Publications

• Paper: 2023, Advancements in synthetic biology-based bacterial cancer therapy: A modular design approach,
  Journal: Critical Reviews in Oncology/Hematology, Number , Volume 190, Pagess: –
  DOI: https://doi.org/10.1016/j.critrevonc.2023.104088 – HANDLE: http://hdl.handle.net/10251/205785
  Authors: Arboleda-García, Mario Andrés; Ivan Alarcon-Ruiz; Boada-Acosta, Lissette Anahi; Boada-Acosta, Yadira Fernanda; Vignoni, Alejandro; Jantus-Lewintre, Eloisa
  

• Book chapter: 2023, Multi-Objective Optimization Tuning Framework for Kinetic Parameter Selection and Estimation,
  Reference: Computational Methods for Estimating the Kinetic Parameters of Biological Systems, Chapter:  4, Pages: –
  Editorial: Humana Press – 978-1-0716-1766-3,
  Authors: Boada-Acosta, Yadira Fernanda; Picó, Jesús; Vignoni, Alejandro

• Paper: 2023, PLATERO: A Calibration Protocol for Plate Reader Green Fluorescence Measurements,
  Journal: Frontiers in Bioengineering and Biotechnology, Number , Volume 11, Pagess: –
  DOI: https://doi.org/10.3389/fbioe.2023.1104445 – HANDLE: http://hdl.handle.net/10251/204157
  Authors: A. González-Cebrián; Borràs-Ferrís, Joan; Boada-Acosta, Yadira Fernanda; Vignoni, Alejandro; Ferrer, Alberto; Picó, Jesús
  

• Paper: 2022, Modeling and Optimization of a Molecular Biocontroller for the Regulation of Complex Metabolic Pathways,
  Journal: Frontiers in Molecular Biosciences, Number , Volume 9, Pagess: 1- 14
  DOI: https://doi.org/10.3389/fmolb.2022.801032 – HANDLE:
  Authors: Boada-Acosta, Yadira Fernanda; Santos-Navarro, Fernando Nóbel; Picó, Jesús; Vignoni, Alejandro
  

• Thesis: 2022, Multi-scale host-aware modeling for analysis and tuning of synthetic gene circuits for bioproduction
  Publication date: 20/05/2022
  Author: Fernando Nóbel Santos Navarro,
  Director/s: Picó, Jesús; Vignoni, Alejandro

• Paper: 2022, Multicolor plate reader fluorescence calibration,
  Journal: Synthetic Biology, Number 1, Volume 7, Pagess: –
  DOI: https://doi.org/10.1093/synbio/ysac010 – HANDLE:
  Authors: Vignoni, Alejandro; Boada-Acosta, Yadira Fernanda
  

• Paper: 2022, OneModel: an open-source SBML modeling tool focused on accessibility, simplicity and modularity,
  Journal: IFAC-PapersOnLine, Number , Volume , Pagess: 125- 130
  DOI: https://doi.org/10.1016/j.ifacol.2022.07.432 – HANDLE:
  Authors: Santos-Navarro, Fernando Nóbel; Navarro Herrero, José Luís; Boada-Acosta, Yadira Fernanda; Vignoni, Alejandro; Picó, Jesús
  

• Paper: 2022, Optimization of the dynamic regulation in a branch-in metabolic pathway,
  Journal: IFAC-PapersOnLine, Number , Volume , Pagess: 119- 124
  DOI: https://doi.org/10.1016/j.ifacol.2022.07.431 – HANDLE:
  Authors: Boada-Acosta, Yadira Fernanda; Santos-Navarro, Fernando Nóbel; Vignoni, Alejandro; Picó, Jesús
  

• Book chapter: 2021, Stochastic Differential Equations for Practical Simulation of Gene Circuits.,
  Reference: Synthetic Gene Circuits. Methods and Protocols, Chapter:  2, Pages: 41-
  Editorial: Springer- ISBN 978-1-0716-1031-2,
  Authors: Picó, Jesús; Vignoni, Alejandro; Boada-Acosta, Yadira Fernanda

• Paper: 2021, RBS and Promoter Strengths Determine the Cell-Growth-Dependent Protein Mass Fractions and Their Optimal Synthesis Rates,
  Journal: ACS Synthetic Biology, Number 12, Volume 10, Pagess: 3290- 3303
  DOI: 10.1021/acssynbio.1c00131 – HANDLE:
  Authors: Santos-Navarro, Fernando Nóbel; Vignoni, Alejandro; Boada-Acosta, Yadira Fernanda; Picó, Jesús
  

• Paper: 2021, Alkylation of a hydrophilic photosensitizer enhances the contact-dependent photo-induced oxidation of phospholipid membranes,
  Journal: Dyes and Pigments, Number 109131, Volume 187, Pagess: 1- 10
  DOI: https://doi.org/10.1016/j.dyepig.2020.109131 – HANDLE:
  Authors: Vignoni, Alejandro; Carla Layana; Helena C. Junqueira; Andrés Thomas; Rosangela Itri; Mauricio S. Baptista; Mariana Vignoni
  

• Paper: 2021, Gene Expression Space Shapes the Bioprocess Trade-Offs among Titer, Yield and Productivity,
  Journal: Applied Sciences, Number 13, Volume 11, Pagess: 5859-
  DOI: https://doi.org/10.3390/app11135859 – HANDLE:
  Authors: Santos-Navarro, Fernando Nóbel; Boada-Acosta, Yadira Fernanda; Vignoni, Alejandro; Picó, Jesús
  

• Paper: 2020, Extended metabolic biosensor design for dynamic pathway regulation of cell factories,
  Journal: iScience, Number 7, Volume 23, Pagess: 1- 25
  DOI: https://doi.org/10.1016/j.isci.2020.101305 – HANDLE:
  Authors: Boada-Acosta, Yadira Fernanda; Vignoni, Alejandro; Picó, Jesús; Carbonell, Pablo
  

• Paper: 2020, Multiobjective Identification of a Feedback Synthetic Gene Circuit,
  Journal: IEEE Transactions on Control Systems Technology, Number 1, Volume 28, Pagess: 208- 223
  DOI: https://doi.org/10.1109/TCST.2018.2885694 – HANDLE:
  Authors: Boada-Acosta, Yadira Fernanda; Vignoni, Alejandro; Picó, Jesús
  

• Paper: 2019, Biomolecular signal tracker with fast time response.,
  Journal: IFAC-PapersOnLine, Number 26, Volume 52, Pagess: 1- 6
  DOI: https://doi.org/10.1016/j.ifacol.2019.12.227 – HANDLE:
  Authors: De Battista, Hernán; Picó, Jesús; Picó-Marco, Enric ; Vignoni, Alejandro
  

• Paper: 2019, Characterization of gene circuits parts based on multi-objective optimization using standard calibrated measurements,
  Journal: ChemBioChem, Number , Volume 20, Pagess: 2653- 2665
  DOI: https://doi.org/10.1002/cbic.201900272 – HANDLE:
  Authors: Boada-Acosta, Yadira Fernanda; Vignoni, Alejandro; Ivan Alarcon-Ruiz; Carlos Andreu-Vilarroig; Roger Monfort-Llorens; Adrián Requena; Picó, Jesús
  

• Paper: 2019, Fluorescence calibration and color equivalence for quantitative synthetic biology,
  Journal: IFAC-PapersOnLine, Number 26, Volume 52, Pagess: 129- 134
  DOI: https://doi.org/10.1016/j.ifacol.2019.12.247 – HANDLE:
  Authors: Vignoni, Alejandro; Boada-Acosta, Yadira Fernanda; Lisset Boada-Acosta; Carlos Andreu-Vilarroig; Ivan Alarcon-Ruiz; Adrián Requena; Picó, Jesús
  

• Paper: 2019, Model mismatch in multi-objective optimisation and preservation of trade-off order,
  Journal: IFAC-PapersOnLine, Number 26, Volume 52, Pagess: 249- 254
  DOI: https://doi.org/10.1016/j.ifacol.2019.12.266 – HANDLE:
  Authors: Reynoso Meza, Gilberto; Vignoni, Alejandro; Boada-Acosta, Yadira Fernanda; Picó, Jesús; Picó-Marco, Enric
  

• Paper: 2018, Host-circuit interactions explain unexpected behavior of a gene circuit.,
  Journal: IFAC-PapersOnLine, Number 19, Volume 51, Pagess: 86- 89
  DOI: https://doi.org/10.1016/j.ifacol.2018.09.030 – HANDLE:
  Authors: Boada-Acosta, Yadira Fernanda; Vignoni, Alejandro; D. Oyarzún; Picó, Jesús
  

• Paper: 2018, Multi-objective identification from fluorescence recovery after photobleaching experiments: Understanding morphogenetic regulation of epithelial polarity,
  Journal: IFAC-PapersOnLine, Number 19, Volume 51, Pagess: 8- 11
  DOI: https://doi.org/10.1016/j.ifacol.2018.09.009 – HANDLE:
  Authors: Vignoni, Alejandro; A. Bajur; E. Knust; I. F. Sbalzarini