Guillermo Rodrigo's publications

    2025

  1. Montagud-Martinez R, Marquez-Costa R, Ruiz R, Martinez-Aviño A, Ballesteros-Garrido R, Navarro D, Campins-Falco P, Rodrigo G (2025) Virus detection by CRISPR-Cas9-mediated strand displacement in a lateral flow assay. ACS Appl. Bio Mater. In press.
  2. Perez-Ropero G, Dolcemascolo R, Perez-Rafols A, Andersson K, Danielson UH, Rodrigo G, Buijs J (2025) Regulatory effects of RNA-protein interactions revealed by reporter assays of bacteria grown on solid media. Biosensors 15: 175.

    2024
  3. Dolcemascolo R, Ruiz R, Baldanta S, Goiriz L, Heras-Hernandez M, Montagud-Martinez M, Rodrigo G (2024) Probing the orthogonality and robustness of the mammalian RNA-binding protein Musashi-1 in Escherichia coli. J. Biol. Eng. 18: 52.
  4. Corell-Sierra J, Marquez-Molins J, Marques MC, Hernandez-Azurdia AG, Montagud-Martinez R, Cebria-Mendoza M, Cuevas JM, Albert E, Navarro D, Rodrigo G, Gomez G (2024) SARS-CoV-2 remodels the landscape of small non-coding RNAs with infection time and symptom severity. npj Syst. Biol. Appl. 10: 41.
  5. Montagud-Martinez R, Marquez-Costa R, Heras-Hernandez M, Dolcemascolo R, Rodrigo G (2024) On the ever-growing functional versatility of the CRISPR-Cas13 system. Microb. Biotechnol. 17: e14418.
  6. Ruiz R, Montagud-Martinez R, Dorta-Gorrin A, Pablo-Marcos D, Gozalo M, Calvo-Montes J, Navas J, Rodrigo G (2024) Rapid and accurate detection of the SARS-CoV‐2 Omicron variant with a CRISPR-Cas12a reaction in the RT-qPCR pot. ACS Omega 9: 18046-18050.
  7. Merwaiss F, Lozano-Sanchez E, Zulaica J, Rusu L, Vazquez-Vilar M, Orzaez D, Rodrigo G, Geller R, Daros JA (2024) Plant virus-derived nanoparticles decorated with genetically encoded SARS-CoV-2 nanobodies display enhanced neutralizing activity. Plant Biotechnol. J. 22: 876-891.
  8. Dolcemascolo R, Heras-Hernandez M, Goiriz L, Montagud-Martinez R, Requena-Menendez A, Ruiz R, Perez-Rafols A, Higuera-Rodriguez RA, Perez-Ropero G, Vranken WF, Martelli T, Kaiser W, Buijs J, Rodrigo G (2024) Repurposing the mammalian RNA-binding protein Musashi-1 as an allosteric translation repressor in bacteria. eLife 12: RP91777.

    2023
  9. Goiriz L, Ruiz R, Garibo-i-Orts O, Conejero JA, Rodrigo G (2023) A variant-dependent molecular clock with anomalous diffusion models SARS-CoV-2 evolution in humans. Proc. Natl. Acad. Sci. USA 120: e2303578120.
  10. Marquez-Costa R, Montagud-Martinez R, Marques MC, Albert E, Navarro D, Daros JA, Ruiz R, Rodrigo G (2023) Multiplexable and biocomputational virus detection by CRISPR-Cas9-mediated strand displacement. Anal. Chem. 95: 9564-9574.
  11. Montagud-Martinez R, Marquez-Costa R, Rodrigo G (2023) Programmable regulation of translation by harnessing the CRISPR-Cas13 system. Chem. Commun. 59: 2616-2619.
  12. Martinez F, Carrasco JL, Toft C, Hillung J, Gimenez-Santamarina S, Yenush L, Rodrigo G, Elena SF (2023) A binary interaction map between turnip mosaic virus and Arabidopsis thaliana proteomes. Commun. Biol. 6: 28.

    2022
  13. Rodrigo G, Ballesteros-Garrido R (2022) Metal-organic frameworks in pursuit of size: the development of macroscopic single crystals. Dalton Trans. 51: 7775-7782.
  14. Marques MC, Sanchez-Vicente J, Ruiz R, Montagud-Martinez R, Marquez-Costa R, Gomez G, Carbonell A, Daros JA, Rodrigo G (2022) Diagnostics of infections produced by the plant viruses TMV, TEV, and PVX with CRISPR-Cas12 and CRISPR-Cas13. ACS Synth. Biol. 11: 2384-2393.
  15. Dolcemascolo R, Goiriz L, Montagud-Martinez R, Rodrigo G (2022) Gene regulation by a protein translation factor at the single-cell level. PLoS Comput. Biol. 18: e1010087.

    2021
  16. Marques MC, Ruiz R, Montagud-Martinez R, Marquez-Costa R, Albert S, Domingo-Calap P, Rodrigo G (2021) CRISPR-Cas12a-based detection of SARS-CoV-2 harboring the E484K mutation. ACS Synth. Biol. 10: 3595-3599.
  17. Montagud-Martinez R, Heras-Hernandez M, Goiriz L, Daros JA, Rodrigo G (2021) CRISPR-mediated strand displacement logic circuits with toehold-free DNA. ACS Synth. Biol. 10: 950-956.
  18. Goiriz L, Rodrigo G (2021) Nonequilibrium thermodynamics of the RNA-RNA interaction underlying a genetic transposition program. Phys. Rev. E 103: 042410.
  19. Ambros S, Gomez-Munoz N, Gimenez-Santamarina S, Sanchez-Vicente J, Navarro-Lopez J, Martinez F, Daros JA, Rodrigo G (2021) Molecular signatures of silencing suppression degeneracy from a complex RNA virus. PLoS Comput. Biol. 17: e1009166.

    2020
  20. Rostain W, Shen S, Cordero T, Rodrigo G, Jaramillo A (2020) Engineering a circular riboregulator in Escherichia coli. BioDesign Res. 2020: 1916789.
  21. Pasin F, Shan H, Garcia B, Muller M, San-Leon D, Ludman M, Fresno DH, Fatyol K, Munne-Bosch S, Rodrigo G, Garcia JA (2020) Abscisic acid connects phytohormone signaling with RNA metabolic pathways and promotes an antiviral response that is evaded by a self-controlled RNA virus. Plant Commun. 1: 100099.
  22. Montagud-Martinez R, Ventura J, Ballesteros-Garrido R, Rosado A, Rodrigo G (2020) Probing the operability regime of an engineered ribocomputing unit in terms of dynamic range maintenance with extracellular changes and time. J. Biol. Eng. 14: 12.
  23. Rodrigo G (2020) Insights about collective decision-making at the genetic level. Biophys. Rev. 12: 19-24.

    2019
  24. Rodrigo G (2019) Ab initio scaling laws between noise and mean of gene expression. Phys. Rev. E 100: 032415.
  25. Ballesteros-Garrido R, Montagud-Martinez R, Rodrigo G (2019) Bacterial population control with macroscopic HKUST crystals. ACS Appl. Mater. Interfaces 11: 19878-19883.
  26. Llabres-Campaner PJ, Zaragoza RJ, Aurell MJ, Ballesteros R, Abarca B, Garcia-Espana E, Rodrigo G, Ballesteros-Garrido R (2019) Empirical modeling of material composition and size in MOFs prepared with ligand mixtures. Dalton Trans. 48: 2881-2885.
  27. Sanz-Carbonell A, Marques MC, Bustamante A, Fares MA, Rodrigo G, Gomez G (2019) Inferring the regulatory network of the miRNA-mediated response to biotic and abiotic stress in melon. BMC Plant Biol. 19: 78.

    2018
  28. Cordero T, Rosado A, Majer E, Jaramillo A, Rodrigo G, Daros JA (2018) Boolean computation in plants using post-translational genetic control and a visual output signal. ACS Synth. Biol. 7: 2322-2330.
  29. Rosado A, Cordero T, Rodrigo G (2018) Binary addition in a living cell based on riboregulation. PLoS Genet. 14: e1007548.
  30. Pacheco CC, Buttel Z, Pinto F, Rodrigo G, Carrera J, Jaramillo A, Tamagnini P (2018) Modulation of intracellular O2 concentration in Escherichia coli strains using Oxygen Consuming Devices. ACS Synth. Biol. 7: 1742-1752.
  31. Rodrigo G, Stocks NG (2018) Suprathreshold stochastic resonance behind cancer. Trends Biochem. Sci. 43: 483-485.
  32. Cervera H, Ambros S, Bernet GP, Rodrigo G, Elena SF (2018) Viral fitness correlates with the magnitude and direction of the perturbation induced in the host's transcriptome: the tobacco etch potyvirus - tobacco case study. Mol. Biol. Evol. 35: 1599-1615.
  33. Rodrigo G (2018) Post-transcriptional bursting in genes regulated by small RNA molecules. Phys. Rev. E 97: 032401.
  34. Rodrigo G, Fares MA (2018) Intrinsic adaptive value and early fate of gene duplication revealed by a bottom-up approach. eLife 7: e29739.

    2017
  35. Rodrigo G, Prakash S, Shen S, Majer E, Daros JA, Jaramillo A (2017) Model-based design of RNA hybridization networks implemented in living cells. Nucleic Acids Res. 45: 9797-9808.
  36. Rodrigo G (2017) Evolutionary impact of copy number variation rates. BMC Res. Notes 10: 393.
  37. Rodrigo G, Bajic D, Elola I, Poyatos JF (2017) Deconstructing a multiple antibiotic resistance regulation through the quantification of its input function. npj Syst. Biol. Appl. 3: 30.
  38. Forment M, Rodrigo G (2017) Molecular noise can minimize the collective sensitivity of a clonal heterogeneous cell population. J. Theor. Biol. 416: 38-44.
  39. Rodrigo G, Daros JA, Elena SF (2017) Virus-host interactome: Putting the accent on how it changes. J. Proteomics 156: 1-4.
  40. Rambla JL, Medina A, Fernandez-del-Carmen A, Barrantes W, Grandillo S, Cammareri M, Lopez-Casado G, Rodrigo G, Alonso A, Garcia-Martinez S, Primo J, Ruiz JJ, Fernandez-Munoz R, Monforte AJ, Granell A (2017) Identification, introgression, and validation of fruit volatile QTLs from a red-fruited wild tomato species. J. Exp. Bot. 68: 429-442.

    2016
  41. Rodrigo G, Poyatos JF (2016) Genetic redundancies enhance information transfer in noisy regulatory circuits. PLoS Comput. Biol. 12: e1005156.
  42. Rodrigo G, Bajic D, Elola I, Poyatos JF (2016) Antagonistic autoregulation speeds up a homogeneous response in Escherichia coli. Sci. Rep. 6: 36196.
  43. Rodrigo G, Prakash S, Cordero T, Kushwaha M, Jaramillo A (2016) Functionalization of an antisense small RNA. J. Mol. Biol. 428: 889-892.
  44. Martinez F, Rodrigo G, Aragones V, Ruiz M, Lodewijck I, Fernandez U, Elena SF, Daros JA (2016) Interaction network of tobacco etch potyvirus NIa protein with the host proteome during infection. BMC Genomics 17: 87.

    2015
  45. Rodrigo G, Majer E, Prakash S, Daros JA, Jaramillo A, Poyatos JF (2015) Exploring the dynamics and mutational landscape of riboregulation with a minimal synthetic circuit in living cells. Biophys. J. 109: 1070-1076.
  46. Sanchez F, Manrique P, Mansilla C, Lunello P, Wang X, Rodrigo G, Lopez-Gonzalez S, Jenner C, Gonzalez-Melendi P, Elena SF, Walsh J, Ponz F (2015) Viral strain-specific differential alterations in Arabidopsis developmental patterns. Mol. Plant Microbe Interact. 28: 1304-1315.
  47. Shen S, Rodrigo G, Prakash S, Majer E, Landrain TE, Kirov B, Daros JA, Jaramillo A (2015) Dynamic signal processing by ribozyme-mediated RNA circuits to control gene expression. Nucleic Acids Res. 43: 5158-5170.
  48. Rostain W, Landrain TE, Rodrigo G, Jaramillo A (2015) Regulatory RNA design through evolutionary computation and strand displacement. Methods Mol. Biol. 1244: 63-78.

    2014
  49. Rodrigo G, Zwart MP, Elena SF (2014) Onset of virus systemic infection in plants is determined by speed of cell-to-cell movement and number of primary infection foci. J. R. Soc. Interface 11: 20140555.
  50. Rodrigo G, Jaramillo A (2014) RiboMaker: computational design of conformation-based riboregulation. Bioinformatics 30: 2508-2510.

    2013
  51. 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.
  52. Rodrigo G, Landrain TE, Shen S, Jaramillo A (2013) A new frontier in synthetic biology: automated design of small RNA devices in bacteria. Trends Genet. 29: 529-536.
  53. Rodrigo G, Landrain TE, Majer E, Daros JA, Jaramillo A (2013) Full design automation of multi-state RNA devices to program gene expression using energy-based optimization. PLoS Comput. Biol. 9: e1003172.
  54. Rodrigo G, Elena SF (2013) MicroRNA precursors are not structurally robust but plastic. Genome Biol. Evol. 5: 181-186.
  55. Rodrigo G, Jaramillo A (2013) AutoBioCAD: full biodesign automation of genetic circuits. ACS Synth. Biol. 2: 230-236.

    2012
  56. Elena SF, Rodrigo G (2012) Towards an integrated molecular model of plant-virus interactions. Curr. Opin. Virol. 2: 719-724.
  57. Rodrigo G, Landrain TE, Jaramillo A (2012) De novo automated design of small RNA circuits for engineering synthetic riboregulation in living cells. Proc. Natl. Acad. Sci. USA 109: 15271-15276.
  58. Rodrigo G, Carrera J, Ruiz-Ferrer V, del-Toro FJ, Llave C, Voinnet O, Elena SF (2012) A meta-analysis reveals the commonalities and differences in Arabidopsis thaliana response to different viral pathogens. PLoS ONE 7: e40526.
  59. Rodrigo G, Fares MA (2012) Describing the structural robustness landscape of bacterial small RNAs. BMC Evol. Biol. 12: 52.
  60. Rodrigo G, Carrera J, Landrain TE, Jaramillo A (2012) Perspectives on the automatic design of regulatory systems for synthetic biology. FEBS Lett. 586: 2037-2042.

    2011
  61. 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.
  62. Elena SF, Carrera J, Rodrigo G (2011) A systems biology approach to the evolution of plant-virus interactions. Curr. Opin. Plant Biol. 14: 372-377.
  63. 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.
  64. Rodrigo G, Jaramillo A, Blazquez MA (2011) Integral control of plant gravitropism through the interplay of hormone signaling and gene regulation. Biophys. J. 101: 757-763.
  65. Rodrigo G, Elena SF (2011) Structural discrimination of robustness in transcriptional feedforward loops for pattern formation. PLoS ONE 6: e16904.
  66. Rodrigo G, Carrera J, Jaramillo A, Elena SF (2011) Optimal viral strategies for bypassing RNA silencing. J. R. Soc. Interface 8: 257-268.

    2010
  67. Rodrigo G, Carrera J, Elena SF (2010) Network design meets in silico evolutionary biology. Biochimie 92: 746-752.
  68. Rodrigo G, Carrera J, Elena SF, Jaramillo A (2010) Robust dynamical pattern formation from a multifunctional minimal genetic circuit. BMC Syst. Biol. 4: 48.

    2009
  69. Suarez M, Rodrigo G, Carrera J, Jaramillo A (2009) Computational design in synthetic biology. Synthetic Biology: the technoscience and its societal consequences (Eds. Schmidt M, et al.) pp 49-63. Springer.
  70. Carrera J, Rodrigo G, Jaramillo A (2009) Towards the automated engineering of a synthetic genome. Mol. BioSyst. 5: 733-743.
  71. Landrain TE, Carrera J, Kirov B, Rodrigo G, Jaramillo A (2009) Modular model-based design for heterologous bioproduction in bacteria. Curr. Opin. Biotechnol. 20: 272-279.
  72. Carrera J, Rodrigo G, Jaramillo A, Elena SF (2009) Reverse-engineering the Arabidopsis thaliana transcriptional network under changing environmental conditions. Genome Biol. 10: R96.
  73. Carrera J, Rodrigo G, Jaramillo A (2009) Model-based redesign of global transcription regulation. Nucleic Acids Res. 37: e38.

    2008
  74. Rodrigo G, Carrera J, Prather KJ, Jaramillo A (2008) DESHARKY: automatic design of metabolic pathways for optimal cell growth. Bioinformatics 24: 2554-2556.
  75. Agudelo-Romero P, Carbonell P, de-la-Iglesia F, Carrera J, Rodrigo G, Jaramillo A, Perez-Amador MA, Elena SF (2008) Changes in the gene expression profile of Arabidopsis thaliana after infection with Tobacco etch virus. Virol. J. 5: 92.
  76. Rodrigo G, Carrera J, Jaramillo A (2008) Computational design and evolution of the oscillatory response under light-dark cycles. Biochimie 90: 888-897.

    2007
  77. Rodrigo G, Carrera J, Jaramillo A (2007) Evolutionary mechanisms of circadian clocks. Cent. Eur. J. Biol. 2: 233-253.
  78. Rodrigo G, Jaramillo A (2007) Computational design of digital and memory biological devices. Syst. Synth. Biol. 1: 183-195.
  79. Rodrigo G, Carrera J, Jaramillo A (2007) Asmparts: assembly of biological model parts. Syst. Synth. Biol. 1: 167-170.
  80. Rodrigo G, Carrera J, Jaramillo A (2007) Genetdes: automatic design of transcriptional networks. Bioinformatics 23: 1857-1858.