Michelle Elias

M.Sc. Biophysics student · Humboldt-Universität zu Berlin Computational systems medicine of the liver · König Lab

About

Background in physiologically based pharmacokinetic and pharmacodynamic (PBPK/PD) modelling, digital twins of drugs and reproducibility studies of published models. Current work moves from the whole body to the tissue scale: AI-based segmentation of whole-slide liver histology, with the resulting feature maps informing spatial PDE–ODE simulations of transport and tissue damage.

Main interests: mechanistic modelling, biomedical image analysis, and open, reproducible research software.

Research

Master project & thesis · M.Sc. Biophysics

From spatial liver imaging to image-informed dynamical simulation (working title)

  1. Whole-slide images
  2. Segmentation
  3. Feature maps
  4. Registration
  5. Meshes
  6. PDE–ODE simulation

  • Master project

    08/2026 – 01/2027

    Humboldt-Universität zu Berlin

    Data and image-analysis foundation: metadata schema, scalable storage of whole-slide images (OME-TIFF/OME-Zarr), AI-assisted necrosis segmentation, quantitative feature maps and interactive 2D visualization.

  • Master thesis

    02/2027 – 09/2027

    Universität zu Lübeck

    Registration of neighbouring tissue sections, image-to-mesh mapping and coupled PDE–ODE simulation (FEniCSx, libRoadRunner), with simulation results returned to the viewer as time-dependent layers. Use cases: APAP-induced liver necrosis and hepatic steatosis.

Supervisor: Prof. Dr. Matthias König

Bachelor thesis · B.Sc. Biology

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

2025

Humboldt-Universität zu Berlin · König Lab

Whole-body PBPK model of the antidiabetic drug glimepiride in SBML, covering renal and hepatic impairment, bodyweight and CYP2C9 genotype, validated against 20 clinical studies. Basis of the published glimepiride digital twin and its interactive web app.

Thesis (PDF, 37 MB) Paper Model Web app App code

Projects

  • SlideViz

    2026 · in development

    Viewer and data layer for whole-slide liver histology: slides with JSON metadata, a queryable slide index and multiscale display in napari. Basis for segmentation results and registered layers in the master project.

    GitHub

  • VisFEM

    2026

    Web platform for interactive visualization of finite-element (FEM) simulation results in biomedical research, developed within DFG SPP 2311. Open source and installable from PyPI; manuscript in preparation.

    GitHub PyPI DOI

  • Polysome resolution & translation prediction

    2025 – 2026 · course project

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

    GitHub

Publications

Journal articles

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

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

    DOI Code

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

    Myshkina M, Elias M, Tensil E, König M · Physiome, 2026

    DOI Code

  3. 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, König M · Pharmaceutics, 2026

    DOI Preprint Code

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

    Elias M, König M · Physiome, 2025

    DOI Code

  5. A Digital Twin of Glimepiride for Personalized and Stratified Diabetes Treatment

    Elias M, König M · Frontiers in Pharmacology, 2025

    DOI Preprint Code Web app

Preprints

  1. An Open and Reproducible Digital Twin for Personalised Anticoagulant Therapy: Modelling Apixaban Pharmacokinetics and Pharmacodynamics

    Myshkina M, Babaeva M, Nguyen LC, Bedón S, Metternich J, Elias M, König M · Preprints, 2026

    DOI

  2. A Digital Twin of Empagliflozin Pharmacokinetics and Pharmacodynamics

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

    DOI Code

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

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

    DOI Code

Submitted

  1. Reproducibility of a Digital Twin of Hydrochlorothiazide Pharmacokinetics and Pharmacodynamics

    Elias M, Myshkina M, Schwaiger A, König M · Physiome

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

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

    Code

  3. Reproducibility of a Digital Twin of Empagliflozin Pharmacokinetics and Pharmacodynamics in Type 2 Diabetes Mellitus

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

    Code

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

    Myshkina M, Elias M, Casabianca E, König M · Physiome

    Code

Experience

  • Student Assistant, DFG Priority Programme SPP 2311

    08/2026 – present

    University of Stuttgart, Institute for Statics and Dynamics of Aerospace Structures (ISD) · with the König Lab

    Development of VisFEM within SPP 2311.

  • Student Assistant, Systems Medicine of the Liver

    01/2026 – 07/2026

    Humboldt-Universität zu Berlin, Institute for Theoretical Biology · König Lab

    PBPK/PD modelling and reproducible model pipelines for Physiome reproducibility studies; contributions to VisFEM and to programme-wide data collection in SPP 2311.