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 (mentoring)
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.
Jan contributes to an online database for running reproducible simulation experiments in computational biology, i.e. tellurium-web.
Jan developed an influenza sub-classification platform based on peptides using data science and machine learning approaches. Part of the work was the development of the data management system required for bioinformatics analysis of peptide-virus binding data FluTypeDB.


Yannick Bartsch
Bachelor student
2019-
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.


Florian Bart
Bachelor student
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.


Adrian Köller
Bachelor student
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.


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


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


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



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.