User:Pablo Carbonell
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Contact Info
- Pablo Carbonell
- SYNBIOCHEM Manchester Institute of Biotechnology
- The University of Manchester
- Email me through OpenWetWare
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.
Education
- 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
- Engineering Biology
- Synthetic Biology
- Systems Biology
- Metabolic Engineering
- Systems Engineering
- Control Engineering
Main Publications
- 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 |
- 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 |
- 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 |
- 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 |
- 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 |
- 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 |
- 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 |
- 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 |
- 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 |
- 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 |
- 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 |
- 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 |
- 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 |
- 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 |
- 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 |
- 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 |