2020

Racovita, Adrian and Jaramillo, Alfonso (2020) Reinforcement learning in synthetic gene circuits. Biochemical Society Transactions, 48 (4). pp. 1637-1643. doi:10.1042/bst20200008

Broedel, A., Rodrigues, R., Jaramillo, Alfonso and Isalan, M. (2020) Accelerated evolution of a minimal 63-amino acid dual transcription factor. Science Advances, 6 (24). eaba2728. doi:10.1126/sciadv.aba2728

Grigonyte, Aurelija, Harrison, Christian, Macdonald, Paul R., Montero-Blay, Ariadna, Tridgett, Matthew, Duncan, John, Sagona, Antonia P., Constantinidou, Chrystala, Jaramillo, Alfonso and Millard, Andrew D. (2020) Comparison of CRISPR and marker-based methods for the engineering of Phage T7. Viruses, 12 (2). e193. doi:10.3390/v12020193

Tridgett, Matthew, Ababi, Maria, Osgerby, Alexander, Ramirez Garcia, Robert and Jaramillo, Alfonso (2020) Engineering bacteria to produce pure phage-like particles for gene delivery. ACS Synthetic Biology . (In Press)

2019

Galizi, Roberto and Jaramillo, Alfonso (2019) Engineering CRISPR guide RNA riboswitches for in vivo applications. Current Opinion in Biotechnology, 55 . pp. 103-113. doi:10.1016/j.copbio.2018.08.007

2018

Cordero, Teresa, Rosado, Arantxa, Majer, Eszter, Jaramillo, Alfonso, Rodrigo, Guillermo and Daròs, José-Antonio (2018) Boolean computation in plants using post-translational genetic control and a visual output signal. ACS Synthetic Biology, 7 (10). 2322–-2330. doi:10.1021/acssynbio.8b00214

Pacheco, Catarina C., Büttel, Zsófia, Pinto, Filipe, Rodrigo, Guillermo, Carrera, Javier, Jaramillo, Alfonso and Tamagnini, Paula (2018) Modulation of intracellular O2 concentration in Escherichia coli strains using oxygen consuming devices. ACS Synthetic Biology, 7 (7). pp. 1742-1752. doi:10.1021/acssynbio.7b00428

Howarth, Mark and Jaramillo, Alfonso (2018) Editorial overview : nanobiotechnology : baby steps and giant strides towards molecular mastery. Current Opinion in Biotechnology, 51 . iv-vi. doi:10.1016/j.copbio.2018.05.001

Brödel, Andreas K., Isalan, Mark and Jaramillo, Alfonso (2018) Engineering of biomolecules by bacteriophage directed evolution. Current Opinion in Biotechnology, 51 . pp. 32-38. doi:10.1016/j.copbio.2017.11.004

Senoussi, Anis, Lee Tin Wah, Jonathan, Shimizu, Yoshihiro, Robert, Jérôme, Jaramillo, Alfonso, Findeiss, Sven, Axmann, Ilka M. and Estevez-Torres, André (2018) Quantitative characterization of translational riboregulators using an in vitro transcription–translation system. ACS Synthetic Biology, 7 (5). pp. 1269-1278. doi:10.1021/acssynbio.7b00387

Ferreira, Eunice A., Pacheco, Catarina C., Pinto, Filipe, Pereira, José, Lamosa, Pedro, Oliveira, Paulo, Kirov, Boris, Jaramillo, Alfonso and Tamagnini, Paula (2018) Expanding the toolbox for Synechocystis sp. PCC 6803 : validation of replicative vectors and characterization of a novel set of promoters. Synthetic Biology, 3 (1). ysy014. doi:10.1093/synbio/ysy014

2017

Rodrigo, Guillermo, Prakash, Satya, Shen, Shensi, Majer, Eszter, Daròs, José-Antonio and Jaramillo, Alfonso (2017) Model-based design of RNA hybridization networks implemented in living cells. Nucleic Acids Research, 45 (16). pp. 9797-9808. doi:10.1093/nar/gkx698

Brodel, Andreas K., Jaramillo, Alfonso and Isalan, Mark (2017) Intracellular directed evolution of proteins from combinatorial libraries based on conditional phage replication. Nature Protocols, 12 (9). pp. 1830-1843. doi:10.1038/nprot.2017.084

Jaramillo, Alfonso (2017) Synthetic biology : engineered stable ecosystems. Nature microbiology, 2 (8). 17119. doi:10.1038/nmicrobiol.2017.119

2016

Brodel, Andreas K., Jaramillo, Alfonso and Isalan, Mark (2016) Engineering orthogonal dual transcription factors for multi-input synthetic promoters. Nature Communications, 7 . 13858 . doi:10.1038/ncomms13858

Sagona, Antonia P., Grigonyte, Aurelija M., MacDonald, Paul and Jaramillo, Alfonso (2016) Genetically modified bacteriophages. Integrative Biology, 8 . pp. 465-474. doi:10.1039/c5ib00267b

Kushwaha, Manish, Rostain, William, Prakash, Satya, Duncan, John and Jaramillo, Alfonso (2016) Using RNA as molecular code for programming cellular function. ACS Synthetic Biology, 5 (8). pp. 795-809. doi:10.1021/acssynbio.5b00297

Pasini, Martina, Fernández-Castané, Alfred , Jaramillo, Alfonso, de Mas, Carles , Caminal, Gloria and Ferrer, Pau (2016) Using promoter libraries to reduce metabolic burden due to plasmid-encoded proteins in recombinant Escherichia coli. New Biotechnology, 33 (1). pp. 78-90. doi:10.1016/j.nbt.2015.08.003

Rodrigo, Guillermo, Prakash, Satya, Cordero, Teresa, Kushwaha, Manish and Jaramillo, Alfonso (2016) Functionalization of an antisense small RNA. Journal of Molecular Biology, 428 Part B (5). pp. 889-892. doi:10.1016/j.jmb.2015.12.022

2015

Rodrigo, Guillermo, Majer, Eszter, Prakash, Satya, Daros, Jose Antonio, Jaramillo, Alfonso and Poyatos, Juan F. (2015) Exploring the dynamics and mutational landscape of riboregulation with a minimal synthetic circuit in living cells. Biophysical Journal, 109 (5). pp. 1070-1076. doi:10.1016/j.bpj.2015.07.021

Amos, Martyn, Axmann, Ilka Maria, Blüthgen, Nils, de la Cruz, Fernando, Jaramillo, Alfonso, Rodriguez-Paton, Alfonso and Simmel, Friedrich (2015) Bacterial computing with engineered populations. Philosophical Transactions of the Royal Society A: Mathematical, Physica and Engineering Sciences, 373 (2046). 20140218. doi:10.1098/rsta.2014.0218

Shen, Shensi, Rodrigo, Guillermo, Prakash, Satya, Majer, Eszter, Landrain, Thomas E., Kiro, Boris, Daros, Jose-Antonio and Jaramillo, Alfonso (2015) Dynamic signal processing by ribozyme-mediated RNA circuits to control gene expression. Nucleic Acids Research, 43 (10). pp. 5158-5170. doi:10.1093/nar/gkv287

Hassall, Jack, MacDonald, Paul, Cordero, Teresa, Rostain, William and Jaramillo, Alfonso (2015) Design and characterization of topological small RNAs. In: Ponchon, Luc, (ed.) RNA Scaffolds. Methods in Molecular Biology, Volume 1316 . Berlin: Springer, pp. 149-167. ISBN 9781493927296

2014

Rostain, William, Landrain, Thomas E., Rodrigo, Guillermo and Jaramillo, Alfonso (2014) Regulatory RNA design through evolutionary computation and strand displacement. In: Marchisio, Mario Andrea , (ed.) Computational Methods in Synthetic Biology. Methods in Molecular Biology, 1244 . New York: Springer, pp. 63-78. ISBN 9781493918775

Rodrigo, Guillermo and Jaramillo, Alfonso (2014) RiboMaker : computational design of conformation-based riboregulation. Bioinformatics, Volume 30 (Number 17). pp. 2508-2510. doi:10.1093/bioinformatics/btu335

2013

Rodrigo, Guillermo, Landrain, Thomas E., Shen, Shensi and Jaramillo, Alfonso (2013) A new frontier in synthetic biology : automated design of small RNA devices in bacteria. Trends in Genetics, Volume 29 (Number 9). pp. 529-536. doi:10.1016/j.tig.2013.06.005

Rodrigo, Guillermo, Landrain, Thomas E., Majer, Eszter, Daròs, José-Antonio and Jaramillo, Alfonso (2013) Full design automation of multi-state RNA devices to program gene expression using energy-based optimization. PLoS Computational Biology, 9 (8). pp. 1-11. e1003172. doi:10.1371/journal.pcbi.1003172

Suárez-Diez, Maria, Pujol, Anaïs M., Matzapetakis, Manolis, Jaramillo, Alfonso and Iranzo, Olga (2013) Computational protein design with electrostatic focusing : experimental characterization of a conditionally folded helical domain with a reduced amino acid alphabet. Biotechnology Journal, 8 (7). pp. 855-864. doi:10.1002/biot.201200380

Rodrigo, Guillermo, Kirov, Boris, Shen, Shensi and Jaramillo, Alfonso (2013) Theoretical and experimental analysis of the forced LacI-AraC oscillator with a minimal gene regulatory model. Chaos: An Interdisciplinary Journal of Nonlinear Science, 23 (2). pp. 1-9. 025109. doi:10.1063/1.4809786

Rodrigo, Guillermo and Jaramillo, Alfonso (2013) AutoBioCAD : full biodesign automation of genetic circuits. ACS Synthetic Biology, 2 (5). pp. 230-236. doi:10.1021/sb300084h

Carrera, Javier and Jaramillo, Alfonso (2013) Automated design of bacterial genome sequences. BMC Systems Biology, Volume 7 (Number 1). Article number 108. doi:10.1186/1752-0509-7-108

2012

Carrera, Javier, Elena, Santiago F. and Jaramillo, Alfonso (2012) Computational design of genomic transcriptional networks with adaptation to varying environments. Proceedings of the National Academy of Sciences of the United States of America, 109 (38). pp. 15277-82. doi:10.1073/pnas.1200030109

Rodrigo, Guillermo, Carrera, Javier, Landrain, Thomas E. and Jaramillo, Alfonso (2012) Perspectives on the automatic design of regulatory systems for synthetic biology. FEBS Letters, 586 (15). pp. 2037-2042. doi:10.1016/j.febslet.2012.02.031

Papin, Jason A., Carrera, Javier, Fernández del Carmen, Asun, Fernández-Muñoz, Rafael, Rambla, Jose Luis, Pons, Clara, Jaramillo, Alfonso, Elena, Santiago F. and Granell, Antonio (2012) Fine-tuning tomato agronomic properties by computational genome redesign. PLoS Computational Biology, 8 (6). e1002528. doi:10.1371/journal.pcbi.1002528

Rodrigo, Guillermo, Landrain, T. E. and Jaramillo, Alfonso (2012) De novo automated design of small RNA circuits for engineering synthetic riboregulation in living cells. Proceedings of the National Academy of Sciences of the United States of America, 109 (38). pp. 15271-15276. doi:10.1073/pnas.1203831109

2011

Rodrigo, Guillermo, Jaramillo, Alfonso and Blázquez, Miguel A. (2011) Integral control of plant gravitropism through the interplay of hormone signaling and gene regulation. Biophysical Journal, 101 (4). pp. 757-763. doi:10.1016/j.bpj.2011.06.047

Jaramillo, Alfonso and Faulon, Jean-Loup (2011) Editorial : synthetic biology - applying new paradigms at the interface of fundamental research and innovation. Biotechnology Journal, 6 (7). pp. 766-767. doi:10.1002/biot.201100254

Carrera, Javier, Rodrigo, Guillermo, Singh, Vijai, Kirov, Boris and Jaramillo, Alfonso (2011) Empirical model and in vivo characterization of the bacterial response to synthetic gene expression show that ribosome allocation limits growth rate. Biotechnology Journal, 6 (7). pp. 773-783. doi:10.1002/biot.201100084

Camsund, Daniel, Lindblad, Peter and Jaramillo, Alfonso (2011) Genetically engineered light sensors for control of bacterial gene expression. Biotechnology Journal, 6 (7). pp. 826-836. doi:10.1002/biot.201100091

Glykys, Doris J., Szilvay, Géza R., Tortosa, Pablo, Suárez Diez, María, Jaramillo, Alfonso and Banta, Scott (2011) Pushing the limits of automatic computational protein design : design, expression, and characterization of a large synthetic protein based on a fungal laccase scaffold. Systems and synthetic biology, 5 (1-2). pp. 45-58. doi:10.1007/s11693-011-9080-9

Rodrigo, G., Carrera, J. and Jaramillo, Alfonso (2011) Computational design of synthetic regulatory networks from a genetic library to characterize the designability of dynamical behaviors. Nucleic Acids Research, 39 (20). e138. doi:10.1093/nar/gkr616

2010

Rodrigo, G., Carrera, J., Jaramillo, Alfonso and Elena, S. F. (2010) Optimal viral strategies for bypassing RNA silencing. Journal of The Royal Society Interface, 8 (55). pp. 257-268. doi:10.1098/rsif.2010.0264