Evolutionary Systems Virology Group
  This is the web page of the Evolutionary Systems Virology Group headed by Prof. Santiago F. Elena at the Instituto de Biologia Integrativa de Sistemas  

List of Publications of the group in the last five years

  1. 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.
  2. 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.
  3. Bedhomme, S., Hillung, J., Elena, S.F. (2015) "Emerging viruses: why they are not jacks of all trades?". Curr. Opin. Virol. 10: 1-6.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. Elena, S.F., Pybus, O.G. (2015) "A home for virology, ecology, epidemiology, and evolutionary biology". Virus Evol. 1: 1-3.
  9. 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.
  10. Zwart, M.P., Elena, S.F. (2015) "Matter of size: geneetic bottlenecks in virus infection and their potential impact on evolution". Annu. Rev. Virol. 2: 161-179.
  11. Galipienso, L., Martínez, C., Willemsen, A., Alfaro-Fernández, A., Font-San Ambrosio, I, Davino, S. y Rubio, L. (2015) Genetic variability and evolutionary analysis of Parietaria mottle virus: role of selection and genetic exchange. Arch. Virol. 160: 2611-2616.
  12. 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.
  13. 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. y Ponz, F. (2015) “Viral strain-specific differential alterations in Arabidopsis developmental patterns”. Mol. Plant-Microb. Interact. 28: 1304-1315.
  14. Frígols, B., Quiles-Puchalt, N., Mir-Sanchis, I., Donderis, J., Elena, S.F., Buckling, A., Novick, R.P., Marina, A., Penadés, J.R. (2015) "Virus satellites drive viral evolution and ecology". PLoS Genet. 11: e1005609.
  15. Velasco, L., Salem, N., Willemsen, A., Lapidot, M., Mansour, A.N., Rubio, L y Galipienso, L. (2016). “Genetic variation and evolutionary forces shaping Cucumber vein yellowing virus populations: risk of emergence of virulent isolates in Europe”. Plant Pathol. 65: 847-856.
  16. 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.
  17. 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.
  18. 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.
  19. 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.
  20. 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.
  21. Elena, S.F. (2016) "Evolutionary transitions during RNA virus experimental evolution". Philos. Trans. R. Soc. B. 371: 20150441.
  22. Cervera, H., Elena, S.F. (2016) "Genetic variation in fitness within a clonal population of a plant RNA virus". Virus Evol. 2: vew006.
  23. 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.
  24. 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.
  25. Cervera, H., Lali?, 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.
  26. Cervera, H., Lali?, 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.
  27. Willemsen, A., Zwart, M.P., Higueras, P., Sardanyés, J., Elena, S.F. (2016). “Predicting the stability of homologous gene duplications in a plant RNA virus”. Genome Biol. Evol. 8: 3065-3082.
  28. 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.
  29. Rodrigo, G., Daròs, J.A., Elena, S.F. (2017). "Virus-host interactome: putting the accent on how it changes". J. Proteomics 156: 1-4.
  30. 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.
  31. Minicka, J., Elena, S.F., Borodynko-Filas, N., Rubis, B., y Hasiów-Jaroszewska, B. (2017). “Strain-dependent mutational effects for Pepino mosaic virus in a natural host”. BMC Evol. Biol. 17: 67.
  32. Elena, S.F. (2017) “Local adaptation of plant viruses: lessons from experimental evolution”. Mol. Ecol. 26: 1711-1719.
  33. Chao, L., Elena, S.F. (2017). "Non-linear tradeoffs allow the cooperation game to evolve from Prisoner's dilemma to snow drift". Proc. R. Soc. B 284: 20170228.
  34. 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. 148: 261-268.
  35. 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.
  36. Kutnjak, D., Elena, S.F. y 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.
  37. Martín, S., Cuevas, J.M., Grande-Pérez, A., Elena, S.F. (2017). “A putative antiviral role of plant cytidine deaminases”. F1000Res. 6: 222.
  38. Valverde, S., Elena, S.F., Solé, R.V. (2017). "Spatially-induced nestedness in a neutral model of phage-bacteria networks" Virus Evol. 3: vex021.
  39. 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.
  40. 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
  41. 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.
  42. Hasiów-Jaroszewska, B., Minicka, J., Zarzynska-Nowak, A., Budzynska, 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.
  43. Sardanyés, J., Arderiu, A., Elena, S.F., Alarcón, T. (2018). "Noise-induced bistability in the quasi-neutral conexistence of viral RNAs under different replication modes". J. R. Soc. Interface 15: 20180129.
  44. Ambrós, S., De la Iglesia, F., Rosario, S.M., Butkovic, A., Elena, S.F. (2018). "Engineered functional redundancy relaxes selective constraints upon endogenous genes in viral RNA genomes". Genome Biol. Evol. 10: 1823-1836.
  45. 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.
  46. 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. y McMinn, P.) pp. 46-62. Springer-Nature Switzerland.
  47. 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.
  48. Solé, R.V. y Elena, S.F. (2019) Virus as Complex Adaptive Systems. Princeton University Press. Princeton NJ, USA. ISBN 9780691158846.
  49. 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.
  50. 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: 154-161.
  51. Pospieszny, H., Borodynko-Filas, N., Hasiów-Jaroszewska, B., Rymelska, N., Elena, S.F. (2019). “Transmission rate of two Polish Tomato torrado virus isolates through tomato seeds”. J. Gen. Plant Pathol. 85: 109-115.
  52. 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
  53. 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
  54. 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.
  55. 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.
  56. 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.
  57. 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.
  58. 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. In press.