@article{arboleda2024dbtl,

title = {DBTL bioengineering cycle for part characterization and refactoring},

author = {A Arboleda-Garcia and M Stiebritz and Y Boada and J Picó and A Vignoni},

year  = {2024},

date = {2024-01-01},

urldate = {2024-01-01},

journal = {IFAC-PapersOnLine},

volume = {58},

number = {23},

pages = {7–12},

publisher = {Elsevier},

keywords = {DBTL},

pubstate = {published},

tppubtype = {article}

}

@article{diaz2024mini,

title = {Mini-bioreactor for parts characterization of a biological circuit: Absorbance and Fluorescence measurement calibration, and online growth rate estimation},

author = {H D'ıaz-Iza and A Arboleda and Y Boada and J Picó and A Vignoni},

year  = {2024},

date = {2024-01-01},

journal = {IFAC-PapersOnLine},

volume = {58},

number = {23},

pages = {97–102},

publisher = {Elsevier},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{maton2024towards,

title = {Towards Constraint-Based Burden-Aware Models for Metabolic Engineering},

author = {M Maton and FN Santos-Navarro and J Picó and Ph Bogaerts and A Vande Wouwer},

year  = {2024},

date = {2024-01-01},

journal = {IFAC-PapersOnLine},

volume = {58},

number = {14},

pages = {247–252},

publisher = {Elsevier},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{gonzalez2023platero,

title = {PLATERO: a calibration protocol for plate reader green fluorescence measurements},

author = {Alba González-Cebrián and Joan Borràs-Ferr'ıs and Yadira Boada and Alejandro Vignoni and Alberto Ferrer and Jesús Picó},

year  = {2023},

date = {2023-01-01},

journal = {Frontiers in Bioengineering and Biotechnology},

volume = {11},

pages = {1104445},

publisher = {Frontiers Media SA},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pushkareva2023towards,

title = {Towards automation of the design-build-test-learn (dbtl) bioengineering cycle: Application to the testing and characterization of standard bioparts},

author = {Anna Pushkareva and Jaime Beltrán and Harold D'ıaz-Iza and Andrés Arboleda-Garc'ıa and Yadira Boada and Alejandro Vignoni and Jesús Picó},

year  = {2023},

date = {2023-01-01},

journal = {XLIV Jornadas de Automática},

pages = {453–458},

publisher = {Universidade da Coruña. Servizo de Publicacións},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{boada2022modeling,

title = {Modeling and optimization of a molecular biocontroller for the regulation of complex metabolic pathways},

author = {Yadira Boada and Fernando N Santos-Navarro and Jesús Picó and Alejandro Vignoni},

year  = {2022},

date = {2022-01-01},

journal = {Frontiers in Molecular Biosciences},

volume = {9},

pages = {801032},

publisher = {Frontiers Media SA},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{santos2022onemodel,

title = {Onemodel: an open-source sbml modeling tool focused on accessibility, simplicity and modularity},

author = {FN Santos-Navarro and JL Navarro and Y Boada and A Vignoni and J Pico},

year  = {2022},

date = {2022-01-01},

journal = {IFAC-PapersOnLine},

volume = {55},

number = {7},

pages = {125–130},

publisher = {Elsevier},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{boada2022optimization,

title = {Optimization of the dynamic regulation in a branch-in metabolic pathway},

author = {Y Boada and FN Santos-Navarro and A Vignoni and J Picó},

year  = {2022},

date = {2022-01-01},

journal = {IFAC-PapersOnLine},

volume = {55},

number = {7},

pages = {119–124},

publisher = {Elsevier},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{santos2021gene,

title = {Gene expression space shapes the bioprocess trade-offs among titer, yield and productivity},

author = {Fernando N Santos-Navarro and Yadira Boada and Alejandro Vignoni and Jesús Picó},

year  = {2021},

date = {2021-01-01},

journal = {Applied Sciences},

volume = {11},

number = {13},

pages = {5859},

publisher = {MDPI},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{santos2021rbs,

title = {RBS and promoter strengths determine the cell-growth-dependent protein mass fractions and their optimal synthesis rates},

author = {Fernando N Santos-Navarro and Alejandro Vignoni and Yadira Boada and Jesús Picó},

year  = {2021},

date = {2021-01-01},

journal = {ACS synthetic biology},

volume = {10},

number = {12},

pages = {3290–3303},

publisher = {American Chemical Society},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pico2021stochastic,

title = {Stochastic differential equations for practical simulation of gene circuits},

author = {Jesús Picó and Alejandro Vignoni and Yadira Boada},

year  = {2021},

date = {2021-01-01},

journal = {Synthetic Gene Circuits: Methods and Protocols},

pages = {41–90},

publisher = {Springer US},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{boada2020extended,

title = {Extended metabolic biosensor design for dynamic pathway regulation of cell factories},

author = {Yadira Boada and Alejandro Vignoni and Jesús Picó and Pablo Carbonell},

year  = {2020},

date = {2020-01-01},

journal = {Iscience},

volume = {23},

number = {7},

publisher = {Elsevier},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nobel2020resources,

title = {Resources allocation explains the differential roles of RBS and promoter strengths in cell mass distribution and optimal protein expression productivity},

author = {Fernando Nóbel and Jesús Picó},

year  = {2020},

date = {2020-01-01},

journal = {bioRxiv},

pages = {2020–11},

publisher = {Cold Spring Harbor Laboratory},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nunez2019analysis,

title = {Analysis of transcriptional feedback strategy for reducing interaction in gene expression processes},

author = {Sebastián Nuñez and Fabricio Garelli and Jesús Picó and Hernán De Battista},

year  = {2019},

date = {2019-01-01},

journal = {IFAC-PapersOnLine},

volume = {52},

number = {1},

pages = {526–531},

publisher = {Elsevier},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{de2019biomolecular,

title = {Biomolecular signal tracker with fast time response.},

author = {Hernán De Battista and J Picó and Enric Picó-Marco and A Vignoni},

year  = {2019},

date = {2019-01-01},

journal = {IFAC-PapersOnLine},

volume = {52},

number = {26},

pages = {1–6},

publisher = {Elsevier},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{boada2019characterization,

title = {Characterization of gene circuit parts based on multiobjective optimization by using standard calibrated measurements},

author = {Yadira Boada and Alejandro Vignoni and Iván Alarcon-Ruiz and Carlos Andreu-Vilarroig and Roger Monfort-Llorens and Adrián Requena and Jesús Picó},

year  = {2019},

date = {2019-01-01},

journal = {ChemBioChem},

volume = {20},

number = {20},

pages = {2653–2665},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{vignoni2019fluorescence,

title = {Fluorescence calibration and color equivalence for quantitative synthetic biology.},

author = {A Vignoni and Y Boada and L Boada Acosta and C Andreu-Vilarroig and I Alarcón and A Requena and J Picó},

year  = {2019},

date = {2019-01-01},

journal = {IFAC-PapersOnLine},

volume = {52},

number = {26},

pages = {129–134},

publisher = {Elsevier},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{boada2019multiobjective,

title = {Multiobjective identification of a feedback synthetic gene circuit},

author = {Yadira Boada and Alejandro Vignoni and Jesús Picó},

year  = {2019},

date = {2019-01-01},

journal = {IEEE Transactions on Control Systems Technology},

volume = {28},

number = {1},

pages = {208–223},

publisher = {IEEE},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nobel2019reference,

title = {Reference conditioning anti-windup for the biomolecular antithetic controller},

author = {F Nóbel and H De Battista and S Nuñez and J Picó},

year  = {2019},

date = {2019-01-01},

journal = {IFAC-PapersOnLine},

volume = {52},

number = {26},

pages = {156–162},

publisher = {Elsevier},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{beguerisse2018flux,

title = {Flux-dependent graphs for metabolic networks},

author = {Mariano Beguerisse-D'ıaz and Gabriel Bosque and Diego Oyarzún and Jesús Picó and Mauricio Barahona},

year  = {2018},

date = {2018-01-01},

journal = {NPJ systems biology and applications},

volume = {4},

number = {1},

pages = {32},

publisher = {Nature Publishing Group UK London},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{de2018global,

title = {Global stabilisation of continuous bioreactors: Tools for analysis and design of feeding laws},

author = {Hernán De Battista and Mart'ın Jamilis and Fabricio Garelli and Jesús Picó},

year  = {2018},

date = {2018-01-01},

journal = {Automatica},

volume = {89},

pages = {340–348},

publisher = {Pergamon},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{boada2018host,

title = {Host-circuit interactions explain unexpected behavior of a gene circuit.},

author = {Y Boada and A Vignoni and D Oyarzún and J Picó},

year  = {2018},

date = {2018-01-01},

journal = {IFAC-PapersOnLine},

volume = {51},

number = {19},

pages = {86–89},

publisher = {Elsevier},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{de2018output,

title = {Output feedback linearization of turbidostats after time scaling},

author = {Hernán De Battista and Enric Picó-Marco and Fernando N Santos-Navarro and Jesús Picó},

year  = {2018},

date = {2018-01-01},

journal = {IEEE Transactions on Control Systems Technology},

volume = {27},

number = {4},

pages = {1668–1676},

publisher = {IEEE},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{boada2017engineered,

title = {Engineered control of genetic variability reveals interplay among quorum sensing, feedback regulation, and biochemical noise},

author = {Yadira Boada and Alejandro Vignoni and Jesús Picó},

year  = {2017},

date = {2017-01-01},

journal = {ACS synthetic biology},

volume = {6},

number = {10},

pages = {1903–1912},

publisher = {American Chemical Society},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{boada2017multib,

title = {Multi-objective optimization for gene expression noise reduction in a synthetic gene circuit},

author = {Yadira Boada and Alejandro Vignoni and Jesús Picó},

year  = {2017},

date = {2017-01-01},

journal = {IFAC-PapersOnLine},

volume = {50},

number = {1},

pages = {4472–4477},

publisher = {Elsevier},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{boada2017promoter,

title = {Promoter and transcription factor dynamics tune protein mean and noise strength in a quorum sensing-based feedback synthetic circuit},

author = {Yadira Boada and Alejandro Vignoni and Jesús Picó},

year  = {2017},

date = {2017-01-01},

journal = {bioRxiv},

pages = {106229},

publisher = {Cold Spring Harbor Laboratory},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{boada2017reduction,

title = {Reduction of population variability in protein expression: A control engineering approach},

author = {Yadira Boada and Alejandro Vignoli and Jesús Picó},

year  = {2017},

date = {2017-01-01},

journal = {Actas de las XXXVIII Jornadas de Automática},

publisher = {Servicio de Publicaciones de la Universidad de Oviedo},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{beguerisse2016context,

title = {Context-dependent metabolic networks},

author = {Mariano Beguerisse-Dıaz and Gabriel Bosque and Diego Oyarzún and Jesús Picó and Mauricio Barahona},

year  = {2016},

date = {2016-01-01},

journal = {arXiv preprint arXiv:1605.01639},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pico2016contractivity,

title = {Contractivity of a genetic circuit with internal feedback and cell-to-cell communication},

author = {Enric Picó-Marco and Yadira Boada and Jesús Picó and Alejandro Vignoni},

year  = {2016},

date = {2016-01-01},

journal = {Ifac-Papersonline},

volume = {49},

number = {26},

pages = {213–218},

publisher = {Elsevier},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{folch2016fusion,

title = {Fusion of genomic, proteomic and phenotypic data: The case of potyviruses},

author = {A Folch-Fortuny and G Bosque and Jesús Picó and A Ferrer and SF Elena},

year  = {2016},

date = {2016-01-01},

journal = {Molecular BioSystems},

volume = {12},

number = {1},

pages = {253–261},

publisher = {Royal Society of Chemistry},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{boada2016multi,

title = {Multi-objective optimization framework to obtain model-based guidelines for tuning biological synthetic devices: an adaptive network case},

author = {Yadira Boada and Gilberto Reynoso-Meza and Jesús Picó and Alejandro Vignoni},

year  = {2016},

date = {2016-01-01},

journal = {BMC systems biology},

volume = {10},

pages = {1–19},

publisher = {BioMed Central},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{boada2016optimization,

title = {Optimization alternatives for robust model-based design of synthetic biological circuits},

author = {Yadira Boada and José Luis Pitarch and Alejandro Vignoni and Gilberto Reynoso-Meza and Jesús Picó},

year  = {2016},

date = {2016-01-01},

journal = {Ifac-Papersonline},

volume = {49},

number = {7},

pages = {821–826},

publisher = {Elsevier},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{boada2016parameter,

title = {Parameter identification in synthetic biological circuits using multi-objective optimization},

author = {Yadira Boada and Alejandro Vignoni and Gilberto Reynoso-Meza and Jesús Picó},

year  = {2016},

date = {2016-01-01},

journal = {Ifac-Papersonline},

volume = {49},

number = {26},

pages = {77–82},

publisher = {Elsevier},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{morales2016pfa,

title = {PFA toolbox: a MATLAB tool for Metabolic Flux Analysis},

author = {Yeimy Morales and Gabriel Bosque and Josep Veh'ı and Jesús Picó and Francisco Llaneras},

year  = {2016},

date = {2016-01-01},

journal = {BMC systems biology},

volume = {10},

pages = {1–10},

publisher = {BioMed Central},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{reynoso2016pid,

title = {PID controller tuning for unstable processes using a multi-objective optimisation design procedure},

author = {Gilberto Reynoso-Meza and J Carrillo-Ahumada and Y Boada and Jesús Picó},

year  = {2016},

date = {2016-01-01},

journal = {IFAC-PapersOnLine},

volume = {49},

number = {7},

pages = {284–289},

publisher = {Elsevier},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{folch2015mcr,

title = {MCR-ALS on metabolic networks: Obtaining more meaningful pathways},

author = {Abel Folch-Fortuny and M Tortajada and José Manuel Prats-Montalbán and F Llaneras and J Picó and A Ferrer},

year  = {2015},

date = {2015-01-01},

journal = {Chemometrics and Intelligent Laboratory Systems},

volume = {142},

pages = {293–303},

publisher = {Elsevier},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pico2015modelado,

title = {Modelado de sistemas bioqu'ımicos: De la ley de acción de masas a la aproximación lineal del ruido},

author = {Jesús Picó and Alejandro Vignoni and Enric Picó-Marco and Yadira Boada},

year  = {2015},

date = {2015-01-01},

journal = {Revista Iberoamericana de Automática e Informática Industrial RIAI},

volume = {12},

number = {3},

pages = {241–252},

publisher = {No longer published by Elsevier},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pico2015modelling,

title = {Modelling biochemical systems: from mass action kinetics to linear noise approximation},

author = {Jesús Picó and Alejandro Vignoni and Enric Picó-Marco and Yadira Boada},

year  = {2015},

date = {2015-01-01},

journal = {REVISTA IBEROAMERICANA DE AUTOMATICA E INFORMATICA INDUSTRIAL},

volume = {12},

number = {3},

pages = {241–252},

publisher = {COMITE ESPANOL AUTOMATICA CEA C VERA 14, APDO 22012, VALENCIA, E-46071, SPAIN},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{zach2014alternativas,

title = {Alternativas de biologıa sintética para el control de rutas metabólicas},

author = {Pavel Zach and Alejandro Vignoni and Daniel Georgiev and Jesús Picó},

year  = {2014},

date = {2014-01-01},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nunez2014diseno,

title = {Diseno de control no lineal para regulación de tasa de crecimiento en cultivos multi-sustrato},

author = {Sebastián Nunez and Fabricio Garelli and Hernán De Battista and Jesús Picó},

year  = {2014},

date = {2014-01-01},

journal = {Actas de las XXXV Jornadas de Automática, Espana},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{gonzalez2014metabolic,

title = {Metabolic flux understanding of Pichia pastoris grown on heterogenous culture media},

author = {José Mar'ıa González-Mart'ınez and Abel Folch-Fortuny and F Llaneras and M Tortajada and J Picó and Alberto Ferrer},

year  = {2014},

date = {2014-01-01},

journal = {Chemometrics and Intelligent Laboratory Systems},

volume = {134},

pages = {89–99},

publisher = {Elsevier},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nunez2014sufficient,

title = {Sufficient conditions for state observability in multi-substrate bioprocesses with additive growth dynamics},

author = {Sebastian Nuñez and Hernan De Battista and Fabricio Garelli and Jesus Picó},

year  = {2014},

date = {2014-01-01},

journal = {IEEE Latin America Transactions},

volume = {12},

number = {5},

pages = {928–934},

publisher = {IEEE},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{bosque2014topology,

title = {Topology analysis and visualization of Potyvirus protein-protein interaction network},

author = {Gabriel Bosque and Abel Folch-Fortuny and Jesús Picó and Alberto Ferrer and Santiago F Elena},

year  = {2014},

date = {2014-01-01},

journal = {BMC systems biology},

volume = {8},

pages = {1–15},

publisher = {BioMed Central},

keywords = {},

pubstate = {published},

tppubtype = {article}

}