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Stefan Hoops
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2020 – today
- 2024
- [j22]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:
Novel multi-cluster workflow system to support real-time HPC-enabled epidemic science: Investigating the impact of vaccine acceptance on COVID-19 spread. J. Parallel Distributed Comput. 191: 104899 (2024) - [i2]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 abs/2401.08124 (2024) - 2023
- [j21]Parantapa Bhattacharya
, Jiangzhuo Chen, Stefan Hoops, Dustin Machi, Bryan L. Lewis, Srinivasan Venkatramanan
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) - [j20]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: 102020 (2023) - [c11]Sami Saliba, Faraz Dadgostari, Stefan Hoops, Henning S. Mortveit, Samarth Swarup:
Active Sensing for Epidemic State Estimation Using ABM-Guided Machine Learning. MABS 2023: 30-45 - [c10]Galen Harrison, Przemyslaw J. Porebski, Jiangzhuo Chen, Mandy L. Wilson, Henning S. Mortveit, Parantapa Bhattacharya, Dawen Xie, Stefan Hoops, Anil Vullikanti
Synthetic Information and Digital Twins for Pandemic Science: Challenges and Opportunities. TPS-ISA 2023: 23-33 - 2022
- [j19]Bilal Shaikh
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
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
BioSimulators: a central registry of simulation engines and services for recommending specific tools. CoRR abs/2203.06732 (2022) - 2021
- [j18]Franziska Hufsky, Kevin Lamkiewicz, Alexandre Almeida
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
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
High Performance Agent-Based Modeling to Study Realistic Contact Tracing Protocols. WSC 2021: 1-12
2010 – 2019
- 2019
- [j17]S. Ha, Elena S. Dimitrova, Stefan Hoops, Doaa Altarawy, Mitra Ansariola, D. Deb, Jane Glazebrook, R. Hillmer, Hossameldin Shahin, Fumiaki Katagiri
PlantSimLab - a modeling and simulation web tool for plant biologists. BMC Bioinform. 20(1): 508 (2019) - [j16]Michael Hucka
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2. J. Integr. Bioinform. 16(2) (2019) - 2018
- [j15]Michael Hucka
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core. J. Integr. Bioinform. 15(1) (2018) - [j14]Michael Hucka
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core. J. Integr. Bioinform. 15(1) (2018) - [j13]Thomas C. Jones Jr
JigCell Model Connector: building large molecular network models from components. Simul. 94(11) (2018) - 2015
- [j12]Pinyi Lu, Vida Abedi
Supervised learning methods in modeling of CD4+ T cell heterogeneity. BioData Min. 8: 27 (2015) - [j11]Yongguo Mei, Vida Abedi
Multiscale modeling of mucosal immune responses. BMC Bioinform. 16(S12): S2 (2015) - [j10]Alida Palmisano
JigCell Run Manager (JC-RM): a tool for managing large sets of biochemical model parametrizations. BMC Syst. Biol. 9: 95 (2015) - [j9]Michael Hucka
Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions. J. Integr. Bioinform. 12(2) (2015) - [j8]Michael Hucka
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core. J. Integr. Bioinform. 12(2) (2015) - [j7]Lucian Paul Smith
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
ENISI multiscale modeling of mucosal immune responses driven by high performance computing. BIBM 2015: 680-684 - 2014
- [j5]Alida Palmisano
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
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
ENISI Visual, an agent-based simulator for modeling gut immunity. BIBM 2012: 1-5 - [c2]Keith R. Bisset, Md. Maksudul Alam
High-Performance Interaction-Based Simulation of Gut Immunopathologies with ENteric Immunity Simulator (ENISI). IPDPS 2012: 48-59 - 2011
- [j2]Dagmar Waltemath, Richard R. Adams
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
COPASI - a COmplex PAthway SImulator. Bioinform. 22(24): 3067-3074 (2006) - [c1]Sven Sahle, Ralph Gauges, Jürgen Pahle
Simulation of biochemical networks using COPASI: a complex pathway simulator. WSC 2006: 1698-1706
Coauthor Index
Madhav V. Marathe
aka: Madhav Vinayak Marathe
aka: Madhav Vinayak Marathe
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