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Stefan Hoops
Stefan Hoops
Research Associate Professor, Biocomplexity Institute & Initiative, University of Virginia
Verified email at virginia.edu
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Year
COPASI—a complex pathway simulator
S Hoops, S Sahle, R Gauges, C Lee, J Pahle, N Simus, M Singhal, L Xu, ...
Bioinformatics 22 (24), 3067-3074, 2006
29872006
Controlled vocabularies and semantics in systems biology
M Courtot, N Juty, C Knüpfer, D Waltemath, A Zhukova, A Dräger, ...
Molecular systems biology 7 (1), 543, 2011
3372011
Computational modeling of biochemical networks using COPASI
P Mendes, S Hoops, S Sahle, R Gauges, J Dada, U Kummer
Systems Biology, 17-59, 2009
2462009
Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core
WDJ Hucka M, Bergmann FT, Dräger A, Hoops S, Keating SM, Le Novère N, Myers ...
Journal of Integrative Bioinformatics, 2018
235*2018
SBML Level 3: an extensible format for the exchange and reuse of biological models
SM Keating, D Waltemath, M König, F Zhang, A Dräger, C Chaouiya, ...
Molecular systems biology 16 (8), e9110, 2020
2092020
Minimum information about a simulation experiment (MIASE)
D Waltemath, R Adams, DA Beard, FT Bergmann, US Bhalla, R Britten, ...
PLoS computational biology 7 (4), e1001122, 2011
1632011
Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research
F Hufsky, K Lamkiewicz, A Almeida, A Aouacheria, C Arighi, A Bateman, ...
Briefings in bioinformatics 22 (2), 642-663, 2021
1442021
Systems modeling of molecular mechanisms controlling cytokine-driven CD4+ T cell differentiation and phenotype plasticity
A Carbo, R Hontecillas, B Kronsteiner, M Viladomiu, M Pedragosa, P Lu, ...
PLoS computational biology 9 (4), e1003027, 2013
1202013
The systems biology markup language (SBML): language specification for level 3 version 2 core release 2
M Hucka, FT Bergmann, C Chaouiya, A Dräger, S Hoops, SM Keating, ...
Journal of integrative bioinformatics 16 (2), 20190021, 2019
1102019
COPASI and its applications in biotechnology
FT Bergmann, S Hoops, B Klahn, U Kummer, P Mendes, J Pahle, S Sahle
Journal of biotechnology 261, 215-220, 2017
932017
Systems biology markup language (SBML) level 2: Structures and facilities for model definitions
M Hucka, S Hoops, S Keating, N Le Novère, S Sahle, D Wilkinson
Nature Precedings, 1-1, 2008
902008
Epidemiological and economic impact of COVID-19 in the US
J Chen, A Vullikanti, J Santos, S Venkatramanan, S Hoops, H Mortveit, ...
Scientific reports 11 (1), 20451, 2021
742021
Predictive computational modeling of the mucosal immune responses during Helicobacter pylori infection
A Carbo, J Bassaganya-Riera, M Pedragosa, M Viladomiu, M Marathe, ...
PloS one 8 (9), e73365, 2013
672013
Condor-COPASI: high-throughput computing for biochemical networks
E Kent, S Hoops, P Mendes
BMC systems biology 6, 1-13, 2012
582012
Prioritizing allocation of COVID-19 vaccines based on social contacts increases vaccination effectiveness
J Chen, S Hoops, A Marathe, H Mortveit, B Lewis, S Venkatramanan, ...
MedRxiv, 2021.02. 04.21251012, 2021
562021
Computational modeling of heterogeneity and function of CD4+ T cells
A Carbo, R Hontecillas, T Andrew, K Eden, Y Mei, S Hoops, ...
Frontiers in cell and developmental biology 2, 31, 2014
542014
A new strategy for assessing sensitivities in biochemical models
S Sahle, P Mendes, S Hoops, U Kummer
Philosophical Transactions of the Royal Society A: Mathematical, Physical …, 2008
522008
SBML level 3 package: hierarchical model composition, version 1 release 3
LP Smith, M Hucka, S Hoops, A Finney, M Ginkel, CJ Myers, I Moraru, ...
Journal of integrative bioinformatics 12 (2), 603-659, 2015
512015
Modeling the regulatory mechanisms by which NLRX1 modulates innate immune responses to Helicobacter pylori infection
CW Philipson, J Bassaganya-Riera, M Viladomiu, B Kronsteiner, V Abedi, ...
PloS one 10 (9), e0137839, 2015
472015
Modeling the Role of Peroxisome Proliferator-Activated Receptor γ and MicroRNA-146 in Mucosal Immune Responses to Clostridium difficile
M Viladomiu, R Hontecillas, M Pedragosa, A Carbo, S Hoops, P Michalak, ...
Public Library of Science 7 (10), e47525, 2012
472012
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