Publications

1. 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

2. 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

3. 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

4. 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

5. 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

6. 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 

7. 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

8. 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

9. 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

10. 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

11. 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

12. 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

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

14. 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

15. 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

16. 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

17. 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

18. 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

19. 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

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

21. 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

22. 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

23. 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

24. 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

25. 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

26. 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

27. 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

28. 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

29. 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

30. 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 

31. 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

32. 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

33. 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

34. 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

35. 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

36. 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

37. 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

38. 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

39. 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

40. 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

41. 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 

42. 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

43. 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

44. 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

45. 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

46. 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

47. 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

48. 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

49. 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

50. 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

51. 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

52. 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.

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

54. 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.

55. 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.

56. 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

57. 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,

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

59. 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

60. 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.

61. 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

62. 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

63. 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

64. 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

65. 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 

66. 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

67. 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

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

69. 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

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

71. 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.

72. 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

73. 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

74. 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

75. 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

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

77. Carbonell, O., Carbonell, P., Stuart, K. Building and implementing pragmatic thesauri through associative networks. In Translation and the Machine: Technology, Meaning, Praxis. Ed.S. Elliot, and S. Berneking, Rome, Edizioni di Storia e Letteratura, 173-182, 2008. 

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

79. 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

80. 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.

81. 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

82. 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.

83. 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.

84. 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.

85. 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

86. 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.

87. P. Carbonell. Local model-based fuzzy logic techniques applied to DC/DC power converters. PhD Thesis. Polytechnic University of Valencia, 2000. doi:10.4995/Thesis/10251/4641

88. P. Carbonell and J. L. Navarro. Local model-based fuzzy control of switch-mode dc/dc converters. IFAC Proceedings Volumes, 32:2, 5404-5409, 1999. doi:10.1016/S1474-6670(17)56920-7

89. P. Carbonell, A. Hilario, and G. Garcera. Fuzzy gain scheduling control of switch-mode dc/dc converters. In Proc. of the IEEE International Symposium on Industrial Electronics ISIE99, Bled (Slovenia), 1999. doi:10.1109/ISIE.1999.801821

90. G. Garcera, P. Carbonell, and A. Abellan. Sensibility study of the control loops of voltage and current mode controlled dc-dc converters by means of robust parametric control. In Proc. of the IEEE International Symposium on Industrial Electronics ISIE99, Bled (Slovenia), 1999. doi:10.1109/ISIE.1999.798682

91. A. Hilario and P.Carbonell Calibración de equipos de medida según ISO 9000 introducción a la calibración de equipos de medida para monitorización y control de procesos industriales según la familia de normas ISO 9000. 104 pp. Barcelona: Cetisa-Boixareu Editores, 2001. ISBN 84931327-2-1.

92. P. Carbonell, A. Hilario, Automatic control. Concepts and simulation exercises, 257 pp., Valencia: Polytechnic University of Valencia, 1998. ISBN 8477216576.

Conference presentations, talks and posters

1. P. Carbonell. The extended metabolic space: from evolution to design. LSC-Retreat 4.0. Canfranc (Spain), 2023,

2. P. Carbonell. Allosteric transcription factor-based biosensors for smart biomanufacturing. BE-I2sysbio: Building & Expanding I2SysBio, València (Spain), 2023.

3. J. Tellechea-Luzardo, P. Carbonell. Sensbio: a biosensor design toolbox for metabolic pathway screening and dynamic regulation. X Bioinformatics and Genomics Symposium (BGS), València (Spain), 2022.

4. C. Fernández, H. Faquir, M. Pájaro, P. Carbonell, I. Otero-Muras. Controlling the behaviour of gene circuits for applications in synthetic biology: stabilization of a stochastic gene switch. X Bioinformatics and Genomics Symposium (BGS), València (Spain), 2022.

5. P. Carbonell. Automated design-build-test-learn (DBTL) pipelines for synthetic biology and biofoundries. I2SysBio seminar, I2SysBio (UV-CSIC), Valencia (Spain), 2022. 

6. I. Blázquez Arenas, P. Carbonell, I. Otero-Muras. Active Learning-based Optimal Experimental Design for efficient biomanufacturing. IWBDA, Paris (France), 2022.

7. P. Carbonell. Integrating DBTL computational tools into automated biofoundries pipelines: SynBioPython and GalaxySynbioCAD. Global Biofoundries Alliance Annual Meeting, Montreal (Canada), 2022.

8. I. Otero-Muras , G. Rodrigo, A. Jaramillo,  M. Porcar, A Pascual-Ahuir, D. Orzáez, A. Vignoni , J. Picó , P. Carbonell. Valencia Biofoundry: A nascent facility for advanced biotechnology and automated biomanufacturing with distinctive assets and global ambition. Global Biofoundries Alliance Annual Meeting, Montreal (Canada), 2022.

9. J. Tellechea-Luzardo, P. Carbonell. Sensbio: an online server for biosensor design. 6th Applied Synthetic Biology in Europe (ASBE VI), Edinburgh (UK), 2022.

10. J. Tellechea-Luzardo, M. Stiebritz, P. Carbonell. Allosteric transcription factor-activated RNA and protein-based biocircuits. RNAct, Valencia (Spain), 2022.

11. J. Tellechea-Luzardo, I. Otero-Muras, P. Carbonell. An integrated approach to meet the challenges of efficient biomanufacturing. SIMB Annual Meeting, San Francisco (USA), 2022.

12. P. Carbonell. Rapid prototyping for metabolic pathway design. IBMCP Biotech Talk, IBMCP (UPV-CSIC), Valencia (Spain), 2022.

13. P. Carbonell. Streamlining the Design-Build-Test-Learn workflow for bio-based production platforms. XI Bioinformatics Open Days, Braga (Portugal), 2022.

14. J. Tellechea-Luzardo, P. Carbonell. Machine learning aided advances in synthetic biology (workshop). IWBDA, 2021.

15. M. Camarena, Y. Boada, J. Picó, P. Carbonell.  Gene variant design space for biosensor-based pathway dynamic regulation. J. Automatica, 2021.

16. P. Carbonell. Automated tools for metabolic pathway design to close the learning loop. Metabolic Engineering 14, 2021.

17. J. L. Faulon, T. Duigou, M. du Lac, J. Hérisson, P. Carbonell. Design automation workflows for synthetic biology and metabolic engineering: the Galaxy-SynbioCAD portal. IWBDA, 2020.

18. Y. Boada, A. Vignoni, A. Fraile, J. Picó, P. Carbonell. Dynamic pathway regulation: extended biosensor and controller tuning with multiobjective optimization. IWBDA, 2020.

19. C. Robinson, P. Carbonell, A. Jervis, C. Yan, K. Hollywood, M. Dunstan, A. Currin, N. Scrutton. Rapid prototyping of microbial chassis for biomanufacturing of a suite of material monomers. Synthetic Biology UK, Warwick (UK), 2019.

20. P. Carbonell, J.L. Faulon, R. Breitling. Efficient learning in metabolic pathway designs through optimal assembling. 8th IFAC Conference on Foundations of Systems Biology in Engineering (FOSBE2019), Valencia (Spain), 2019.

21. P. Carbonell. Biomanufacturing: towards a new bioeconomy. Difutec, Alcoy (Spain), 2019.

22. P. Carbonell. Bioretrosynthesis and rapid prototyping for automated synthetic pathway redesign. 9th Int. CeBiTec Research Conference:  Advances in Industrial Biotechnology , Bielefeld (Germany), 2019.

23. P. Carbonell, R. Breitling, J.L. Faulon. OptBioDes: optimal design for the synbio toolchain. IWBDA, Cambridge (UK), 2019.

24. P.Carbonell. An agile engineering design approach to biomanufacturing. New Vistas in Computational Systems and Synthetic Biology, Vigo (Spain), 2019.

25. T. Duigou, P. Carbonell, J.L. Faulon. RetroRules: an online resource for reaction rules in biological engineering, Synthetic Biology UK, Bristol (UK), 2018.

26. A. Roberts, P. Kelly, J. Bain, P. Carbonell, J.L. Faulon, J. Blaker, S. Hay, S. Yeats, N. Scrutton. Synthetic biology as a route to high-strength poly(aromatic amide) fibres, Synthetic Biology UK, Bristol (UK), 2018.

27. P. Carbonell. A framework for portability and predictability of genetic circuits in the pathway engineering pipeline, Centre for Synthetic Biology and the Bioeconomy (CSBB), Newcastle University (UK), 2018.

28. P. Carbonell. Design to Learn, Learn to Design: The Manchester SYNBIOCHEM automated Design-Build-Test-Learn pipeline for microbial production of fine chemicals, JBEI (USA), 2018.

29. P. Carbonell, S. Taylor, R. Sung, A. J Jervis, R. Breitling, J.L. Faulon, N. S. Scrutton. Context-aware predictive tools for portable genetic circuit engineering, IWBDA, Berkeley (USA), 2018.

30. P. Carbonell. Annual Debate 2018: Synthetic Biology. Linnean Society, London (UK), 2018.

31. P. Carbonell, N. Swainston, A. Jervis, N.S. Scrutton, E. Takano, D.B. Kell, R. Breitling, J.L. Faulon. Machine learning for the automated synthetic biology pipeline. Synthetic Biology UK, Manchester (UK), 2017.

32. B. Delépine, T. Duigou, P. Carbonell, J.L. Faulon. RetroPath2.0: open-source retrosynthesis workflow for metabolic engineering. Synthetic Biology UK, Manchester (UK), 2017.

33. N. Swainston, M. Dustan, A. Jervis, C. Robinson, P. Carbonell, A. Williams, R. Breitling, N.S. Scrutton. PartsGenie: an integrated tool for optimising and sharing synthetic biology parts. Synthetic Biology UK, Manchester (UK), 2017.

34. J. Bain, P. Kelly, S. Yeates, J. Bleaker, P. Carbonell, J.L. Faulon, S. Hay, N.S. Scrutton.   Synthetic Biology Approaches to Sustainable Production of Aramid Fibre Precursors. Synthetic Biology UK, Manchester (UK), 2017.

35. P. Carbonell. Observability and controllability of engineered metabolic circuits for microbial chemical production. International Workshop on Control Engineering and Synthetic Biology, London (UK), 2017.

36. B. Delepine, T. Duigou, P. Carbonell, J.L. Faulon. RetroPath 2.0. A versatile reaction network prediction tool for biological engineers. SB 7.0. The Seventh International Meeting on Synthetic Biology, Singapore, 2017.

37. P. Carbonell, J.L. Faulon. Screening biosynthetic accessibility of novel biomaterials building blocks with improved properties. Scientific and Technological Challenges in Defining a New Paradigm for Sustainable Biomaterials, Manchester (UK), 2017.

38. P. Carbonell, N. Swainston, A. Jervis, M. Vinaixa, M. Dunstan, C. Robinson, K. Hollywood, C. Yan, A. Currin. The expansion/contraction data paradigm to enhance chemical diversity production in industrial biotechnology. Data-driven biotechnology – Bench, Bioreactor and Bedside, Novo Nordisk Favrholm Campus, Hillerod (DK), 2017.

39. P. Carbonell, S. Heux. Retro-biosynthesis in metabolic engineering. Advances in Systems and Synthetic Biology, Thematic Research School, Lyon (France), 2017.

40. P. Carbonell. SYNBIOCHEM: Harnessing industrial partnerships for added impact. Synthetic Biology for Growth Networking. Edinburgh (UK), 2016.

41. J. Bain, W. Finnigan. L. Heap, C. Jensen, P. Kelly, J. Blaker, R. Breitling, P. Carbonell, M. Corbett, J.L. Faulon, S. Hay, E. Takano, N. Turner, S. Yeates, N. Scrutton. Synthetic biology for high performance materials. Synthetic Biology UK, Edinburgh (UK), 2016.

42. P. Carbonell, A. Gök, P. Shapira, J.L Faulon. A patent landscape for the synbio of fine and speciality chemical production. Synthetic Biology UK, Edinburgh (UK), 2016.

43. P. Carbonell, O. Lopez, A. Amberg, M. Pastor, F. Sanz. Systems biology-based drug toxicity prediction using gene expression data and its application to hepatotoxicity. eTOX Final Conference, Novartis Campus Basel (Switzerland), 2016.

44. P. Carbonell. SynBio Design. EuroScience Open Forum ESOF16, Manchester (UK), 2016.

45. P. Carbonell. Automating engineering design in SynBio foundries. BioSynSys, Bordeaux (France), 2016. 

46. P. Carbonell. Retro-biosynthesis in metabolic engineering. Advances in Systems and Synthetic Biology, Thematic Research School, Evry (France), 2016.

47. B. Delépine, T. Duigou, P. Carbonell, J.L Faulon. Diving into the metabolic space: some insights from a retrosynthesis standpoint. BioSynSys, Bordeaux (France), 2016. 

48. M. Dunstan, A. Jervis, C. Robinson, N. Swainston, J.L. Faulon, P. Carbonell. SBCDOE: a design of experiments-based part planner for synthetic biology production of chemicals. IWBDA, Newcastle (UK), 2016.

49. N. Swainston, P. Carbonell, A. Jervis, C. Robinson, M. Dunstan, J.L. Faulon. PathwayGenie - pathway design from selection to plasmid. IWBDA, Newcastle (UK), 2016.

50. V. Kulkarni, L. E. Menjra, P. Carbonell, J.L. Faulon. Integrated predictive genome-scale models to improve the metabolic re-engineering efficiency. IWBDA, Newcastle (UK), 2016.

51. N. Swainston, P. Carbonell, et al. Integrated informatics to support SYNBIOCHEM Design-Build-Test cycle for production of fine and speciality chemicals. Cellular and Molecular Biotechnology, Paris (France), 2015.

52. J. Mellor, P. Carbonell, J.L. Faulon. Gaussian process-based model for automated enzyme selection in pathway design. Synthetic Biology UK, London (UK), 2015.

53. P. Carbonell, J.L Faulon. Modelling and redesign of synergistic antimicrobial activities between peptides and proteins for synthetic biology applications. Application of Synthetic Biology for the production of next generation biologics. COEBP 4th Annual Scientific Symposium, Manchester (UK), 2015.

54. P. Carbonell. Retro-biosynthesis in metabolic engineering. Advances in Systems and Synthetic Biology, Thematic Research School, Strasbourg (France), 2015.

55. P. Carbonell, M.A. Mayer, A. Bravo. Exploring brand-name drug mentions on Twitter for pharmacovigilance. Medical Informatics Europe MIE, Madrid (Spain), 2015.

56. J. Mellor, P. Carbonell, J.L. Faulon. Automated enzyme selection for pathway design using Gaussian process-based models. BioSynSys, Paris (France), 2015.

57. P. Carbonell. System-level assessment of tissue-specific drug toxicity. II Bioinformatics and Computational Biology Symposium, Barcelona (Spain), 2014.

58. P. Carbonell. Retrosynthetic circuit design. 3S Biology Summer School Systems, Synthetic and Semantic Biology, Trento (Italy), 2014.

59. P. Carbonell. Automated Modeling, Design & Optimization of Microbial Biosynthesis for Industrial Biotechnology. The Novo Nordisk Foundation Center for Biosustainability (CFB), Technical University of Denmark (DTU), 2014.

60. P. Carbonell. Towards predictive integrative biology. Institute of Genetics and Microbiology (IGM), CNRS, Paris-Sud University (France), 2014.

61. P. Carbonell. Towards multi-scale refactoring of microbial biosynthesis pathways. Paris Interdisciplinary Energy Research Institute, Paris (France), 2014.

62. P. Carbonell. Retro-biosynthesis in metabolic engineering. Advances in Systems and Synthetic Biology, Thematic Research School, Evry (France), 2014.

63. T. Feher, P. Carbonell, V. Libis, J.L. Faulon. The rational design-build-test cycle applied to metabolic pathway engineering. BioSynSys, Toulouse (France), 2014.

64. B. Delepine, P. Carbonell, J.L. Faulon. XTMS in action: retrosynthetic design in the extended metabolic space of heterologous pathways for high-value compounds. The 12th Conference on Computational Methods in Systems Biology, University of Manchester (UK), 2014.

65. P. Carbonell. TaxaTox: System-level assessment of taxa-specific differences in drug toxicity. 12th Symposium in Bioinformatics, Seville (Spain), 2014.

66. P. Carbonell. The Extended Metabolic Space: Unveiling latent capabilities towards biosynthesis, sensing and regulation. The Netherlands Institute for Systems Biology, University of Amsterdam (Netherlands), 2013.

67. P. Carbonell. Unfolding diversity: Modeling promiscuity and toxicity in the metabolic space and beyond. GRIB, Barcelona (Spain), 2013.

68. P. Carbonell. Towards in silico whole-cell modeling for regulation and design. CGM, Gif sur Yvette (France), 2013.

69. P. Carbonell, P. Parutto, J.L. Faulon. RetroPath: Automated pipeline for embedded metabolic circuits. IWBDA, London (UK), 2013.

70. P. Carbonell, P. Parutto. Unraveling evolutionary mechanisms driving metabolic diversity. JOBIM, Toulouse (France), 2013.

71. P. Carbonell. Retro-biosynthesis in metabolic engineering. Advances in Systems and Synthetic Biology, Thematic Research School, La Colle-sur-Loup (France), 2013.

72. P. Carbonell. Unfolding chemical and metabolic diversity for advanced biotechnological applications. LISBP, Toulouse (France), 2013.

73. P. Carbonell, T. Feher. Metabolic circuits: modeling, design and optimization. Journée Biologie Synthétique iSSB/Genoscope, Evry (France), 2013.

74. P. Carbonell. In silico biological modeling and design: integrating top-down and bottom-up approaches. BIOS Seminar, Tours, 2013.

75. P. Carbonell. A journey into retrosynthesis: exploring the origins of promiscuity in biosynthetic pathways. Jena Life Science Forum 2012: Designing Living Matter, Jena (Germany), 2012 (invited).

76. P. Carbonell, I. Grigoras, A.G. Planson, J.L. Faulon. Modelling synergistic antimicrobial activities in peptide cocktails: Strategies for production and delivery. AMP2012 - International Symposium on Antimicrobial Peptides, Lille (France), 2012.

77. P. Carbonell, D. Fichera, J.L. Faulon. Constructive biosynthetic pathway selection in the reaction signature space. In 71st Harden Conference - Metabolic Pathway Analysis 2011, University of Chester (UK), 2011.

78. P. Carbonell, D. Fichera, F. Green, E. Paillard, A.G. Planson, J.L. Faulon. Using retrosynthetic biology to design metabolic pathways for therapeutics production. In SB5.0: the Fifth International Meeting on Synthetic Biology, Stanford University, Stanford (USA), 2011.

79. P. Carbonell. Determinants of protein affinity and promiscuity for in-silico engineering of biological circuits and devices. In LRI Laboratory for Computer Science Seminars, Université Paris-Sud, Orsay (France), 2011 (invited).

80. A.G. Planson, P. Carbonell, D. Fichera, E. Paillard, C. Sarnowski, J.L. Faulon. A roadmap to implementing novel therapeutic circuits in E. coli. In ICSynBio, International Conference on Synthetic Biology, Evry (France), 2010.

81. P. Carbonell, D. Fichera, J.L. Faulon. Predicting heterologous compound-forming reaction pathways through retrosynthesis hypergraphs. In LIX Bioinformatics Colloquium 2010, Ecole Polytechnique, Palaiseau (France), 2010.

82. P. Carbonell. Systems approach to language networks mapping: pull up by the bootstraps. In Mapping language across cultures: Textual analysis in cross-cultural and intercultural communication (MLAC10), Salamanca (Spain), 2010 (invited). 

83. D. Fichera, P. Carbonell and J.L. Faulon. Signatures of chemical diversity in metabolic networks. In Modelling Complex Biological Systems in the Context of Genomics, Evry (France), 2010. 

84. P. Carbonell. Determinants of protein binding promiscuity: insights into protein-protein interactions. In SaarLorLux09 Workshop on Systems Biology, Nancy (France), 2009. 

85. P. Carbonell and J.L. Faulon. Catalytic promiscuity prediction using molecular signatures. In European Systems & Synthetic Biology ESSB09, Evry (France), 2009.

86. P. Carbonell and A. del Sol. Specificity and affinity in protein-protein interactions: From a systems biology to a molecular point of view. In 12th Annual International Conference on Research in Computational Molecular Biology RECOMB2008, Singapore (Singapore), 2008.

87. O. Carbonell, K. Stuart, and P. Carbonell. Building and implementing pragmatic thesauri through associative networks: A necessary step in computer-assisted translation technology. In International Conference on Translating with Computer-Assisted Technology, Rome (Italy), 2004.

88. A. Hilario and P. Carbonell. Prototipo experimental para la identificacion y control de actuadores por musculo neumatico. In XXIV Jornadas de Automatica, Leon (Spain), 2003.

89. P. Carbonell and M. A. Satorre. Prototipo de un sistema de monitorizacion y control de la temperatura en un criostato. In XXIV Jornadas de Automatica, Leon (Spain), 2003.

90. M. A. Satorre, P. Carbonell, J.J. Ferre, J. Jaen, and A. Quiles. Controlador de temperatura para criostato de he. In XXIX Reunion Bienal de Fisica, volume I, pages 50-51, Madrid (Spain), 2003.

91. P. Carbonell. Control fuzzy adaptativo en redes complejas. In Actas del XI Congreso Espanol sobre Tecnologias y Logica Fuzzy, Leon (Spain), 2002.

92. P. Carbonell, X. Wang, and Z. P. Jiang. On the suppression of flow-induced vibration with a simple control algorithm. In ASME Symposium on the Vibration and Control of Mechanical Systems, New York (USA), 2001.

93. P. Carbonell, A. Hilario, and S. Valero. Elaboracion de notas tecnicas de control avanzado para la practica profesional. In XXII Jornadas de Automatica, Barcelona (Spain), 2001.

94. A. Hilario, P. Carbonell, and S. Valero. Desarrollo de un sistema de informacion electronico sobre normalizacion en el ambito de la instrumentacion, calibracion y control industrial. In First International Workshop on Multimedia Applications INTERMEDIA 2001, Valencia (Spain), 2001.

95. P. Carbonell and A. Hilario. Iso 9000 calibration requirements and implications for robust control design. In Proc. of the CONTROL000, Guimaraes (Portugal), 2000.

96. P. Carbonell. Metodologia para la seleccion de modelos locales borrosos en el espacio de regimenes de traba jo. In Actas del X Espanol sobre Tecnologias y Logica Fuzzy ESTYLF00, Sevilla (Spain), 2000.

97. A. Hilario, P, and Carbonell. Cuaderno tecnico: calibracion de equipos de medida industriales segun iso 9000. In Actas de las XXI Jornadas de Automatica, Sevilla (Spain), 2000.

98. A. Hilario and P. Carbonell. Integracion de herramientas de simulacion y multimedia: un caso practico con matlab/simulink y macromedia director 7. In I Jornadas de Trabajo Ensenanza via Internet/web de la Ingenieria de Sistemas y Automatica EIWISA00, Valencia, (Spain), 2000.

99. P. Carbonell and A. Hilario. Empleo de la incertidumbre estimada por calibracion segun iso 9000 en el diseno de lazos robustos de regulacion. In Actas de las XX Jornadas de Automatica, Salamanca (Spain), 1999.

100. P. Carbonell. Control borroso adaptativo de un convertidor dc/dc conmutado. In Actas del VII Espanol sobre Tecnologias y Logica Fuzzy ESTYLF97, Tarragona (Spain), 1997.

101. P. Carbonell. Nuevos enfoques en inteligencia artificial aplicada a la traduccion automatica: redes neuronales y sistemas borrosos. In X Simposio sobre Traduccion Literaria y Cientfico-Tecnica, Caceres (Spain), 1996.

102. P. Carbonell. Aportaciones de la inteligencia artificial a la teoria de la traduccion. In XI Simposio sobre Traduccion Literaria y Cientifico-Tecnica, Caceres (Spain), 1997. 

103. P. Carbonell, J.J. Beltran, M. Carbonell, M. Diaz, and J. Masia. Libreria de sistemas fisicos en simulink para su empleo en el campo de la simulacion y el control. In Actas del II Congreso de Usuarios de Matlab MATLAB96, Madrid (Spain), 1996. 

104. D. Carrica, J. Fernandez, A. San Martin, J.L. Diaz, P. Carbonell, A.Guerrero, M. Armada, and B. Kuchen. Low-cost commercial igbt inverter. In Proc. of ECLA94 Workshop on Advanced Automation, Madrid (Spain), 1994.