| 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 | 2478 | 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 | 270 | 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 | 207 | 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 | 135 | 2011 |
| 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 | 109* | 2018 |
| 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 | 99 | 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 computational biology 9 (4), e1003027, 2013 | 97 | 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 | 86 | 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 | 86 | 2008 |
| 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 | 56 | 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 | 49 | 2008 |
| 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 | 47 | 2020 |
| Condor-COPASI: high-throughput computing for biochemical networks E Kent, S Hoops, P Mendes BMC systems biology 6 (1), 1-13, 2012 | 43 | 2012 |
| 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 | 40 | 2021 |
| 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 | 39 | 2017 |
| 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 | 39 | 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 | 38 | 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 | 37 | 2014 |
| 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 | 35 | 2015 |
| 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 | 33 | 2015 |
Pedro MendesUniversity of ConnecticutVerified email at uchc.edu
