Jonathan R. Karr

Publication Activity (10 Years)

Years Active: 2008-2024
Publications (10 Years): 14

Top Topics

Computational Model

Parameter Identification

Markup Language

Top Venues

Nucleic Acids Res.

J. Integr. Bioinform.

IEEE Trans. Biomed. Eng.

Publications

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)
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 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 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 S. Saglam, Dilawar Singh, Ankur Sinha, Jacky L. Snoep, Hugh Sorby, Ryan K. Spangler, Jörn Starruß, Payton J. Thomas, David 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) (2022)
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 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 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 S. Saglam, Dilawar Singh, Ankur Sinha, Jacky Snoep, Hugh Sorby, Ryan K. Spangler, Jörn Starruß, Payton J. Thomas, David 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 (2022)
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)
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) (2021)
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) (2021)
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)
Andreas Dräger, Tomás Helikar, Matteo Barberis, Marc 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) (2021)
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 (2020)
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) (2020)
Jonathan R. Karr, Wolfram Liebermeister, Arthur P. Goldberg, John A. P. Sekar, Bilal Shaikh
Structured spreadsheets with ObjTables enable data reuse and integration. CoRR (2020)
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) (2016)
Arthur P. Goldberg, Yin Hoon Chew, Jonathan R. Karr
Toward Scalable Whole-Cell Modeling of Human Cells. SIGSIM-PADS (2016)
J. Kyle Medley, Arthur P. Goldberg, Jonathan R. Karr
Guidelines for Reproducibly Building and Simulating Systems Biology Models. IEEE Trans. Biomed. Eng. 63 (10) (2016)
Rui Chang, Jonathan R. Karr, Eric E. Schadt
Causal Inference in Biology Networks with Integrated Belief Propagation. Pacific Symposium on Biocomputing (2015)
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 (2015)
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 (2015)
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 (2015)
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)
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)
Ruby Lee, Jonathan R. Karr, Markus W. Covert
WholeCellViz: data visualization for whole-cell models. BMC Bioinform. 14 (2013)
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) (2013)
Markus W. Covert, Nan Xiao, Tiffany J. Chen, Jonathan R. Karr
. Bioinform. 24 (18) (2008)