• Darlington A.P., Kim J., Jimenez J.I., Bates D.G. Engineering translational allocation controllers: Mechanistic models, design guidelines, and potential biological implementations. Submitted (bioRxiv)
  • Darlington A.P.¹, Kim J.¹, Jimenez J.I.², Bates D.G.² Dynamic allocation of orthogonal ribosomes facilitates uncoupling of co-expressed genes. (2018)  Nature Communications. 9:695 (¹equal contribution, ²corresponding authors) (bioRxiv) (link)
  • Cavaliere M., Fang S. Soyer O. and Jimenez J.I. Cooperation in microbial communities and their biotechnological applications. (2017) Environ Microbiol.19(8):2949-2963. (link) (pdf)
  • Qian Y., Huang HH., Jimenez J.I. and Del Vecchio D. Resource competition shapes the response of genetic circuits. ACS Synth Biol. 6(7):1263-1272. (pdf) (SI) (bioRxiv) (link)
  • Jimenez J.I. Shedding light on the black box models of the cell. (2017) Microb Biotechnol. 10(1):43-45 (pdf) (link)
  • Kim J., Salvador M., Saunders E., Gutierrez J., Avignone-Rossa C. and Jimenez J.I. Properties of alternative microbial hosts used in Synthetic Biology: Towards the modular design of a chassis. (2016) Essays Biochem. 60(4):303-313. (link)
  • Avendaño R., Chaves N., Fuentes P., Sanchez E., Jimenez J.I. and Chavarria M. Production of selenium nanoparticles in Pseudomonas putida (2016) Sci Rep. 6:37155 (link)
  • Xulvi-Brunet R., Campbell G.W., Rajamani S., Jimenez I. and Chen I.A. Computational analysis of fitness landscapes and evolutionary networks from in vitro evolution experiments. (2016) Methods. 106:86-96. (link)
  • Jimenez J.I., Fraile S., Zafra O., de Lorenzo V. Phenotypic knockouts of selected metabolic pathways by targeting enzymes with camel derived nanobodies (VHHs). (2015) Metab Eng. 30:40-48. (link)
  • Gyorgy A., Jimenez J.I., Yazbek J., Huang H.H., Chung H., Weiss R. and Del Vecchio D. Isocost lines describe the cellular economy of genetic circuits. (2015) Biophys J. 109(3):639-646. (link)
  • Nilgiriwala K., Jimenez J.I., Rivera P.M. and Del Vecchio D. A synthetic tunable amplifying genetic circuit in coli. (2015) ACS Synth Biol. 4(5):577-84. (link)
  • Freese P., Korolev K., Jimenez J.I. and Chen I.A. Genetic drift suppresses bacterial conjugation in spatially structured populations. (2014) Biophys J. 106(4):944-54. (link)
  • Jimenez J.I., Perez-Pantoja D., Chavarria M, Diaz E. and de Lorenzo V. A second chromosomal copy of the catA gene endows Pseudomonas putida mt-2 with an enzymatic safety valve for excess of catechol. (2014). Environ Microbiol. 16(6):1767-78. (link)
  • Jimenez J.I., Xulvi-Brunet R., Campbell G.W., Turk-McLeod R. and Chen I.A. Comprehensive experimental fitness landscape and evolutionary network for RNA. (2013) PNAS. 110(37):14984-9. (link)
  • Fraile S., Jimenez J.I., Gutierrez C. and de Lorenzo V. NanoPad: an integrated platform for bacterial production of camel nanobodies aimed at detecting environmental biomarkers. (2013) Proteomics. 13(18-19):2766-75. (link)
  • Diaz E., Jimenez J.I. and Nogales J. Aerobic degradation of aromatic compounds. (2013) Curr Opin Biotechnol. 24:1-12.
  • Lin A., Jimenez J.I., Derr J., Vera P., Manapat M.L., Esvelt K.M., Villanueva L., Liu D.R. and Chen I.A. Inhibition of bacterial conjugation by phage M13 and its protein g3p: quantitative analysis and model. (2011) PLoS One. 6(5):e19991. (link)
  • Jimenez J.I., Juarez J.F., Garcia J.L. and Diaz E. A finely tuned regulatory circuit of the nicotinic acid degradation pathway in Pseudomonas putida. (2011) Environ Microbiol. 13(7):1718-32. (link)
  • Zafra O., Fraile S., Gutierrez C., Haro A., Paez A.D., Jimenez J.I. and de Lorenzo V. Monitoring biodegradative enzymes with nanobodies raised in Camelus dromedarius with mixtures of catabolic proteins. (2011) Environ Microbiol. 13(4):960-74. (link)
  • Jimenez J.I., Acebron-Avalos I., Diaz E. and Mancheño. A preliminary crystallographic study of recombinant NicX, an Fe2+-dependent 2,5-dihydroxypyridine dioxygenase from Pseudomonas putida (2010) Acta Crystallogr Sect F Struct Biol Cryst Commun. 66(Pt 5):549-53. (link)
  • Jimenez J.I., Canales A., Jimenez-Barbero J., Ginalski K., Rychlewski L., Garcia J.L. and Diaz E. Deciphering the genetic determinants for aerobic nicotinic acid degradation: The nic cluster from Pseudomonas putida KT2440. (2008) PNAS. 105(32):11329-34. (link)
  • Yuste L., Hervas A.B., Canosa I., Tobes R., Jimenez J.I., Nogales J., Santero E., Díaz E., Ramos J.L., de Lorenzo V. and Rojo F. Growth-phase dependent expression of the Pseudomonas putida KT2440 transcriptional machinery throughout the growth           phase analyzed by means of a genome-wide microarray. (2006) Environ Microbiol. 8(1):165-177. (link)
  • Jimenez J.I., Minambres B., Garcia J.L. and Diaz E. Genomic analysis of the aromatic catabolic pathways from Pseudomonas putida (2002) Environ Microbiol. 4(12):824-841. (link)


Book chapters

  • Xulvi-Brunet R., Campbell G.W., Rajamani S., Jimenez J.I. and Chen I.A. Quantitative analysis of synthesized nucleic acid pools. (2016) In Non-linear events in Biology. Springer Publishers. 7:19-41. (link)
  • de Lorenzo V., Fraile S. and Jimenez J.I. Emerging Systems and Synthetic Biology approaches to Hydrocarbon Biotechnology. (2009) In Handbook of Hydrocarbon and Lipid Microbiology. Chapter 41, 1411-1435 Ed.: K. Timmis, Springer Publishers. (link)
  • Jimenez J.I., Nogales J., García J.L. and Diaz E. A genomic view of the catabolism of aromatic compounds in Pseudomonas. (2009) In Handbook of Hydrocarbon and Lipid Chapter 35, 1297-1325 Ed.: K. Timmis, Springer Berlin Heidelberg Publishers. (link)
  • Jimenez J.I., Minambres B., Garcia J.L. and Diaz E. Genomic insights in the metabolism of Pseudomonas putida KT2440. (2004) In Pseudomonas. Vol. 3, chapter 15, 425-462 Ed. J.L. Ramos. Kluwer Publishers.