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David Saque Henriques
David Saque Henriques
Post-Doctoral Researcher, IIM-CSIC
Verified email at iim.csic.es
Title
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Cited by
Year
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, 1-14, 2012
2422012
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, 1-9, 2014
1852014
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
1552016
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, 1-15, 2015
902015
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
892012
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
532017
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
382016
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
332018
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
252015
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), 10.1128/msystems. 00260-21, 2021
212021
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
212017
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
212017
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
92021
A multiphase multiobjective dynamic genome-scale model shows different redox balancing among yeast species of the
D Henriques, R Minebois, SN Mendoza, LG Macías, R Pérez-Torrado, ...
Saccharomyces, 2021
92021
Modeling signaling networks with different formalisms: a preview
A MacNamara, D Henriques, J Saez-Rodriguez
In Silico Systems Biology, 89-105, 2013
72013
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
42023
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 120 (7), 1998-2012, 2023
32023
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 11 (3), e03519-22, 2023
22023
A New GIMME–Based Heuristic for Compartmentalised Transcriptomics Data Integration
D Troitiño-Jordedo, L Carvalho, D Henriques, V Pereira, M Rocha, ...
International Conference on Practical Applications of Computational Biology …, 2023
12023
A continuous dynamic genome-scale model explains batch fermentations led by species of the Saccharomyces genus.
A R. Moimenta, D Troitino-Jordedo, D Henriques, A Contreras-Ruiz, ...
bioRxiv, 2024.05. 03.592398, 2024
2024
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