Dr. Matthias König
Group leader
2016-
Data scientist, data analyst, computational modeller, bioinformatician, group leader. Application of computational modelling and machine learning to biological, medical, and clinical questions and datasets. Predictive modeling of physiological processes and systems with focus on metabolic research.
Research projects on glucose homeostasis in normal subjects and diabetes, personalization of liver function tests for the improvement of diagnosis, and stratification and individualization of computer models for precision medicine.


Jan Grzegorzewski
Ph.D. student
2017-
Jan works on the stratification and personalization of computational models. He develops methods and software for semi-automatic data curation of pharmacokinetics information and a pharmacokinetics database for the storage and FAIR access of such data (PK-DB).


Helen Leal Pujol
Bachelor student
2021-
Helen Leal Pujol works on a physiological based model of pravastatin. Key questions are the effect of genotypes and hepatic and renal disease on pravastatin pharmacokinetics.


Jonas Küttner
Master student
2022-
Jonas Küttner works on a physiological based model of chlorzoxazone for hepatic CYP2E1 phenotyping. Key questions are the effect of CYP2E1 induction/inhibition and zonation on phenotyping using chlorzoxazone.


Beatrice Stemmer Mallol
Bachelor student
2022-
Beatrice Stemmer Mallol works on a physiological based model for the characterization of intestinal P-glycoprotein using talinolol as a probe drug.


Adrian Köller
Bachelor student, student assistant
2020-
Adrian Köller works on a physiological based model of indocyanine green (ICG) clearance. Key questions are the effect of blood flow and plasma proteins on ICG clearance and corresponding liver function tests.


Florian Bartsch
Bachelor student, student assistant
2020-
Florian Bartsch works on a physiological based model of statin metabolism clearance. Key questions are the effect of statins (atorvastatin and simvasting) on cholesterol plasma levels, and drug-drug interactions due to medications.


Paula Ogata
Humboldt Intership Student
2020-2021
Paula Ogata works on a pharmacokinetics/pharmacodynamics model of metorpolol. Key questions are the effect of dosing and formulation on metoprolol pharmacokinetics and reduction in exercise heart rate (EHR).


Deepa Maheshvare
Ph.D. student (internship)
2019-
Deepa Maheshvare works on a kinetic model of the pancreatic beta-cell. Key questions are the effect of various amino acids on the insulin secretion of the pancreas.

Alumni



Janosch Brandhorst
Student assistant
2019-2022
Janosch Brandhorst works on the computational modeling of paracetamol by the liver and curating data for PKDB.


Sükrü Balci
Bachelor student
2020-2021
Sükrü Balci works on a physiological based model of omeprazole. Key questions are the effect of omeprazole formulation and dosing on the pharmacodynamic effects of omeprazole.


Sankha Das
Google summer of code student (2021)
2021
In cooperation with Ralf Steuer from the Humboldt-University Berlin we are implementing an SBML report for Humans in sbmlutils. The full proposal is available here.


Yannick Duport
Bachelor student
2019-2021
Yannick Duport works on a physiological based model of midazolam clearance. Key questions are the effect of inhibitors and inducers on the metabolism of midazolam.


Danny Ke
Humboldt Internship Student 2020
2020-2021
Danny Ke works on a physiological based model of benzodiazepines. Key questions are the effect of genetic variance on clearance of diazepam.


Sara de Angelis
Humboldt Internship Student 2020
2020
Sara de Angelis works on a physiological based model of torasemide. Key questions are the effect of sex on torasemide pharmacokinetics and pharmacodynamics.


Hemant Yadav
Google summer of code student (2020)
2020
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.


Hemil Panchiwala
Google summer of code student (2020)
2020
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.


Kaustubh Trivedi
Google summer of code student (2019)
2019
In cooperation with Andreas Dräger from the University of Tübingen we are working on the extension of ModelPolisher to a universal annotation tool.


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.


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.


Shalin Shah
Google Summer of Code 2018
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/.


Takahiro Yamada
Google Summer of Code 2017
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/.


Dimitra Eleftheriadou
Student assistant
2016-2017
Dimitra (Master Toxicology) worked on the analysis and digitalization of literature data for liver function tests.