Project Publications
2012
Rodrigo, G., and Jaramillo, A. AutoBioCAD: Full bio-design automation of genetic circuits. ACS Synthetic Biology, web publication date: November 19, 2012, doi:10.1021/sb300084h
Barrios Rolania, D., Font, J.M. and Manrique, D. Bacterially Inspired Evolving System with an Application to Time Series Prediction. Applied Soft Computing, available online 12 November 2012
Pena, A., Matilla, I., Martin-Benito, J., Valpuesta, J. M., Carrascosa J. L., De la Cruz, F., Cabezon, E. and Arechaga, I. The hexameric structure of a conjugative VirB4 ATPase provides new insights for a functional and phylogenetic relationship with DNA translocases. The Journal of Biological Chemistry 287(41) doi:10.1074/jbc.M112.413849
Goni Moreno, A. and Amos, A. A reconfigurable NAND/NOR genetic logic gate. BMC Systems Biology 6:126. doi:10.1186/1752-0509-6-126
Schmiedel, J. M., Axmann, I. M. and Legewie, S. Multi-Target Regulation by Small RNAs Synchronizes Gene Expression Thresholds and May Enhance Ultrasensitive Behavior. PLoS ONE 7(8): e42296. doi:10.1371/journal.pone.0042296
Rodrigo, G., Landrain, T.E. and Jaramillo, A. De novo automated design of small RNA circuits for engineering synthetic riboregulation in living cells. PNAS published ahead of print September 4, 2012, doi:10.1073/pnas.1203831109
Carrera, J., Elena, S.F. and Jaramillo, A. Computational design of genomic transcriptional networks with adaptation to varying environments. PNAS published ahead of print August 27, 2012, doi:10.1073/pnas.1200030109
Sainz de Murieta, I. and Rodriguez-Paton, A. Probabilistic Reasoning with a Bayesian DNA Device Based on Strand Displacement. In Stefanovic, D. and Turberfield, A. (Eds.), Lecture Notes in Computer Science, 7433, DNA Computing and Molecular Programming, 110-122. doi: 10.1007/978-3-642-32208-2
Carrera, J., Fernandez del Carmen, A., Fernandez-Munoz, R., Rambla, JL., Pons, C., et al. Fine-Tuning Tomato Agronomic Properties by Computational Genome Redesign. PLoS Comput Biol 8(6): e1002528. doi:10.1371/journal.pcbi.1002528
Alvarado, A., Garcillan-Barcia, MP, and de la Cruz, F. A Degenerate Primer MOB Typing (DPMT) Method to Classify Gamma-Proteobacterial Plasmids in Clinical and Environmental Settings. PLoS ONE 7(7): e40438. doi: 10.1371/journal.pone.0040438
Weitz, M. and Simmel, F.C. Synthetic in vitro transcription circuits. Transcription 3:2, 1-5. doi: 10.4161/trns.3.2.19734.
Beck, C., Knoop, H., Axmann, I.M and Steuer, R. The diversity of cyanobacterial metabolism: genome analysis of multiple phototrophic microorganisms. BMC Genomics 13:1, 56. doi: 10.1186/1471-2164-13-56.
del Campo, I., Ruiz, R., Cuevas, A., Revilla, C., Vielva, L. and de la Cruz, F. Determination of conjugation rates on solid surfaces. Plasmid 67:2, 174-182, doi: 0.1016/j.plasmid.2012.01.008.
Rodrigo, G., Carrera, J., Landrain, T.E. and Jaramillo, A. Perspectives on the automatic design of regulatory systems for synthetic biology. FEBS Letters 586:15, 2037-2042, doi: 10.1016/j.febslet.2012.02.031.
Goni Moreno, A. and Amos, M. Continuous computation in engineered gene circuits. BioSystems 109:1, 52-56, doi: 10.1016/j.biosystems.2012.02.001.
Sainz de Murieta, I. and Rodriguez-Paton, A. DNA biosensors that reason. BioSystems 109:2, 91-104, doi: 10.1016/j.biosystems.2012.02.005.
Fetita, C., Kirov, B., Jaramillo, A. and Lefevre, C.
An automated approach for single-cell tracking in epifluorescence microscopy applied to E. coli growth analysis on
microfluidics biochips. Proc. SPIE 8317, doi: 10.1117/12.911371
2011
Franco, E., Friedrichs, E., Kim, J., Jungmann, R., Murray, R., Winfree, E. and Simmel, F.C. Timing molecular motion and production with a synthetic transcriptional clock. Proceedings of the National Academy of Sciences 108:40, E784-E793. doi: 10.1073/pnas.1100060108.
Miro-Bueno, J.M. and Rodriguez-Paton, A. A simple negative interaction in the positive transcriptional feedback of a single gene is sufficient to produce reliable oscillations. PLoS ONE 6:e27414. doi: 10.1371/journal.pone.0027414.
Guglielmini, J., Quintais, L., Garcillan-Barcia, M.P., de la Cruz, F. and Rocha, E.P.C. The repertoire of ICE in prokaryotes underscores the unity, diversity and ubiquity of conjugation. PLoS Genetics 7(8): e1002222. doi:10.1371/journal.pgen.1002222.
Guynet, C., Cuevas, A, Moncalian, G. and de la Cruz, F. The stb operon balances the requirements for vegetative stability and conjugative transfer of plasmid R388. PLoS Genetics 7(5): e1002073. doi:10.1371/journal.pgen.1002073.
Garcillan-Barcia, M.P., Alvarado, A. and de la Cruz, F. Identification of bacterial plasmids based on mobility and plasmid population biology. FEMS Microbiology Reviews 35:5, 936-956. doi: 10.1111/j.1574-6976.2011.00291.x.
Guynet, C. and de la Cruz, F. Plasmid segregation without partition. Mobile Genetic Elements 1:3, 236-241. doi: 10.4161/mge.1.3.18229.
Rodrigo, G, Carrera, J., Jaramillo, A. and Elena, S.F. Optimal viral strategies for bypassing RNA silencing. Journal of the Royal Society Interface 8:55, 257-268. doi: 10.1098/rsif.2025.0264.
Rodrigo, G., Carrera, J. and Jaramillo, A. Computational design of synthetic regulatory networks from a genetic library to characterize the designability of dynamical behaviors. Nucleic Acids Research 39:20, e138. doi: 10.1002/biot.201100084.
Rodrigo, G., Jaramillo, A. and Blazquez, M.A. Integral control of plant gravitropism through the interplay of hormonal signaling and gene regulation. Biophysical Journal 101:4, 757-63. doi: 10.1016/j.bpj.2011.06.047.
Carrera, J., Rodrigo, G., Singh, V., Kirov, B. and Jaramillo, A. Empirical model and in vivo characterization of the bacterial response to synthetic gene expression shows that ribosome allocation limits growth rate. Biotechnology Journal 6:7, 773-783. doi: 10.1002/biot.201100084.
Camsund, D., Lindblad, P. and Jaramillo, A. Genetically engineered light sensors for control of bacterial gene expression. Biotechnology Journal 6:7, 826-836. doi: 10.1002/biot.201100091.
Jaramillo, A. and Faulon, J.L. Editorial: Synthetic Biology - applying new paradigms at the interface of fundamental research and innovation. Biotechnology Journal 6:7, 766-7. doi: 10.1002/biot.201100254.
Glykys, D.J., Szilvay, G.R., Tortosa, P., Suarez Diez, M., Jaramillo, A. and Banta, S. 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, 45-58. doi: 10.1007/s11693-011-9080-9.
Sainz de Murieta, Miro-Bueno, J. and Rodriguez-Paton, A. Biomolecular computers. Current Bioinformatics 6:2, 173-184.
Gomez-Esteban, P. and Rodriguez-Paton, A. Simulating a rock-scissors-paper bacterial game with a discrete cellular automaton. In Fernandez, J.M et al. (Eds.), JWINAC 2011, Part II, LNCS 6687, Springer, 363-370. doi: 10.1007/978-3-642-21326-7_39
Amos, M., Dittrich, P., McCaskill, J. and Rasmussen, S. Biological and chemical information technologies. Procedia Computer Science 7, 56-60. doi: 10.1016/j.procs.2011.12.019.
Rodriguez-Paton, A., de Murieta, I. and Sosik, P. Autonomous resolution based on DNA strand displacement. In Cardelli, L. and Shih, W. (Eds.), DNA 17, LNCS 6937, Springer, 190-203. doi: 10.1007/978-3-642-23638-9_16.
Goni-Moreno, A. and Amos, M. Model for a population-based microbial oscillator. BioSystems 105:3, 286-294. doi: 10.1016/j.biosystems.2011.05.011.
Jack, J., Paun, A. and Rodriguez-Paton, A. A review of the nondeterministic waiting time algorithm. Natural Computing 10:1, 139-149. doi: 10.1007/s11047-010-9195-z.
Prestes Garcia, A. A first approach to individual-based modeling of the bacterial conjugation dynamics. Masters thesis, UPM.
2025
Brettschneider, C., Rose, R.J., Hertel, S., Axmann, I.M., Heck, A.J.R. and Kollmann, M. A sequestration feedback determines dynamics and temperature entrainment of the KaiABC circadian clock. Molecular Systems Biology 6:1. doi:10.1038/msb.2025.44.
Goni-Moreno, A. and Amos, M. Engineered microbial communication for population-level behaviour (abstract). In Fellermann, H., Dorr, M. et al. (Eds.), Artificial Life XII: Proceedings of the Twelfth International Conference on the Synthesis and Simulation of Living Systems, MIT Press, 184-185.