List of Publications of the group in the last five years

1. Lin, S.S., Wu, H.W., Elena, S.F., Chen, K.C., Niu, Q.W., Yeh, S.D., Chen, C.C., Chua, N.H. (2009). "Molecular evolution of a viral non-coding sequence under the selective pressure of amiRNA-mediated silencing". PLoS Pathog. 5: e1000312.
2. Gago, S., Elena, S.F., Flores, R., Sanjuán, R. (2009). "Extremely high mutation rate of a hammerhead viroid". Science 323: 1308.
3. Carrera, J., Rodrigo, G., Jaramillo, A. (2009). “Model-based redesign of global transcription regulation”. Nucl. Acids Res. 37(5):e38.
4. Elena, S.F., Agudelo-Romero, P, Lalic, J. (2009) “The evolution of viruses in multi-host fitness landscapes”. Open Virol. J. 3: 1-6.
5. Sanjuán, R., Agudelo-Romero, P., Elena, S.F. (2009). "Upper-limit mutation rate estimation for a plant RNA virus". Biol. Lett. 5: 394-396.
6. Martín, S., Sambade, A., Rubio, L, Vives, M.C., Moya, P., Guerri, J., Elena, S.F., Moreno, P. (2009). “Contribution of recombination and selection to molecular evolution of Citrus tristeza virus”. J. Gen. Virol. 90: 1527-1538.
7. Carrera, J., Rodrigo, G., Jaramillo, A. (2009). "Towards the automated engineering of a synthetic genome". Mol. Biosyst. 5: 733-743.
8. Bernard, L., Duran-Vila, N., Elena, S.F. (2009). "Effect of citrus hosts on the generation, maintenance and evolutionary fate of genetic variability of Cirtrus exocortis viroid (CEVd)". J. Gen. Virol. 90: 2040-2049.
9. Landrain, T.E., Carrera, J., Kirov, B., Rodrigo, G., Jaramillo, A. (2009). "Modular model-based design for heterologous bioproduction in bacteria". Curr. Opin. Biotechnol. 20: 272-279.
10. Elena, S.F., Gómez, G., Daròs, J.A. (2009). "Evolutionary constraints to viroid evolution". Viruses 1: 241-254.
11. Carrera, J., Rodrigo, G., Jaramillo, A. (2009). "Towards the automated engineering of a synthetic genome". Mol. Biosyst. 5: 733-743.
12. Carrera, J., Rodrigo, G., Jaramillo, A., Elena, S.F. (2009). "Reverse-engineering Arabidopsis thaliana transcriptional network under changing environmental conditions". Genome Biol. 10: R96.
13. Martín, S., Elena, S.F. (2009). "Application of game theory to the interaction between plant viruses during mixed infections". J. Gen. Virol. 90: 2815-2820.
14. Gómez, P., Sempere, R.N., Elena, S.F., Aranda, M. (2009). “Mixed infections of Pepino mosaic virus strains modulate the evolutionary dynamics of this emergent virus”. J. Virol. 83: 12378-12387.
15. Sardanyés, J., Solé, R.V., Elena, S.F. (2009). "Replication mode and landscape topology affect differentially RNA virus mutational load and robustness". J. Virol. 83: 12579-12589.
16. Duarte, J., Januário, C., Martins, N., Sardanyés, J. (2009). "Chaos and crises in a model for cooperative hunting: a symbolic dynamics approach". Chaos 19: 043102.
17. Torres-Barceló, C., Daròs, J.A., Elena, S.F. (2010). "HC-Pro hypo- and hypersuppressor mutants: differences in viral siRNA accumulation in vivo and siRNA binding activity in vitro". Arch. Virol. 155: 251-254.
18. Torres-Barceló, C., Daròs, J.A., Elena, S.F. (2010). "Compensatory molecular evolution of HC-Pro, and RNA-silencing suppressor from a plant RNA virus". Mol. Biol. Evol. 27: 543-551.
19. Sardanyés, J., Fontich, E. (2010). "On the metapopulation dynamics of autocatalysis: extinction transients related to ghosts". Int. J. Bif. Chaos. 20: 1261-1268.
20. Elena, S.F., Froissart, R. (2010). "Preface: New experimental and theoretical approaches towards the understanding of the emergence of viral infections". Phil Trans. R. Soc. B. 365: 1867-1869.
21. Lalic, J., Agudelo-Romero, P., Carrasco, P., Elena, S.F. (2010). "Adaptation of Tobacco etch potyvirus to a susceptible ecotype of Arabidopsis thaliana capacitates it for systemic infection of other resistant ecotypes". Phil Trans. R. Soc. B. 365: 1997-2008.
22. Rodrigo, G., Carrera, J., Elena, S.F., Jaramillo, A. (2010). "Robust dynamical pattern formation from a multifunctional minimal genetic circuit". BMC Syst. Biol. 4: 48.
23. Rodrigo, G., Carrera, J., Elena, S.F. (2010). "Network design meets in silico evolutionary biology". Biochimie 92: 746-752.
24. Sardanyés, J., Elena, S.F. (2010). "Error threshold in RNA quasispecies models with complementation". J. Theor. Biol. 265: 278-286.
25. Elena, S.F., Solé, R.V., Sardanyés, J. (2010). "Simple genomes, complex interactions: epistasis in RNA virus". Chaos 20: 026106.
26. Elena, S.F. (2010). "Evolutionary and systems biology of plant RNA virus emergence". Phytopathology 100: s149.
27. Sardanyés, J., Duarte, J., Januário, C., Martins, N. (2010). "Quantifying chaos for ecological stoichiometry". Chaos 20: 0331025.
28. Tromas, N., Elena, S.F. (2010). "The rate and spectrum of spontaneous mutations in a plant RNA virus". Genetics 185: 983-989.
29. Elena, S.F. (2010). "Evolución viral: desentrañando los papeles de la mutación, la selección y el azar". Pp. 27-38 in Encuentros con la Ciencia (eds. E. Viguera, A. Grande-Pérez y J. Lozano). Servicio de Publicaciones de la Universidad de Málaga.
30. Amorós-Moya, D., Bedhomme, S., Hermann, M., Bravo, I. (2010). "Evolution in regulatory regions rapidly compensates the cost of nonoptimal codon usage". Mol. Biol. Evol. 27: 2141-51.
31. Dieu, B.T., Zwart, M.P., Vlak, J.M. (2010). "Can VNTRs be used to study genetic variation within white spot syndrome virus isolates?". J. Fish Dis. 33: 689-693.
32. Abbott, J.K., Bedhomme, S., Chippindale, A.K. (2010). "Sexual conflict in wing size and shape in Drosophila melanogaster". J. Evol. Biol. 23: 1989-1997.
33. Zwart, M.P., Dieu, B.T.M., Hemerik, L., Vlak, J.M. (2010). "Evolutionary trajectory of white spot syndrome virus (WSSV) genome shrinkage during spread in Asia". PLoS ONE 5: e13400.
34. Sardanyés, J. (2010). "Estudiant els virus d’RNA: equacions dins el tub d’assaig?". Omnis Cellula 25: 10-15.
35. Elena, S.F. (2011). "Evolutionary constraints on emergence of plant RNA viruses". Chap. 14, pp. 283-300 in Recent Advances in Plant Virology (eds. C. Caranta, M.A. Aranda, M. Tepfer y J.J. López-Moya). Caister Academic Press.
36. Rodrigo, G., Carrera, J., Jaramillo, A., Elena, S.F. (2011). "Optimal viral strategies for bypassing RNA silencing". J. R. Soc. Interface 8: 257-268.
37. Castaño, A., Ruiz, L., Elena, S.F., Hernández, C. (2011) "Population differentiation and selective constraints in Pelargonium line pattern virus". Virus Res. 155: 274-282.
38. Elena, S.F., Bedhomme, S., Carrasco, P., Cuevas, J.M., de la Iglesia, F., Lafforgue, G., Lalic, J., Pròsper, À., Tromas, N., Zwart, M.P. (2011). "The evolutionary genetics of emerging plant RNA viruses". Mol. Plant-Microb. Interact. 24: 287-293.
39. Wu, B., Blanchard-Letort, A., Liu, Y., Zhou, G., Wang, X., Elena, S.F. (2011). "Dynamics of molecular evolution and phylogeography of Barley yellow dwarf virus-PAV". PLoS ONE 6: e16896.
40. Rodrigo, G., Elena, S.F. (2011). "Structural discrimination of robustness in transcriptional feedforward loops for pattern formation". PLoS ONE 6: e16904.
41. Hoa, T., Zwart, M.P., Phuong, N.T., Oanh, D.T., de Jong, M., Vlak, J.M. (2011). "Mixed-genotype WSSV infections of shrimp are correlated with low virulence in ponds. J. Gen. Virol. 92: 675-680.
42. Bedhomme, S., Elena, S.F. (2011). "Virus infection suppresses Nicotiana benthamiana adaptive phenotypic plasticity". PLoS ONE 6: e17275.
43. Hoa, T.T.T., Zwart, M.P., Phuong, N.T., Vlak, J.M., de Jong, M.C.M. (2011). “Transmission of white spot syndrome virus in improved-extensive and semi-intensive shrimp production systems: A molecular epidemiology study”. Aquaculture. 313: 7-14.
44. Lafforgue, G., Sardanyés, J., Elena, S.F. (2011). "Differences in accumulation and virulence determine the outcome of competition during Tobacco etch virus coinfection". PLoS ONE 6: e17917.
45. Sardanyés, J. (2011). "Low dimensional homeochaos in coevolving host-parasitoid dimorphic populations: extinction thresholds under local noise". Commun. Nonlin. Sci. Num. Sim. 16:3896-3903.
46. Elena, S.F., Carrera, J., Rodrigo, G. (2011). "A systems biology approach to the evolution of plant-virus interactions". Curr. Op. Plant Biol. 14: 372-377.
47. Martínez, F., Sardanyés, J., Elena, S.F., Daròs, J.A. (2011). "Dynamics of a plant RNA virus intracellular accumulation: stamping machine vs. geometric replication". Genetics 188: 637-646.
48. Acosta-Leal, R., Duffy, S., Xiong, Z., Hammond, R.W., Elena, S.F. (2011). "Advances in plant virus evolution: translating evolutionary insights into better disease management". Phytopathology 101 1136-1148.
49. Zwart, M.P., Daròs, J.A., Elena, S.F. (2011). "One is enough: In vivo effective population size is dose-dependent for a plant RNA virus". PLoS Pathog. 7: e1002122.
50. Carrera, J., Rodrigo, G., Singh, V., Kirov,B., Jaramillo, A. (2011). "Empirical model and in vivo characterization of the bacterial response to synthetic gene expression shows that ribosome allocation limits growth rate". Biotech. J. 6: 773-783.
51. Hasiów-Jaroszewska, B., Czerwoniec, A., Pospieszny, H., Elena, S.F. (2011). "Tridimensional model structure and patterns of molecular evolution of Pepino mosaic virus TGBp3 protein". Virol. J. 8: 318.
52. Van der Werf, W., Hemerik, L., Vlak, J.M., Zwart, M.P. (2011). "Heterogeneous host susceptibility enhances prevalence of mixed-genotype micro-parasite infections". PLoS Comp. Biol. 7: e1002097.
53. Lafforgue, G., Martínez, F., Sardanyés, J., de la Iglesia, F., Niu, Q.W., Lin, S.S., Solé, R.V., Chua, N.H, Daròs, J.A., Elena, S.F. (2011). "Tempo and mode of plant RNA virus escape from RNAi-mediated resistance". J. Virol. 85: 9686-9695.
54. Rodrigo, G., Jaramillo, A., Blázquez, M.A. (2011). “Integral control of plant gravitropism through the interplay of hormone signaling and gene regulation”. Biophys. J. 101: 757-763.
55. Sardanyés, J., Elena, S.F. (2011). "Quasispecies spatial models for RNA viruses with different replication modes and infection strategies". PLoS ONE. 6: e24884.
56. De Visser, J.A.G.M., Cooper, T.F., Elena, S.F. (2011). “The causes of epistasis”. Proc. R. Soc. B 278: 3617-3624.
57. Zhang, X., Ryu, S.H., Xu, Y., Elbaz, T., Zekri, A.R.N., Abdelaziz, A.O., Abdel-Hamid, M., Thiers, V., Elena, S.F., Fan, X. y Di Bisceglie, A.M. (2011). "The Core/E1 domain of Hepatitis C virus genotype 4a in Egypt does not contain viral mutations or strains specific for hepatocellular carcinoma". J. Clin. Virol. 52: 333-338.
58. Lalic, J., Cuevas, J.M., Elena, S.F. (2011). "Effect of host species on the distribution of mutational fitness effects for an RNA virus". PLoS Genet. 7: e1002378.
59. Jiang, P.P., Bedhomme, S., Prasad, N.G, Chippindale, A. (2011) “Sperm competition and mate harm unresponsive to male-limited selected in Drosophila: an evolving genetic architecture under domestication”. Evolution 65: 2448-2460.
60. Bedhomme, S., Chippindale, A.K., Prasad, N.G., Delcourt, M., Abbott, J.K., Mallet, M.A., Rundle, H.D. (2011). “Male-limited evolution suggests no extant intralocus sexual conflict over the sexually dimorphic cuticular hydrocarbons of Drosophila melanogaster”. J. Genet. 90: 443-452.
61. Sardanyés, J., Duarte, J., Januário, C., Martins, N. (2012). “Topological entropy of catalytic sets: hypercycles revisited”. Commun. Nonlin. Sci. Num. Sim. 17: 795-803.
62. Duarte, J., Januário, C., Martins, N., Sardanyés, J. (2012). “Symbolic dynamics and control in chaotic systems”. Chap. 1 in Advanced Topics in Chaos Theory and Dynamics, (ed. E. Zeraoulia). Science Publishers. Pp. 1-41.
63. Duarte, J., Januário, C., Martins, N., Sardanyés, J. (2012). "Scaling law in saddle-node bifurcations for one dimensional maps: a complex variable approach". Nonlin. Dynamics 67: 541-547.
64. Gallet, R., Cooper, T.F., Elena, S.F., Lenormand, T. (2012). "Measuring selection coefficients below 10^-3: method, questions and prospects". Genetics 190: 175-186.
65. Macía, J., Solé, R.V., Elena, S.F. (2012). "The causes of epistasis in genetic networks". Evolution 66: 586-596.
66. Sardanyés, J., Martínez, F., Daròs, J.A., Elena, S.F. (2012). "Dynamics of alternative modes of RNA replication for positive-sense RNA viruses". J. R. Soc. Interface 9: 768-776.
67. De la Iglesia, F., Martínez, F., Hillung, J., Cuevas, J.M., Gerrish, P.J., Daròs, J.A., Elena, S.F. (2012). "Luria-Delbrück estimation of Turnip mosaic virus mutation rate in vivo. J. Virol. 86: 3386-3388.
68. Duarte, J., Januário, C., Martins, N., Sardanyés, J. (2012). “On chaos, transient chaos and ghost in single populations models with Allee effects”. Nonlin. Anal. 13: 1647-1661.
69. Hillung, J., Ruiz-López, E., Bellón-Echeverría, I., Clemente-Casares, P., Más, A. (2012). “Characterization of the interaction between Hepatitis C virus NS5B and the human oestrogen receptor alpha”. J. Gen. Virol. 93: 780-785.
70. Bedhomme, S., Lafforgue, G., Elena, S.F. (2012). “Multihost experimental evolution of a plant RNA virus reveals local adaptation and host specific mutations”. Mol. Biol. Evol. 29: 1481-1492.
71. Lalic, J., Elena, S.F. (2012). "Magnitude and sign epistasis among deleterious mutations in a positive-sense plant RNA virus". Heredity 109: 71-77.
72. Carrera, J., Fernández del Carmen, A., Fernández-Muñoz, R., Rambla, J.L., Pons, C., Jaramillo, A., Elena, S.F. y Granell, A. (2012). “Fine-tuning tomato agronomic properties by computational genome redesign”. PLoS Comput. Biol. 8: e1002528.
73. Sardanyés, J., Duarte, J., Januário, C., y Martins, N. (2012). “Controlling delayed transitions with applications to prevent single species extinctions”. Adv. Diff. Eq. Contl. Proc. 10: 29-41.
74. Rodrigo, G., Fares, M.A. (2012). "Describing the structural robustness landscape of bacterial small RNAs". BMC Evol. Biol. 12: 52.
75. Cuevas, J.M., Delaunay, A., Visser, J.C., Bellstedt, D.U., Jacquot, E. y Elena, S.F. (2012). "Phylogeography and molecular evolution of Potato virus Y". PLoS ONE 7: e37853.
76. Martínez, F., Lafforgue, G., Morelli, M.J., González-Candelas, F., Chua, N.H., Daròs, J.A., Elena, S.F. (2012). "Ultra-deep sequencing analysis of population dynamics of virus escape mutants in RNAi-mediated resistant plants". Mol. Biol. Evol. 29: 3297-3307.
77. Hoa, T.T.T., Zwart, M.P., Phuong, N.T., Oanh, D.T.H., de Jong, M.C.M., Vlak, J.M. (2012). “Indel-II region deletion sizes in the White spot syndrome virus genome correlate with shrimp disease outbreaks in southern Vietnam”. Dis. Aquat. Org. 99: 153-162.
78. Gómez, P., Sempere, R.N., Aranda, M.A. y Elena, S.F. (2012). “Phylodynamics of Pepino mosaic virus in Spain”. Eur. J. Plant Pathol. 134: 445-449.
79. Hillung, J., Cuevas, J.M., Elena, S.F. (2012). "Transcript profiling of different Arabidopsis thaliana ecotypes in response to Tobacco etch potyvirus infection". Front. Microbiol. 3: 229.
80. Rodrigo, G., Carrera, J., Ruiz-Ferrer, V, del Toro, F.J., Llave, C., Voinnet, O., Elena, S.F. (2012). “A meta-analysis reveals the commonalities and differences in Arabidopsis thaliana response to different viral pathogens”. PLoS ONE 7: e40526.
81. Lalic, J., Elena, S.F. (2012). "Epistasis between mutations is host-dependent for an RNA virus". Biol. Lett. 9: 20120396
82. Elena, S.F. (2012). “RNA virus genetic robustness: possible causes and some consequences”. Curr. Opin. Virol. 2: 525-530.
83. Hoa, T.T.T., Zwart, M.P., Phuong, N.T., de Jong, M.C.M., Vlak, J.M. (2012). "Low numbers of repeat units in variable number of tandem repeats (VNTR) regions of White syndrome virus are correlated with disease outbreak". J. Fish Dis. 35: 817-826.
84. Cuevas, J.M., Delaunay, A., Rupar, M., Jacquot, E., Elena, S.F. (2012). "Molecular evolution and phylogeography of Potato virus Y based on the CP gene". J. Gen. Virol. 93: 2496-2501.
85. Carrera, J., Elena, S.F., Jaramillo, A. (2012) “Computational design of genomic transcriptional networks with adaptation to varying environments”. Proc. Natl. Acad. Sci. USA 109: 15277-15282.
86. Rodrigo, G., Landrain, T.E., Jaramillo, A. (2012). "De novo automated design of small RNA circuits for engineering synthetic riboregulation in living cells". Proc. Natl. Acad. Sci. USA 109: 15271-15276.
87. Zwart, M.P., Daròs, J.A., Elena, S.F. (2012). “Effect of Potyvirus effective population size in inoculated leaves on viral accumulation and the onset of symptoms”. J. Virol. 86: 9737-9747.
88. Rodrigo, G., Carrera, J., Landrain, T.E., Jaramillo, A. (2012). "Perspectives on the automatic design of regulatory systems for synthetic biology". FEBS Lett. 586: 2037-2042.
89. Elena, S.F., Rodrigo, G. (2012). "Towards an integrated molecular model of plant-virus interactions". Curr. Opin. Virol. 2: 713-718.
90. Lafforgue, G., Tromas, N., Elena, S.F., Zwart, M.P. (2012). "Dynamics of potyvirus systemic infection establishment: independent yet cumulative action of primary infection sites”. J. Virol. 86: 12912-12922.
91. Carrera, J., Elena, S.F. (2012). "Computational design of host transcription-factors sets whose misregulation mimics the transcriptomic effect of viral infections". Sci. Rep. 2: 1002.
92. Rodrigo, G., Elena, S.F. (2013). "MicroRNA precursors are not structurally robust but plastic". Genome Biol. Evol. 5: 181-186.
93. Bedhomme, S., Lafforgue, G., Elena, S.F. (2013). "Genotypic but not phenotypic historical contingency revealed by viral experimental evolution". BMC Evol. Biol. 13: 46.
94. Martínez, F., Elena, S.F., Daròs, J.A. (2013) “Fate of artificial microRNA-mediated resistance to plant viruses in mixed infections”. Phytopathology In press.
95. Zwart, M.P., Pijlman, G.P., Sardanyés, J., Duarte, J., Januário, C., Elena S.F. (2013) “Complex dynamics of defective interfering baculoviruses during serial passage in insect cells". J. Biol. Phys. 39: 327-342.
96. Zwart, M.P., Tromas, N., Elena, S.F. (2013) “Model-selection-based approach for calculating cellular multiplicity of infection during virus colonization of multi-cellular hosts”. PLoS ONE 8: e64657.
97. Lafforgue, G., Martínez, F., Niu, Q.W., Chua, N.H., Daròs, J.A., Elena, S.F. (2013) “Improving the effectiveness of amiRNA-mediated resistance against Turnip mosaic virus by combining two amiRNAs or by targeting highly conserved viral genomic regions”. J. Virol. In press.
98. Lalic, J., Elena, S.F. (2013) “Plant RNA virus fitness predictability: contribution of genetic and environmental factors”. Plant Pathol. In press.
99. Davino, S., Willemsen, A., Panno, S., Davino, M., Catara, A., Elena, S.F., Rubio, L. (2013) “Emergence and phylodynamics of Citrus tristeza virus in Sicily, Italy”. PLoS ONE In press.
100. Kassem, M., Juárez, M., Gómez, P., Mengual, C.M., Sempere, R.N., Plaza, M., Elena, S.F., Moreno, A., Fereres, A., Aranda, M.A. (2013) "Genetic diversity and potential vectors and reservoirs of Cucurbit aphid-borne yellows virus in southeastern Spain". Phytopathology In press.