User:Pablo Carbonell

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Pablo Carbonell
SYNBIOCHEM Manchester Institute of Biotechnology
The University of Manchester
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Synthetic Bio

I work at the Manchester Synthetic Biology Centre for fine and speciality chemicals (SYNBIOCHEM). My field of research is engineering biology design.

I have developed several bioretrosynthesis-based pathway design tools, including RetroPath, XTMS, EcoliTox, and protein design Promis. I am interested in applying the principles of control engineering and machine learning to sustainable biological design. I've joined OpenWetWare because I am participating as a researcher in several projects on synthetic biology.


  • Habilitation Systems Biology, UniverSud Paris
  • Ph.D. Control Engineering, Polytech Univ Valencia
  • M.S. Bioinformatics and Computational Biology, Complutense Univ Madrid
  • M.S. Industrial Electronics Engineering, Polytech Univ Madrid
  • B.S. Industrial Electronics, Polytech Univ Valencia

Research interests

  1. Engineering Biology
  2. Synthetic Biology
  3. Systems Biology
  4. Metabolic Engineering
  5. Systems Engineering
  6. Control Engineering

Main Publications

  1. Carbonell P, Currin A, Jervis AJ, Rattray NJ, Swainston N, Yan C, Takano E, and Breitling R. Bioinformatics for the synthetic biology of natural products: integrating across the Design-Build-Test cycle. Nat Prod Rep. 2016 Aug 27;33(8):925-32. DOI:10.1039/c6np00018e | PubMed ID:27185383 | HubMed [Paper10]
  2. Delépine B, Libis V, Carbonell P, and Faulon JL. SensiPath: computer-aided design of sensing-enabling metabolic pathways. Nucleic Acids Res. 2016 Jul 8;44(W1):W226-31. DOI:10.1093/nar/gkw305 | PubMed ID:27106061 | HubMed [Paper11]
  3. Fehér T, Libis V, Carbonell P, and Faulon JL. A Sense of Balance: Experimental Investigation and Modeling of a Malonyl-CoA Sensor in Escherichia coli. Front Bioeng Biotechnol. 2015;3:46. DOI:10.3389/fbioe.2015.00046 | PubMed ID:25905101 | HubMed [Paper12]
  4. Fehér T, Planson AG, Carbonell P, Fernández-Castané A, Grigoras I, Dariy E, Perret A, and Faulon JL. Validation of RetroPath, a computer-aided design tool for metabolic pathway engineering. Biotechnol J. 2014 Nov;9(11):1446-57. DOI:10.1002/biot.201400055 | PubMed ID:25224453 | HubMed [Paper13]
  5. Carbonell P, Parutto P, Baudier C, Junot C, and Faulon JL. Retropath: automated pipeline for embedded metabolic circuits. ACS Synth Biol. 2014 Aug 15;3(8):565-77. DOI:10.1021/sb4001273 | PubMed ID:24131345 | HubMed [Paper14]
  6. Carbonell P, Parutto P, Herisson J, Pandit SB, and Faulon JL. XTMS: pathway design in an eXTended metabolic space. Nucleic Acids Res. 2014 Jul;42(Web Server issue):W389-94. DOI:10.1093/nar/gku362 | PubMed ID:24792156 | HubMed [Paper15]
  7. Carbonell P, Carlsson L, and Faulon JL. Stereo signature molecular descriptor. J Chem Inf Model. 2013 Apr 22;53(4):887-97. DOI:10.1021/ci300584r | PubMed ID:23527586 | HubMed [Paper16]
  8. Planson AG, Carbonell P, Paillard E, Pollet N, and Faulon JL. Compound toxicity screening and structure-activity relationship modeling in Escherichia coli. Biotechnol Bioeng. 2012 Mar;109(3):846-50. DOI:10.1002/bit.24356 | PubMed ID:22038678 | HubMed [Paper17]
  9. Carbonell P, Fichera D, Pandit SB, and Faulon JL. Enumerating metabolic pathways for the production of heterologous target chemicals in chassis organisms. BMC Syst Biol. 2012 Feb 6;6:10. DOI:10.1186/1752-0509-6-10 | PubMed ID:22309974 | HubMed [Paper18]
  10. Carbonell P, Lecointre G, and Faulon JL. Origins of specificity and promiscuity in metabolic networks. J Biol Chem. 2011 Dec 23;286(51):43994-44004. DOI:10.1074/jbc.M111.274050 | PubMed ID:22052908 | HubMed [Paper19]
  11. Carbonell P, Planson AG, Fichera D, and Faulon JL. A retrosynthetic biology approach to metabolic pathway design for therapeutic production. BMC Syst Biol. 2011 Aug 5;5:122. DOI:10.1186/1752-0509-5-122 | PubMed ID:21819595 | HubMed [Paper20]
  12. Carbonell P and Faulon JL. Molecular signatures-based prediction of enzyme promiscuity. Bioinformatics. 2010 Aug 15;26(16):2012-9. DOI:10.1093/bioinformatics/btq317 | PubMed ID:20551137 | HubMed [Paper1]
  13. Carbonell P and del Sol A. Methyl side-chain dynamics prediction based on protein structure. Bioinformatics. 2009 Oct 1;25(19):2552-8. DOI:10.1093/bioinformatics/btp463 | PubMed ID:19648137 | HubMed [Paper2]
  14. Carbonell P, Nussinov R, and del Sol A. Energetic determinants of protein binding specificity: insights into protein interaction networks. Proteomics. 2009 Apr;9(7):1744-53. DOI:10.1002/pmic.200800425 | PubMed ID:19253304 | HubMed [Paper3]
  15. del Sol A and Carbonell P. The modular organization of domain structures: insights into protein-protein binding. PLoS Comput Biol. 2007 Dec;3(12):e239. DOI:10.1371/journal.pcbi.0030239 | PubMed ID:18069884 | HubMed [Paper4]
  16. Colinge J, Masselot A, Carbonell P, and Appel RD. InSilicoSpectro: an open-source proteomics library. J Proteome Res. 2006 Mar;5(3):619-24. DOI:10.1021/pr0504236 | PubMed ID:16512677 | HubMed [Paper5]

All Medline abstracts: PubMed | HubMed

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