Dr. Matthias König

Junior Group Leader
LiSyM - Systems Medicine of the Liver
Institute for Biology, Institute for Theoretical Biology
Humboldt Universität zu Berlin
Invalidenstraße 43, 10117 Berlin, Germany
+49 30 2093-8450

Institute for Biology  Institute for Theoretical Biology  Humboldt University Berlin

Dr. Matthias König

Matthias König (PhD. in Biophysics) leads an independent junior research group for Systems Biology and Systems Medicine of the liver with focus on metabolic research at the Humboldt University Berlin. His research areas include computational modeling, data science, development of bioinformatics methods and machine learning based on biological, medical and clinical data for predictive modeling of physiological processes and systems. He has been actively involved in the development of SBML, SED-ML and software supporting these standards: Lead-developer of cy3sbml and sbmlutils; co-developer of the SBML simulation software libroadrunner and tellurium.
Key projects are the personalized evaluation of liver function tests and multi-scale modeling of the liver. For more information have a look at our projects.




2018-2020 SBML Editor
Systems Biology Markup Language
2017-2019 SED-ML Editor
Simulation Experiment Description Language

Participation in Research Projects

2016-2020 Junior group leader in Systems Medicine of the Liver project funded by the Federal Ministry of Education and Research (BMBF).
2010-2015 PhD in Systems Biology and Systems Medicine of liver project funded by the Federal Ministry of Education and Research (BMBF).
2005-2010 Student assistant and PhD in Systems Biology and Systems Medicine of liver project funded by the Federal Ministry of Education and Research (BMBF).


2018 König M., Wünsch T., Lill D., Lock JF., Mohr J., Taheri P., Timmer J., Stockmann M.
Computational Modeling of Dynamical Liver Function Tests: LiMAx and Methacetin Breath Test (MBT)
preprint 2018
2018 Choi K., Medley K., König M., Stocking K., Smith L., Gu S., and Sauro HM.
Tellurium: An Extensible Python-based Modeling Environment for Systems and Synthetic Biology
Biosystems. 2018 Jul 24. pii: S0303-2647(18)30125-4. doi: 10.1016/j.biosystems.2018.07.006.
2018 Berndt N., Bulik S., Wallach I., Wünsch T., König M., Stockmann M., Meierhofer M., Holzhütter HG.
HEPATOKIN1: A Biochemistry-Based Model of Liver Metabolism Suited for Applications in Medicine and Pharmacology
Nat Commun. 2018 Jun 19;9(1):2386. doi: 10.1038/s41467-018-04720-9.
2018 Bergmann, FT., Cooper, J., König, M.*, Moraru, I., Nickerson, D., Le Novère N., Olivier, BG., Sahle, S., Smith, L., Waltemath, D.
* corresponding author
Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3)
Journal of Integrative Bioinformatics, 15(1), 2018
2018 Neal, M.; König, M.; Nickerson, D.; Misirli, G.; Kalbasi, R.; Dräger, A.; Atalag, K.; Chelliah, V.; Cooling, M.; Cook, D.; Crook, S.; de Alba, M.; Friedman, S.; Garny, A.; Gennari, J.; Gleeson, P.; Golebiewski, M.; Hucka, M.; Juty, N.; Novère, N. L.; Myers, C.; Olivier, B.; Sauro, H.; Scharm, M.; Snoep, J.; Touré, V.; Wipat, A.; Wolkenhauer, O. & Waltemath, D.
Harmonizing semantic annotations for computational models in biology
bioRxiv 246470; doi: doi.org/10.1101/246470 [Briefings in Bioinformatics, accepted 2018-08-20]
2018 Watanabe L.*, König* M., and Myers C.
* equal contribution
Dynamic Flux Balance Analysis Models in SBML
bioRxiv 245076; doi: doi.org/10.1101/245076 [submitted]
2018 Medley K., Choi K., König M., Smith L., Gu S., Hellerstein J., Sealfon S., and Sauro HM.
Tellurium Notebooks — An Environment for Reproducible Dynamical Modeling in Systems Biology.
PLoS computational biology 14, no. 6 (2018): e1006220.
2017 Christ, B.*, Dahmen, U.*, Herrmann, K.H.*, König, M.*, Reichenbach, J.R*., Ricken, T.*, Schleicher, J.*, Ole Schwen, L.*, Vlaic, S.* and Waschinsky, N.*
* equal contribution
Computational Modeling in Liver Surgery
Frontiers in physiology, 8, p.906; doi: doi.org/10.3389/fphys.2017.00906
2016 König M.*, Oellrich A.*, Waltemath D.*, Dobson R., Hubbard T., and Wolkenhauer O.
* equal contribution
Challenges and opportunities for system biology standards and tools in medical research
ODLS, p1-6, 2016; article
2016 König M.
cy3sabiork: A Cytoscape app for visualizing kinetic data from SABIO-RK
[version 1; referees: awaiting peer review]. F1000Research 2016, 5:1736 (doi: 10.12688/f1000research.9211.1)
2016 Choi K., Medley JK., Cannistra C., König M., Smith L., Stocking K., and Sauro HM.
Tellurium: A Python Based Integrated Environment for Biological Modeling and Simulation
bioRxiv 054601; doi: doi.org/10.1101/054601
2016 Wholecell Consortium (König M.)
Toward community standards and software for whole-cell modeling
IEEE Trans Biomed Eng. 2016 Jun 10. [PubMed]
2015 Kerstin A.*, König M.*, Hoppe A., Thomas M., Müller I., Ebert M., Weng H., Holzhütter HG., Zanger UM., Bode J., Vollmar B. and Dooley S.
* equal contribution
Pathobiochemical signatures of cholestatic liver disease in bile duct ligated mice
BMC Syst Biol. 2015 Nov 20;9(1):83. doi: 10.1186/s12918-015-0229-0 [PubMed]
2015 Werner D., Ricken T., Dahmen U., Dirsch O., Holzhütter HG., König M.
On the Influence of Growth in Perfusion Dependent Biological Systems - at the Example of the Human Liver.
PAMM 15 (1), 119-120, 2015 [doi:10.1002/pamm.201510050]
2015 Somogyi ET., Bouteiller JM., Glazier JA., König M., Medley JK., Swat MH and Sauro HM.
LibRoadRunner: a high performance SBML simulation and analysis library.
Bioinformatics. 2015 Jun 17. pii: btv363. [PubMed]
2014 Ricken T., Werner D., Holzhütter HG., König M., Dahmen U., Dirsch O.
Modeling function-perfusion behavior in liver lobules including tissue, blood, glucose, lactate and glycogen by use of a coupled two-scale PDE-ODE approach.
Biomech Model Mechanobiol. 2014 Sep 19. [doi, PubMed]
2014 König M. and Holzhütter HG.
Homeostasis of blood glucose - Computer simulations of central liver functions.
systembiologie.de 2014; 8:p.53-57 [PDF (de), PDF (en)]
2013 König M., Holzhütter HG., Berndt N.
Metabolic Gradients as Key Regulators in Zonation of Tumor Energy Metabolism: A Tissue-scale Model Based Study.
Biotechnol J. 2013 Apr 16. [doi, PubMed]
2012 König M. and Holzhütter HG.
Kinetic Modeling of Human Hepatic Glucose Metabolism in T2DM Predicts Higher Risk of Hypoglycemic Events in Rigorous Insulin Therapy
J Biol Chem. 2012 [DOI 10.1074/jbc.M112.382069]
2012 König M., Dräger A. and Holzhütter HG.
CySBML: a Cytoscape plugin for SBML
Bioinformatics. 2012 Jul 5. [PubMed]
2012 König M., Bulik S. and Holzhütter HG.
Quantifying the Contribution of the Liver to the Homeostasis of Plasma Glucose: A Detailed Kinetic Model of Hepatic Glucose Metabolism Integrated with the Hormonal Control by Insulin, Glucagon and Epinephrine
PLoS Comput Biol. 2012 Jun;8(6):e1002577. Epub 2012 Jun 21. [PubMed]
2011 Herling A, König M, Bulik S, Holzhütter HG.
Enzymatic Features of the Glucose Metabolism in Tumor Cells.
FEBS J. 2011 Jul;278(14):2436-59. [doi, PubMed]
2011 König M. and Holzhütter HG.
FluxViz - Cytoscape Plug-in for Vizualisation of Flux Distributions in Networks
Genome Informatics 2010, Vol.24, p.96-103 [PubMed]
2010 Gille C, Bölling C, Hoppe A, Bulik S, Hoffmann S, Hübner K, Karlstädt A, Ganeshan R, König M, Rother K, Weidlich M, Behre J, Holzhütter HG.
HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology.
Mol Syst Biol., 6:411. [PubMed]