Curriculum Vitae
Dr. Matthias König
Junior Group Leader
LiSyM - Systems Medicine of the Liver
Institute for Biology, Institute for Theoretical Biology
Humboldt Universität zu Berlin
Invalidenstraße 110, 10117 Berlin, Germany
+49 30 2093-98435
koenigmx@hu-berlin.de
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.
Funding
Participation in Research Projects
| 2016-2020 |
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Junior group leader in Systems Medicine of the Liver project funded by the Federal Ministry of Education and Research (BMBF). |
| 2010-2015 |
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PhD in Systems Biology and Systems Medicine of liver project funded by the Federal Ministry of Education and Research (BMBF). |
| 2005-2010 |
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Student assistant and PhD in Systems Biology and Systems Medicine of liver project funded by the Federal Ministry of Education and Research (BMBF). |
Publications
| 2022 |
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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; |
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| 2022 |
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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 |
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| 2022 |
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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] |
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| 2022 |
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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 |
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| 2022 |
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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 |
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| 2022 |
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Kausthubh Ramachandran, Matthias König, Martin Scharm, Dagmar Waltemath, Henning Hermjakob, Rahuman Sheriff FAIR sharing of reproducible and reusable COVID-19 models [submitted, 2022-02-16] |
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| 2021 |
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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 |
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| 2021 |
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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. |
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| 2021 |
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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 |
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| 2021 |
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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 |
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| 2021 |
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Sükrü Balci (supervisor: Matthias König) Computational modelling of omeprazole - pharmacokinetics and pharmacodynamics Bachelor Thesis, October 2021 |
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| 2021 |
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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). |
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| 2021 |
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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 |
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| 2021 |
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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. |
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| 2021 |
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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] |
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| 2021 |
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John Gennari, Matthias König, Goskel Misirli, Maxwell Neal, David Nickerson, Dagmar Waltemath OMEX Metadata Specification Version 1.2 [Submitted to JIB, 2021-08-08] |
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| 2021 |
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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] |
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| 2021 |
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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 |
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| 2020 |
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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 |
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| 2020 |
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Florian Bartsch (supervisor: Matthias König) Computational Modelling of Simvastatin - Effects on HMG-CoA Reductase Activity and Cholesterol Bachelor Thesis, November 2020 |
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| 2020 |
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Yannick Duport (supervisor: Matthias König) Computational Modelling of Midazolam Clearance: Effect of Inhibitors and Inducers Bachelor Thesis, August 2020 |
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| 2020 |
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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 |
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| 2020 |
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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 |
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| 2020 |
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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 |
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| 2020 |
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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 |
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| 2020 |
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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 |
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| 2020 |
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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 |
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| 2020 |
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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 |
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| 2020 |
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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] |
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| 2019 |
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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 |
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| 2019 |
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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 |
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| 2019 |
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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 |
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| 2018 |
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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 |
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| 2018 |
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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. |
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| 2018 |
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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 |
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| 2018 |
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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 |
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| 2018 |
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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] |
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| 2018 |
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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 |
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| 2017 |
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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 |
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| 2016 |
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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 |
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| 2016 |
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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) |
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| 2016 |
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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 |
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| 2016 |
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Wholecell Consortium (König M.) Toward community standards and software for whole-cell modeling IEEE Trans Biomed Eng. 2016 Jun 10. [PubMed] |
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| 2015 |
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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] |
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| 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] |
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| 2015 |
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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] |
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| 2014 |
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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] |
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| 2014 |
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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)] |
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| 2013 |
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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] |
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| 2012 |
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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] |
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| 2012 |
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König M., Dräger A. and Holzhütter HG. CySBML: a Cytoscape plugin for SBML Bioinformatics. 2012 Jul 5. [PubMed] |
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| 2012 |
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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] |
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| 2011 |
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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] |
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| 2011 |
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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] |
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| 2010 |
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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] |