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Evolving by deleting: patterns of molecular evolution of Apple stem pitting virus isolates from Poland.

Komorowska B, Hasiów-Jaroszewska B, Elena SF.

J Gen Virol. 2019 Oct;100(10):1442-1456. doi: 10.1099/jgv.0.001290. Epub 2019 Aug 19.


Evolution and ecology of plant viruses.

Lefeuvre P, Martin DP, Elena SF, Shepherd DN, Roumagnac P, Varsani A.

Nat Rev Microbiol. 2019 Oct;17(10):632-644. doi: 10.1038/s41579-019-0232-3. Epub 2019 Jul 16. Review.


Parsimonious Scenario for the Emergence of Viroid-Like Replicons De Novo.

Catalán P, Elena SF, Cuesta JA, Manrubia S.

Viruses. 2019 May 9;11(5). pii: E425. doi: 10.3390/v11050425.


Mutagenesis Scanning Uncovers Evolutionary Constraints on Tobacco Etch Potyvirus Membrane-Associated 6K2 Protein.

González R, Wu B, Li X, Martínez F, Elena SF.

Genome Biol Evol. 2019 Apr 1;11(4):1207-1222. doi: 10.1093/gbe/evz069.


Theoretical conditions for the coexistence of viral strains with differences in phenotypic traits: a bifurcation analysis.

Nurtay A, Hennessy MG, Sardanyés J, Alsedà L, Elena SF.

R Soc Open Sci. 2019 Jan 9;6(1):181179. doi: 10.1098/rsos.181179. eCollection 2019 Jan.


Complete nucleotide sequence of a novel mycovirus from Trichoderma harzianum in China.

Liu C, Li M, Redda ET, Mei J, Zhang J, Elena SF, Wu B, Jiang X.

Arch Virol. 2019 Apr;164(4):1213-1216. doi: 10.1007/s00705-019-04145-9. Epub 2019 Feb 12.


Viral replication modes in single-peak fitness landscapes: A dynamical systems analysis.

Fornés J, Tomás Lázaro J, Alarcón T, Elena SF, Sardanyés J.

J Theor Biol. 2019 Jan 7;460:170-183. doi: 10.1016/j.jtbi.2018.10.007. Epub 2018 Oct 6.


The utility of fitness landscapes and big data for predicting evolution.

de Visser JAGM, Elena SF, Fragata I, Matuszewski S.

Heredity (Edinb). 2018 Nov;121(5):401-405. doi: 10.1038/s41437-018-0128-4. Epub 2018 Aug 20. No abstract available.


Engineered Functional Redundancy Relaxes Selective Constraints upon Endogenous Genes in Viral RNA Genomes.

Ambrós S, de la Iglesia F, Rosario SM, Butkovic A, Elena SF.

Genome Biol Evol. 2018 Jul 1;10(7):1823-1836. doi: 10.1093/gbe/evy141.


Noise-induced bistability in the quasi-neutral coexistence of viral RNAs under different replication modes.

Sardanyés J, Arderiu A, Elena SF, Alarcón T.

J R Soc Interface. 2018 May;15(142). pii: 20180129. doi: 10.1098/rsif.2018.0129.


Going, going, gone: predicting the fate of genomic insertions in plant RNA viruses.

Willemsen A, Carrasco JL, Elena SF, Zwart MP.

Heredity (Edinb). 2018 Nov;121(5):499-509. doi: 10.1038/s41437-018-0086-x. Epub 2018 May 10.


Defective RNA particles derived from Tomato black ring virus genome interfere with the replication of parental virus.

Hasiów-Jaroszewska B, Minicka J, Zarzyńska-Nowak A, Budzyńska D, Elena SF.

Virus Res. 2018 May 2;250:87-94. doi: 10.1016/j.virusres.2018.04.010. Epub 2018 Apr 14.


Viral Fitness Correlates with the Magnitude and Direction of the Perturbation Induced in the Host's Transcriptome: The Tobacco Etch Potyvirus-Tobacco Case Study.

Cervera H, Ambrós S, Bernet GP, Rodrigo G, Elena SF.

Mol Biol Evol. 2018 Jul 1;35(7):1599-1615. doi: 10.1093/molbev/msy038.


Exploring the role of cellular homologous of the 30K-superfamily of plant virus movement proteins.

Carrasco JL, Sánchez-Navarro JA, Elena SF.

Virus Res. 2019 Mar;262:54-61. doi: 10.1016/j.virusres.2018.02.015. Epub 2018 Feb 21.


Spatially induced nestedness in a neutral model of phage-bacteria networks.

Valverde S, Elena SF, Solé R.

Virus Evol. 2017 Aug 2;3(2):vex021. doi: 10.1093/ve/vex021. eCollection 2017 Jul.


Within-host Evolution of Segments Ratio for the Tripartite Genome of Alfalfa Mosaic Virus.

Wu B, Zwart MP, Sánchez-Navarro JA, Elena SF.

Sci Rep. 2017 Jul 10;7(1):5004. doi: 10.1038/s41598-017-05335-8.


A putative antiviral role of plant cytidine deaminases.

Martín S, Cuevas JM, Grande-Pérez A, Elena SF.

Version 2. F1000Res. 2017 May 3 [revised 2017 Jan 1];6:622. doi: 10.12688/f1000research.11111.2. eCollection 2017.


Time-Sampled Population Sequencing Reveals the Interplay of Selection and Genetic Drift in Experimental Evolution of Potato Virus Y.

Kutnjak D, Elena SF, Ravnikar M.

J Virol. 2017 Jul 27;91(16). pii: e00690-17. doi: 10.1128/JVI.00690-17. Print 2017 Aug 15.


Nonlinear trade-offs allow the cooperation game to evolve from Prisoner's Dilemma to Snowdrift.

Chao L, Elena SF.

Proc Biol Sci. 2017 May 17;284(1854). pii: 20170228. doi: 10.1098/rspb.2017.0228.


Strain-dependent mutational effects for Pepino mosaic virus in a natural host.

Minicka J, Elena SF, Borodynko-Filas N, Rubiś B, Hasiów-Jaroszewska B.

BMC Evol Biol. 2017 Mar 6;17(1):67. doi: 10.1186/s12862-017-0920-4.


2b or Not 2b: Experimental Evolution of Functional Exogenous Sequences in a Plant RNA Virus.

Willemsen A, Zwart MP, Ambrós S, Carrasco JL, Elena SF.

Genome Biol Evol. 2017 Feb 1;9(2):297-310. doi: 10.1093/gbe/evw300.


High virulence does not necessarily impede viral adaptation to a new host: a case study using a plant RNA virus.

Willemsen A, Zwart MP, Elena SF.

BMC Evol Biol. 2017 Jan 19;17(1):25. doi: 10.1186/s12862-017-0881-7.


Virus-host interactome: Putting the accent on how it changes.

Rodrigo G, Daròs JA, Elena SF.

J Proteomics. 2017 Mar 6;156:1-4. doi: 10.1016/j.jprot.2016.12.007. Epub 2016 Dec 20. Review.


Genetic variation in fitness within a clonal population of a plant RNA virus.

Cervera H, Elena SF.

Virus Evol. 2016 Mar 30;2(1):vew006. eCollection 2016 Jan.


Local adaptation of plant viruses: lessons from experimental evolution.

Elena SF.

Mol Ecol. 2017 Apr;26(7):1711-1719. doi: 10.1111/mec.13836. Epub 2016 Sep 22. Review.


Predicting the Stability of Homologous Gene Duplications in a Plant RNA Virus.

Willemsen A, Zwart MP, Higueras P, Sardanyés J, Elena SF.

Genome Biol Evol. 2016 Oct 12;8(9):3065-3082.


Effect of Host Species on Topography of the Fitness Landscape for a Plant RNA Virus.

Cervera H, Lalić J, Elena SF.

J Virol. 2016 Oct 28;90(22):10160-10169. doi: 10.1128/JVI.01243-16. Print 2016 Nov 15.


Efficient escape from local optima in a highly rugged fitness landscape by evolving RNA virus populations.

Cervera H, Lalić J, Elena SF.

Proc Biol Sci. 2016 Aug 17;283(1836). pii: 20160984. doi: 10.1098/rspb.2016.0984.


Changes in the composition of the RNA virome mark evolutionary transitions in green plants.

Mushegian A, Shipunov A, Elena SF.

BMC Biol. 2016 Aug 15;14:68. doi: 10.1186/s12915-016-0288-8.


Evolutionary transitions during RNA virus experimental evolution.

Elena SF.

Philos Trans R Soc Lond B Biol Sci. 2016 Aug 19;371(1701). pii: 20150441. doi: 10.1098/rstb.2015.0441. Review.


The transcriptomics of an experimentally evolved plant-virus interaction.

Hillung J, García-García F, Dopazo J, Cuevas JM, Elena SF.

Sci Rep. 2016 Apr 26;6:24901. doi: 10.1038/srep24901.


Matters of Size: Genetic Bottlenecks in Virus Infection and Their Potential Impact on Evolution.

Zwart MP, Elena SF.

Annu Rev Virol. 2015 Nov;2(1):161-79. doi: 10.1146/annurev-virology-100114-055135. Review.


Multiple Barriers to the Evolution of Alternative Gene Orders in a Positive-Strand RNA Virus.

Willemsen A, Zwart MP, Tromas N, Majer E, Daròs JA, Elena SF.

Genetics. 2016 Apr;202(4):1503-21. doi: 10.1534/genetics.115.185017. Epub 2016 Feb 11.


Assessing parallel gene histories in viral genomes.

Mengual-Chuliá B, Bedhomme S, Lafforgue G, Elena SF, Bravo IG.

BMC Evol Biol. 2016 Feb 5;16:32. doi: 10.1186/s12862-016-0605-4.


Interaction network of tobacco etch potyvirus NIa protein with the host proteome during infection.

Martínez F, Rodrigo G, Aragonés V, Ruiz M, Lodewijk I, Fernández U, Elena SF, Daròs JA.

BMC Genomics. 2016 Feb 1;17:87. doi: 10.1186/s12864-016-2394-y.


Viral Strain-Specific Differential Alterations in Arabidopsis Developmental Patterns.

Sánchez F, Manrique P, Mansilla C, Lunello P, Wang X, Rodrigo G, López-González S, Jenner C, González-Melendi P, Elena SF, Walsh J, Ponz F.

Mol Plant Microbe Interact. 2015 Dec;28(12):1304-15. doi: 10.1094/MPMI-05-15-0111-R. Epub 2015 Dec 8.


Distribution of mutational fitness effects and of epistasis in the 5' untranslated region of a plant RNA virus.

Bernet GP, Elena SF.

BMC Evol Biol. 2015 Dec 7;15:274. doi: 10.1186/s12862-015-0555-2.


Fusion of genomic, proteomic and phenotypic data: the case of potyviruses.

Folch-Fortuny A, Bosque G, Picó J, Ferrer A, Elena SF.

Mol Biosyst. 2016 Jan;12(1):253-61. doi: 10.1039/c5mb00507h.


Virus Satellites Drive Viral Evolution and Ecology.

Frígols B, Quiles-Puchalt N, Mir-Sanchis I, Donderis J, Elena SF, Buckling A, Novick RP, Marina A, Penadés JR.

PLoS Genet. 2015 Oct 23;11(10):e1005609. doi: 10.1371/journal.pgen.1005609. eCollection 2015 Oct.


The impact of high-order epistasis in the within-host fitness of a positive-sense plant RNA virus.

Lalić J, Elena SF.

J Evol Biol. 2015 Dec;28(12):2236-47. doi: 10.1111/jeb.12748. Epub 2015 Sep 22.


Evaluating the within-host fitness effects of mutations fixed during virus adaptation to different ecotypes of a new host.

Hillung J, Cuevas JM, Elena SF.

Philos Trans R Soc Lond B Biol Sci. 2015 Aug 19;370(1675). pii: 20140292. doi: 10.1098/rstb.2014.0292.


Corrigendum: Variability in mutational fitness effects prevents full lethal transitions in large quasispecies populations.

Sardanyés J, Simó C, Martínez R, Solé RV, Elena SF.

Sci Rep. 2015 Jun 30;5:11167. doi: 10.1038/srep11167. No abstract available.


Editorial: A home for virology, ecology, epidemiology, and evolutionary biology.

Elena SF, Pybus OG.

Virus Evol. 2015 Mar 26;1(1):1-3. eCollection 2015. No abstract available.


Temporal dynamics of intrahost molecular evolution for a plant RNA virus.

Cuevas JM, Willemsen A, Hillung J, Zwart MP, Elena SF.

Mol Biol Evol. 2015 May;32(5):1132-47. doi: 10.1093/molbev/msv028. Epub 2015 Feb 6.


Global-scale computational analysis of genomic sequences reveals the recombination pattern and coevolution dynamics of cereal-infecting geminiviruses.

Wu B, Shang X, Schubert J, Habekuß A, Elena SF, Wang X.

Sci Rep. 2015 Jan 30;5:8153. doi: 10.1038/srep08153.


Evolution of plant virus movement proteins from the 30K superfamily and of their homologs integrated in plant genomes.

Mushegian AR, Elena SF.

Virology. 2015 Feb;476:304-315. doi: 10.1016/j.virol.2014.12.012. Epub 2015 Jan 7.


Emerging viruses: why they are not jacks of all trades?

Bedhomme S, Hillung J, Elena SF.

Curr Opin Virol. 2015 Feb;10:1-6. doi: 10.1016/j.coviro.2014.10.006. Epub 2014 Nov 19. Review.


Topology analysis and visualization of Potyvirus protein-protein interaction network.

Bosque G, Folch-Fortuny A, Picó J, Ferrer A, Elena SF.

BMC Syst Biol. 2014 Nov 20;8:129. doi: 10.1186/s12918-014-0129-8.


Experimental virus evolution reveals a role of plant microtubule dynamics and TORTIFOLIA1/SPIRAL2 in RNA trafficking.

Peña EJ, Ferriol I, Sambade A, Buschmann H, Niehl A, Elena SF, Rubio L, Heinlein M.

PLoS One. 2014 Aug 18;9(8):e105364. doi: 10.1371/journal.pone.0105364. eCollection 2014.


Testing the independent action hypothesis of plant pathogen mode of action: a simple and powerful new approach.

Zwart MP, Elena SF.

Phytopathology. 2015 Jan;105(1):18-25. doi: 10.1094/PHYTO-04-14-0111-R.

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