| The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models M Hucka, A Finney, HM Sauro, H Bolouri, JC Doyle, H Kitano, AP Arkin, ... Bioinformatics 19 (4), 524-531, 2003 | 3843 | 2003 |
| 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 | 3054 | 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 | 341 | 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 | 250 | 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 | 245* | 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 | 230 | 2020 |
| 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 | 172 | 2011 |
| 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 | 151 | 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 | 121 | 2013 |
| 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 | 111 | 2019 |
| 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 | 102 | 2017 |
| 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 | 91 | 2008 |
| 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 | 81 | 2021 |
| 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 | 67 | 2013 |
| Condor-COPASI: high-throughput computing for biochemical networks E Kent, S Hoops, P Mendes BMC systems biology 6, 1-13, 2012 | 61 | 2012 |
| 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 | 59 | 2021 |
| 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 | 57 | 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 | 56 | 2015 |
| 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 | 51 | 2008 |
| 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 | 49 | 2015 |
Pedro MendesUniversity of ConnecticutVerified email at uchc.edu
