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]