Jens Timmer

PEtab Select provides a standardized format and software for automated model selection in systems biology, supporting diverse modeling frameworks and enabling efficient evaluation of large model spaces.

The paper identifies parameters for stable Her6 oscillations in zebrafish neural stem cells, showing they require equal transcript and protein degradation rates.

This paper introduces a latent-space calibration method for rare disease ODE models using synthetic data, improving parameter recovery and trajectory prediction from sparse clinical observations.

The paper shows brain metastases form gap-junction-coupled networks with coordinated calcium activity that drives proliferation and is inhibited by gap junction blockers.

The paper introduces 1100 synthetic benchmark problems for dynamic cellular process modeling to improve algorithm evaluation.

The paper uses 18O-water labeling to study phosphate group dynamics in inositol phosphates across species, revealing distinct pools with different cycling behaviors.

This study uses mathematical modeling to show that 1,5-InsP8 synthesis follows a linear pathway in yeast and human cells, challenging previous assumptions about IPP metabolism.

The paper identifies elevated basal MET phosphorylation as a marker of hepatocyte dysregulation in liver disease, correlating with patient outcomes after surgery.

PenTag enables specific, covalent conjugation of proteins to ligands for biohybrid material synthesis, demonstrating applications in hydrogels and computational systems.

The paper designs a biohybrid materials circuit with binary decoder functionality using protease-based modules to detect small molecules and produce regulated protease outputs.

This paper investigates likelihood-ratio test statistics for nonlinear ODE models in finite-sample settings and finds that corrections are needed to avoid anti-conservative results.

The paper investigates how Pou5f3 and Nanog regulate enhancer types during zygotic genome activation through an activator-blocker mechanism.

This paper introduces a regularization method for identifying cell-type specific mechanisms in dynamical models, demonstrating its effectiveness with synthetic and biological data.

The paper develops a material-genetic interface as a safety switch for engineered cells in hydrogels to control therapeutic agent production based on the presence of the embedding material.

BlotIt aligns relative experimental measurements from Western blot and qPCR by estimating scaling factors and providing confidence intervals for comparable data analysis.

The paper identifies a mutual repression network between JNK/AP-1 and JAK/STAT signaling that spatially segregates cell behaviors during tissue regeneration in Drosophila.

The paper shows Pou5f3 and Sox19b independently regulate enhancer chromatin accessibility, affecting zygotic gene expression in zebrafish embryos.

The paper models single-cell variability in JAK2/STAT5 signaling and cytoplasmic volume to explain how erythroid progenitor cells transition from binary survival/apoptosis decisions to graded population responses upon Epo stimulation.

This study identifies IL1β as an amplifier of IFN-induced antiviral responses through mathematical modeling and experimental validation.

The paper presents 20 ODE-based benchmark models for evaluating dynamic modeling methods in systems biology, including parameter estimation and uncertainty analysis.

This paper introduces the R package dMod for dynamic modeling, parameter estimation, and uncertainty analysis in complex systems.

The paper predicts ligand-dependent tumor growth in cell lines and patient samples using a mechanistic signaling model and Bagged Decision Trees, finding a correlation between growth factor expression and predicted response.