Team

Prof. Dr. Matthias König Group Leader

Data scientist, data analyst, computational modeler, bioinformatician, group leader. Application of computational modeling and machine learning to biological, medical and...

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Prof. Dr. Matthias König

Group Leader 2016-

Data scientist, data analyst, computational modeler, bioinformatician, group leader. Application of computational modeling and machine learning to biological, medical and clinical questions and data sets. Predictive modeling of physiological processes and systems with a focus on metabolic research.
Research projects on glucose homeostasis in normal and diabetic subjects, personalization of liver function tests to improve diagnosis, and stratification and individualization of computational models for precision medicine.

Publications (110)

• A Digital Twin of Canagliflozin Pharmacokinetics and Pharmacodynamics in Type 2 Diabetes Mellitus (2026)
• Reproducibility of a Digital Twin of the Angiotensin II Receptor Blocker Losartan (2026)
• A Digital Twin of the Angiotensin II Receptor Blocker Losartan: Physiologically Based Modeling of Blood Pressure Regulation (2026)
• A Physiologically Based Pharmacokinetic and Pharmacodynamic (PBPK/PD) Model of Dapagliflozin in Type 2 Diabetes Mellitus: The Effect of Dosing, Hepatorenal Impairment, and Food (2026)
• User-driven development and evaluation of an agentic framework for analysis of large pathway diagrams (2026)
• A Digital Twin of Empagliflozin Pharmacokinetics and Pharmacodynamics (2026)
• From FAIR to CURE: Guidelines for Computational Models of Biological Systems (2026)
• Parameter Uncertainty in the Optimization of Pharmacokinetic Models: A Reproducible Bayesian Approach (2026)
• Automated Segmentation of Hepatic Vessels and Lobules in Whole-Slide Images Using U-Net Models (2026)
• An Open and Reproducible Digital Twin for Personalised Anticoagulant Therapy: Modelling Apixaban Pharmacokinetics and Pharmacodynamics (2026)
• A PBPK Digital Twin of Rapamycin for Predicting Dose–Exposure Relationships, Organ Impairment Effects, and Drug–Drug Interactions (2026)
• Reproducibility of a Physiologically Based Pharmacokinetic and Pharmacodynamic (PBPK/PD) Model of Dapagliflozin (2026)
• TabularQual: A spreadsheet-based format for annotating and curating logical models in SBML-qual (2026)
• A Physiologically Based Pharmacokinetic/Pharmacodynamic Model of the Diuretic Hydrochlorothiazide (2026)
• EFECT enables reliable and reproducible stochastic simulations across disciplines (2026)
• The Parameter Estimation tables (PEtab) format version 2 (2026)
• SBML Level 3 Package: Flux Balance Constraints version 3 (2026)
• A system for FAIR assessment of computational biology models and simulations based on RDA indicators (2026)
• Physiologically based pharmacokinetic/pharmacodynamic modeling of the direct renin inhibitor aliskiren: Exploring the impact of hepatorenal impairment and drug-drug interactions (2025)
• Computational Model Development Using SBML: sbmlutils, sbm4humans, cy3sbml (2025)
• Reproducible digital twins for personalized liver function assessment (2025)
• Anti-Endoglin monoclonal antibody prevents the progression of liver sinusoidal endothelial inflammation and fibrosis in MASH (2025)
• A Physiologically-Based Pharmacokinetic Model of Tirzepatide (2025)
• FAIRification of computational models in biology (2025)
• Inflammation and autophagy in peripheral nerves of rodent models with metabolic syndrome and type 2 diabetes mellitus (2025)
• A physiological-based pharmacokinetic (PBPK) model of the sulfonylurea glimepiride (2025)
• Physiologically-Based Pharmacokinetic/Pharmacodynamic Modeling of Dapagliflozin: Exploring the Impact of Dosing, Hepatorenal Impairment and Food Intake (2025)
• A physiological-based pharmacokinetic/ pharmacodynamic (PBPK/PD) model of the angiotensin II receptor blocker (ARB) losartan (2025)
• A Systems Pharmacology Approach to Rivaroxaban: Physiologically Based Modeling of Pharmacokinetics and Coagulation Dynamics (2025)
• A Systems Pharmacology Approach to Rivaroxaban: Physiologically Based Modeling of Pharmacokinetics and Coagulation Dynamics (2025)
• Assessing the Impact of AI and Digital Twins on Clinical Decision-Making in Hepatology and Hepatobiliary Surgery (2025)
• Reproducibility of a Digital Twin of Glimepiride for Personalized and Stratified Diabetes Treatment (2025)
• A Digital Twin of Glimepiride for Personalized and Stratified Diabetes Treatment (2025)
• A physiologically-based pharmacokinetic (PBPK) model of sorafenib for investigating the effect of sorafenib parameters in hepatorenal impairment (2024)
• SimLivA – Modelling ischemia reperfusion injury in the liver: A first step towards a clinical decision support tool. (2024)
• Quantifying fat zonation in liver lobules: an integrated multiscale in silico model combining disturbed microperfusion and fat metabolism via a continuum biomechanical bi-scale, tri-phasic approach (2024)
• Simulation of zonation-function relationships in the liver using coupled multiscale models: Application to drug-induced liver injury (2024)
• The simulation experiment description markup language (SED-ML): language specification for level 1 version 5 (2024)
• Bayesian modelling of time series data (BayModTS)-a FAIR workflow to process sparse and highly variable data (2024)
• A systematic overview of protein variability in cytochrome P450 and UDP-glucuronosyltransferase enzymes in the human liver (2024)
• Enhancing Our Understanding of Enalapril’s Pharmacokinetics: A Physiologically Based Modeling Approach (2024)
• Cross-Species Variability in Lobular Geometry and Cytochrome P450 Hepatic Zonation: Insights into CYP1A2, CYP2E1, CYP2D6 and CYP3A4 (2024)
• Specifications of standards in systems and synthetic biology: status, developments, and tools in 2024 (2024)
• Modulation of endoglin and soluble endoglin in NASH: Computational modeling and monoclonal antibody therapeutic benefits (2024)
• Quantitative Image Analysis of Hepatic Zonation in Cytochrome P450 and Steatosis Using Whole Slide Scans (2024)
• FROG Analysis Ensures the Reproducibility of Genome Scale Metabolic Models (2024)
• libRoadRunner 2.0: A High-Performance SBML Simulation and Analysis Library (2023)
• Physiologically based pharmacokinetic (PBPK) modeling for dynamical liver function tests and CYP phenotyping (2023)
• Simvastatin therapy in different subtypes of hypercholesterolemia - a physiologically based modelling approach (2023)
• standard-GEM: standardization of open-source genome-scale metabolic models (2023)
• Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2022 and the COMBINE meeting 2022 (2023)
• A physiologically based pharmacokinetic model for CYP2E1 phenotyping via chlorzoxazone (2023)
• A physiologically based pharmacokinetic (PBPK) model of the probe drug talinolol for the characterization of intestinal P-glycoprotein (2023)
• A pathway model of glucose-stimulated insulin secretion in the pancreatic β-cell (2023)
• Insights into Intestinal P-glycoprotein Function using Talinolol: A PBPK Modeling Approach (2023)
• Eleven Strategies for Making Reproducible Research and Open Science Training the Norm at Research Institutions (2023)
• Pharmacokinetics of caffeine: A systematic analysis of reported data for application in metabolic phenotyping and liver function testing (2022)
• Dynamic Flux Balance Analysis Models in SBML (2022)
• A physiologically based model of pravastatin - The role of genotypes and hepatic or renal impairment on the pharmacokinetics of pravastatin (2022)
• BioSimulators: a central registry of simulation engines and services for recommending specific tools (2022)
• FAIR Sharing of Reproducible Models of Epidemic and Pandemic Forecast (2022)
• Physiologically based pharmacokinetic (PBPK) modeling of the role of CYP2D6 polymorphism for metabolic phenotyping with dextromethorphan (2022)
• Cytochrome p450 enzymes in periportal steatosis: Modulation of drug metabolizing activity but not of pericentral expression pattern (2022)
• A Physiologically Based Model of Indocyanine Green Liver Function Tests - Effects of Physiological Factors, Hepatic Disease and Hepatic Surgery (2021)
• SED-ML Validator: tool for debugging simulation experiments (2021)
• OMEX Metadata Specification Version 1.2 (2021)
• Ten Simple Rules for FAIR Sharing of Experimental and Clinical Data with the Modeling Community (2021)
• The Systems Biology Simulation Core Library (2021)
• The simulation experiment description markup language (SED-ML): language specification for level 1 version 4 (2021)
• SBMLWebApp: Web-based Simulation, Steady-State Analysis, and Parameter Estimation of Systems Biology Models (2021)
• Computational modelling of omeprazole - pharmacokinetics and pharmacodynamics (2021)
• Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2021 (2021)
• Hepatectomy-Induced Alterations in Hepatic Perfusion and Function - Toward Multi-Scale Computational Modeling for a Better Prediction of Post-hepatectomy Liver Function (2021)
• Physiologically based modeling of the effect of physiological and anthropometric variability on indocyanine green based liver function tests (2021)
• Prediction of survival after hepatectomy using a physiologically based pharmacokinetic model of indocyanine green liver function tests (2021)
• Executable Simulation Model of the Liver (2020)
• MEMOTE for standardized genome-scale metabolic model testing (2020)
• The Distributions Package for SBML Level 3 (2020)
• The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE) (2020)
• Specifications of Standards in Systems and Synthetic Biology:Status and Developments in 2020 (2020)
• Open modeling and exchange (OMEX) metadata specification version 1.0 (2020)
• SBML Level 3: an extensible format for the exchange and reuse of biological models (2020)
• PK-DB: pharmacokinetics database for individualized and stratified computational modeling (2020)
• Computational Modelling of Midazolam Clearance: Effect of Inhibitors and Inducers (2020)
• Computational Modelling of Simvastatin - Effects on HMG-CoA Reductase Activity and Cholesterol (2020)
• QuaLiPerF – Multi-X Liver Modelling (2020)
• The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core (2019)
• Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019 (2019)
• Model Order Reduction (MOR) of Function-Perfusion-Growth Simulation in the Human Fatty Liver via Artificial Neural Network (ANN) (2019)
• Tellurium Notebooks — An Environment for Reproducible Dynamical Modeling in Systems Biology. (2018)
• Harmonizing semantic annotations for computational models in biology (2018)
• Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3) (2018)
• HEPATOKIN1: A Biochemistry-Based Model of Liver Metabolism Suited for Applications in Medicine and Pharmacology (2018)
• Tellurium: An Extensible Python-based Modeling Environment for Systems and Synthetic Biology (2018)
• Computational Modeling in Liver Surgery (2017)
• Toward community standards and software for whole-cell modeling (2016)
• cy3sabiork: A Cytoscape app for visualizing kinetic data from SABIO-RK (2016)
• Challenges and opportunities for system biology standards and tools in medical research (2016)
• LibRoadRunner: a high performance SBML simulation and analysis library. (2015)
• On the Influence of Growth in Perfusion Dependent Biological Systems - at the Example of the Human Liver. (2015)
• Pathobiochemical signatures of cholestatic liver disease in bile duct ligated mice (2015)
• Homeostasis of blood glucose - Computer simulations of central liver functions. (2014)
• Modeling function-perfusion behavior in liver lobules including tissue, blood, glucose, lactate and glycogen by use of a coupled two-scale PDE-ODE approach. (2014)
• Metabolic Gradients as Key Regulators in Zonation of Tumor Energy Metabolism: A Tissue-scale Model Based Study. (2013)
• Quantifying the Contribution of the Liver to the Homeostasis of Plasma Glucose: A Detailed Kinetic Model of Hepatic Glucose Metabolism Integrated with the Hormonal Control by Insulin, Glucagon and Epinephrine (2012)
• CySBML: a Cytoscape plugin for SBML (2012)
• Kinetic Modeling of Human Hepatic Glucose Metabolism in T2DM Predicts Higher Risk of Hypoglycemic Events in Rigorous Insulin Therapy (2012)
• FluxViz - Cytoscape Plug-in for Vizualisation of Flux Distributions in Networks (2011)
• Enzymatic Features of the Glucose Metabolism in Tumor Cells. (2011)
• HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology. (2010)

Projects (25)

• Analysis of hepatic zonation patterns from whole-slide images
• Physiologically based pharmacokinetic (PBPK) model of creatinine and inulin
• Physiologically based pharmacokinetic (PBPK) model of CYP2D6 polymorphism
• Digital twins of SGLT2 inhibitors
• Digital twins for blood pressure regulation
• Digital twin of glimepiride for personalized diabetes therapy
• Digital twins of direct oral anticoagulants (DOACs)
• Digital twin of rapamycin for personalized immunosuppressive therapy
• PBPK model of montelukast
• Protein distributions in the human liver
• ATLAS - AI and Simulation for Tumor Liver ASsessment
• Hepatic zonation patterns of Cytochrome P450 enzymes
• Simvastatin therapy in different subtypes of hypercholesterolemia
• Computational Modeling of Dynamical Liver Function Tests: LiMAx
• Reproducible simulation studies targeting COVID-19
• TabularQual: A spreadsheet-based format for logical models
• VisFEM: 3D visualization of digital twins
• Modeling Hepatic Central Metabolism
• Stratification and personalization of computational models
• Multi-scale Model of Hepatic Metabolism
• Liver Function Tests
• Biomarker signatures in liver disease
• High Performance Simulators and Simulation Software
• Reproducible simulation experiments
• FluType: Influenza Classification based on Machine Learning

Software (11)

• PK-DB — Pharmacokinetics database
• sbmlutils — Python utilities for SBML
• SBML4Humans — SBML simulation made easy
• sbmlsim — SBML simulation made easy
• cysbml — Cytoscape 3 app for the Systems Biology Markup Language
• brendapy — BRENDA in python
• libsbgnpy — Python library for SBGN
• roadrunner — High-performance simulator for SBML
• COBRApy — COBRA python package
• tellurium — systems biology simulation library
• VisFEM — Web visualization of FEM models

Mariia Myshkina Ph.D. Student

Mariia works on ATLAS, a decision support tool for hepatocellular carcinoma (HCC). Based on AI methods, ATLAS processes all relevant...

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Mariia Myshkina

Ph.D. Student 2024-

Mariia works on ATLAS, a decision support tool for hepatocellular carcinoma (HCC). Based on AI methods, ATLAS processes all relevant patient data from databases, systems medicine and continuum biomechanical in silico prognosis models as well as individual patient data. The tool is being developed in a co-design approach by experts in surgical oncology, mathematical modeling and machine learning.

Publications (6)

• Reproducibility of a Digital Twin of the Angiotensin II Receptor Blocker Losartan (2026)
• A Digital Twin of the Angiotensin II Receptor Blocker Losartan: Physiologically Based Modeling of Blood Pressure Regulation (2026)
• An Open and Reproducible Digital Twin for Personalised Anticoagulant Therapy: Modelling Apixaban Pharmacokinetics and Pharmacodynamics (2026)
• Reproducibility of a Physiologically Based Pharmacokinetic and Pharmacodynamic (PBPK/PD) Model of Dapagliflozin (2026)
• A Systems Pharmacology Approach to Rivaroxaban: Physiologically Based Modeling of Pharmacokinetics and Coagulation Dynamics (2025)
• Assessing the Impact of AI and Digital Twins on Clinical Decision-Making in Hepatology and Hepatobiliary Surgery (2025)

Projects (5)

• Digital twins of SGLT2 inhibitors
• Digital twins for blood pressure regulation
• Digital twins of direct oral anticoagulants (DOACs)
• ATLAS - AI and Simulation for Tumor Liver ASsessment
• VisFEM: 3D visualization of digital twins

Software (2)

• PK-DB — Pharmacokinetics database
• VisFEM — Web visualization of FEM models

Shubhankar Palwankar Scientific Researcher

Shubhankar worked on enhancing our understanding of enalapril's pharmacokinetics and dynamics based on a physiologically based modeling approach. The work...

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Shubhankar Palwankar

Master Thesis · Scientific Researcher 2023-10/2024-05, 2026-07-

Shubhankar worked on enhancing our understanding of enalapril's pharmacokinetics and dynamics based on a physiologically based modeling approach. The work will build on top of existing models of the ACE inhibitors lisinopril and ramipril.

Publications (1)

• Enhancing Our Understanding of Enalapril’s Pharmacokinetics: A Physiologically Based Modeling Approach (2024)

Projects (1)

• ATLAS - AI and Simulation for Tumor Liver ASsessment

Martina Grohs Technische Assistentin (TA)

Martina works on data management and metadata of clinical samples.

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Martina Grohs

Technische Assistentin (TA) 2026-06-

Martina works on data management and metadata of clinical samples.

Michelle Elias Master Thesis

Michelle develops a physiologically based pharmacokinetic/ pharmacodynamic (PBPK) model of the sulfonylurea glimepiride. The objective is to enhance our understanding...

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Michelle Elias

Bachelor Thesis · Student Assistant · Master Thesis 2024-09/2025-12

Michelle develops a physiologically based pharmacokinetic/ pharmacodynamic (PBPK) model of the sulfonylurea glimepiride. The objective is to enhance our understanding of the underlying causes of intraindividual variability in insulin secretion and T2DM treatment with sulfonylurea, e.g., differences in hepatorenal function.

Publications (9)

• A Digital Twin of Canagliflozin Pharmacokinetics and Pharmacodynamics in Type 2 Diabetes Mellitus (2026)
• Reproducibility of a Digital Twin of the Angiotensin II Receptor Blocker Losartan (2026)
• A Physiologically Based Pharmacokinetic and Pharmacodynamic (PBPK/PD) Model of Dapagliflozin in Type 2 Diabetes Mellitus: The Effect of Dosing, Hepatorenal Impairment, and Food (2026)
• A Digital Twin of Empagliflozin Pharmacokinetics and Pharmacodynamics (2026)
• An Open and Reproducible Digital Twin for Personalised Anticoagulant Therapy: Modelling Apixaban Pharmacokinetics and Pharmacodynamics (2026)
• Reproducibility of a Physiologically Based Pharmacokinetic and Pharmacodynamic (PBPK/PD) Model of Dapagliflozin (2026)
• A physiological-based pharmacokinetic (PBPK) model of the sulfonylurea glimepiride (2025)
• Reproducibility of a Digital Twin of Glimepiride for Personalized and Stratified Diabetes Treatment (2025)
• A Digital Twin of Glimepiride for Personalized and Stratified Diabetes Treatment (2025)

Projects (5)

• Digital twins of SGLT2 inhibitors
• Digital twins for blood pressure regulation
• Digital twin of glimepiride for personalized diabetes therapy
• Digital twins of direct oral anticoagulants (DOACs)
• VisFEM: 3D visualization of digital twins

Software (1)

• VisFEM — Web visualization of FEM models

Mariia Babaeva Student Assistant

Mariia works on a physiologically based model of lisinopril. Key questions are the effect of hepatic and renal disease on...

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Mariia Babaeva

Master Project · Student Assistant 2025-04/2026

Mariia works on a physiologically based model of lisinopril. Key questions are the effect of hepatic and renal disease on lisinopril pharmacokinetics and pharmacodynamics.

Publications (2)

• A Digital Twin of Empagliflozin Pharmacokinetics and Pharmacodynamics (2026)
• An Open and Reproducible Digital Twin for Personalised Anticoagulant Therapy: Modelling Apixaban Pharmacokinetics and Pharmacodynamics (2026)

Projects (2)

• Digital twins of SGLT2 inhibitors
• Digital twins of direct oral anticoagulants (DOACs)

Amanda Schwaiger Medical Thesis

Amanda develops a physiologically based pharmacokinetic/ pharmacodynamic (PBPK/PD) model of the diuretic hydrochlorothiazide. The objective is to enhance our understanding...

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Amanda Schwaiger

Medical Thesis 2023-09/2026-09

Amanda develops a physiologically based pharmacokinetic/ pharmacodynamic (PBPK/PD) model of the diuretic hydrochlorothiazide. The objective is to enhance our understanding of how hydrochlorothiazide changes urinary volume and plasma volume and ion balance (sodium, potassium, chloride).

Publications (1)

• A Physiologically Based Pharmacokinetic/Pharmacodynamic Model of the Diuretic Hydrochlorothiazide (2026)

Projects (1)

• Digital twins for blood pressure regulation

Minjun Kim Humboldt Internship Project

Kim is developing a physiologically based pharmacokinetic/ pharmacodynamic (PBPK/PD) model of the GLP-1 receptor agonist dulaglutide to better understand its...

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Minjun Kim

Humboldt Internship Project 2025-05/2025-08, 2025-09/2026-08

Kim is developing a physiologically based pharmacokinetic/ pharmacodynamic (PBPK/PD) model of the GLP-1 receptor agonist dulaglutide to better understand its absorption, distribution, metabolism, and effects on glucose regulation.

Jessica Cruz Humboldt Internship Project

Jessica Cruz is developing a physiologically based pharmacokinetic (PBPK) model of the leukotriene receptor antagonist montelukast to better understand its...

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Jessica Cruz

Humboldt Internship Project 2026-06/2026-09

Jessica Cruz is developing a physiologically based pharmacokinetic (PBPK) model of the leukotriene receptor antagonist montelukast to better understand its absorption, distribution, metabolism, and excretion. The project focuses on interindividual variability in montelukast pharmacokinetics, particularly the impact of hepatic metabolism, CYP2C9/CYP3A4 variability, drug-drug interactions, and age-dependent differences in pediatric and adult populations.

Projects (1)

• PBPK model of montelukast

Shelee Bedón Internship Project

Shelee is developing a physiologically based pharmacokinetic (PBPK) model of the multikinase inhibitor lenvatinib to better understand its absorption, distribution,...

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Shelee Bedón

Internship Project 2026-04/2026-11

Shelee is developing a physiologically based pharmacokinetic (PBPK) model of the multikinase inhibitor lenvatinib to better understand its absorption, distribution, metabolism, and excretion. The project focuses on characterizing interindividual variability in treatment response, with particular emphasis on hepatic metabolism, drug-drug interactions, and the impact of liver function in patients with hepatocellular carcinoma.

Publications (1)

• An Open and Reproducible Digital Twin for Personalised Anticoagulant Therapy: Modelling Apixaban Pharmacokinetics and Pharmacodynamics (2026)

Projects (1)

• Digital twins of direct oral anticoagulants (DOACs)

Chang Linh Nguyen Bachelor Project

Chang Linh is developing a physiologically based pharmacokinetic (PBPK) model of the β2-adrenergic receptor agonist albuterol (salbutamol) to better understand...

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Chang Linh Nguyen

Bachelor Project 2026-04/2026-11

Chang Linh is developing a physiologically based pharmacokinetic (PBPK) model of the β2-adrenergic receptor agonist albuterol (salbutamol) to better understand its absorption, distribution, metabolism, and excretion. The project focuses on route-specific pharmacokinetics, particularly inhalation delivery, and investigates variability in drug response across different patient populations, including the impact of formulation, dosing, and pulmonary physiology.

Sandeep Konaka Gautamdas Internship Project

Sandeep is developing a physiologically based pharmacokinetic (PBPK) model of the multi-kinase inhibitor regorafenib to better understand its absorption, distribution,...

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Sandeep Konaka Gautamdas

Internship Project 2026-06/2026-12

Sandeep is developing a physiologically based pharmacokinetic (PBPK) model of the multi-kinase inhibitor regorafenib to better understand its absorption, distribution, metabolism, and excretion. The project focuses on characterizing dose–exposure relationships and interindividual variability, with particular emphasis on hepatic metabolism, active metabolites, organ impairment, and clinically relevant factors affecting regorafenib pharmacokinetics in cancer therapy.

Antonio Aquiles Alvarez Aguilar Internship Project

Antonio will delve into the influence of parameter variability in PBPK models, focusing on the consequential effects for dynamic liver...

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Antonio Aquiles Alvarez Aguilar

Master Thesis · Internship Project 2023-10/2025-12

Antonio will delve into the influence of parameter variability in PBPK models, focusing on the consequential effects for dynamic liver function assessments. The overarching objective of this project is to augment our comprehension of how inherent variability in parameters translates into intra-individual variability in pharmacokinetics.

Publications (1)

• Parameter Uncertainty in the Optimization of Pharmacokinetic Models: A Reproducible Bayesian Approach (2026)

Open Positions

Internship

We offer internships online or in-person for instance via the Humboldt Internship Program.

We support ERASMUS student internships.

Bachelor Thesis

Undergraduate (Bachelor) students are always welcome. Projects can take place in Lübeck or Berlin.

Master Thesis

Graduate (Master) students are always welcome. Projects can take place in Lübeck or Berlin.

PhD

We have a fully funded open position available as PhD in Lübeck as a Research Software Engineer (RSE) or Informatician.

We also supervise doctoral projects if you have a fellowship or similar funding source.

PostDoc

We have a fully funded open position available as PostDoc in Lübeck as a Research Software Engineer (RSE) or Informatician.

We also supervise postdoctoral projects if you have a fellowship or similar funding source.

We offer projects on the following topics

Digital Twins

Physiologically based models that mirror individual patients, from molecule to whole body.

AI

Mechanistic modeling meets machine learning for predictive, personalized medicine.

Digital Pathology

AI-driven analysis of whole-slide histology to quantify liver structure and disease at scale.

Pharmacometrics

Physiologically based pharmacokinetic/ pharmacodynamic models for precision dosing.

Open & FAIR

Reproducible, standardized models and data that the community can build on.

Interested in joining the group? Contact Prof. Matthias König.

Alumni

2025

Yusuf Ali Kulanoglu Bachelor Thesis Biophysics

Yusuf works on a physiologically based pharmacokinetic/ pharmacodynamic model of the direct renin inhibitor aliskiren.

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Yusuf Ali Kulanoglu Bachelor Thesis Biophysics

Yusuf Ali Kulanoglu

Study Project · Bachelor Thesis Biophysics 2024-04/2025-01

Yusuf works on a physiologically based pharmacokinetic/ pharmacodynamic model of the direct renin inhibitor aliskiren.

Publications (1)

• Physiologically based pharmacokinetic/pharmacodynamic modeling of the direct renin inhibitor aliskiren: Exploring the impact of hepatorenal impairment and drug-drug interactions (2025)

Abhinav Mishra Master Internship

Abhinav develops a physiologically based pharmacokinetic (PBPK) model of the GIP and GLP-1 receptor agonist tirzepatide (Mounjaro). The objective is to enhance our understanding...

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Abhinav Mishra Master Internship

Abhinav Mishra

Master Internship 2025-01/2025-03

Abhinav develops a physiologically based pharmacokinetic (PBPK) model of the GIP and GLP-1 receptor agonist tirzepatide (Mounjaro). The objective is to enhance our understanding of the underlying causes of intraindividual variability in weight loss.

Publications (1)

• A Physiologically-Based Pharmacokinetic Model of Tirzepatide (2025)

Michael Gaas Google Summer of Code (GSOC)

Michael Gaas is enhancing the Systems Biology Simulation Core Library (SBSCL) by developing a solver-agnostic framework that enables seamless integration of open-source and commercial...

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Michael Gaas Google Summer of Code (GSOC)

Michael Gaas

Google Summer of Code (GSOC) 2025-05/2025-08

Michael Gaas is enhancing the Systems Biology Simulation Core Library (SBSCL) by developing a solver-agnostic framework that enables seamless integration of open-source and commercial optimization solvers. This upgrade will make Flux Balance Analysis faster, more flexible, and fully compatible with modern hardware architectures, empowering researchers worldwide to model complex biological systems more effectively.

Emre Hikmet Google Summer of Code (GSOC)

Emre works on CySBML Reloaded: Smarter, Simpler, Automated, a project focused on upgrading CySBML — a Cytoscape app for visualizing computational models encoded in...

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Emre Hikmet Google Summer of Code (GSOC)

Emre Hikmet

Google Summer of Code (GSOC) 2025-05/2025-08

Emre works on CySBML Reloaded: Smarter, Simpler, Automated, a project focused on upgrading CySBML — a Cytoscape app for visualizing computational models encoded in SBML. The project will enhance usability, improve stability, and introduce automation features, making it easier for researchers to explore, validate, and interact with complex biomedical models through an intuitive and streamlined interface based on network visualization.

Rohit Chakraborty Data Curation

Rohit supports the data curation for morphine pharmacokinetics.

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Rohit Chakraborty Data Curation

Rohit Chakraborty

Data Curation 2024-05/2025-12

Rohit supports the data curation for morphine pharmacokinetics.

Rohini Chakraborty Data Curation

Rohini supports the data curation for morphine pharmacokinetics.

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Rohini Chakraborty Data Curation

Rohini Chakraborty

Data Curation 2024-03/2025-12

Rohini supports the data curation for morphine pharmacokinetics.

Olivia Yau Humboldt Internship Project (HIP)

During Program Day at Humboldt-Universität zu Berlin, Isabella Tan, Olivia Yau, and Minjun Kim presented their physiologically based pharmacokinetic/ pharmacodynamic (PBPK/PD) modeling projects on...

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Olivia Yau Humboldt Internship Project (HIP)

Olivia Yau

Humboldt Internship Project (HIP) 2025-05/2025-08

During Program Day at Humboldt-Universität zu Berlin, Isabella Tan, Olivia Yau, and Minjun Kim presented their physiologically based pharmacokinetic/ pharmacodynamic (PBPK/PD) modeling projects on GLP-1 receptor agonists. Minjun Kim is developing a model of dulaglutide to investigate its absorption, distribution, metabolism, and effects on glucose regulation. Isabella Tan is building a model of liraglutide to study its pharmacological behavior and impact on glucose homeostasis, focusing on individualized treatment strategies. Olivia Yau is working on a model of lixisenatide to explore its kinetics and therapeutic effects, aiming to advance personalized approaches to diabetes therapy.

Isabella Tan Humboldt Internship Project (HIP)

Isabella is building a PBPK/PD model of the GLP-1 receptor agonist liraglutide to explore its pharmacological behavior and impact on glucose homeostasis, with a...

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Isabella Tan Humboldt Internship Project (HIP)

Isabella Tan

Humboldt Internship Project (HIP) 2025-05/2025-08

Isabella is building a PBPK/PD model of the GLP-1 receptor agonist liraglutide to explore its pharmacological behavior and impact on glucose homeostasis, with a focus on individualized treatment strategies.

Nike Nemitz Bachelor Project

Nike develops a physiologically based pharmacokinetic/ pharmacodynamic (PBPK) model of SGLT2 inhibitor dapagliflozin. The objective is to enhance our understanding of the underlying causes...

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Nike Nemitz Bachelor Project

Nike Nemitz

Bachelor Project 2024-2025

Nike develops a physiologically based pharmacokinetic/ pharmacodynamic (PBPK) model of SGLT2 inhibitor dapagliflozin. The objective is to enhance our understanding of the underlying causes of intraindividual variability in diabetes treatment with SGLT2 inhibitors, e.g., differences in hepatorenal function.

Publications (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 (2026)
• Reproducibility of a Physiologically Based Pharmacokinetic and Pharmacodynamic (PBPK/PD) Model of Dapagliflozin (2026)
• Physiologically-Based Pharmacokinetic/Pharmacodynamic Modeling of Dapagliflozin: Exploring the Impact of Dosing, Hepatorenal Impairment and Food Intake (2025)

Projects (1)

• Digital twins of SGLT2 inhibitors

Helen Leal Pujol Student Assistant

Helen worked on a physiologically based model of pravastatin. Key questions are the effect of genotypes and hepatic and renal disease on pravastatin pharmacokinetics...

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Helen Leal Pujol Student Assistant

Helen Leal Pujol

Bachelor Student · Student Assistant 2021/2025-09

Helen worked on a physiologically based model of pravastatin. Key questions are the effect of genotypes and hepatic and renal disease on pravastatin pharmacokinetics and coupling to a pharmacodynamic model of LDL-C reduction. Currently, Helen works on a physiologically based model of omeprazol.

Publications (2)

• Simvastatin therapy in different subtypes of hypercholesterolemia - a physiologically based modelling approach (2023)
• A physiologically based model of pravastatin - The role of genotypes and hepatic or renal impairment on the pharmacokinetics of pravastatin (2022)

Elisabetta Casabianca Master Thesis

Elisabetta develops a physiologically based pharmacokinetic/ pharmacodynamic (PBPK) model of the direct oral anticoagulant (DOAC) rivaroxaban. The objective is to enhance our understanding of...

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Elisabetta Casabianca Master Thesis

Elisabetta Casabianca

ERASMUS · Master Thesis 2025-02/2025-07

Elisabetta develops a physiologically based pharmacokinetic/ pharmacodynamic (PBPK) model of the direct oral anticoagulant (DOAC) rivaroxaban. The objective is to enhance our understanding of the underlying causes of intraindividual variability in anticoagulation treatment with DOACs.

Publications (3)

• A Systems Pharmacology Approach to Rivaroxaban: Physiologically Based Modeling of Pharmacokinetics and Coagulation Dynamics (2025)
• A Systems Pharmacology Approach to Rivaroxaban: Physiologically Based Modeling of Pharmacokinetics and Coagulation Dynamics (2025)
• Assessing the Impact of AI and Digital Twins on Clinical Decision-Making in Hepatology and Hepatobiliary Surgery (2025)

Projects (1)

• Digital twins of direct oral anticoagulants (DOACs)

Ennie Tensil Bachelor Thesis

Ennie develops a physiologically based pharmacokinetic/ pharmacodynamic (PBPK) model of the direct angiotensin II receptor (ARB) inhibitor losartan. The objective is to enhance our...

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Ennie Tensil Bachelor Thesis

Ennie Tensil

Bachelor Project · Bachelor Thesis 2024-09/2025-06

Ennie develops a physiologically based pharmacokinetic/ pharmacodynamic (PBPK) model of the direct angiotensin II receptor (ARB) inhibitor losartan. The objective is to enhance our understanding of the underlying causes of intraindividual variability in hypertension treatment with ARB inhibitors, e.g., differences in hepatorenal function and CYP2C9 genotype.

Publications (3)

• Reproducibility of a Digital Twin of the Angiotensin II Receptor Blocker Losartan (2026)
• A Digital Twin of the Angiotensin II Receptor Blocker Losartan: Physiologically Based Modeling of Blood Pressure Regulation (2026)
• A physiological-based pharmacokinetic/ pharmacodynamic (PBPK/PD) model of the angiotensin II receptor blocker (ARB) losartan (2025)

Projects (1)

• Digital twins for blood pressure regulation

Juan Pablo Ramos Mendoza Master Student

Juan Pablo is developing a closed-loop control system to optimize anesthesia delivery, aiming to enhance precision and patient safety during surgical procedures.

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Juan Pablo Ramos Mendoza Master Student

Juan Pablo Ramos Mendoza

Master Student 2025-04/2025-09

Juan Pablo is developing a closed-loop control system to optimize anesthesia delivery, aiming to enhance precision and patient safety during surgical procedures.

Monika Jesionek ERASMUS Student

Monika is developing a PBPK model of immune suppressant rapamycin (sirolimus) as part of our contribution to the Immune Digital Twin (IDT).

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Monika Jesionek ERASMUS Student

Monika Jesionek

ERASMUS Student 2025-07/2025-11

Monika is developing a PBPK model of immune suppressant rapamycin (sirolimus) as part of our contribution to the Immune Digital Twin (IDT).

Publications (1)

• A PBPK Digital Twin of Rapamycin for Predicting Dose–Exposure Relationships, Organ Impairment Effects, and Drug–Drug Interactions (2026)

Projects (1)

• Digital twin of rapamycin for personalized immunosuppressive therapy

2024

Afruja Hossain Bachelor Student

Afruja worked on a systematic overview of the protein variability of cytochrome P450 (CYP450) isoforms in the human liver.

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Afruja Hossain Bachelor Student

Afruja Hossain

Bachelor Student 2022-2024

Afruja worked on a systematic overview of the protein variability of cytochrome P450 (CYP450) isoforms in the human liver.

Publications (1)

• A systematic overview of protein variability in cytochrome P450 and UDP-glucuronosyltransferase enzymes in the human liver (2024)

Projects (1)

• Protein distributions in the human liver

Prerna Parakkat Humboldt Internship Student

Prerna worked on an advanced Large Language Model (LLM) to serve as an expert system for efficiently and accurately curating pharmacokinetic data from scientific...

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Prerna Parakkat Humboldt Internship Student

Prerna Parakkat

Humboldt Internship Student 2024-05/2024-08

Prerna worked on an advanced Large Language Model (LLM) to serve as an expert system for efficiently and accurately curating pharmacokinetic data from scientific literature.

Jonas Küttner QuaLiPerF

Jonas worked on a physiologically based model of chlorzoxazone for hepatic CYP2E1 phenotyping. Key questions are the effect of CYP2E1 induction/inhibition and zonation on...

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Jonas Küttner QuaLiPerF

Jonas Küttner

Master Project · Master Student · QuaLiPerF 2022-2024

Jonas worked on a physiologically based model of chlorzoxazone for hepatic CYP2E1 phenotyping. Key questions are the effect of CYP2E1 induction/inhibition and zonation on chlorzoxazone phenotyping. Jonas now analyses whole-slide images of the liver to evaluate zonation patterns in the liver using digital pathology methods. In his master thesis Jonas developed methods for quantitative image analysis of hepatic zonation in cytochrome P450 and steatosis using whole slide scans.

Publications (2)

• Quantitative Image Analysis of Hepatic Zonation in Cytochrome P450 and Steatosis Using Whole Slide Scans (2024)
• A physiologically based pharmacokinetic model for CYP2E1 phenotyping via chlorzoxazone (2023)

Projects (2)

• Analysis of hepatic zonation patterns from whole-slide images
• Hepatic zonation patterns of Cytochrome P450 enzymes

Samira Eissazedeh ERASMUS

Samira works to enhance our understanding of the role of endoglin in TGF-β signaling. She develops a computational model that explores the nuances of...

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Samira Eissazedeh ERASMUS

Samira Eissazedeh

ERASMUS 2023-09/2023-12, 2024-08/2024-09

Samira works to enhance our understanding of the role of endoglin in TGF-β signaling. She develops a computational model that explores the nuances of L-endoglin's role within this pathway and evaluates the effects of targeted interventions on this signaling.

Vera Tereshchuk Humboldt Internship Student

Vera developed a physiologically based pharmacokinetic/ pharmacodynamic (PBPK) model of SGLT2 inhibitor canagliflozin. The objective is to enhance our understanding of the underlying causes...

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Vera Tereshchuk Humboldt Internship Student

Vera Tereshchuk

Humboldt Internship Student 2024-07/2024-09

Vera developed a physiologically based pharmacokinetic/ pharmacodynamic (PBPK) model of SGLT2 inhibitor canagliflozin. The objective is to enhance our understanding of the underlying causes of intraindividual variability in diabetes treatment with SGLT2 inhibitors, e.g., differences in hepatorenal function.

Publications (1)

• A Digital Twin of Canagliflozin Pharmacokinetics and Pharmacodynamics in Type 2 Diabetes Mellitus (2026)

Projects (1)

• Digital twins of SGLT2 inhibitors

Beatrice Stemmer Mallol Student Assistant

Beatrice works on a physiologically based model to characterize intestinal P-glycoprotein using talinolol as a probe drug.

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Beatrice Stemmer Mallol Student Assistant

Beatrice Stemmer Mallol

Bachelor Student · Student Assistant 2022-2024

Beatrice works on a physiologically based model to characterize intestinal P-glycoprotein using talinolol as a probe drug.

Publications (2)

• A physiologically based pharmacokinetic (PBPK) model of the probe drug talinolol for the characterization of intestinal P-glycoprotein (2023)
• Insights into Intestinal P-glycoprotein Function using Talinolol: A PBPK Modeling Approach (2023)

Deepa Maheshvare Humboldt Internship Student

Deepa worked on a kinetic model of glucose stimulated insulin secretion (GSIS) of the pancreatic beta-cell, studying changes in glycolysis during insulin secretion, and...

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Deepa Maheshvare Humboldt Internship Student

Deepa Maheshvare

Ph.D. Student (Internship) · Humboldt Internship Student 2019-2023, 2023-2024

Deepa worked on a kinetic model of glucose stimulated insulin secretion (GSIS) of the pancreatic beta-cell, studying changes in glycolysis during insulin secretion, and later on enhancing our understanding of morphine pharmacokinetics based on a physiologically based modeling approach.

Publications (1)

• A pathway model of glucose-stimulated insulin secretion in the pancreatic β-cell (2023)

Jennesse Alejandro Humboldt Internship Student (Brown University)

Jennesse develops a physiologically based pharmacokinetic/ pharmacodynamic (PBPK) model of SGLT2 inhibitor canagliflozin. The objective is to enhance our understanding of the underlying causes...

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Jennesse Alejandro Humboldt Internship Student (Brown University)

Jennesse Alejandro

Humboldt Internship Student (Brown University) 2024-08/2024-11

Jennesse develops a physiologically based pharmacokinetic/ pharmacodynamic (PBPK) model of SGLT2 inhibitor canagliflozin. The objective is to enhance our understanding of the underlying causes of intraindividual variability in diabetes treatment with SGLT2 inhibitors, e.g., differences in hepatorenal function.

Publications (1)

• A Digital Twin of Empagliflozin Pharmacokinetics and Pharmacodynamics (2026)

Projects (1)

• Digital twins of SGLT2 inhibitors

Luca Samuel Sawady Internship

Luca works on a physiologically based model of the oral contraceptive component ethinylestradiol. By the end of this project, we offer a robust and...

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Luca Samuel Sawady Internship

Luca Samuel Sawady

Internship 2023-09/2024-01

Luca works on a physiologically based model of the oral contraceptive component ethinylestradiol. By the end of this project, we offer a robust and validated PBPK model for ethinylestradiol that can serve as a valuable tool for researchers, clinicians, and the pharmaceutical industry.

2023

Sophie Silberhorn Internship

Sophie worked on a systematic overview of the protein variability of ABC and SLC transporters in the human liver.

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Sophie Silberhorn Internship

Sophie Silberhorn

Internship 2023-05/2023-06

Sophie worked on a systematic overview of the protein variability of ABC and SLC transporters in the human liver.

Projects (1)

• Protein distributions in the human liver

Jan Grzegorzewski Ph.D. Student

Jan worked on the stratification and personalization of computational models. He develops methods and software for semi-automatic data curation of pharmacokinetic information and a...

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Jan Grzegorzewski Ph.D. Student

Jan Grzegorzewski

Ph.D. Student 2017-2023

Jan worked on the stratification and personalization of computational models. He develops methods and software for semi-automatic data curation of pharmacokinetic information and a pharmacokinetic database for storage and the storage and FAIR access of such data (PK-DB).

Publications (12)

• Cross-Species Variability in Lobular Geometry and Cytochrome P450 Hepatic Zonation: Insights into CYP1A2, CYP2E1, CYP2D6 and CYP3A4 (2024)
• Physiologically based pharmacokinetic (PBPK) modeling for dynamical liver function tests and CYP phenotyping (2023)
• Simvastatin therapy in different subtypes of hypercholesterolemia - a physiologically based modelling approach (2023)
• A physiologically based pharmacokinetic model for CYP2E1 phenotyping via chlorzoxazone (2023)
• Insights into Intestinal P-glycoprotein Function using Talinolol: A PBPK Modeling Approach (2023)
• Pharmacokinetics of caffeine: A systematic analysis of reported data for application in metabolic phenotyping and liver function testing (2022)
• Dynamic Flux Balance Analysis Models in SBML (2022)
• Physiologically based pharmacokinetic (PBPK) modeling of the role of CYP2D6 polymorphism for metabolic phenotyping with dextromethorphan (2022)
• Ten Simple Rules for FAIR Sharing of Experimental and Clinical Data with the Modeling Community (2021)
• Physiologically based modeling of the effect of physiological and anthropometric variability on indocyanine green based liver function tests (2021)
• Prediction of survival after hepatectomy using a physiologically based pharmacokinetic model of indocyanine green liver function tests (2021)
• PK-DB: pharmacokinetics database for individualized and stratified computational modeling (2020)

Projects (5)

• Physiologically based pharmacokinetic (PBPK) model of CYP2D6 polymorphism
• Simvastatin therapy in different subtypes of hypercholesterolemia
• Stratification and personalization of computational models
• Reproducible simulation experiments
• FluType: Influenza Classification based on Machine Learning

Software (1)

• PK-DB — Pharmacokinetics database

Nurudeen Sojimade Internship

Nurudeen works on a physiologically based pharmacokinetic (PBPK) model of the contrast agent Gd-EOB-DTPA. Key questions are to study the effect of hepatorenal impairment,...

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Nurudeen Sojimade Internship

Nurudeen Sojimade

Internship 2023-03/2023-05

Nurudeen works on a physiologically based pharmacokinetic (PBPK) model of the contrast agent Gd-EOB-DTPA. Key questions are to study the effect of hepatorenal impairment, perfusion and OATP activity on Gd-EOB-DTPA pharmacokinetics.

Adrian Köller Student Assistant

Adrian worked on a physiologically based model of indocyanine green (ICG) clearance. Key questions are the effect of blood flow and plasma proteins on...

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Adrian Köller Student Assistant

Adrian Köller

Bachelor Student · Master Project · Student Assistant 2020-2023

Adrian worked on a physiologically based model of indocyanine green (ICG) clearance. Key questions are the effect of blood flow and plasma proteins on ICG clearance and related liver function tests. Currently, Adrian analyzes the changes in OGTT during impaired glucose tolerance and diabetes type 2.

Publications (5)

• Pharmacokinetics of caffeine: A systematic analysis of reported data for application in metabolic phenotyping and liver function testing (2022)
• A Physiologically Based Model of Indocyanine Green Liver Function Tests - Effects of Physiological Factors, Hepatic Disease and Hepatic Surgery (2021)
• Physiologically based modeling of the effect of physiological and anthropometric variability on indocyanine green based liver function tests (2021)
• Prediction of survival after hepatectomy using a physiologically based pharmacokinetic model of indocyanine green liver function tests (2021)
• PK-DB: pharmacokinetics database for individualized and stratified computational modeling (2020)

Zahra Bahri Humboldt Internship Student

Zhara works on a physiologically based pharmacokinetic (PBPK) model to estimate the glomerular filtration rate (eGFR) using creatinine. The objective is to enhance our...

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Zahra Bahri Humboldt Internship Student

Zahra Bahri

Humboldt Internship Student 2023-07/2023-09

Zhara works on a physiologically based pharmacokinetic (PBPK) model to estimate the glomerular filtration rate (eGFR) using creatinine. The objective is to enhance our understanding of how variations in creatinine production, muscle mass, and tubular secretion of creatinine influence eGFR calculations.

Projects (1)

• Physiologically based pharmacokinetic (PBPK) model of creatinine and inulin

Xenia Petukhova Humboldt Internship Student

Xenia works on a physiologically based pharmacokinetic (PBPK) model of inulin to assess the glomerular filtration rate (GFR). Our goal is to gain a...

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Xenia Petukhova Humboldt Internship Student

Xenia Petukhova

Humboldt Internship Student 2023-07/2023-09

Xenia works on a physiologically based pharmacokinetic (PBPK) model of inulin to assess the glomerular filtration rate (GFR). Our goal is to gain a deeper understanding of the impact of various inulin protocols on GFR measurement and the influence of physiological factors, such as body composition, on GFR determination using inulin.

Projects (1)

• Physiologically based pharmacokinetic (PBPK) model of creatinine and inulin

Sankha Das Research Internship

Sankha worked on the analysis and quantification of microcirculation data recorded in Humans and Rats, developing a workflow for the analysis of orthogonal polarization...

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Sankha Das Research Internship

Sankha Das

Google Summer of Code Student · Research Internship 2021, 2022-11/2023-05 · Birla Institute of Technology and Science Pilani

Sankha worked on the analysis and quantification of microcirculation data recorded in Humans and Rats, developing a workflow for the analysis of orthogonal polarization spectroscopy (OPS) and IDF as part of QuaLiPerF. As part of Google Summer of Code 2021, in cooperation with Ralf Steuer from the Humboldt-University Berlin, he also implemented an SBML report for Humans in sbmlutils.

Frances Okibedi Internship

Frances works on a physiologically based pharmacokinetic (PBPK) model of sorafenib for systemic treatment of hepatocellular carcinoma (HCC). Key questions are to study the...

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Frances Okibedi Internship

Frances Okibedi

Internship 2023-03/2023-12

Frances works on a physiologically based pharmacokinetic (PBPK) model of sorafenib for systemic treatment of hepatocellular carcinoma (HCC). Key questions are to study the effect of OATP activity and CYP3A4 inhibition on sorafenib pharmacokinetics and efficiency.

Publications (1)

• A physiologically-based pharmacokinetic (PBPK) model of sorafenib for investigating the effect of sorafenib parameters in hepatorenal impairment (2024)

Hülya Karaboğa ERASMUS

Huelya will develop a physiologically based pharmacokinetic (PBPK) model of the ACE inhibitor captopril.

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Hülya Karaboğa ERASMUS

Hülya Karaboğa

ERASMUS 2023-10/2023-12

Huelya will develop a physiologically based pharmacokinetic (PBPK) model of the ACE inhibitor captopril.

Hannah Menghis Humboldt Internship Student (Brown University)

Hannah will establish a pharmacokinetic dataset of semaglutide and develop an initial version of a physiologically based pharmacokinetic (PBPK) model of the GLP-1 inhibitor...

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Hannah Menghis Humboldt Internship Student (Brown University)

Hannah Menghis

Humboldt Internship Student (Brown University) 2023-08/2023-10

Hannah will establish a pharmacokinetic dataset of semaglutide and develop an initial version of a physiologically based pharmacokinetic (PBPK) model of the GLP-1 inhibitor semaglutide. The objective is to enhance our understanding of the underlying causes of intraindividual variability in semaglutide treatment, e.g., differences in renal function.

2022

Janosch Brandhorst Student Assistant

Janosch works on the computational modeling of acetaminophen through the liver and curates data for the pharmacokinetics database PK-DB.

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Janosch Brandhorst Student Assistant

Janosch Brandhorst

Student Assistant 2019-2022

Janosch works on the computational modeling of acetaminophen through the liver and curates data for the pharmacokinetics database PK-DB.

Publications (2)

• Physiologically based pharmacokinetic (PBPK) modeling of the role of CYP2D6 polymorphism for metabolic phenotyping with dextromethorphan (2022)
• PK-DB: pharmacokinetics database for individualized and stratified computational modeling (2020)

Projects (1)

• Physiologically based pharmacokinetic (PBPK) model of CYP2D6 polymorphism

Paula Ogata Humboldt Internship Student

Paula works on a pharmacokinetics/pharmacodynamics model of metoprolol. Key questions are the effect of dosing and formulation on metoprolol pharmacokinetics and exercise heart rate...

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Paula Ogata Humboldt Internship Student

Paula Ogata

Humboldt Internship Student 2020-2022

Paula works on a pharmacokinetics/pharmacodynamics model of metoprolol. Key questions are the effect of dosing and formulation on metoprolol pharmacokinetics and exercise heart rate (EHR) reduction.

2021

Danny Ke Humboldt Internship Student

Danny Ke works on a physiologically based model of benzodiazepines. Key questions are the effect of genetic variance on clearance of diazepam.

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Danny Ke Humboldt Internship Student

Danny Ke

Humboldt Internship Student 2020-2021

Danny Ke works on a physiologically based model of benzodiazepines. Key questions are the effect of genetic variance on clearance of diazepam.

Publications (1)

• PK-DB: pharmacokinetics database for individualized and stratified computational modeling (2020)

Yannick Duport Bachelor Student

Yannick Duport works on a physiologically based model of midazolam clearance. Key questions are the effect of inhibitors and inducers on the metabolism of...

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Yannick Duport Bachelor Student

Yannick Duport

Bachelor Student 2019-2021

Yannick Duport works on a physiologically based model of midazolam clearance. Key questions are the effect of inhibitors and inducers on the metabolism of midazolam.

Publications (2)

• PK-DB: pharmacokinetics database for individualized and stratified computational modeling (2020)
• Computational Modelling of Midazolam Clearance: Effect of Inhibitors and Inducers (2020)

Sükrü Balci Bachelor Student

Sükrü Balci works on a physiologically based model of omeprazole. Key questions are the effect of omeprazole formulation and dosing on the pharmacodynamic effects...

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Sükrü Balci Bachelor Student

Sükrü Balci

Bachelor Student 2020-2021

Sükrü Balci works on a physiologically based model of omeprazole. Key questions are the effect of omeprazole formulation and dosing on the pharmacodynamic effects of omeprazole.

Publications (1)

• Computational modelling of omeprazole - pharmacokinetics and pharmacodynamics (2021)

2020

Hemil Panchiwala Google Summer of Code Student

In cooperation with Andreas Dräger from the University of Tübingen we are extending SBML support for The Systems Biology Simulation Core Library. The full...

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Hemil Panchiwala Google Summer of Code Student

Hemil Panchiwala

Google Summer of Code Student 2020 · Indian Institute of Technology, Roorkee

In cooperation with Andreas Dräger from the University of Tübingen we are extending SBML support for The Systems Biology Simulation Core Library. The full proposal is available here.

Publications (1)

• The Systems Biology Simulation Core Library (2021)

Hemant Yadav Google Summer of Code Student

In cooperation with Andreas Dräger from the University of Tübingen we are extending SBML and JSON support for cobrapy. The full proposal is available...

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Hemant Yadav Google Summer of Code Student

Hemant Yadav

Google Summer of Code Student 2020 · Indian Institute of Technology, Roorkee

In cooperation with Andreas Dräger from the University of Tübingen we are extending SBML and JSON support for cobrapy. The full proposal is available here.

Sara de Angelis Humboldt Internship Student

Sara de Angelis works on a physiologically based model of torasemide. Key questions are the effect of sex on torasemide pharmacokinetics and pharmacodynamics.

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Sara de Angelis Humboldt Internship Student

Sara de Angelis

Humboldt Internship Student 2020

Sara de Angelis works on a physiologically based model of torasemide. Key questions are the effect of sex on torasemide pharmacokinetics and pharmacodynamics.

Publications (1)

• PK-DB: pharmacokinetics database for individualized and stratified computational modeling (2020)

Florian Bartsch Master Project

Florian works on a physiologically based model of statin clearance. Key questions are the effect of statins (atorvastatin and simvastatin) on cholesterol plasma levels...

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Florian Bartsch Master Project

Florian Bartsch

Bachelor Student · Student Assistant · Master Project 2020-

Florian works on a physiologically based model of statin clearance. Key questions are the effect of statins (atorvastatin and simvastatin) on cholesterol plasma levels and drug-drug interactions.

Publications (3)

• Simvastatin therapy in different subtypes of hypercholesterolemia - a physiologically based modelling approach (2023)
• Pharmacokinetics of caffeine: A systematic analysis of reported data for application in metabolic phenotyping and liver function testing (2022)
• Computational Modelling of Simvastatin - Effects on HMG-CoA Reductase Activity and Cholesterol (2020)

Projects (1)

• Simvastatin therapy in different subtypes of hypercholesterolemia

2019

Patrick Pett Ph.D. Student (Mentoring)

Patrick works on the analysis of mammalian circadian clock in the human liver based on the analysis of OMICS datasets.

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Patrick Pett Ph.D. Student (Mentoring)

Patrick Pett

Ph.D. Student (Mentoring) 2017-2019

Patrick works on the analysis of mammalian circadian clock in the human liver based on the analysis of OMICS datasets.

Kaustubh Trivedi Google Summer of Code Student

In cooperation with Andreas Dräger from the University of Tübingen we are working on the extension of ModelPolisher to a universal annotation tool.

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Kaustubh Trivedi Google Summer of Code Student

Kaustubh Trivedi

Google Summer of Code Student 2019 · Indian Institute of Technology, Roorkee

In cooperation with Andreas Dräger from the University of Tübingen we are working on the extension of ModelPolisher to a universal annotation tool.

2018

Shalin Shah Google Summer of Code

The Systems Biology Simulation Core Library (SBSCL) provides an efficient and exhaustive Java™ implementation of methods to interpret the content of models encoded in...

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Shalin Shah Google Summer of Code

Shalin Shah

Google Summer of Code 2018

The Systems Biology Simulation Core Library (SBSCL) provides an efficient and exhaustive Java™ implementation of methods to interpret the content of models encoded in the Systems Biology Markup Language (SBML) and its numerical solution. This library is based on the JSBML project and can be used on every operating system for which a Java Virtual Machine is available. Within this project SBSCL was extended among others with better support for SED-ML and COMBINE archives. See also https://ssdoesgsoc.wordpress.com/.

Publications (1)

• The Systems Biology Simulation Core Library (2021)

Roman Schulte Bachelor Thesis

Within his thesis the concept of an Modular Research Environment (MRE) was developed. An MRE is a modular application framework that can be extended...

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Roman Schulte Bachelor Thesis

Roman Schulte

Bachelor Thesis 2018

Within his thesis the concept of an Modular Research Environment (MRE) was developed. An MRE is a modular application framework that can be extended with plugins to create a new tool. InSilico is the working proof-of-principle implementation of such an MRE and was developed alongside this work. The created infrastructure of InSilico can be used to create, share and reuse custom research tools with less effort, time, and resources compared to the traditional approach.

2017

Dimitra Eleftheriadou Student Assistant

Dimitra (Master Toxicology) worked on the analysis and digitalization of literature data for liver function tests.

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Dimitra Eleftheriadou Student Assistant

Dimitra Eleftheriadou

Student Assistant 2016-2017

Dimitra (Master Toxicology) worked on the analysis and digitalization of literature data for liver function tests.

Publications (1)

• PK-DB: pharmacokinetics database for individualized and stratified computational modeling (2020)

Projects (1)

• Liver Function Tests

Takahiro Yamada Google Summer of Code

Within this project as part of Google Summer of Code 2017 a Web App for SBML models was implemented which provides functionality for time...

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Takahiro Yamada Google Summer of Code

Takahiro Yamada

Google Summer of Code 2017

Within this project as part of Google Summer of Code 2017 a Web App for SBML models was implemented which provides functionality for time course simulation, steady state analysis, and parameter estimation. The Web App provides options for uploading SBML models and experimental data files and run the respective simulations with the models. See also https://gsoc2017developwebservice.blogspot.com/.

Publications (1)

• SBMLWebApp: Web-based Simulation, Steady-State Analysis, and Parameter Estimation of Systems Biology Models (2021)