

A. Schulze-Bonhage, J. Timmer, B. Schelter, 2008 .

Noisy signaling through promoter logic gates.

J. Timmer, M. Gerstung, Christian Fleck, 2009, Physical review. E, Statistical, nonlinear, and soft matter physics.

Optogenetic control of gene expression in plants in the presence of ambient white light

Matias D. Zurbriggen, J. Timmer, R. Simon, 2020, Nature Methods.

Biofunctionalized Materials Featuring Feedforward and Feedback Circuits Exemplified by the Detection of Botulinum Toxin A

Jens Timmer, Raphael Engesser, Svenja Kemmer, 2018, Advanced science.

Modeling system states in liver cells: Survival, apoptosis and their modifications in response to viral infection

C. Borner, J. Timmer, T. Dandekar, 2009, BMC Systems Biology.

Spleen tyrosine kinase is overexpressed and represents a potential therapeutic target in chronic lymphocytic leukemia.

J. Gribben, J. Timmer, K. Bartholomé, 2009, Cancer research.

Parametric Versus Nonparametric Transfer Function Estimation of Cerebral Autoregulation from Spontaneous Blood-Pressure Oscillations

J. Timmer, B. Schelter, M. Jachan, 2009, Cardiovascular engineering.

Detection of improper installation from the sensor signal of vortex flowmeters

Jens Timmer, Frank Dipl.-Ing. Buhl, Jörg Dipl.-Ing. Herwig, 2004 .

Photoconversion and Nuclear Trafficking Cycles Determine Phytochrome A's Response Profile to Far-Red Light

J. Timmer, E. Schäfer, C. Fleck, 2011, Cell.

Selecting relevant electrode positions for classification tasks based on the electro-encephalogram

T. Mergner, T. Müller, T. Ball, 2006, Medical and Biological Engineering and Computing.

An Application for the Analysis of Human Tremor Time-Series

Jens Timmer, C. H. Lücking, Günther Deuschl, 2003 .

Comparison of approaches for parameter identifiability analysis of biological systems

J. Timmer, M. Jirstrand, A. Raue, 2014, Bioinform..

Confidence Regions for Spectral Peak Frequencies

Jens Timmer, C. H. Lücking, M. Lauk, 1997 .

A common strategy and database to compare the performance of seizure prediction algorithms

J. Gotman, A. Schulze-Bonhage, J. Timmer, 2010, Epilepsy & Behavior.

Modeling system states in liver cells: Survival, apoptosis and their modifications in response to viral infection

C. Borner, J. Timmer, T. Dandekar, 2009, BMC Systems Biology.

Time-variant estimation of connectivity and Kalman's filter

Jens Timmer, Celso Grebogi, Wolfgang Mader, 2014 .

Dynamic Modeling, Parameter Estimation and Uncertainty Analysis in 𝗥

Jens Timmer, Daniel Kaschek, Wolfgang Mader, 2016, bioRxiv.

Estimation of Gene Induction Enables a Relevance-Based Ranking of Gene Sets

J. Timmer, C. Kreutz, K. Bartholomé, 2009, J. Comput. Biol..

J. Timmer, B. Schelter, J. Vesper, 2008, Neuroscience Letters.

Analyzing the dynamics of hand tremor time series

Jens Timmer, Josef Honerkamp, C. Gantert, 1992, Biological Cybernetics.

Dynamical modelling of measured time series from a Q-switched CO2 laser

Jens Timmer, Riccardo Meucci, Marco Ciofini, 2003 .

Estimating parameters in differential equations with application to laser data

J. Timmer, M. Bünner, W. Horbelt, 2000 .

Oscillatory cerebral hemodynamics – the macro- versus microvascular level

C. Weiller, J. Timmer, B. Guschlbauer, 2006, Clinical Neurophysiology.

Multivariate analysis of dynamical processes

J. Timmer, M. Jachan, B. Hellwig, 2008 .

Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems

Fabian J Theis, J. Hasenauer, J. Timmer, 2015, Bioinform..

Profile likelihood in systems biology

J. Timmer, A. Raue, C. Kreutz, 2013, The FEBS journal.

Contents List of Contributors 9 1 Handbook of Time Series Analysis : Introduction and Overview 13 2 Nonlinear Analysis of Time Series Data (

S. Boccaletti, S. Bressler, H. Abarbanel, 2022 .

presence of non-identifiability methodology: a study for inference in the Joining forces of Bayesian and frequentist

Fabian J Theis, J. Timmer, A. Raue, 2013 .

Testing for the Number of States in Hidden Markov Models with Application to Ion Channel Data

Jens Timmer, J. Timmer, M. Wagner, 1999 .