Matthias König

According to our database, Matthias König authored at least 28 papers between 2012 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2024

The simulation experiment description markup language (SED-ML): language specification for level 1 version 5.

Lucian P. Smith, Frank T. Bergmann, Alan Garny, Tomás Helikar, Jonathan R. Karr, David P. Nickerson, Herbert M. Sauro, Dagmar Waltemath, Matthias König

J. Integr. Bioinform., 2024

Specifications of standards in systems and synthetic biology: status, developments, and tools in 2024.

Martin Golebiewski, Gary D. Bader, Padraig Gleeson, Thomas E. Gorochowski, Sarah M. Keating, Matthias König, Chris J. Myers, David P. Nickerson, Björn Sommer, Dagmar Waltemath, Falk Schreiber

J. Integr. Bioinform., 2024

2023

Specifications of standards in systems and synthetic biology: status and developments in 2022 and the COMBINE meeting 2022.

Matthias König, Padraig Gleeson, Martin Golebiewski, Thomas E. Gorochowski, Michael Hucka, Sarah M. Keating, Chris J. Myers, David P. Nickerson, Björn Sommer, Dagmar Waltemath, Falk Schreiber

J. Integr. Bioinform., March, 2023

libRoadRunner 2.0: a high performance SBML simulation and analysis library.

Ciaran M. Welsh, Jin Xu, Lucian P. Smith, Matthias König, Kiri Choi, Herbert M. Sauro

Bioinform., January, 2023

2022

BioSimulators: a central registry of simulation engines and services for recommending specific tools.

Bilal Shaikh, Lucian P. Smith, Dan Vasilescu, Gnaneswara Marupilla, Michael Wilson, Eran Agmon, Henry Agnew, Steven S. Andrews, Azraf Anwar, Moritz E. Beber, Frank T. Bergmann, David Brooks, Lutz Brusch, Laurence Calzone, Kiri Choi, Joshua Cooper, John Detloff, Brian Drawert, Michel Dumontier, G. Bard Ermentrout, James R. Faeder, Andrew P. Freiburger, Fabian Fröhlich, Akira Funahashi, Alan Garny, John H. Gennari, Padraig Gleeson, Anne Goelzer, Zachary B. Haiman, Jan Hasenauer, Joseph L. Hellerstein, Henning Hermjakob, Stefan Hoops, Jon C. Ison, Diego Jahn, Henry V. Jakubowski, Ryann Jordan, Matús Kalas, Matthias König, Wolfram Liebermeister, Rahuman S. Malik-Sheriff, Synchon Mandal, Robert A. McDougal, J. Kyle Medley, Pedro Mendes, Robert Müller, Chris J. Myers, Aurélien Naldi, Tung V. N. Nguyen, David P. Nickerson, Brett G. Olivier, Drashti Patoliya, Loïc Paulevé, Linda R. Petzold, Ankita Priya, Anand K. Rampadarath, Johann M. Rohwer, Ali Sinan Saglam, Dilawar Singh, Ankur Sinha, Jacky L. Snoep, Hugh Sorby, Ryan K. Spangler, Jörn Starruß, Payton J. Thomas, David D. van Niekerk, Daniel Weindl, Fengkai Zhang, Anna Zhukova, Arthur P. Goldberg, James C. Schaff, Michael L. Blinov, Herbert M. Sauro, Ion I. Moraru, Jonathan R. Karr

Nucleic Acids Res., 2022

BioSimulators: a central registry of simulation engines and services for recommending specific tools.

Bilal Shaikh, Lucian P. Smith, Dan Vasilescu, Gnaneswara Marupilla, Michael Wilson, Eran Agmon, Henry Agnew, Steven S. Andrews, Azraf Anwar, Moritz E. Beber, Frank T. Bergmann, David Brooks, Lutz Brusch, Laurence Calzone, Kiri Choi, Joshua Cooper, John Detloff, Brian Drawert, Michel Dumontier, G. Bard Ermentrout, James R. Faeder, Andrew P. Freiburger, Fabian Fröhlich, Akira Funahashi, Alan Garny, John H. Gennari, Padraig Gleeson, Anne Goelzer, Zachary B. Haiman, Joseph L. Hellerstein, Stefan Hoops, Jon C. Ison, Diego Jahn, Henry V. Jakubowski, Ryann Jordan, Matús Kalas, Matthias König, Wolfram Liebermeister, Synchon Mandal, Robert A. McDougal, J. Kyle Medley, Pedro Mendes, Robert Müller, Chris J. Myers, Aurélien Naldi, Tung V. N. Nguyen, David P. Nickerson, Brett G. Olivier, Drashti Patoliya, Loïc Paulevé, Linda R. Petzold, Ankita Priya, Anand K. Rampadarath, Johann M. Rohwer, Ali Sinan Saglam, Dilawar Singh, Ankur Sinha, Jacky L. Snoep, Hugh Sorby, Ryan K. Spangler, Jörn Starruß, Payton J. Thomas, David D. van Niekerk, Daniel Weindl, Fengkai Zhang, Anna Zhukova, Arthur P. Goldberg, Michael L. Blinov, Herbert M. Sauro, Ion I. Moraru, Jonathan R. Karr

CoRR, 2022

The systems biology simulation core library.

Hemil Panchiwala, Shalin Shah, Hannes Planatscher, Mykola Zakharchuk, Matthias König, Andreas Dräger

Bioinform., 2022

2021

PK-DB: pharmacokinetics database for individualized and stratified computational modeling.

Jan Grzegorzewski, Janosch Brandhorst, Kathleen Green, Dimitra Eleftheriadou, Yannick Duport, Florian Barthorscht, Adrian Köller, Danny Yu Jia Ke, Sara De Angelis, Matthias König

Nucleic Acids Res., 2021

The simulation experiment description markup language (SED-ML): language specification for level 1 version 4.

Lucian P. Smith, Frank T. Bergmann, Alan Garny, Tomás Helikar, Jonathan R. Karr, David P. Nickerson, Herbert M. Sauro, Dagmar Waltemath, Matthias König

J. Integr. Bioinform., 2021

Specifications of standards in systems and synthetic biology: status and developments in 2021.

Falk Schreiber, Padraig Gleeson, Martin Golebiewski, Thomas E. Gorochowski, Michael Hucka, Sarah M. Keating, Matthias König, Chris J. Myers, David P. Nickerson, Björn Sommer, Dagmar Waltemath

J. Integr. Bioinform., 2021

OMEX metadata specification (version 1.2).

John H. Gennari, Matthias König, Goksel Misirli, Maxwell Lewis Neal, David P. Nickerson, Dagmar Waltemath

J. Integr. Bioinform., 2021

2020

The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE).

Dagmar Waltemath, Martin Golebiewski, Michael L. Blinov, Padraig Gleeson, Henning Hermjakob, Michael Hucka, Esther Thea Inau, Sarah M. Keating, Matthias König, Olga Krebs, Rahuman S. Malik-Sheriff, David P. Nickerson, Ernst Oberortner, Herbert M. Sauro, Falk Schreiber, Lucian P. Smith, Melanie I. Stefan, Ulrike Wittig, Chris J. Myers

J. Integr. Bioinform., 2020

Systems Biology Markup Language (SBML) Level 3 Package: Distributions, Version 1, Release 1.

Lucian P. Smith, Stuart L. Moodie, Frank T. Bergmann, Colin S. Gillespie, Sarah M. Keating, Matthias König, Chris J. Myers, Maciek J. Swat, Darren J. Wilkinson, Michael Hucka

J. Integr. Bioinform., 2020

Specifications of standards in systems and synthetic biology: status and developments in 2020.

Falk Schreiber, Björn Sommer, Tobias Czauderna, Martin Golebiewski, Thomas E. Gorochowski, Michael Hucka, Sarah M. Keating, Matthias König, Chris J. Myers, David P. Nickerson, Dagmar Waltemath

J. Integr. Bioinform., 2020

Open modeling and exchange (OMEX) metadata specification version 1.0.

Maxwell Lewis Neal, John H. Gennari, Dagmar Waltemath, David P. Nickerson, Matthias König

J. Integr. Bioinform., 2020

2019

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019.

Falk Schreiber, Björn Sommer, Gary D. Bader, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Sarah M. Keating, Matthias König, Chris J. Myers, David P. Nickerson, Dagmar Waltemath

J. Integr. Bioinform., 2019

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2.

Michael Hucka, Frank T. Bergmann, Claudine Chaouiya, Andreas Dräger, Stefan Hoops, Sarah M. Keating, Matthias König, Nicolas Le Novère, Chris J. Myers, Brett G. Olivier, Sven Sahle, James C. Schaff, Rahuman S. Malik-Sheriff, Lucian P. Smith, Dagmar Waltemath, Darren J. Wilkinson, Fengkai Zhang

J. Integr. Bioinform., 2019

Harmonizing semantic annotations for computational models in biology.

Maxwell Lewis Neal, Matthias König, David P. Nickerson, Goksel Misirli, Reza Kalbasi, Andreas Dräger, Koray Atalag, Vijayalakshmi Chelliah, Michael T. Cooling, Daniel L. Cook, Sharon M. Crook, Miguel de Alba, Samuel H. Friedman, Alan Garny, John H. Gennari, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Nick S. Juty, Chris J. Myers, Brett G. Olivier, Herbert M. Sauro, Martin Scharm, Jacky L. Snoep, Vasundra Touré, Anil Wipat, Olaf Wolkenhauer, Dagmar Waltemath

Briefings Bioinform., 2019

2018

Tellurium notebooks - An environment for reproducible dynamical modeling in systems biology.

J. Kyle Medley, Kiri Choi, Matthias König, Lucian P. Smith, Stanley Gu, Joseph L. Hellerstein, Stuart C. Sealfon, Herbert M. Sauro

PLoS Comput. Biol., 2018

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3).

Frank T. Bergmann, Jonathan Cooper, Matthias König, Ion I. Moraru, David P. Nickerson, Nicolas Le Novère, Brett G. Olivier, Sven Sahle, Lucian P. Smith, Dagmar Waltemath

J. Integr. Bioinform., 2018

Tellurium: An extensible python-based modeling environment for systems and synthetic biology.

Kiri Choi, J. Kyle Medley, Matthias König, Kaylene Stocking, Lucian P. Smith, Stanley Gu, Herbert M. Sauro

Biosyst., 2018

2016

Toward Community Standards and Software for Whole-Cell Modeling.

Dagmar Waltemath, Jonathan R. Karr, Frank T. Bergmann, Vijayalakshmi Chelliah, Michael Hucka, Marcus Krantz, Wolfram Liebermeister, Pedro Mendes, Chris J. Myers, Pinar Pir, Begum Alaybeyoglu, Naveen K. Aranganathan, Kambiz Baghalian, Arne T. Bittig, Paulo E. Pinto Burke, Matteo Cantarelli, Yin Hoon Chew, Rafael S. Costa, Joseph Cursons, Tobias Czauderna, Arthur P. Goldberg, Harold F. Gómez, Jens Hahn, Tuure Hameri, Daniel F. Hernandez Gardiol, Denis Kazakiewicz, Ilya Kiselev, Vincent Knight-Schrijver, Christian Knüpfer, Matthias König, Daewon Lee, Audald Lloret-Villas, Nikita Mandrik, J. Kyle Medley, Bertrand Moreau, Hojjat Naderi-Meshkin, Sucheendra K. Palaniappan, Daniel Priego-Espinosa, Martin Scharm, Mahesh Sharma, Kieran Smallbone, Natalie J. Stanford, Je-Hoon Song, Tom Theile, Milenko Tokic, Namrata Tomar, Vasundra Touré, Jannis Uhlendorf, Thawfeek M. Varusai, Leandro H. Watanabe, Florian Wendland, Markus Wolfien, James T. Yurkovich, Yan Zhu, Argyris Zardilis, Anna Zhukova, Falk Schreiber

IEEE Trans. Biomed. Eng., 2016

cy3sabiork: A Cytoscape app for visualizing kinetic data from SABIO-RK.

Matthias König

F1000Research, 2016

Challenges and opportunities for system biology standards and tools in medical research.

Matthias König, Anika Oellrich, Dagmar Waltemath, Richard J. B. Dobson, Tim J. P. Hubbard, Olaf Wolkenhauer

Proceedings of the 7th Workshop on Ontologies and Data in Life Sciences, 2016

2015

Pathobiochemical signatures of cholestatic liver disease in bile duct ligated mice.

Kerstin Abshagen, Matthias König, Andreas Hoppe, Isabell Müller, Matthias Ebert, Honglei Weng, Hermann-Georg Holzhütter, Ulrich M. Zanger, Johannes G. Bode, Brigitte Vollmar, Maria Thomas, Steven Dooley

BMC Syst. Biol., 2015

libRoadRunner: a high performance SBML simulation and analysis library.

Endre T. Somogyi, Jean-Marie Bouteiller, James A. Glazier, Matthias König, J. Kyle Medley, Maciej H. Swat, Herbert M. Sauro

Bioinform., 2015

2012

Quantifying the Contribution of the Liver to Glucose Homeostasis: A Detailed Kinetic Model of Human Hepatic Glucose Metabolism.

Matthias König, Sascha Bulik, Hermann-Georg Holzhütter

PLoS Comput. Biol., 2012

CySBML: a Cytoscape plugin for SBML.

Matthias König, Andreas Dräger, Hermann-Georg Holzhütter

Bioinform., 2012