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. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. Elena, S.F. (2016) "Evolutionary transitions during RNA virus experimental evolution". Philos. Trans. R. Soc. B. 371: 20150441.
  8. Cervera, H., Elena, S.F. (2016) "Genetic variation in fitness within a clonal population of a plant RNA virus". Virus Evol. 2: vew006.
  9. 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.
  10. 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.
  11. 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.
  12. 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.
  13. 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.
  14. 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.
  15. Rodrigo, G., Daròs, J.A., Elena, S.F. (2017). "Virus-host interactome: putting the accent on how it changes". J. Proteomics 156: 1-4.
  16. 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.
  17. 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.
  18. Elena, S.F. (2017) “Local adaptation of plant viruses: lessons from experimental evolution”. Mol. Ecol. 26: 1711-1719.
  19. 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.
  20. 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.
  21. 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.
  22. 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.
  23. Martín, S., Cuevas, J.M., Grande-Pérez, A., Elena, S.F. (2017). “A putative antiviral role of plant cytidine deaminases”. F1000Res. 6: 222.
  24. Valverde, S., Elena, S.F., Solé, R.V. (2017). "Spatially-induced nestedness in a neutral model of phage-bacteria networks" Virus Evol. 3: vex021.
  25. 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.
  26. 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
  27. 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.
  28. 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.
  29. 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.
  30. 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.
  31. 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.
  32. 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.
  33. 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.
  34. Solé, R.V. y Elena, S.F. (2019) Virus as Complex Adaptive Systems. Princeton University Press. Princeton NJ, USA. ISBN 9780691158846.
  35. 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.
  36. 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.
  37. 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.
  38. 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
  39. 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
  40. 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.
  41. 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.
  42. González, R., Butkovic, 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.
  43. 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.
  44. 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.
  45. 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.
  46. 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.
  47. González, R., Butkovic, A., Elena, S.F. (2020) “From foes to friends: viral infections expand the limits of host phenotypic plasticity”. Adv. Virus Res. 106: In press.