Stefan Hoops
Stefan Hoops
Research Associate Professor, Biocomplexity Institute & Initiative, University of Virginia
Verified email at
Cited by
Cited by
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
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
Computational modeling of biochemical networks using COPASI
P Mendes, S Hoops, S Sahle, R Gauges, J Dada, U Kummer
Systems Biology, 17-59, 2009
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
The systems biology markup language (SBML): Language specification for level 3 version 1 core
L Smith, D Wilkinson, M Hucka, F Bergmann, S Hoops, S Keating, S Sahle, ...
Nature Precedings, 1-1, 2010
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 Comput Biol 9 (4), e1003027, 2013
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
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
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
COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project
FT Bergmann, R Adams, S Moodie, J Cooper, M Glont, M Golebiewski, ...
BMC bioinformatics 15 (1), 1-9, 2014
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
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
Condor-COPASI: high-throughput computing for biochemical networks
E Kent, S Hoops, P Mendes
BMC systems biology 6 (1), 91, 2012
Hybrid modeling and simulation of stochastic effects on progression through the eukaryotic cell cycle
Z Liu, Y Pu, F Li, CA Shaffer, S Hoops, JJ Tyson, Y Cao
The Journal of chemical physics 136 (3), 034105, 2012
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, ...
PLoS One 7 (10), e47525, 2012
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
ENteric Immunity SImulator: a tool for in silico study of gastroenteric infections
KV Wendelsdorf, M Alam, J Bassaganya-Riera, K Bisset, S Eubank, ...
IEEE transactions on nanobioscience 11 (3), 273-288, 2012
Enzyme kinetics and computational modeling for systems biology
P Mendes, H Messiha, N Malys, S Hoops
Methods in enzymology 467, 583-599, 2009
Systems modeling of interactions between mucosal immunity and the gut microbiome during clostridium difficile infection
A Leber, M Viladomiu, R Hontecillas, V Abedi, C Philipson, S Hoops, ...
PLoS One 10 (7), e0134849, 2015
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
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