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Project Publications


2016

Sagredo, S., Pirzer, T., Aghebat Rafat, A., Goetzfried, M. A., Moncalian, G., Simmel, F. C., and de la Cruz, F. Orthogonal protein assembly on DNA nanostructures using relaxases. Angewandte Chemie International Edition. doi: 10.1002/anie.201510313.

Ramalho, T., Meyer, A., Mückl, A., Kapsner, K., Gerland, U. and Simmel, F.C. Single Cell Analysis of a Bacterial Sender-Receiver System. PLOS ONE, 11(1). doi: 10.1371/journal.pone.0145829


2015

Amos, M., Axmann, I., Bluethgen, N., de la Cruz, F., Jaramillo, A., Rodriguez-Paton, A. and Simmel, F. Bacterial computing with engineered populations. Philosophical Transactions of the Royal Society A 373:2046. doi: 10.1098/rsta.2014.0218.

Goñi-Moreno, A. and Amos, M. DiSCUS: A simulation platform for conjugation computing. In Calude, C.S. & Dineen, M.J. (Eds), Unconventional and Natural Computation (UCNC 2015), Auckland, New Zealand, August 31-September 4, 2015, p.p. 181-191, Springer.


2014

Rostain, W., Landrain, T.E., Rodrigo, G. and Jaramillo, A. Regulatory RNA design through evolutionary computation and strand displacement. In Computational Methods in Synthetic Biology, Marchisio, M.A. (Ed.), pp. 63-78. Springer.


2013

Blanco, J., Mora, A., Mamani, R., López, C., Blanco, M., Dahbi, G., Herrera, A., Marzoa, J., Fernández, V., de la Cruz, F., Martínez-Martínez, L., Alonso, M.P., Nicolas-Chanoine, M.H., Johnson, J.R., Johnston, B., López-Cerero, L., Pascual, A., and Rodríguez-Baño, J., Four Main Virotypes among Extended-Spectrum β-Lactamase-Producing Isolates of Escherichia coli O25b:H4-B2-ST131: Bacterial, Epidemiological, and Clinical Characteristics. Journal of Clinical Microbiology 51(10): 3358-3367. doi:10.1128/JCM.01555-13

Mata, C., Miró, E., Alvarado, A., Garcillán-Barcia, M.P., Toleman, M., Walsh, T.R., de la Cruz, F., and Navarro, F., Plasmid typing and genetic context of AmpC β-lactamases in Enterobacteriaceae lacking inducible chromosomal ampC genes: findings from a Spanish hospital 1999-2007. Journal of Antimicrobial Chemotherapy 67(1): 115-122. doi:10.1093/jac/dkr412

Bentele, K., Saffert, P., Rauscher, R., Ignatova, Z., and Blüthgen, N., Efficient translation initiation dictates codon usage at gene start. Molecular Systems Biology 9(1): 675. doi:10.1038/msb.2013.32

Suárez‐Diez, M., Pujol, A.M., Matzapetakis, M., Jaramillo, A., and Iranzo, O., Computational protein design with electrostatic focusing: Experimental characterization of a conditionally folded helical domain with a reduced amino acid alphabet. Biotechnology Journal 8(7): 855-864. doi:10.1002/biot.201200380

Rodrigo, G., Landrain, T.E., Majer, E., Daròs, J-A., and Jaramillo, A., Full Design Automation of Multi-State RNA Devices to Program Gene Expression Using Energy-Based Optimization. PLoS Computational Biology 9(8): e1003172. doi:10.1371/journal.pcbi.1003172

Chandler, M., de la Cruz, F., Dyda, F., Hickman, A.B., Moncalian, G., and Ton-Hoang, B., Breaking and joining single-stranded DNA: the HUH endonuclease superfamily. Nature Reviews Microbiology 11: 525-538. doi:10.1038/nrmicro3067

Francia, M.V., Clewell, D.B., de la Cruz, F., and Moncalián, G. Catalytic domain of plasmid pAD1 relaxase TraX defines a group of relaxases related to restriction endonucleases. Proceedings of the National Academy of Sciences 110(33): 13606-13611. doi:10.1073/pnas.1310037110

Larrea, D., de Paz, H.D., Arechaga, I., de la Cruz, F., and Llosa, M., Structural independence of conjugative coupling protein TrwB from its Type IV secretion machinery. Plasmid 70(1): 146-153. doi:10.1016/j.plasmid.2013.03.006

Ripoll-Rozada, J., Zunzunegui, S., de la Cruz, F., Arechaga, I., and Cabezón, E., Functional interactions of VirB11 traffic ATPases with VirB4 and VirD4 molecular motors in Type IV secretion systems. Journal of Bacteriology 195(18): 4195-4201. doi:10.1128/JB.00437-13

Garcillán-Barcia, M.P., and de la Cruz, F., Ordering the bestiary of genetic elements transmissible by conjugation. Mobile Genetic Elements 3(1): e24263. doi:10.4161/mge.24263

Goñi-Moreno, A., Amos, M., and de la Cruz, F., Multicellular Computing Using Conjugation for Wiring. PLoS ONE 8(6): e65986. doi:10.1371/journal.pone.0065986

Hertel, S., Brettschneider, C., and Axmann, I. M., Revealing a Two-Loop Transcriptional Feedback Mechanism in the Cyanobacterial Circadian Clock. PLoS Computational Biology 9(3): e1002966. doi:10.1371/journal.pcbi.1002966


2012

Murphy, N., and Rodriguez-Paton, A., Distributed Computing with Prokaryotic Immune Systems. Artificial Immune Systems, LCNS 7597: 286-288. doi:10.1007/978-3-642-33757-4_22

Guglielmini, P., de la Cruz, F., and Rocha, E. P. C. Evolution of conjugation and type IV secretion systems. Molecular Biology and Evolution 30(2):315-331. doi:10.1093/molbev/mss221

Rodrigo, G., and Jaramillo, A. AutoBioCAD: Full bio-design automation of genetic circuits. ACS Synthetic Biology 2(5): 230-236. 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 13(2): 1136-1146. doi:10.1016/j.asoc.2012.10.012

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):39925-39932. doi:10.1074/jbc.M112.413849

Goni Moreno, A., and Amos, M. 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. Proceedings of the National Academy of Sciences 109(38): 15271-15276. doi:10.1073/pnas.1203831109

Carrera, J., Elena, S.F., and Jaramillo, A. Computational design of genomic transcriptional networks with adaptation to varying environments. Proceedings of the National Academy of Sciences 109(38): 15277-15282. doi:10.1073/pnas.1200030109

Sainz de Murieta, I., and Rodriguez-Paton, A. Probabilistic Reasoning with a Bayesian DNA Device Based on Strand Displacement. DNA Computing and Molecular Programming, LCNS 7433: 110-122. doi:10.1007/978-3-642-33757-4_22

Carrera, J., Fernandez del Carmen, A., Fernandez-Munoz, R., Rambla, JL., Pons, C., Jaramillo, A., Elena, S.F., and Granell, A. Fine-Tuning Tomato Agronomic Properties by Computational Genome Redesign. PLoS Computational Biology 8(6): e1002528. doi:10.1371/journal.pcbi.1002528

Alvarado, A., Garcillan-Barcia, M.P., 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): 87-91. 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(1): 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

Paun, A., Paun, M., Rodriguez-Paton, A., and Sidoroff, M. P systems with proteins on membranes: A survey. International Journal of Foundations of Computer Science 22(1): 39-53. doi:10.1142/S0129054111007812

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(11):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.2010.0264

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): 757-763. 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): 766-767. 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(12)

Gomez-Esteban, P., and Rodriguez-Paton, A. Simulating a rock-scissors-paper bacterial game with a discrete cellular automaton. New Challenges on Bioinspired Applications, LCNS 6687: 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. DNA Computing and Molecular Programming, LNCS 6937: 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


2010

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 6:389. doi:10.1038/msb.2010.44

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 2010. MIT Press, 184-185