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Jonathan R. Karr
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2020 – today
- 2024
- [j17]Lucian P. Smith, Frank T. Bergmann, Alan Garny, Tomás Helikar, Jonathan R. Karr, David P. Nickerson, Herbert M. Sauro, Dagmar Waltemath, Matthias König:
The simulation experiment description markup language (SED-ML): language specification for level 1 version 5. J. Integr. Bioinform. 21(1) (2024) - 2022
- [j16]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:
BioSimulators: a central registry of simulation engines and services for recommending specific tools. Nucleic Acids Res. 50(W1): 108-114 (2022) - [i4]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:
BioSimulators: a central registry of simulation engines and services for recommending specific tools. CoRR abs/2203.06732 (2022) - 2021
- [j15]Alexander Mazein, Adrien Rougny, Jonathan R. Karr, Julio Saez-Rodriguez, Marek Ostaszewski, Reinhard Schneider:
Reusability and composability in process description maps: RAS-RAF-MEK-ERK signalling. Briefings Bioinform. 22(5) (2021) - [j14]Andreas Dräger, Tomás Helikar, Matteo Barberis, Marc R. Birtwistle, Laurence Calzone, Claudine Chaouiya, Jan Hasenauer, Jonathan R. Karr, Anna Niarakis, María Rodríguez Martínez, Julio Saez-Rodriguez, Juilee Thakar:
SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems. Bioinform. 37(21): 3702-3706 (2021) - [j13]Lucian P. Smith, Frank T. Bergmann, Alan Garny, Tomás Helikar, Jonathan R. Karr, David P. Nickerson, Herbert M. Sauro, Dagmar Waltemath, Matthias König:
The simulation experiment description markup language (SED-ML): language specification for level 1 version 4. J. Integr. Bioinform. 18(3) (2021) - [j12]Yosef D. Roth, Zhouyang Lian, Saahith Pochiraju, Bilal Shaikh, Jonathan R. Karr:
Datanator: an integrated database of molecular data for quantitatively modeling cellular behavior. Nucleic Acids Res. 49(Database-Issue): D516-D522 (2021) - [j11]Bilal Shaikh, Gnaneswara Marupilla, Mike Wilson, Michael L. Blinov, Ion I. Moraru, Jonathan R. Karr:
RunBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats. Nucleic Acids Res. 49(Webserver-Issue): 597-602 (2021) - 2020
- [j10]Arthur P. Goldberg, Jonathan R. Karr:
DE-Sim: an object-oriented, discrete-event simulation tool for data-intensive modeling of complex systems in Python. J. Open Source Softw. 5(55): 2685 (2020) - [i3]Jonathan R. Karr, Wolfram Liebermeister, Arthur P. Goldberg, John A. P. Sekar, Bilal Shaikh:
Structured spreadsheets with ObjTables enable data reuse and integration. CoRR abs/2005.05227 (2020) - [i2]Arthur P. Goldberg, John A. P. Sekar, Jonathan R. Karr:
Exact Parallelization of the Stochastic Simulation Algorithm for Scalable Simulation of Large Biochemical Networks. CoRR abs/2005.05295 (2020)
2010 – 2019
- 2016
- [j9]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:
Toward Community Standards and Software for Whole-Cell Modeling. IEEE Trans. Biomed. Eng. 63(10): 2007-2014 (2016) - [j8]J. Kyle Medley, Arthur P. Goldberg, Jonathan R. Karr:
Guidelines for Reproducibly Building and Simulating Systems Biology Models. IEEE Trans. Biomed. Eng. 63(10): 2015-2020 (2016) - [c2]Arthur P. Goldberg, Yin Hoon Chew, Jonathan R. Karr:
Toward Scalable Whole-Cell Modeling of Human Cells. SIGSIM-PADS 2016: 259-262 - 2015
- [j7]Jonathan R. Karr, Harendra Guturu, Edward Y. Chen, Stuart L. Blair, Jonathan M. Irish, Nikesh Kotecha, Markus W. Covert:
NetworkPainter: dynamic intracellular pathway animation in Cytobank. BMC Bioinform. 16: 172:1-172:7 (2015) - [j6]Denis Kazakiewicz, Jonathan R. Karr, Karol M. Langner, Dariusz Plewczynski:
A combined systems and structural modeling approach repositions antibiotics for Mycoplasma genitalium. Comput. Biol. Chem. 59: 91-97 (2015) - [j5]Jonathan R. Karr, Alex H. Williams, Jeremy D. Zucker, Andreas Raue, Bernhard Steiert, Jens Timmer, Clemens Kreutz, Simon Wilkinson, Brandon A. Allgood, Brian M. Bot, Bruce R. Hoff, Michael R. Kellen, Markus W. Covert, Gustavo A. Stolovitzky, Pablo Meyer:
Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models. PLoS Comput. Biol. 11(5) (2015) - [c1]Rui Chang, Jonathan R. Karr, Eric E. Schadt:
Causal Inference in Biology Networks with Integrated Belief Propagation. Pacific Symposium on Biocomputing 2015: 359-370 - [i1]Thomas Cokelaer, Mukesh Bansal, Christopher Bare, Erhan Bilal, Brian M. Bot, Elias Chaibub Neto, Federica Eduati, Mehmet Gönen, Steven M. Hill, Bruce R. Hoff, Jonathan R. Karr, Robert Küffner, Michael P. Menden, Pablo Meyer, Raquel Norel, Abhishek Pratap, Robert J. Prill, Matthew T. Weirauch, James C. Costello, Gustavo Stolovitzky, Julio Saez-Rodriguez:
DREAMTools: a Python package for scoring collaborative challenges. F1000Research 4: 1030 (2015) - 2014
- [j4]Jonathan R. Karr, Nolan C. Phillips, Markus W. Covert:
WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions. Database J. Biol. Databases Curation 2014 (2014) - 2013
- [j3]Ruby Lee, Jonathan R. Karr, Markus W. Covert:
WholeCellViz: data visualization for whole-cell models. BMC Bioinform. 14: 253 (2013) - [j2]Jonathan R. Karr, Jayodita C. Sanghvi, Derek N. Macklin, Abhishek Arora, Markus W. Covert:
WholeCellKB: model organism databases for comprehensive whole-cell models. Nucleic Acids Res. 41(Database-Issue): 787-792 (2013)
2000 – 2009
- 2008
- [j1]Markus W. Covert, Nan Xiao, Tiffany J. Chen, Jonathan R. Karr:
Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli. Bioinform. 24(18): 2044-2050 (2008)
Coauthor Index
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