Matthias König

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About Matthias König:

We are investigating liver metabolism and function with the help of computational models and methods.

Group Leader Dr. Matthias König

Institute for Theoretical Biology
Humboldt-University Berlin
Philippstraße 13, 10115 Berlin, Germany
phone +49 30 2093-98435
koenigmx@hu-berlin.de https://www.livermetabolism.com

The König group works on computational modeling, data science, data management, bioinformatics methods and machine learning on biological, medical and clinical data. Main research topics are (i) predictive modeling of biomedical systems with special focus on the liver; and (ii) databases and FAIR data. Key projects are the personalized evaluation of liver function tests, multi-scale modeling of the liver, development of a database for pharmacokinetics data. For more information have a look at our publications and projects.

SEEK ID: https://fairdomhub.org/people/678

Location: Germany

ORCID: https://orcid.org/0000-0003-1725-179X

Joined: 29th May 2016

Expertise: Computational modelling, Metabolic Models, Kinetic modelling, Liver, Metabolic Networks, Computational Biology, PBPK modeling, Physiological-based pharmacokinetics model

Tools: SBML, SED-ML, ODE, roadrunner, tellurium, Cytoscape, jupyter notebooks

Their tags

Blood sampling caffeine human Multi-cellular model Pharmacokinetics SABIO-RK SBML

Project positions

Project Coordinator: Kinetics on the move - Workshop 2016 (Charité University Medicine Berlin)

Other Projects: Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF) (Charité University Medicine Berlin) ; Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF) (Humboldt-Universität zu Berlin) ; FAIRDOM user meeting (Humboldt University Berlin) ; COMBINE Multicellular Modelling (Humboldt-Universität zu Berlin) ; FAIRDOM & LiSyM & de.NBI Data Structuring Training (Humboldt University Berlin)

This is the exchange platform of the COMBINE network.

COMBINE is an initiative to coordinate the development of various community standards and formats for computational models: BioPax, CellML, NeuroML, Synthetic Biology Open Language (SBOL), Systems Biology Graphical Notation (SBGN), Systems Biology Markup Language (SBML), Simulation Experiment Description Markup Language (SED-ML).

Projects: COMBINE Multicellular Modelling, ModeleXchange initiative

Web page: http://co.mbine.org

LiSyM - Systems Medicine of the Liver

LiSyM (Liver Systems Medicine) represents a research network of German centers and institutions, brought together by a 20 Million Euro funding program of the German Government, in which mathematicians, modelers, pharmacologists, molecular biologists and clinical scientists work together to develop a Systems Medicine approach to study early and advanced liver disease. The aim of this unique research program is to acquire and use new experimental data and data from existing data bases to build ...

Projects: Early Metabolic Injury (LiSyM-EMI - Pillar I), Chronic Liver Disease Progression (LiSyM-DP - Pillar II), Regeneration and Repair in Acute-on-Chronic Liver Failure (LiSyM-ACLF - Pillar III), LiSyM Core Infrastructure and Management (LiSyM-PD), Liver Function Diagnostics (LiSyM-LiFuDi - Pillar IV), Model Guided Pharmacotherapy In Chronic Liver Disease (LiSyM-MGP), Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF), The Hedgehog Signalling Pathway (LiSyM-JGMMS), Molecular Steatosis - Imaging & Modeling (LiSyM-MSIM), FAIRDOM & LiSyM & de.NBI Data Structuring Training, New LiSyM project

Web page: http://www.lisym.org

FAIRDOM

FAIRDOM is establishing a support and service network for European Systems Biology. FAIRDOM is a joint action of ERA-Net ERASysAPP and European Research Infrastructure ISBE to establish a data and model management service facility for Systems Biology. Our prime mission is to support researchers, students, trainers, funders and publishers by enabling Systems Biology projects to make their Data, Operating procedures and Models, Findable, Accessible, Interoperable and Reusable (FAIR).

Projects: FAIRDOM, FAIRDOM user meeting, FAIRDOM Community Workers

Web page: http://fair-dom.org

de.NBI Systems Biology Service Center (de.NBI-SysBio)

The German Network for Bioinformatics Infrastructure - de.NBI offers first class bioinformatics services including training and education to users in basic and applied life sciences research. In this network 40 projects belonging to eight service centers provide services that cover a wide variety of methods (genomics, proteomics, ...) and applications (from plants to humans). de.NBI-SysBio is the Systems Biology Service Center of de.NBI. In collaboration with FAIRDOM, de.NBI-SysBio serves the ...

Projects: de.NBI-SysBio, ExtremoPharm, ZucAt, Kinetics on the move - Workshop 2016, Example use cases, MIX-UP, Working Group Nicole Radde, MPIEvolBio-SciComp

Web page: http://www.denbi.de

FAIRDOM user meeting

Good data and model management improves the longevity and impact of your interdisciplinary research. FAIRDOM offers software and expertise to support you in better managing your interdisciplinary life-science projects, particularly in systems and synthetic biology. If you have never heard of data and model management, or are curious about it, or you are an expert keen to exchange ideas, our user meeting is the place for you!

At our users meeting you can:

Learn why data and model management is ...

Programme: FAIRDOM

Public web page: Not specified

Organisms: Homo sapiens

Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF)

We will contribute to the LiSyM Research Network an open source, freely available and reproducible multiscale model of the human liver from single cell metabolism to whole liver function. The model will be available in existing standards of systems biology, provide standardized interfaces for data integration and be fully annotated to available biological, medical and computational ontologies. All data, models and source code will be shared within the LiSyM Research Network and made available to ...

Programme: LiSyM - Systems Medicine of the Liver

Public web page: https://livermetabolism.com

Organisms: Homo sapiens, Mus musculus, Rattus norvegicus

COMBINE Multicellular Modelling

No description specified

Programme: COMBINE (Computational Modeling in Biology Network)

Public web page: https://multicellml.org/

Organisms: Not specified

FAIRDOM & LiSyM & de.NBI Data Structuring Training

No description specified

Programme: LiSyM - Systems Medicine of the Liver

Public web page: https://www.fairdomhub.org/events/96

Organisms: Not specified

Kinetics on the move - Workshop 2016

The workshop focuses on the publication, curation, retrieval, and usage of kinetic data from the reaction kinetics database SABIO-RK and on the use of data in modeling. There will be experience reports from scientists who successfully used experimental data to formulate or verify biological hypotheses with the computer, and you will experience how experimental data can be used with computational models.

Programme: de.NBI Systems Biology Service Center (de.NBI-SysBio)

Public web page: http://www.h-its.org/event/kinetics-on-the-move/

Organisms: Bacillus subtilis, Acidithiobacillus caldus, Arabidopsis thaliana

Charité University Medicine Berlin