| 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 | 2817 | 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 | 309 | 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 | 226 | 2009 |
| 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 | 209* | 2018 |
| 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 | 149 | 2011 |
| 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 | 142 | 2020 |
| 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 | 120 | 2021 |
| 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 | 107 | 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 | 89 | 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 | 89 | 2008 |
| 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 | 76 | 2017 |
| 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 | 73 | 2019 |
| 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 | 60 | 2013 |
| Condor-COPASI: high-throughput computing for biochemical networks E Kent, S Hoops, P Mendes BMC systems biology 6 (1), 1-13, 2012 | 50 | 2012 |
| 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 | 50 | 2008 |
| 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 | 49 | 2014 |
| 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 | 46 | 2015 |
| 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 | 45 | 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 | 44 | 2012 |
| 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 | 43 | 2015 |
Pedro MendesUniversity of ConnecticutVerified email at uchc.edu
