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Identificação

Identificação pessoal

Nome completo
Pablo Carbonell

Nomes de citação

  • Carbonell, Pablo

Identificadores de autor

Ciência ID
801A-4FF1-9BCF
ORCID iD
0000-0002-0993-5625
Formação
Grau Classificação
1999
Concluído
 Pablo Carbonell (Doctor)
Universitat Politècnica de València, Espanha
Percurso profissional

Ciência

Categoria Profissional
Instituição de acolhimento 		Empregador
2015/05/01 - 2020/04/01 Investigador (Investigação) The University of Manchester Manchester Institute of Biotechnology, Reino Unido

Docência no Ensino Superior

Categoria Profissional
Instituição de acolhimento 		Empregador
2020/04/01 - Atual Professor Coordenador (Docente Ensino Superior Politécnico) Universitat Politècnica de València, Espanha
Projetos

Bolsa

Designação Financiadores
2019 - 2023 Shikifactory100: Modular cell factories for the production of 100 compounds from the shikimate pathway. Horizon2020 BIOTEC-03-2018.
814408
Investigador responsável
Produções

Publicações

Artigo em conferência
  1. Sarnowski, C.; Carbonell, P.; Elati, M.; Faulon, J.L.. "Prediction of catalytic efficiency to discover new enzymatic activities". 2010.
  2. Carbonell, P.; Jiang, Z.-P.; Panwar, S.. "Fuzzy TCP: A preliminary study". 2002.
    10.3182/20020721-6-es-1901.00687
  3. Carbonell, P; Jiang, Z-P; Repperger, DW. "A fuzzy backstepping controller for a pneumatic muscle actuator system". 2001.
    10.1109/isic.2001.971535
  4. Carbonell, P.; Wang, X.; Jiang, Z.-P.. "On the suppression of flow-induced vibration with a simple control algorithm". 2001.
  5. Carbonell, P; Jiang, Z-P; Repperger, DW. "Nonlinear control of a pneumatic muscle actuator: backstepping vs. sliding-mode". 2001.
  6. Carbonell, Pablo; Garcera, Gabriel; Hilario, Adolfo. "Fuzzy gain scheduling control of switch-mode dc/dc converters". 1999.
    10.1109/isie.1999.801821
  7. Garcer{\'a. "Sensibility study of the control loops of voltage and current mode controlled DC-DC converters by means of robust parametric control theory". 1999.
    10.1109/isie.1999.798682
Artigo em revista
  1. Jonathan Tellechea-Luzardo; Irene Otero-Muras; Angel Goñi-Moreno; Pablo Carbonell. "Fast biofoundries: coping with the challenges of biomanufacturing". Trends in Biotechnology (2022): https://doi.org/10.1016/j.tibtech.2021.12.006.
    10.1016/j.tibtech.2021.12.006
  2. Christopher J. Robinson; Jonathan Tellechea-Luzardo; Pablo Carbonell; Adrian J. Jervis; Cunyu Yan; Katherine A. Hollywood; Mark S. Dunstan; et al. "Prototyping of microbial chassis for the biomanufacturing of high-value chemical targets". Biochemical Society Transactions 49 3 (2021): 1055-1063. https://doi.org/10.1042/BST20200017.
    10.1042/BST20200017
  3. Irene Otero-Muras; Pablo Carbonell. "Automated engineering of synthetic metabolic pathways for efficient biomanufacturing". Metabolic Engineering 63 (2021): 61-80. https://doi.org/10.1016/j.ymben.2020.11.012.
    10.1016/j.ymben.2020.11.012
  4. "Engineering Escherichia coli towards de novo production of gatekeeper (2S)-flavanones: naringenin, pinocembrin, eriodictyol and homoeriodictyol". Synthetic Biology (2020): http://dx.doi.org/10.1093/synbio/ysaa012.
    10.1093/synbio/ysaa012
  5. Christopher J. Robinson; Pablo Carbonell; Adrian J. Jervis; Cunyu Yan; Katherine A. Hollywood; Mark S. Dunstan; Andrew Currin; et al. "Rapid prototyping of microbial production strains for the biomanufacture of potential materials monomers". Metabolic Engineering (2020): https://doi.org/10.1016/j.ymben.2020.04.008.
    10.1016/j.ymben.2020.04.008
  6. Pablo Carbonell; Rosalind Le Feuvre; Eriko Takano; Nigel S Scrutton. "In silico design and automated learning to boost next-generation smart biomanufacturing". Synthetic Biology (2020): https://doi.org/10.1093/synbio/ysaa020.
    10.1093/synbio/ysaa020
  7. Sidorova, J.; Carbonell, P.; Cukic, M.. "Blood Glucose Estimation From Voice: First Review of Successes and Challenges". Journal of Voice (2020): http://www.scopus.com/inward/record.url?eid=2-s2.0-85092216394&partnerID=MN8TOARS.
    10.1016/j.jvoice.2020.08.034
  8. Pablo Carbonell; Jean-Loup Faulon; Rainer Breitling. "Efficient learning in metabolic pathway designs through optimal assembling". IFAC-PapersOnLine 52 26 (2019): 7-12. https://www.research.manchester.ac.uk/portal/en/publications/efficient-learning-in-metabolic-pathway-designs-through-optimal-assembling(26ba9709-ab78-42f5-be3b-ae7a5dd3b8a3).html.
    10.1016/j.ifacol.2019.12.228
  9. Lewis Grozinger; Martyn Amos; Thomas E. Gorochowski; Pablo Carbonell; Diego A. Oyarzún; Ruud Stoof; Harold Fellermann; et al. "Pathways to cellular supremacy in biocomputing". Nature Communications (2019): https://doi.org/10.1038/s41467-019-13232-z.
    10.1038/s41467-019-13232-z
  10. Carbonell, Pablo. "Opportunities at the Intersection of Synthetic Biology, Machine Learning, and Automation". ACS Synthetic Biology (2019): http://dx.doi.org/10.1021/acssynbio.8b00540.
    10.1021/acssynbio.8b00540
  11. Adrian J. Jervis; Pablo Carbonell; Sandra Taylor; Rehana Sung; Mark S. Dunstan; Christopher J. Robinson; Rainer Breitling; Eriko Takano; Nigel S. Scrutton. "SelProm: A Queryable and Predictive Expression Vector Selection Tool for Escherichia coli". ACS Synthetic Biology (2019): https://doi.org/10.1021/acssynbio.8b00399.
    10.1021/acssynbio.8b00399
  12. Adrian J. Jervis; Pablo Carbonell; Maria Vinaixa; Mark S. Dunstan; Katherine A. Hollywood; Christopher J. Robinson; Nicholas J. W. Rattray; et al. "Machine Learning of Designed Translational Control Allows Predictive Pathway Optimization in Escherichia coli". ACS Synthetic Biology 8 1 (2019): 127-136. https://www.research.manchester.ac.uk/portal/en/publications/machine-learning-of-designed-translational-control-allows-predictive-pathway-optimization-in-escherichia-coli(0de93b3a-59ca-47af-9390-3d1dc913a435).html.
    10.1021/acssynbio.8b00398
  13. Andrew Currin; Neil Swainston; Mark S Dunstan; Adrian J Jervis; Paul Mulherin; Christopher J Robinson; Sandra Taylor; et al. "Highly multiplexed, fast and accurate nanopore sequencing for verification of synthetic DNA constructs and sequence libraries". Synthetic Biology (2019): https://doi.org/10.1093/synbio/ysz025.
    10.1093/synbio/ysz025
  14. Kurgan, G.; Kurgan, L.; Schneider, A.; Onyeabor, M.; Rodriguez-Sanchez, Y.; Taylor, E.; Martinez, R.; et al. "Identification of major malate export systems in an engineered malate-producing Escherichia coli aided by substrate similarity search". Applied Microbiology and Biotechnology 103 21-22 (2019): 9001-9011. http://www.scopus.com/inward/record.url?eid=2-s2.0-85074563836&partnerID=MN8TOARS.
    10.1007/s00253-019-10164-y
  15. Pablo Carbonell; Adrian J. Jervis; Christopher J. Robinson; Cunyu Yan; Mark Dunstan; Neil Swainston; Maria Vinaixa; et al. "An automated Design-Build-Test-Learn pipeline for enhanced microbial production of fine chemicals". Communications Biology 1 1 (2018): https://doi.org/10.1038/s42003-018-0076-9.
    10.1038/s42003-018-0076-9
  16. Carbonell, Pablo. "RetroRules: a database of reaction rules for engineering biology". Nucleic Acids Research (2018): gky940-gky940. http://dx.doi.org/10.1093/nar/gky940.
    10.1093/nar/gky940
  17. Pablo Carbonell; Mathilde Koch; Thomas Duigou; Jean-Loup Faulon. "Enzyme Discovery". Methods in Enzymology 608 (2018): 3-27. https://www.research.manchester.ac.uk/portal/en/publications/enzyme-discovery(2fad9c8b-2a52-4099-913a-62fd8508b2be).html.
    10.1016/bs.mie.2018.04.005
  18. Neil Swainston; Mark Dunstan; Adrian J Jervis; Christopher J Robinson; Pablo Carbonell; Alan R Williams; Jean-Loup Faulon; et al. "PartsGenie: an integrated tool for optimizing and sharing synthetic biology parts". Bioinformatics (2018): https://doi.org/10.1093/bioinformatics/bty105.
    10.1093/bioinformatics/bty105
  19. Pablo Carbonell; Jerry Wong; Neil Swainston; Eriko Takano; Nicholas J Turner; Nigel S Scrutton; Douglas B Kell; et al. "Selenzyme: enzyme selection tool for pathway design". Bioinformatics (2018): https://doi.org/10.1093/bioinformatics/bty065.
    10.1093/bioinformatics/bty065
  20. López-Massaguer O; Pastor M; Sanz F; Carbonell P. "Hepatotoxicity Prediction by Systems Biology Modeling of Disturbed Metabolic Pathways Using Gene Expression Data.". Methods in molecular biology (Clifton, N.J.) (2018): http://europepmc.org/abstract/med/29934908.
    10.1007/978-1-4939-7899-1_23
  21. Carbonell P; Delépine B; Faulon JL. "Extended Metabolic Space Modeling.". Methods in molecular biology (Clifton, N.J.) (2018): http://europepmc.org/abstract/med/29170954.
    10.1007/978-1-4939-7295-1_6
  22. Koch M; Duigou T; Carbonell P; Faulon JL. "Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0.". Journal of Cheminformatics (2017): http://europepmc.org/abstract/med/29260340.
    10.1186/s13321-017-0252-9
  23. Delépine B; Duigou T; Carbonell P; Faulon JL. "RetroPath2.0: A retrosynthesis workflow for metabolic engineers.". Metabolic engineering (2017): http://europepmc.org/abstract/med/29233745.
    10.1016/j.ymben.2017.12.002
  24. Neil Swainston; Andreas Prlic; Riza Batista-Navarro; Pablo Carbonell; Paul D. Dobson; Mark Dunstan; Adrian J. Jervis; et al. "biochem4j: Integrated and extensible biochemical knowledge through graph databases". PLOS ONE (2017):
    10.1371/journal.pone.0179130
  25. Le Feuvre RA; Carbonell P; Currin A; Dunstan M; Fellows D; Jervis AJ; Rattray NJW; et al. "SYNBIOCHEM Synthetic Biology Research Centre, Manchester – A UK foundry for fine and speciality chemicals production". Synthetic and Systems Biotechnology 1 4 (2016): 271-275. https://doi.org/10.1016/j.synbio.2016.07.001.
    10.1016/j.synbio.2016.07.001
  26. Del{\'e. "SensiPath: computer-aided design of sensing-enabling metabolic pathways". Nucleic acids research (2016): gkw305-gkw305.
    10.1093/nar/gkw305
  27. Pablo Carbonell; Andrew Currin; Adrian J. Jervis; Nicholas J. W. Rattray; Neil Swainston; Cunyu Yan; Eriko Takano; Rainer Breitling. "Bioinformatics for the synthetic biology of natural products: integrating across the Design–Build–Test cycle". Natural Product Reports 33 8 (2016): 925-932. https://doi.org/10.1039/C6NP00018E.
    10.1039/C6NP00018E
  28. Martiny VY; Carbonell P; Chevillard F; Moroy G; Nicot AB; Vayer P; Villoutreix BO; Miteva MA. "Integrated structure- and ligand-based in silico approach to predict inhibition of cytochrome P450 2D6.". Bioinformatics (Oxford, England) (2015): http://europepmc.org/abstract/med/26315915.
    10.1093/bioinformatics/btv486
  29. Trosset, Jean-Yves; Carbonell, Pablo. "Synthetic biology for pharmaceutical drug discovery". Drug design, development and therapy 9 (2015): 6285-6285.
    10.2147/DDDT.S58049
  30. Carbonell P; Trosset JY. "Computational protein design methods for synthetic biology.". Methods in molecular biology (Clifton, N.J.) (2015): http://europepmc.org/abstract/med/25487090.
    10.1007/978-1-4939-1878-2_1
  31. Ceroni F; Carbonell P; François JM; Haynes KA. "Editorial - Synthetic Biology: Engineering Complexity and Refactoring Cell Capabilities.". Frontiers in bioengineering and biotechnology (2015): http://europepmc.org/abstract/med/26347864.
    10.3389/fbioe.2015.00120
  32. Carbonell P; Mayer MA; Bravo À. "Exploring brand-name drug mentions on Twitter for pharmacovigilance.". Studies in health technology and informatics (2015): http://europepmc.org/abstract/med/25991101.
    doi:10.3233/978-1-61499-512-8-55
  33. Fehér T; Libis V; Carbonell P; Faulon JL. "A Sense of Balance: Experimental Investigation and Modeling of a Malonyl-CoA Sensor in Escherichia coli.". Frontiers in bioengineering and biotechnology (2015): http://europepmc.org/abstract/med/25905101.
    10.3389/fbioe.2015.00046
  34. Fernández-Castané A; Fehér T; Carbonell P; Pauthenier C; Faulon JL. "Computer-aided design for metabolic engineering.". Journal of biotechnology (2014): http://europepmc.org/abstract/med/24704607.
    10.1016/j.jbiotec.2014.03.029
  35. Fehér T; Planson AG; Carbonell P; Fernández-Castané A; Grigoras I; Dariy E; Perret A; Faulon JL. "Validation of RetroPath, a computer-aided design tool for metabolic pathway engineering.". Biotechnology journal (2014): http://europepmc.org/abstract/med/25224453.
    10.1002/biot.201400055
  36. Carbonell, Pablo; Parutto, Pierre; Herisson, Joan; Pandit, Shashi Bhushan; Faulon, Jean-Loup. "XTMS: pathway design in an eXTended metabolic space". Nucleic acids research 42 W1 (2014): W389-W394.
    10.1093/nar/gku362
  37. Carbonell, Pablo; Trosset, Jean-Yves. "Overcoming drug resistance through in silico prediction". Drug Discovery Today: Technologies 11 (2014): 101-107.
    10.1016/j.ddtec.2014.03.012
  38. Martiny, Virginie Y; Carbonell, Pablo; Lagorce, David; Villoutreix, Bruno O; Moroy, Gautier; Miteva, Maria A. "In silico mechanistic profiling to probe small molecule binding to sulfotransferases". PloS one 8 9 (2013): e73587-e73587.
    10.1371/journal.pone.0073587
  39. Trosset, Jean-Yves; Carbonell, Pablo. "Synergistic synthetic biology: units in concert". Frontiers in bioengineering and biotechnology 1 (2013):
    10.3389/fbioe.2013.00011
  40. Sendren Sheng-Dong Xu; Hao Ying; Pablo Carbonell; Ching-Hung Lee; Wei-Sheng Wu. "Fuzzy Logic Applications in Control Theory and Systems Biology". Advances in Fuzzy Systems 2013 (2013): 1-1. http://dx.doi.org/10.1155/2013/504728.
    10.1155/2013/504728
  41. Carbonell P; Planson AG; Faulon JL. "Retrosynthetic design of heterologous pathways.". Methods in molecular biology (Clifton, N.J.) (2013): http://europepmc.org/abstract/med/23417804.
    10.1007/978-1-62703-299-5_9
  42. Planson, Anne-Ga{\. "A retrosynthetic biology approach to therapeutics: from conception to delivery". Current opinion in biotechnology 23 6 (2012): 948-956.
    10.1016/j.copbio.2012.03.009
  43. Pablo Carbonell; Davide Fichera; Shashi B Pandit; Jean-Loup Faulon. "Enumerating metabolic pathways for the production of heterologous target chemicals in chassis organisms.". BMC Systems Biology 6 1 (2012): https://www.research.manchester.ac.uk/portal/en/publications/enumerating-metabolic-pathways-for-the-production-of-heterologous-target-chemicals-in-chassis-organisms(6448fe2d-239d-453e-8a43-36556cd2787e).html.
    10.1186/1752-0509-6-10
  44. Anne-Gaëlle Planson; Pablo Carbonell; Elodie Paillard; Nicolas Pollet; Jean-Loup Faulon. "Compound toxicity screening and structure-activity relationship modeling in Escherichia coli". Biotechnology and Bioengineering 109 3 (2012): 846-850. https://www.research.manchester.ac.uk/portal/en/publications/compound-toxicity-screening-and-structureactivity-relationship-modeling-in-escherichia-coli(5e6d3f25-d112-4bdf-9657-6312ae5350da).html.
    10.1002/bit.24356
  45. Carbonell, Pablo; Lecointre, Guillaume; Faulon, Jean-Loup. "Origins of specificity and promiscuity in metabolic networks". Journal of Biological Chemistry 286 51 (2011): 43994-44004.
    10.1074/jbc.m111.274050
  46. Pablo Carbonell; Anne-Gaëlle G Planson; Davide Fichera; Jean-Loup Faulon. "A retrosynthetic biology approach to metabolic pathway design for therapeutic production.". BMC Systems Biology 5 1 (2011): https://www.research.manchester.ac.uk/portal/en/publications/a-retrosynthetic-biology-approach-to-metabolic-pathway-design-for-therapeutic-production(051074f9-3d25-408e-9851-508979552a3a).html.
    10.1186/1752-0509-5-122
  47. Carbonell, P; del Sol, A. "Methyl side-chain dynamics prediction based on protein structure". Bioinformatics 25 19 (2009): 2552-2558.
    10.1093/bioinformatics/btp463
  48. Faulon, Jean-Loup; Carbonell, Pablo. "Reaction Network Generation". Handbook of Chemoinformatics Algorithms 33 (2009): 317-317.
  49. Pablo Carbonell. "Efficient Fuzzy Logic-Based Algorithm for Microarray Network Identification and Prediction in Bioinformatics". Elektronika ir Elektrotechnika 67 3 (2006): 37-40. https://www.research.manchester.ac.uk/portal/en/publications/efficient-fuzzy-logicbased-algorithm-for-microarray-network-identification-and-prediction-in-bioinformatics(0af3588e-6c08-4e78-928f-43f8f4643ad5).html.
  50. Carbonell, P.. "Decentralized control of transmission networks based on adaptive fuzzy techniques,Control descentralizado de redes de transmisión basado en técnicas fuzzy adaptativas". Informacion Tecnologica 14 4 (2003): 59-64. http://www.scopus.com/inward/record.url?eid=2-s2.0-0041426651&partnerID=MN8TOARS.
Livro
  1. Pablo Carbonell. Metabolic Pathway Design. Springer Nature. 2019.
  2. Delépine, B.; Carbonell, P.; Faulon, J.-L.. XTMS in action: Retrosynthetic design in the extended metabolic space of heterologous pathways for high-value compounds. 2014.
    10.1007/978-3-319-12982-2_21

Outros

Outra produção
  1. Selenzyme: Enzyme selection tool for pathway design. 2017. Pablo Carbonell; Jerry Wong; Neil Swainston; Eriko Takano; Nicholas J. Turner; Nigel S. Scrutton; Douglas B. Kell; Rainer Breitling; Jean-Loup Faulon. https://doi.org/10.1101/188979.
    10.1101/188979
  2. PartsGenie: an integrated tool for optimising and sharing synthetic biology parts. 2017. Neil Swainston; Mark Dunstan; Adrian J. Jervis; Christopher J. Robinson; Pablo Carbonell; Alan R. Williams; Jean-Loup Faulon; Nigel S. Scrutton; Douglas B. Kell. https://doi.org/10.1101/189357.
    10.1101/189357
  3. RetroPath2.0: a retrosynthesis workflow for metabolic engineers. 2017. Baudoin Delépine; Thomas Duigou; Pablo Carbonell; Jean-Loup Faulon. https://doi.org/10.1101/141721.
    10.1101/141721