Dr. Matthias König

Junior Group Leader
LiSyM - Systems Medicine of the Liver
Institute for Biology, Institute for Theoretical Biology
Humboldt Universität zu Berlin
Philippstraße 13, 10115 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.

COMBINE coordinator (2018-)

Our lab works actively on the standardization and reproducibility of computational models in biology. The 'COmputational Modeling in BIology' NEtwork (COMBINE) is an initiative to coordinate the development of the various community standards and formats for computational models.

SBML editor (2018-2020, 2021-2023)

Systems Biology Markup Language (SBML) is a free and open interchange format for computer models of biological processes. SBML is useful for models of metabolism, cell signaling, and more. It continues to be evolved and expanded by an international community.

SED-ML editor (2017-2019, 2020-2022)

The Simulation Experiment Description Markup Language (SED-ML) is an XML-based format for encoding simulation setups, to ensure exchangeability and reproducibility of simulation experiments.



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).


2022 M. Albadry, S. Höpfl, N. Ehteshamzad, M. König, M. Böttcher, J. Neumann, A. Lupp, O. Dirsch, N. Radde, B. Christ, M. Christ, L.O. Schwen, H. Laue, R. Klopfleisch and Uta Dahmen
Cytochrome p450 enzymes in periportal steatosis: Modulation of drug metabolizing activity but not of pericentral expression pattern
[submitted 2022-09-12]
2022 Grzegorzewski, J., Brandhorst, J., König, M.*
Physiologically based pharmacokinetic (PBPK) modeling of the role of CYP2D6 polymorphism for metabolic phenotyping with dextromethorphan
bioRxiv 2022.08.23.504981; doi: https://doi.org/10.1101/2022.08.23.504981 [Accepted Frontiers Pharmacology, 2022-09-23]
2022 Ramachandran, K.*; König, M.*; Scharm, M.; Nguyen, T.V.N.; Hermjakob, H.; Waltemath, D.; Malik Sheriff, R.S. (* equal contribution)
FAIR Sharing of Reproducible Models of Epidemic and Pandemic Forecast
Preprints 2022, 2022060137 (doi: 10.20944/preprints202206.0137.v1).
2022 Shaikh B, Smith LP, Vasilescu D, Marupilla G, Wilson M, Agmon E, Agnew H, Andrews SS, Anwar A, Beber ME, Bergmann FT, Brooks D, Brusch L, Calzone L, Choi K, Cooper J, Detloff J, Drawert B, Dumontier M, Ermentrout GB, Faeder JR, Freiburger AP, Fröhlich F, Funahashi A, Garny A, Gennari JH, Gleeson P, Goelzer A, Haiman Z, Hasenauer J, Hellerstein JL, Hermjakob H, Hoops S, Ison JC, Jahn D, Jakubowski HV, Jordan R, Kalaš M, König M, Liebermeister W, Sheriff RSM, Mandal S, McDougal R, Medley JK, Mendes P, Müller R, Myers CJ, Naldi A, Nguyen TVN, Nickerson DP, Olivier BG, Patoliya D, Paulevé L, Petzold LR, Priya A, Rampadarath AK, Rohwer JM, Saglam AS, Singh D, Sinha A, Snoep J, Sorby H, Spangler R, Starruß J, Thomas PJ, van Niekerk D, Weindl D, Zhang F, Zhukova A, Goldberg AP, Schaff JC, Blinov ML, Sauro HM, Moraru II, Karr JR.
BioSimulators: a central registry of simulation engines and services for recommending specific tools
Nucleic Acids Res. 2022 May 7:gkac331. doi: 10.1093/nar/gkac331. Epub ahead of print. PMID: 35524558. 2022 Mar 16;
2022 Helena Leal Pujol (supervisor: Matthias König)
A physiologically based model of pravastatin - The role of genotypes and hepatic or renal impairment on the pharmacokinetics of pravastatin
Bachelor Thesis, May 2022
2022 Matthias König*, Leandro H. Watanabe*, Jan Grzegorzewski, and Chris J. Myers
* equal contribution
Dynamic Flux Balance Analysis Models in SBML
bioRxiv 245076; doi: doi.org/10.1101/245076 [submitted]
2022 Ciaran Welsh, Jin Xu, Lucian Smith, Matthias König, Kiri Choi, Herbert M. Sauro
libRoadRunner 2.0: A High-Performance SBML Simulation and Analysis Library
arXiv preprint arXiv:2203.01175. 2022 Feb 26; doi: https://doi.org/10.48550/arXiv.2203.01175
2022 Jan Grzegorzewski, Florian Bartsch, Adrian Köller, and Matthias König
Pharmacokinetics of caffeine: A systematic analysis of reported data for application in metabolic phenotyping and liver function testing
Frontiers in Pharmacology 2022, Vol12; doi: 10.3389/fphar.2021.752826
2021 Adrian Köller, Jan Grzegorzewski, Michael Tautenhahn, Matthias König
Prediction of survival after hepatectomy using a physiologically based pharmacokinetic model of indocyanine green liver function tests
Front. Physiol., 22 November 2021; doi: 10.3389/fphys.2021.730418
2021 Adrian Köller, Jan Grzegorzewski and Matthias König
Physiologically based modeling of the effect of physiological and anthropometric variability on indocyanine green based liver function tests
Front Physiol. 2021 Nov 22;12:757293. doi: 10.3389/fphys.2021.757293. eCollection 2021.
2021 Adrian Köller, Jan Grzegorzewski and Matthias König
24th Surgical Research Days. Eur Surg Res., Abstract: ID 17, Physiological Based Pharmacokinetic Models of Dynamical Liver Function Tests as a Promising Tool in Hepatectomy
2021;62(3):161-220. doi: 10.1159/000518793. Epub 2021 Aug 31. PMID: 34515110.
2021 S. Höpfl, M. König, N. Radde
24th Surgical Research Days. Eur Surg Res., Abstract: ID 101, Bayesian Statistics for Uncertainty Quantification of a Physiologically Based Model of Indocyanine Green Liver Function Tests
2021;62(3):161-220. doi: 10.1159/000518793. Epub 2021 Aug 31. PMID: 34515110.
2021 Bruno Christ∗, Maximilian Collatz*, Uta Dahmen*, Karl-Heinz Herrmann*, Sebastian Höpfl*, Matthias König*, Lena Lambers*, Manja Marz*, Daria Meyer*, Nicole Radde*, Jürgen R. Reichenbach*, Tim Ricken*, and Hans-Michael Tautenhahn* (* equal contribution)
Hepatectomy-Induced Alterations in Hepatic Perfusion and Function - Toward Multi-Scale Computational Modeling for a Better Prediction of Post-hepatectomy Liver Function
Front. Physiol. 2021; doi: 10.3389/fphys.2021.733868
2021 F. Schreiber, P. Gleeson, M. Golebiewski, T. Gorochowski, M. Hucka, S. Keating, M. König, C. Myers, D. Nickerson, D. Walthemath
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2021
J Integr Bioinform. 2021 Oct 22;18(3):20210026. doi: 10.1515/jib-2021-0026. PMID: 34674411
2021 Sükrü Balci (supervisor: Matthias König)
Computational modelling of omeprazole - pharmacokinetics and pharmacodynamics
Bachelor Thesis, October 2021
2021 Takahiro G. Yamada, Kaito Ii, Matthias König, Martina Feierabend, Andreas Dräger, and Akira Funahashi
SBMLWebApp: Web-based Simulation, Steady-State Analysis, and Parameter Estimation of Systems Biology Models
Processes 9, no. 10: 1830. https://doi.org/10.3390/pr9101830 (doi: https://doi.org/10.3390/pr9101830).
2021 Smith, Lucian P., Bergmann, Frank T., Garny, Alan, Helikar, Tomáš, Karr, Jonathan, Nickerson, David, Sauro, Herbert, Waltemath, Dagmar and König, Matthias.
The simulation experiment description markup language (SED-ML): language specification for level 1 version 4
Journal of Integrative Bioinformatics, vol. 18, no. 3, 2021, pp. 20210021. doi: 10.1515/jib-2021-0021, PMID: 35330701
2021 Panchiwala, H.; Shah, S.; Planatscher, H.; Zakharchuk, M.; König, M.; Dräger, A.
The Systems Biology Simulation Core Library
Bioinformatics. 2021 Sep 23:btab669. doi: 10.1093/bioinformatics/btab669. Epub ahead of print. PMID: 34554191.
2021 Matthias König*, Jan Grzegorzewski, Martin Golebiewski, Henning Hermjakob, Mike Hucka, Brett Olivier, Sarah M. Keating, David Nickerson, Falk Schreiber, Rahuman Sheriff, Dagmar Waltemath
Ten Simple Rules for FAIR Sharing of Experimental and Clinical Data with the Modeling Community
Preprints 2021, 2021080303, doi: 10.20944/preprints202108.0303.v2 [Submitted PLoS Computational Biology, 2021-11-19]
2021 John Gennari, Matthias König, Goskel Misirli, Maxwell Neal, David Nickerson, Dagmar Waltemath
OMEX Metadata Specification Version 1.2
[Submitted to JIB, 2021-08-08]
2021 Bilal Shaikh, Andrew Philip Freiburger, Matthias König, Frank T. Bergmann, David P. Nickerson, Herbert M. Sauro, Michael L. Blinov, Lucian P. Smith, Ion I. Moraru, Jonathan R. Karr
SED-ML Validator: tool for debugging simulation experiments
arXiV, 2021, 2106.00844, [Submitted to Bioinformatics 2021-06-02]
2021 Adrian Köller (supervisor: Matthias König)
A Physiologically Based Model of Indocyanine Green Liver Function Tests - Effects of Physiological Factors, Hepatic Disease and Hepatic Surgery
Bachelor Thesis, March 2021
2020 Tim Ricken, Lena Lambers, Bruno Christ, Uta Dahmen, Karl-Heinz Herrmann, Matthias König, Manja Marz, Nicole Radde, Jürgen R. Reichenbach, Lars Ole Schwen & Hans-Michael Tautenhahn
QuaLiPerF – Multi-X Liver Modelling
GACM - German Association for Computational Mechanics Report, winter 2020: No. 13
2020 Florian Bartsch (supervisor: Matthias König)
Computational Modelling of Simvastatin - Effects on HMG-CoA Reductase Activity and Cholesterol
Bachelor Thesis, November 2020
2020 Yannick Duport (supervisor: Matthias König)
Computational Modelling of Midazolam Clearance: Effect of Inhibitors and Inducers
Bachelor Thesis, August 2020
2020 Grzegorzewski J, Brandhorst J, Green K, Eleftheriadou D, Duport Y, Barthorscht F, Köller A, Ke DYJ, De Angelis S, König M.
PK-DB: pharmacokinetics database for individualized and stratified computational modeling
Nucleic Acids Res. 2020 Nov 5:gkaa990. doi: 10.1093/nar/gkaa990. Epub ahead of print. PMID: 33151297
2020 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
Mol Syst Biol. 2020;16(8):e9110. doi:10.15252/msb.20199110
2020 Neal ML, Gennari JH, Waltemath D, Nickerson DP, König M
Open modeling and exchange (OMEX) metadata specification version 1.0
J Integr Bioinform. 2020;/j/jib.ahead-of-print/jib-2020-0020/jib-2020-0020.xml. doi:10.1515/jib-2020-0020
2020 F. Schreiber, B. Sommer, G. Bader, P. Gleeson, M. Golebiewski, T. Gorochowski, M. Hucka, S. Keating, M. König, C. Myers, D. Nickerson, D. Walthemath
Specifications of Standards in Systems and Synthetic Biology:Status and Developments in 2020
J Integr Bioinform. 2020;/j/jib.ahead-of-print/jib-2020-0022/jib-2020-0022.xml; doi:10.1515/jib-2020-0022
2020 D Waltemath, M Golebiewski, M Blinov, P Gleeson, H Hermjakob, E Inau, S Keating, M König, O Krebs, R Malik-Sheriff, D Nickerson, E Oberortner, H Sauro, F Schreiber, L Smith, M Stefan, U Wittig, C Myers
The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE)
J Integr Bioinform. 2020;/j/jib.ahead-of-print/jib-2020-0005/jib-2020-0005.xml. doi:10.1515/jib-2020-0005
2020 L Smith, S Moodie, F Bergmann, C Gillespie, S Keating, M. König, C Myers, M Swat, D Wilkinson, M Hucka
The Distributions Package for SBML Level 3
J Integr Bioinform. 2020 Aug 4;/j/jib.ahead-of-print/jib-2020-0018/jib-2020-0018.xml. doi: 10.1515/jib-2020-0018
2020 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 for standardized genome-scale metabolic model testing
Nat Biotechnol. 2020;38(3):272-276. doi: 10.1038/s41587-020-0446-y
2020 Matthias König
Executable Simulation Model of the Liver
bioRxiv 2020.01.04.894873; doi: https://doi.org/10.1101/2020.01.04.894873 [accepted, 04-2020]
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]