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 Nature Communications [accepted 05-2018]
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, in revision]
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		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 [accepted, 2017-07-17]
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]