Dr. Matthias König

Junior Group Leader
LiSyM - Systems Medicine of the Liver
Institute for Biology, Institute for Theoretical Biology
Humboldt Universität zu Berlin
Invalidenstraße 110, 10117 Berlin, Germany
+49 30 2093-98435

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).


2019 Christian Lieven, Moritz Emanuel Beber, Brett G. Olivier, Frank T. Bergmann, Meric Ataman, Parizad Babaei, Jennifer A. Bartell, Lars M. Blank, Siddharth Chauhan, Kevin Correia, Christian Diener, Andreas Dräger, Birgitta Elisabeth Ebert, Janaka N. Edirisinghe, Jose P. Faria, Adam Feist, Georgios Fengos, Ronan M. T. Fleming, Beatriz Garcia-Jimenez, Vassily Hatzimanikatis, Wout van Helvoirt, Christopher Henry, Henning Hermjakob, Markus J. Herrgard, Hyun Uk Kim, Zachary King, Jasper Jan Koehorst, Matthias König, Steffen Klamt, Edda Klipp, Meiyappan Lakshmanan, Nicolas Le Novere, Dong-Yup Lee, Sang Yup Lee, Sunjae Lee, Nathan E. Lewis, Hongwu Ma, Daniel Machado, Radhakrishnan Mahadevan, Paulo Maia, Adil Mardinoglu, Greg L. Medlock, Jonathan Monk, Jens Nielsen, Lars K. Nielsen, Juan Nogales, Intawat Nookaew, Osbaldo Resendis, Bernhard Palsson, Jason A. Papin, Kiran Raosaheb Patil, Mark Poolman, Nathan D. Price, Anne Richelle, Isabel Rocha, Benjamin Sanchez, Peter Schaap, Rahuman S. Malik Sheriff, Saeed Shoaie, Nikolaus Sonnenschein, Bas Teusink, Paulo Vilaca, Jon Olav Vik, Judith A. Wodke, Joana C. Xavier, Qianqian Yuan, Maksim Zakhartsev, Cheng Zhang
Memote: A community-driven effort towards a standardized genome-scale metabolic model test suite
Nature Biotechnology [accepted, 2019-11-04]
2019 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, and SBML Community members
SBML Level 3: an extensible format for the exchange and reuse of biological models
Molecular Systems Biology [11-2019, in revision]
2019 Jan Grzegorzewski, Janosch Brandhorst, Dimitra Eleftheriadou, Kathleen Green, Matthias König
PK-DB: PharmacoKinetics DataBase for Individualized and Stratified Computational Modeling
bioRxiv 760884; doi: 10.1101/760884 [09-09-2019]
2019 Lambers L., Ricken T., and König M.
Model Order Reduction (MOR) of Function-Perfusion-Growth Simulation in the Human Fatty Liver via Artificial Neural Network (ANN)
Proceedings in Applied Mathematics & Mechanics, PAMM, 10.1002/pamm.201900429, 2019
2019 F Schreiber, G Bader, P Gleeson, M Golebiewski, M Hucka, SM Keating, M König, C Myers, D Nickerson, B Sommer, D Waltemath
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019
J Integr Bioinform. 2019 Jul 13;16(2); 10.1515/jib-2019-0035
2019 M. Hucka, F. Bergmann, C. Chaouiya, A. Dräger, S. Hoops, S. Keating, M. König, N Le Novere, C. Myers, B. Olivier, S. Sahle, J. Schaff, R. Sheriff, L. Smith, D. Waltemath, D. Wilkinson, F. Zhang
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core
J Integr Bioinform. 2019 Jun 20;16(2); 10.1515/jib-2019-0021
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)
J Integr Bioinform. 2018 Mar 19;15(1); doi: 10.1515/jib-2017-0086
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
Brief Bioinform. 2018 Nov 21. doi: 10.1093/bib/bby087
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.; doi: 10.1371/journal.pcbi.1006220
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: 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]