| CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms C Terfve, T Cokelaer, D Henriques, A MacNamara, E Goncalves, ... BMC systems biology 6 (1), 1-14, 2012 | 220 | 2012 |
| MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics JA Egea, D Henriques, T Cokelaer, AF Villaverde, A MacNamara, ... BMC bioinformatics 15 (1), 1-9, 2014 | 171 | 2014 |
| AMIGO2, a toolbox for dynamic modeling, optimization and control in systems biology E Balsa-Canto, D Henriques, A Gábor, JR Banga Bioinformatics 32 (21), 3357-3359, 2016 | 141 | 2016 |
| State–time spectrum of signal transduction logic models A MacNamara, C Terfve, D Henriques, BP Bernabé, J Saez-Rodriguez Physical biology 9 (4), 045003, 2012 | 85 | 2012 |
| BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology AF Villaverde, D Henriques, K Smallbone, S Bongard, J Schmid, ... BMC systems biology 9 (1), 1-15, 2015 | 84 | 2015 |
| Data-driven reverse engineering of signaling pathways using ensembles of dynamic models D Henriques, AF Villaverde, M Rocha, J Saez-Rodriguez, JR Banga PLoS computational biology 13 (2), e1005379, 2017 | 49 | 2017 |
| SYNBADm: a tool for optimization-based automated design of synthetic gene circuits I Otero-Muras, D Henriques, JR Banga Bioinformatics 32 (21), 3360-3362, 2016 | 31 | 2016 |
| Saccharomyces cerevisiae and S. kudriavzevii Synthetic Wine Fermentation Performance Dissected by Predictive Modeling D Henriques, J Alonso-del-Real, A Querol, E Balsa-Canto Frontiers in Microbiology 9, 88, 2018 | 24 | 2018 |
| Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach D Henriques, M Rocha, J Saez-Rodriguez, JR Banga Bioinformatics 31 (18), 2999-3007, 2015 | 21 | 2015 |
| Systems pharmacology dissection of cholesterol regulation reveals determinants of large pharmacodynamic variability between cell lines P Blattmann, D Henriques, M Zimmermann, F Frommelt, U Sauer, ... Cell systems 5 (6), 604-619. e7, 2017 | 17 | 2017 |
| A parallel metaheuristic for large mixed-integer dynamic optimization problems, with applications in computational biology DR Penas, D Henriques, P González, R Doallo, J Saez-Rodriguez, ... PLoS One 12 (8), e0182186, 2017 | 15 | 2017 |
| A Multiphase Multiobjective Dynamic Genome-Scale Model Shows Different Redox Balancing among Yeast Species of the Saccharomyces Genus in Fermentation D Henriques, R Minebois, SN Mendoza, LG Macías, R Pérez-Torrado, ... Msystems 6 (4), e00260-21, 2021 | 11 | 2021 |
| The Monod model is insufficient to explain biomass growth in nitrogen-limited yeast fermentation D Henriques, E Balsa-Canto Applied and environmental microbiology 87 (20), e01084-21, 2021 | 8 | 2021 |
| A multi-phase multi-objective dynamic genome-scale model shows different redox balancing among yeast species in fermentation D Henriques, R Minebois, S Mendoza, LG Macías, R Pérez-Torrado, ... bioRxiv, 2021.03. 08.434513, 2021 | 8 | 2021 |
| Modeling signaling networks with different formalisms: a preview A MacNamara, D Henriques, J Saez-Rodriguez In Silico Systems Biology, 89-105, 2013 | 5 | 2013 |
| A Dynamic Genome-Scale Model Identifies Metabolic Pathways Associated with Cold Tolerance in Saccharomyces kudriavzevii D Henriques, R Minebois, D Dos Santos, E Barrio, A Querol, ... Microbiology Spectrum, e03519-22, 2023 | | 2023 |
| Dynamic genome‐scale modeling of Saccharomyces cerevisiae unravels mechanisms for ester formation during alcoholic fermentation WT Scott, D Henriques, EJ Smid, RA Notebaart, E Balsa‐Canto Biotechnology and Bioengineering, 2023 | | 2023 |
| Modelling the physiological status of yeast during wine fermentation enables the prediction of secondary metabolism AR Moimenta, D Henriques, R Minebois, A Querol, E Balsa‐Canto Microbial biotechnology 16 (4), 847-861, 2023 | | 2023 |
| Dynamic genome-scale modeling of Saccharomyces cerevisiae unravels mechanisms for higher alcohol and ester formation during alcoholic fermentation WT Scott Jr, D Henriques, EJ Smid, RA Notebaart, E Balsa-Canto bioRxiv, 2022.05. 27.493771, 2022 | | 2022 |
| Optimización de procesos fermentativos basada en el análisis multiómico de las diferencias del metabolismo entre levaduras del género Saccharomyces A Querol, R Minebois, S Albillos, D Henriques, E Balsa-Canto, E Barrio | | 2022 |
Julio Saez RodriguezHeidelberg UniversityVerified email at bioquant.uni-heidelberg.de
