Stefan Hoops

Publication Activity (10 Years)

Years Active: 2006-2024
Publications (10 Years): 24

Top Topics

Systems Biology

Markup Language

Top Venues

J. Integr. Bioinform.

BMC Syst. Biol.

Publications

Joy Kitson, Ian J. Costello, Jiangzhuo Chen, Diego Jiménez, Stefan Hoops, Henning S. Mortveit, Esteban Meneses, Jae-Seung Yeom, Madhav V. Marathe, Abhinav Bhatele
A Large-Scale Epidemic Simulation Framework for Realistic Social Contact Networks. CoRR (2024)
Sami Saliba, Faraz Dadgostari, Stefan Hoops, Henning S. Mortveit, Samarth Swarup
Active Sensing for Epidemic State Estimation Using ABM-Guided Machine Learning. MABS (2023)
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) (2023)
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
Synthetic Information and Digital Twins for Pandemic Science: Challenges and Opportunities. TPS-ISA (2023)
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
Augmenting the Social Vulnerability Index using an agent-based simulation of Hurricane Harvey. Comput. Environ. Urban Syst. 105 (2023)
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)
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)
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)
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) (2021)
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)
Parantapa Bhattacharya, Dustin Machi, Jiangzhuo Chen, Stefan Hoops, Bryan L. Lewis, Henning S. Mortveit, Srinivasan Venkatramanan, Mandy L. Wilson, Achla Marathe, Przemyslaw Porebski, Brian Klahn, Joseph Outten, Anil Vullikanti, Dawen Xie, Abhijin Adiga, Shawn Brown, Christopher L. Barrett, Madhav Marathe
AI-Driven Agent-Based Models to Study the Role of Vaccine Acceptance in Controlling COVID-19 Spread in the US. IEEE BigData (2021)
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)
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)
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)
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)
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)
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)
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 (2015)
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) (2015)
Yongguo Mei, Vida Abedi, Adria Carbo, Xiaoying Zhang, Pinyi Lu, Casandra W. Philipson, Raquel Hontecillas, Stefan Hoops, Nathan Liles, Josep Bassaganya-Riera
Multiscale modeling of mucosal immune responses. BMC Bioinform. 16 (S12) (2015)
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)
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)
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 (2015)
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)
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 (2014)
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)
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)
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)
Edward Kent, Stefan Hoops, Pedro Mendes
Condor-COPASI: high-throughput computing for biochemical networks. BMC Syst. Biol. 6 (2012)
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)
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) (2006)
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)