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2020 – today
- 2023
[j18]Parantapa Bhattacharya, Jiangzhuo Chen, Stefan Hoops, Dustin Machi, Bryan L. Lewis, Srinivasan Venkatramanan, Mandy L. Wilson, Brian Klahn, Aniruddha Adiga, Benjamin Hurt, Joseph Outten, Abhijin Adiga, Andrew S. Warren, Young Yun Baek, Przemyslaw J. Porebski, Achla Marathe, Dawen Xie, Samarth Swarup, Anil Vullikanti, Henning S. Mortveit, Stephen G. Eubank, Christopher L. Barrett, Madhav Vinayak Marathe:
Data-driven scalable pipeline using national agent-based models for real-time pandemic response and decision support. Int. J. High Perform. Comput. Appl. 37(1): 4-27 (2023)- 2022
- [j17]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): 108-114 (2022) - [c9]Jiangzhuo Chen, Stefan Hoops, Achla Marathe, Henning S. Mortveit, Bryan L. Lewis, Srinivasan Venkatramanan, Arash Haddadan, Parantapa Bhattacharya, Abhijin Adiga, Anil Vullikanti, Aravind Srinivasan, Mandy L. Wilson, Gal Ehrlich, Maier Fenster, Stephen G. Eubank, Christopher L. Barrett, Madhav V. Marathe:
Effective Social Network-Based Allocation of COVID-19 Vaccines. KDD 2022: 4675-4683 - [i1]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 L. 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 abs/2203.06732 (2022) - 2021
- [j16]Franziska Hufsky, Kevin Lamkiewicz, Alexandre Almeida, Abdel Aouacheria, Cecilia N. Arighi, Alex Bateman, Jan Baumbach, Niko Beerenwinkel, Christian Brandt, Marco Cacciabue, Sara Chuguransky, Oliver Drechsel, Robert D. Finn, Adrian Fritz, Stephan Fuchs, Georges Hattab, Anne-Christin Hauschild, Dominik Heider, Marie Hoffmann, Martin Hölzer, Stefan Hoops, Lars Kaderali, Ioanna Kalvari, Max von Kleist, Renó Kmiecinski, Denise Kühnert, Gorka Lasso, Pieter Libin, Markus List, Hannah F. Löchel, Maria Jesus Martin, Roman Martin, Julian O. Matschinske, Alice C. McHardy, Pedro Mendes, Jaina Mistry, Vincent Navratil, Eric P. Nawrocki, Áine Niamh O'toole, Nancy Ontiveros-Palacios, Anton I. Petrov, Guillermo Rangel-Pineros, Nicole Redaschi, Susanne Reimering, Knut Reinert, Alejandro Reyes, Lorna J. Richardson, David L. Robertson, Sepideh Sadegh, Joshua B. Singer, Kristof Theys, Chris Upton, Marius Welzel, Lowri Williams, Manja Marz:
Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research. Briefings Bioinform. 22(2): 642-663 (2021) - [c8]Parantapa Bhattacharya, Dustin Machi, Jiangzhuo Chen, Stefan Hoops, Bryan L. Lewis, Henning S. Mortveit, Srinivasan Venkatramanan, Mandy L. Wilson, Achla Marathe, Przemyslaw J. Porebski, Brian Klahn, Joseph Outten, Anil Vullikanti, Dawen Xie, Abhijin Adiga, Shawn Brown, Christopher L. Barrett, Madhav V. Marathe:
AI-Driven Agent-Based Models to Study the Role of Vaccine Acceptance in Controlling COVID-19 Spread in the US. IEEE BigData 2021: 1566-1574 - [c7]Dustin Machi, Parantapa Bhattacharya, Stefan Hoops, Jiangzhuo Chen, Henning S. Mortveit, Srinivasan Venkatramanan, Bryan L. Lewis, Mandy L. Wilson, Arindam Fadikar, Tom Maiden, Christopher L. Barrett, Madhav V. Marathe:
Scalable Epidemiological Workflows to Support COVID-19 Planning and Response. IPDPS 2021: 639-650 - [c6]Stefan Hoops, Jiangzhuo Chen, Abhijin Adiga, Bryan L. Lewis, Henning S. Mortveit, Hannah Baek, Mandy L. Wilson, Dawen Xie, Samarth Swarup, Srinivasan Venkatramanan, Justin Crow, Elena Diskin, Seth Levine, Helen Tazelaar, Brooke Rossheim, Chris Ghaemmaghami, Rebecca Early, Chris Barrett, Madhav V. Marathe, Carter Price:
High Performance Agent-Based Modeling to Study Realistic Contact Tracing Protocols. WSC 2021: 1-12
2010 – 2019
- 2019
- [j15]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:
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2. J. Integr. Bioinform. 16(2) (2019) - 2018
- [j14]Michael Hucka, Frank T. Bergmann, Andreas Dräger, Stefan Hoops, Sarah M. Keating, Nicolas Le Novère, Chris J. Myers, Brett G. Olivier, Sven Sahle, James C. Schaff, Lucian P. Smith, Dagmar Waltemath, Darren J. Wilkinson:
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core. J. Integr. Bioinform. 15(1) (2018) - [j13]Michael Hucka, Frank T. Bergmann, Andreas Dräger, Stefan Hoops, Sarah M. Keating, Nicolas Le Novère, Chris J. Myers, Brett G. Olivier, Sven Sahle, James C. Schaff, Lucian P. Smith, Dagmar Waltemath, Darren J. Wilkinson:
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core. J. Integr. Bioinform. 15(1) (2018) - [j12]Thomas C. Jones Jr, Stefan Hoops, Layne T. Watson, Alida Palmisano, John J. Tyson, Clifford A. Shaffer:
JigCell Model Connector: building large molecular network models from components. Simul. 94(11) (2018) - 2015
- [j11]Pinyi Lu, Vida Abedi, Yongguo Mei, Raquel Hontecillas, Stefan Hoops, Adria Carbo, Josep Bassaganya-Riera:
Supervised learning methods in modeling of CD4+ T cell heterogeneity. BioData Min. 8: 27 (2015) - [j10]Alida Palmisano, Stefan Hoops, Layne T. Watson, Thomas C. Jones Jr, John J. Tyson, Clifford A. Shaffer:
JigCell Run Manager (JC-RM): a tool for managing large sets of biochemical model parametrizations. BMC Syst. Biol. 9: 95 (2015) - [j9]Michael Hucka, Frank T. Bergmann, Andreas Dräger, Stefan Hoops, Sarah M. Keating, Nicolas Le Novère, Chris J. Myers, Brett G. Olivier, Sven Sahle, James C. Schaff, Lucian P. Smith, Dagmar Waltemath, Darren J. Wilkinson:
Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions. J. Integr. Bioinform. 12(2) (2015) - [j8]Michael Hucka, Frank T. Bergmann, Stefan Hoops, Sarah M. Keating, Sven Sahle, James C. Schaff, Lucian P. Smith, Darren J. Wilkinson:
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core. J. Integr. Bioinform. 12(2) (2015) - [j7]Lucian Paul Smith, Michael Hucka, Stefan Hoops, Andrew Finney, Martin Ginkel, Chris J. Myers, Ion I. Moraru, Wolfram Liebermeister:
SBML Level 3 package: Hierarchical Model Composition, Version 1 Release 3. J. Integr. Bioinform. 12(2) (2015) - [j6]Yongguo Mei, Adria Carbo, Stefan Hoops, Raquel Hontecillas, Josep Bassaganya-Riera:
ENISI SDE: A New Web-Based Tool for Modeling Stochastic Processes. IEEE ACM Trans. Comput. Biol. Bioinform. 12(2): 289-297 (2015) - [c5]Vida Abedi, Raquel Hontecillas, Stefan Hoops, Nathan Liles, Adria Carbo, Pinyi Lu, Casandra W. Philipson, Josep Bassaganya-Riera:
ENISI multiscale modeling of mucosal immune responses driven by high performance computing. BIBM 2015: 680-684 - 2014
- [j5]Alida Palmisano, Stefan Hoops, Layne T. Watson, Thomas C. Jones Jr, John J. Tyson, Clifford A. Shaffer:
Multistate Model Builder (MSMB): a flexible editor for compact biochemical models. BMC Syst. Biol. 8: 42 (2014) - [c4]Yongguo Mei, Adria Carbo, Raquel Hontecillas, Stefan Hoops, Nathan Liles, Pinyi Lu, Casandra W. Philipson, Josep Bassaganya-Riera:
ENISI MSM: A novel multi-scale modeling platform for computational immunology. BIBM 2014: 391-396 - 2013
- [j4]Adria Carbo, Raquel Hontecillas, Barbara Kronsteiner, Monica Viladomiu, Mireia Pedragosa, Pinyi Lu, Casandra W. Philipson, Stefan Hoops, Madhav V. Marathe, Stephen G. Eubank, Keith R. Bisset, Katherine V. Wendelsdorf, Abdul Salam Jarrah, Yongguo Mei, Josep Bassaganya-Riera:
Systems Modeling of Molecular Mechanisms Controlling Cytokine-driven CD4+ T Cell Differentiation and Phenotype Plasticity. PLoS Comput. Biol. 9(4) (2013) - 2012
- [j3]Edward Kent, Stefan Hoops, Pedro Mendes:
Condor-COPASI: high-throughput computing for biochemical networks. BMC Syst. Biol. 6: 91 (2012) - [c3]Yongguo Mei, Raquel Hontecillas, Xiaoying Zhang, Keith R. Bisset, Stephen G. Eubank, Stefan Hoops, Madhav V. Marathe, Josep Bassaganya-Riera:
ENISI Visual, an agent-based simulator for modeling gut immunity. BIBM 2012: 1-5 - [c2]Keith R. Bisset, Md. Maksudul Alam, Josep Bassaganya-Riera, Adria Carbo, Stephen G. Eubank, Raquel Hontecillas, Stefan Hoops, Yongguo Mei, Katherine V. Wendelsdorf, Dawen Xie, Jae-Seung Yeom, Madhav V. Marathe:
High-Performance Interaction-Based Simulation of Gut Immunopathologies with ENteric Immunity Simulator (ENISI). IPDPS 2012: 48-59 - 2011
- [j2]Dagmar Waltemath, Richard R. Adams, Daniel A. Beard, Frank T. Bergmann, Upinder S. Bhalla, Randall Britten, Vijayalakshmi Chelliah, Mike T. Cooling, Jonathan Cooper, Edmund J. Crampin, Alan Garny, Stefan Hoops, Michael Hucka, Peter J. Hunter, Edda Klipp, Camille Laibe, Andrew K. Miller, Ion I. Moraru, David P. Nickerson, Poul M. F. Nielsen, Macha Nikolski, Sven Sahle, Herbert M. Sauro, Henning Schmidt, Jacky L. Snoep, Dominic P. Tolle, Olaf Wolkenhauer, Nicolas Le Novère:
Minimum Information About a Simulation Experiment (MIASE). PLoS Comput. Biol. 7(4) (2011)
2000 – 2009
- 2006
- [j1]Stefan Hoops, Sven Sahle, Ralph Gauges, Christine Lee, Jürgen Pahle, Natalia Simus, Mudita Singhal, Liang Xu, Pedro Mendes, Ursula Kummer:
COPASI - a COmplex PAthway SImulator. Bioinform. 22(24): 3067-3074 (2006) - [c1]Sven Sahle, Ralph Gauges, Jürgen Pahle, Natalia Simus, Ursula Kummer, Stefan Hoops, Christine Lee, Mudita Singhal, Liang Xu, Pedro Mendes:
Simulation of biochemical networks using COPASI: a complex pathway simulator. WSC 2006: 1698-1706
Coauthor Index
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