Dieses Bild zeigt Matthias König

Matthias König

Herr Dr. rer. nat.

Gruppenleiter Computergestützte Biomechanik, Wissenschaftler
Institut für Statik und Dynamik der Luft- und Raumfahrtkonstruktionen

Kontakt

Persönlicher Webex-Raum
 +49 711 685 63706

Pfaffenwaldring 27
70569 Stuttgart
Deutschland

  1. 2026

    1. Elias, M., Myshkina, M., Nemitz, N., & König, M. (2026). Reproducibility of a Physiologically Based Pharmacokinetic and Pharmacodynamic (PBPK/PD) Model of Dapagliflozin. https://doi.org/10.36903/physiome.31368556
    2. Myshkina, M., Elias, M., Tensil, E., & König, M. (2026). Reproducibility of a Digital Twin of the Angiotensin II Receptor Blocker Losartan. https://doi.org/10.36903/physiome.31359823
    3. Nemitz, N., Elias, M., & König, M. (2026). A Physiologically Based Pharmacokinetic and Pharmacodynamic (PBPK/PD) Model of Dapagliflozin in Type 2 Diabetes Mellitus: The Effect of Dosing, Hepatorenal Impairment, and Food. Pharmaceutics, 18, Article 3. https://doi.org/10.3390/pharmaceutics18030287
    4. Tensil, E., Myshkina, M., & König, M. (2026). A Digital Twin of the Angiotensin II Receptor Blocker Losartan: Physiologically Based Modeling of Blood Pressure Regulation. Pharmaceutics, 18, Article 2. https://doi.org/10.3390/pharmaceutics18020262
    5. Tereshchuk, V., Elias, M., & König, M. (2026). A Digital Twin of Canagliflozin Pharmacokinetics and Pharmacodynamics in Type 2 Diabetes Mellitus. https://doi.org/10.20944/preprints202601.2095.v1

  2. 2025

    1. Nemitz, N., Elias, M., & König, M. (2025). A Digital Twin of Dapagliflozin Pharmacokinetics and Pharmacodynamics in Type 2 Diabetes Mellitus: Modeling Variability in Dosing, Hepatorenal Impairment, and Food Effects. https://doi.org/10.20944/preprints202511.0981.v1
    2. Tensil, E., & König, M. (2025). A Digital Twin of the Angiotensin II Receptor Blocker Losartan: Physiologically Based Modeling of Blood Pressure Regulation. https://doi.org/10.20944/preprints202510.1254.v1
    3. Elias, M., & König, M. (2025). Reproducibility of a Digital Twin of Glimepiride for Personalized and Stratified Diabetes Treatment. Physiome. https://doi.org/10.36903/physiome.28379193
    4. Myshkina, M., Casabianca, E., Schnurpel, A., Ricken, T., Tautenhahn, H.-M., & König, M. (2025). Assessing the Impact of AI and Digital Twins on Clinical Decision-Making in Hepatology and Hepatobiliary Surgery. https://doi.org/10.20944/preprints202509.1164.v1
    5. Bafna, M., König, M., Saalfeld, S., Moulisova, V., Liska, V., Dahmen, U., & Albadry, M. (2025). Automated Segmentation of Hepatic Vessels and Lobules in Whole-Slide Images Using U-Net Models. https://doi.org/10.1101/2025.09.08.674181
    6. Casabianca, E., Myshkina, M., & König, M. (2025). A Systems Pharmacology Approach to Rivaroxaban: Physiologically Based Modeling of Pharmacokinetics and Coagulation Dynamics. https://doi.org/10.20944/preprints202507.1945.v1
    7. Baum, P., Ebert, T., Klöting, N., Krupka, S., König, M., Paeschke, S., Stock, P., Bulc, M., Blüher, M., Palus, K., Nowicki, M., & Kosacka, J. (2025). Inflammation and autophagy in peripheral nerves of rodent models with metabolic syndrome and type 2 diabetes mellitus. Neuroscience Research. https://doi.org/10.1016/j.neures.2025.04.002
    8. Elias, M., & König, M. (2025). A Digital Twin of Glimepiride for Personalized and Stratified Diabetes Treatment. https://doi.org/10.20944/preprints202506.1264.v1
    9. Balaur, I., Nickerson, D. P., Welter, D., Wodke, J. A. H., Ancien, F., Gebhardt, T., Grouès, V., Hermjakob, H., König, M., Radde, N., Rougny, A., Schneider, R., Malik-Sheriff, R. S., Shiferaw, K. B., Stefan, M., Satagopam, V., & Waltemath, D. (2025). FAIRification of computational models in biology. https://doi.org/10.1101/2025.03.21.644517

  3. 2024

    1. Raman, K., Kratochvíl, M., Olivier, B. G., König, M., Sengupta, P., Baskaran, D. K. K., Nguyen, T. V. N., Lobo, D., Wilken, S. E., Tiwari, K. K., Raghu, A. K., Palanikumar, I., Raajaraam, L., Ibrahim, M., Balakrishnan, S., Umale, S., Bergmann, F., Malpani, T., Satagopam, V. P., et al. (2024). FROG Analysis Ensures the Reproducibility of Genome Scale Metabolic Models. https://doi.org/10.1101/2024.09.24.614797
    2. Golebiewski, M., Bader, G., Gleeson, P., Gorochowski, T. E., Keating, S. M., König, M., Myers, C. J., Nickerson, D. P., Sommer, B., Waltemath, D., & Schreiber, F. (2024). Specifications of standards in systems and synthetic biology: status, developments, and tools in 2024. Journal of Integrative Bioinformatics. https://doi.org/10.1515/jib-2024-0015
    3. Smith, L. P., Bergmann, F. T., Garny, A., Helikar, T., Karr, J., Nickerson, D., Sauro, H., Waltemath, D., & König, M. (2024). The simulation experiment description markup language (SED-ML): language specification for level 1 version 5. Journal of Integrative Bioinformatics. https://doi.org/10.1515/jib-2024-0008
    4. Gerhäusser, S., Lambers, L., Mandl, L., Franquinet, J., Ricken, T., & König, M. (2024). Simulation of zonation-function relationships in the liver using coupled multiscale models: Application to drug-induced liver injury. https://doi.org/10.1101/2024.03.26.586870

  4. 2023

    1. Mallol, B. S., Grzegorzewski, J., Tautenhahn, H.-M., & König, M. (2023). Insights into Intestinal P-glycoprotein Function using Talinolol: A PBPK Modeling Approach. https://doi.org/10.1101/2023.11.21.568168
    2. Küttner, J., Grzegorzewski, J., Tautenhahn, H.-M., & König, M. (2023). A physiologically based pharmacokinetic model for CYP2E1 phenotyping via chlorzoxazone. https://doi.org/10.1101/2023.04.12.536571
    3. König, M., Gleeson, P., Golebiewski, M., Gorochowski, T. E., Hucka, M., Keating, S. M., Myers, C. J., Nickerson, D. P., Sommer, B., Waltemath, D., & Schreiber, F. (2023). Specifications of standards in systems and synthetic biology: status and developments in 2022 and the COMBINE meeting 2022. Journal of Integrative Bioinformatics. https://doi.org/10.1515/jib-2023-0004
    4. Anton, M., Almaas, E., Benfeitas, R., Benito-Vaquerizo, S., Blank, L. M., Dräger, A., Hancock, J. M., Kittikunapong, C., König, M., Li, F., Liebal, U. W., Lu, H., Ma, H., Mahadevan, R., Mardinoglu, A., Nielsen, J., Nogales, J., Pagni, M., Papin, J. A., et al. (2023). standard-GEM: standardization of open-source genome-scale metabolic models. https://doi.org/10.1101/2023.03.21.512712
    5. Maheshvare, M. D., Raha, S., König, M., & Pal, D. (2023). A Consensus Model of Glucose-Stimulated Insulin Secretion in the Pancreaticβ-Cell. https://doi.org/10.1101/2023.03.10.532028
    6. Bartsch, F., Grzegorzewski, J., Pujol, H. L., Tautenhahn, H.-M., & König, M. (2023). Simvastatin therapy in different subtypes of hypercholesterolemia – a physiologically based modelling approach. https://doi.org/10.1101/2023.02.01.23285358
    7. Welsh, C., Xu, J., Smith, L., König, M., Choi, K., & Sauro, H. M. (2023). libRoadRunner 2.0: a high performance SBML simulation and analysis library. Bioinformatics. https://doi.org/10.1093/bioinformatics/btac770

  5. 2022

    1. Grzegorzewski, J., Brandhorst, J., & König, M. (2022). Physiologically based pharmacokinetic (PBPK) modeling of the role of CYP2D6 polymorphism for metabolic phenotyping with dextromethorphan. https://doi.org/10.1101/2022.08.23.504981
    2. Panchiwala, H., Shah, S., Planatscher, H., Zakharchuk, M., König, M., & Dräger, A. (2022). The systems biology simulation core library. Bioinformatics. https://doi.org/10.1093/bioinformatics/btab669

  6. 2021

    1. König, M., Grzegorzewski, J., Golebiewski, M., Hermjakob, H., Hucka, M., Olivier, B., Keating, S., Nickerson, D., Schreiber, F., Sheriff, R., & Waltemath, D. (2021). Ten Simple Rules for FAIR Sharing of Experimental and Clinical Data with the Modeling Community. https://doi.org/10.20944/preprints202108.0303.v2
    2. Smith, L. P., Bergmann, F. T., Garny, A., Helikar, T., Karr, J., Nickerson, D., Sauro, H., Waltemath, D., & König, M. (2021). The simulation experiment description markup language (SED-ML): language specification for level 1 version 4. Journal of Integrative Bioinformatics. https://doi.org/10.1515/jib-2021-0021
    3. Yamada, T. G., Ii, K., König, M., Feierabend, M., Dräger, A., & Funahashi, A. (2021). SBMLWebApp: Web-Based Simulation, Steady-State Analysis, and Parameter Estimation of Systems Biology Models. Processes. https://doi.org/10.3390/pr9101830
    4. Schreiber, F., Gleeson, P., Golebiewski, M., Gorochowski, T. E., Hucka, M., Keating, S. M., König, M., Myers, C. J., Nickerson, D. P., Sommer, B., & Waltemath, D. (2021). Specifications of standards in systems and synthetic biology: status and developments in 2021. Journal of Integrative Bioinformatics, 18, Article 3. https://doi.org/10.1515/jib-2021-0026
    5. Gennari, J. H., König, M., Misirli, G., Neal, M. L., Nickerson, D. P., & Waltemath, D. (2021). OMEX metadata specification (version 1.2). Journal of Integrative Bioinformatics, 18, Article 3. https://doi.org/10.1515/jib-2021-0020
    6. Köller, A., Grzegorzewski, J., & König, M. (2021). Physiologically based modeling of the effect of physiological and anthropometric variability on indocyanine green based liver function tests. https://doi.org/10.1101/2021.08.11.455999
    7. König, M., Grzegorzewski, J., Golebiewski, M., Hermjakob, H., Hucka, M., Olivier, B., Keating, S., Nickerson, D., Schreiber, F., Sheriff, R., & Waltemath, D. (2021). Ten Simple Rules for Sharing Experimental and Clinical Data with the Modeling Community. https://doi.org/10.20944/preprints202108.0303.v1
    8. Grzegorzewski, J., Bartsch, F., Köller, A., & König, M. (2021). Pharmacokinetics of caffeine: A systematic analysis of reported data for application in metabolic phenotyping and liver function testing. https://doi.org/10.1101/2021.07.12.452094
    9. Köller, A., Grzegorzewski, J., Tautenhahn, M., & König, M. (2021). Prediction of survival after hepatectomy using a physiologically based pharmacokinetic model of indocyanine green liver function tests. https://doi.org/10.1101/2021.06.15.448411

  7. 2020

    1. Panchiwala, H., Shah, S., Planatscher, H., Zakharchuk, M., König, M., & Dräger, A. (2020). The Systems Biology Simulation Core Library. https://doi.org/10.20944/preprints202012.0296.v1
    2. Grzegorzewski, J., Brandhorst, J., Green, K., Eleftheriadou, D., Duport, Y., Barthorscht, F., Köller, A., Ke, D. Y. J., Angelis, S. D., & König, M. (2020). PK-DB: pharmacokinetics database for individualized and stratified computational modeling. Nucleic Acids Research. https://doi.org/10.1093/nar/gkaa990
    3. Keating, S. M., Waltemath, D., König, M., Zhang, F., Dräger, A., Chaouiya, C., Bergmann, F. T., Finney, A., Gillespie, C. S., Helikar, T., Hoops, S., Malik-Sheriff, R. S., Moodie, S. L., Moraru, I. I., Myers, C. J., Naldi, A., Olivier, B. G., Sahle, S., Schaff, J. C., et al. (2020). SBML Level 3: an extensible format for the exchange and reuse of biological models. Molecular Systems Biology, 16, Article 8. https://doi.org/10.15252/msb.20199110
    4. Smith, L. P., Moodie, S. L., Bergmann, F. T., Gillespie, C., Keating, S. M., König, M., Myers, C. J., Swat, M. J., Wilkinson, D. J., & Hucka, M. (2020). Systems Biology Markup Language (SBML) Level 3 Package: Distributions, Version 1, Release 1. Journal of Integrative Bioinformatics, 17, Article 2–3. https://doi.org/10.1515/jib-2020-0018
    5. Waltemath, D., Golebiewski, M., Blinov, M. L., Gleeson, P., Hermjakob, H., Hucka, M., Inau, E. T., Keating, S. M., König, M., Krebs, O., Malik-Sheriff, R. S., Nickerson, D., Oberortner, E., Sauro, H. M., Schreiber, F., Smith, L., Stefan, M. I., Wittig, U., & Myers, C. J. (2020). The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE). Journal of Integrative Bioinformatics, 17, Article 2–3. https://doi.org/10.1515/jib-2020-0005
    6. Neal, M. L., Gennari, J. H., Waltemath, D., Nickerson, D. P., & König, M. (2020). Open modeling and exchange (OMEX) metadata specification version 1.0. Journal of Integrative Bioinformatics, 17, Article 2–3. https://doi.org/10.1515/jib-2020-0020
    7. König, M. (2020). Executable Simulation Model of the Liver. https://doi.org/10.1101/2020.01.04.894873

  8. 2019

    1. Grzegorzewski, J., Brandhorst, J., Eleftheriadou, D., Green, K., & König, M. (2019). PK-DB: PharmacoKinetics DataBase for Individualized and Stratified Computational Modeling. https://doi.org/10.1101/760884
    2. Schreiber, F., Sommer, B., Bader, G. D., Gleeson, P., Golebiewski, M., Hucka, M., Keating, S. M., König, M., Myers, C., Nickerson, D., & Waltemath, D. (2019). Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019. Journal of Integrative Bioinformatics, 16, Article 2. https://doi.org/10.1515/jib-2019-0035
    3. Hucka, M., Bergmann, F. T., Chaouiya, C., Dräger, A., Hoops, S., Keating, S. M., König, M., Novere, N. L., Myers, C. J., Olivier, B. G., Sahle, S., Schaff, J. C., Sheriff, R., Smith, L. P., Waltemath, D., Wilkinson, D. J., & Zhang, F. (2019). The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2. Journal of Integrative Bioinformatics, 16, Article 2. https://doi.org/10.1515/jib-2019-0021

  9. 2018

    1. Neal, M. L., König, M., Nickerson, D., Misirli, G., Kalbasi, R., Dräger, A., Atalag, K., Chelliah, V., Cooling, M. T., Cook, D. L., Crook, S., de Alba, M., Friedman, S. H., Garny, A., Gennari, J. H., Gleeson, P., Golebiewski, M., Hucka, M., Juty, N., et al. (2018). Harmonizing semantic annotations for computational models in biology. Briefings in Bioinformatics, 20, Article 2. https://doi.org/10.1093/bib/bby087
    2. Berndt, N., Bulik, S., Wallach, I., Wünsch, T., König, M., Stockmann, M., Meierhofer, D., & Holzhütter, H.-G. (2018). HEPATOKIN1 is a biochemistry-based model of liver metabolism for applications in medicine and pharmacology. Nature Communications. https://doi.org/10.1038/s41467-018-04720-9
    3. Medley, J. K., Choi, K., König, M., Smith, L., Gu, S., Hellerstein, J., Sealfon, S. C., & Sauro, H. M. (2018). Tellurium notebooks—An environment for reproducible dynamical modeling in systems biology. PLOS Computational Biology, 14, Article 6. https://doi.org/10.1371/journal.pcbi.1006220
    4. Bergmann, F. T., Cooper, J., König, M., Moraru, I., Nickerson, D., Novere, N. L., Olivier, B. G., Sahle, S., Smith, L., & Waltemath, D. (2018). Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3). Journal of Integrative Bioinformatics, 0, Article 0. https://doi.org/10.1515/jib-2017-0086
    5. König, M., Watanabe, L. H., Grzegorzewski, J., & Myers, C. J. (2018). Dynamic Flux Balance Analysis Models in SBML. https://doi.org/10.1101/245076
    6. Neal, M. L., König, M., Nickerson, D., Mısırlı, G., Kalbasi, R., Dräger, A., Atalag, K., Chelliah, V., Cooling, M., Cook, D. L., Crook, S., de Alba, M., Friedman, S. H., Garny, A., Gennari, J. H., Gleeson, P., Golebiewski, M., Hucka, M., Juty, N., et al. (2018). Harmonizing semantic annotations for computational models in biology. bioRxiv. https://doi.org/10.1101/246470

  10. 2017

    1. Christ, B., Dahmen, U., Herrmann, K.-H., König, M., Reichenbach, J. R., Ricken, T., Schleicher, J., Schwen, L. O., Vlaic, S., & Waschinsky, N. (2017). Computational modeling in liver surgery. Frontiers in Physiology, 8, Article NOV.

  11. 2016

    1. König, M. (2016). cy3sabiork: A Cytoscape app for visualizing kinetic data from SABIO-RK. https://doi.org/10.1101/062091
    2. König, M. (2016). Cy3sabiork: A Cytoscape app for visualizing kinetic data from SABIO-RK version 1; referees: 2 approved with reservations. F1000Research, 5.
    3. Waltemath, D., Karr, J. R., Bergmann, F. T., Chelliah, V., Hucka, M., Krantz, M., Liebermeister, W., Mendes, P., Myers, C. J., Pir, P., Alaybeyoglu, B., Aranganathan, N. K., Baghalian, K., Bittig, A. T., Burke, P. E. P., Cantarelli, M., Chew, Y. H., Costa, R. S., Cursons, J., et al. (2016). Toward Community Standards and Software for Whole-Cell Modeling. IEEE Transactions on Biomedical Engineering, 63, Article 10.
    4. König, M., Oellrich, A., Waltemath, D., Dobson, R. J. B., Hubbard, T. J. P., & Wolkenhauer, O. (2016). Challenges and opportunities for system biology standards and tools in medical research. CEUR Workshop Proceedings, 1692.

  12. 2015

    1. Somogyi, E., Bouteiller, J., Glazier, J., König, M., Medley, J., Swat, M., & Sauro, H. (2015). libRoadRunner: a high performance SBML simulation and analysis library. https://doi.org/10.1093/bioinformatics/btv363
    2. Ricken, T., Werner, D., Holzhütter, H., König, M., Dahmen, U., & Dirsch, O. (2015). Modeling function-perfusion behavior in liver lobules including tissue, blood, glucose, lactate and glycogen by use of a coupled two-scale PDE-ODE approach. https://doi.org/10.1007/s10237-014-0619-z
    3. Abshagen, K., König, M., Hoppe, A., Müller, I., Ebert, M., Weng, H., Holzhütter, H., Zanger, U., Bode, J., Vollmar, B., Thomas, M., & Dooley, S. (2015). Pathobiochemical signatures of cholestatic liver disease in bile duct ligated mice. https://doi.org/10.1186/s12918-015-0229-0

  13. 2013

    1. König, M., Holzhütter, H., & Berndt, N. (2013). Metabolic gradients as key regulators in zonation of tumor energy metabolism: a tissue-scale model-based study. https://doi.org/10.1002/biot.201200393

  14. 2012

    1. König, M., & Holzhütter, H.-G. (2012). Kinetic modeling of human hepatic glucose metabolism in type 2 diabetes mellitus predicts higher risk of hypoglycemic events in rigorous insulin therapy. Journal of Biological Chemistry, 287, Article 44.
    2. König, M., Dräger, A., & Holzhütter, H.-G. (2012). CySBML: A cytoscape plugin for SBML. Bioinformatics, 28, Article 18.
    3. König, M., Bulik, S., & Holzhütter, H.-G. (2012). Quantifying the contribution of the liver to glucose homeostasis: A detailed kinetic model of human hepatic glucose metabolism. PLoS Computational Biology, 8, Article 6.

  15. 2011

    1. Herling, A., König, M., Bulik, S., & Holzhütter, H.-G. (2011). Enzymatic features of the glucose metabolism in tumor cells. FEBS Journal, 278, Article 14.

  16. 2010

    1. 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, H.-G. (2010). HepatoNet1: A comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology. Molecular Systems Biology, 6.
    2. König, M., & Holzhütter, H. G. (2010). Fluxviz - Cytoscape plug-in for visualization of flux distributions in networks. Genome Informatics. International Conference on Genome Informatics, 24, 96–103.
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