Engineering organism-specific virus-like antibiotics. Engineering synthetic RNA circuits in living cells.
After a PhD in Particle Physics (1999), AJ he worked on the computational design of proteins, using molecular modeling techniques. Afterwards, after moving as Assistant Professor to Ecole Polytechnique, he developed computational design methods for metabolic networks, transcriptional networks, and particularly RNA networks. In 2009, after moving to CNRS-Genopole as senior researcher, he started his experimental microbiology lab where he could validate experimentally his computational methodologies. He then developed and used automated microscopy and microfluidics chips for single-cell validations. In 2013, he moved to the University of Warwick as Full Professor, where he is developing new cell-culture bioreactors for directed evolution, which he applies to engineer the first synthetic bacteriophage. He also is developing a novel gene regulation relying on RNA. He has coordinated several Synthetic Biology international consortia and he is member of the editorial boards of ACS Synthetic Biology and the J. of Biol. Engineering.
- Goicoechea Serrano, Eduardo, Blázquez-Bondia, Carlos, Jaramillo, Alfonso, 2024. T7 phage-assisted evolution of riboswitches using error-prone replication and dual selection. Scientific Reports, 14 (1)
- Tridgett, Matthew, Ababi, Maria, Osgerby, Alexander, Ramirez Garcia, Robert, Jaramillo, Alfonso, 2021. Engineering bacteria to produce pure phage-like particles for gene delivery. ACS Synthetic Biology, 10 (1), pp. 107-114
- Grigonyte, Aurelija, Harrison, Christian, Macdonald, Paul R., Montero-Blay, Ariadna, Tridgett, Matthew, Duncan, John, Sagona, Antonia P., Constantinidou, Chrystala, Jaramillo, Alfonso, Millard, Andrew D., 2020. Comparison of CRISPR and marker-based methods for the engineering of Phage T7. Viruses, 12 (2)
- Broedel, A., Rodrigues, R., Jaramillo, Alfonso, Isalan, M., 2020. Accelerated evolution of a minimal 63-amino acid dual transcription factor. Science Advances, 6 (24)
- Racovita, Adrian, Jaramillo, Alfonso, 2020. Reinforcement learning in synthetic gene circuits. Biochemical Society Transactions, 48 (4), pp. 1637-1643
- Galizi, Roberto, Duncan, John, Rostain, William, Quinn, Charlotte M., Storch, Marko, Kushwaha, Manish, Jaramillo, Alfonso, 2020. Engineered RNA-interacting CRISPR guide RNAs for genetic sensing and diagnostics. The CRISPR Journal, 3 (5), pp. 398-408
- Galizi, Roberto, Jaramillo, Alfonso, 2019. Engineering CRISPR guide RNA riboswitches for in vivo applications. Current Opinion in Biotechnology, 55, pp. 103-113
- Cordero, Teresa, Rosado, Arantxa, Majer, Eszter, Jaramillo, Alfonso, Rodrigo, Guillermo, Daròs, José-Antonio, 2018. Boolean computation in plants using post-translational genetic control and a visual output signal. ACS Synthetic Biology, 7 (10), pp. 2322?-2330
- Pacheco, Catarina C., Büttel, Zsófia, Pinto, Filipe, Rodrigo, Guillermo, Carrera, Javier, Jaramillo, Alfonso, Tamagnini, Paula, 2018. Modulation of intracellular O2 concentration in Escherichia coli strains using oxygen consuming devices. ACS Synthetic Biology, 7 (7), pp. 1742-1752
- Senoussi, Anis, Lee Tin Wah, Jonathan, Shimizu, Yoshihiro, Robert, Jérôme, Jaramillo, Alfonso, Findeiss, Sven, Axmann, Ilka M., Estevez-Torres, André, 2018. Quantitative characterization of translational riboregulators using an in vitro transcription?translation system. ACS Synthetic Biology, 7 (5), pp. 1269-1278
- Brödel, Andreas K., Isalan, Mark, Jaramillo, Alfonso, 2018. Engineering of biomolecules by bacteriophage directed evolution. Current Opinion in Biotechnology, 51, pp. 32-38
- Ferreira, Eunice A., Pacheco, Catarina C., Pinto, Filipe, Pereira, José, Lamosa, Pedro, Oliveira, Paulo, Kirov, Boris, Jaramillo, Alfonso, 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)
- Howarth, Mark, Jaramillo, Alfonso, 2018. Editorial overview : nanobiotechnology : baby steps and giant strides towards molecular mastery. Current Opinion in Biotechnology, 51, pp. iv-vi
- Brodel, Andreas K., Jaramillo, Alfonso, Isalan, Mark, 2017. Intracellular directed evolution of proteins from combinatorial libraries based on conditional phage replication. Nature Protocols, 12 (9), pp. 1830-1843
- Rodrigo, Guillermo, Prakash, Satya, Shen, Shensi, Majer, Eszter, Daròs, José-Antonio, Jaramillo, Alfonso, 2017. Model-based design of RNA hybridization networks implemented in living cells.. Nucleic Acids Research, 45 (16), pp. 9797-9808
- Brodel, Andreas K., Jaramillo, Alfonso, Isalan, Mark, 2016. Engineering orthogonal dual transcription factors for multi-input synthetic promoters. Nature Communications, 7
- Pasini, Martina, Fernández-Castané, Alfred, Jaramillo, Alfonso, de Mas, Carles, Caminal, Gloria, 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
- Kushwaha, Manish, Rostain, William, Prakash, Satya, Duncan, John, Jaramillo, Alfonso, 2016. Using RNA as molecular code for programming cellular function. ACS Synthetic Biology, 5 (8), pp. 795-809
- Sagona, Antonia P., Grigonyte, Aurelija M., MacDonald, Paul, Jaramillo, Alfonso, 2016. Genetically modified bacteriophages. Integrative Biology, 8, pp. 465-474
- Rodrigo, Guillermo, Prakash, Satya, Cordero, Teresa, Kushwaha, Manish, Jaramillo, Alfonso, 2016. Functionalization of an antisense small RNA. Journal of Molecular Biology, 428 Part B (5), pp. 889-892
- Amos, Martyn, Axmann, Ilka Maria, Blüthgen, Nils, de la Cruz, Fernando, Jaramillo, Alfonso, Rodriguez-Paton, Alfonso, Simmel, Friedrich, 2015. Bacterial computing with engineered populations. Philosophical Transactions of the Royal Society A: Mathematical, Physica and Engineering Sciences, 373 (2046)
- Shen, Shensi, Rodrigo, Guillermo, Prakash, Satya, Majer, Eszter, Landrain, Thomas E., Kiro, Boris, Daros, Jose-Antonio, Jaramillo, Alfonso, 2015. Dynamic signal processing by ribozyme-mediated RNA circuits to control gene expression. Nucleic Acids Research, 43 (10), pp. 5158-5170
- Rodrigo, Guillermo, Majer, Eszter, Prakash, Satya, Daros, Jose Antonio, Jaramillo, Alfonso, 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
- Rodrigo, Guillermo, Jaramillo, Alfonso, 2014. RiboMaker : computational design of conformation-based riboregulation. Bioinformatics, 30 (17), pp. 2508-2510
- Suárez-Diez, Maria, Pujol, Anaïs M., Matzapetakis, Manolis, Jaramillo, Alfonso, 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
- Rodrigo, Guillermo, Landrain, Thomas E., Majer, Eszter, Daròs, José-Antonio, 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
- Rodrigo, Guillermo, Kirov, Boris, Shen, Shensi, 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
- Rodrigo, Guillermo, Jaramillo, Alfonso, 2013. AutoBioCAD : full biodesign automation of genetic circuits. ACS Synthetic Biology, 2 (5), pp. 230-236
- Carrera, Javier, Jaramillo, Alfonso, 2013. Automated design of bacterial genome sequences. BMC Systems Biology, 7 (1)
- Rodrigo, Guillermo, Landrain, Thomas E., Shen, Shensi, Jaramillo, Alfonso, 2013. A new frontier in synthetic biology : automated design of small RNA devices in bacteria. Trends in Genetics, 29 (9), pp. 529-536
- Carrera, Javier, Elena, Santiago F, 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
- Rodrigo, Guillermo, Landrain, T. E., 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
- Rodrigo, Guillermo, Carrera, Javier, Landrain, Thomas E., Jaramillo, Alfonso, 2012. Perspectives on the automatic design of regulatory systems for synthetic biology. FEBS Letters, 586 (15), pp. 2037-2042
- Papin, Jason A., Carrera, Javier, Fernández del Carmen, Asun, Fernández-Muñoz, Rafael, Rambla, Jose Luis, Pons, Clara, Jaramillo, Alfonso, Elena, Santiago F., Granell, Antonio, 2012. Fine-tuning tomato agronomic properties by computational genome redesign. PLoS Computational Biology, 8 (6)
- Glykys, Doris J., Szilvay, Géza R., Tortosa, Pablo, Suárez Diez, María, Jaramillo, Alfonso, 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
- Camsund, Daniel, Lindblad, Peter, Jaramillo, Alfonso, 2011. Genetically engineered light sensors for control of bacterial gene expression. Biotechnology Journal, 6 (7), pp. 826-836
- Carrera, Javier, Rodrigo, Guillermo, Singh, Vijai, Kirov, Boris, 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
- Jaramillo, Alfonso, 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
- Rodrigo, Guillermo, Jaramillo, Alfonso, 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
- Rodrigo, G., Carrera, J., 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)
- Rodrigo, G., Carrera, J., Jaramillo, Alfonso, Elena, S. F., 2010. Optimal viral strategies for bypassing RNA silencing. Journal of The Royal Society Interface, 8 (55), pp. 257-268
- Hassall, Jack, MacDonald, Paul, Cordero, Teresa, Rostain, William, Jaramillo, Alfonso, 2015. Design and characterization of topological small RNAs. In Ponchon, Luc (ed.), RNA Scaffolds, Berlin, Springer, pp. 149-167
- Rostain, William, Landrain, Thomas E., Rodrigo, Guillermo, Jaramillo, Alfonso, 2014. Regulatory RNA design through evolutionary computation and strand displacement. In Marchisio, Mario Andrea (ed.), Computational Methods in Synthetic Biology, New York, Springer, pp. 63-78
- Jaramillo, Alfonso, 2017. Synthetic biology : engineered stable ecosystems. Nature microbiology, Nature Publishing Group
Title | Funder | Award start | Award end |
---|---|---|---|
Warwick Integrative Synthetic Biology Centre (WISB) extension - related to 46082 | BBSRC | 01 Apr 2020 | 31 Mar 2022 |
EVO-ENGINE: A directed evolution engine for engineering proteins and logic gates | BBSRC | 01 Oct 2017 | 30 Sep 2021 |
Warwick Integrative Synthetic Biology Centre (WISB) | BBSRC | 14 Nov 2014 | 31 May 2020 |
MetaRNA - RNA-based technologies for single-cell metabolite analysis (Marie Curie ITN) | European Commission | 01 Jun 2015 | 30 Jun 2019 |
PROMYS: Programming synthetic networks for bio-based production of value chemicals | EU | 01 Jan 2014 | 31 Dec 2017 |
General-Purpose Programmable Evolution Machine on a Chip (EVOPROG) | EU | 01 Jan 2014 | 31 Dec 2016 |
Engineering bacterial circuits | BBSRC | 22 Jun 2015 | 28 Sep 2015 |
iGEM Glasgow student stipend competition February 2014 - | University of Glasgow | 23 Jun 2014 | 30 Sep 2014 |