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Publications

78. Brödel, A.K., Jaramillo, A. & Isalan M. Intracellular directed evolution of proteins from combinatorial libraries based on conditional phage replication. Nature Protocols (2017). In press.

77. Brödel, A.K., Jaramillo, A. & Isalan M. (2016) Engineering orthogonal dual transcription factors for multi- input synthetic promoters. Nat Comms 7:13858.

76. A. P. Sagona, A. M. Grigonyte, P. MacDonald, and A. Jaramillo, “Genetically modified bacteriophages,” Integr. Biol., Feb. 2016. doi: 10.1039/C5IB00267B

75. G. Rodrigo, S. Prakash, T. Cordero, M. Kushwaha, and A. Jaramillo, “Functionalization of an Antisense Small RNA.,” J Mol Biol. 428, 889-892. (2016) doi: 10.1016/j.jmb.2015.12.022

74. M. Pasini, A. Fernández-Castané, A. Jaramillo, C. de Mas, G. Caminal, P. Ferrer, Using promoter libraries to reduce metabolic burden due to plasmid-encoded proteins in recombinant Escherichia coli, New Biotechnol. 33 (2015) 78–90. doi: 10.1016/j.nbt.2015.08.003.

73. M. Amos, I.M. Axmann, N. Bluthgen, F. de la Cruz, A. Jaramillo, A. Rodriguez-Paton and F. Simmel, Bacterial computing with engineered populations, Philos Trans a Math Phys Eng Sci. 373 (2015) 20140218. doi: 10.1098/rsta.2014.0218.

72. G. Rodrigo, E. Majer, S. Prakash, J.-A. Daròs, A. Jaramillo, J.F. Poyatos, Exploring the dynamics and mutational landscape of riboregulation with a minimal synthetic circuit in living cells, Biophys J. 109 (2015) 1070–1076.

71. S. Shen, G. Rodrigo, S. Prakash, E. Majer, T.E. Landrain, B. Kirov, and A. Jaramillo. Dynamic signal processing by ribozyme-mediated RNA circuits to control gene expression, Nucleic Acids Res. 43 (2015) 5158–5170. doi: 10.1093/nar/gkv287.

70. J. Hassall, P. MacDonald, T. Cordero, W. Rostain, A. Jaramillo, Design and Characterization of Topological Small RNAs, Methods Mol. Biol. 1316 (2015) 149–167. doi: 10.1007/978-1-4939-2730-2_13.

69. Rodrigo, G. & Jaramillo, A. 2014 RiboMaker: computational design of conformation-based riboregulation. Bioinformatics (doi:10.1093/bioinformatics/btu335)

68. Rostain, W., Landrain, T.E., Rodrigo, G. and Jaramillo, A. 2014 Regulatory RNA design through evolutionary computation and strand-displacement. Methods in Molecular Biology. (in press). (doi:10.1101/004580)

67. Rodrigo, G., Landrain, T. E., Majer, E., Daròs, J.-A. & Jaramillo, A. 2013 Full design automation of multi-state RNA devices to program gene expression using energy-based optimization. PLoS Comp Biol 9, e1003172.(doi:10.1371/journal.pcbi.1003172)

66. Rodrigo, G., Kirov, B., Shen, S. & Jaramillo, A. 2013 Theoretical and experimental analysis of the forced LacI-AraC oscillator with a minimal gene regulatory model. Chaos 23, 025109.(doi:10.1063/1.4809786)

65. Carrera, J. & Jaramillo, A. 2013 Automated design of bacterial genome sequences. BMC systems biology 7, 108.(doi:10.1186/1752-0509-7-108)

64. Suárez Diez, M., Pujol, A. M., Matzapetakis, M., Jaramillo, A. & Iranzo, O. 2013 Computational protein design with electrostatic focusing: Experimental characterization of a conditionally folded helical domain with a reduced amino acid alphabet. Biotechnol. J. 8, 855–864.(doi:10.1002/biot.201200380)

63. Rodrigo, G., Landrain, T. E., Shen, S. & Jaramillo, A. 2013 A new frontier in synthetic biology: automated design of small RNA devices in bacteria. Trends Genet 29, 529–536. (doi:10.1016/j.tig.2013.06.005)

62. Rodrigo, G., Carrera, J., Landrain, T. E. & Jaramillo, A. 2012 Perspectives on the automatic design of regulatory systems for synthetic biology. FEBS Lett 586, 2037–2042.(doi:10.1016/j.febslet.2012.02.031)

61. Rodrigo, G. & Jaramillo, A. 2013 AutoBioCAD: full biodesign automation of genetic circuits. ACS Synth. Biol. 2, 230–236. (doi:10.1021/sb300084h)

60. Jaramillo, A. & Zeliszewski, D. 2013 La conception du vivant s' automatise. Biofutur 339, 36–39.

59. Rodrigo, G., Landrain, T. E. & Jaramillo, A. 2012 De novo automated design of small RNA circuits for engineering synthetic riboregulation in living cells. Proc Natl Acad Sci U S A 109, 15271–15276. (doi:10.1073/pnas.1203831109)

58. Carrera, J., Elena, S. F. & Jaramillo, A. 2012 Computational design of genomic transcriptional networks with adaptation to varying environments. Proc Natl Acad Sci U S A 109, 15277–15282. (doi:10.1073/pnas.1200030109)

57. Carrera, J., Fernández Del Carmen, A., Fernández-Muñoz, R., Rambla, J. L., Pons, C., Jaramillo, A., Elena, S. F. & Granell, A. 2012 Fine-tuning tomato agronomic properties by computational genome redesign. PLoS Comp Biol 8, e1002528.(doi:10.1371/journal.pcbi.1002528)

56. Fetita, C., Kirov, B., Jaramillo, A. & Lefevre, C. 2012 An automated approach for single-cell tracking in epifluorescence microscopy applied to E. coli growth analysis on microfluidics biochips. Proceedings of SPIE 8317, 83170Z.(doi:10.1117/12.911371)

55. Rodrigo, G., Carrera, J. & Jaramillo, A. 2011 Computational design of synthetic regulatory networks from a genetic library to characterize the designability of dynamical behaviors. Nucleic Acids Res 39, e138–e138.(doi:10.1093/nar/gkr616)

54. Rodrigo, G., Jaramillo, A. & Blázquez, M. A. 2011 Integral Control of Plant Gravitropism through the Interplay of Hormone Signaling and Gene Regulation. Biophys J 101, 757–763.(doi:10.1016/j.bpj.2011.06.047)

53. Carrera, J., Rodrigo, G., Singh, V., Kirov, B. & Jaramillo, A. 2011 Empirical model and in vivo characterization of the bacterial response to synthetic gene expression show that ribosome allocation limits growth rate. Biotechnol. J. 6, 773–783. (doi:10.1002/biot.201100084)

52. Glykys, D. J., Szilvay, G. R., Tortosa, P., Suárez Diez, M., Jaramillo, A. & Banta, S. 2011 Pushing the limits of automatic computational protein design: design, expression, and characterization of a large synthetic protein based on a fungal laccase scaffold. Syst Synth Biol, 1–14. (doi:10.1007/s11693-011-9080-9)

51. Camsund, D., Lindblad, P. & Jaramillo, A. 2011 Genetically engineered light sensors for control of bacterial gene expression. Biotechnol. J. 6, 826–836.(doi:10.1002/biot.201100091)

50. Jaramillo, A. & Faulon, J.-L. 2011 Editorial: Synthetic Biology - applying new paradigms at the interface of fundamental research and innovation. Biotechnol. J. 6, 766–767.(doi:10.1002/biot.201100254)

49. Rodrigo, G., Carrera, J., Jaramillo, A. & Elena, S. F. 2011 Optimal viral strategies for bypassing RNA silencing. J R Soc Interface 8, 257–268.(doi:10.1098/rsif.2010.0264)

48. Rodrigo, G., Carrera, J., Elena, S. F. & Jaramillo, A. 2010 Robust dynamical pattern formation from a multifunctional minimal genetic circuit. BMC systems biology 4, 48.(doi:10.1186/1752-0509-4-48)

47. Gilbert, D., Jaramillo, A., Krasnogor, N., de Lorenzo, V. 2010 Synthetic biology gains momentum in Europe. Syst Synth Biol. 4, 145-147. (doi:10.1007/s11693-010-9065-0)

46. Suarez, M., Tortosa, P., Garcia-Mira, M. M., Rodríguez-Larrea, D., Godoy-Ruiz, R., Ibarra-Molero, B., Sanchez-Ruiz, J. M. & Jaramillo, A. 2010 Using multi-objective computational design to extend protein promiscuity. Biophys. Chem. 147, 13–19. (doi:10.1016/j.bpc.2009.12.003)

45. Carrera, J., Rodrigo, G., Jaramillo, A. & Elena, S. F. 2009 Reverse-engineering the Arabidopsis thaliana transcriptional network under changing environmental conditions. Genome Biol 10, R96.(doi:10.1186/gb-2009-10-9-r96)

44. Prather, K. L. J. & Jaramillo, A. 2009 Editorial: Focus on synthetic biology. Biotechnol. J. 4, 1367.(doi:10.1002/biot.200990084)

43. Suarez, M., Tortosa, P. & Jaramillo, A. 2008 PROTDES: CHARMM toolbox for computational protein design. Syst Synth Biol 2, 105–113.(doi:10.1007/s11693-009-9026-7)

42. Moltó, G., Suarez, M., Tortosa, P., Alonso, J. M., Hernández, V. & Jaramillo, A. 2009 Protein design based on parallel dimensional reduction. J Chem Inf Model 49, 1261–1271.(doi:10.1021/ci8004594)

41. Carrera, J., Rodrigo, G. & Jaramillo, A. 2009 Model-based redesign of global transcription regulation. Nucleic Acids Res 37, e38–e38.(doi:10.1093/nar/gkp022)

40. Sciretti, D., Bruscolini, P., Pelizzola, A., Pretti, M. & Jaramillo, A. 2009 Computational protein design with side-chain conformational entropy. Proteins 74, 176–191.(doi:10.1002/prot.22145)

39. Landrain, T. E., Carrera, J., Kirov, B., Rodrigo, G. & Jaramillo, A. 2009 Modular model-based design for heterologous bioproduction in bacteria. Curr Opin Biotechnol 20, 272–279.(doi:10.1016/j.copbio.2009.06.003)

38. Carrera, J., Rodrigo, G. & Jaramillo, A. 2009 Towards the automated engineering of a synthetic genome. Mol. BioSyst. 5, 733–743.(doi:10.1039/b904400k)

37. Suarez, M. & Jaramillo, A. 2009 Challenges in the computational design of proteins. J R Soc Interface 6 Suppl 4, S477–91.(doi:10.1098/rsif.2008.0508.focus)

36. Suarez, M., Rodrigo, G., Carrera, J. & Jaramillo, A. 2009 Chapter 4: Computational Design in Synthetic Biology. In (eds M. Schmidt M. Kelle A. Ganguli & A. de Vriend), pp. 49–63. Synthetic Biology.(doi:10.1007/978-90-481-2678-1_4)

35. Carrera, J., Rodrigo, G. & Jaramillo, A. 2008 Computational Design of Enzymes and Their Networks Using High Performance Computing. In (eds S. BassiniG Erbacci), pp. 411–415. Science and Supercomputing in Europe.

34. Carrera, J., Rodrigo, G. & Jaramillo, A. 2008 High Performance Computing in Synthetic Biology. In (eds S. BassiniG Erbacci), pp. 416–419. Science and Supercomputing in Europe.

33. Rodrigo, G., Suarez, M., Carrera, J. & Jaramillo, A. 2008 Computational Design of Biofuel Cells. In (eds S. BassiniG Erbacci), pp. 454–456. Science and Supercomputing in Europe.

32. Rodrigo, G., Carrera, J., Prather, K. J. & Jaramillo, A. 2008 DESHARKY: automatic design of metabolic pathways for optimal cell growth. Bioinformatics (Oxford, England) 24, 2554–2556.(doi:10.1093/bioinformatics/btn471)

31. Agudelo-Romero, P., Carbonell, P., la Iglesia, de, F., Carrera, J., Rodrigo, G., Jaramillo, A., Perez-Amador, M. A. & Elena, S. F. 2008 Changes in the gene expression profile of Arabidopsis thaliana after infection with Tobacco etch virus. Virol J 5, 92.(doi:10.1186/1743-422X-5-92)

30. Suarez, M., Tortosa, P., Carrera, J. & Jaramillo, A. 2008 Pareto optimization in computational protein design with multiple objectives. J Comput Chem 29, 2704–2711. (doi:10.1002/jcc.20981)

29. Rodrigo, G., Carrera, J. & Jaramillo, A. 2008 Computational design and evolution of the oscillatory response under light-dark cycles. Biochimie 90, 888–897.(doi:10.1016/j.biochi.2008.02.012)

28. Noirel, J., Ow, S. Y., Sanguinetti, G., Jaramillo, A. & Wright, P. C. 2008 Automated extraction of meaningful pathways from quantitative proteomics data. Brief Funct Genomic Proteomic 7, 136–146.(doi:10.1093/bfgp/eln011)

27. Sciretti, D., Bruscolini, P., Pelizzola, A., Pretti, M. & Jaramillo, A. 2008 Protein design at room temperature: the role of side-chain conformational entropy. pp. 82–97.(doi:10.1063/1.3033363)

26. Rodrigo, G., Carrera, J. & Jaramillo, A. 2008 Combinatorial Optimisation to Design Gene Regulatory Networks. Proceedings of the Workshop on Machine Constraint Based Methods for Bioinformatics.

25. Rodrigo, G., Carrera, J. & Jaramillo, A. 2007 Automatic model-based design of genetic circuits. Proceedings of the 2007 Conference on Machine Learning in Systems Biology

24. Rodrigo, G., Carrera, J. & Jaramillo, A. 2007 ECOLITASTER: cellular biosensor. BMC systems biology 1, P38.

23. Jaramillo, A., Tortosa, P., Rodrigo, G. & Suarez, M. 2007 Computational design of proteins with new functions. BMC systems biology 1, S15.

22. Rodrigo, G. & Jaramillo, A. 2007 Computational design of digital and memory biological devices. Syst Synth Biol 1, 183–195. (doi:10.1007/s11693-008-9017-0)

21. Rodrigo, G., Carrera, J. & Jaramillo, A. 2007 Asmparts: assembly of biological model parts. Syst Synth Biol 1, 167–170. (doi:10.1007/s11693-008-9013-4)

20. Rodrigo, G., Carrera, J. & Jaramillo, A. 2007 Genetdes: automatic design of transcriptional networks. Bioinformatics 23, 1857–1858. (doi:10.1093/bioinformatics/btm237)

19. Rodrigo, G., Carrera, J. & Jaramillo, A. 2007 Evolutionary mechanisms of circadian clocks. Central European Journal of Biology 2, 233–253. (doi:10.2478/s11535-007-0016-z)

18. Suarez, M. & Jaramillo, A. 2007 Computational Design of a Thioredoxin Protein with Esterase Activity. In (eds S. BassiniG Erbacci), pp. 735–736. Science and Supercomputing in Europe.

17. Rodrigo, G., Tortosa, P., Suarez, M. & Jaramillo, A. 2007 Improved Biofuel Cells Through Computational Biology. In (eds S. BassiniG Erbacci), pp. 769–770. Science and Supercomputing in Europe.

16. Rodrigo, G. et al. 2007 Vanillin cell sensor. IET Synthetic Biology 1, 74–78.

15. Tortosa, P. & Carrera, J. 2006 Optimisation in enzyme design: The combinatorial problem of grafting an esterase site into a Thioredoxin protein. In (eds S. BassiniG Erbacci), pp. 797–799. Science and Supercomputing in Europe.

14. Tortosa, P. & Jaramillo, A. 2006 Active Sites by Computational Protein Design. AIP Conf. Proc. 851, 96–101.(doi:10.1063/1.2345625)

13. Jaramillo, A. & Wodak, S. J. 2005 Computational protein design is a challenge for implicit solvation models. Biophys J 88, 156–171.(doi:10.1529/biophysj.104.042044)

12. Ogata, K., Jaramillo, A., Cohen, W., Briand, J.-P., Connan, F., Choppin, J., Muller, S. & Wodak, S. J. 2003 Automatic sequence design of major histocompatibility complex class I binding peptides impairing CD8+ T cell recognition. J Biol Chem 278, 1281–1290.(doi:10.1074/jbc.M206853200)

11. Jaramillo, A., Wernisch, L., Hery, S. & Wodak, S. J. 2002 Folding free energy function selects native-like protein sequences in the core but not on the surface. Proc Natl Acad Sci U S A 99, 13554–13559.(doi:10.1073/pnas.212068599)

10. Jaramillo, A., Wernisch, L., Hery, S. & Wodak, S. J. 2001 Automatic procedures for protein design. Comb. Chem. High Throughput Screen. 4, 643–659.

9. Jaramillo, A. & Mansfield, P. 2000 Finite VEVs from a Large Distance Vacuum Wave Functional. Int. J. Mod. Phys. A 15, 581–600.(doi:10.1142/S0217751X00000288)

8. Jaramillo, A. & Mansfield, P. 1998 Non-Perturbative VEVs from a Local Expansion. Acta Phys Pol B 29, 2487–2492.

7. Baig, M., Clua, J. & Jaramillo, A. 1998 Numerical simulation of random paths with a curvature dependent action. Int. J. Mod. Phys. A 13, 2131–2138. (doi:10.1142/S0217732398002254)

6. Ferrando, A., Jaramillo, A. & Shabanov, S. 1997 Confinement in 3D Gluodynamics as a 2D Critical Phenomenon. Proceedings edited by N. Brambilla and G.M. Prosperi, World Scientific (1997).

5. Ferrando, A. & Jaramillo, A. 1995 The role of temperature in a dimensional approach to QCD 3. Nuclear Physics B 457, 57–77.

4. Ferrando, A. & Jaramillo, A. 1995 Two dimensional quantum chromodynamics as the limit of higher dimensional theories. Physics Letters B 341, 342–348.

3. Ferrando, A., Jaramillo, A. & Vento, V. 1995 On the relation between 2-D quantum chromodynamics and higher dimensional gauge theories. Proceedings of ‘Como 1994, Quark confinement and the hadron spectrum’. 235–237

2. Ferrando, A., Jaramillo, A. & Vento, V. 1995 Dimensional transition in gauge theories. Proceedings of ‘Paris 1994, Quantum infrared physics’. 200–204.

1. Jaramillo, A., Parente, G., Cruz, J. D. & Sampayo, O. A. 1994 Using F L as a test of compositeness. Physics Letters B 336, 80–84.

Alfonso Jaramillo. Non-perturbative methods in quantum field theory, PhD thesis Theoretical Physics, University of Valencia (Spain), 29 July 1999. DOI: 10.13140/RG.2.2.21055.71843