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.
Most of the information related to LiSyM is managed within the FairdomHub at
https://www.fairdomhub.org/people/678
https://www.fairdomhub.org/projects/46
SEEK ID: https://seek.lisym.org/people/17
Location: Germany
ORCID: https://orcid.org/0000-0003-1725-179X
Joined: 28th Apr 2017
Roles
PAL
- LiSyM PALs
- Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF)
- LiSyM Pillar IV: Liver Function Diagnostics (LiSyM-LiFuDi)
- LiSyM network
Project administrator
Asset housekeeper
Related items
- Programmes (2)
- Projects (5)
- Institutions (1)
- Investigations (4)
- Studies (2)
- Assays (14)
- Data files (28+5)
- Publications (23)
- Presentations (17+2)
- Events (1)
- Documents (0+1)
LiSyM-Krebs ist ein nationales Forschungsnetz zur Früherkennung und Prävention von Leberkrebs, das unter Verwendung des systemmedizinischen Forschungsansatzes die komplexen, dynamischen Prozesse der Krankheitsprogression analysiert, um ausgehend von den Erkenntnissen aus dem Forschungsnetz LiSyM die Entstehung von Leberkrebs besser zu verstehen, vorherzusagen und im besten Fall sogar zu verhindern. LiSyM-Krebs setzt die erfolgreichen Forschungsaktivitäten der BMBF-Vorgängerprogramme ...
Projects: LiSyM-Krebs Partnering, Forschungsnetzwerk LiSyM-Krebs, SMART-NAFLD, DEEP-HCC network, C-TIP-HCC network
Web page: https://www.lisym-cancer.org
Liver Systems Medicine : striving to develop non-invasive methods for diagnosing and treating NAFLD by combining mathematical modeling and biological research. LiSyM, is a multidisciplinary research network, in which molecular and cell biologists, clinical researchers, pharmacologists and experts in mathematical modeling examine the liver in its entirety. LiSyM research focuses on the metabolic liver disease non-alcoholic fatty liver disease (NAFLD), which includes non-alcoholic steatohepatitis ...
Projects: LiSyM Core Infrastructure and Management (LiSyM-PD), LiSyM Pillar I: Early Metabolic Injury (LiSyM-EMI), LiSyM Pillar II: Chronic Liver Disease Progression (LiSyM-DP), LiSyM Pillar III: Regeneration and Repair in Acute-on-Chronic Liver Failure (LiSyM-ACLF), LiSyM Pillar IV: Liver Function Diagnostics (LiSyM-LiFuDi), Model Guided Pharmacotherapy In Chronic Liver Disease (LiSyM-MGP), Molecular Steatosis - Imaging & Modeling (LiSyM-MSIM), The Hedgehog Signalling Pathway (LiSyM-JGMMS), Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF), LiSyM PALs, Project Management PTJ, LiSyM network, LiSyM Scientific Leadership Team (LiSyM-LT)
Web page: https://www.lisym.org/
Disorders of the liver show up through changes in blood tests. These blood tests indicate markers for events taking place in the liver. Usually studies of liver tissue cannot be performed: as liver samples would need to be obtained through a liver biopsy, and this procedure is not without risk, therefore these samples are usually unavailable. Complex metabolism models based on existing and new scientific data can simulate changes in the liver caused by disease. They often reveal unknown relationships ...
Programme: LiSyM: Liver Systems Medicine
Public web page: http://www.lisym.org/our-work/pillar-research/the-liver-is-very-patient
Start date: 1st Jan 2016
Organisms: Homo sapiens
This generic project is intended to be a forum for all LiSyM partner and external stakeholders interested in participating in the BMBF initiative LiSyM-Krebs.
Programme: LiSyM-Krebs - Systemmedizinisches Forschungsnetz zur Früherkennung und Prävention von Leberkrebs
Public web page: https://www.ptj.de/projektfoerderung/gesundheitsforschung/lisym-krebs
Organisms: Not specified
This comprises the whole LiSyM network
Programme: LiSyM: Liver Systems Medicine
Public web page: http://www.lisym.org
Start date: 1st Jan 2016
Organisms: Rattus norvegicus, Rattus rattus, Mus musculus, Homo sapiens
This is a generic project that comprises all LiSyM data management PALs and associated FAIRDOM PALs, as well as the LiSyM data management team. Olga Maja Alain
Programme: LiSyM: Liver Systems Medicine
Public web page: Not specified
Organisms: Not specified
Dr. Matthias König (Humboldt University, Berlin) models the human liver on the computer. His simulations show the extent of individual differences in liver function and the external factors influencing it. König has shown that smoking falsifies the result of an important liver test (LiMAx). With his models, drug doses can be calculated so that they can be administered in doses that do not harm the liver.
Programme: LiSyM: Liver Systems Medicine
Public web page: https://livermetabolism.com
Start date: 1st Jan 2016
Organisms: Homo sapiens
We face a crisis in reproducibility, where it is impossible to believe most of the computational results shown in conferences and papers. Recent replication efforts and theoretical considerations indicate that most published research findings in biomedical research are wrong. This is especially problematic for the translation of computational models into the clinics. Modelling standards, software, and community initiatives are fundamental for reproducibility in systems biology and systems medicine. ...
Snapshots: No snapshots
Test for SEEK API upload.
Submitter: Matthias König
Studies: PKDB Caffeine Study
Assays: Digitized pharmacokinetics data (Akinyinka2000), Digitized pharmacokinetics data (Amchin1999), Digitized pharmacokinetics data (Blanchard1983a), Digitized pharmacokinetics data (Haller2002), Digitized pharmacokinetics data (Healy1991), Digitized pharmacokinetics data (Hetzler1990), Digitized pharmacokinetics data (Jeppesen1996), Digitized pharmacokinetics data (Kakuda2014), Digitized pharmacokinetics data (Kaplan1997), Digitized pharmacokinetics data (Magnusson2008), Digitized pharmacokinetics data (Oh2012), Digitized pharmacokinetics data (Perera2011), Digitized pharmacokinetics data (Spigset1999a), Digitized pharmacokinetics data (Tanaka2014)
Snapshots: No snapshots
Introduction: The field of pharmacokinetics describe the kinetics of substances administered to the body, consisting of absorption, distribution, metabolization and elimination (ADME) of the substance. An important use case is the testing of liver function via test substances like caffeine, methacetin or galactose in dynamical liver function tests. Understanding the kinetics of test substances and drugs is crucial to evaluate therapeutic outcome and diagnostic value.
Results: Physiologically based ...
Submitter: Matthias König
Studies: PK-DB: PharmacoKinetics DataBase for Individualized and Stratified Compu...
Assays: No Assays
Snapshots: No snapshots
Collection of Presentations and Posters from Dresden LiSyM Jamboree (LiFuDi & MM-PLF)
Pillar IV Jamboree • (10 min) Introduction to Pillar IV (Hergo Holzhütter) • (20 min) Precise Measurement of Hepatic Elasticity for Fibrosis Detection (Christian Hudert) • (20 min) Tissue Scale Metabolic Modelling (Sascha Bulik) • (10 min) Multi-scale models for liver function tests (Matthias König) • (20 min) Improving the diagnostic precision of the 13C-methacetin dynamic liver function test (LiMAx) (Tilo ...
Snapshots: No snapshots
A multitude of pharmacokinetics studies have been published. However, due to the lack of an open database, pharmacokinetics data, as well as the corresponding meta-information, have been difficult to access. We present PK-DB (https://develop.pk-db.com), an open database for pharmacokinetics information from clinical trials including pre-clinical research. PK-DB provides curated information on (i) characteristics of studied patient cohorts and subjects (e.g. age, bodyweight, smoking status); (ii) ...
Submitter: Matthias König
Investigation: Stratification and Personalization of Computati...
Assays: No Assays
Snapshots: No snapshots
Pharmacokinetics data set for caffeine
Submitter: Matthias König
Investigation: Caffeine investigation
Assays: Digitized pharmacokinetics data (Akinyinka2000), Digitized pharmacokinetics data (Amchin1999), Digitized pharmacokinetics data (Blanchard1983a), Digitized pharmacokinetics data (Haller2002), Digitized pharmacokinetics data (Healy1991), Digitized pharmacokinetics data (Hetzler1990), Digitized pharmacokinetics data (Jeppesen1996), Digitized pharmacokinetics data (Kakuda2014), Digitized pharmacokinetics data (Kaplan1997), Digitized pharmacokinetics data (Magnusson2008), Digitized pharmacokinetics data (Oh2012), Digitized pharmacokinetics data (Perera2011), Digitized pharmacokinetics data (Spigset1999a), Digitized pharmacokinetics data (Tanaka2014)
Snapshots: No snapshots
Data digitized from publication.
Hetzler1990 Description
Submitter: Matthias König
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Caffeine investigation
Study: PKDB Caffeine Study
Organisms: Homo sapiens
SOPs: No SOPs
Data files: CSV (Hetzler1990), PNG (Hetzler1990)
Snapshots: No snapshots
Data digitized from publication.
Spigset1999a Description
Submitter: Matthias König
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Caffeine investigation
Study: PKDB Caffeine Study
Organisms: Homo sapiens
SOPs: No SOPs
Data files: CSV (Spigset1999a), PNG (Spigset1999a)
Snapshots: No snapshots
Data digitized from publication.
Akinyinka2000 Description
Submitter: Matthias König
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Caffeine investigation
Study: PKDB Caffeine Study
Organisms: Homo sapiens
SOPs: No SOPs
Data files: CSV (Akinyinka2000), PNG (Akinyinka2000)
Snapshots: No snapshots
Data digitized from publication.
Perera2011 Description
Submitter: Matthias König
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Caffeine investigation
Study: PKDB Caffeine Study
Organisms: Homo sapiens
SOPs: No SOPs
Data files: CSV (Perera2011), PNG (Perera2011)
Snapshots: No snapshots
Data digitized from publication.
Amchin1999 Description
Submitter: Matthias König
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Caffeine investigation
Study: PKDB Caffeine Study
Organisms: Homo sapiens
SOPs: No SOPs
Data files: CSV (Amchin1999), PNG (Amchin1999)
Snapshots: No snapshots
Digitized pharmacokinetics data.
Creator: Matthias König
Submitter: Matthias König
Investigations: Caffeine investigation
Studies: PKDB Caffeine Study
Digitized pharmacokinetics data.
Creator: Matthias König
Submitter: Matthias König
Investigations: Caffeine investigation
Studies: PKDB Caffeine Study
Digitized pharmacokinetics data.
Creator: Matthias König
Submitter: Matthias König
Investigations: Caffeine investigation
Studies: PKDB Caffeine Study
Digitized pharmacokinetics data.
Creator: Matthias König
Submitter: Matthias König
Investigations: Caffeine investigation
Studies: PKDB Caffeine Study
Digitized pharmacokinetics data.
Creator: Matthias König
Submitter: Matthias König
Investigations: Caffeine investigation
Studies: PKDB Caffeine Study
Abstract (Expand)
Authors: J. Grzegorzewski, J. Brandhorst, K. Green, D. Eleftheriadou, Y. Duport, F. Barthorscht, A. Koller, D. Y. J. Ke, S. De Angelis, M. Konig
Date Published: 5th Nov 2020
Publication Type: Journal
PubMed ID: 33151297
Citation: Nucleic Acids Res. 2020 Nov 5. pii: 5957165. doi: 10.1093/nar/gkaa990.
Abstract (Expand)
Authors: Lucian P. Smith, Stuart L. Moodie, Frank T. Bergmann, Colin Gillespie, Sarah M. Keating, Matthias König, Chris J. Myers, Maciek J. Swat, Darren J. Wilkinson, Michael Hucka
Date Published: 1st Aug 2020
Publication Type: Journal
Abstract (Expand)
Authors: SM Keating, D Waltemath, M König, F Zhang, A Dräger, C Chaouiya, FT Bergmann, A Finney, CS Gillespie, T Helikar, S Hoops, RS Malik-Sheriff, SL Moodie, II Moraru, CJ Myers, A Naldi, BG Olivier, S Sahle, JC Schaff, LP Smith, MJ Swat, DT, L Watanabe, DJ Wilkinson, ML Blinov, K Begley, JR Faeder, HF Gómez, TM Hamm, Y Inagaki, W Liebermeister, AL Lister, D Lucio, E Mjolsness, CJ Proctor, K Raman, N Rodriguez, CA Shaffer, BE Shapiro, J Stelling, N Swainston, N Tanimura, J Wagner, M Meier-Schellersheim, HM Sauro, B Palsson, H Bolouri, H Kitano, Akira Funahashi, H Hermjakob, JC Doyle, M Hucka, SBML Community members
Date Published: 1st Jul 2020
Publication Type: Journal
Citation: Mol Syst Biol.
Abstract
Author: Matthias König
Date Published: 1st Jul 2020
Publication Type: Misc
Citation:
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
Citation: Journal of Integrative Bioinformatics 17(2-3)
PK-DB: PharmacoKinetics DataBase for Individualized and Stratified Computational Modeling Jan Grzegorzewski, Janosch Brandhorst, Dimitra Eleftheriadou, Kathleen Green, Matthias König bioRxiv 760884; doi: https://doi.org/10.1101/760884
Creators: Matthias König, Jan Grzegorzewski
Submitter: Matthias König
We face a reproducibility crisis and computational science, with most published models neither being accessible nor reproducible. The Systems Biology Markup Language (SBML) is the de facto standard format for encoding pathway based models, which provides a means for exchanging process based models between researchers and tools. The talk gives an overview of SBML and SBML-based tools.
Creator: Matthias König
Submitter: Matthias König
Assessment of liver function is a key task in hepatology but accurate quantification of hepatic function has remained a clinical challenge. Dynamic liver function tests are a promising tool for the non-invasive evaluation of liver function in vivo. Quantitative dynamical liver function tests evaluate the function of the liver via the clearance of a given test substance, thereby providing in vivo information on the metabolic capacity of the liver. Here, we present recent results in establishing ...
Creator: Matthias König
Submitter: Matthias König
Hünfeld 2018 presention on reproducible research and open science.
Creator: Matthias König
Submitter: Matthias König
Improved evaluation of caffeine-based dynamical liver function tests by accounting for lifestyle and pharmacological modifiers like smoking and oral contraceptive use
Matthias König1,*, Ute Hofmann2, Jan Grzegorzewski1, Reinhold Kerb2, Svitlana Igel2, Elke Schäffeler2 and Matthias Schwab2,3
1Institute for Theoretical Biology, Institute of Biology, Humboldt University, Berlin, Germany, koenigmx@hu-berlin.de, orcid.org/0000-0003-1725-179X 2Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, ...
Creator: Matthias König
Submitter: Matthias König
Modeling tutorial as part of the 1st LiSyM Retreat Meeting in Hünfeld (20-22 November 2017).
This tutorial gives a quick introduction into standards used in computational modeling and visualizes, simulates and analysis showcase example models. A basic introduction to simple kinetic models is provided.
The latest material is available from https://github.com/matthiaskoenig/lisym-tutorial under https://github.com/matthiaskoenig/lisym-tutorial/releases. The presentation is available from the within ...
Start Date: 21st Nov 2017
End Date: 22nd Nov 2017
Event Website: https://github.com/matthiaskoenig/lisym-tutorial
Country: Not specified
City: Not specified