Matthias König

TabularQual provides a spreadsheet-based format for annotating logical models, with tools to convert between spreadsheets and SBML-qual, enhancing model reuse and interoperability.

The paper develops a deep learning pipeline using U-Net models to segment hepatic vessels and lobules in histological images, achieving high Dice scores for various structures.

The paper describes the development and evaluation of an agentic framework using LLMs to explore molecular interaction maps through user-driven prototyping and testing.

The paper proposes adapting FAIR indicators to assess and improve the quality and transparency of computational models in biology.

The paper introduces FROG analysis to standardize reproducibility assessments of genome-scale metabolic models, resulting in full reproducibility of all tested models.

This study compares lobular geometry and CYP450 zonation across four species using whole slide imaging, identifying species differences and determining the minimum number of lobules needed for statistical analysis.

The paper presents a multiscale liver model coupling PDE and ODE-based approaches to simulate drug-induced liver injury and zonation patterns.

This paper develops a PBPK model of talinolol to study P-gp function and its impact on pharmacokinetics under various conditions.

This study develops a PBPK model to assess CYP2E1 activity using chlorzoxazone, showing how ethanol consumption, abstinence, and liver impairment affect its metabolism.

Standard-GEM provides a template for reproducible genome-scale metabolic model development following FAIR principles and software best practices.

The paper develops a consensus model of glucose-stimulated insulin secretion in pancreatic beta-cells using a systematic workflow, showing glucose-dependent increases in glycolytic intermediates and ATP/ADP ratios drive insulin secretion.

This paper introduces a method to encode dynamic FBA models in SBML, enabling exchange and simulation of hybrid models across tools.

This paper uses computational modeling to analyze how physiological and anthropometric factors affect indocyanine green elimination in liver function tests.

PK-DB provides an open database of pharmacokinetics data from clinical and pre-clinical studies, enabling meta-analysis and integration with computational models for individualized and stratified modeling.

The paper introduces an executable simulation model (EXSIMO) to improve reproducibility in computational modeling and applies it to replicate a study on hepatic glucose metabolism.

Memote, open-source Python software, runs a community-maintained, partly scored test suite (consistency, biomass, annotations, optional experimental data) on SBML-encoded genome-scale metabolic models, once or through continuous integration.

Tellurium Notebook enables reproducible and reusable dynamical models in systems biology by integrating community standards and literate coding practices.