Publications

Martín Lázaro, M., Marín Bautista, R., Carbonell, P. DetSpace: a web server for engineering detectable pathways for bio-based chemical production. Nucleic Acids Research, W1-W5, 2024. doi:10.1093/nar/gkae287

Stoney, R., Hanko, E.K.R., Carbonell, P., Breitling, R. SelenzymeRF: updated enzyme suggestion software for unbalanced biochemical reactions. Computational and Structural Biotechnology Journal, 21, 5868-5876, 2023. doi:10.1016/j.csbj.2023.11.039

Tellechea-Luzardo, J., Martín Lázaro, H., Moreno López, R., Carbonell, P. Sensbio: an online server for biosensor design. BMC Bioinformatics, 24, 71, 2023. doi:10.1186/s12859-023-05201-7

Tellechea-Luzardo, J., Stiebritz, M. T., Carbonell, P. Transcription factor-based biosensors for screening and dynamic regulation. Frontiers in Bioengineering and Biotechnology, 11, 147, 2023. doi:10.3389/fbioe.2023.1118702

Hérisson, J., Duigou, T., du Lac, M., Bazi-Kabbaj, K., Sabeti Azad, M., Buldum, G., Telle, O., el Moubayed, Y., Carbonell, P., Swainston, N., Zulkower, V., Kushwaha, M., Baldwin, G. S., Faulon, J.-L. The automated Galaxy-SynBioCAD pipeline for synthetic biology design and engineering. Nature Communications, 13:1, 13:5082, 2022. doi:10.1038/s41467-022-32661-x

Tellechea-Luzardo, J., Otero-Muras, I., Goñi-Moreno, A., Carbonell, P. Fast biofoundries: coping with the challenges of biomanufacturing. Trends in Biotechnology, 40:7, 831-842, 2022. doi:10.1016/j.tibtech.2021.12.006

Carbonell, P. A retrobiosynthetic approach for production, conversion, sensing, dynamic regulation and degradation of molecules. New Frontiers and Applications of Synthetic Biology, 205-214, 2022. doi:10.1016/B978-0-12-824469-2.00024-5

Robinson, C. J., Tellechea-Luzardo, J., Carbonell, P., Jervis, A. J., Yan, C., Hollywood, K. A., Dunstan, M.S., Currin, A., Takano, E., Scrutton, N. S. Prototyping of microbial chassis for the biomanufacturing of high-value chemical targets. Biochemical Society Transactions, 49 (3): 1055–1063, 2021. doi:10.1042/BST20200017

Otero-Muras, I., Carbonell, P. Automated engineering of synthetic metabolic pathways for efficient biomanufacturing. Metabolic Engineering, 63, 61-80, 2021. doi:10.1016/j.ymben.2020.11.012

Yeoh JW, Swainston N, Vegh P, Zulkower V, Carbonell P, Holowko MB, Peddinti G, Poh CL. SynBiopython: an open-source software library for Synthetic Biology. Synthetic Biology, 6(1), ysab001, 2021. doi:10.1093/synbio/ysab001

Carbonell, P. Synthetic biology design tools for metabolic engineering. Microbial Cell Factories Engineering for Production of Biomolecules. Academic Press Elsevier, 65-77, 2021. ISBN: 9780128214770

Carbonell, P., Le Feuvre, R., Takano, E., Scrutton, N. S. In silico design and automated learning to boost next-generation smart biomanufacturing. Synthetic Biology, 5:1, ysaa020, 2020. doi:10.1093/synbio/ysaa020

Dunstan, M, Robinson, C, Jervis, A, Yan, C, Carbonell, P, Hollywood, K, Currin, A, Swainston, N, Le Feuvre, R, Micklefield, J, Faulon, JL, Breitling, R, Turner, N, Takano, E, Scrutton, N. Engineering Escherichia coli towards de novo production of gatekeeper (2S)-flavanones: naringenin, pinocembrin, eriodictyol and homoeriodictyol. Synthetic Biology, 5(1), ysaa012, 2020. doi:10.1093/synbio/ysaa012

Sidorova, J, Carbonell, P, Čukić, M. Blood glucose estimation from voice: First review of successes and challenges. Journal of Voice, 2020. doi:10.1016/j.jvoice.2020.08.034

Carbonell, P. Genome Engineering via CRISPR-Cas9 System. Academic Press, 2020. doi:10.1016/B978-0-12-818140-9.06001-3

Boada Y, Vignoni A, Picó J, Carbonell P. Extended metabolic biosensor design for dynamic pathway regulation of cell factories. iScience, 101305, 2020. doi:10.1016/j.isci.2020.101305

Robinson CJ, Carbonell P, Jervis AJ, Yan C, Hollywood KA, Dunstan MS, Currin A, Swainston N, Spiess R, Taylor S, Mulherin P, Parker, S, Rowe, W, Matthews, N, Malone, K, Le Feuvre, R, Shapira, P, Barran, P, Turner, NJ, Micklefield, J, Breitling, R, Takano, E, Scrutton, NS. Rapid prototyping of microbial production strains for the biomanufacture of potential materials monomers. Metabolic Engineering, 60, 168-182, 2020. doi:10.1016/j.ymben.2020.04.008

Grozinger, L., Amos, M., Gorochowski, T. E., Carbonell, P., Oyarzún, D. A., Stoof, R., Fellermann, H., Zuliani, P., Tas, H., Goñi-Moreno, A. Pathways to cellular supremacy in biocomputing. Nature Communications, 10(1), 5250, 2019. doi:10.1038/s41467-019-13232-z

Currin, A., Swainston, N., Dunstan, M. S., Jervis, A. J., Mulherin, P., Robinson, C. J., Taylor, S., Carbonell, P., Hollywood, K.A., Yan, C., Takano, E., Scrutton, N.S., Breitling, R. Highly multiplexed, fast and accurate nanopore sequencing for verification of synthetic DNA constructs and sequence libraries. Synthetic Biology, 2019. doi:10.1093/synbio/ysz025

P. Carbonell, J.L. Faulon, R. Breitling. Efficient learning in metabolic pathway designs through optimal assembling. IFAC-PapersOnLine. 52, 7-12, 2019. doi:10.1016/j.ifacol.2019.12.228

Kurgan G, Kurgan L, Schneider A, Onyeabor M, Rodriguez-Sanchez Y, Taylor E, Martinez R, Carbonell P, Shi X, Gu H, Wang X. Identification of major malate export systems in an engineered malate-producing Escherichia coli aided by substrate similarity search. Appl Microbiol Biotechnol, 2019 . doi:10.1007/s00253-019-10164-y

Carbonell, P. Metabolic Pathway Design. A Practical Guide. Learning Materials in Biosciences. Springer, 2019. doi:10.1007/978-3-030-29865-4

Carbonell, P., Radivojevic, T., García Martín, H. Opportunities at the intersection of synthetic biology, machine learning, and automation. ACS Synthetic Biology, 8, 1474–1477, 2019. doi:10.1021/acssynbio.8b00540

Jervis, A. J., Carbonell, P., Taylor, S., Sung, R., Dunstan, M. S., Robinson, C. J., Breitling, R., Takano, E., Scrutton, N. S. SelProm: A queryable and predictive expression vector selection tool for Escherichia coli. ACS Synthetic Biology, 8, 1478-1483, 2019. doi:10.1021/acssynbio.8b00399

Jervis, A. J., Carbonell, P., Vinaixa, M., Dunstan, M. S., Hollywood, K. A., Robinson, C. J., Rattray, N. J. , Yan, C., Swainston, N., Currin, A., Sung, R., Toogood, H. S., Taylor, S., Faulon, J. L., Breitling, R., Takano, E., Scrutton, N. S. Machine learning of designed translational control allows predictive pathway optimisation in Escherichia coli. ACS Synthetic Biology, 8, 127-136, 2019. doi:10.1021/acssynbio.8b00398

Duigou, T., du Lac, M., Carbonell, P., Faulon, J.L. RetroRules: a database of reaction rules for engineering biology, Nucleic Acids Research, 47:D1, D1229–D1235, 2019. doi:10.1093/nar/gky940

Carbonell, P., Jervis, A. J., Robinson, C. J., Yan, C., Dunstan, M., Swainston, N., Vinaixa, M., Hollywood, K. A., Currin, A., Rattray, N. J. W., Taylor, S., Spiess, R., Sung, R., Williams, A. R., Fellows, D., Stanford, N. J., Mulherin, P., Le Feuvre, R., Barran, P., Goodacre, R., Turner, N. J., Goble, C., Chen, G. G., Kell, D. B., Micklefield, J., Breitling, R., Takano, E., Faulon, J. L., Scrutton, N. S. An automated Design-Build-Test-Learn pipeline for enhanced microbial production of fine chemicals, Communications Biology, 1, 66, 2018. doi:10.1038/s42003-018-0076-9

Carbonell, P., Koch, M., Duigou, T., Faulon, J.L. Enzyme Discovery: Enzyme Selection and Pathway Design, Methods in Enzymology, volume “Enzymes in Synthetic Biology”, 608, 2018. doi:10.1016/bs.mie.2018.04.005

Carbonell, P., Wong, J., Swainston, N., Takano, E., Turner, N.J., Scrutton, N.S., Kell, D.B., Breitling, R., Faulon, J.L. Selenzyme: Enzyme selection tool for pathway design, Bioinformatics, 34, 2153–2154, 2018. doi:10.1093/bioinformatics/bty065

Swainston, N., Dunstan, M., Jervis, A. J., Robinson, C. J., Carbonell, P., Williams, A. R., Faulon, J.L., Scrutton, N. S., Kell, D. B. PartsGenie: an integrated tool for optimising and sharing synthetic biology parts, Bioinformatics, bty105, 2018. doi:10.1093/bioinformatics/bty105

Delépine, B., Duigou, T., Carbonell, P., Faulon, J.L. RetroPath2.0: A retrosynthesis workflow for metabolic engineers, Metabolic Engineering, 45, 158–170, 2018. doi:10.1016/j.ymben.2017.12.002

López-Messeguer, 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, volume “Computational Toxicology”, 1800, 505-518, 2018. doi:10.1007/978-1-4939-7899-1

Koch, M., Duigou, T., Carbonell, P., Faulon, J.L. Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0. Journal of Cheminformatics, 9, 64, 2017. doi:10.1186/s13321-017-0252-9

Carbonell, P., Delépine, B., Faulon, J. L. Extended metabolic space modeling. Methods in Molecular Biology, volume “Synthetic Metabolic Pathways”, 1671, 83-97, 2017. doi:10.1007/978-1-4939-7295-1

Swainston, N., Batista-Navarro, R., Carbonell, P., Dobson, P. D. , Dunstan, M. , Jervis, A. J. , Vinaixa, M., Williams, A. R., Ananiadou, S., Faulon, J. L., Mendes, P., Kell, D. B., Scrutton, N. S., Breitling, R. biochem4j: integrated and extensible biochemical knowledge through graph databases, PloS One, 12 (7), e0179130, 2017. doi:10.1371/journal.pone.0179130

Carbonell, P, Lopez, O., Amberg, A., Pastor, M., Sanz, F. Hepatotoxicity prediction by systems biology modeling of disturbed metabolic pathways using gene expression data. ALTEX: Alternatives to Animal Experimentation, 34 (2), 219-234, 2017. doi:10.14573/altex.1602071

Carbonell, P., Gök, A., Shapira, P., Faulon, J.L. Mapping the patent landscape of synthetic biology for fine chemical production pathways. Microbial Biotechnology, 9 (5), 687-695, 2016. doi:10.1111/1751-7915.12401

le Feuvre, R., Carbonell, P., Currin, A., Dunstan, M., Fellows, D., Jervis, A., Rattray, . N.J.W., Robinson, C.J., Swainston, N., Vinaixa, M., Williams, A., Yan, C., Barran, P. Breitling, R., Chen, G.G., Faulon, J.L., Goble, C., Goodacre, R., Kell, D.B., Micklefield, J., Scrutton, N.S., Shapira, P., Takano, E., Turner, N.J. SYNBIOCHEM synthetic biology research centre, Manchester – a UK foundry for fine and speciality chemicals production. Synthetic and Systems Biotechnology, 1 (4), 271-275, 2016. doi:10.1016/j.synbio.2016.07.001

Carbonell, P., Currin, A., Dunstan, M., Fellows, D., Jervis, A., Rattray, N. J. W., Robinson, C. J., Swainston, N., Vinaixa, M., Williams, A., Yan, C., Barran, P., Breitling, R., Chen, G. G., Faulon, J.-L., Goble, C., Goodacre, R., Kell, D. B., Feuvre, R. L., Micklefield, J., Scrutton, N. S., Shapira, P., Takano, E., Turner, N. J. SYNBIOCHEM–a SynBio foundry for the biosynthesis and sustainable production of fine and speciality chemicals. Biochemical Society Transactions, 44 (3), 675-677, 2016. doi:10.1042/BST20160009

Carbonell, P., Currin, A., Jervis, A., Rattray, N., Swainston, N., Yan, C., Takano, E., Breitling, R. Bioinformatics for the synthetic biology of natural products: Integrating across the Design-Build-Test cycle. Natural Products Reports, 33, 925-932, 2016. doi:10.1039/c6np00018e

Delépine, B., Libis, V., Carbonell, P., Faulon, J.L. SensiPath: computer-aided design of Sensing-enabling metabolic Pathways. Nucleic Acids Research, 44 (W1): W226-W231, 2016. doi:10.1093/nar/gkw305

Mellor, J., Grigoras, I., Carbonell, P., Faulon, J.L. Semisupervised Gaussian process for automated enzyme search. ACS Synthetic Biology, 5 (6), 518–528, 2016. doi:10.1021/acssynbio.5b00294

Ceroni, F., Carbonell, P., François, J.M., Haynes, K.A. Editorial – Synthetic Biology: engineering complexity and refactoring cell capabilities. Frontiers in Synthetic Biology, 3, 120, 2015. doi:10.3389/fbioe.2015.00120

Martiny, V., Carbonell, P., Chevillard, F., Moroy, G., Nicot. A., Vayer, P., Villoutreix, B., Miteva, M. Integrated structure- and ligand-based in silico approach to predict inhibition of cytochrome P450 2D6. Bioinformatics, 31 3930-3937, 2015. doi:10.1093/bioinformatics/btv486

Trosset, J.Y., Carbonell, P. Synthetic biology for pharmaceutical drug discovery. Journal of Drug Design, Development and Therapy, 9:6285-6302, 2015. doi:10.2147/DDDT.S58049

Carbonell, P., Trosset, J.Y. Computational protein design methods for synthetic biology. Methods in Molecular Biology, volume “Computational Methods in Synthetic Biology”, 1244: 3-21, 2015. doi:10.1007/978-1-4939-1878-2_1

Feher, T., Libis, V., Carbonell, P., Faulon, J.L. A sense of balance: Experimental investigation and modeling of a malonyl-CoA sensor in Escherichia coli. Frontiers in Synthetic Biology, 3, 46, 2015. doi:10.3389/fbioe.2015.00046

Carbonell P, Mayer MA, Bravo À. Exploring brand-name drug mentions on twitter for pharmacovigilance. Stud Health Technol Inform, 210:55-9, 2015. doi: 10.3233/978-1-61499-512-8-55

Carbonell, P., Parutto, P., Herisson, J., Pandit, S., Faulon, J.L. XTMS: Pathway design in an eXTended Metabolic Space. Nucleic Acids Research, 42 (W1): W389-W394, 2014. doi:10.1093/nar/gku362

Feher, T., Planson, A.G., Carbonell, P., Fernandez-Castane, A., Grigoras, I., Dariy, E., Perret, A., Faulon, J.L. Validation of RetroPath, a computer aided design tool for metabolic pathway engineering. Biotechnology Journal, 9(11), 1446-1457, 2014. doi:10.1002/biot.201400055

Carbonell, P., Parutto, P., Baudier, C., Junot, C., Faulon, J.L. Retropath: automated pipeline for embedded metabolic circuits. ACS Synthetic Biology, 3 (8), 565-577, 2014. doi:10.1021/sb4001273

Fernandez-Castane, A., Feher, T., Carbonell, P., Pauthenier, C., Faulon, J.L. Computer-aided design for metabolic engineering. Journal of Biotechnology, 192(B), 302-313, 2014. doi:10.1016/j.jbiotec.2014.03.029

Delepine, B., Carbonell, P., Faulon. J.L. XTMS in Action: Retrosynthetic Design in the Extended Metabolic Space of Heterologous Pathways for High-Value Compounds. Computational Methods in Systems Biology, Lecture Notes in Computer Science, 8859, 256-259, 2014. doi:10.1007/978-3-319-12982-2_21

Carbonell, P., Trosset, J.Y. Overcoming drug resistance through in silico prediction. Drug Discovery Today: Technologies, 11: 101-107, 2014. doi:10.1016/j.ddtec.2014.03.012.

Carbonell, P., Faulon, J.L, Capasso, E., Volpati, L. A microbial organism for producing terephthalate from biomass. International Patent Application WO2014102280 A1, July 2014.

Carbonell, P., Feher, T., Grigoras, I., Faulon, J.L. Retropath: retrosynthesis design of metabolic pathways. In Advances in Systems and Synthetic Biology, 49-56, 2014.

Carbonell, P. Systems approach to language networks mapping: pull up by the bootstraps. In Language analysis in cross-cultural and intercultural communication, 41-50, 2014.

Carbonell, P., Carlsson, L., Faulon, J.L. Stereo signature molecular descriptor. Journal of Chemical Information and Modeling, 53(4): 887-897, 2013. doi:10.1021/ci300584r

Martiny, V.Y., Carbonell, P., Lagorce, D., Villoutreix, B.O., Moroy, G., Miteva, M.A. In silico mechanistic profiling to probe small molecule binding to sulfotransferases. PLoS ONE, 8(9): e73587, 2013. doi:10.1371/journal.pone.0073587,

Trosset, J.Y, Carbonell, P. Synergistic synthetic biology: units in concert. Frontiers in Synthetic Biology, 1:11, 2013. doi:10.3389/fbioe.2013.00011

Carbonell, P., Planson, A.G., Faulon, J.L. Retrosynthetic design of heterologous pathways. In Methods in Molecular Biology, volume “Systems Metabolic Engineering: Methods and Protocols”, 985:149-73, 2013. doi:10.1007/978-1-62703-299-5_9

Pauthenier, C., Carbonell, P., Faulon, J.L. La conception rationnelle de ferments biologiques : comment concevoir un micro-organisme pour produire un composé chimique spécifique. L’Actualité Chimique, 375: 30-36, 2013.

Xu, S., Ying, H., Carbonell, P., Hu, J., Lee, C. Wu, W. Fuzzy logic applications in control theory and systems biology. Advances in Fuzzy Systems, 504728, 2013. doi:10.1155/2013/504728

Planson, A.G., Carbonell, P., Grigoras, I., Faulon, J.L. A retrosynthetic biology approach to therapeutics: from conception to delivery. Current Opinion in Biotechnology, 23:948-956, 2012.doi:10.1016/j.copbio.2012.03.009

Carbonell, P., Fichera, D., Pandit, S.B., Faulon, J.L. Enumerating metabolic pathways for the production of heterologous target chemicals in chassis organisms. BMC Systems Biology, 6:10, 2012.doi:10.1186/1752-0509-6-10

Planson, A.G., Carbonell, P., Paillard, E., Pollet, N., Faulon, J.L. Compound toxicity screening and structure-activity relationship modeling in Escherichia coli. Biotechnology and Bioengineering, 109(3):846-850, 2012. doi:10.1002/bit.24356

Carbonell, P., Lecointre, G., Faulon, J.L. Origins of specificity and promiscuity in metabolic networks. Journal of Biological Chemistry, 286:43994-44004, 2011. doi:10.1074/jbc.M111.274050

Carbonell P., Planson A.G., Fichera D., Faulon J.L. A retrosynthetic biology approach to metabolic pathway design for therapeutic production. BMC Systems Biology, 5:122, 2011. doi:10.1186/1752-0509-5-122

Planson, A.G., Carbonell, P., Grigoras, I., Faulon, J.L. Engineering antibiotic production and overcoming bacterial resistance. Biotechnology Journal, 6(7): 812-825, 2011. doi:10.1002/biot.201100085

Carbonell P., Faulon J.L. Molecular signatures-based prediction of enzyme promiscuity. Bioinformatics, 26(16): 2012-2019, 2010. doi:10.1093/bioinformatics/btq317

Faulon, J.L., Carbonell, P. Reaction network generation. In Handbook Of Chemoinformatics Algorithms. Boca Raton: Chapman & Hall/CRC Series on Mathematical & Computational Biology. 2010. ISBN:9781420082920

Carbonell, P. Large-scale in silico identification of determinants of protein affinity and promiscuity, Habilitation Thesis, University of Evry, 2010. [pdf]

C. Sarnowski, P. Carbonell, M. Elati and J.L. Faulon. Prediction of catalytic efficiency to discover new enzymatic activities. In Proc. of MLSB10, the Fourth International Workshop on Machine Learning in Systems Biology, pages 153-156, Edinburgh (Scotland), 2010.

Carbonell, P., del Sol, A. Methyl side-chain dynamics prediction based on protein structure. Bioinformatics, 25(19): 2552-2558, 2009. doi:10.1093/bioinformatics/btp463

Carbonell, P., Nussinov, R., del Sol, A. Energetic determinants of protein binding specificity: Insights into protein interaction networks. Proteomics, 9(7): 1744-1753, 2009. doi:10.1002/pmic.200800425

del Sol, A., Carbonell, P. The modular organization of domain structures: insights into protein-protein binding. PLoS Computational Biology, 3(12): e239, 2007. doi:10.1371/journal.pcbi.0030239

Colinge, J., Masselot, A., Carbonell, P., Appel, R.D. Insilicospectro: An open-source proteomics library. Journal of Proteome Research, 5(3): 781-786, 2006. doi:10.1021/pr0504236

Carbonell. P. Efficient fuzzy logic-based algorithm for microarray network identification and prediction in bioinformatics. Elektronika Ir Elektrotechnika, 67(3): 37-40, 2006.

Carbonell, P. Decentralized control of telecommunications networks using fuzzy logic techniques. Information Technology, 14 (4), Jul-Aug 2003.

Carbonell, P., Wang, X., Jiang, Z.P. On the suppression of flow-induced vibration with a simple control algorithm. Communications in Nonlinear Science and Numerical Simulation, 8(1):49-64, March 2003. doi:10.1016/S1007-5704(02)00017-5

Carbonell, P., Diez, J.L., Navarro, J.L. Aplicaciones de técnicas de modelos locales en sistemas complejos .Inteligencia artificial: Revista Iberoamericana de Inteligencia Artificial, 4:10, 111-118, 2000.

P. Carbonell, Z. P. Jiang, and S. Panwar. Fuzzy TCP: A preliminary study. IFAC Proceedings Volumes, 35: 1, 205-210, 2002. doi:10.3182/20020721-6-ES-1901.00687

P. Carbonell, Z. P. Jiang, and D. Repperger. Comparative study of three nonlinear control strategies for a pneumatic muscle actuator. In Proc. of the 5th IFAC Symposium Nonlinear Control Systems (NOLCOS 2001), St Petersburg (Russia), 2001.

A. Hilario, P. Carbonell, and S. Valero. Development of an electronic reference and consulting tool in standardization, calibration and industrial control. In Proc. of the IFAC Workshop on Internet Based Control Education, pages 13-18, Madrid (Spain), 2001.

P. Carbonell and Z. P. Jiang. Fuzzy backstepping control technique for mechanical systems. In Proceedings of the IFAC Workshop on Advanced Fuzzy/Neural Control, volume pp. 167-172, page Valencia (Spain), 2001.

P. Carbonell, Z. P. Jiang, and D. Repperger. A fuzzy backstepping controller for a pneumatic muscle actuator system. In Proc. of the IEEE Conference on Intelligent Control Systems, Mexico D.F. (Mexico), 2001. doi:10.1109/ISIC.2001.971535

P. Carbonell, Z. P. Jiang, and D. Repperger. Nonlinear control of a pneumatic muscle actuator: Backstepping vs. sliding-mode. In Proc. of the IEEE International Conference on Control Applications, Mexico D.F. (Mexico), 2001.