Publications

• Paper: 2024, Computer-aided design and implementation of efficient biosynthetic pathways to produce high added-value products derived from tyrosine in Escherichia coli,
  Journal: Frontiers in Bioengineering and Biotechnology, Number , Volume 12, Pagess: –
  DOI: https://doi.org/10.3389/fbioe.2024.1360740 – HANDLE: http://hdl.handle.net/10251/208932
  Authors: Ferreira, Sofia; Balola, Alexandra; Sveshnikova, Anastasia; Hatzimanikatis, Vassily; Vilaça, Paulo; Maia, Paulo; Carreira, Rafael; Stoney, Ruth; Carbonell, Pablo; Souza, Caio Silva; Correia, Joao; Lousa, Diana; Soares, Claudio M.; Rocha, Isabel
  

• Paper: 2024, DetSpace: a web server for engineering detectable pathways for bio-based chemical production,
  Journal: Nucleic Acids Research, Number , Volume 1, Pagess: –
  DOI: https://doi.org/10.1093/nar/gkae287 – HANDLE: https://riunet.upv.es/handle/10251/220681
  Authors: Martín-Làzaro, Héctor; Marín Bautista, Ricardo; Carbonell, Pablo
  

• Paper: 2023, SelenzymeRF: updated enzyme suggestion software for unbalanced biochemical reactions,
  Journal: Computational and Structural Biotechnology Journal, Number , Volume , Pagess: –
  DOI: https://doi.org/10.1016/j.csbj.2023.11.039 – HANDLE: http://hdl.handle.net/10251/212245
  Authors: Ruth A Stoney; Erik K. R. Hanko; Carbonell, Pablo; R. Breitling
  

• Paper: 2023, Sensbio: an online server for biosensor design,
  Journal: BMC Bioinformatics, Number , Volume , Pagess: –
  DOI: https://doi.org/10.1186/s12859-023-05201-7 – HANDLE: http://hdl.handle.net/10251/205715
  Authors: Jonathan Tellechea-Luzardo; Martín-Làzaro, Héctor; Moreno-López, Raúl; Carbonell, Pablo
  

• Paper: 2023, Transcription factor-based biosensors for screening and dynamic regulation,
  Journal: Frontiers in Bioengineering and Biotechnology, Number , Volume 11, Pagess: –
  DOI: https://doi.org/10.3389/fbioe.2023.1118702 – HANDLE: http://hdl.handle.net/10251/204155
  Authors: Jonathan Tellechea-Luzardo; Stiebritz, Martin Tillmann; Carbonell, Pablo
  

• Book chapter: 2022, A retrobiosynthetic approach for production, conversion, sensing, dynamic regulation and degradation of molecules,
  Reference: New Frontiers and Applications of Synthetic Biology, Chapter:  14, Pages: 205- 214
  Editorial: Elsevier – ISBN 978-0-12-824469-2,
  Authors: Carbonell, Pablo

• Paper: 2022, Fast biofoundries: coping with the challenges of biomanufacturing,
  Journal: Trends in Biotechnology, Number , Volume , Pagess: –
  DOI: https://doi.org/10.1016/j.tibtech.2021.12.006 – HANDLE:
  Authors: Tellechea-Luzardo, Jonathan ; Irene Otero-Muras; A. Goñi-Moreno; Carbonell, Pablo
  

• Paper: 2022, The automated Galaxy-SynBioCAD pipeline for synthetic biology design and engineering,
  Journal: Nature Communications, Number , Volume 13, Pagess: –
  DOI: https://doi.org/10.1038/s41467-022-32661-x – HANDLE:
  Authors: Hérisson, J; Thomas Duigou; Melchior Du Lac; Kenza Bazi-Kabbaj; Mahnaz Sabeti Azad; Gizem Buldum; Olivier Telle; Carbonell, Pablo; Yorgo El Mouyabed; Neil Swainston; Zulkower, Valentin; Kushwaha M; Geoff Baldwin; Jean-Loup Faulon
  

• Book chapter: 2021, Synthetic biology design tools for metabolic engineering,
  Reference: Microbial Cell Factories Engineering for Production of Biomolecules, Chapter:  5, Pages: 65-
  Editorial: Academic Press Elsevier- ISBN 978-0-12-821477-0,
  Authors: Carbonell, Pablo

• Paper: 2021, SynBiopython: an open-source software library for Synthetic Biology,
  Journal: Synthetic Biology, Number , Volume , Pagess: ysab001-
  DOI: https://doi.org/10.1093/synbio/ysab001 – HANDLE:
  Authors: Yeoh, Jing Wui; Neil Swainston; Vegh, Peter; Zulkower, Valentin; Carbonell, Pablo; Holowko, Maciej B; Peddinti, Gopal; Poh, Chueh Loo
  

• Paper: 2021, Prototyping of microbial chassis for the biomanufacturing of high-value chemical targets,
  Journal: Biochemical Society Transactions, Number , Volume , Pagess: –
  DOI: https://doi.org/10.1042/BST20200017 – HANDLE:
  Authors: Christopher Robinson; Jonathan Tellechea-Luzardo; Carbonell, Pablo; Adrian Jervis; Cunyu Yan; Katherine A. Hollywood; Mark Dunstan; Andrew Currin; Eriko Takano; Nigel S. Scrutton
  

• Book chapter: 2020, Extended Metabolic Space Modeling,
  Reference: Synthetic Metabolic Pathways, Chapter:  6, Pages: 83-
  Editorial: Springer- ISBN 978-1-4939-7294-4,
  Authors: Carbonell, Pablo; Delepine, B.; Faulon, Jean-Loup

• Paper: 2020, In silico design and automated learning to boost next-generation smart biomanufacturing,
  Journal: Synthetic Biology, Number 1, Volume 5, Pagess: –
  DOI: https://doi.org/10.1093/synbio/ysaa020 – HANDLE:
  Authors: Carbonell, Pablo; Rosalind le Feuvre; Eriko Takano; Nigel S. Scrutton
  

• Paper: 2020, Automated engineering of synthetic metabolic pathways for efficient biomanufacturing,
  Journal: Metabolic Engineering, Number , Volume , Pagess: –
  DOI: https://doi.org/10.1016/j.ymben.2020.11.012 – HANDLE:
  Authors: Carbonell, Pablo; Otero-Muras, Irene
  

• 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, Rapid prototyping of microbial production strains for the biomanufacture of potential materials monomers,
  Journal: Metabolic Engineering, Number , Volume 60, Pagess: 168- 182
  DOI: https://doi.org/10.1016/j.ymben.2020.04.008 – HANDLE:
  Authors: Christopher Robinson; Carbonell, Pablo; Adrian Jervis; Cunyu Yan; Katherine A. Hollywood; Mark Dunstan; Andrew Currin; Neil Swainston; Spiess, Reynard; Sandra Taylor; Mulherin, P.; Parker, Stephen; Rowe, William; Matthews, Nicholas E.; Malone, Kirk
  

• Paper: 2020, Blood Glucose Estimation from Voice: First Review of Successes and Challenges,
  Journal: Journal of Voice, Number , Volume , Pagess: –
  DOI: https://doi.org/10.1016/j.jvoice.2020.08.034 – HANDLE:
  Authors: Sidorova, Julia; Carbonell, Pablo; Cukic, Milena
  

• Paper: 2019, Efficient learning in metabolic pathway designs through optimal assembling,
  Journal: IFAC-PapersOnLine, Number 26, Volume 52, Pagess: 7- 12
  DOI: https://doi.org/10.1016/j.ifacol.2019.12.228 – HANDLE:
  Authors: Carbonell, Pablo; Jean-Loup Faulon; R. Breitling
  

• Paper: 2019, Highly multiplexed, fast and accurate nanopore sequencing for verification of synthetic DNA constructs and sequence libraries,
  Journal: Synthetic Biology, Number , Volume , Pagess: –
  DOI: https://doi.org/10.1093/synbio/ysz025 – HANDLE:
  Authors: Andrew Currin; Neil Swainston; Mark Dunstan; Adrian Jervis; Mulherin, P.; Christopher Robinson; Sandra Taylor; Carbonell, Pablo; Katherine A. Hollywood; Cunyu Yan; Eriko Takano; Nigel S. Scrutton; R. Breitling
  

• Paper: 2019, Identification of major malate export systems in an engineered malate-producing Escherichia coli aided by substrate similarity search,
  Journal: Applied Microbiology and Biotechnology, Number , Volume 103, Pagess: 9001- 9011
  DOI: https://doi.org/10.1007/s00253-019-10164-y – HANDLE:
  Authors: Kurgan, Gavin; Kurgan, Logan; Schneider, Aidan; Onyeabor, Moses; Rodriguez-Sanchez, Yesenia; Taylor, Eric; Carbonell, Pablo; Martinez, Rodrigo; Xiaojian, Shi; Gu, Haiwei; Wang, Xuan
  

• Paper: 2019, Machine learning of designed translational control allows predictive pathway optimisation in Escherichia coli,
  Journal: ACS Synthetic Biology, Number , Volume 8, Pagess: 127- 136
  DOI: https://doi.org/10.1021/acssynbio.8b00398 – HANDLE:
  Authors: Adrian Jervis; Carbonell, Pablo; Maria Vinaixa; Mark Dunstan; Katherine A. Hollywood; Christopher Robinson; Nicholas Rattray; Cunyu Yan; Neil Swainston; Andrew Currin; Rehana Sung; Helen Toogood; Sandra Taylor; Jean-Loup Fauon; R. Breitling; Eriko Takano;
  

• Paper: 2019, Opportunities at the intersection of synthetic biology, machine learning, and automation.,
  Journal: ACS Synthetic Biology, Number 8, Volume , Pagess: 1474- 1477
  DOI: https://doi.org/10.1021/acssynbio.8b00540 – HANDLE:
  Authors: Carbonell, Pablo; Radivojevic, Tijiana; Garcia-Martin, Hector
  

• Paper: 2019, Pathways to cellular supremacy in biocomputing,
  Journal: Nature Communications, Number 1, Volume 10, Pagess: 5250-
  DOI: https://doi.org/10.1038/s41467-019-13232-z – HANDLE:
  Authors: L. Grozinger; Thomas E. Gorochowski; Martyn Amos; Carbonell, Pablo; D. Oyarzún; Rudd Stoof; H. Fellermann; P. Zuliani; H. Tas; A. Goñi-Moreno
  

• Paper: 2019, RetroRules: a database of reaction rules for engineering biology,
  Journal: Nucleic Acids Research, Number D1, Volume 41, Pagess: D1229- D1235
  DOI: https://doi.org/10.1093/nar/gky940 – HANDLE:
  Authors: Thomas Duigou; Melchior Du Lac; Carbonell, Pablo; Jean-Loup Fauon
  

• Paper: 2019, SelProm: A queryable and predictive expression vector selection tool for Escherichia coli,
  Journal: ACS Synthetic Biology, Number , Volume 8, Pagess: 1478- 1483
  DOI: https://doi.org/10.1021/acssynbio.8b00399 – HANDLE:
  Authors: Adrian Jervis; Carbonell, Pablo; Sandra Taylor; Rehana Sung; Mark Dunstan; Christopher Robinson; R. Breitling; Eriko Takano; Nigel S. Scrutton
  

• Book chapter: 2018, Hepatotoxicity prediction by systems biology modeling of disturbed metabolic pathways using gene expression data,
  Reference: Methods in Molecular Biology, volume “Computational Toxicology”,, Chapter:  23, Pages: 505- 518
  Editorial: Springer- ISBN 978-1-4939-7899-1,
  Authors: Lopez, Oriol; Pastor, Manuel; Sanz, Ferran; Carbonell, Pablo

• Book chapter: 2018, Enzyme Discovery: Enzyme Selection and Pathway Design,
  Reference: Enzymes in Synthetic Biology, Chapter:  1, Pages: 3- 30
  Editorial: Academic Press Elsevier- ISBN 9780128151488,
  Authors: Carbonell, Pablo; Koch, Mathilde; Duigou, Thomas; Faulon, Jean-Loup

• Paper: 2018, An automated Design-Build-Test-Learn pipeline for enhanced microbial production of fine chemicals,
  Journal: Communications Biology, Number , Volume 1, Pagess: 66-
  DOI: https://doi.org/10.1038/s42003-018-0076-9 – HANDLE:
  Authors: Carbonell, Pablo; Adrian Jervis; Christopher Robinson; Cunyu Yan; Neil Swainston; Maria Vinaixa; Katherine A. Hollywood; Andrew Currin; Nicholas Rattray; Sandra Taylor; Spiess, Reynard; Rehana Sung; Williams, Alan R; Fellos, Donal; Stanford, Natalie
  

• Paper: 2018, PartsGenie: an integrated tool for optimising and sharing synthetic biology parts,
  Journal: Bioinformatics, Number , Volume , Pagess: –
  DOI: https://doi.org/10.1093/bioinformatics/bty105 – HANDLE:
  Authors: Neil Swainston; Mark Dunstan; Adrian Jervis; Christopher Robinson; Carbonell, Pablo; Williams, Alan R; Faulon, Jean-Loup; Nigel S. Scrutton; Kell, Douglas B
  

• Paper: 2018, RetroPath2.0: A retrosynthesis workflow for metabolic engineers,
  Journal: Metabolic Engineering, Number , Volume 45, Pagess: 158- 170
  DOI: https://doi.org/10.1016/j.ymben.2017.12.002 – HANDLE:
  Authors: Delepine, B.; Thomas Duigou; Carbonell, Pablo; Faulon, Jean-Loup
  

• Paper: 2018, Selenzyme: Enzyme selection tool for pathway design,
  Journal: Bioinformatics, Number , Volume 34, Pagess: 2153- 2154
  DOI: https://doi.org/10.1093/bioinformatics/bty065 – HANDLE:
  Authors: Carbonell, Pablo; Wong, Jerry; Neil Swainston; Eriko Takano; Turmner, Nicholas J; Nigel S. Scrutton; Kell, Douglas B; R. Breitling; Faulon, Jean-Loup