Stefan Hoops

According to our database, Stefan Hoops authored at least 35 papers between 2006 and 2024.

Collaborative distances:

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

2024

Novel multi-cluster workflow system to support real-time HPC-enabled epidemic science: Investigating the impact of vaccine acceptance on COVID-19 spread.

Parantapa Bhattacharya, Dustin Machi, Jiangzhuo Chen, Stefan Hoops, Bryan 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

J. Parallel Distributed Comput., 2024

A Large-Scale Epidemic Simulation Framework for Realistic Social Contact Networks.

Joy Kitson, Ian J. Costello, Jiangzhuo Chen, Diego Jiménez, Stefan Hoops, Henning S. Mortveit, Esteban Meneses, Jae-Seung Yeom, Madhav V. Marathe, Abhinav Bhatele

CoRR, 2024

2023

Augmenting the Social Vulnerability Index using an agent-based simulation of Hurricane Harvey.

Anna E. Brower, Balaji Ramesh, Kazi Ashik Islam, Henning S. Mortveit, Stefan Hoops, Anil Vullikanti, Madhav V. Marathe, Benjamin F. Zaitchik, Julia M. Gohlke, Samarth Swarup

Comput. Environ. Urban Syst., October, 2023

Data-driven scalable pipeline using national agent-based models for real-time pandemic response and decision support.

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

Int. J. High Perform. Comput. Appl., 2023

Synthetic Information and Digital Twins for Pandemic Science: Challenges and Opportunities.

Galen Harrison, Przemyslaw J. Porebski, Jiangzhuo Chen, Mandy L. Wilson, Henning S. Mortveit, Parantapa Bhattacharya, Dawen Xie, Stefan Hoops, Anil Vullikanti, Li Xiong, James Joshi, Madhav V. Marathe

Proceedings of the 5th IEEE International Conference on Trust, 2023

Active Sensing for Epidemic State Estimation Using ABM-Guided Machine Learning.

Sami Saliba, Faraz Dadgostari, Stefan Hoops, Henning S. Mortveit, Samarth Swarup

Proceedings of the Multi-Agent-Based Simulation XXIV - 24th International Workshop, 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

Effective Social Network-Based Allocation of COVID-19 Vaccines.

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

Proceedings of the KDD '22: The 28th ACM SIGKDD Conference on Knowledge Discovery and Data Mining, Washington, DC, USA, August 14, 2022

2021

Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research.

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

Briefings Bioinform., 2021

High Performance Agent-Based Modeling to Study Realistic Contact Tracing Protocols.

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

Proceedings of the Winter Simulation Conference, 2021

Scalable Epidemiological Workflows to Support COVID-19 Planning and Response.

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

Proceedings of the 35th IEEE International Parallel and Distributed Processing Symposium, 2021

AI-Driven Agent-Based Models to Study the Role of Vaccine Acceptance in Controlling COVID-19 Spread in the US.

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

Proceedings of the 2021 IEEE International Conference on Big Data (Big Data), 2021

2019

PlantSimLab - a modeling and simulation web tool for plant biologists.

S. Ha, Elena S. Dimitrova, Stefan Hoops, Doaa Altarawy, Mitra Ansariola, D. Deb, Jane Glazebrook, R. Hillmer, Hossameldin Shahin, Fumiaki Katagiri, J. McDowell, Molly Megraw, João C. Setubal, B. M. Tyler, Reinhard C. Laubenbacher

BMC Bioinform., December, 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

2018

JigCell Model Connector: building large molecular network models from components.

Thomas C. Jones Jr, Stefan Hoops, Layne T. Watson, Alida Palmisano, John J. Tyson, Clifford A. Shaffer

Simul., 2018

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

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

J. Integr. Bioinform., 2018

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core.

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

J. Integr. Bioinform., 2018

2015

Multiscale modeling of mucosal immune responses.

Yongguo Mei, Vida Abedi, Adria Carbo, Xiaoying Zhang, Pinyi Lu, Casandra W. Philipson, Raquel Hontecillas, Stefan Hoops, Nathan Liles, Josep Bassaganya-Riera

BMC Bioinform., December, 2015

ENISI SDE: A New Web-Based Tool for Modeling Stochastic Processes.

Yongguo Mei, Adria Carbo, Stefan Hoops, Raquel Hontecillas, Josep Bassaganya-Riera

IEEE ACM Trans. Comput. Biol. Bioinform., 2015

SBML Level 3 package: Hierarchical Model Composition, Version 1 Release 3.

Lucian Paul Smith, Michael Hucka, Stefan Hoops, Andrew Finney, Martin Ginkel, Chris J. Myers, Ion I. Moraru, Wolfram Liebermeister

J. Integr. Bioinform., 2015

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core.

Michael Hucka, Frank T. Bergmann, Stefan Hoops, Sarah M. Keating, Sven Sahle, James C. Schaff, Lucian P. Smith, Darren J. Wilkinson

J. Integr. Bioinform., 2015

Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions.

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

J. Integr. Bioinform., 2015

JigCell Run Manager (JC-RM): a tool for managing large sets of biochemical model parametrizations.

Alida Palmisano, Stefan Hoops, Layne T. Watson, Thomas C. Jones Jr, John J. Tyson, Clifford A. Shaffer

BMC Syst. Biol., 2015

Supervised learning methods in modeling of CD4+ T cell heterogeneity.

Pinyi Lu, Vida Abedi, Yongguo Mei, Raquel Hontecillas, Stefan Hoops, Adria Carbo, Josep Bassaganya-Riera

BioData Min., 2015

ENISI multiscale modeling of mucosal immune responses driven by high performance computing.

Vida Abedi, Raquel Hontecillas, Stefan Hoops, Nathan Liles, Adria Carbo, Pinyi Lu, Casandra W. Philipson, Josep Bassaganya-Riera

Proceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine, 2015

2014

Multistate Model Builder (MSMB): a flexible editor for compact biochemical models.

Alida Palmisano, Stefan Hoops, Layne T. Watson, Thomas C. Jones Jr, John J. Tyson, Clifford A. Shaffer

BMC Syst. Biol., 2014

ENISI MSM: A novel multi-scale modeling platform for computational immunology.

Yongguo Mei, Adria Carbo, Raquel Hontecillas, Stefan Hoops, Nathan Liles, Pinyi Lu, Casandra W. Philipson, Josep Bassaganya-Riera

Proceedings of the 2014 IEEE International Conference on Bioinformatics and Biomedicine, 2014

2013

Systems Modeling of Molecular Mechanisms Controlling Cytokine-driven CD4+ T Cell Differentiation and Phenotype Plasticity.

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

PLoS Comput. Biol., 2013

2012

Condor-COPASI: high-throughput computing for biochemical networks.

Edward Kent, Stefan Hoops, Pedro Mendes

BMC Syst. Biol., 2012

High-Performance Interaction-Based Simulation of Gut Immunopathologies with ENteric Immunity Simulator (ENISI).

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

Proceedings of the 26th IEEE International Parallel and Distributed Processing Symposium, 2012

ENISI Visual, an agent-based simulator for modeling gut immunity.

Yongguo Mei, Raquel Hontecillas, Xiaoying Zhang, Keith R. Bisset, Stephen G. Eubank, Stefan Hoops, Madhav V. Marathe, Josep Bassaganya-Riera

Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine, 2012

2011

Minimum Information About a Simulation Experiment (MIASE).

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

PLoS Comput. Biol., 2011

2006

COPASI - a COmplex PAthway SImulator.

Stefan Hoops, Sven Sahle, Ralph Gauges, Christine Lee, Jürgen Pahle, Natalia Simus, Mudita Singhal, Liang Xu, Pedro Mendes, Ursula Kummer

Bioinform., 2006

Simulation of biochemical networks using COPASI: a complex pathway simulator.

Sven Sahle, Ralph Gauges, Jürgen Pahle, Natalia Simus, Ursula Kummer, Stefan Hoops, Christine Lee, Mudita Singhal, Liang Xu, Pedro Mendes

Proceedings of the Winter Simulation Conference WSC 2006, 2006