Philippi, Nicole, Walter, Dorothee, Schlatter, Rebekka, Ferreira, Karine, Ederer, Michael, Sawodny, Oliver, ...
Abstract Background The decision pro- or contra apoptosis is complex, involves a number of different inputs, and is central for the homeostasis of an individual cell as well as for the maintenance...
A Quantitative and Dynamic Model for Plant Stem Cell Regulation (2009)
Florian Geier, Jan U. Lohmann, Moritz Gerstung, Annette T. Maier, Jens Timmer
Plants maintain pools of totipotent stem cells throughout their entire life. These stem cells are embedded within specialized tissues called meristems, which form the growing points of the organism....
Estimation of gene induction enables a relevance-based ranking of (2009)
Kilian Bartholomé, Clemens Kreutz, Jens Timmer
gene sets
Dynamical modeling and multi-experiment fitting with
Pages 1–7 Dynamical Modeling and Multi-Experiment Fitting with (2009)
Received on; revised on; accepted on
Simona Digiuni, Swen Schellmann, Florian Geier, Bettina Greese, Martina Pesch, Katja Wester, ...
Supplementary Information: A competitive complex formation mechanism underlies trichome
Detection of directed information flow in biosignals (2009)
Matthias Winterhalder, Björn Schelter, Wolfram Hesse, Karin Schwab, Lutz Leistritz, Jens Timmer, ...
Several analysis techniques have been developed for time series to detect interactions in multidimensional dynamic systems. When analyzing biosignals generated by unknown dynamic systems, awareness...
A spatial approach to soil-ecological experimentation at landscape scale § (2009)
Monika Joschko, Jörg Oehley, Robin Gebbers, Martina Wiemer, Jens Timmer, Catherine A. Fox
The upscaling of soil-ecological processes to larger landscape units represents a special challenge to soil ecology. Results from micro- or mesocosms cannot easily be transferred to other scales...
Macmillan Publishers, Limited All, Simona Digiuni, Swen Schellmann, Florian Geier, Bettina Greese, ...
www.molecularsystemsbiology.com A competitive complex formation mechanism underlies trichome patterning on Arabidopsis leaves
Host Cell Responses Induced by Hepatitis C Virus Binding (2009)
Xinhua Fang, Mirjam B. Zeisel, Jochen Wilpert, Bettina Gissler, Robert Thimme, Clemens Kreutz, ...
Initiation of hepatitis C virus (HCV) infection is mediated by docking of the viral envelope to the hepatocyte cell surface membrane followed by entry of the virus into the host cell. Aiming to...
Supporting Online Material Material and Methods (2009)
Stefanie Sick, Stefan Reinker, Jens Timmer, Thomas Schlake
In order to account for the characteristics of the WNT signaling pathway, we modified the Gierer-Meinhardt equations that take the form ∂a ∂t = D a ∆ a + ρ a F(a,h) − µ a a, ∂h ∂t = D h...
Noykova, Neli, Müller, Thorsten, Gyllenberg, Mats, Timmer, Jens
We investigate the problem of identifying the parameters of a non-linear fifth order model describing the population dynamics of two main bacterial groups in an anaerobic wastewater treatment...
Müller, Thorsten, Noykova, Neli, Gyllenberg, Mats, Timmer, Jens
In this paper we investigate two second order models of batch anaerobic digestion processes: one includes the Monod model of the specific growth rate of methanogenic bacteria, while the other...
Holger Steltner, Michael Vogel, Eva Sprung, Jens Timmer
Lung function W Multi-exponential modelling W
WNT and DKK Determine Hair Follicle Spacing Through a Reaction-Diffusion Mechanism (2008)
M. A. Ward, P. S. Burgoyne, Biol Reprod, M. Gomendio, A. H. Harcourt, ...
Mathematical reaction-diffusion models have been suggested to describe formation of animal pigmentation patterns and distribution of epidermal appendages. However, the crucial signals and in vivo...
high-density SNP arrays (2008)
Dietmar Pfeifer, Milena Pantic, Ilona Skatulla, Justyna Rawluk, Clemens Kreutz, Uwe M. Martens, ...
Recurrent genomic aberrations are important prognostic parameters in chronic lymphocytic leukemia (CLL). High-resolution 10k and 50k Affymetrix SNP arrays were evaluated as a diagnostic tool for CLL...
ABSTRACT Aggregated Markov models are a widely used tool to model patch clamp data measured from single ion channels. These channels must obey the principle of detailed balance in thermodynamic...
Data-Based Mathematical Modeling of Vectorial Transport across (2008)
Kilian Bartholomé, Maria Rius, Katrin Letschert, Daniela Keller, Jens Timmer
Vectorial transport of endogenous small molecules, toxins, and drugs across polarized epithelial cells contributes to their half-life in the organism and to detoxification. To study vectorial...
BIOPHYSICS LETTER Ste€en Michalek á Holger Lerche á Mirko Wagner (2008)
Nenad Mitrovicâ, Michael Schiebe, Frank Lehmann-horn, Jens Timmer
Abstract Transitions between distinct kinetic states of an ion channel are described by a Markov process. Hidden Markov models (HMM) have been successfully applied in the analysis of single ion...
Florian Geier, Jens Timmer, Christian Fleck
gene-regulatory networks from time series,
Fabb AQ: I Data-Based Mathematical Modeling of Vectorial Transport across (2008)
Kilian Bartholomé, Maria Rius, Katrin Letschert, Daniela Keller, Jens Timmer
Vectorial transport of endogenous small molecules, toxins, and drugs across polarized epithelial cells contributes to their half-life in the organism and to detoxification. To study vectorial...
Daniel Bouyer, Florian Geier, Friedrich Kragler, Arp Schnittger, Martina Pesch, Katja Wester, ...
Trichome patterning in Arabidopsis serves as a model system to study how single cells are selected within a field of initially equivalent cells. Current models explain this pattern by an...
A systems biology approach to analyse amplification in the JAK2-STAT5 signalling pathway (2008)
Vera, Julio, Bachmann, Julie, Pfeifer, Andrea C, Becker, Verena, Hormiga, Jose A, Darias, Nestor, ...
Abstract Background The amplification of signals, defined as an increase in the intensity of a signal through networks of intracellular reactions, is considered one of the essential properties in...
Hybrid optimization method with general switching strategy for parameter estimation (2008)
Balsa-Canto, Eva, Peifer, Martin, Banga, Julio R, Timmer, Jens, Fleck, Christian
Abstract Background Modeling and simulation of cellular signaling and metabolic pathways as networks of biochemical reactions yields sets of non-linear ordinary differential equations. These models...
Hybrid optimization method with general switching strategy for parameter estimation (2008)
Balsa-Canto, Eva, Peifer, Martin, Banga, Julio R., Timmer, Jens, Fleck, Christian
This article is available from: http://www.biomedcentral.com/1752-0509/2/26
Analyzing X-Ray Variability by Linear State Space Models (2008)
Michael König, Jens Timmer, Hermann-herder Str
54> A ~x(t \Gamma 1) + ~ffl(t) ~ffl(t) ¸ N (0; Q) (1) y(t) = C ~x(t) + j(t) j(t) ¸ N (0; R) (2) The AR model expresses the temporal correlations in the process in terms of memory, in the sense...
Analyzing X-Ray Variability by State Space Models - Application to an EXOSAT AGN sample (2008)
Michael König, Michael K, Rüdiger Staubert, Jens Timmer
. In recent years, autoregressive models have had a profound impact on the description of astronomical time series as the observation of a stochastic process. These methods have advantages compared...
BMC Systems Biology BioMed Central (2008)
Eva Balsa-canto, Martin Peifer, Julio R Banga, Jens Timmer
Research article Hybrid optimization method with general switching strategy for parameter estimation
Matthias Reinhard, Zora Waldkircher, Jens Timmer, Cornelius Weiller, Andreas Hetzel
autoregulation dynamics in humans
Dynamical Modeling and Multi-Experiment Fitting with PottersWheel – Supplement (2008)
This supplement provides detailed information about the functionalities of the Potters-Wheel toolbox as described in the main text. For further information please use the
BMC Systems Biology BioMed Central (2008)
Julio Vera, Julie Bachmann, Andrea C Pfeifer, Verena Becker, Jose A Hormiga, ...
Research article A systems biology approach to analyse amplification in the JAK2-STAT5 signalling pathway
Dynamical modeling and multi-experiment fitting with PottersWheel (2008)
Motivation: Modelers in Systems Biology need a flexible framework that allows them to easily create new dynamic models, investigate their properties and fit several experimental datasets...
Induction level determines signature of gene expression noise in cellular systems (2007)
Rausenberger, Julia, Fleck, Christian, Timmer, Jens, Kollmann, Markus
Noise in gene expression, either due to inherent stochasticity or to varying inter- and intracellular environment, can generate significant cell-to-cell variability of protein levels in clonal...
Steffen Michalek, Holger Lerche, Mirko Wagner, Michael Schiebe, Frank Lehmann-horn, Jens Timmer
channel gating schemes using moving-average filtered hidden Markov models
Aggregated Markov models are a widely used tool to model patch clamp data measured from single ion channels. These channels must obey the principle of detailed balance in thermodynamic equilibrium,...
Reconstructing gene-regulatory networks from time series, knock-out data, and prior knowledge (2007)
Geier, Florian, Timmer, Jens, Fleck, Christian
Abstract Background Cellular processes are controlled by gene-regulatory networks. Several computational methods are currently used to learn the structure of gene-regulatory networks from data. This...
Florian Geier, Jens Timmer, Christian Fleck
Research article Reconstructing gene-regulatory networks from time series, knock-out data, and prior knowledge
J Neurol (200■) 25■:000–000 DOI 10.1007/s00415-008-0865-z ORIGINAL COMMUNICATION (2007)
Matthias Reinhard, Thomas A. Gerds, Daniel Grabiak, Markus Roth, Brigitte Guschlbauer, Jens Timmer, ...
Cerebral dysautoregulation and the risk of ischemic events in occlusive carotid artery disease
Stefanie Sick, Stefan Reinker, Jens Timmer, Thomas Schlake
Mathematical reaction-diffusion models have been suggested to describe formation of animal pigmentation patterns and distribution of epidermal appendages. However, the crucial signals and in vivo...
Björn Schelter, Matthias Winterhalder, Thomas Maiwald, Armin Br, Ariane Schad, Jens Timmer, ...
are accompanied by high numbers of false predictions to achieve high sensitivity. Little is known about the extent to which changes in EEG dynamics contribute to false predictions. This study...
NDES2005 Submission Style (2006)
Matthias Winterhalder, Björn Schelter, Jens Timmer
Detecting coupling directions in multivariate oscillatory systems
Peter C. Warnke, Klaus Kopitzki, Jens Timmer, Christoph B. Ostertag, Abteilung Stereotaktische Neurochirurgie
BACKGROUND. Advances in the treatment of medulloblastoma have largely been attributed to the introduction of chemotherapy, although Phase III trials have shown advantages for chemotherapy only in...
Gene profiling of polycystic kidneys (2006)
Schieren, Gisela, Rumberger, Brigitta, Klein, Marinella, Kreutz, Clemens, Wilpert, Jochen, Geyer, Marcel, ...
Background. While the genetic basis of autosomal dominant polycystic kidney disease (ADPKD) has been clearly established, the pathogenesis of renal failure in ADPKD remains elusive. Cyst formation...
Gene profiling of polycystic kidneys (2006)
Schieren, Gisela, Rumberger, Brigitta, Klein, Marinella, Kreutz, Clemens, Wilpert, Jochen, Geyer, Marcel, ...
Background. While the genetic basis of autosomal dominant polycystic kidney disease (ADPKD) has been clearly established, the pathogenesis of renal failure in ADPKD remains elusive. Cyst formation...
Gene profiling of polycystic kidneys (2006)
Schieren, Gisela, Rumberger, Brigitta, Klein, Marinella, Kreutz, Clemens, Wilpert, Jochen, Geyer, Marcel, ...
Background. While the genetic basis of autosomal dominant polycystic kidney disease (ADPKD) has been clearly established, the pathogenesis of renal failure in ADPKD remains elusive. Cyst formation...
Host cell responses induced by hepatitis C virus binding. (2006)
Fang, Xinhua, Zeisel, Mirjam B, Wilpert, Jochen, Gissler, Bettina, Thimme, Robert, Kreutz, Clemens, ...
Initiation of hepatitis C virus (HCV) infection is mediated by docking of the viral envelope to the hepatocyte cell surface membrane followed by entry of the virus into the host cell. Aiming to...
Host cell responses induced by hepatitis C virus binding. (2006)
Fang, Xinhua, Zeisel, Mirjam B, Wilpert, Jochen, Gissler, Bettina, Thimme, Robert, Kreutz, Clemens, ...
Initiation of hepatitis C virus (HCV) infection is mediated by docking of the viral envelope to the hepatocyte cell surface membrane followed by entry of the virus into the host cell. Aiming to...
Host cell responses induced by hepatitis C virus binding. (2006)
Fang, Xinhua, Zeisel, Mirjam B, Wilpert, Jochen, Gissler, Bettina, Thimme, Robert, Kreutz, Clemens, ...
Initiation of hepatitis C virus (HCV) infection is mediated by docking of the viral envelope to the hepatocyte cell surface membrane followed by entry of the virus into the host cell. Aiming to...
Björn Schelter, Matthias Winterhalder, Jens Timmer
In Nonlinear Dynamics synchronization of oscillators is examined. Alternatively for linear stochastic systems, coherence analysis is utilized to detect interdependencies in transfer function systems....
Matthias Winterhalder, Björn Schelter, Jens Timmer
Determination of synchronization phenomena between pairs of coupled multivariate processes is of particular interest in Nonlinear Dynamics. Besides synchronization phenomena, coupling directions...
Marcel Schilling, Thomas Maiwald, Sebastian Bohl, Markus Kollmann, Clemens Kreutz, Jens Timmer, ...
processing and error reduction strategies
Capillary Physiology and Drug Delivery in Central Nervous System Lymphomas (2004)
Peter C. Warnke, Jens Timmer, Christoph B. Ostertag, Klaus Kopitzki
To evaluate whether the chemosensitivity of primary central nervous system lymphomas to water-soluble drugs could result from improved drug delivery, we quantitatively assessed pharmacokinetic...
Institute of Mechanics and Biomechanics, (2004)
A qualitative model of cell cycle control is presented and its transition from bistability to limit cycle oscillations and vice versa is discussed. The origin of this model is the two-dimensional...
An Open Source Protein Gel Documentation System for Proteome Analyses (2003)
Daniel Faller, Thomas Reinheckel, Daniel Wenzler, Sascha Hagemann, Ke Xiao, Josef Honerkamp, ...
Data organization and data mining represents one of the main challenges for modern high throughput technologies in pharmaceutical chemistry and medical chemistry. The presented open source...
NONLINEAR DYNAMICAL SYSTEM IDENTIFICATION FROM UNCERTAIN AND INDIRECT MEASUREMENTS (2002)
We review the problem of estimating parameters and unobserved trajectory components from noisy time series measurements of continuous nonlinear dynamical systems. It is first shown that in parameter...
Dynamic annual daylight simulations based on one-hour and one-minute means of irradiance data (2002)
Oliver Walkenhorst, Joachim Luther, Christoph Reinhart, Jens Timmer
Abstract—This study investigates the influence of the short-term dynamics of daylight on simulation-based predictions of the annual daylight availability in a building. To this end annual indoor...
Diagnosis of Sleep Apnea by . . . (2002)
Richard Staats, Jens Timmer, Michael Vogel, Josef Guttmann, Heinrich Matthys, ...
This article has an online data supplement, which is accessible from this issue's table of contents at www.atsjournals.org Diagnosis of Sleep Apnea by Automatic Analysis of Nasal Pressure and...
Identifiability problems in a mathematical model of anaerobic digestion (2001)
Noykova, Neli, Müller, Thorsten, Gylleberg, Mats, Timmer, Jens
We investigate the problem of identifying the parameters of a non-linear fifth order modified Hill and Barth model describing the population dynamics of two main bacterial groups (hydrolitic and acid...
Nelly Noykova, Mats Gyllenberg, Jens Timmer
Abstract: We investigated the problem of identifying the parameters of a nonlinear ®fth order model describing the population dynamics of two main bacterial groups in an anaerobic wastewater...
Michael Lauk, Jens Timmer, Brigitte Guschlbauer, Bernhard Hellwig, Carl-herrmann Lücking
ABSTRACT: We investigated the electromyographic activity (EMG) of flexor and extensor muscles with different hand positions in patients with essential (ET) and parkinsonian (PD) tremor. Using a...
Model selection in nonnested hidden Markov models (2001)
An important task in the application of Markov models to the analysis of ion channel data is the determination of the correct gating scheme of the ion channel under investigation. Some prior...
Model selection in nonnested hidden Markov models (2001)
Mirko Wagner, Jens Timmer, M. Wagner, J. Timmer
Abstract. An important task in the application of Markov models to the analysis of ion channel data is the determination of the correct gating scheme of the ion channel under investigation. Some...
A new approximate likelihood estimator for ARMA-filtered hidden Markov models. submitted to (2000)
Steffen Michalek, Mirko Wagner, Jens Timmer
Hidden Markov models (HMM) are successfully applied in various fields of time series analysis. Colored noise, e.g. due to filtering, violates basic assumptions of the model. While it is well-known...
Estimating Parameters in Differential Equations with Application to Laser Data (2000)
Jens Timmer, Werner Horbelt, Martin Bunner, Ricardo Meucci, Marco Ciofini
. Many physical problems can be described by systems of ordinary differential equations (ODE) comprising system states and parameters not accessible by direct measurements. The goal is to estimate...
Pathological tremors: Deterministic chaos or nonlinear stochastic oscillators? (1999)
Jens Timmer, Siegfried Hauler, Michael Lauk, Carl Lücking
. Pathological tremors exhibit a nonlinear oscillation that is not strictly periodic. We investigate whether the deviation from periodicity is due to nonlinear deterministic chaotic dynamics or due...
Estimating rate constants in Hidden Markov Models by the EM algorithm (1999)
The EM algorithm, e.g. as Baum-Welch reestimation, is an important tool for parameter estimation in discrete-time Hidden Markov Models. We present a direct reestimation of rate constants for...
Detecting multimodality in saccadic reaction time distributions in gap and overlap tasks (1998)
Abstract. In many cases the distribution of saccadic reaction times (SRT) deviates considerably from a unimodal distribution and may often exhibit several peaks. We present a statistical approach to...
Modeling Volatility Using State Space Models (1997)
Timmer, Jens, Weigend, Andreas S.
In time series problems, noise can be divided into two categories: dynamic noise which drives the process, and observational noise which is added in the measurement process, but does not influence...
Modeling Volatility Using State Space Models (1997)
Timmer, Jens, Weigend, Andreas S.
In time series problems, noise can be divided into two categories: dynamic noise which drives the process, and observational noise which is added in the measurement process, but does not influence...
Modeling Volatility Using State Space Models (1997)
Timmer, Jens, Weigend, Andreas S.
In time series problems, noise can be divided into two categories: dynamic noise which drives the process, and observational noise which is added in the measurement process, but does not influence...
Modeling Volatility Using State Space Models (1997)
Timmer, Jens, Weigend, Andreas S.
In time series problems, noise can be divided into two categories: dynamic noise which drives the process, and observational noise which is added in the measurement process, but does not influence...
Analyzing X-Ray Variability by Linear State Space Models (1997)
. In recent years, autoregressive models have had a profound impact on the description of astronomical time series as the observation of a stochastic process. These methods have advantages compared...
Modeling Volatility Using State Space Models (1997)
Jens Timmer, Andreas S. Weigend
this article can also be helpful for understanding and characterizing stochastic volatility models. This article is organized as follows: Section 2 discusses observational noise and dynamic noise and...
www.fdm.uni-freiburg.de/Njeti (1997)
Jens Timmer, Fakultat Fur Physik, Andreas S. Weigend, Jens Timmer, Andreas S. Weigend
Abstract. In time series problems, noise can be divided into two categories: dynamic noise which drives the process, and observational noise which is added in the measurement process, but does not...
Analyzing X-ray variability by Linear State Space Models (1996)
In recent years, autoregressive models have had a profound impact on the description of astronomical time series as the observation of a stochastic process. These methods have advantages compared...
The Seyfert Galaxy NGC 6814 -- a highly variable X-ray source (1996)
Koenig, Michael, Friedrich, Susanne, Staubert, Ruediger, Timmer, Jens
The Seyfert galaxy NGC 6814 is a highly variable X-ray source despite the fact that it has recently been shown not to be the source of periodic variability. The 1.5 year monitoring by ROSAT has...
AND ASTROPHYSICS The Seyfert galaxy NGC 6814 – a highly variable X-ray source (1996)
Michael König, Susanne Friedrich, Rüdiger Staubert, Jens Timmer
Abstract. The Seyfert galaxy NGC 6814 is a highly variable X-ray source despite the fact that it has recently been shown not to be the source of periodic variability. The 1.5 year monitoring by ROSAT...
Zugl.: Freiburg (Breisgau), Universiẗat, Diss., 1994.
Analysis of single ion channel data incorporating time-interval omission and sampling
Hidden Markov models are widely used to describe single channel currents from patch-clamp experiments. The inevitable anti-aliasing filter limits the time resolution of the measurements and therefore...
Hybrid optimization method with general switching strategy for parameter estimation
Balsa-Canto, Eva, Peifer, Martin, Banga, Julio R, Timmer, Jens, Fleck, Christian
A systems biology approach to analyse amplification in the JAK2-STAT5 signalling pathway
Vera, Julio, Bachmann, Julie, Pfeifer, Andrea C, Becker, Verena, Hormiga, Jose A, Darias, Nestor V Torres, ...
Bouyer, Daniel, Geier, Florian, Kragler, Friedrich, Schnittger, Arp, Pesch, Martina, Wester, Katja, ...
Trichome patterning in Arabidopsis serves as a model system to study how single cells are selected within a field of initially equivalent cells. Current models explain this pattern by an...
Dynamical modeling and multi-experiment fitting with PottersWheel
Motivation: Modelers in Systems Biology need a flexible framework that allows them to easily create new dynamic models, investigate their properties and fit several experimental datasets...
A competitive complex formation mechanism underlies trichome patterning on Arabidopsis leaves
Digiuni, Simona, Schellmann, Swen, Geier, Florian, Greese, Bettina, Pesch, Martina, Wester, Katja, ...
Trichome patterning in Arabidopsis serves as a model system for de novo pattern formation in plants. It is thought to typify the theoretical activator–inhibitor mechanism, although this hypothesis...
A Quantitative and Dynamic Model for Plant Stem Cell Regulation
Geier, Florian, Lohmann, Jan U., Gerstung, Moritz, Maier, Annette T., Timmer, Jens, Fleck, Christian
Plants maintain pools of totipotent stem cells throughout their entire life. These stem cells are embedded within specialized tissues called meristems, which form the growing points of the organism....
Systems-level interactions between insulin–EGF networks amplify mitogenic signaling
Borisov, Nikolay, Aksamitiene, Edita, Kiyatkin, Anatoly, Legewie, Stefan, Berkhout, Jan, Maiwald, Thomas, ...
Crosstalk mechanisms have not been studied as thoroughly as individual signaling pathways. We exploit experimental and computational approaches to reveal how a concordant interplay between the...