The Library
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Number of items: 46.
2024
Goicoechea Serrano, Eduardo, BlΓ‘zquez-Bondia, Carlos and Jaramillo, Alfonso (2024) T7 phage-assisted evolution of riboswitches using error-prone replication and dual selection. Scientific Reports, 14 (1). 2377. doi:10.1038/s41598-024-52049-9 ISSN 2045-2322.
2022
Cunliffe, Tabitha G., Parker, Alan L. and Jaramillo, Alfonso (2022) Pseudotyping bacteriophage P2 tail fibers to extend the host range for biomedical applications. ACS Synthetic Biology, 11 (10). pp. 3207-3215. doi:10.1021/acssynbio.1c00629 ISSN 2161-5063.
2021
Camsund, Daniel, Jaramillo, Alfonso and Lindblad, Peter (2021) Engineering of a promoter repressed by a light-regulated transcription factor in escherichia coli. BioDesign Research, 2021 (9857418). doi:10.34133/2021/9857418 ISSN 2693-1257.
Tridgett, Matthew, Ababi, Maria, Osgerby, Alexander, Ramirez Garcia, Robert and Jaramillo, Alfonso (2021) Engineering bacteria to produce pure phage-like particles for gene delivery. ACS Synthetic Biology, 10 (1). pp. 107-114. doi:10.1021/acssynbio.0c00467 ISSN 2161-5063.
2020
Galizi, Roberto, Duncan, John, Rostain, William, Quinn, Charlotte M., Storch, Marko, Kushwaha, Manish and Jaramillo, Alfonso (2020) Engineered RNA-interacting CRISPR guide RNAs for genetic sensing and diagnostics. The CRISPR Journal, 3 (5). pp. 398-408. doi:10.1089/crispr.2020.0029 ISSN 2573-1602.
Racovita, Adrian and Jaramillo, Alfonso (2020) Reinforcement learning in synthetic gene circuits. Biochemical Society Transactions, 48 (4). pp. 1637-1643. doi:10.1042/bst20200008 ISSN 0300-5127.
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 ISSN 2375-2548.
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 ISSN 1999-4915.
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 ISSN 0958-1669.
2018
Cordero, Teresa, Rosado, Arantxa, Majer, Eszter, Jaramillo, Alfonso, Rodrigo, Guillermo and DarΓ²s, JosΓ©-Antonio (2018) Boolean computation in plants using post-translational genetic control and a visual output signal. ACS Synthetic Biology, 7 (10). 2322β-2330. doi:10.1021/acssynbio.8b00214 ISSN 2161-5063.
Pacheco, Catarina C., BΓΌttel, ZsΓ³fia, 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 ISSN 2161-5063.
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 ISSN 0958-1669.
BrΓΆdel, 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 ISSN 0958-1669.
Senoussi, Anis, Lee Tin Wah, Jonathan, Shimizu, Yoshihiro, Robert, JΓ©rΓ΄me, Jaramillo, Alfonso, Findeiss, Sven, Axmann, Ilka M. and Estevez-Torres, AndrΓ© (2018) Quantitative characterization of translational riboregulators using an in vitro transcriptionβtranslation system. ACS Synthetic Biology, 7 (5). pp. 1269-1278. doi:10.1021/acssynbio.7b00387 ISSN 2161-5063.
Ferreira, Eunice A., Pacheco, Catarina C., Pinto, Filipe, Pereira, JosΓ©, 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 ISSN 2397-7000.
2017
Rodrigo, Guillermo, Prakash, Satya, Shen, Shensi, Majer, Eszter, DarΓ²s, JosΓ©-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 ISSN 0305-1048.
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 ISSN 1750-2799.
Jaramillo, Alfonso (2017) Synthetic biology : engineered stable ecosystems. Nature microbiology, 2 (8). 17119. ISSN 2058-5276 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 ISSN 2041-1723.
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 ISSN 1757-9694.
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 ISSN 2161-5063.
Pasini, Martina, FernΓ‘ndez-CastanΓ©, 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 ISSN 1871-6784 .
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 ISSN 0022-2836.
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 ISSN 0006-3495.
Amos, Martyn, Axmann, Ilka Maria, BlΓΌthgen, 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 ISSN 1364-503X.
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 ISSN 0305-1048.
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 ISSN 1367-4803.
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 ISSN 0168-9525.
Rodrigo, Guillermo, Landrain, Thomas E., Majer, Eszter, DarΓ²s, JosΓ©-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 ISSN 1553-7358.
SuΓ‘rez-Diez, Maria, Pujol, AnaΓ―s 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 ISSN 18606768.
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 ISSN 1054-1500.
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 ISSN 2161-5063.
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 ISSN 1752-0509.
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 ISSN 0027-8424.
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 ISSN 0014-5793.
Papin, Jason A., Carrera, Javier, FernΓ‘ndez del Carmen, Asun, FernΓ‘ndez-MuΓ±oz, 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 ISSN 1553-7358.
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 ISSN 0027-8424.
2011
Rodrigo, Guillermo, Jaramillo, Alfonso and BlΓ‘zquez, 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 ISSN 0006-3495.
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 ISSN 1860-6768.
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 ISSN 1860-6768.
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 ISSN 1860-6768.
Glykys, Doris J., Szilvay, GΓ©za R., Tortosa, Pablo, SuΓ‘rez Diez, MarΓa, 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 ISSN 1872-5325.
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 ISSN 0305-1048.
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 ISSN 1742-5689.
This list was generated on Thu Mar 28 20:37:25 2024 GMT.