Matthias König
We are investigating liver metabolism and function with the help of computational models and methods.
Read more about the LiSyM junior group at: www.livermetabolism.com
Junior Group Leader
Dr. Matthias König
Institute for Theoretical Biology
Humboldt-University Berlin
Invalidenstraße 43, 10117 Berlin, Germany
phone +49 30 2093-8450
konigmatt@googlemail.com
The liver is the central metabolic organ of our body playing a crucial role in the clearance of drugs, xenobiotics and numerous metabolites from the bloodstream. The quantification of these liver functions is essential to assess the status of the liver, obtain information about the degree of impairment, to evaluate treatment response or to select transplant recipients.
Within the Systems Medicine of the Liver (LiSyM) consortium we establish a standardized multiscale model framework of the human liver readily adaptable to various quantitative liver function tests currently used in the clinics. The resulting models will be personalized with individual imaging data from CT and PET in combination with anthropomorphic information like gender, age, body weight and height and used for the evaluation of quantitative liver function tests in a personalized context.
SEEK ID: https://fairdomhub.org/people/678
Location:
Germany
Expertise: Computational modelling, Metabolic Models, Kinetic modelling, Liver, Metabolic Networks, Computational Biology
Tools: SBML, SED-ML, ODE, roadrunner, tellurium, Cytoscape, jupyter notebooks
https://orcid.org/0000-0003-1725-179X 
Project roles
Project administrator
Asset gatekeeper
Asset housekeeper
Their tagsKinetics on the move - Workshop 2016 (Charité University Medicine Berlin)
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)
Related items
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
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Programme: LiSyM - Systems Medicine of the Liver
Public web page: https://livermetabolism.com
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
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Programme: Test program
Public web page: http://fair-dom.org/communities/users/barcelona-2016-first-user-meeting/
Programme: COMBINE (Computational Modeling in Biology Network)
Public web page: https://multicellml.org/
Programme: LiSyM - Systems Medicine of the Liver
Public web page: https://www.fairdomhub.org/events/96
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/
Understanding how liver function arises from the complex interaction of morphology, perfusion, and metabolism from single cells up to the entire organ requires systems-levels computational approaches.
Snapshots: Snapshot 1, Snapshot 2, Snapshot 3, Snapshot 4
Personalized liver function tests: A Multiscale Computational Model Predicts Individual Human Liver Function From Single-Cell Metabolism
Understanding how liver function arises from the complex interaction of morphology, perfusion, and metabolism from single cells up to the entire organ requires systems-levels computational approaches. We report a multiscale mathematical model of the Human liver comprising the scales from single hepatocytes, over representation of ultra-structure and micro-circulation
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Person responsible: Matthias König
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Spigset1999a Description
Submitter: Matthias König
Assay type: /assay_types?uri=http%3A%2F%2Fwww.mygrid.org.uk%2Fontology%2FJERMOntology%23metabolomics
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Jeppesen1996 Description
Submitter: Matthias König
Assay type: /assay_types?uri=http%3A%2F%2Fwww.mygrid.org.uk%2Fontology%2FJERMOntology%23metabolomics
Technology type: /technology_types?uri=http%3A%2F%2Fwww.mygrid.org.uk%2Fontology%2FJERMOntology%23metabolomics
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Oh2012 Description
Submitter: Matthias König
Assay type: /assay_types?uri=http%3A%2F%2Fwww.mygrid.org.uk%2Fontology%2FJERMOntology%23metabolomics
Technology type: /technology_types?uri=http%3A%2F%2Fwww.mygrid.org.uk%2Fontology%2FJERMOntology%23metabolomics
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Healy1991 Description
Submitter: Matthias König
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Technology type: /technology_types?uri=http%3A%2F%2Fwww.mygrid.org.uk%2Fontology%2FJERMOntology%23metabolomics
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Akinyinka2000 Description
Submitter: Matthias König
Assay type: /assay_types?uri=http%3A%2F%2Fwww.mygrid.org.uk%2Fontology%2FJERMOntology%23metabolomics
Technology type: /technology_types?uri=http%3A%2F%2Fwww.mygrid.org.uk%2Fontology%2FJERMOntology%23metabolomics
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Kakuda2014 Description
Submitter: Matthias König
Assay type: /assay_types?uri=http%3A%2F%2Fwww.mygrid.org.uk%2Fontology%2FJERMOntology%23metabolomics
Technology type: /technology_types?uri=http%3A%2F%2Fwww.mygrid.org.uk%2Fontology%2FJERMOntology%23metabolomics
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Haller2002 Description
Submitter: Matthias König
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Technology type: /technology_types?uri=http%3A%2F%2Fwww.mygrid.org.uk%2Fontology%2FJERMOntology%23metabolomics
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Amchin1999 Description
Submitter: Matthias König
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Technology type: /technology_types?uri=http%3A%2F%2Fwww.mygrid.org.uk%2Fontology%2FJERMOntology%23metabolomics
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Kaplan1997 Description
Submitter: Matthias König
Assay type: /assay_types?uri=http%3A%2F%2Fwww.mygrid.org.uk%2Fontology%2FJERMOntology%23metabolomics
Technology type: /technology_types?uri=http%3A%2F%2Fwww.mygrid.org.uk%2Fontology%2FJERMOntology%23metabolomics
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Blanchard1983a Description
Submitter: Matthias König
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Tanaka2014 Description
Submitter: Matthias König
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Technology type: /technology_types?uri=http%3A%2F%2Fwww.mygrid.org.uk%2Fontology%2FJERMOntology%23metabolomics
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Perera2011 Description
Submitter: Matthias König
Assay type: /assay_types?uri=http%3A%2F%2Fwww.mygrid.org.uk%2Fontology%2FJERMOntology%23metabolomics
Technology type: /technology_types?uri=http%3A%2F%2Fwww.mygrid.org.uk%2Fontology%2FJERMOntology%23metabolomics
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Magnusson2008 Description
Submitter: Matthias König
Assay type: /assay_types?uri=http%3A%2F%2Fwww.mygrid.org.uk%2Fontology%2FJERMOntology%23metabolomics
Technology type: /technology_types?uri=http%3A%2F%2Fwww.mygrid.org.uk%2Fontology%2FJERMOntology%23metabolomics
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Hetzler1990 Description
Submitter: Matthias König
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Technology type: /technology_types?uri=http%3A%2F%2Fwww.mygrid.org.uk%2Fontology%2FJERMOntology%23metabolomics
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Creator: Matthias König
Submitter: Matthias König
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Not specified
Abstract (Expand)
Authors: Dagmar Waltemath, Martin Golebiewski, Michael L Blinov, Padraig Gleeson, Henning Hermjakob, Michael Hucka, Esther Thea Inau, Sarah M Keating, Matthias König, Olga Krebs, Rahuman S Malik-Sheriff, David Nickerson, Ernst Oberortner, Herbert M Sauro, Falk Schreiber, Lucian Smith, Melanie I Stefan, Ulrike Wittig, Chris J Myers
Date Published: 29th Jun 2020
Publication Type: Journal
Abstract (Expand)
Authors: Falk Schreiber, Björn Sommer, Tobias Czauderna, Martin Golebiewski, Thomas E. Gorochowski, Michael Hucka, Sarah M. Keating, Matthias König, Chris Myers, David Nickerson, Dagmar Waltemath
Date Published: 29th Jun 2020
Publication Type: Journal
Abstract (Expand)
Authors: Falk Schreiber, Björn Sommer, Gary D. Bader, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Sarah M. Keating, Matthias König, Chris Myers, David Nickerson, Dagmar Waltemath
Date Published: 13th Jul 2019
Publication Type: Journal
Abstract (Expand)
Authors: Maxwell Lewis Neal, Matthias König, David Nickerson, Göksel Mısırlı, Reza Kalbasi, Andreas Dräger, Koray Atalag, Vijayalakshmi Chelliah, Michael T Cooling, Daniel L Cook, Sharon Crook, Miguel de Alba, Samuel H Friedman, Alan Garny, John H Gennari, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Nick Juty, Chris Myers, Brett G Olivier, Herbert M Sauro, Martin Scharm, Jacky L Snoep, Vasundra Touré, Anil Wipat, Olaf Wolkenhauer, Dagmar Waltemath
Date Published: 1st Mar 2019
Publication Type: Journal
Abstract (Expand)
Authors: D. Waltemath, J. Karr, F. Bergmann, V. Chelliah, M. Hucka, M. Krantz, W. Liebermeister, P. Mendes, C. Myers, P. Pir, B. Alaybeyoglu, N. Aranganathan, K. Baghalian, A. Bittig, P. Burke, M. Cantarelli, Y. Chew, R. Costa, J. Cursons, T. Czauderna, A. Goldberg, H. Gomez, J. Hahn, T. Hameri, D. Gardiol, D. Kazakiewicz, I. Kiselev, V. Knight-Schrijver, C. Knupfer, M. Konig, D. Lee, A. Lloret-Villas, N. Mandrik, J. Medley, B. Moreau, H. Naderi-Meshkin, S. Palaniappan, D. Priego-Espinosa, M. Scharm, M. Sharma, K. Smallbone, N. Stanford, J. H. Song, T. Theile, M. Tokic, N. Tomar, V. Toure, J. Uhlendorf, T. Varusai, L. Watanabe, F. Wendland, M. Wolfien, J. Yurkovich, Y. Zhu, A. Zardilis, A. Zhukova, F. Schreiber
Date Published: 16th Jun 2016
Publication Type: Not specified
Abstract (Expand)
Author: Matthias König
Date Published: 2016
Publication Type: Not specified
An overview over important lessons from the experience with SBML Level 3 extension for the MultiCellML language.
Creator: Matthias König
Submitter: Matthias König
PAL report during COMBINE2019 SEEK user meeting.
A short overview of the SEEK API and using it to upload caffeine data and images.
The code is available from
https://github.com/matthiaskoenig/ipython_for_SEEK-API
Creator: Matthias König
Submitter: Matthias König
Report about PAL experience and data management solutions in MM-PLF LiSyM.
Creator: Matthias König
Submitter: Matthias König
Our group develops computational models of the liver within the German systems biology projects VLN (Virtual Liver Network) and LiSyM (Systems Medicine of the Liver). In this talk we present our experiences in data and model management in recent years and future directions towards reproducible computational research we plan to implement.
We give an overview over the role of Fairdom and SEEK within our data management solution and how this integrates with and complements other approaches such as
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Creator: Matthias König
Submitter: Matthias König
