Michelle Elias

About

M.Sc. student in Biophysics at Humboldt University of Berlin
Working as student assistant in the research group of Dr. Matthias König
Focus on systems biology, systems medicine, and computational pharmacology
Research interests include PBPK modeling and digital twins
Development of reproducible model pipelines for model-informed precision dosing

Currently

Developing VisFEM, a web platform for FEM simulation visualization, as part of DFG SPP 2311
Supporting manuscript development and editing for ongoing publications in the König Lab
Working on reproducible PBPK modeling workflows
M.Sc. coursework in systems biology, dynamic modeling, and medical biophysics

Modeling PBPK/PD SBML Docker Git Data Analysis Python Marimo PyTorch Trame PyVista

Projects

VisFEM: Web Visualization of FEM Models

Elias M and König M · 2026

An interactive web-based tool for visualization of Finite Element Method (FEM) simulation results, with a focus on biomedical applications. Developed as part of DFG SPP 2311 and installable as an open-source Python package via PyPI.

GitHub DOI PyPI

Polysome Resolution & Translation Prediction

Course Project · 2025/2026

CNN-based prediction of mean ribosome load (MRL) from 5′ UTR sequences, investigating how reducing polysome profiling resolution affects model performance. Trained on 280,000 sequences with 5-fold cross-validation across five resolution schemes; model interpretation via Integrated Gradients (Captum).

GitHub

Glimepiride Digital Twin Web Application

Elias M and König M · 2024–2025

Interactive web application implementing the glimepiride digital twin for personalized and stratified diabetes treatment, built with Marimo and deployable via Docker. Accompanies the glimepiride PBPK/PD model and the corresponding publication in Frontiers in Pharmacology.

Web App GitHub

Glimepiride PBPK Model

Elias M and König M · 2024–2025

Physiologically based pharmacokinetic (PBPK) model of glimepiride distributed in SBML format, including liver, kidney, intestine, and whole-body submodels. Accompanied by a COMBINE archive, FAIR assessment, and reproducible simulation pipeline.

GitHub DOI

Publications

Featured

A digital twin of glimepiride for personalized and stratified diabetes treatment

Elias M and König M · Frontiers in Pharmacology, 2025 · First Author

Published DOI Preprint Code Web App

Reproducibility of a Digital Twin of Glimepiride for Personalized and Stratified Diabetes Treatment

Elias M and König M · Physiome, 2025 · First Author

Published DOI Code

First Author

Reproducibility of a Digital Twin of Empagliflozin Pharmacokinetics and Pharmacodynamics

Elias M, Myshkina M, Alejandro J, Babaeva M, and König M · Physiome, 2026

Submitted Code

Reproducibility of a Digital Twin of Canagliflozin Pharmacokinetics and Pharmacodynamics in Type 2 Diabetes Mellitus

Elias M, Myshkina M, Tereshchuk V, and König M · Physiome, 2026

Submitted Code

Reproducibility of a Physiologically Based Pharmacokinetic and Pharmacodynamic (PBPK/PD) Model of Dapagliflozin

Elias M, Myshkina M, Nemitz N, and König M · Physiome, 2026

Accepted DOI Code

Co-Author

A Digital Twin of Empagliflozin Pharmacokinetics and Pharmacodynamics

Alejandro J, Elias M, Babaeva M, and König M · Preprints, 2026

Submitted Preprint Code

A Digital Twin of Canagliflozin Pharmacokinetics and Pharmacodynamics in Type 2 Diabetes Mellitus

Tereshchuk V, Elias M, and König M · Preprints, 2026

Submitted Preprint Code

Rivaroxaban Pharmacokinetics and Coagulation Effects: Reproducibility of a Physiologically Based Modeling Approach

Myshkina M, Elias M, Casabianca E, and König M · Physiome, 2026 · Second Author

Submitted Code

Reproducibility of a Digital Twin of the Angiotensin II Receptor Blocker Losartan

Myshkina M, Elias M, Tensil E, and König M · Physiome, 2026 · Second Author

Accepted DOI Code

A Physiologically Based Pharmacokinetic and Pharmacodynamic (PBPK/PD) Model of Dapagliflozin in Type 2 Diabetes Mellitus: The Effect of Dosing, Hepatorenal Impairment, and Food

Nemitz N, Elias M, and König M · Pharmaceutics, 2026

Published DOI Preprint Code

Thesis

A physiological-based pharmacokinetic (PBPK) model of the sulfonylurea glimepiride

Bachelor's Thesis · B.Sc. Biology · Systems Medicine of the Liver · Humboldt University of Berlin · 2025

Development of a whole-body PBPK model of glimepiride based on curated clinical data, investigating pharmacokinetic variability due to renal and hepatic impairment, bodyweight and CYP2C9 genetic variants.

Bachelor's Thesis PDF