CURRICULUM VITAE:

Family Name: Elena Fito Given Name: Santiago F.

Spain Passport Number: AAB541567

Date and Place of Birth: 1967 April 17th, in València (Spain)

Profession: Biologist

Professional Address: Instituto de Biología Integrativa de Sistemas, CSIC-UV. Parc Cientific UV, Catedrático

Agustín Escardino 9, Paterna, 46980 València, Spain Phone: +34 963 544 779

E-mail: santiago.elena@uv.es

ORCID: 0000-0001-8249-5593, Publons/Research ID: A-4191-2011, Scopus ID: 7006364449

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1.- ACADEMIC FORMATION:

1. BSc in Biology, Universitat de València. 1985-1990.

2. MSc in Biochemistry. Dissertation thesis titled "Phylogenetic analysis of viroids and viroidlike RNA satellites. Study of its variability". Universitat de València. 1990.

3. Postgraduate Course in "Networks and databases in Molecular Biology". Universitat de València. 1992.

4. PhD in Molecular and Evolutionary Genetics. Dissertation thesis titled “Evolution of biological fitness in experimental populations of vesicular stomatitis virus”. Universitat de València. 1991-1995.

2.- PROFESSIONAL EXPERIENCE

1. 1991 System Manager, Bioinformatics Service, Universitat de València

2. October 1st, 1991 to September 30th, 1995. PhD Student Fellow, Department of Genetics, Universitat de València

3. June 1st to August 31st, 1994. Visiting scientist, Department of Biology, University of California San Diego.

4. October 1st, 1995 to September 30th, 1997. Postdoctoral Fellow, Center for Microbial Ecology, Michigan State University.

5. October 1st to December 10th, 1997. Associate Researcher, Center for Microbial Ecology, Michigan State University.

6. October 17th, 1997 to September 3rd, 2001. Assistant Professor of Genetics and Evolution, Department of Genetics, Universitat de València.

7. September 3rd, 2001 to June 31st, 2002. Associate Professor of Population Genetics, Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València. Leave of absence.

8. July 1st, 2002 to May 1st, 2006. Senior Scientist, Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas.

9. July 8th, 2002 to October 8th, 2002. Visiting Professor, Department of Microbiology and Molecular Genetics, Michigan State University.

10. Since May 2nd, 2006. Research Professor, Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas.

11. Since June 1st, 2008. External Professor, Santa Fe Institute, Santa Fe (NM), USA.

12. April 1st to September 30th, 2016. Visiting professor, Division of Biological Sciences, University of California San Diego.

13. July 1st, 2018 to June 31st, 2022. Adjunct Profesor. Institut of Plant Protection, Chinese Academy of Agricultural Sciences.

14. January 27th to February 7th, 2020. Visiting professor, Departamento de Biologia Celular, Universidade de Brasília. Brasília DF, Brazil.

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3.- PUBLICATIONS:

Hirsch’s h index: 64 (as in November 15th, 2019 in Google Scholar)

1. Rodríguez-Cerezo, E., Elena, S.F., Moya, A. and García-Arenal, F. (1991) High genetic stability in natural populations of the plant RNA virus U5-TMV. J. Mol. Evol. 32: 328-332.

2. Elena, S.F., Dopazo, J., Diener, T.O., Flores, R. and Moya, A. (1991) Phylogeny of viroids, viroid-like satellite RNAs ant the viroid-like domain of Human Hepatitis Delta virus" Proc. Natl. Acad. Sci. USA 88: 5631-5634.

3. Elena, S.F. and Moya, A. (1991) Some evolutionary parameters of viroids and viroidlike satellite RNAs. Rev. Cièn. 8: 9-15.

4. Elena, S.F., González-Candelas, F. and Moya, A. (1992) Does the VP1 gene of Foot-and-Mouth Disease Virus behave as a molecular clock?. J. Mol. Evol. 35: 223-229.

5. Hernández, C., Elena, S.F., Moya, A. and Flores, R. (1992) Pear blister canker viroid is a member of the apple scar skin subgroup (apscaviroids) and has also sequence homologies with viroids from other subgroups. J. Gen. Virol. 73: 2503-2507.

6. Quinones, S., Bernal, D., García-Sogo, M., Elena, S.F. and Saus, J. (1992) Exon/intron structure of the human a3(IV) gene encompassing the Goodpasture antigen (a3(IV)NC1): Identification of a potentially antigenic region at the triple helix/NC1 domain junction. J. Biol. Chem. 267: 19780-19784. A correction in J. Biol. Chem. 269: 17358 (1994).

7. Hernández, C., Daròs, J.A., Elena, S.F., Moya, A. and Flores, R. (1992) The strands of both polarities of a circular RNA from carnation self-cleave in vitro through alternative double- and single- hammerhead structures. Nucl. Acids Res. 20: 6323-6329.

8. Clarke, D.K., Duarte, E.A., Moya, A., Elena, S.F., Domingo, E., and Holland, J.J. (1993) Genetic bottlenecks and population passages cause profound fitness differences in RNA viruses. J. Virol. 67: 222-228.

9. Duarte, E. A., Clarke, D.K., Moya, A., Elena, S.F., Domingo, E. and Holland, J.J. (1993) Many trillionfold amplification of single RNA virus particles fails to overcome the Muller's ratchet effect. J. Virol. 67: 3620-3623.

10. Elena, S.F., Marcos, J.F., Dopazo, J., Flores, R. and Moya, A. (1994) The viroid sequences showed intramolecular correlataion and the hability to form pseudoknots and tetraloops. In Biología Computacional, A. Moya (ed.), pp: 163-175. Servei de Publicacions, Universitat de València. ISBN 8437013208.

11. Clarke, D.K., Duarte, E.A., Elena, S.F., Moya, A., Domingo, E. and Holland, J.J. (1994) The Red Queen reigns in the kingdom of RNA viruses. Proc. Natl. Acad. Sci. USA 91: 4821-4824.

12. Duarte, E.A., Novella, I.S., Ledesma, S., Clarke, D.K., Moya, A., Elena, S.F., Domingo, E. and Holland, J.J. (1994) The subclonal components of consensus fitness in an RNA virus clone. J. Virol. 68: 4295-4301.

13. Duarte, E.A., Novella, I.S., Weaver, S.C., Domingo, E., Wain-Hobson, S., Clarke, D.K., Moya, A., Elena, S.F., de la Torre, J.C. and Holland, J.J. (1994) RNA virus quasispecies: significance for viral disease and epidemiology. Infect. Agents Dis. 3: 201-214.

14. Elena, S.F., Flores, R. and Moya A. (1994) Phylogenetic evidence supports the concept that viroid and viroidlike satellite RNAs are relics of the RNA world. Orig. Life Evol. Biosph. 24: 218-219.

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15. Novella, I.S., Elena, S.F., Moya, A., Domingo, E. and Holland, J.J. (1995) Size of genetic bottleneck leading to virus fitness loss is determined by mean initial population fitness. J. Virol. 69: 2869-2872.

16. Novella, I.S., Duarte, E.A., Elena, S.F., Moya, A., Domingo, E. and Holland, J.J. (1995) Exponential increases of RNA virus fitness during repeated transmission. Proc. Natl. Acad. Sci. USA 92: 5841-5844.

17. González-Candelas, F., Elena, S.F. and Moya, A. (1995) Approximate variance of nucleotide divergence between two sequences when restiction fragment data are available. Genetics 140: 1443-1446.

18. Novella, I.S., Clarke, D.K., Quer, J., Duarte, E.A., Lee, C.H., Weaver, S.C., Elena, S.F., Moya, A., Domingo, E. and Holland, J.J. (1995) Extreme fitness differences in mammalian and insect hosts after continuous replication of vesicular stomatitis virus in sandfly cells. J. Virol. 69: 6805-6809.

19. Elena, S.F., González-Candelas, F., Novella, I.S., Duarte, E.A., Clarke, D.K., Domingo, E., Holland, J.J. and Moya, A. (1996) Evolution of fitness in experimental populations of vesicular stomatitis virus. Genetics 142: 673-679.

20. Elena, S. F. (1996) Evolution of biological fitness in experimental populations of vesicular stomatitis virus. Servei de Publicacions, Universitat de València. ISBN 8437022223.

21. Elena, S.F., Cooper, V.S. and Lenski, R.E. (1996) Punctuated evolution caused by selection of rare beneficial mutations. Science 272: 1802-1804.

22. Domingo, E., Escarmís, C., Sevilla, N., Moya, A., Elena, S.F., Quer, J., Novella, I.S. and Holland, J.J. (1996) Basic concepts in RNA virus evolution. FASEB J.10: 859-864.

23. Novella, I.S., Celnis, M. Elena, S.F., Kohn, J., Moya, A., Domingo, E. and Holland, J.J. (1996) Large population passages of vesicular stomatitis virus in interferon-treated cells select variants of only limited resistence. J. Virol.70: 6414-6417.

24. Novella, I.S., Elena, S.F., Moya, A., Domingo, E. and Holland, J.J. (1996) Repeated transfer of small RNA virus populations leading to balanced fitness with infrequent stochastic drift. Mol. Gen. Genet. 252: 733-738.

25. Elena, S.F., Cooper, V.S. and Lenski, R.E. (1996) Mechanisms of punctuated evolution-Reply. Science 274: 1749-1750.

26. Elena, S.F., Moya, A. and González-Candelas, F. (1996) About the simulation of Molecular Evolution processes: considerations about the derivation and checking of a nucleotide divergence variance estimator when restriction fragment data ara available. Qüestiió 20: 327-344.

27. Elena, S.F., Miralles, R. and Moya, A. (1997) Frequency-dependent selection in a mammalian RNA virus. Evolution 51: 984-987.

28. Miralles, R., Moya, A. and Elena, S.F. (1997) Is group selection a factor modulating the virulence of RNA viruses?. Genet. Res., Camb. 68. 165-172.

29. Elena, S.F. and Lenski, R.E. (1997) Long-term experimental evolution in Escherichia coli. VII. mechanisms maintaining the genetic variability within populations. Evolution 51: 1058-1067.

30. Elena, S.F. and Lenski, R.E. (1997) Test of synergistic interactions between deleterious mutations in bacteria. Nature 390: 395-398.

31. Elena, S.F., Dávila, M., Novella, I.S., Holland, J.J., Domingo, E. and Moya, A. (1998) Evolutionary dynamics of fitness recovery from the debilitating effects of Muller’s ratchet. Evolution 52: 309-314.

32. Elena, S.F., Ekunwe, L., Hajeela, N., Oden, S.A. and Lenski, R.E. (1998) Distribution of fitness effects caused by random insertion mutations in Escherichia coli. Genetica 102-103: 359-367. Reedited in

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Contemporary Issues in Genetics and Evolution. (Eds. R.C. Woodruff and J.N. Thomson, Jr.). Kluwer Academic Publishers.

33. Miralles, R., Moya, A. and Elena, S.F. (1999) Effect of population patchiness and migration rates on the adaptation and divergence of vesicular stomatitis virus quasispecies populations. J. Gen. Virol. 80: 2051-2059.

34. Miralles, R., Gerrish, P.J., Moya, A. and Elena, S. F. (1999) Clonal interference and the evolution of RNA virus. Science 285: 1745-1747.

35. Elena, S.F. and Moya, A. (1999) Rate of deleterious mutation and the distribution of its effects on fitness in vesicular stomatitis virus. J. Evol. Biol. 12: 1078-1088.

36. Elena, S.F. (1999) Little evidence for synergism among deleterious mutations in a non-segmented RNA virus. J. Mol. Evol. 49: 703-707.

37. Elena, S.F., Miralles, R., Cuevas, J.M., Turner, P.E. and Moya, A. (2000) The two faces of mutation: extinction and adaptation in RNA viruses. IUBMB Life. 49: 5-9.

38. Miralles, R., Moya, A. and Elena, S.F. (2000) Diminishing returns of population size in the rate of RNA virus adaptation. J. Virol. 74: 3566-3571.

39. de la Peña, M., Elena, S.F. and Moya, A. (2000) Effect of deleterious mutation-accumulation on the fitness of RNA bacteriophage MS2. Evolution 54: 686-691.

40. Moya, A., Elena, S.F., Bracho, M.A., Miralles, R. and Barrio, E. (2000) The evolution of RNA viruses: Population Genetics view. Proc. Natl. Acad. Sci. USA. 97: 6967-6973. Reedited in Variation and Evolution in Plants and Microorganisms. (Eds. F.J. Ayala, W.M. Fitch and M.T. Clegg). National Academy of Sciences Press.

41. Turner, P.E. and Elena, S.F. (2000) Cost of host radiation in an RNA virus. Genetics. 156: 1465-1470.

42. Elena, S.F., Dopazo, J., de la Peña, M., Flores, R., Diener, T.O. and Moya, A. (2001) Phylogenetic analysis of viroid and viroid-like satellite RNAs from plants: a reassessment. J. Mol. Evol. 53: 155-159.

43. Elena, S.F., Sanjuán, R., Bordería, A.V. and Turner, P.E. (2001) Transmisión bottlenecks and the evolution of fitness in rapidly evolving RNA viruses. Infect. Genet. Evol. 1: 41-48.

44. Miralles, R., Ferrer, R., Solé, R.V., Moya, A. and Elena, S.F. (2001) Multiple infection dynamics has pronounced effects on the fitness of RNA viruses. J. Evol. Biol. 14: 654-662.

45. Elena, S.F. and Lenski, R.E. (2001) Epistasis between new mutations and genetic background, and a test of genetic canalisation. Evolution 55: 1746-1752.

46. Elena, S.F. (2001) Evolutionary consequences and costs of plasmid-borne resistance to antibiotics. Chap. 11 in Antibiotic Development and Resistance, (eds. D. Hughes y D. Andersson). Harwood Academic Publishers. Pp. 163-180.

47. Elena, S.F. (2001) Evolutionary history conditions the timing of transmission in vesicular stomatitis virus. Infect. Genet. Evol. 1: 151-159.

48. Fares, M.A., Ruiz-González, M.X., Moya, A., Elena, S.F. and Barrio, E. (2002) Endosymbiotic bacteria: GroEL buffers against deleterious mutations”. Nature 417: 398.

49. Elena, S.F., Sanjuán, R., Bordería, A.V. and Turner, P.E. (2002) Differential effects of vertical and horizontal transmission in the fitness of an RNA virus: A reanalysis. Infect. Genet. Evol. 1: 307-309

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50. Elena, S.F. (2002) Environmental restrictions to viral adaptation: an experimental approach. Antoine van Leewenhoek 81: 135-142.

51. Elena, S.F. (2002) Evolution and adaptation of RNA viruses. Investigación y Ciencia (spanish edition of Scientific American) 313: 46-55. Reedited in Temas Investigación y Ciencia. Virus y Bacterias 48: 39-47 (2007).

52. Cuevas, J.M., Elena, S.F. and Moya, A. (2002) Molecular basis of adaptive convergence in experimental populations of RNA viruses. Genetics 162: 533-542.

53. Elena, S.F. (2002) Evolution in experimental populations of RNA viruses. Chap. 26 in Evolución: la base de la Biología, (ed. M. Soler). Proyecto Sur Ediciones. Pp. 439-451.

54. Bordería, A.V. and Elena, S.F. (2002) r and K selection in experimental populations of vesicular stomatitis virus and the adaptation to the multiplicity of infection. Infect. Genet. Evol. 2: 137-143.

55. Fares, M.A., Elena, S.F., Ortiz, J., Moya, A. and Barrio, E. (2002) A sliding window-based method to detect selective constraints in protein-coding genes and its application to RNA viruses. J. Mol. Evol. 55: 509-521.

56. Saldaña, J., Elena, S.F. and Solé, R.V. (2003) Coinfection and superinfection in RNA virus populations: a selection-mutation model. Math. Biosci. 183: 135-160.

57. Cuevas, J.M., Moya, A. and Elena, S.F. (2003) Evolution of RNA virus in spatially-structured heterogeneous environments. J. Evol. Biol. 16: 456-466.

58. Elena, S.F., Codoñer, F.M. and Sanjuán, R. (2003) Intra-clonal variation in RNA viruses: generation, maintenance and consequences. Biol. J. Linn. Soc. 79: 17-26.

59. Elena, S.F. and Lenski, R.E. (2003) Evolution experiments with micro-organisms: dynamics and genetic bases of adaptation. Nat. Rev. Genet. 4: 457-469.

60. Elena, S.F., Codoñer, F.M., Cuevas, J.M. and Sanjuán, R. (2003) Adaptive dynamics during experimental evolution of RNA viruses. Biology Int. 44: 75-77.

61. Elena, S.F. and de Visser, J.A.G.M. (2003) Environmental stress and the effects of mutation. J. Biol. 2: 12.

62. de Visser, J.A.G.M., Hermisson, J., Wagner, G.P., Ancel-Meyers, L., Bagheri-Chaichian, H., Blanchard, J.L., Chao, L., Cheverud, J.M., Elena, S.F., Fontana, W., Gibson, G., Hansen, T.F., Krakauer, D., Lewontin, R.C., Ofria, C., Rice, S.H., von Dassow, G., Wagner, A. y Whitlock, M.C. (2003) Evolution and detection of genetic robutness. Evolution 57: 1959-1972.

63. Elena, S.F. and Sanjuán, R. (2003) Climb every mountain?. Science 302: 2074-2075.

64. Sanjuán, R., Moya, A. and Elena, S.F. (2004) The distribution of fitness effects caused by single-nucleotide substitutions in an RNA virus. Proc. Natl. Acad. Sci. USA 101: 8396-8401.

65. Sanjuán, R., Codoñer, F.M., Moya, A. and Elena, S.F. (2004) Natural selection and the organ-specific differentiation of HIV-1 V3 hypervariable region. Evolution 58: 1185-1194.

66. Sanjuán, R., Moya, A. and Elena, S. F. (2004) The contribution of epistasis to the architecture of fitness in an RNA virus. Proc. Natl. Acad. Sci. USA 101: 15376-15379.

67. Cuevas, J.M., Sanjuán, R., Moya, A. and Elena, S.F. (2005) Mode of selection and experimental evolution of antiviral drugs resistance in vesicular stomatitis virus. Infect. Genet. Evol. 5: 55-65.

68. Cooper, T. F., Lenski, R. E. and Elena, S. F. (2005) Parasites and mutational load: an experimental test of a pluralistic theory for the evolution of sex. Proc. R. Soc. B. 272: 311-317.

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69. Elena, S.F. and Sanjuán, R. (2005) RNA viruses as complex adaptive systems. Biosystems 81: 31-41.

70. Elena, S.F. and Bracho, M.A. (2005) Origin and evolution of viruses. Mètode 45: 95-104.

71. Sanjuán, R., Cuevas, J.M., Moya, A. and Elena, S.F. (2005) Epistasis and the adaptability of an RNA virus. Genetics 170: 1001-1008.

72. Elena, S.F., and Sanjuán, R. (2005) Adaptive value of high mutation rates in RNA viruses: seaparating causes from consequences. J. Virol. 79: 11555-11558.

73. Codoñer, F.M., Cuevas, J.M., Sánchez-Navarro, J.A., Pallás, V. and Elena, S.F. (2005) Molecular evolution of the plant virus family Bromoviridae based on RNA 3 encoded proteins. J. Mol. Evol. 61: 697-705.

74. Elena, S.F., Whittam, T.S., Winkworth, C.L., Riley, M.A. and Lenski, R.E. (2005) “Genomic divergente of Escherichia coli strains, with evidence for horizontal transfer and variation in mutation rates”. Int. Microbiol. 8: 271-278.

75. Codoñer, F.M., and Elena, S.F. (2006) Evolutionary relationships among members of the Bromoviridae deduced from whole proteome analysis. Arch. Virol. 151: 299-307.

76. Elena, S.F., Carrasco, P., Daròs, J.A. and Sanjuán, R. (2006) Mechanisms of genetic robustness in RNA viruses. EMBO Reports 7: 168-173.

77. Codoñer, F.M., Fares, M.A., and Elena, S.F. (2006) Adaptive covariation between the coat and movement proteins of prunus necrotic ringspot virus. J. Virol. 80: 5833-5840.

78. Daròs, J.A., Elena, S.F., and Flores, R. (2006) Viroids: an Ariadne’s thread into the RNA labyrinth. EMBO Reports 7: 593-598.

79. Sanjuán, S.F., Forment, J., and Elena, S.F. (2006) In silico predicted robustness of viroids RNA secondary structures. I. The effect of single mutations. Mol. Biol. Evol. 23: 1427-1436.

80. Rico, P., Ivars, P., Elena, S.F., and Hernández, C. (2006) Insights into the selective pressures restricting pelargonium flower break virus genome variability: evidences for host adaptation. J. Virol. 80: 8124-8132.

81. Sanjuán, R. and Elena, S.F. (2006) Epistasis correlates to genome complexity. Proc Natl. Acad. Sci. USA 103: 14402-14405. Scored as exceptional (9) by Faculty1000.

82. Sanjuán, R., Forment, J. and Elena, S.F. (2006) In silico predicted robustness of viroids RNA secondary structures. II. Interaction between mutation pairs. Mol. Biol. Evol. 23: 2123-2130.

83. Codoñer, F.M., Daròs, J.A., Solé, R.V. and Elena, S.F. (2006) The fittest versus the flattest: experimental confirmation of the quasispecies effect with subviral pathogens. PLoS Pathog. 2: e136.

84. Carrasco, P., Daròs, J.A., Agudelo-Romero, P. and Elena, S.F. (2007) A real-time RT-PCR assay for quantifying the fitness of tobacco etch virus in competition experiments. J. Virol. Meth. 139: 181-188.

85. de Visser, J.A.G.M. and Elena, S.F. (2007) The evolution of sex: empirical insights into the roles of epistasis and drift. Nat. Rev. Genet. 8: 139-149.

86. Elena, S.F., Wilke, C.O., Ofria, C. and Lenski, R.E. (2007) Effects of population size and mutation rate on the evolution of mutational robustness. Evolution 61: 666-674.

87. Martin, G., Elena, S.F. and Lenormand, T. (2007) Distribution of epistasis in microbes fit predictions from a fitness landscape model. Nat. Genet. 39: 555-560.

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88. Beerenwinkel, N., Pachter, L., Sturmfels, B., Elena, S.F. and Lenski, R.E. (2007) Analysis of epistatic interactions and fitness landscapes using a new geometric approach. BMC Evol. Biol. 7: 60.

89. de la Iglesia, F. and Elena, S.F. (2007) Fitness declines in tobacco etch virus upon serial bottleneck transfers. J. Virol. 81: 4941-4947.

90. Carrasco, P., de la Iglesia, F. and Elena, S.F. (2007) The distribution of fitness and virulence effects caused by single-nucleotide substitutions in tobacco etch virus. J. Virol. 81: 12979-12984. Scored as recommended (3) by Faculty1000.

91. Elena, S.F. and Sanjuán, R. (2007) Virus evolution: insights from an experimental approach. Annu. Rev. Ecol. Syst. Evol. 38: 27-52.

92. Elena, S.F., and Codoñer, F.M. (2007) Bioinformatic tools in phytopathology. Chap. 2 in Herramientas Biotecnológicas en Fitopatología, (eds. V. Pallás, P. Rodríguez-Valenzuela, J.F. Marcos, and C. Escobar) pp: 109-134. Mundi Prensa.

93. Sardanyés, J., Elena, S.F. and Solé, R.V. (2008) Simple quasispecies models for the survival-of-the-flattest effect: the role of space. J. Theor. Biol. 250: 560-568.

94. Herranz, M.C., Al Rwahnih, M., Sánchez-Navarro, J.A., Elena, S.F., Choueiri, E., Myrta, A. and Pallás, V. (2008) Low genetic variability in the coat and movement proteins of American plum line pattern virus from different geographic origins. Arch. Virol. 153: 367-373.

95. Agudelo-Romero, P. and Elena, S.F. (2008) The degree of plant resilience to infection corraltes with virus virulence and host-range. Span. J. Agricult. Res. 6: 160-169.

96. Fiore, N., Fajardo, T.V.M., Prodan, S., Herranz, M.C., Aparicio, F., Montealegre, J., Elena, S.F., Pallás, V. y Sánchez-Navarro, J. (2008) Genetic diversity of the movement and coat protein genes of South American isolates of Prunus necrotic ringspot virus. Arch. Virol. 153: 909-919.

97. Elena, S.F., Agudelo-Romero, P., Carrasco, P., Codoñer, F.M., Martín, S., Torres-Barceló, C. and Sanjuán, R. (2008) Experimental evolution of plant RNA viruses. Heredity 100: 478-483.

98. Duran-Vila, N., Elena, S.F., Daròs, J.A., and Flores, R. (2008) Structure and evolution of viroids. Chap. 2 in Origin and Evolution of Viruses 2nd Edition (eds. E. Domingo, C. Parrish and J.J. Holland) pp: 43-65. Elsevier.

99. Codoñer, F.M., and Elena, S.F. (2008) The promiscuous evolutionary history of the Bromoviridae family. J. Gen. Virol. 89: 1739-1747.

100. Agudelo-Romero, P., Carbonell, P., de la Iglesia, F., Carrera, J., Rodrigo, G., Jaramillo, A., Pérez-Amador, M.A. and Elena, S.F. (2008) Changes in the gene expression profile of Arabidopsis thaliana after infection with Tobacco etch virus. Virol. J. 5: 92.

101. Agudelo-Romero, P., Carbonell, P., Pérez-Amador, M.A., and Elena, S.F. (2008) Virus adaptation by manipulation of host’s gene expression. PLoS ONE 3: e2397.

102. Clune, J., Misevic, D., Ofria, C., Lenski, R.E., Elena, S.F., and Sanjuán, R. (2008) Natural selection fails to optimize mutation rates for long-term adaptation on rugged fitness landscapes. PLoS Comput. Biol. 4: e1000187.

103. Elena, S.F. and Sanjuán, R. (2008) The effect of genetic robustness on evolvability in digital organisms. BMC Evol. Biol. 8: 284.

104. Torres-Barceló, C., Martín, S., Daròs, J.A. and Elena, S.F. (2008) From hypo- to hyper-suppression: Effect of amino acid substitutions on the RNA silencing suppressor activity of Tobacco etch virus HC-Pro. Genetics 180: 1039-1049.

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105. Agudelo-Romero, P., de la Iglesia, F. and Elena, S.F. (2008) The pleiotropic cost of host-specialization in Tobacco etch potyvirus. Infect. Genet. Evol. 8: 806-814.

106. Lin, S.S., Wu, H.W., Elena, S.F., Chen, K.C., Niu, Q.W., Yeh, S.D., Chen, C.C. and Chua, N.M. (2009). Molecular evolution of a viral non-coding sequence under the selective pressure of amiRNA-mediated silencing. PLoS Pathog. 5: e1000312.

107. Gago, S., Elena, S.F., Flores, R. and Sanjuán, R. (2009). Extremely high mutation rate of a hammerhead viroid. Science 323: 1308. Scored as must read (6) by Faculty1000.

108. Elena, S.F., Agudelo-Romero, P, and Lalic, J. (2009) The evolution of viruses in multi-host fitness landscapes. Open Virol. J. 3: 1-6.

109. Sanjuán, R., Agudelo-Romero, P. and Elena, S.F. (2009). Upper-limit mutation rate estimation for a plant RNA virus. Biol. Lett. 5: 394-396.

110. Martín, S., Sambade, A., Rubio, L, Vives, M.C., Moya, P., Guerri, J., Elena, S.F., and Moreno, P. (2009). Contribution of recombination and selection to molecular evolution of Citrus tristeza virus. J. Gen. Virol. 90: 1527-1538.

111. Bernard, L., Duran-Vila, N. and Elena, S.F. (2009). Effect of citrus hosts on the generation, maintenance and evolutionary fate of genetic variability of Citrus exocortis viroid (CEVd). J. Gen. Virol. 90: 2040-2049.

112. Elena, S.F., Gómez, G. and Daròs, J.A. (2009) Evolutionary constraints to viroid evolution. Viruses 1: 241-254.

113. Carrera, J., Rodrigo, G., Jaramillo, A., and Elena, S.F. (2009). Reverse-engineering Arabidopsis thaliana transcriptional network under changing environmental conditions. Genome Biol. 10: R96.

114. Martín, S. and Elena, S.F. (2009) Application of game theory to the interaction between plant viruses during mixed infections. J. Gen. Virol. 90: 2815-2820.

115. Gómez, P., Sempere, R.N., Elena, S.F., and Aranda, M.A. (2009). Mixed infections of Pepino mosaic virus strains modulate the evolutionary dynamics of this emergent virus. J. Virol. 83: 12378-12387.

116. Sardanyés, J., Solé, R.V. and Elena, S.F. (2009). Replication mode and landscape topology affect differentially RNA virus mutational load and robustness. J. Virol. 83: 12579-12589.

117. Torres-Barceló, C., Daròs, J.A. and Elena, S.F. (2010). HC-Pro hypo- and hyperssuppressor mutants: differences in viral siRNA accumulation in vivo and siRNA binding activity in vitro. Arch. Virol. 155: 251-254.

118. Torres-Barceló, C., Daròs, J.A. and Elena, S.F. (2010). Compensatory molecular evolution of HC-Pro, an RNA-silending suppressor from a plant RNA virus”. Mol. Biol. Evol. 27: 543-551.

119. Rodrigo, G., Carrera, J., Elena, S.F. and Jaramillo, A. (2010). Robust dynamical pattern formation from a multifunctional minimal genetic circuit. BMC Syst. Biol. 4: 48.

120. Elena, S.F. and Froissart, R. (2010) Preface: New experimental and theoretical approaches towards the understanding of the emergente of viral infections. Philos. Trans. R. Soc. B 365: 1867-1869.

121. Lalic, J., Agudelo-Romero, P., Carrasco, P. and Elena S.F. (2010). Adaptation of Tobacco etch potyvirus to a susceptible ecotype of Arabidopsis thaliana capacitates it for systemic infection of resistant ecotypes. Philos. Trans. R. Soc. B 365: 1997-2008.

122. Sardanyés, J. and Elena, S.F. (2010). Error threshold in RNA quasispecies models with complementation. J. Theor. Biol. 265: 278-286.

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123. Rodrigo, G., Carrera, J. and Elena, S.F. (2010). Network design meets in silico evolutionary biology. Biochimie 92: 746-752.

124. Elena, S.F., Solé, R.V. and Sardanyés, J. (2010). Simple genomes, complex interactions: epistasis in RNA virus. Chaos 20: 026106.

125. Tromas, N. and Elena, S.F. (2010). The rate and spectrum of spontaneous mutations in a plant RNA virus. Genetics 185: 983-989.

126. Elena, S.F. (2010) “Evolución viral: desentrañando los papeles de la mutación, la selección y el azar”. En Encuentros con la Ciencia II. Del Macrocosmos and Microcosmos (ed. E. Viguera, A. Grande-Pérez & J. Lozano) pp: 27-38. Servicio de Publicaciones Málaga University.

127. Elena, S.F. (2011) Evolutionary constraints on emergence of plant RNA viruses. Chap. 14 in Recent Advances in Plant Virology, (eds. C. Caranta, M.A., Aranda M. Tepfer & J.J. López-Moya) pp: 283-300. Caister Academic Press.

128. Rodrigo, G., Carrera, J., Jaramillo, A. and Elena, S.F. (2011). Optimal viral strategies for bypassing RNA silencing. J. R. Soc. Interface. 8: 257-268.

129. Castaño, A., Ruiz, L., Elena, S.F. and Hernández, C. (2011). Population differentiation and selective constraints in Pelargonium line pattern virus. Virus Res. 155: 274-282.

130. Elena, S.F., Bedhomme, S., Carrasco, P., Cuevas, J.M., de la Iglesia, F., Lafforgue, G., Lalic, J., Pròsper, À., Tromas, N. and Zwart, M.P. (2011). The evolutionary genetics of emerging plant RNA viruses. Mol. Plant-Microb. Interact. 24: 287-293.

131. Wu, B., Blanchard-Letort, A., Liu, Y., Zhou, G., Wang, X. and Elena, S.F. (2011). Dynamics of molecular evolution and phylogeography of Barley yellow dwarf virus-PAV. PLoS ONE 6: e16896.

132. Rodrigo, G. and Elena, S.F. (2011). Structural discrimination of robustness in transcriptional feedforward loops for pattern formation. PLoS ONE 6: 16904.

133. Bedhomme, S. and Elena, S.F. (2011). Virus infections suppresses Nicotiana benthamiana adaptive phenotypic plasticity. PLoS ONE 6: e17275.

134. Lafforgue, G., Sardanyés, J. and Elena, S.F. (2011). Differences in accumulation and virulence determine the outcome of competition during Tobacco etch virus coinfection. PLoS ONE 6: e17917.

135. 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.

136. Zwart, M.P., Daròs, J.A. and Elena, S.F. (2011). One is enough: In vivo effective population size is dose-dependent for a plant RNA virus. PLoS Pathog. 7: e1002122.

137. Martínez, F., Sardanyés, J., Elena, S.F. and Daròs, J.A. (2011). Dynamics of a plant RNA virus intracellular accumulation: stamping machine vs. geometric replication”. Genetics 188: 637-646.

138. Elena, S.F., Carrera, J. and Rodrigo, J. (2011). A systems biology approach to the evolution of plant-virus interactions. Curr. Opin. Plant Biol. 14: 372-377.

139. 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., and Elena, S.F. (2011). Tempo and mode of plant virus escape from RNAi-mediated resistance. J. Virol. 85: 9686-9695.

140. Sardanyés, J. and Elena, S.F. (2011). Quasispecies spatial models for RNA viruses with different replication modes and infection strategies. PLoS ONE 6: e24884.

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141. Acosta-Leal, R., Duffy, S., Xiong, Z., Hammond, R.W. and Elena, S.F. (2011). Advances in plant virus evolution: translating evolutionary insights into better disease management. Phytopathology 101: 1136-1148.

142. 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. and 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.

143. 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.

144. De Visser, J.A.G.M., Cooper, T.F. and Elena, S.F. (2011). The causes of epistasis. Proc. R. Soc. B 278: 3617-3624.

145. Gallet, R., Cooper, T.F., Elena, S.F., and Lenormand, T. (2012). Measuring selection coefficients below 10-

3: method, questions and prospects. Genetics 190: 175-186.

146. Macía, J., Solé, R.V. and Elena, S.F. (2012). The causes of epistasis in genetic networks. Evolution 66: 586-596.

147. De la Iglesia, F., Martínez, F., Hillung, J., Cuevas, J.M., Gerrish, P.J., Daròs, J.A. and Elena, S.F. (2012). Luria-Delbrück estimation of Turnip mosaic virus mutation rate in vivo. J. Virol. 86: 3386-3388.

148. Sardanyés, J., Martínez, F., Daròs, J.A., and Elena, S.F. (2012). Dynamics of alternative modes of RNA replication for positive-sense RNA viruses. J. R. Soc. Interface 9: 768-776.

149. Bedhomme, S., Lafforgue, G., and 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.

150. Cuevas, J.M., Delaunay, A., Visser, J.C., Bellstedt, D.U., Jacquot, E. and Elena, S.F. (2012). Phylogeography and molecular evolution of Potato virus Y. PLoS ONE 7: e7853.

151. Hillung, J., Cuevas, J.M. and Elena, S.F. (2012) Transcription profiling of different Arabidopsis thaliana ecotypes in response to Tobacco etch potyvirus infection. Front. Microbiol. 3: 229.

152. Carrera, J., Fernández del Carmen, A., Fernández-Muñoz, R., Rambla, J.L., Pons, C., Jaramillo, A., Elena, S.F. and Granell, A. (2012). Fine-tuning tomato agronomic properties by computational genome redesign. PLoS Comput. Biol. 8: e1002528.

153. Rodrigo, G., Carrera, J., Ruiz-Ferrer, V, del Toro, F.J., Llave, C., Voinnet, O. and Elena, S.F. (2012). A meta-analysis reveals the commonalities and differences in Arabidopsis thaliana response to different viral pathogens. PLoS ONE 7: e40526.

154. Valverde, S., Solé, R.V. and Elena, S.F. (2012). Evolved modular epistasis in artificial organisms. Chap. 16 in Artificial Life XIII: Proceedings of the 13rd International Conference on the Simulation and Synthesis of Living Systems, (eds. C. Adami, D.M. Bryson, C. Ofria, & R.T. Pennock) pp. 111-115. MIT Press.

155. Lalic, J. and Elena, S.F. (2012). Magnitude and sign epistasis among deleterious mutations in a positive-sense plant RNA virus. Heredity 109: 71-77.

156. Zwart, M.P., Daròs, J.A. and 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.

157. Carrera, J., Elena, S.F. and Jaramillo, A. (2012) “Computational design of genomic transcriptional networks with adaptation to varying environments”. Proc. Natl. Acad. Sci. USA 109: 15277-15282.

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158. Gómez, P., Sempere, R.N., Aranda, M.A. and Elena, S.F. (2012). Phylodynamics of Pepino mosaic virus in Spain. Eur. J. Plant Pathol. 134: 445-449.

159. Cuevas, J.M., Delaunay, A., Rupar, M., Jacquot, E. and Elena, S.F. (2012) Molecular evolution and phylogeography of Potato virus Y based on the CP gene. J. Gen. Virol. 93: 2496-2501.

160. Elena, S.F. (2012). RNA virus genetic robustness: possible causes and some consequences. Curr. Opin. Virol. 2: 525-530.

161. Martínez, F., Lafforgue, G., Morelli, M.J., González-Candelas, F., Chua, N.H., Daròs, J.A. and 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.

162. Lafforgue, G., Tromas, N., Elena, S.F. and Zwart, M.P. (2012) Dynamics of potyvirus systemic infection establishment: independent yet cumulative action of primary infection sites. J. Virol. 86: 12912-12922.

163. Elena, S.F. and Rodrigo, G. (2012) Towards an integrated molecular model of plant-virus interactions. Curr. Opin. Virol. 2: 713-718.

164. Carrera, J. and Elena, S.F. (2012). Computational design of host transcription-factors sets whose misregulation mimics the transcriptomic effect of viral infections. Sci. Rep. 2: 1002.

165. Lalic, J. and Elena, S.F. (2013). Epistasis between mutations is host-dependent for an RNA virus. Biol. Lett. 9: 20120396.

166. Rodrigo, G. and Elena, S.F. (2013) MicroRNA precursors are not structurally robust but plastic. Genome Biol. Evol. 5: 181-186.

167. Bedhomme, S., Lafforgue, G. and Elena, S.F. (2013) Genotypic but not phenotypic historical contingency revealed by viral experimental evolution. BMC Evol. Biol. 13: 46.

168. Zwart, M.P., Pijlman, G.P., Sardanyés, J., Duarte, J., Januário, C. and Elena, S.F. (2013) Complex dynamics of defective interfering baculoviruses during serial passage in insect cells. J. Biol. Phys. 39: 327-342.

169. Zwart, M.P., Tromas, N. and 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.

170. Davino, S., Willemsen, A., Panno, S., Davino, M., Catara, A., Elena, S.F. and Rubio, L. (2013) “Emergence and phylodynamics of Citrus tristeza virus in Sicily, Italy”. PLoS ONE 8: e66700.

171. Lafforgue, G., Martínez, F., Niu, Q.W., Chua, N.H., Daròs, J.A. and Elena, S.F. (2013) “Improving the effectiveness of artificial microRNA (amiRNA)-mediated resistance against Turnip mosaic virus by combining two amiRNAs or by targeting highly conserved viral genomic regions”. J. Virol. 87: 8254-8256.

172. Martínez, F., Elena, S.F. and Daròs, J.A. (2013) “Fate of artificial microRNA-mediated resistance to plant viruses in mixed infections”. Phytopathology 103: 870-876.

173. Sánchez-Navarro, J.A., Zwart, M.P. and Elena, S.F. (2013) “Effects of the number of genome segments on primary and systemic infection for a multipartite plant RNA virus”. J. Virol. 87: 10805-10815.

174. Kassem, M., Juárez, M., Gómez, P., Mengual, C.M., Sempere, R.N., Plaza, M., Elena, S.F., Moreno, A., Fereres, A. and Aranda, M.A. (2013) “Genetic diversity and potential vectrors and reservoirs of Cucurbit aphid-borne yellows virus in southeastern Spain”. Phytopathology 103: 1188-1197.

175. Hillung, J., Elena, S.F. and Cuevas, J.M. (2013) “Intra-specific variability and biological relevance of P3N-PIPO protein length in potyviruses”. BMC Evol. Biol. 13: 249.

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176. Lalic, J. and Elena, S.F. (2013) “Plant RNA virus fitness predictability: contribution of genetic and environmental factors”. Plant Pathol. 62 (Suppl. 1): 10-18.

177. Elena, S.F., Fraile, A. and García-Arenal, F. (2014) “Evolution and emergence of plant viruses”. Adv. Virus Res. 88: 161-191.

178. Zwart, M.P., Willemsen, A., Daròs, J.A. and Elena, S.F. (2014) “Experimental evolution of pseudogenization and gene loss in a plant RNA virus”. Mol. Biol. Evol. 31: 121-134.

179. Hasiów-Jaroszewska, B., Fares, M.A., and Elena, S.F. (2014) “Molecular evolution of viral multifunctional proteins: the case of Potyvirus HC-Pro”. J. Mol. Evol. 78: 75-86.

180. Tromas, N., Zwart, M.P., Poulain, M. and Elena, S.F. (2014) “Estimation of the in vivo recombination rate for a plant RNA virus”. J. Gen. Virol. 95: 724-732.

181. Tromas, N., Zwart, M.P., Lafforgue, G. and Elena, S.F. (2014) “Within-host spatiotemporal dynamics of plant virus infection at the cellular level”. PLoS Genet. 10: e1004186.

182. Tromas, N., Zwart, M.P., Forment, J. and Elena, S.F. (2014) “Shrinkage of genome size in a plant RNA virus upon transfer of an essential gene into the host genome”. Genome Biol. Evol. 6: 538-550.

183. Majer, E., Salvador, Z., Zwart, M.P., Willemsen, A., Elena, S.F. and Daròs, J.A. (2014) “Relocation of the NIb gene in the tobacco etch potyvirus genome”. J. Virol. 88: 4586-4590.

184. Sardanyés, J., Simó, C., Martínez, R., Solé, R.V., Elena, S.F. (2014) “Variability in mutational fitness effects prevents full lethal transitions in large quasispecies populations”. Sci. Rep. 4: 4625.

185. Flores, R., Gago-Zachert, S., Serra, P., Sanjuán, R., Elena, S.F. (2014) “Viroids: survivors from the RNA world?”. Annu. Rev. Microbiol. 68: 395-414.

186. Rodrigo, G., Zwart, M.P., Elena, S.F. (2014) “Onset of virus systemic infection in plants is determined by speed of cell-to-cell movement and number of primary infection foci”. J. R. Soc. Interface 11: 20140555.

187. Elena, S.F., Bernet, G.P., Carrasco, J.L. (2014) “The games plant viruses play”. Curr. Opin. Virol. 8: 62-67.

188. Peña, E.J., Ferriol, I., Sambade, A., Buschmann, H., Niehl, A., Elena, S.F., Rubio, L., Heinlein, M. (2014) “Experimental virus evolution reveals a role of plan microtubule dynamics and TORTIFOLIA1/SPIRAL2 in RNA trafficking”. PLoS ONE. 9: e105364.

189. Hillung, J., Cuevas, J.M., Valverde, S., Elena, S.F. (2014) “Experimental evolution of an emerging plant virus in host genotypes that differ in their susceptibility to infection”. Evolution 68: 2467-2480.

190. Bergua, M., Zwart, M.P., El-Mohtar, C., Shilts, T., Elena, S.F., Folimonova, S.Y. (2014) “A viral protein mediates superinfection exclusion at the whole organism level while is not required for exclusion at the cellular level”. J. Virol. 88: 11327-11338.

191. Bosque, G., Folch-Fortuny, A., Picó, J., Ferrer, A., Elena, S.F. (2014) “Topology analysis and visualization of Potyvirus protein-protein interaction network”. BMC Syst. Biol. 8: 129.

192. Elena, S.F. (2014) “Tracking the population dynamics of plant virus escape mutants”. Ch. 17 in Trends in Mathematics: Research Perspectives CRM Barcelona Workshop on Virus Dynamics and Evolution, (eds. Corbera, M., Cors, J.M., Llibre, J., & Korobeinikov, A.) pp. 101-105. Springer-Birkhäusen Basel.

193. Mushegian, A.R., Elena, S.F. (2015) “Evolution of plant virus movement proteins from the 30K superfamily and of their homologs integrated in plant genomes”. Virology 476: 304-315. (Editor’s choice for Virology Highlights Blog http://www.virologyhighlights.com/?p=499)

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194. Zwart, M.P., Elena, S.F. (2015) “Testing the independent action hypothesis of plant pathogen mode of action: a simple and powerful new approach”. Phytopathology 105: 18-25.

195. Bedhomme, S., Hillung, J., Elena, S.F. (2015) “Emerging viruses: why they are not jacks of all trades?”. Curr. Opin. Virol. 10: 1-6.

196. Wu, B., Shang, X., Schubert, J., Habekuss, A., Elena, S.F., Wang, X. (2015) “Global-scale computational analysis of genomic sequences reveals the recombination pattern and coevolution dynamics of cereal-infecting geminiviruses”. Sci. Rep. 5: 8153.

197. Minicka, J., Rymelska, N., Elena, S.F., Czerwoniec, A., Hasiów-Jaroszewska, B. (2015) “Molecular evolution of Pepino mosaic virus during long-term passaging in different hosts and its impact on virus virulence”. Ann. Appl. Biol. 166: 389-401.

198. Cuevas, J.M., Willemsen, A., Hillung, J., Zwart, M.P., Elena, S.F. (2015) “Temporal dynamics of intra-host molecular evolution for a plant RNA virus”. Mol. Biol. Evol. 32: 1132-1147.

199. Janzac, B., Willemsen, A., Cuevas, J.M., Glais, L., Tribodet, M., Verrier, J.L., Elena, S.F., Jacquot, E. (2015) “Brazilian Potato virus Y isolates identified as members of a new clade facilitate the reconstruction of evolutionary traits within this species”. Plant Pathol. 64: 799-807.

200. Elena, S.F., Pybus, O.G. (2015). “A home for virology, ecology, epidemiology, and evolutionary biology”. Virus Evol. 1: vev001.

201. Hillung, J., Cuevas, J.M., Elena, S.F. (2015) “Evaluating the within-host fitness effects of mutations fixed during virus adaptation to different ecotypes of a new host”. Philos. Trans. R. Soc. B 370: 20140292.

202. Frígols, B., Quiles-Puchalt, N., Mir-Sanchis, I., Donderis, J., Elena, S.F., Buckling, A., Novick, R.P., Marina, A. y Penadés, J.R. (2015). Virus satellites drive viral evolution and ecology. PLoS Genet. 11: e1005609.

203. Zwart, M.P., Elena, S.F. (2015) “Matters of size: genetic bottlenecks in virus infection and their potential impact on evolution”. Annu. Rev. Virol. 2: 161-179.

204. Bernet, G.P., Elena, S.F. (2015) “Distribution of mutational fitness effects and of epistasis in the 5’ untranslated region of a plant RNA virus”. BMC Evol. Biol. 15: 274.

205. Lalic, J., Elena, S.F. (2015) “The impact of high-order epistasis in the within-host fitness of a positive-sense plant RNA virus”. J. Evol. Biol. 28: 2236-2247.

206. Sánchez, F., Manrique, P., Mansilla, C., Lunello, P., Wang, X., Rodrigo, G., López-González, S., Jenner, C., González-Melendi, P., Elena, S.F., Walsh, J., Ponz, F. (2015) “Viral strain-specific differential alterations in Arabidopsis developmental patterns”. Mol. Plant-Microb. Interact. 28: 1304-1315.

207. Elena, S.F., Fraile, A., García-Arenal, F. (2016) “Evolución y emergencia de virus de plantas”. Cap. 12 en Enfermedades de Plantas Causadas por Virus y Viroides (eds. M.A. Ayllón, M. Cambra, E. Moriones y C. Llave) pp. 337-365. Sociedad Española de Fitopatología.

208. Folch-Fortuny, A., Bosque, G., Picó, J., Ferrer, A., Elena, S.F. (2016) “Fusion of genomic, proteomic and phenotypic data: the case of potyviruses”. Mol. BioSyst. 12: 253-261.

209. Martínez, F., Rodrigo, G., Aragonés, V., Ruiz, M., Lodewijk, I., Fernández, U., Elena, S.F., Daròs, J.A. (2016) “Interaction network of tobacco etch potyvirus NIa protein with the host proteome during infection”. BMC Genomics 17: 87.

210. Mengual-Chuliá, B., Bedhomme, S., Lafforgue, G., Elena, S.F., Bravo, I.G. (2016) “Assessing parallel gene histories in viral genomes”. BMC Evol. Biol. 16: 32.

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211. Cervera, H., Elena, S.F. (2016) “Genetic variation in fitness within a clonal population of a plant RNA virus”. Virus Evol. 2: vew006.

212. Willemsen, A., Zwart, M.P., Tromas, N., Majer, E., Daròs, J.A., Elena, S.F. (2016) “Multiple barriers to the evolution of alternative gene orders in a positive-strand RNA virus”. Genetics 202: 1503-1521.

213. Hillung, J., García-García, F., Dopazo, J., Cuevas, J.M., Elena, S.F. (2016) “The transcriptomics of an experimentally evolved plant-virus interaction”. Sci. Rep. 6: 24901.

214. Mushegian, A.R., Shypunov, A., Elena, S.F. (2016) “Changes in the composition of RNA virome mark evolutionary transitions in green plants”. BMC Biology 14: 68.

215. Elena, S.F. (2016) “Evolutionary transitions during RNA virus experimental evolution”. Philos. Trans. R. Soc. B. 371: 20150441.

216. Cervera, H., Lalic, J., Elena, S.F. (2016) “Efficient escape from local optima in a highly rugged fitness landscape by evolving RNA virus populations”. Proc. R. Soc. B. 283: 20160984.

217. Willemsen, A., Zwart, M.P., Higueras, P., Sardanyés, J., Elena, S.F. (2016). “Predicting the statibility of homologous gene duplications in a plant RNA virus”. Genome Biol. Evol. 8: 3065-3082.

218. Cervera, H., Lalic, J., Elena, S.F. (2016) “Effect of host species on the topography of fitness landscape for a plant RNA virus”. J. Virol. 90: 10160-10169. Elegido por los editores para el Spotlight.

219. Willemsen, A., Zwart, M.P., Elena, S.F. (2017) “High virulence does not necessarily impede viral adaptation to a new host: a case study using a plant RNA virus”. BMC Evol. Biol. 17: 25.

220. Rodrigo, G., Daròs J.A., Elena, S.F. (2017). “Virus-host interactome: putting the accent on how it changes”. J. Proteomics 156: 1-4.

221. Willemsen, A., Zwart, M.P., Ambrós, S., Carrasco, J.L., Elena, S.F. (2017). “2b or not 2b: experimental evolution of functional exogenous sequences in a plant RNA virus”. Genome Biol. Evol. 9: 297-310.

222. Minicka, J., Elena, S.F., Borodynko-Filas, N., Rubis, B., Hasiów-Jaroszewska, B. (2017). “Strain-dependent mutational effects for Pepino mosaic virus in a natural host”. BMC Evol. Biol. 17: 67.

223. Elena, S.F. (2017) “Local adaptation of plant viruses: lessons from experimental evolution”. Mol. Ecol. 26: 1711-1719.

224. Chao, L., Elena, S.F. (2017). “Nonlinear trade-offs allow the cooperation game to evolve from prisoner’s dilemma to snow drift”. Proc. R. Soc. B 284: 20170228.

225. Martín, S., Cuevas, J.M., Grande-Pérez, A., Elena, S.F. (2017). “A putative antiviral role of plant cytidine deaminases”. F1000Res. 6: 222.

226. Wu, B., Zwart, M.P., Sánchez-Navarro, J., Elena, S.F. (2017) “Within-host evolution of segments ratio for the tripartite genome of Alfafa mosaic virus”. Sci. Rep. 7: 5004.

227. Kutnjak, D., Elena, S.F., Ravnikar, M. (2017) “Time-sampled population sequencing reveals the interplay of selection and genetic drift in experimental evolution of Potato virus Y”. J. Virol. 91: e00690-17.

228. Valverde, S., Elena, S.F., Solé, R.V. (2017). “Spatially-induced nestedness in a neutral model of phage-bacteria networks”. Virus Evol. 3: vex021.

229. Ambrós, S., Martínez, F., Ivars, P., Hernández, C., de la Iglesia, F., Elena, S.F. (2017). “Molecular and biological characterization of an isolate of Tomato mottle mosaic virus (ToMMV) infecting tomato and other experimental hosts in eastern Spain”. Eur. J. Plant Pathol. 149: 261-268.

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230. Navarro, R., Ambrós, S., Martínez, F., Elena, S.F. (2017). “Diminishing returns of inoculum size on the rate of a plant RNA virus evolution”. Europhys. Lett. 120: 38001.

231. Sardanyés, J., Arderiu, A., Elena, S.F., Alarcón, T. (2018). “Noise-induced bistability in the quasi-neutral coexistence of viral RNAs under different replication modes”. J. R. Soc. Interface. 15: 20180129.

232. Cervera, H., Ambrós, S., Bernet, G.P., Rodrigo, G., Elena, S.F. (2018). “Viral fitness correlates with the magnitude and direction of the perturbation induced in the host’s transcriptome: the tobacco etch potyvirus – tobacco case study”. Mol. Biol. Evol. 35: 1599-1615

233. Hasiów-Jaroszewska, B., Minicka, J., Zarzyńska-Nowak, A., Budzyńska, D., Elena, S.F. (2018). “Defective RNA particles derived from tomato black ring virus genome interfere with the replication of the parental virus”. Virus Res. 250: 87-94.

234. De Visser, J.A.G.M., Elena, S.F., Fragata. I., Matuszewski, S. (2018). “The utility of fitness landscapes and big data for predicting evolution”. Heredity 121: 401-405.

235. Willemsen, A., Carrasco, J.L., Elena, S.F., Zwart, M.P. (2018). “Going, going, gone: predicting the fate of genomic insertions in plant RNA viruses”. Heredity 121: 499-509.

236. Ambrós, S., de la Iglesia, F., Rosario, S.M., Butković, A., Elena, S.F. (2018). “Engineered functional redundancy relaxes selective constraints upon endogenous genes in viral RNA genomes”. Genome Biol. Evol. 10: 1823-1836.

237. Beslon, G., Elena, S.F., Hogeweg, P., Schneider, D., Stepney, S. (2018) “Evolving living technologies – insights from the EvoEvo project”. Lecture Notes in Computer Sciences: Search-Based Software Engineering (eds. Colanzi, T.E. & McMinn, P.) pp. 46-62. Springer-Nature Switzerland.

238. Solé, R.V., Elena, S.F. (2019) Virus as Complex Adaptive Systems. Princeton University Press. Princeton NJ, USA. ISBN 9780691158846.

239. Fornés, J., Lázaro, J.T., Alarcón, T., Elena, S.F., Sardanyés, J. (2019). “Viral replication modes in single-peak fitness landscapes: a dynamical systems analysis”. J. Theor. Biol. 460: 170-183.

240. Nurtay, A., Hennessy, M.G., Sardanyés, J., Alsedà, L., Elena, S.F. (2019) “Theoretical conditions for the coexistence of viral strains with differences in phenotypic traits: a bifurcation analysis”. R. Soc. Open Sci. 6: 181179.

241. Carrasco, J.L., Sánchez-Navarro, J.A., Elena, S.F. (2019). “Exploring the role of cellular homologous of the 30K-superfamily of plant virus movement proteins”. Virus Res. 262: 54-61.

242. Pospieszny, H., Borodynko-Filas, N., Hasiów-Jaroszewska, B., Rymelska, N., Elena, S.F. (2018). “Transmission rate of two Polish Tomato torrado virus isolates through tomato seeds”. J. Gen. Plant Pathol. 85: 109-115.

243. Liu, C., Li, M., Redda, E.T., Mei, J., Zhang, J., Elena, S.F., Wu, B., Jiang, X. (2019). “Complete nucleotide sequence of a novel mycovirus from Trichoderma harzianum in China”. Arch. Virol. 164: 1213-1216.

244. Shaikhet, L., Elena, S.F., Korobeinikov, A. (2019). “Stability of a stochastically perturbed model of intracellular single-stranded RNA virus replication”. J. Biol. Syst. 27: 69-82.

245. González, R., Wu, B., Li, X., Martínez, F., Elena, S.F. (2019). “Mutagenesis scanning uncovers evolutionary constraints on tobacco etch potyvirus membrane-associated 6K2 protein”. Genome Biol. Evol. 11: 1207-1222.

246. Catalán, P., Elena, S.F., Cuesta, J.A., Manrubia, S. (2019). “Parsimonious scenario for the emergence of viroid-like replicons de novo”. Viruses 11: 425.

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247. González, R., Butković, A., Elena S.F. (2019) “Role of host genetic diversity for susceptibility-to-infection in the evolution of virulence of a plant virus”. Virus Evol. 5: vez024.

248. Lefeuvre, P., Martin, D. P., Elena, S.F., Shepherd, D.N., Roumagnac, P., Varsani, A. (2019) “Evolution and ecology of plant viruses”. Nat. Rev. Microbiol. 17: 632-644.

249. Komorowska, B., Hasiów-Jaroszewska, B., Elena, S.F. (2019) “Evolving by deleting: patterns of molecular evolution of Apple stem pitting virus isolates from Poland”. J. Gen. Virol. 100: 1442-1456.

250. Nurtay, A., Hennessy, G., Alsedà, L., Elena, S.F., Sardanyés, J. (2019). “Host-virus evolutionary dynamics with specialist and generalist infection strategies: bifurcations, bistability and chaos”. arXiv 1911.06025v1.

251. Pospieszny, H., Borodynko-Filas, N., Hasiów-Jaroszewska, B., Czerwonka, B., Elena, S.F. (2020) “An assessment of the transmission rate of Tomato black ring virus (TBRV) through tomato seeds”. Plant Protect. Sci. 56: 9-12.

252. Tarazona, A., Forment, J., Elena, S.F. (2020). “Identifying early-warning signals for the sudden transition from mild to severe tobacco etch disease by dynamical network biomarkers”. Viruses 12: 16.

253. González, R., Butković, A., Elena, S.F. (2020) “From foes to friends: viral infections expand the limits of host phenotypic plasticity”. Adv. Virus Res. 106: doi: 10.1016/bs.aivir.2020.01.003.

254. Manrubia, S., Cuesta, J.A., Aguirre, J., Ahnert, S.E., Atenberg, L., Cano, A.V., Catalán, P., Díaz-Uriarte, R., Elena, S.F., García-Martín, J.A., Hogeweg, P., Khatri, B.S., Krug, J., Louis, A.A., Martin, N.S., Payne, J.L., Tarnowski, M.J., Weiss, M. (2020). “From genotypes to organisms: state-of-the-art and perspectives of a cornerstone in evolutionary dynamics”. arXiv 2002.00363v1.

255. Solé, R.V., Sardanyés, J., Elena, S.F. (2020). “Phase transitions in virology”. Preprints 2020020261.

256. Zwart, M.P., Elena, S.F. (2020) “Modeling multipartite virus evolution: the genome formula facilitates rapid adaptation to heterogeneous environments”. Virus Evol. In press.

257. Corrêa, R.L., Sanz-Carbonell, A., Kogej, Z., Müller, S.Y., Ambrós, S., López-Mogollón, S., Gómez, G., Baulcombe, D.C., Elena, S.F. (2020). “Viral fitness determines the magnitude of transcriptomic and epigenomic reprogramming of defense responses in plants”. Mol. Biol. Evol. doi: 10.1093/molbev/msaa091.

258. Butković, A., González, R., Elena, S.F. (2020). “Revisiting Orthotospovirus phylogeny using whole genomic data and a hypothesis for their geographic origin and diversification”. bioRxiv 031120.

4.- INTERNATIONAL PATENTS:

1. Givert X, Sitjà, M., Fenech, M.M., Elena, S.F., García, S. 2018. Porcine reproductive and respiratory syndrome virus cDNA clone and uses thereof. WO 2018/024677 A1.

5.- CONFERENCES:

1. Rodríguez-Cerezo, E., Elena, S.F., Moya, A. and García-Arenal, F. (1989) Variability and evolution of field isolates of plant RNA viruses. 2nd International Symposium on Positive Strand RNA Viruses. Viena (Austria).

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2. Elena, S.F., Dopazo, J., Flores, R. and Moya, A. (1990) A first phylogeny of viroids. II Congreso Nacional de Virología. Valladolid (Spain).

3. Dopazo, J., Elena, S.F., Flores, R. and Moya, A. (1990). A first phylogeny of viroids and viroid-like satellite RNAs. International Meeting on Biology: Genome expression and pathogenesis of plant RNA viruses. Fundación Juan March. Madrid (Spain).

4. Elena, S.F., Dopazo, J., Flores, R., Diener, T.O. and Moya, A. (1990) A phylogenetic reconstruction for viroids and viroid-like satellite RNAs. VIIIth International Congress of Virology (ICV-90). Berlin (Germany).

5. Elena, S.F., Flores, R. and Dopazo, J. (1990) Study of the intraspecific variability of viroids. XXV Jornadas de Genética Luso-Españolas. Alcalá de Henares (Spain).

6. González-Quintanilla, M., Elena, S.F., Buades, C., Dopazo, J. and Moya, A. (1990) Analysis of the variability of viroids and viroidlike RNA satellites. XXV Jornadas de Genética Luso-Españolas. Alcalá de Henares (Spain).

7. Elena, S.F., Rubio, L., González-Candelas, F., Domingo, E. and Moya, A. (1991) Does the phylogeny of Foot-and-Mouth Disease Virus behave as a molecular clock?. International Meeting on Biology: Workshop on Coevolution of viruses, their hosts and vectors. Fundación Juan March. Madrid (Spain).

8. Elena, S.F., Marcos, J.F., Dopazo, J., Flores, R. and Moya, A. (1992) The sequences of viroids shwon intramolecular correlation and the potential to form pseudokonts and tetraloops. III Congreso Nacional de Virología. Barcelona (Spain).

9. Elena, S.F., Muñoz, A., Domingo, E. and Moya, A. (1992) A stochastic model to predict the genetic variability during a viral infection. III Congreso Nacional de Virología. Barcelona (Spain).

10. Hernández, C., Elena, S.F., Moya, A. and Flores, R. (1992) The peach blister cranker viroid has the central conserved region of apscaviroids and homologous sequences with other viroidal subgroups. III Congreso Nacional de Virología. Barcelona (Spain).

11. Nieto, A., Elena, S.F., Sentandreu, R. and del Castillo, L. (1992) Isolation and sequentiation of SEC18 gen of Candida albicans. Biotec-92. Santiago de Compostela (Spain).

12. Member of the organization comitee of the I Reunión Nacional about “Computational analysis of the structure and evolution of biological macromolecules”. Valencia (Spain), (1992).

13. Moya, A., Buades, C., Elena, S.F., González-Candelas, F., Barrio, E. and Latorre, A. (1992) The resolution of three evolutionary problems by means of the maximum-likelihood phylogenetic reconstruction method. I Reunión Nacional about "Computational analysis of the structure and evolution of biological macromolecules". Valencia (Spain).

14. Moya, A., Latorre, A., González, A., Carrió. R., Elena, S.F., Fernández-Pedrosa, V. and Martínez-Torres, D. (1993) The Population Genetics as the theoretical framework of Molecular Evolution: some examples. IX Seminarios de Genética de Poblaciones y Evolución. Granada (Spain).

15. Elena, S.F., Flores, R. and Moya, S. (1993) Phylogenetic evidence supports the concept that viroid and viroidlike satellite RNAs are relics of the RNA world. 7th ISSOL Meeting, 10th International Conference on the Origin of Life. Barcelona (Spain).

16. Elena, S.F., Flores, R. and Moya, A. (1993) Statistical evaluation of recombination events in viroids evolution. IXth International Congress of Virology (ICV-93). Glasgow (Scotland).

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17. Elena, S.F., Clarke, D.K., Duarte, E.A., Domingo, E., Holland, J.J. and Moya, A. (1993) Rate of fitness evolution of VSV under different population dynamics. IXth International Congress of Virology (ICV-93). Glasgow (Scotland).

18. Moya, A., Bracho, A. and Elena, S.F. (1994) How much experimental confirmation of Population Genetical theories could be obtained with RNA viruses as model?. XXIX Jornadas de Genética Luso-Españolas. Lleida (Spain).

19. Assistance to the X Seminarios de Genética de Poblaciones y Evolución. Miraflores de la Sierra (Spain), (1995).

20. González-Candelas, F., Elena, S.F. and Moya, A. (1995) About the simulation of molecular evolutionary processes. V Conferencia española de Biometría. Valencia (Spain).

21. Elena, S.F., Cooper, V.S. and Lenski, R.E. (1996) Punctuated equilibria of quantitative characters caused by periodic selection in experimental populations of Escherichia coli. 19th Midwest Ecology and Evolution Conference. East Lansing, MI (USA).

22. Elena, S.F., Cooper, V.S. and Lenski, R.E. (1996) Punctuated equilibria of quantitative characters caused by periodic selection in experimental populations of Escherichia coli. 50th Annual Meeting of the American Sociaties for the Study of Evolution and Systematic Biologists. Saint Louis, MO (USA).

23. Elena, S.F. and Lenski, R.E. (1996) Mechanisms maintaining the genetic variability within populations in Escherichia coli. Forum on Environmental Remediation & Environmental Toxicology and Microbial Ecology Forum. Lansing, MI (USA).

24. Oden, S.A., Elena, S.F. and Lenski, R.E. (1996) Synergistic interactions and distribution of mutational effects on the fitness of Escherichia coli. Forum on Environmental Remediation & Environmental Toxicology and Microbial Ecology Forum. Lansing, MI (USA).

25. Elena, S.F., Cooper, V.S. and Lenski, R.E. (1996) Punctuated evolution caused by selection of rare beneficial mutations. Forum on Environmental Remediation & Environmental Toxicology and Microbial Ecology Forum. Lansing, MI (USA).

26. Moya, A., Bracho, A., Miralles, R., Barrio, E. and Elena, S.F. (1996) The population genetics of RNA viruses. Workshop on RNA viral quasispecies. International Meeting on Biology. Fundación Juan March. Madrid (Spain).

27. Miralles, R., Elena, S.F. and Moya, A. (1996) Is group selection a factor modulating the virulence of RNA viruses?. International Meeting on Biology. Workshop on RNA viral quasispecies. Fundación Juan March. Madrid (Spain).

28. Elena, S.F. and Lenski, R. E. (1997) Test of synergistic interactions among deleterious mutations in bacteria. 51th Annual Meeting of the American Societies of Naturalists, Systematic Biologists and for the Study of Evolution. Boulder, CO (USA).

29. Elena, S.F. and Lenski, R. E. (1997) Distribution of fitness effects caused by the random insertion of transposons into the genome of Escherichia coli. Gordon Research Conferences on Microbial Population Biology. Plymouth, NH (USA).

30. Gerrish, P.J. and Elena, S.F. (1998) Life history evolution of HIV. Alcalá 1st International Conference on Mathematical Ecology. Alcalá de Henares (Spain).

31. Elena, S.F., Lenski, R.E. and Moya, A. (1998) Deletereous mutations and their effect on the fitness of microbes. XII Seminarios de Genética de Poblaciones y Evolución. Begur (Spain).

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32. Elena, S.F., Miralles, R., Gerrish, P.J. and Moya, A. (1999) Clonal interference and the evolution of RNA virus. VII European Society for Evolutionary Biology Congress. Barcelona (Spain).

33. Miralles, R., Moya, A. and Elena, S.F. (1999) Differences in the evolutionary outcome induced by dynamics of coinfection and superinfection in Vesicular Stomatitis Virus. VII European Society for Evolutionary Biology Congress. Barcelona (Spain).

34. Cuevas, J.M., Miralles, R., Moya, A. and Elena, S.F. (1999) Efecto de la tasa de migración y la estructura poblacional en la adaptación y divergencia del virus de la estomatitis vesicular. II Congreso de la Sociedad Española de Genética. A Coruña (Spain).

35. Member of the organization comitee of the meeting “Evolution: from molecules to ecosystems”. Valencia (Spain), (2000).

36. Elena, S.F., Turner, P.E., Cuevas, J.M. and Moya, A. (2000) Adaptive radiation of RNA viruses: host-range expansion. XIII Seminarios de Genética de Poblaciones y Evolución. Baiona (Spain).

37. Cuevas, J.M., Elena, S.F. and Moya, A. (2001) Evolutionary convergence in experimental populations of RNA viruses. VIIIth Congress of the European Society for Evolutionary Biology. Aarhus (Danemark). Poster.

38. Elena, S.F. (2001) Environmental restrictions to viral adaptation. An experimental approach. 9th International Symposium on Microbial Ecology. Amsterdam (The Netherlands). Invited talk.

39. Elena, S.F. (2001) Exploring the role of symbionine (GroEL) in buffering deleterious mutational effects during vertical transmission of bacteria. ESF/LESC Exploratory Workshop: “Long Term Evolution with Microbes”. Aussois (France). Invited speach.

40. Member of the organization comitee of the “VII Congreso de la Sociedad Española de Virología”. Valencia (Spain) (September 2001).

41. Cuevas, J.M., Moya, A. and Elena, S.F. (2001) Effect of migration rate and host-heterogeneity in the divergence and adaptation of the vesicular stomatitis virus. VII Congreso Nacional de Virología. Valencia (Spain). Poster.

42. Sanjuán, R., Bordería, A.V., Turner, P.E. and Elena, S.F. (2001) Bottlenecks during ribovirus transmission: evolution of biological fitness. VII Congreso Nacional de Virología. Valencia (Spain). Poster.

43. Fares, M.A., Elena, S.F., Moya, A. and Barrio, E. (2001) A new method for analyzing selective constraints in protein-coding genes based on sliding windows. III Congreso de la Sociedad Española de Genética. Seville (Spain). Poster.

44. Elena, S.F., Codoñer, F.M., and Sanjuán, R. (2002). Evolutionary genetics: lessons from bacteria and RNA viruses. Workshop on “Intraclonal Genetic Variation: Ecological and Evolutionary Aspects”, organized by The Linnean Society of London & Royal Entomological Society. London (UK). Invited talk.

45. Workshop on “Detection and Evolution of Genetic Robustness”. Santa Fe Institute. Fanta Fe, NM (USA). April 2002.

46. Elena, S.F. (2002). Adaptive dynamics during experimental evolution of RNA viruses. International Symposium on “Integrative Biology and Complexity in Natural Systems”, organized by IUBS/UNESCO/CNRS. París (France). Invited talk.

47. Elena, S.F. (2002). Is viral adaptation a self-organized phenomenon?. 2nd Workshop on Viral Evolution, organiced by the S. R. Nobel Foundation. Ardmore, OK (USA). Invited talk.

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48. Member of the organization comitee of the “XIV Seminarios de Genética de Poblaciones y Evolución”. Gandía (Valencia, Spain) (November 2002).

49. 1st Workshop of the “Red Nacional de Virología de Plantas”. Xàvea (Valencia, Spain) (March 2003).

50. Co-organizer (with G. Bell and J.A.G.M. de Visser) of the symposium “Experimental microbial evolution: the roles of sex, recombination and mutation” within the IXth of the European Society for Evolutionary Biology. Leeds (UK) (August 2003).

51. Elena, S.F. and Lenski, R.E. (2003). Experimental evolution of gene regulation and expression: the tetAR operon in E. coli. IXth European Society for Evolutionary Biology Congress. Leeds (UK). Talk.

52. Codoñer, F.M., Cuevas, J.M., Sánchez-Navarro, J.A., Pallás, V. and Elena, S.F. (2003). Molecular evolution of the plant virus family Bromoviridae based on RNA 3 encoded proteins. IXth European Society for Evolutionary Biology Congress. Leeds (UK). Poster.

53. Sanjuán, R., Moya, A. and Elena, S.F. (2003). Characterization of the distribution of mutational effects for an RNA virus. IXth European Society for Evolutionary Biology Congress. Leeds (UK). Poster.

54. Elena, S.F. (2003). Experimental evolution of plant viruses: disentangling the roles of mutation, selection and chance. AAB Advances in Plant Virology. Montpellier (France). Invited talk.

55. Cuevas, J.M., Moya, A. and Elena, S.F. (2003). Adaptive dynamics of RNA viruses in presence of antiviral drugs. VIII Congreso Nacional de Virología. Barcelona (Spain) Talk.

56. Codoñer, F.M., Cuevas, J.M., Sánchez-Navarro, J.A., Pallás, V. and Elena, S.F. (2003). Molecular evolution of the plant virus family Bromoviridae based on RNA 3 encoded proteins. VIII Congreso Nacional de Virología. Barcelona (Spain) Talk.

57. Elena, S.F., Cooper, T.F. and Lenski, R.E. (2004). Parasites and mutational load: an experimental test of a pluralistic theory for the maintenance of sex. 2nd PARTNER Workshop: Origin and spread of asexuals. European Science Foundation. Valencia (Spain). Invited talk.

58. Elena, S.F. (2004). How can microbial experimental evolution help to understand pathogens natural evolution?. VII International Meeting on Molecular Epidemiology and Evolutionary Genetics of Infectious Diseases. Valencia. Organizer.

59. Elena, S.F. (2004). Distribution of mutational effects and contribution of epistasis to fitness architecture in RNA viruses. Experimental Evolution Workshop. University of Fribourg. Fribourg (Switzerland). Invited talk.

60. Workshop on “Robustness of specialist/generalist strategies”. Santa Fe Institute. Fanta Fe, NM (USA). October 2004.

61. Sanjuán, R., Moya, A. and Elena, S.F. (2004). The distribution of fitness effects caused by single-nucleotide substitutions in an RNA virus. 3rd Workshop on Viral Evolution. S. R. Nobel Foundation. Ardmore, OK (USA). Talk.

62. Sanjuán, R., Moya, A. and Elena, S.F. (2004). The contribution of epistasis to the architecture of fitness in an RNA virus. 3rd Workshop on Viral Evolution. S. R. Nobel Foundation. Ardmore, OK (USA). Talk.

63. Carrasco, P., Agudelo-Romero, P., Daròs, J.A. and Elena, S.F. (2004). Quantifying the fitness of tobacco etch Potyvirus by jeans of competition assays based on RT-qPCR with TaqMan. 3rd Workshop on Viral Evolution. S. R. Nobel Foundation. Ardmore, OK (USA). Poster.

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64. Elena, S.F., Agudelo-Romero, S.P., Carrasco, M.P., Codoñer, F.M. and Daròs, J.A. (2004). Experimental evolucion of plant viruses: ongoing projects and perspectives. XV Seminarios de Genética de Poblaciones y Evolución. Sigüenza (Spain). Talk.

65. Elena, S.F. (2005). Deleterious mutations, epistasis and the evolution of genome robustness in RNA viruses. 10ème Rencontres de Virologie Végétale. Aussois (France). Invited talk.

66. Elena, S.F. (2005). Experimental evolution of RNA phytoviruses. 5th EMBO Young Investigator Program Meeting. Heidelberg (Germany). Talk.

67. EMBO Young Investigator Program 3rd Symposium on Quantitative Biology. Heidelberg (Germany) (June 2005).

68. Codoñer, F.M., Daròs, J.A., Solé, R.V. and Elena, S.F. (2005). Selection for fitness versus selection for robustness in subviral RNA phytopathogens. Congreso de la Sociedad Española de Genética. Almería. Invited talk.

69. Elena, S.F. (2005). Deleterious mutations, epistasis and the evolution of genome robustness in riboviruses. V EMBO-Spain meeting. Alicante. Invited talk.

70. Elena, S.F. (2005) What can we learn about the mechanisms of genome evolution using viroids as model system? Mathematical Biosciences Institute Workshop on Aspects of Self-Organization in Evolution. Ohio State University, Columbus, OH (USA). Invited talk.

71. Elena, S.F. (2005) Individual hypersensitivity versus population robustness in RNA viruses. Workshop on Frontiers in Evolutionary Ecology. MPI für Limnologie, Plön (Germany). Invited talk.

72. Elena, S.F. (2005) Some thoughts about virus origin and the mechanisms of viral evolution. II Simposium Omnis Cellula Origin of Life and Evolution. Societat Catalana de Biología, Barcelona. Invited talk.

73. Elena S.F. March 2005 Mechanisms of genetic robustness in RNA viruses. Workshop on New Directions in Infection Biology and Immunity. MPI für Infektionsbiologie, Berlin (Germany). Invited talk.

74. Elena, S.F. May 2006. The fittest versus the flattest: experimental confirmation of the quasispecies effect with subviral pathogens. 6th EMBO YIP Meeting. Vienna (Austria). Talk.

75. Co-organizer (with A. Buckling) of the symposium “Evolutionary Ecology” within the XIth International Symposium on Microbial Ecology-ISME 11. Vienna (Austria) (August 2006).

76. Elena, S.F., Carrasco, P., Daròs, J.A., and Sanjuán, R. August 2006. Evolution of mutational robustness in RNA viruses. XIth International Symposium on Microbial Ecology-ISME 11. Vienna (Austria). Invited talk.

77. Elena, S.F. and de la Iglesia, F. 2006. Fitness declines in tobacco etch virus upon serial bottleneck transfers. 4th Workshop on Viral Evolution. S. R. Nobel Foundation. Ardmore, OK (USA). Talk.

78. III Meeting EMBO Young Investigator Program Spain. Valencia, Octubre 2006. Organizer.

79. Elena, S.F. 2006. RNA virus replicate in an always fluctuating world: organ-specific adaptation, gene flow and metapopulation structure. ESF/CONGEN Workshop: “Experimental metapopulations in evolutionary biology”. Montpellier (France). Invited Talk.

80. Elena, S.F. 2007. Experimental RNA virus evolution. IXth Congreso Nacional de Virología. Zaragoza (Spain). Invited closing conference.

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81. Agudelo-Romero, P., Sanjuán, R. and Elena, S.F. 2007. TEV experimental evolution: evolutionary dynamics and the molecular basis of adaptation. IXth Congreso Nacional de Virología. Zaragoza (Spain). Poster.

82. Torres-Barceló, C., Martín, S., Daròs, J.A. and Elena, S.F. 2007. RNA silencing suppression as an adaptive strategy of plant RNA viruses. IXth Congreso Nacional de Virología. Zaragoza (Spain). Poster.

83. Elena, S.F., Torres-Barceló, C., Martín, S. and Daròs, J.A. 2007. “The evolution of silencing suppression and other ways viruses have to escape from silencing”. First BiosafeNET Seminar Balancing resistance and risk: plant endogenous viral sequences and virus-resistant transgenic plants as possible sources of resistance and virus emergence. Ca’Tron di Roncade, Italia. Invited Talk.

84. Elena, S.F. 2007. “The evolution of silencing suppression activity in multifunctional proteins encoded by plant RNA viruses”. 7th EMBO YIP Meeting. Heidelberg (Germany). Talk.

85. Elena, S.F. 2007. “The evolution of silencing suppression and other ways viruses have to escape from silencing”. Conferences Jacques Monod on Evolutionary Genetics of Host-Parasite Relationships. Roscoff, Francia. Invited Talk.

86. 3rd Meeting of the Spanish Systems Biology Network (REBS). Murcia, November 2007. Organizer.

87. Rodrigo, G., Carrera, J., Jaramillo, A. and Elena, S.F. 2007. Modeling and optimization of the interaction between RNA silencing pathway and viral suppressors of silencing. CAMDA 07 Conference. Valencia (Spain). Poster.

88. Agudelo-Romero, P., Carbonell, P., Pérez-Amador, M.A. and Elena, S.F. 2007. Virus adaptation by manipulation of host’s gene expression. CAMDA 07 Conference. Valencia (Spain). Poster.

89. Elena, S.F. 2008. Viral adaptation and manipulation of the transcriptome of the host. IIM-CSIC Workshop on Systems Biology. Vigo (Spain). Invited Talk.

90. Elena, S.F. 2008. Virus evolution. 1st meeting of the PVYwide Organization. Paris (France). Invited Talk.

91. Elena, S.F. 2008. Virus fitness and host switching. Technical CIDD Workshop on virus adaptation on multi-host fitness landscapes. Center for Infectious Diseases Dynamics, Pennsylvania State University, State College, PA (USA). Invited Talk.

92. Sanjuán, R., Gago, S. and Elena, S.F. 2008. Direct estimation of mutation rate for Chrysanthemum chlorotic mottle viroid (CChMVd). Viroid-2008 International conference on viroids and viroid-like RNAs. Berlin (Germany). Talk.

93. Elena, S.F. 2008. Virus adaptation by manipulation of host’s gene expression. 5th Workshop on Viral Evolution, organized by the S. R. Nobel Foundation. Ardmore, OK (USA). Talk.

94. Torres-Barceló, C., Martín, S., Daròs, J.A. and Elena, S.F. 2008. From hypo- to hyper-suppression: effect of amino acid substitutions on the RNA silencing suppressor activity of Tobacco etch virus HC-Pro. 5th Workshop on Viral Evolution, organized by the S. R. Nobel Foundation. Ardmore, OK (USA). Poster.

95. Agudelo-Romero, P., de la Iglesia, F. and Elena, S.F. 2008. The pleiotropic cost of host-range expansion in Tobacco etch potyvirus. 5th Workshop on Viral Evolution, organized by the S. R. Nobel Foundation. Ardmore, OK (USA). Poster.

96. Sardanyés, J., Elena, S.F. and Solé, R. 2008 “Simple quasispecies models for the survival-of-the-flattest effect: the role of space”. Workshop on Spatial Evolutionary Dynamics, organizado por Institut des Systèmes Complexes. Paris (France). Talk.

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97. Santa Fe Institute 2008 Annual Bussiness Network and Board of Trustees’ Symposium. Santa Fe, NM (USA). Noviembre 2008. Assistence.

98. Elena, S.F. 2008 “The evolutionary genetics of plant virus emergence”. International Conference Genetic Control of Plant Pathogenic Viruses and their Vectors: Towards New Resistance Strategies. El Puerto de Santa María (Spain). Invited Talk.

99. 4th Meeting of the Spanish Systems Biology Network (REBS). Valencia, December 2008. Organizer.

100. Elena, S.F. 2008 “Virus adaptation by manipulation of host’s gene expression”. 4th Meeting of the Spanish Systems Biology Network (REBS). Valencia (Spain). Talk.

101. Agudelo-Romero, P., Carbonell, P., de la Iglesia, F., Carrera, J., Rodrigo, G., Jaramillo, A., Pérez-Amador, MA. and Elena, S.F. 2008 “Changes in the gene expression profile of Arabidopsis thaliana after infection with Tobacco etch virus”. 4th Meeting of the Spanish Systems Biology Network (REBS). Valencia (Spain). Poster.

102. Rodrigo, G., Carrera, J., Jaramillo, A. and Elena, S.F. 2008 “Modeling and optimization of the interaction between RNA silencing pathway and viral suppressors of silencing”. 4th Meeting of the Spanish Systems Biology Network (REBS). Valencia (Spain). Poster.

103. Daròs, J.A., Martínez, F., Lafforgue, G., de la Iglesia, F., Chua, N.H. and Elena, S.F. 2009 “Resistencia a virus de plantas mediada por microRNAs artificiales”. Xth Congreso Nacional de Virología. Salamanca (Spain). Talk.

104. Gómez, P., Sempere, R.N., Aranda, M.A. and Elena, S.F. 2009 “Dinámica evolutiva del virus del mosaico del pepino dulce (PepMV) en cultivos de tomate del sureste de España”. Xth Congreso Nacional de Virología. Salamanca (Spain). Talk.

105. Gago, S., Elena, S.F., Flores, R. and Sanjuán, R. 2009 “Un viroide con ribozima de cabeza de martillo presenta la tasa de mutación más elevada descrita para una entidad biológica”. Xth Congreso Nacional de Virología. Salamanca (Spain). Talk.

106. Castaño, A., Ruiz, L., Elena, S.F. and Hernández, C. 2009 “Evolución extremadamente rápida del virus del arabesco del pelargonium en un huésped experimental”. Xth Congreso Nacional de Virología. Salamanca (Spain). Poster.

107. Jacques Monod Conference Understanding emergence of infectious diseases: focus on new experimental and theoretical approaches to virus evolution. September 2009. Roscoff (France). President.

108. Elena, S.F. 2009 “Experimental evaluation of the durability of resistance to plant viruses mediated by artificial microRNAs”. Conferences Jacques Monod on Understanding emergence of infectious diseases: Focus on new experimental and theoretical approaches to virus evolution. Roscoff, France. Invited talk.

109. Bedhomme, S. and Elena, S.F. 2009 “Interaction between virulence and host intraspecific competition in the early steps of host switching”. Conferences Jacques Monod on Understanding emergence of infectious diseases: Focus on new experimental and theoretical approaches to virus evolution. Roscoff, France. Poster.

110. Blanchard, A., Delaunay, A., Elena, S.F. and Jacquot, E. 2009 “Importance of recombination during Potato virus Y (PVY) evolution”. Conferences Jacques Monod on Understanding emergence of infectious diseases: Focus on new experimental and theoretical approaches to virus evolution. Roscoff, France. Poster.

111. Gómez, P., Sempere, R.N., Aranda, M.A. and Elena, S.F. 2009 “Evolutionary dynamics of Pepino mosaic virus during epidemics in Southeastern Spain”. Conferences Jacques Monod on Understanding emergence of infectious diseases: Focus on new experimental and theoretical approaches to virus evolution. Roscoff, France. Poster.

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112. Lafforgue, G., Martínez, F., de la Iglesia, F., Chua, N.H., Daròs, J.A. and Elena, S.F. 2009 “amiR-mediated resistance to virus infection: estimating the likelihood of escape mutants”. Conferences Jacques Monod on Understanding emergence of infectious diseases: Focus on new experimental and theoretical approaches to virus evolution. Roscoff, France. Poster.

113. Lalic, J., Carrasco, P. and Elena, S.F. 2009 “Adaptation of TEV to the susceptible ecotype Arabidopsis thaliana Ler increases its infectivity in other resistant ecotypes”. Conferences Jacques Monod on Understanding emergence of infectious diseases: Focus on new experimental and theoretical approaches to virus evolution. Roscoff, France. Poster.

114. Lalic, J., Carrasco, P. and Elena, S.F. 2009 “Systemic movement determinants of TEV in Arabidopsis thaliana”. Conferences Jacques Monod on Understanding emergence of infectious diseases: Focus on new experimental and theoretical approaches to virus evolution. Roscoff, France. Poster.

115. Sardanyés, J., Solé, R.V. and Elena, S.F. 2009 “The survival-of-the-flattest: a dynamical systems approach to viroids and RNA viruses evolution”. Conferences Jacques Monod on Understanding emergence of infectious diseases: Focus on new experimental and theoretical approaches to virus evolution. Roscoff, France. Poster.

116. Tromas, N. and Elena, S.F. 2009 “Experimental evolution of plant viruses: estimating the in vivo mutation rate of Tobacco etch potyvirus (TEV)”. Conferences Jacques Monod on Understanding emergence of infectious diseases: Focus on new experimental and theoretical approaches to virus evolution. Roscoff, France. Poster.

117. XXXVII Congress of the Spanish Genetical Society. Torremolinos, Málaga, September 2009. Scientific board and organizer of the Evolutionary Genetics session.

118. Elena, S.F. 2009 “Virus emergentes y biología de sistemas: identificando las dianas de la adaptación viral”. XXXVII Congreso de la Sociedad Española de Genética. Torremolinos, Málaga. Talk.

119. 2nd Congress of the Spanish Society of Evolutionary Biology. Valencia, December 2009. Scientific board and chairman in session 6.

120. Bedhomme, S. and Elena, S.F. 2009 “Interaction between virulence and host intraspecific competition in the early steps of host switching”. II Congress of the Spanish Society of Evolutionary Biology. València, Spain. Poster.

121. Lafforgue, G., Martínez, F., de la Iglesia, F., Chua, N.H., Daròs, J.A. and Elena, S.F. 2009 “amiR-mediated resistance to virus infection: estimating the likelihood of escape mutants”. II Congress of the Spanish Society of Evolutionary Biology. València, Spain. Poster.

122. Lalic, J., Carrasco, P. and Elena, S.F. 2009 “Adaptation of TEV to the susceptible ecotype Arabidopsis thaliana Ler increases its infectivity in other resistant ecotypes”. II Congress of the Spanish Society of Evolutionary Biology. València, Spain. Talk.

123. Sardanyés, J., Solé, R.V. and Elena, S.F. 2009 “Efecto del modo de replicación y del paisaje adaptativo en la acumulación de mutaciones y en la robustez de virus de RNA”. II Congress of the Spanish Society of Evolutionary Biology. València, Spain. Poster.

124. Tromas, N. and Elena, S.F. 2009 “Experimental evolution of plant viruses: estimating the in vivo mutation rate of Tobacco etch potyvirus (TEV)”. II Congress of the Spanish Society of Evolutionary Biology. València, Spain. Poster.

125. Member of the organizing comittee and chairman in on session. 5th Meeting of the Spanish Systems Biology Network (REBS). Madrid, Spain. Diciembre 2009.

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126. Elena, S.F., Carrera, J. and Rodrigo, G. 2009 “An evolutionary systemic approach to virus-host interaction”. 5th Meeting of the Spanish Network of Systems Biology (REBS). Madrid, Spain. Invited Talk.

127. Sardanyés, J., Solé, R.V. and Elena, S.F. 2009 “Replication mode and landscape topology differentially affect RNA virus mutational load and robustness”. 5th Meeting of the Spanish Network of Systems Biology (REBS). Madrid, Spain. Talk.

128. Elena, S.F. 2010 “Experimental evolution of RNA viruses: disentangling the roles of mutation, selection and chance”. II Meeting of the Spanish Network of Plant Virology (REVIPLANT). Puerto de Santa María, Spain. Opening conference.

129. Gago Zachert, S., Elena, S.F., Flores, R. and Sanjuán, R. 2010 “Members of both viroid families show different mutation rates”. II Meeting of the Spanish Network of Plant Virology (REVIPLANT). Puerto de Santa María, Spain. Oral presentation.

130. Lalic, J., Agudelo-Romero, P., Carrasco, P. and 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”. II Meeting of the Spanish Network of Plant Virology (REVIPLANT). Puerto de Santa María, Spain. Oral presentation.

131. Sardanyés, J. and Elena, S.F. 2010 “Error threshold in RNA quasispecies models with complementation.” II Meeting of the Spanish Network of Plant Virology (REVIPLANT). Puerto de Santa María, Spain. Oral presentation.

132. Bedhomme, S. and Elena, S.F. 2010 “Strategies of adaptation to new hosts and evolution through consecutive host switches”. II Meeting of the Spanish Network of Plant Virology (REVIPLANT). Puerto de Santa María, Spain. Poster.

133. Tromas, N. and Elena, S.F. 2010 “Estimation of the in vivo mutation rate and mutant spectrum of Tobacco etch potyvirus”. II Meeting of the Spanish Network of Plant Virology (REVIPLANT). Puerto de Santa María, Spain. Poster.

134. Carrera, J., Rodrigo, G. and Elena, S.F. 2010 “An evolutionary systemic approach to virus-host interactions”. II Meeting of the Spanish Network of Plant Virology (REVIPLANT). Puerto de Santa María, Spain. Poster.

135. Martínez, F., Lafforgue, G., De la Iglesia, F., Chua, N.H., Elena, S.F. and Daròs, J.A. 2010 “Resistance to plant viruses mediated by artificial microRNAs”. II Meeting of the Spanish Network of Plant Virology (REVIPLANT). Puerto de Santa María, Spain. Poster.

136. Sardanyés, J. and Elena, S.F. 2010 “Exploring the interplay between RNA virus replication mode and landscape topologies: theoretical and computational models”. XVIII Seminarios de Genética de Poblaciones y Evolución. Guitiriz, Spain. Oral presentation.

137. Gago, S., Elena, S.F., Sanjuán, R. and Flores, R. 2010 “Differences in mutation rates of members of the families Asvunviroidae and Pospiviroidae”. 4th European Congress of Virology. Cernobbio (Italy). Poster.

138. Elena, S.F. 2010 “Vagaries of ribovirus evolution: durability of plant amiR-mediated resistance”. ESF-EMBO Symposium Antiviral applications of RNA interference. Sant Feliu de Guíxols, Spain. Invited talk.

139. Martínez, F., Lafforgue, G., Elena, S.F. and Daròs, J.A. 2010 “Fate of artificial microRNA-mediated resistance to plant virus in mixed infections”. ESF-EMBO Symposium Antiviral applications of RNA interference. Sant Feliu de Guíxols, Spain. Poster.

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140. Lafforgue, G., Martínez, F., De la Iglesia, F., Daròs, J.A. and Elena, S.F. 2010 “AmiR-mediated resistance to virus infection: estimating the likelihood of escape mutants”. ESF-EMBO Symposium Antiviral applications of RNA interference. Sant Feliu de Guíxols, Spain. Poster.

141. Li., S.S., Wu, H.W., Elena, S.F., Chen, K.C., Niu, Q.W., Yeh, S.D. and Chua, N.H. 2010 “Applications of artificial microRNA in plant biotechnology”. ESF-EMBO Symposium Antiviral applications of RNA interference. Sant Feliu de Guíxols, Spain. Poster.

142. Gago, S., Elena, S.F., Flores, R. and Elena, S.F. 2010 “Nuclear and chloroplastic viroids replicate with different mutation rates”. EMBO Workshop Genomic Approaches to interactions between plant viruses, their hosts and their vectors. Fenestrelle (Italy). Poster.

143. Lafforgue, G., Martínez, F., De la Iglesia, F., Daròs, J.A. and Elena, S.F. 2010 “AmiR-mediated resistance to virus infection: estimating the likelihood of escape mutants”. EMBO Workshop Genomic Approaches to interactions between plant viruses, their hosts and their vectors. Fenestrelle (Italy). Poster.

144. Elena, S.F. 2010 “Emerging viruses: changes in viral genome result in a better manipulation of host regulatory networks”. Collaborative Research Center Conference Molecular Basis of Evolutionary Innovations. Marche-en-Famenne (Belgium). Invited talk.

145. Elena, S.F. 2010 “Evolutionary and Systems Biology of plant RNA virus emergente”. American Phytopathological Society 2010 Meeting. Charlotte NC (USA). Invited talk. (Published in Phytopathology 100: S149, 2010).

146. Elena, S.F. 2010 “Vagaries of ribovirus evolution: durability of plant amiR-mediated resistance”. 6th Workshop on Viral Evolution, organizado por la S. R. Nobel Foundation. Ardmore, OK (USA). Invited talk.

147. Bedhomme, S., Lafforgue, G. and Elena, S.F. 2010 “Experimental evolution of generalist and specialist lineages of Tobacco etch virus”. 6th Workshop on Viral Evolution, organizado por la S. R. Nobel Foundation. Ardmore, OK (USA). Oral presentation.

148. Lalic, J., Pròsper, A., Cuevas, J.M. and Elena, S.F. 2010 “Evaluating the distribution of mutations fitness effects for Tobacco etch potyvirus across hosts species”. 6th Workshop on Viral Evolution, organizado por la S. R. Nobel Foundation. Ardmore, OK (USA). Poster.

149. Tromas, N., Lafforgue, G. and Elena, S.F. 2010 “MOI and its relationship to recombination rate for Tobacco etch potyvirus”. 6th Workshop on Viral Evolution, organizado por la S. R. Nobel Foundation. Ardmore, OK (USA). Poster.

150. Lalic, J., Pròsper, À., Cuevas, J.M. and Elena, S.F. 2010 “Evaluating the distribution of mutations fitness effects for Tobacco etch potyvirus across hosts species”. X Jornada de Virologia, Societat Catalana de Virologia. Barcelona (Spain). Oral presentation.

151. Sardanyés, J. and Elena, S.F. 2010 “Approaching to virologically realistic quasispecies models: the interplay between space, replication mode, fitness landscape, and superinfection”. 6th Meeting of the Spanish Network of Systems Biology (REBS). Barcelona (Spain). Oral presentation.

152. Carrera, J., Rodrigo, G., Elena, S.F. and Jaramillo, A. 2010 “All-genome rewiring of transcription regulation under dynamic environments”. International Conference on Synthetic Biology. Université d’Évry-Val-D’Essonne (Francia). Poster.

153. Kavli Institute for Theoretical Physics Workshop on Bacterial and Viral Evolution. University of California Santa Barbara (USA), January – March 2011. Organizer.

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154. Elena, S.F. 2011 “Presentación del grupo de virología evolutiva y de sistemas (EvolSysVir)”. I Reunión de la Red Española Interdisciplinar de Biofísica de Virus (BioFiViNet). Barcelona (Spain). Comunicación oral.

155. Sardanyés, J., Elena, S.F. 2011 “Approaching to virologically realistic quasispecies models: interplay between space, replication mode, fitness landscape, and superinfection”. I Reunión de la Red Española Interdisciplinar de Biofísica de Virus (BioFiViNet). Barcelona (Spain). Oral presentation.

156. Elena, S.F., Carrera, J., Rodrigo, G. 2011 “A Systems Biology approach to the evolution of virus-host interactions”. XII International Conference on Molecular Systems Biology. Lleida (Spain). Invited talk.

157. XI Congreso Nacional de Virología. Granada (Spain), 2011. Member of the Scientific Committee and chairman of session Virus Replication (I).

158. Martínez, F., Lafforgue, G., Sardanyés, J., de la Iglesia, F., Solé, R.V., Chua, N.H., Elena, S.F., Daròs, J.A. 2011 “Durabilidad de la resistencia al potyvirus del mosaico del nabo mediada por un microRNA artificial”. XI Congreso Nacional de Virología. Granada (Spain). Oral presentation. (Published in Virología 14: S16-S17, 2011).

159. Cuevas, J.M., Grande-Pérez, A., Martín, S., de la Iglesia, F., Elena, S.F. 2011 “Importancia de las citidina-deaminasas como agente mutagénico en virus de plantas”. XI Congreso Nacional de Virología. Granada (Spain). Oral presentation. (Published in Virología 14: S47-S48, 2011).

160. Martínez, F., Sardanyés, J., Elena, S.F., Daròs, J.A. 2011 “Dinámica de la acumulación intracelular de un virus de RNA de plantas: replicación geométrica versus stamping machine”. XI Congreso Nacional de Virología. Granada (Spain). Oral presentation. (Published in Virología 14: S107, 2011).

161. Zwart, M.P., Daròs, J.A., Elena, S.F. 2011 “A single virion can cause systemic infection: a test of the independent action hypothesis model with a plant RNA virus”. XI Congreso Nacional de Virología. Granada (Spain). Oral presentation. (Published in Virología 14: S114, 2011).

162. Bedhomme, S., Lafforgue, G., Elena, S.F. 2011 “Experimental multihost evolution of Tobacco etch virus”. XI Congreso Nacional de Virología. Granada (Spain). Oral presentation. (Published in Virología 14: S115-S116, 2011).

163. Sardanyés, J., Martínez, F., Daròs, J.A., Elena, S.F. 2011 “Modeling viral RNA intracellular accumulation under differential replication modes: a dynamical systems approach”. XI Congreso Nacional de Virología. Granada (Spain). Poster. (Published in Virología 14: S145, 2011).

164. Hillung, J., de la Iglesia, F., Cuevas, J.M., Elena, S.F. 2011 “Cuantificación de la infección primaria en un sistema experimental virus-planta”. XI Congreso Nacional de Virología. Granada (Spain). Poster. (Published in Virología 14: S160-S161, 2011).

165. Lalic, J., Pròsper, À., Cuevas, J.M., Elena, S.F. 2011 “Evaluating the distribution of mutational fitness effects for Tobacco etch potyvirus across host species”. XI Congreso Nacional de Virología. Granada (Spain). Poster. (Published in Virología 14: S163-S164, 2011).

166. Tromas, N., Pròsper, A., Elena, S.F. 2011 “Evolution of genetic and functional redundancy in a RNA virus”. XI Congreso Nacional de Virología. Granada (Spain). Poster. (Published in Virología 14: S167, 2011).

167. FEMS2011 4th Congress of European Microbiologists. Geneve (Switzerland), 2011. Organizer session Virus Ecology and Evolution.

168. Lalic, J., Cuevas, J.M., Elena, S.F. 2011 “Evaluating the distribution of mutational fitness effects of a plant RNA virus across different host species”. FEMS2011 4th Congress of European Microbiologists. Geneva (Switzerland). Oral presentation.

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169. Carrera, J., Elena, S.F., Jaramillo, A. 2011 “All-genome rewiring of transcription regulation under dynamic environments”. SB5.0 5th International Meeting on Synthetic Biology. Stanford, CA (USA).

170. Gordon Research Conferences on Microbial Population Biology. Andover, NH (USA), 2011. Organizer session Evolutionary Virology.

171. Elena, S.F. 2011. “Evolution of virus-host interactions”. Gordon Research Conference on Microbial Population Biology. Andover, NH (USA).

172. Clune, J., Misevic, D., Ofria, C., Lenski, R.E., Elena, S.F., Sanjuán, R. 2011. “Natural selection fails to optimiza mutation rate for long-term adaptation in rugged fitness landscapes”. European Conference on Artificial Life (ECAL 11). Paris (Francia). Oral presentation.

173. XIIIrd Congress of the European Society for Evolutionary Biology. Tübingen (Germany), 2011. Organizer symposium Origin of Epistasis.

174. XIIIrd Congress of the European Society for Evolutionary Biology. Tübingen (Germany), 2011. Organizer symposium Microbe/macrobe experimental evolution.

175. Lafforgue, G., Elena, S.F., Bedhomme, S. 2011. “Experimental multihost evolution of Tobacco etch virus and role of historical contingencies in evolution”. XIIIrd Congress of the European Society for Evolutionary Biology. Tübingen (Germany). Oral presentation.

176. Bedhomme, S., Elena, S.F. 2011. “Virus infection supresses Nicotiana benthamiana adaptive phenotypic plasticity”. XIIIrd Congress of the European Society for Evolutionary Biology. Tübingen (Germany). Poster.

177. Elena, S.F., Macía, J., Solé, R.V. 2011. “The causes of epistasis in genetic networks”. XIIIrd Congress of the European Society for Evolutionary Biology. Tübingen (Germany). Poster.

178. Elena, S.F. 2011. “Evaluating the distribution of mutational fitness effects of a plant RNA virus accross different host species”. An Evolutionary Journey II. Universidad Carlos III. Madrid (Spain). Invited talk.

179. Lalic, J., Elena, S.F. 2011. “Magnitude and sign epistasis among deleterious mutations in a positive-sense plant RNA virus”. XI Jornada de Virologia, Societat Catalana de Biologia. Barcelona (Spain). Oral presentation.

180. International Symposium Understanding plant disease emergence: evolutionary ecology meets genomics. Fundación Ramón Areces. Madrid, 2011. Chairman of one session.

181. Elena, S.F. 2012. “The genetic basis of unpredictability in plant RNA virus evolution: G´G, G´E and G´G´E”. International Symposium Understanding plant disease emergence: evolutionary ecology meets genomics. Fundación Ramón Areces. Madrid (Spain). Invited talk.

182. Elena, S.F., Lalic, J. 2012. “Uncertainties in estimating viral fitness”. Cologne Spring Meeting 2012 Molecular Ecology and Evolution. Cologne (Germany). Invited talk.

183. Elena, S.F. 2012. “Population dynamics of virus escape mutants in RNAi-mediated resistant plants”. ESF-EMBO Symposium Antiviral RNAi: from Molecular Biology towards applications. Pultusk (Poland). Invited talk.

184. Sánchez, F., Manrique, P., Grinvalds, C., Mansilla, C., Lunello, P., Ponz, F., Rodrigo, G., Carrera, J., Elena, S.F. 2012. “Transcriptomic characterization of the differential interactions established in Arabidopsis by two different strains of Turnip mosaic virus”. XI Reunión de Biología Molecular de Plantas. Segovia (Spain). Poster.

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185. Elena, S.F. 2012. “The evolution of silencing suppression and other ways viruses have to escape from RNA silencing”. Society for Molecular Biology and Evolution Congress. Dublin (Ireland). Invited talk.

186. ALife XIII. Co-chairman of Track II: Evolution in Action. East Lansing, MI (USA), July 2012.

187. Elena, S.F. 2012. “Evolutionary and systems biology of RNA viruses”. EMBO Members Meeting. Heidelberg (Germany). Oral presentation.

188. Lalic, J., Elena, S.F. 2012. “The genetic architecture of RNA virus fitness”. British Society for Plant Pathology Presidential Meeting 2012. Norwich (UK). Invited talk.

189. Martín, S., Cuevas, J.M., Grande-Pérez, A., Elena, S.F. 2013. “A putative antiviral role of plant cytidine deaminases”. 7th Workshop on Viral Evolution, Pennsylvania State University. State College, PA (USA). Oral presentation.

190. Hillung, J., Elena, S.F., Cuevas, J.M. 2013. “Adaptative value of Potyvirus P3N-PIPO protein length intraspecific variability”. 7th Workshop on Viral Evolution, organizado por la Pennsylvania State University. State College, PA (USA). Poster.

191. Willemsen, A., Zwart, M.P., Elena, S.F. 2013. “Experimental evolution of genome architecture and complexity in RNA virus”. 7th Workshop on Viral Evolution, organizado por la Pennsylvania State University. State College, PA (USA). Poster.

192. Elena, S.F. 2013. “Vagaries and trivialities in plant RNA virus experimental evolution”. Symposium on Experimental Evolution in Honor of Prof. Richard E. Lenski. Wageningen (The Netherlands). Invited talk.

193. Elena, S.F., de la Iglesia, F., Lalic, J. 2013. “Empirical fitness landscapes reveals a limited number of accesible adaptive pathways for an RNA virus”. II Reunión de la Red Española Interdisciplinar de Biofísica de Virus (BioFiViNet). Madrid (Spain). Talk.

194. Rodrigo, G., Carrera, J., Elena, S.F. 2013. “An evolutionary systemic approach to virus-host interactions”. II Reunión de la Red Española Interdisciplinar de Biofísica de Virus (BioFiViNet). Madrid (Spain). Poster.

195. Elena, S.F. 2013. “Experimental evolution of virus-host interactions”. 113th General Meeting of the American Society for Microbiology. Denver, CO (USA). Invited talk.

196. XII Congreso Nacional de Virología. Burgos (Spain), 2013. Member of the Scientific Committee and chairman of session Virus Evolution.

197. Ferriol, I., Peña, E., Sambade, A., Buschmann, H., Niehl, A., Elena, S.F., Heinlein, M., Rubio, L. 2013. “Experimental evolution of Tobacco mosaic virus in Arabidopsis thaliana plants with altered cytoskeleton dynamics”. XII Congreso Nacional de Virología. Burgos (Spain). Talk. (Published in Virología 16: S127-S128, 2013).

198. Willemsen, A., Majer, E., Salvador, Z., Zwart, M.P., Daròs, J.A., Elena, S.F. 2013. “Experimental evolution of genome architecture and complexity in RNA virus”. XI Congreso Nacional de Virología. Burgos (Spain). Poster. (Published in Virología 16: S254-S255, 2013).

199. Zwart, M.P., Willemsen, A., Daròs, J.A., Elena, S.F. 2013. “Holding on the future: experimental evolution of pseudogenization in viral genomes”. XI Congreso Nacional de Virología. Burgos (Spain). Poster. (Published in Virología 16: S256-S257, 2013).

200. Hillung, J., Cuevas, J.M., Elena, S.F. 2013. “Some ecotypes of Arabidopsis thaliana favor local adaptation of Tobacco etch potyvirus while others select for generalist viruses”. XI Congreso Nacional de Virología. Burgos (Spain). Poster. (Published in Virología 16: S257-S258, 2013).

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201. Elena, S.F. 2013. “Evolutionary genetics factors underlying the emergence and spread of plant RNA viruses”. American Phytopathological Society 2013 Meeting. Austin (TX, USA). Invited talk. (Published in Phytopathology 103: S2.179, 2013).

202. XIVth Congress of the European Society for Evolutionary Biology. Lisbon (Portugal), 2013. Organizer symposium Experimental Evolution on Empirical Fitness Landscapes.

203. Elena, S.F., Lalic, J., Franke, J., de la Iglesia, F. 2013. “Empirical fitness landscapes reveals a limited number of accesible adaptive pathways for an RNA virus”. XIVth ESEB Congress. Lisbon (Portugal). Poster.

204. Bedhomme, S., Lafforgue, G., Elena, S.F. 2013. “Viral experimental evolution reveals genotypic but not phenotypic historical contingency”. XIVth ESEB Congress. Lisbon (Portugal). Poster.

205. Elena, S.F. 2013. “The evolution of plant virus hsot range: lessons from experimental evolution”. Xth International Congress of Plant Pathology. Beijing (China). Invited talk. (Published in Acta Phytopathol. Sinica 43: S476-S477, 2013).

206. Lalic, J., de la Iglesia, F., Elena, S.F. 2013. “Topography and ruggedness of Tobacco etch Potyvirus adaptive fitness landscapes”. EMBO Workshop: Green viruses, from gene to landscape. Hyères-les-Palmieres (France). Invited talk.

207. Member of the Scientific Advisory Board, workshop Viral Evolution and Quasispecies. Vth European Congress of Virology. Lyon (France), September 2013.

208. Elena, S.F. 2013. “Mechanisms of mutational robustness in RNA virus populations”. NIH Workshop: Protein homeostasis and viral infection – mechanisms to therapeutics. Bethesda (MD, USA). Invited talk.

209. Elena, S.F. 2013. “Evolutionary and systems biology of RNA viruses”. EMBO-IndiaBioscience Young Scientist Networking Meeting. Bangalore (India). Invited talk.

210. Elena, S.F. 2014. “An experimental approach to the emergence of plant RNA viruses”. Jacques Monod Conference From emerging to pandemic viruses: interplay between host ecology and viral evolution. Roscoff (France). Invited talk.

211. Minicka, J., Rimelska, N., Elena, S.F., Czerwoniec, A., Hasiów-Jaroszewska, B. 2014. “Genome evolution of Pepino mosaic virus populations during long-term passaging in different hosts”. Jacques Monod Conference From emerging to pandemic viruses: interplay between host ecology and viral evolution. Roscoff (France). Poster.

212. Hillung, J., García-García, F., Cuevas, J.M., Elena, S.F. 2014. “The effect of genetic diversity of the host species on the adaptation of an emerging plant RNA virus”. Jacques Monod Conference From emerging to pandemic viruses: interplay between host ecology and viral evolution. Roscoff (France). Poster.

213. Willemsen, A., Tromas, N., Majer, E., Daròs, J.A., Elena, S.F., Zwart, M.P. 2014. “Experimental evolution of genome rearrangements in plant RNA virus”. Jacques Monod Conference From emerging to pandemic viruses: interplay between host ecology and viral evolution. Roscoff (France). Poster.

214. Minicka, J., Rymelska, N., Elena, S.F., Borodynko, N., Hasiów-Jaroszewska, B. 2014. Pepino mosaic virus genome evolution during long-term passaging in diverse hosts. Society for Molecular Biology and Evolution Congress. San Juán (PR, USA). Poster.

215. López-González, S., Sánchez, F., Manrique, P., Mansilla, C., González-Melendi, P., Rodrigo, G., Elena, S.F., Ponz, F. 2014. Developmental alterations of Arabidopsis thaliana induced by Turnip mosaic virus infection. XII Reunión de Biología Molecular de Plantas. Cartagena (Spain). Poster.

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216. Member of the Organizing Comittee, 1st ASM Conference on Experimental Microbial Evolution. Washington (USA), Junio 2014.

217. Elena, S.F. 2014. “Experimental evolution of an emerging plant virus in host genotypes that differ in their degree of susceptibility and tolerance to infection”. 1st ASM Conference on Experimental Microbial Evolution. Washington DC (USA). Invited talk.

218. Willemsen, A., Tromas, N., Majer, E., Daròs, J.A., Elena, S.F., Zwart, M.P. 2014. “Experimental evolution of genome rearrangements in plant RNA virus”. 1st ASM Conference on Experimental Microbial Evolution. Washington DC (USA). Oral presentation.

219. Hillung, J., García-García, F., Cuevas, J.M., Elena, S.F. 2014. “The effect of genetic diversity of the host species on the adaptation of an emerging plant RNA virus”. 1st ASM Conference on Experimental Microbial Evolution. Washington DC (USA). Poster.

220. Bergua, M., Zwart, M.P., Elena, S.F., El-Mohtar, C., Shilts, T., Folimonova, S.Y. 2014. “Citrus tristeza virus p33 protein mediates superinfection exclusion at the whole organism level while is not required for excluion at the cellular level”. 33rd Annual Meeting of the American Society for Virology. Fort Collins (CO, USA). Poster.

221. Member of the Organizing Comittee and chairman of one session, CRM Workshop on Virus Dynamics and Evolution. Barcelona (Spain).

222. Elena, S.F. 2014. “Tracking the population dynamics of plant virus escape mutants”. CRM Workshop on Virus Dynamics and Evolution. Bellaterra (Spain). Invited talk.

223. Elena, S.F. 2014. “An experimental evolutiona approach to the emergence of plant RNA viruses”. 16th Annual Meeting of the Society of Evolutionary Studies Japan. Osaka (Japan). Invited talk.

224. Elena, S.F. 2014. “A systems biology approach to the evolution of virus-plant interactions”. 6th Slovenian Symposium on Plant Biology. Maribor (Slovenia). Invited talk.

225. Elena, S.F. 2014. “Experimenal evolution of genome architecture and complexity in RNA virus”. 1st Symposium on Molecular Aspects of Virology. México DF (México). Invited talk.

226. Elena, S.F. 2014. “Resistance to RNA viruses mediated by artificial-microRNAs: promises and disappointments”. XVII Congreso de la Sociedad Española de Fitopatología – REVIPLANT Symposium. Lleida (Spain). Invited talk.

227. Elena, S.F. 2014. “The rugged adaptive landscape of an emerging plant RNA virus”. EMBO YIP Sectorial Meeting Systems Biology and Evolution. Barcelona (Spain). Oral presentation.

228. Elena, S.F., Willemsen, A., Carrasco, J.L., Zwart, M.P. 2014. “Experimenal evolution of genome architecture and complexity in RNA virus”. XXX Congreso Nacional de Bioquímica. Guadalajara (México). Invited talk.

229. Folch-Fortuny, A., Bosque, G., Picó, J., Ferrer, A., Elena, S.F. 2014. “Latent structures-based modeling of mutated protein-protein interaction networks”. XII Conference on Computational Methods in Systems Biology. Manchester (UK). Poster.

230. Elena, S.F. 2014. “Major transitions observed during experimental virus evolution”. SFI Workshop on Major Transitions in Natural, Synthetic and Artificial Evolution. Santa Fe (NM, USA). Oral presentation.

231. Lalic, J., Cervera, H., Elena, S.F. 2015. “The ruggedness of adaptive fitness landscapes and the predictability of virus evolution”. III Reunión de la Red Española Interdisciplinar de Biofísica de Virus (BioFiViNet). Bilbao (Spain). Invited talk.

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232. Folch-Fortuny, A., Bosque, G., Picó, J., Ferrer, A., Elena, S.F. 2015. “Genomic, proteomic and phenotypic data fusion: the case of potyviruses”. III Reunión de la Red Española Interdisciplinar de Biofísica de Virus (BioFiViNet). Bilbao (Spain). Poster.

233. Lalic, J., Cervera, H., De la Iglesia, F., Elena, S.F. 2015. “The ruggedness of adaptive fitness landscape and the predictability of virus evolution”. 8th Workshop on Viral Evolution, Pennsylvania State University. State College, PA (USA). Oral presentation.

234. Willemsen, A., Tromas, N., Majer, E., Daròs, J.A., Elena, S.F. 2015. “Experimental evolution of genome rearrangements in plant RNA virus”. 8th Workshop on Viral Evolution, Pennsylvania State University. State College, PA (USA). Oral presentation.

235. Elena, S.F., Tromas, N., Lafforgue, G., Zwart, M.P. 2015. “Genetic bottlenecks during virus infection and host colonization and their impact on genetic diversity and evolution”. Xth International Symposium on Thysanoptera and Tospoviruses. Asilomar Conference Grounds, Pacific Grove, CA (USA). Invited talk.

236. Hillung, J., García-García, F., Dopazo, J., Cuevas, J.M., Elena, S.F. 2015. “The molecular evolution and gene expression analyses of an evolved plant-virus gene-forgene interaction”. Gordon Research Conference on Molecular Mechanisms in Evolution. Easton, MA (USA). Poster.

237. Willemsen, A., Zwart, M.P., Elena, S.F. 2015. “Experimental evolution of genetic redundancy in a plant RNA virus”. Gordon Research Conference on Molecular Mechanisms in Evolution. Easton, MA (USA). Poster.

238. Lalic, J., Cervera, H., Elena, S.F. 2015. “The ruggedness of adaptive fitness landscapes and the predictability of virus evolution”. American Society of Virology 2015 Congress. London, ON (Canada). Invited talk.

239. Elena, S.F. 2015. “Trade-off between virulence and host specificity in experimental Potyvirus-plant pathosystems. British Ecological Society Symposium on The Ecology and Evolution of Emerging Plant Pests and Pathogens. University of Exeter, Penryn (UK). Invited talk.

240. Member of the organizing committee, ECAL 2015 EvoEvo Workshop. York (UK), July 2015.

241. Member of the scientific board, Vth Congress of the Spanish Society of Evolutionary Biology. Murcia (Spain), January 2016.

242. Elena, S.F., Hillung, J., Cuevas, J.M. García-García, F., Dopazo, J. 2016. “The transcriptomics of an experimentally evolved plant-virus gene-for-gene interaction”. Conference on Evolutionary Systems Biology. Wellcome Genome Campus, Hinxton (UK). Invited talk.

243. Elena, S.F. 2016 “Fitness-tradeoffs and host specificity in experimental potyvirus-plant pathosystems”. Pathogen Host Shift Workshop. University of Cambridge, Cambridge (UK). Invited talk.

244. Elena, S.F. 2016. “RNA plant viruses as model systems to tackle the problema of the evolution of generalists and specialists pathogens during host switching”. EMBO Symposium New Model Systems for Linking Evolution and Ecology. Heidelberg (Germany). Invited talk.

245. Member of the scientific board, XIII Symposium on Bioinformatics. Valencia (Spain), May 2016.

246. Kutnjak, D., Gutiérrez-Aguirre, I, Elena, S.F., Ravnikar, M. 2016. “Deep sequencing of small RNAs for studies of plant virus diversity and evolution”. 13rd International Plant Virus Epidemiology Symposium. Avignon (France). Poster.

247. Elena, S.F. 2016. “To which extent can RNA virus evolution be predicted?”. CIFAR Integrated Microbial Biodiversity Program Symposium. Toronto, ON ( Canada). Invited talk.

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248. Member of the Organizing Comittee, 2nd ASM Conference on Experimental Microbial Evolution. Washington (USA), August 2016.

249. Willemsen, A., Zwart, M.P., Tromas, N., Ambrós, S., Carrasco, J.L., Elena, S.F. 2016. “A roadmap to genome architecture: experimental evolution in an RNA virus”. ISME 2016. Montreal, QC (Canada). Poster.

250. Kutnjak, D., Gutiérrez-Aguirre, I., Elena, S.F., Ravnikar, M. 2016. “Using deep sequencing of small RNAs to track plant virus population structure changes during experimental evolution”. AAB International Advances in Plant Virology. Greenwich (UK). Poster.

251. Member of the scientific board, International Conference on Systems Biology 2016. Barcelona (Spain), September 2016.

252. Somovilla, P., Pigolotti, S., Elena, S.F., Cuesta, J.A, Manrubia, S. 2016. “Inference of fitness landscapes from next-generation sequencing data”. International Conference on Systems Biology 2016. Barcelona (Spain). Poster.

253. Elena, S.F. 2016. “Evolutionary and systems biology of viral emergence”. XXVII Congresso Brasileiro de Virologia/XI Encuentro de Virología de Mercosur. Pirenópolis, GO (Brasil). Plenary conference.

254. Elena S.F. 2016. “Resistance to RNA virus based on the expression of amiRNAs: promisses and disappointments”. XXVII Congresso Brasileiro de Virologia/XI Encuentro de Virología de Mercosur. Pirenópolis, GO (Brasil). Oral presentation.

255. Member of the scientific board, EvoEvo Workshop, 2016 Conference on Complex Systems. Amsterdam (The Netherlands), September 2016.

256. Beslon G., Liard, V., Elena, S.F. 2016. “Evolvability drives innovation in viral genomes”. EvoEvo Workshop, 2016 Conference on Complex Systems. Amsterdam (The Netherlands). Talk.

257. González, R., Ambrós, S., Martorell, P., Ramón, D., Elena, S.F. 2017. “Evaluation of Caenorhabditis elegans as experimental host for a thrip-transmitted plant RNA virus”. VI Spanish Worm Meeting. Valencia (Spain). Poster and talk. (Published in F1000Res. 6: 295, doi: 10.7490/f1000research.1113766.1)

258. Ambrós, S., Elena, S.F. 2017. “Comparison of the rates and molecular signatures of compensatory evolution in coding and non-coding sequences of a plant RNA virus”. 9th Workshop in Virus Evolution. Pennsylvania State University. State College, PA (USA). Poster.

259. Cervera, H., Ambrós, S., Bernet, G.P., Bakker, R., Rodrigo, G., Elena, S.F. 2017. “Host determinants of differences in viral fitness”. 9th Workshop in Virus Evolution. State College, PA (USA). Poster.

260. Chao, L., Elena, S.F. 2017. “Non-linear tradeoffs allow cooperation to evolve from Prisoner’s dilemma to Snow Drift”. 9th Workshop in Virus Evolution. Pennsylvania State University. State College, PA (USA). Talk.

261. Minicka, J., Rymelska, N., Elena, S.F., Czerwoniec, A., Hasiów-Jaroszewska, B. 2015. “Molecular evolution of Pepino mosaic virus in different hosts”. 9th Workshop in Virus Evolution. Pennsylvania State University. State College, PA (USA). Poster.

262. Elena, S.F. 2017. “Host variability in resistance genes conditions the evolutionary fate of an emerging RNA plant virus”. XIV Congreso Nacional de Virología. Cádiz (Spain). Invited talk.

263. Martínez, F., Elena, S.F. 2017. “Towards a host-potyvirus protein-protein interaction network”. XIV Congreso Nacional de Virología. Cádiz (Spain). Poster. (Published in Virología 20: S84, 2017).

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264. Cervera, H., Ambrós, S., Rodrigo, G., Bernet, G.P., Bakker, R., Elena, S.F. 2017. “Identifying host factors whose whose expression correlates with differences in viral fitness”. XIV Congreso Nacional de Virología. Cádiz (Spain). Poster. (Published in Virología 20: S106-S107, 2017).

265. Ambrós, S., Elena, S.F. 2017. “Comparison of the rates of compensatory evolution in coding and non-coding sequences of a plant RNA virus”. XIV Congreso Nacional de Virología. Cádiz (Spain). Poster. (Published in Virología 20: S107-S108, 2017).

266. Chairman session on Systems Biology in the XXIII Reunión de la Sociedad Española de Fisiología Vegetal/XV Spanish Portuguese Congress of Plant Physiology. Barcelona (Spain), Junio 2017.

267. Elena, S.F. 2017. “A systems biology perspective to the evolution of virus-plant Interactions”. XXIII Reunión de la Sociedad Española de Fisiología Vegetal/XV Spanish Portuguese Congress of Plant Physiology. Barcelona (Spain). Keynote talk.

268. Gordon Research Conferences on Microbial Population Biology. Andover, NH (USA), 2017. Organizer session Evolutionary Consequences of Epistasis.

269. Coorganizer symposium Fitness landscapes, big data and the predictability of evolution, XVIth ESEB Congress. Groningen (Netherlands), 2017.

270. Beslon, G., Liard, V., Elena, S.F. 2017. “Testing evolution predictability using the aevol software”. XVIth ESEB Congress, Groningen (Netherlands). Poster.

271. Elena, S.F. 2017. “Experimental evolution of plant-RNA virus interactions: a game of resistances and virulence”. KITP program Eco-ecolutionary dynamics in Nature and the lab. University of California Santa Barbara (CA, USA). Invited talk.

272. Chairman of one session. 2017. EMBO Members Meeting 2017. Heidelberg (Germany).

273. Elena, S.F. 2017. “Population heterogeneity in host’s susceptibility to infection drives the evolution of virulence of a plant RNA virus”. FISABIO Workshop on Experimental Evolution. Segorbe (Spain). Invited talk.

274. Elena, S.F. 2018. “Mechanisms of virus evolution and emergence”. Australasian Plant Virology Workshop. Waiheke Island (Auckland, New Zealand). Richard Forster Memorial Lecture.

275. Scientific Committee. LVIII Scientific Session Institute of Plant Protection – National Research Institute. Poznań (Poland), April 2018.

276. Elena, S.F. 2018. “Petites grans transicions evolutives: l’origen evolutiu de les innovacions en el món viral”. XIX Matinal de l’Evolució (València, Spain).

277. Chairman session Evolutionary and Molecular Virology, Conference The Power of Viruses, Poreč (Croatia), May 2018.

278. Elena, S.F. 2018. “The contribution of plant RNA viruses to address fundamental questions in evolutionary biology”. Conference The Power of Viruses. Poreč (Croatia). Keynote lecture.

279. Hasiów-Jaroszewska, B., Minicka, J., Zarzyńska-Nowak, A., Budyńska, D., Elena, S.F. 2018. “Defective RNA particles of Tomato black ring virus: origin, structure and biological effect”. Conference The Power of Viruses. Poreč (Croatia). Poster.

280. Hasiów-Jaroszewska, B., Budzyńska, D., Zarzyńska-Nowak, A., Elena, S.F. 2018. “Genetic diversity of Tomato black ring virus isolates collected from different hosts”. Conference on Virus Genomics and Evolution 2018. Wellcome Genome Campus, Hinxton (UK). Poster.

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281. Elena, S.F. 2018 “Experimental host-range expansion in a plant RNA virus: an interplay between viral fitness and regulation of host’s transcriptome “. The Ramon Margalef Summer Colloquia: Ecology Through the Omics Lens. Barcelona (Spain). Invited talk.

282. Elena, S.F. 2018 “Differences among A. thaliana ecotypes in response to infection drive patterns of virus adaptation”. B-Debate When Development Meets Stress: Understanding Developmental Reprogramming Upon Pathogenesis in Plants. Barcelona (Spain). Invited talk.

283. Organizer SFI Workshop Integrating Critical Phenomena and Multiscale Selection in Virus Evolution, Santa Fe (NM, USA). November 2018.

284. Elena, S.F., Ambrós, S., Butković, A., Carrasco, J.L., de la Iglesia, F., González, R., Martínez, F., Navarro, R. 2018. “Host variability in resistance genes conditions the evolution of emerging plant RNA viruses”. XIII Reunión de Biología Vegetal. Puerto Varas (Chile). Invited talk.

285. Elena, S.F. 2019. “To which extent can we predict RNA virus evolution?”. CNB-CSIC Colloquium on Programability and Predictability of Biological Systems. Madrid (Spain). Invited talk.

286. Navarro, R., de la Iglesia, F., Ambrós, S., Martínez, F., Carrasco, J.L., Elena, S.F. 2019. “Host variability in resistance genes conditions the evolution of emerging plant RNA viruses”. 10th Workshop in Virus Evolution. State College, PA (USA). Talk.

287. González, R., Butković, A., de la Iglesia, F., Elena, S.F. 2019. “Role of host population structure in the evolution of virulence in a plant virus”. 10th Workshop in Virus Evolution. State College, PA (USA). Talk.

288. González, R., Butković, A., Martínez-Latorre, J., de la Iglesia, F., Elena, S.F. 2019. “Evolving in drought conditions: consequences in the interaction between a potyvirus and Arabidopsis thaliana”. 10th Workshop in Virus Evolution. State College, PA (USA). Poster.

289. Elena, S.F. 2019. “RNA virus: living in rugged and fluctuating landscapes”. Workshop From Sequences to Functions: Challenges in the Computation of Realistic Genotype-Phenotype Maps. Centre Européen de Calcul Atomique et Moléculaire (CECAM). Zaragoza (Spain). Invited talk.

290. González, R., de la Iglesia, F., Butković, A., Elena, S.F. 2019. “Evolution of virulence of an emerging RNA virus in homogeneous vs heterogeneous plant populations”. XXIes Journées Francophones de Virologie. Lyon (France). Invited talk. (Published in Virologie 22: 59, 2019).

291. Scientific Committee and chairman session Plant Virology. 2019 Congress of the European Society of Virology. Rotterdam (Netherlands), April 2019.

292. Elena, S.F., Ambrós, S., Butković, A., Carrasco, J.L., de la Iglesia, F., González, R., Martínez, F., Navarro, R. 2019. “Host variability in resistance genes conditions the evolution of emerging plant RNA viruses”. European Congress of Virology 2019. Rotterdam (Netherlands). Invited talk.

293. Elena, S.F., Ambrós, S., Butković, A., Carrasco, J.L., de la Iglesia, F., González, R., Martínez, F., Navarro, R. 2019. “Variability in resistance genes conditions the evolution of emerging plant RNA viruses”. 14th Internation Plant Virus Epidemiology Symposium. Seoul (Korea). Invited keynote talk.

294. Elena, S.F. 2019. “Adaptive dynamics of viral populations - perspective from complex systems theory”. International Workshop New Vistas in Computational Systems and Synthetic Biology. Vigo (Spain). Invited talk.

295. Elena, S.F. 2019. “Experimental evolution of RNA viruses in fluctuating fitness landscapes”. Physics of Evolution. Francis Crick Institute, London (UK). Invited talk.

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296. Elena, S.F. 2019. “Experimental evolution of host range in RNA virus”. EMBO YIP Workshop on Evolutionary and Computational Biology, Basel (Switzerland). Invited talk.

297. González, R., Butković, A., Martínez-Latorre, J., Melero, I., de la Iglesia, F., Elena, S.F. 2019 “Environmental stress shapes the evolution of a potyvirus towards a mutualistic relationship with its host”. Conferences Jacques Monod on Virus Evolution on the Mutualism-Parasite Continuum. Roscoff (Francia). Talk.

298. Organizer SFI Working Group Critical Phenomena and Phase Transitions in the Viral World, Santa Fe (NM, USA). November 2019.

299. Elena, S.F. 2019. “Within- and between-hosts dynamics of plant virus diversity in reservoir and novel hosts”. SFI Working Group Critical Phenomena and Phase Transitions in the Viral World, Santa Fe (NM, USA). Talk.

300. Catalán, P., Elena, S.F., Cuesta, J.A., Manrubia, S. 2020. “Parsimonious scenario for the emergence of viroid-like replicons de novo”. VII Congress of the Spanish Society for Evolutionary Biology. Seville (Spain). Poster.

301. González, R., Butković, A., Martínez-Latorre, J., Melero, I., Pérez-Parets, E., de la Iglesia, F., Elena, S.F. 2020. Virus evolution in the pathosystem turnip mosaic potyvirus – Arabidopsis thaliana under drought conditions selects for viruses who enhance the host tolerance to water deficiency. Conference on Evolutionary Systems Biology. Wellcome Genome Campus, Hinxton (UK). Poster.

302. Butković, A., González, R., Elena, S.F. 2020. Mapping Arabidopsis thaliana genes involved in plant response to a turnip mosaic potyvirus (TuMV) infection. Conference on Evolutionary Systems Biology. Wellcome Genome Campus, Hinxton (UK). Talk.

303. Elena, S.F. 2020. Integrative systems biology approaches to characterize the evolution of plant-virus interactions. Future Biotech Winter Retreat. Novosibirsk (Russian Federation). Invited talk.

304. Elena, S.F. 2020. Identifying early-warning signals for the sudden transition from mild to severe tobacco etch disease by dynamical network biomarkers (DNB). CAL Workshop Down of the Molecular Pathways as Deterministic Circuits Paradigm. LSC Canfranc, Huesca (Spain). Invited talk.

6.- PARTICIPATION IN FUNDED RESEARCH PROJECTS:

1. Project PB91-0051-C02-02 "Genetic variability of RNA viruses: Biological fitness of variants and the effect of deleterious mutations accumulation" funded by the Comisión Interministerial de Ciencia y Tecnología, Spain. (1992-1995). PI: Prof. Andrés Moya.

2. Project PB94-0034-C02-02 “Genetic variability of RNA viruses: Population dynamics between viral variants” funded by the Comisión Interministerial de Ciencia y Tecnología, Spain (1995-1998). PI: Prof. Andrés Moya.

3. Project PM97-0060-C02-02 “Genetic variability of RNA viruses: Molecular basis and quantification of biological fitness gains” funded by the Dirección General de Investigación Sanitaria, Spain (1998-2001). PI: Prof. Andrés Moya.

4. Project 1FD97-2328 “Molecular epidemiology of high-prevalence viral diseases: large-scale study of the hepatitis C virus in the Valencian Comunity”funded by the FEDER program of the European Union (2000-2002). PI: Prof. Andrés Moya.

5. Project GV01-65 “Effect of epistasis and genome complexity in the dynamics of viral evolution” funded by the Generalitat Valenciana, Spain (2002-2003). PI: Dr. Santiago F. Elena.

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6. Project BMC2001-3096 “Adaptive evolution and genetic variability in viral coinfections” funded by the Ministerio de Ciencia y Tecnología, Spain (2002). PI: Prof. Andrés Moya.

7. Project BMC2003-00066 "Experimental evolution of plat viruses: characterization of mutational effects and the evolutionary implications of genome segmentation” funded by the Ministerio de Ciencia y Tecnología, Spain (2003 – 2006). PI: Dr. Santiago F. Elena.

8. Project GRUPOS03/064 for R+D consolidated groups funded by the Generaltiat Valenciana (2003 - 2004). PI: Prof. Ricardo Flores.

9. Project GV04B280 “PTGS suppression as an adaptive response in plant viruses” funded by the Generalitat Valenciana, Spain (2004-2005). PI: Dr. Santiago F. Elena.

10. EMBO Young Investigator Program – MEC Special actions BFU2004-22607-E and BFU2005-23720-E/BMC (2005 – 2007). PI: Dr. Santiago F. Elena.

11. Joint Action with France HF2005-0284 “Coevolutionary synergistic interactions among phytoviruses” financed by the Spanish Ministerio de Educación y Ciencia (2006 – 2007). Spanish PI: Dr. Santiago F. Elena. French co-PI: Dr. Rémy Froissart (CNRS-INRA-CIRAD, Montpellier)

12. Project BFU2005-24995-E/BMC “Spanish Network for Systems Molecular Biology” funded by the Ministerio de Educación y Ciencia, Spain (2006 – 2007). PI: Santiago F. Elena

13. Project ACOMP2006/015 Complementary funds to R+D Projects funded by the Generalitat Valenciana, Spain (2006). PI: Prof. Santiago F. Elena.

14. Project BFU2006-14819-CO2-01/BMC “Experimental evolution of plant viruses: deleterious mutations, mechanisms of genomic robustness and the evolution of the interaction with plant defence mechanisms” funded by the Ministerio de Educación y Ciencia, Spain (2007-2009). PI: Prof. Santiago F. Elena.

15. Project ACOMP2007/263 Complementary funds to R+D Projects funded by the Generalitat Valenciana, Spain (2007). PI: Prof. Santiago F. Elena.

16. Joint Action with France HF2007-0098 “The interplay between mutation and adaptation across fixed or variable environments in RNA viruses” financed by the Spanish Ministerio de Educación y Ciencia (2008 – 2009). Spanish PI: Prof. Santiago F. Elena. French co-PI: Dr. Guillaume Martin (CNRS-IRD, Montpellier).

17. Project RGP12/2008 “Evolutionary implications of virus-encoded gene-silencing suppression” financed by the Human Frontier Science Program Organization. 2008-2011. PI: Prof. Santiago F. Elena.

18. Project ACOMP2009/023 Complementary funds to R+D Projects funded by the Generalitat Valenciana, Spain (2009). PI Prof. Santiago F. Elena.

19. Project BFU2009-06993/BMC “Evolutionary systems virology of plant RNA virus emergence” funded by the Ministerio de Ciencia e Innovación, Spain (2010-2012). PI: Prof. Santiago F. Elena.

20. Project ACOMP2010/089 Complementary funds to R+D Projects funded by Generalitat Valenciana (2010). PI: Prof. Santiago F. Elena.

21. Project PROMETEO/2010/019 “Evolutionary implications of virus-encoded gene-silencing suppression” funded by Generalitat Valenciana (2010-2012). PI: Prof. Santiago F. Elena.

22. FORMOSA Joint Action 2010TW0015 “Evaluation of the durability of artificial microRNA-mediated strategies for plant resistance to RNA viruses” funded by CSIC-Taiwan NCS (2011-2013). Spanish PI: Dr. José A. Daròs. Taiwanish co-PI: Dr. Shih-Shun Lin (NCS Institute of Biotechonology).

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23. I+D Contract with Laboratorios Hipra SA “Study of the genetic variability of the reproductive and respiratory syndrome virus (PRRSV)”. PI: Prof. Santiago F. Elena.

24. Project JTF22371 “Experimental evolution of genome architecture and complexity in RNA virus” funded by John Templeton Foundation (2012-2013). PI: Prof. Santiago F. Elena.

25. Project BFU2012-30805 “Evolutionary systems virology: epistasis and the ruggedness of adaptive landscapes, mutations in regulatory sequences, and the host determinants of viral fitness”. Funded by the Ministerio de Economía y Competitividad (2013-2015). PI: Prof. Santiago F. Elena.

26. Project ICT-610427 “Evolution of evolution – EvoEvo”. Funded by the EU FP7 Program (2013-2016). Spanish PI: Santiago F. Elena.

27. Project PROMETEOII/2014/021 “Comparative systems biology of host-virus interactions” funded by Generalitat Valenciana (2014-2017). PI: Santiago F. Elena.

28. Project EUIN2015-62632 “Dinámicas de poblaciones de virus de RNA a escala de células individuales” funded by Ministerio de Economía y Competitividad (2015). PI: Santiago F. Elena Fito.

29. Project BFU2015-65037-P “Evolution of viruses in hosts with variable susceptibility: consequences in fitness and virulence and changes in the virus-host interaction networks”. Funded by Agencia Nacional de Investigación (2016-2019). PI: Santiago F. Elena Fito.

30. Project GRISOLIAP/2018/005 “Epigenetic complexes as host organizers of plant viral evolution”. Funded by Generalitat Valenciana (2018-2021). PI: Santiago F. Elena Fito.

31. Project DEB1830688 “RoL:FELS Integrating critical phenomena and multi-scale selection in virus evolution”. Funded by USA National Science Foundation (2018-2019). PI: Santiago F. Elena Fito.

32. Project PROMETEU/2019/012 “Plant-virus dynamic interactores: identifying early-warnings of critical transitions to disease”. Funded by Generalitat Valenciana (2019-2022). PI: Santiago F. Elena Fito.

33. Project PIE202020E094 “Setting up Caenorhabditis elegans as experimental pathosystem to study host-virus interactions”. Funded by CSIC (2020-2021). PI: Santiago F. Elena Fito.

7.- DIRECTION OF THESIS AND SUPERVISSION OF POSTDOCTORAL AND VISITING RESEARCHERS:

Supervised PhD Theses

1. M. Rosario Miralles Borrego. “Efecto del tamaño y estructuración poblacional en poblaciones experimentales del virus de la estomatitis vesicular (VSV)”. Universitat de València. Cosupervirsor: Prof. Andrés Moya. May 9th, 2000. Qualification: Excellent Cum Laude.

2. José M. Cuevas Torrijos “Restricciones adaptativas durante la evolución experimental del virus de la estomatitis vesicular (VSV)”. Universitat de València. Cosupervirsor: Prof. Andrés Moya. September 24th, 2003. Qualification: Excellent Cum Laude. Currently Ramón y Cajal Researcher at the University of Valencia.

3. Rafael Sanjuán Verdeguer. “Robustez genética, epistasia y evolución de los virus de RNA”. Universitat de València. Cosupervirsor: Prof. Andrés Moya. February 15th, 2005. Qualification: Excellent Cum Laude. Currently Associate Professor at the University of Valencia.

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4. Francisco M. Codoñer Cortés. “Evolución molecular y relaciones taxonómicas de la familia Bromoviridae de virus de plantas”. Universitat de València. September 15th, 2006. Qualification: Excellent Cum Laude. Currently R+D Director at Life Sequencing LTD, a biotech company.

5. S. Patricia Agudelo Romero. “Evolución experimental de la gama de huéspedes del virus del grabado del tabaco (TEV)”. Universidad Politécnica de Valencia. Cosupervisor: Dr. Rafael Sanjuán. April 28th, 2009. Qualification: Excellent Cum Laude. Currently researcher at the Murdoch Children’s Research Institute, Perth, Australia.

6. Clara Torres Barceló. “Evolución molecular de la proteína HC-Pro del TEV, supresor del silenciamiento del RNA”. Universitat de València. Cosupervisor: Dr. José A. Daròs. September 22nd, 2009, Qualification: Excellent Cum Laude. Currently INRA CR1 scientist, Avignon, France.

7. Guillermo Rodrigo Tárraga. “Computational design and designability of gene regulatory networks”. Universidad Politécnica de Valencia. Cosupervisor: Dr. Alfonso Jaramillo. December 19th, 2011, Qualification: Excellent Cum Laude. Currently CSIC associate profesor at IBMCP, Valencia.

8. Javier Carrera Montesinos. “Automatic computational design of synthetic genomes”. Universidad Politécnica de Valencia. Cosupervisor: Dr. Alfonso Jaramillo. July 17th, 2012, Qualification: Excellent Cum Laude. Currently bioinformatics scientist III at Zymergen Inc., USA.

9. Jasna Lalić. “Nonlinearities in plant RNA virus fitness”. December 10th, 2012. Universitat de València. Qualification: Excellent Cum Laude. Currently Projects Development Manager at Sandoz-Novartis Development Center, Slovenia.

10. Nicolas Tromas. “Evaluating fundamental life-history traits for Tobacco etch potyvirus”. July 3rd, 2013. Universitat de València. Qualification: Excellent Cum Laude. Currently research associated at the Department of Biology, University of Montreal, Canada.

11. Guillame C.G. Lafforgue. “Resistance to virus infection mediated by artificial microRNAs: estimating the likelihood of escape mutants”. Universitat de València. Cosupervisor: Dr. José A. Daròs. November 5th, 2013. Qualification: Excellent Cum Laude. Currently postdoctoral researcher at CNRS, Toulouse, France.

12. Fernando Martínez García. “Análisis de la dinámica de replicación de un virus de RNA de plantas y del uso de microRNAs artificiales como estrategia antiviral”. Universidad Politécnica de Valencia. Cosupervisor: Dr. José A. Daròs. January 24th, 2014. Qualification: Excellent Cum Laude.

13. Julia Hillung. “La emergencia viral como consecuencia de la interacción entre las variabilidades genéticas del virus y huésped”. Universitat de València. Cosupervisor: Dr. José M. Cuevas. November 5th, 2015. Qualification: Excellent Cum Laude. Currently postdoctoral researcher at FISABIO, Spain.

14. Anouk Willemsen. “Experimental evolution of genome architecture and complexity in an RNA virus”. Universitat de València. Cosupervisor: Dr. Mark P. Zwart. May 24th, 2016. Qualification: Excellent Cum Laude. Currently Marie Sklodowska-Curie postdoctoral fellow at University of Vienna, Vienna, Austria.

15. Héctor Cervera Benet. “Epistasia multidimensional y rugosidad de los paisajes adaptativos y factores del huésped que determinan la eficacia viral”. January 26th, 2018. Universidad Politécnica de Valencia. Qualification: Excellent Cum Laude.

16. Anel Nurtay. “Mathematical modelling of pathogen specialization”. Universitat Autònoma de Barcelona. Cosupervisor: Prof. Lluís Alsedà. February 25th, 2019. Qualification: Excellent Cum Laude. Currently postdoctoral researcher at Oxford Big Data Institute, UK.

17. Rebeca Navarro Canales. 2014 -.

18. Rubén González Miguelez. Fellow from MCIU. 2017- .

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19. Anamarija Butković. GRISOLIA fellow from Generalitat Valenciana. 2018 -.

20. Javier Falgueras Cano. 2018 -.

Supervised Master Theses

1. M. Rosario Miralles Borrego. “Caracterización de los niveles de selección en poblaciones experimentales del virus de la estomatitis vesicular”. December 18th, 1995, Universitat de València. Cosupervisor: Prof. Andrés Moya. Qualification: Excellent.

2. Rafael Sanjuán Verdeguer. “Pruebas estadísticas para filogenias obtenidas mediante matrices de distancias: cómo evaluar las ramas cuando otros métodos no son aplicables”. September 15th, 2002, Universitat de València. Qualification: Excellent.

3. Francisco Manuel Codoñer Cortés. “Estructura poblacional intra-paciente del HIV-1”. September 15th, 2002, Universitat de València. Qualification: Excellent.

4. Clara Torres Barceló. “La supresión del silenciamiento génico post-transcripcional como estrategia evolutiva de los virus de plantas”. December 14th, 2005, Universitat de València. Qualification: Excellent.

5. Josep Sardanyés i Cayuela. “Error threshold and sensitivity to mutations depend on whether RNA virus replication occurs geometrically or via a stamping machine”. June 30th, 2008, Universitat Pompeu Fabra. Cosupervisor: Prof. Ricard V. Solé. Qualification: Excellent.

6. Pablo Hernández Alonso. “Evolution of gene duplications in context of genetic networks of increasing complexity”. September 19th, 2011, Universidad Politécnica de Valencia. Qualification: Excellent.

7. Rubén González Miguélez. “Evaluating the potential of Caenorhabditis elegans as experimental host for arboviruses”. January 23rd, 2017. Universidad Politécnica de Valencia. Cosupervisor: Dr. Silvia Ambrós. Qualification: Excellent.

8. Sttefany M. Rosario. “Evolución compensatoria del coste asociado a la adición de genes al genoma del potyvirus del grabado del tabaco”. September 19th, 2017. Universitat de València. Qualification: Excellent.

9. Inés Cobo Diego. “Comparative analysis of the dynamical network biomarkers marking phase transitions for different viruses”. Universitat de València. In progress.

Supervised Final Degree Works

1. Ariadna Albó Delgado. “Interference of defective particles in the replication of RNA viruses with satellites”. Universitat Politècnica de Catalunya, Fac. Matemàtiques. Cosupervisors: Dr. J. Tomás Lázaro and Dr. Josep Sardanyés. September 10th, 2018. Qualification: Excellent.

2. Juan C. Muñoz Sánchez. “Anaysis of phase transitions between health and disease cellular stages to identify early warning signals”. Universitat de València, Fac. Física. Tutor: Dr. José A. Oteo. July 16th, 2019. Qualification: Excellent.

3. Adrián Tarazona Sánchez. “Detection of early warning signals for the transtion between healthy and disease states during the infection of Nicotiana tabacum with tobacco etch virus”. Universitat Politécnica de València, ETSIAMN. Tutor: Dr. Javier Forment. September 16th, 2019. Qualification: Excellent.

Postdoctoral students

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1. Dr. Paul E. Turner. Postdoctoral student. Postdoctoral fellow from the National Academy of Sciences-NATO, 1999. Currently Professor at the Department of Ecology and Evolutionary Biology, Yale University, USA.

2. Dr. M. Purificación Carrasco Valero. Postdoctoral associated. September 2003 – Decembre 2007 + November 2008 - 2011. Currently Associate Researcher at the University of Valencia.

3. Dr. Rafael Sanjuán Verdeguer. Postdoctoral I3P CSIC research associate. April 2005 - December 2007. Currently Associate Professor at the University of Valencia.

4. Dr. Susana Martin García. Postdoctoral fellow from the Juan de la Cierva program (MEC). January 2006 – December 2008. Postdoctoral associated. May 2011 - .

5. Dr. Alexandra Blanchard-Letort. Postdoctoral fellow from the INRA (France). September 2008 – August 2009. Currently INRA CR2 scientist, Tours, France.

6. Dr. Josep Sardanyés Cayuela. Postdoctoral fellow from UPF. September 2009 – May 2011. Currently, postdoctoral researcher, Universitat Pompeu Fabra, Barcelona.

7. Dr. Stéphanie Bedhomme. JAE-Doc Postdoctoral Associate (CSIC). May 2009 – August 2012. Currently CNRS Teanured Scientist, Center of Functional Ecology, Montpellier, France

8. Dr. José M. Cuevas Torrijos. JAE-Doc Postdoctoral Associate (CSIC). May 2010 – April 2012. Currently Associate Researcher at the University of Valencia.

9. Dr. Mark P. Zwart. Postdoctoral fellow RUBICON program, Dutch government. March 2010 – February 2012. P ostdoctoral fellow from the Juan de la Cierva program (MINECO). March 2012 – April 2014. Currently postdoctoral resarcher at the University of Cologne, Germany.

10. Dr. Nicolas Tromas, postdoctoral associated (June 2013 – December 2014). Currently postdoctoral researcher at the University of Montreal, Canada.

11. Dr. Guillermo P. Bernet Zamanillo, postdoctoral associate (August 2013 – March 2015).

12. Dr. José L. Carrasco Jiménez, postdoctoral associate (November 2013 – December 2017).

13. Dr. Beilei Wu, postdoctoral associate (September 2014 – February 2016).

14. Dr. Fernando Martínez García, postdoctoral associate (October 2014 – December 2017).

15. Dr. Silvia Ambrós Palaguerri, postdoctoral associate (April 2015 -).

16. Dr. Denis Kutnjak, postdoctoral associate (February 2019 – March 2020).

Visiting scientists

1. Dr. Howard Ochman. Sabbatic from the University of Arizona. August 2000 – January 2001.

2. Antonio V. Bordería Giner. PhD student. Fellow from the Spanish National Institutes of Health (ISCIII), January-July 2001.

3. Sherri Goings. PhD student Michigan State University. January-June 2007.

4. Jeffrey Clune. PhD student. Michigan State University. January-July 2007.

5. Guillaume Lafforgue. FEMS Fellow. September-December 2007.

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6. Jasna Lalic. FEMS Fellow. September-December 2007.

7. Dr. Romain Gallet. CNRS. March-May 2009.

8. Dr. Ana Grande-Pérez. University of Málaga. June-September 2009.

9. Dr. Virginia Ruiz-Ferrer. CNRS. June-July 2009.

10. Carme Zaragoza. JAE-Intro Fellow. July-September 2009.

11. Enric Cosme. JAE-Intro Fellow. July-September 2009.

12. Dr. Alfonso Jaramillo, CNRS. August 2008, 2009.

13. Dr. Beata Hasiów-Jaroszewska. Polish National Research Institute of Plant Protection. EMBO Short Term Fellow, January – March 2011.

14. Dr. Beilei Wu. Institute of Plant Protection – Chinese Academy of Agricultural Sciences. April – June 2011.

15. Dr. Arcady Mushigian. USA National Science Foundation. June-July 2014, June-July 2015.

16. Julia Minicka. Polish National Research Institute of Plant Protection. November 2014.

17. Denis Kutnjak. Slovenian National Institute of Biology. February 2016.

18. Ruben Bakker, University of Amsterdam, The Netherlands. ERASMUS+ fellow. October 2016 –March 2017.

19. Anamarija Butković, University of Zagreg, Croatia. ERASMUS+ fellow. October 2016 - February 2017.

20. Dr. Régis Lopes Corrêa, Universidade Federal do Rio de Janeiro, Brazil. May 2017 – April 2019.

21. Zala Kogej, University of Ljubljana, Eslovenia. ERASMUS+ fellow. September 2017 – December 2017.

22. Dr. Rachel Whitaker, sabbatical. University of Illinois at Urbana. August 2017 – July 2018.

23. Javier Martínez-Latorre. JAE-Intro Fellow. June – December 2018.

24. Swarnalock De, University of Helsinki, Finland. October – November 2018.

25. Daria Budzynska, National Research Institute of Plant Protection Poznan, Poland. Jauary 2019.

26. Izan Melero. ADEIT/Universitat de València Practicum. February – April 2019.

27. Mark Paul S. Rivarez, University of Philippines Los Baños, Philippines. April – June 2019.

28. Enric Pérez. ADEIT/Universitat de València Practicum. May – July 2019.

29. Aleksandra Zarzyńska-Nowak, National Research Institute of Plant Protection, Poznan, Poland. June - July 2019.

30. Paul Banse, École Normal Supérieure-INRIA, Rennes, France. February – June 2020.

31. João M. Fagundes Silva, Instituto de Ciências Biológica, Universidade de Brasília. March – September 2020.

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International mentoring programs

1. Dr. Beata Hasiów-Jaroszewska, National Research Institute of Plant Protection, Poznan, Poland. Programme, Foundation for Polish Science. January 2011 - 2014.

2. Dr. Erdal Toprak, Sabanci University, Istanbul, Turkey. EMBO Installation Grants Mentorship. May 2013 -

8.- INVITED TALKS:

1. “Viroids, viroidlike domain of the hepatitis d factor and RNA satellites: study of primitive living forms". July 30th, 1991. Centro de Biología Molecular Severo Ochoa (Madrid, Spain).

2. “Evolutionary Biology of RNA viruses”. November 20th, 1991. Ecology and Evolutionary Biology Program, Michigan State University (East Lansing MI, USA).

3. “Beneficial and deleterious mutations in microbes”. March 3rd, 1999. Instituto Gulbenkian do Ciência (Oeiras, Portugal).

4. “Deleterious mutations, epistasis and sex in bacteria and RNA virus”. March 9th, 1999. Centro Nacional de Biología Fundamental, Instituto de Salud Carlos III (Majadahonda, Spain).

5. “Deleterious mutations, epistasis and sex in bacteria and RNA virus”. April 9th, 1999. Instituto de Biología Molecular y Celular de Plantas (València, Spain).

6. “The two faces of mutation: extinction and adaptation in viruses”. November 22nd, 1999. Caja de Ahorros del Mediterráneo (València, Spain).

7. “The two faces of mutation: extinction and adaptation in viruses”. March 23rd, 2000. Caja de Ahorros del Mediterráneo (Torrent, Spain).

8. “Experimental evolution in viruses: Is there a limit to viral adaptation? We hope so!“. October 20th, 2000. Institut für Tierzuncht und Genetik, Veterinärmedizinische Universität Wien.

9. “Extinction and adaptation in the viral world”. February 1st, 2001. Department of Ecology and Evolutionary Biology, University of Arizona (Tucson AZ, USA).

10. “Why endosymbiontic bacteria had not got extincted a thousand and one times by genomic mutational load?”. February 1st 2002. Instituto de Biología Molecular y Celular de Plantas (València, Spain).

11. “Adaptive dynamics during experimental evolution of RNA viruses”. May 30th, 2002. Centre d’Etudes sur le Polymorphisme des Micro-Organismes (CNRS-IRD, Montpellier, France).

12. “Experimental evolution of RNA viruses: exploring the roles of mutation, seelction and chance”. March 10th, 2004. Instituto de Biomedicina de Valencia (València, Spain).

13. “Experimental RNA virus evolution”. May 25th, 2004. Friedrich Miescher Institute (Novartis) (Basel, Switzerland).

14. “Distribution of mutational effects and contribution of epistasis to the genetic architecture of RNA virus fitness”. April 15th, 2005. IRSI-Caixa Foundation (Badalona, Spain).

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15. “Individual hypersensitivity versus population robustness in RNA virus”. November 9th, 2005. Centre d’Ecologie Functionnelle et Evolutive (CNRS, Montpellier, France).

16. “Individual hypersensitivity versus population robustness in RNA viruses”. February 6th, 2006. Sainsbury Laboratory-John Innes Center (Norwich, UK).

17. “Mecanismos de robustez mutacional en virus de RNA”. February 10th, 2006. Department of Biotechnology, Universidad Complutense de Madrid (Madrid, Spain).

18. “Individual hypersensitivity versus population robustness in RNA viruses”. February 17th, 2006. Department of Biology, National University of Ireland ( Maynooth, Ireland).

19. “Mecanismos de robustez mutacional en virus de RNA”. May 11st, 2006. Centro Nacional de Biotecnología, CSIC (Madrid, Spain).

20. “Mechanisms of mutational robustness in RNA viruses”. July 5th, 2006. Amsterdam Medical Center (Amsterdam, The Neatherlands).

21. “Mechanisms of genetic robustness in RNA viruses”. September 19th, 2006. MPI for Developmental Biology (Tübingen, Germany).

22. “Neutrality and robustness in RNA subviral pathogens: in silico and in vivo studies”. September 21st, 2006. Institute for Evolution and Biodiversity, University of Münster (Münster, Germany).

23. “Genomic complexity and mutational robustness”. November 24th, 2006. Centro Andaluz de Biología del Desarrollo, CSIC-UPO (Seville, Spain).

24. “Una aproximación experimental a la evolución viral: desentrañando los papeles de la mutación, la selección y el azar”. December 4th, 2006. IVth Cycle of Conferences “Encuentros con la Ciencia” organiced by Ámbito Cultural de El Corte Inglés and the Universidad de Málaga (Málaga, Spain).

25. “Mechanisms of genetic robustness in RNA viruses”. October 22nd, 2007. Department of Pathobiology, University of Illinous (Urbana IL, USA).

26. “Mechanisms of genetic robustness in RNA viruses”. January 11st, 2008. Instituto Gulbenkian de Ciência (Oeiras, Portugal).

27. “Mechanisms of genetic robustness in RNA viruses”. February 12nd, 2008. Evolutionary Biology Program, Ludwig Maximiliam University (Munich, Germany).

28. “Experimental RNA virus evolution”. May 5th, 2008. Rockefeller University (New York, USA).

29. “Evolutionary Biology of host-range expanssion in RNA viruses”. September 30th, 2008. Wageningen University and Research (Wageningen, The Netherlands).

30. “Experimental RNA virus evolution: disentangling the roles of mutation, selection and chance”. March 13rd, 2009 Santa Fe Institute (Santa Fe NM, USA).

31. “Virus emergentes y Biología de Sistemas: identificando las dianas de la adaptación viral”. May 8th, 2009. Estación Experimental El Zaidín, CSIC (Granada, Spain).

32. “Darwin meets RNA viruses: what small bugs can tell us about big evolutionary questions?”. June 2nd, 2009. Plant Research International (Wageningen, The Neatherlands).

33. “Biología evolutiva de la expansión de la gama de huéspedes en virus de RNA”. June 26th, 2009. Instituto Valenciano de Investigaciones Agrarias (Valencia, Spain).

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34. “Evolutionary Genetics and Systems Biology of RNA virus emergence”. October 13rd, 2009. Department of Ecology and Evolutionary Biology, Yale University (New Haven CT, USA).

35. “Evolutionary systems virology of plant RNA virus emergence”. November 5th, 2009. INRA Toulouse (France).

36. “Mechanisms of genetic robustness in RNA viruses”. November 19th, 2009. Wageningen Ecology and Evolution Semminars, Wageningen University and Research (Wageningen, The Netherlands).

37. “Evolución a tiempo real: el uso de los virus de RNA como modelos experimentales en Biología Evolutiva”. November 24th, 2009. Seminarios de Evolución, Universidad de Vigo (Vigo, Spain).

38. “Experimental evolution of RNA virues: disentangling the role of mutation, selection and chance” March 24th, 2010. Institute of Science and Technology Austria, Vienna (Austria).

39. “Darwin y virus de RNA: ¿qué respuestas a grandes cuestiones nos pueden dar estos pequeños seres?”. April 16th, 2010. Instituto de Bioingeniería, Universidad Miguel Hernández (Elche, Spain).

40. “Silenciamiento del RNAs y evolución de virus”. May 28th, 2010. Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, CSIC-U. Málaga (Algarrobo-Costa, Spain).

41. “Causas y consecuencias de la evolución de virus de RNA”. June 17th, 2010. Laboratorios Veterinarios Hipra S.A. (Àmers).

42. “Mechanisms of mutational robustness in RNA viruses”. September 14th, 2010. Plant Protection Institute, Chinese Academy of Agronomical Sciences. Beijing (P.R. China).

43. “Evolutionary genetics of host shifting”. September 15th, 2010. Plant Protection Institute, Chinese Academy of Agronomical Sciences. Beijing (P.R. China).

44. “AmiRNA-mediated resistance to viruses and ways they have to escape”. September 17th, 2010. Plant Protection Institute, Chinese Academy of Agronomical Sciences. Beijing (P.R. China).

45. “Evolutionary systems virology of plant RNA virus emergence”. October 26th, 2010. iBEST Program, University of Idaho (Moscow ID, USA).

46. “Evolutionary systems biology of RNA virus host range expansion”. November 12nd, 2010. Department of Life Science, University of Manchester (Manchester, UK).

47. “The evolutionary genetics of emerging viruses”. February 28th, 2011. Kavlin Instute of Theoretical Physics, University of California Santa Barbara (Goleta CA, USA).

48. “Biología de sistemas evolutiva de la interacción virus-huésped”. May 27th, 2011. Centro Nacional de Biotecnología-CSIC (Madrid, Spain).

49. “Biología de sistemas evolutiva de la interacción virus-huésped”. June 17th, 2011. Centre de Recerca Agrigenòmica, CSIC-IRTA-UAB-UB (Barcelona, Spain).

50. “Darwin meets RNA viruses: what small bugs can tell us about big evolutionary questions?”. September 1st, 2011. Academia Sinica-National Taiwan University (Taipei, Taiwan).

51. “Eficiencia del silenciamiento del RNA como estrategia antiviral: tu me silencias, yo evoluciono y me escapo”. December 1st, 2011. Facultat de Ciències Biològiques, Universitat de València (Valencia, Spain).

52. “Sources of unpredictability in viral fitness”. December 13rd, 2011. The Santa Fe Institute (Santa Fe NM, USA).

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53. “Genética evolutiva de la emergencia de virus de RNA”. January 13rd, 2012. Departamento de Genética, Universidad de Sevilla (Sevilla, Spain).

54. “Evolutionary Systems Biology of plant-virus interactions”. May 25th, 2012. Centro de Biotecnología y Genómica de Plantas, UPM-INIA (Madrid, Spain).

55. “Biología evolutiva y de sistemas de la expansión de la gama de huéspedes de virus de RNA”. May 30th, 2012. Centro Nacional de Microbiología, ISCIII (Madrid, Spain).

56. “Evolution of genetic robustness in RNA virus populations”. September 18th, 2012. Institute Pasteur (Paris, France).

57. “A systems biology approach to the evolution of virus-host interactions”. February 28th, 2013. Institute of Integrative Biology, ETH (Zürich, Switzerland).

58. “Evolutionary genetics of emerging viral infections”. April 26th, 2013. INRIA (Lyon, France).

59. “Evolutionary and systems biology of plant-virus interactions”. September 22nd, 2013. Department of Plant Pathology, University of Florida (Gainesville FL, USA).

60. “On the durability of amiR-mediated resistance to plant RNA viruses”. September 23rd, 2013. Department of Plant Pathology, University of Florida (Gainesville FL, USA).

61. “The evolutionary genetics of emerging viral infections”. Octuber 11st, 2013. Centro de Astrobiología, INTA-CSIC-NASA (Madrid, Spain).

62. “Resistance to RNA viruses mediated by artificial-microRNAs: promises and disappointments”. October 25th, 2013. Instituto de Biomedicina de Valencia, CSIC (Valencia, Spain).

63. “Artificial microRNAs as a therapeutic approach: durability and virus population dynamics”. December 17th, 2013. Institute for Evolution and Biodiversity, University of Münster (Münster, Germany).

64. “Darwin meets RNA viruses: small answers to big questions”. April 10th, 2014. Faculty of Engineering and Natural Sciences, Sabanci University (Istanbul, Turkey).

65. “Experimental evolution of genome architecture and complexity in RNA viruses”. August 21st, 2014. Department of Bioinformatic Engineering, Osaka University (Osaka, Japan).

66. “Artificial microRNAs as antivirals: durability and virus population dynamics”. August 25th, 2014. Institut of Biotechnology, National Taiwan University (Taipei, Taiwan).

67. “Darwin meets RNA viruses: small answers to big questions”. November 6th, 2014. Instituto de Ecología, Universidad Nacional Autónoma de México (México DF, Mexico).

68. “A systems biology approach to the interaction between plants and viruses”. November 13rd, 2014. Departament of Microbiology, University of Helsinki (Helsinki, Finland).

69. “To what extent can we predict virus evolution?”. March 23rd, 2015. Departament of Biology and Biochemistry, University of Houston (Houston TX, USA).

70. “Impact of population bottlenecks on virus genetic diversity and evolution during infection and host colonization”. May 21st, 2015. Departament of Microbiology & Immunology, University of California San Francisco (San Francisco CA, USA).

71. “How predictable is the evolution of RNA virus fitness?”. September 14th, 2015. FISABIO (Valencia, Spain).

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72. “Evolution, viruses and new diseases: a Darwinian perspective of the emergence of new viral diseases”. December 27th, 2015. Skeptics in the Pub (Valencia, Spain).

73. “Experimental evolution of genome architecture and complexity in RNA viruses”. May 20th, 2016. Section of Ecology, Behaviour and Evolution, University of California San Diego (La Jolla CA, USA).

74. “The ruggedness of fitness landscapes and the reproducibility of RNA virus evolution”. September 1st, 2016. Department of Biology, Georgia Institute of Technology (Atlanta GA, USA).

75. “Evolutionary and Systems Biology of viral emergence”. Septiembre 2nd, 2016. Department of Biology, Emory University (Atlanta GA, USA).

76. “Experimental evolution of genome architecture and complexity in RNA viruses”. September 12nd, 2016. Department of Integrative Biology, University of Texas Austin (Austin TX, USA).

77. “Experimental evolution of genome architecture and complexity in RNA viruses”. September 23rd, 2016. Department of Ecology and Evolutionary Biology, University of California Irvine (Irvine CA, USA).

78. “Exploring the constraints to increase genome complexity in RNA viruses”. March 2nd, 2017. Center for Infectious Disease Dynamics, Pennsylvania State University (State College PA, USA).

79. “Epistasis, pleiotropy, the ruggedness of fitness landscapes and the predictability of RNA virus evolution”. November 14th, 2017. Weizmann Institute of Sciences (Rehovot, Israel).

80. “Evolutionary and Systems Biology approaches to plant-virus interactions”. February 1st, 2018. IRB Universitat de Lleida (Lleida, Spain).

81. “Host-range expansión in a plant RNA virus: interplay between viral fitness and regulation of host’s transcriptome”. June 13rd, 2018. Plant Protection Institute, Chinese Academy of Agronomical Sciences (Beijing, P.R. China).

82. “What evolutionary biologist can learn from Artificial Life?”. April 10th, 2019 en la ETSI Informatics, Universidad de Málaga (Málaga, Spain).

83. “Differences in resistance and susceptibility to infection modulate the rate of plant virus evolution”. June 13rd, 2019. Plant Protection Institute, Chinese Academy of Agronomical Sciences (Beijing, P.R. China).

84. “To which extent can we predict RNA virus evolution?”. January 31st, 2020. Instituto de Ciências Biológica, Universidade de Brasília (Brazilia, Brazil).

85. “To which extent can we predict RNA virus evolution?”. March 4th, 2020. MPI Mathematik in den Naturwissenschaften (Leipzig, Germany)

9.- STAYS IN OTHER RESEARCH CENTERS:

1. Centro de Biología Molecular Severo Ochoa (CSIC-UAM). Two months (1993). PhD Student. Supervisor: Dr. Esteban Domingo.

2. Department of Biology and Center for Molecular Genetics, University of California San Diego. Three months (1994). PhD Student. Supervisor: Dr. John J. Holland.

3. Center for Microbial Ecology, Michigan State University. Twenty seven months (from October 3rd, 1995 to December 10th, 1997). Postdoc. Supervisor: Dr. Richard E. Lenski.

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4. Department of Microbiology and Molecular Genetics, Michigan State University. Three months (from July 8th, 2002 to- October 8th, 2002). Visiting Associate Professor. Host: Dr. Richard E. Lenski.

5. Department of Microbiology and Molecular Genetics, Michigan State University. Fifteen days (November 2006). Visiting Professor. Host: Dr. Richard E. Lenski.

6. Laboratory of Genetics, Wageningen University and Reseach. Fifteen days (November – December 2009). Vissiting Professor. Host: Dr. J. Arjan G. M. de Visser.

7. The Santa Fe Institute. One hundred fourteen days (several stays between 2009 - 2019). External Professor.

8. Division of Biological Sciences, University of California San Diego. Six months (2016). Visiting Professor. Host: Dr. Lin Chao.

9. Departamento de Biologia Celular, Universidade de Brasília. Two weeks (2020). Visiting Professor. Host: Dr. Tatsuya Nagata.

10.- HONORS AND AWARDS:

1. Schoolarship for undergraduate studes from the Ministerio de Educación y Ciencia. Years 1985-86, 1986-87 and 1987-88.

2. Fellowship for undergraduate research assistants from the Ministerio de Educación y Ciencia in the Department of Genetics, Universitat de València. Years 1988-89 and 1989-90.

3. Fellowship from the Universitat de València for graduate students. Year 1991-1992.

4. Fellowship from the Consellería d’Educació i Ciència de la Generalitat Valenciana. Years 1991-92, 1992-93, 1993-94 and 1994-95.

5. Fellowship from the Consellería d’Educació i Ciència de la Generalitat Valenciana for a visit to the University of California at San Diego (three months) with Prof. John J. Holland (1994).

6. Extraordinary doctorate award. Universitat de València. 1994-95.

7. Postdoctoral fellowship from the Spanish Ministerio de Educación y Ciencia to stay in the Center for Microbial Ecology (Michigan State University) with Prof. Richard E. Lenski (1995-1997).

8. Award from the National Academy of Sciences of the U.S.A. for attending to the Colloquium on Genetics and the Origin of Species. Irvine, CA.

9. Award from the Conselleria de Cultura, Educació i Ciència de la Generalitat Valencia for attending the XIII Seminarios de Genética de Poblaciones y Evolución. Baiona, Spain.

10. Sabbatical (three months) fellowpship from the Spanish Ministerio de Educación, Cultura y Deporte to stay in the Center for Microbial Ecology (Michigan State University) with Prof. Richard E. Lenski (2002).

11. Award from the Universidad Politécnica de Valencia for attending the IIIrd Noble Foundation Workshop on Virus Evolution.

12. Award from the Universidad Politécnica de Valencia for attending the IVth Noble Foundation Workshop on Virus Evolution.

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13. Award from the Universidad Politécnica de Valencia for attending the 2009 Gordon Research Conference in Microbial Population Biology.

14. Elected EMBO Young Investigator in 2005.

15. Awarded Junior Virologist by the Spanish Society of Virology in 2006.

16. Elected EMBO Member in 2011.

17. Sabbatical (six months) fellowpship from the Spanish Ministerio de Educación, Cultura y Deporte to stay in the Department of Biology (University of California San Diego) with Prof. Lin Chao (2016).

18. Grant from the Brazilian Federal Foundation for Support and Evaluation of Graduate Education (CAPES) for visiting professors into Departamento de Biologia Celular (Universidade de Brasília) with Dr. Tatsuya Nagata (2020).

11.- TEACHING EXPERIENCE:

1. 1991-1992, Universitat de València: A Practical Course of Genetics (60 hours). Teaching assistant.

2. 1992-1993, Universitat de València: Introduction to networks an data bases in Molecular Biology (25 hours). Teaching assistant.

3. 1993-1994, Universitat de València: Problems and Questions in Genetics (60 hours). Teaching assistant.

4. 1994-1995, Universitat de València: A Practical Course of Genetics (60 hours). Teaching assistant.

5. 1997-1998, Universitat de València: Genetic Análisis Techniques (60 hours). A Practical Course of Molecular Evolution (30 hours). Computational Molecular Biology for graduated students (10 hours). Assistant professor.

6. 1998-1999, Universitat de València: Genetics (25 hours). Evolutionary Biology (30 hours). A Practical Course of Molecular Evolution (30 hours). Computational Molecular Biology for graduated students (10 hours). Advanced Molecular Evolution for graduated students (10 hours). Microbial Experimental Evolution (Centro de Astrobiología, INTA-NASA; 10 hours). Assistant professor.

7. 1999-2000, Universitat de València: Genetics (37.5 hours). Evolutionary Biology (30 hours). A Practical Course of Genetics (50 hours). A Practical Course of Molecular Evolution (30 hours). Computational Molecular Biology for graduated students (30 hours). Assistant professor.

8. 2000-2001, Universitat de València: Genetics (37.5 hours). Evolutionary Biology (67.5 hours). A Practical Course of Genetics (60 hours). Assistant professor.

9. 2001-2002. Universitat de València: Evolutionary Biology (115 hours). A Practical Course of Genetics (30 hours). Computational Molecular Biology for graduated students (30 hours). Associate professor.

10. 2005-2006. EMBO YIP PhD Course: Experimental Viral Evolution (8 hours).

11. 2010-2011. Master in Virology, Universidad Complutense de Madrid. “Virus-Host Interaction: Evolutionary Biology of emerging RNA viruses” (1.5 hours).

12. 2011-2012. Master in Virology, Universidad Complutense de Madrid; “Virus-Host Interaction: Evolutionary Biology of emerging RNA viruses” (1.5 hours).

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13. 2012-2013. Master in Virology, Universidad Complutense de Madrid; “Virus-Host Interaction: Evolutionary Biology of emerging RNA viruses” (1.5 hours). Master in Plant Molecular and Cellular Biotechnology, Universidad Politécnica de Valencia; “Systems Biology” (5 hours). Master in Virology, Universidad Complutense de Madrid; “Virus-Host Interaction: Evolutionary Biology of emerging RNA viruses” (1.5 hours).

14. 2013-2014. Master in Biomedicine and Molecular Biology, Universidad de Cantabria. “Experimental Microbial Evolution” (3 hours). Master in Plant Molecular and Cellular Biotechnology, Universidad Politécnica de Valencia. “Systems Biology” (5 hours). Master in Virology, Universidad Complutense de Madrid; “Virus-Host Interaction: Evolutionary Biology of emerging RNA viruses” (1.5 hours). Master in Integrative Evolutionary Biology, Universitat de València. “Evolucion of Complex Systems” (10 hours). Curso Avanzado “Mathematical Methods of Biological Evolution”, Universitat Autònoma de Barcelona (6 hours).

15. 2014-2015. Next Generation Sequencing Course, Vetmeduni Vienna. “Applications of NGS to experimental RNA virus evolution” (1 hour).

16. 2015-2016. Master in Virology, Universidad Complutense de Madrid; “Virus-Host Interaction: Evolutionary Biology of emerging RNA viruses” (1.5 hours).

17. 2016-2017. Master in Virology, Universidad Complutense de Madrid; “Virus-Host Interaction: Evolutionary Biology of emerging RNA viruses” (1.5 hours).

18. 2017-2018. Frontiers in Systems Biology Program, Weizmann Institute of Science, Rehovot (Israel). “A systems biology perspective to the evolution of virus-plants interactions” (2 hours). Master in Virology, Universidad Complutense de Madrid; “Virus-Host Interaction: Evolutionary Biology of emerging RNA viruses” (1.5 hours). 3rd Population Genetics and Evolution School, International Center for Theoretical Sciences, Bangalore (India) : “Experimental microbial evolution” (7.5 hours). II Congreso del Master in Molecular and Cellular Biology and Genetics, Universitat de València: “Evolution of viruses and their interaction with hosts” (1.5 hours).

19. 2018-2019. Master in Virology, Universidad Complutense de Madrid; “Virus-Host Interaction: Evolutionary Biology of emerging RNA viruses” (1.5 hours).

20. 2019-2020. PhD programs in Microbiology, Plant Pathology and Molecular Biology, Universidade de Brasília, Brasilia (Brasil). “Virus as Complex Adaptive Systems” (10 horas).

21. Member of 17 PhD thesis committees, including 6 in foreing countries.

22. Member of the Advanced Studies Diplomme committee for the program Biodiversity and Evolutionary Biology of the Universitat de València. 2004-05, 2005-06, 2006-07.

23. Representative of the IBMCP in the Biotechnology PhD Progam Coordinating Committee, Universitat de València (2007-08 to the present).

12.- ADDITIONAL PROFESSIONAL ACTIVITIES:

1. Assistant of Citology and Histology. Department of Microscopical Morphology. Universitat de València. 1986-87.

2. Assistant of Microbiology. Department of Microbiology. Universitat de València. 1987-88.

4. System Manager of the Bioinformatics Unit. Universitat de València. 1991-1995.

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5. Coordinator of the Section of Cell and Tissue Cultures of the S.C.S.I.E. Universitat de València. From April 1998 to February 1999.

6. Referee for Advances in Ecological Research; ALife; American Journal of Botany; American Naturalist; Archives of Virology; Bioessays; Biology Letters; BMC Evolutionary Biology; BMC Infectious Diseases; BMC Microbiology; Evolution; Genetics; Infection, Genetics and Evolution; Journal of Biology; Journal of Evolutionary Biology; Journal of General Virology; Journal of Virology; Molecular Biology and Evolution; Molecular Ecology; Nature; Nature Review Genetics; Phycological Research; Phylosophical Transactions of the Royal Society B; Plant Pathology; PLoS Biology; PLoS ONE; PLoS Pathogens; Proceedings of the National Academy of Sciences of the USA; Proceedings of the Royal Society B; Science; Spanish Journal of Agronomical Research; The American Naturalist; Trends in Ecology & Evolution and Trends in Microbiology; Virus Research.

7. Referee for the following founding agencies: Spanish MEC (BMC-BFU Program, 2007, 2010), Spanish ANEP, CNRS program “Maladies Infectieuses Emergentes” (France), FWF of Austria, Wageningen University (The Netherlands), French Ministery of Research and New Technologies (Microbiology program), EEUU National Science Foundation (Genes and Genome Systems program), The Neatherlands NWO (From Molecule to Organisms ALW), The South African NRF.

8. Associated editor of Infection, Genetics and Evolution (2001 - 2009); Evolution (2002 – 2005); Frontiers in Virology (2011 - 2015); Journal of Evolutionary Biology (2002 - 2005); BMC Evolutionary Biology (2005 - ); The Open Genomics Journal (2007 - 2012); The Open Parasitology Journal (2007 - 2012); The Open Virology Journal (2007 - 2012); International Journal of Evolutionary Biology (2009 - 2017); The American Naturalist (2008 - 2012); Proceedings of the Royal Society B (2010 - 2012), PLoS Pathogens (guess editor). Virus Evolution (co-editor in chief, 2015 - ).

9. Faculty member, Faculty of 1000 Microbial Evolution & Genomics section (2011 - 2017). Member Peer Community in Evolutionary Biology (2016 - ).

10. Editor of the Special Topic Issue “New experimental and theoretical approaches towards the understanding of the emergence of viral infections” of the Phil. Trans. R. Soc. B (vol. 365, number 1548, ISSN 0962-8436)

11. Translation to Spanish of the book “Evolutionary Analysis 2nd edition” by S. Freeman y J.C. Herron, for Prentice Hall, 2002. In cooperation with Prof. José L. Ménsua Fernández.

12. Member selection committee CSIC Senior Scientist area Molecuar and Cellular Biology and Genetics.

13. Chairman of the Stress Biology Department of the IBMCP (June 1st, 2005 – October 23rd, 2009).

14. Chairman of the Virology Department of the IBMCP (January 1st, 2011 – January 31st, 2014).

15. Coordinator Scientific Comission of the IBMCP (June 1st, 2005 – October 23rd, 2009).

16. Member of the Genetic Variation and Evolution Study Section (Center for Scientific Review), National Institutes of Health, USA. (October 2006 - 2010).

17. Member of the committee “Habilitation à Diriger des Recherches” of Dr. Emmanuel Jacquot, University of Rénnes (France). December 19th, 2007.

18. Member of the Scientific Advisory Panels of ERASysBio+ and SysMO2.

19. President Selection Board for a Senior Bioinformatician for the Isaac Peral program from the UPM-Fundación BBVA. September 12nd, 2011.

20. Member of the ESEB Council from 2003 – 2007 and 2011 - 2019.

21. Member of the ESEB Outreach Committee from 2011 - 2015.

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22. Member of the EMBO Fellowship Committee from 2013 - .

23. Member of the IST Austria Postdoctoral Fellowships Selection Committee from 2014 - 2015.

24. Evaluator for the IBS Korea Research Director Search Committee (2016).

25. Evaluator for the G. Gustafsson Prize 2016 (Sweden).

26. President selection committee CSIC Teanured Scientist area Synthetic and Systems Biology (2017)

27. Member of the ISTplus Austria Postdoctoral Fellowships Selection Committee from 2018 - 2019.

28. President selection committee CSIC Teanured Scientist area Biotechonology and Systems Biology of microorganisms of agronomical interest (2019).

29. Chairman of the Program for Pathogens Systems Biology of the I2SysBio (September 12nd 2018 – present).

30. External Evaluation Committee, Minerva Center on Life Emulation of Evolution in the Lab, Rehovot (Israel) (2020).

13.- MEMBER OF THE FOLLOWING SCIENTIFIC ORGANIZATIONS:

1. Member of the Spanish Association of Biologists.

2. Member of the Catalan Society of Biology.

3. Member of the Spanish Society of Virology.

4. Member of the American Society for the Study of the Evolution.

5. Former member of the American Asociation for the Advance of Science (1996 – 2005).

6. Member of the Spanish Society of Genetics.

7. Member of the Spanish Society of Biochemistry and Molecular Biology.

8. Member of the European Society of Evolutionary Biology (ESEB).

9. Member of the Society of Molecular Epidemiology and Evolutionary Genetics of Infections Diseases.

10. Founder member of the Spanish Society of Evolutionary Biology.

11. Founder member of the Spanish Network for Systems Biology (REBS).

12. Member of the Spanish Network for Plant Viology (REVIPLANT).

13. Member of the Spanish Network for Virus Biophysics (BioFiViNet).