Publications

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 Bioinformatics, accepted [2022-11-24], arXiv preprint arXiv:2203.01175. 2022 Feb 26; doi: https://doi.org/10.48550/arXiv.2203.01175
2022		Grzegorzewski, J., Brandhorst, J., König, M.* Physiologically based pharmacokinetic (PBPK) modeling of the role of CYP2D6 polymorphism for metabolic phenotyping with dextromethorphan Front. Pharmacol., 24 October 2022; doi: 10.3389/fphar.2022.1029073
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		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		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]