Publications

You can also see my publications in PubMed or in my Google Scholar profile. My ORCID iD is 0000-0001-7622-5482.

*denotes co-lead authors

†denotes co-corresponding authors

Preprints

[1] *Jakobson, C., *Aguilar-Rodríguez, J., Jarosz, D.F. (2023). Hsp90 shapes adaptation by controlling the fitness consequences of regulatory variation. bioRxiv.

Refereed Journal Publications

[16] *Alvarez-Ponce, D., *Aguilar-Rodríguez, J., Fares, M. A. (2019). Molecular chaperones accelerate the evolution of their protein clients in yeast. Genome Biology and Evolution, 11(8): 2360–2375.

[15] Aguilar-Rodríguez, J., Fares, M. A., Wagner, A. (2019). Chaperonin overproduction and metabolic erosion caused by mutation accumulation in Escherichia coli. FEMS Microbiology Letters, 336(10): fnz121.

[14] †Aguilar-Rodríguez, J., †Wagner, A. (2018). Metabolic determinants of enzyme evolution in a genome-scale bacterial metabolic network. Genome Biology and Evolution, 10(11): 3076-3088.

Runner-up to the SMBE Best GBE Graduate Paper Award. [link]

[13] Sprouffske, K, Aguilar-Rodríguez, J., Sniegowski, P., Wagner, A. (2018). High mutation rates limit evolutionary adaptation in Escherichia coli. PLOS Genetics, 14(4): e1007324.

[12] Aguilar-Rodríguez, J., Peel, L., Stella, M., †Wagner, A., †Payne, J. (2018). The architecture of an empirical genotype-phenotype map. Evolution, 72(6): 1242-1260.

[11] *Aguilar-Rodríguez, J., *Payne, J. L., Wagner, A. (2017). A thousand empirical adaptive landscapes and their navigability. Nature Ecology & Evolution, 1: 0045.

SIB Best Swiss Bioinformatics Graduate Paper Award. [link] [link]

Navigating adaptive landscapes. [link] 

[10] Blattner, A. C., Aguilar-Rodríguez, J., Kränzlin, M., Wagner, A., Lehner, C. F. (2017). Drosophila Nnf1 paralogs are partially redundant for somatic and germ line kinetochore function. Chromosoma, 126(1): 145–163.

[9] *Aguilar-Rodríguez, J., *Sabater-Muñoz, B, Montagud-Martínez, R., Berlanga, V., Alvarez-Ponce, D., †Wagner, A., †Fares, M. A. (2016). The molecular chaperone DnaK is a source of mutational robustness. Genome Biology and Evolution, 8(9): 2979–2991.

Research highlight in Genome Biology and Evolution. [link]

[8] Khalid, F., Aguilar-Rodríguez, J., †Wagner, A., †Payne, J. L. (2016). Genonets Server–a web server for the construction, analysis and visualization of genotype networks. Nucleic Acids Research, 44: W70-76.

[7] Sprouffske, K., Aguilar-Rodríguez, J., Wagner, A. (2016). How archiving by freezing affects the genome-scale diversity of Escherichia coli populations. Genome Biology and Evolution, 8(5): 1290-1298.

[6] SIB Swiss Institute of Bioinformatics Members (including José Aguilar-Rodríguez) (2016). The SIB Swiss Institute of Bioinformatics’ resources: focus on curated databases. Nucleic Acids Research, 44: D27-37.

[5] *Sabater-Muñoz, B., *Prats-Escriche, M., Montagud-Martínez, R., López-Cerdán, A., Toft, C., Aguilar-Rodríguez, J., Wagner, A., Fares, M. A. (2015). Fitness trade-offs determine the role of the molecular chaperonin GroEL in buffering mutations. Molecular Biology and Evolution, 32(10): 2681-2693.

[4] Ashikaga, H., Aguilar-Rodríguez, J., Gorsky, S., Lusczek, E., Marquitti, F. M. D., Thompson, B., Wu, D., Garland, J. (2015). Modelling the heart as a communication system. Journal of the Royal Society Interface, 12: 20141201.

John Hopkins Medicine News, March 10, 2015. [link]

[3] Llorens, C., Futami, R., Covelli, L., Domínguez-Escribá, L., Viu, J. M., Tamarit, D., Aguilar-Rodríguez, J., Vicente-Ripolles, V., Fuster, G., Bernet, G. P., Maumus, F., Munoz-Pomer, A., Sempere, J. M., Latorre, A., Moya, A. (2011). The Gypsy Database (GyDB) of mobile genetic elements: release 2.0. Nucleic Acids Research, 39: D70-74.

[2] Baquero, F., Aguilar-Rodríguez, J., Moya., A. (2011). La biología como forma de representación: Wittgenstein y la partitura de la vida. Ludus Vitalis: Journal of Philosophy of Life Sciences, 19: 29-46. [In Spanish]

[1] The International Aphid Genomics Consortium (including José Aguilar) (2010). Genome sequence of the pea aphid Acyrthosiphon pisum. PLoS Biology, 8: e1000313.

Refereed Book Chapters

[1] Aguilar-Rodríguez, J., Payne, J. L.. (2021). Robustness and evolvability in transcriptional regulation. In Evolutionary Systems Biology, vol. 2, Ed. A Crombach.

Other Publications

[1] Aguilar Rodríguez, J. (2011). Explorant l’emergència de les primeres cèl·lules [Book Review of First Life: Discovering the Connections between Stars, Cells and How Life Began, by David Deamer, Princeton University Press, 2011]. Mètode: Journal of Public Understanding of Science, 72. [In Catalan]

PhD Dissertation

Aguilar-Rodríguez, J. (2017) "Genotype-Phenotype Maps in Complex Living Systems." University of Zurich. [link]