All Stories

  1. Plant virus evolution under strong drought conditions results in a transition from parasitism to mutualism

    Article • Proceedings of the National Academy of Sciences, February 2021, Proceedings of the National Academy of Sciences

    Professor Santiago F Elena

  2. A putative antiviral role of plant cytidine deaminases

    Article • F1000Research, June 2017, Faculty of 1000, Ltd.

    Professor Santiago F Elena

  3. A putative antiviral role of plant cytidine deaminases

    Article • F1000Research, May 2017, Faculty of 1000, Ltd.

    Professor Santiago F Elena, Dr Ana Grande-Perez, José Manuel Cuevas

  4. Local adaptation of plant viruses: lessons from experimental evolution

    Article • Molecular Ecology, September 2016, Wiley

    Professor Santiago F Elena

  5. Predicting the stability of homologous gene duplications in a plant RNA virus

    Article • Genome Biology and Evolution, September 2016, Oxford University Press (OUP)

    Professor Santiago F Elena

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

    Article • Journal of Virology, August 2016, ASM Journals

    Professor Santiago F Elena

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

    Article • Proceedings of the Royal Society B Biological Sciences, August 2016, Royal Society Publishing

    Professor Santiago F Elena

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

    Article • BMC Biology, August 2016, Springer Science + Business Media

    Professor Santiago F Elena

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

    Article • July 2016, Cold Spring Harbor Laboratory Press

    Professor Santiago F Elena

  10. Evolutionary transitions during RNA virus experimental evolution

    Article • Philosophical Transactions of the Royal Society B Biological Sciences, July 2016, Royal Society Publishing

    Professor Santiago F Elena

  11. Molecular and biological characterization of an isolate of Tomato mottle mosaic virus (ToMMV) infecting tomato and other experimental hosts in a greenhouse in Valencia, Spain

    Article • July 2016, Cold Spring Harbor Laboratory Press

    Professor Santiago F Elena

  12. Predicting the stability of homologous gene duplications in a plant RNA virus

    Article • June 2016, Cold Spring Harbor Laboratory Press

    Professor Santiago F Elena

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

    Article • June 2016, Cold Spring Harbor Laboratory Press

    Professor Santiago F Elena

  14. The transcriptomics of an experimentally evolved plant-virus interaction

    Article • Scientific Reports, April 2016, Nature

    Professor Santiago F Elena

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

    Article • Genetics, February 2016, Genetics Society of America

    Professor Santiago F Elena

  16. Assessing parallel gene histories in viral genomes

    Article • BMC Evolutionary Biology, February 2016, Springer Science + Business Media

    Professor Santiago F Elena

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

    Article • BMC Genomics, February 2016, Springer Science + Business Media

    Professor Santiago F Elena

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

    Article • Virus Evolution, January 2016, Oxford University Press (OUP)

    Professor Santiago F Elena

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

    Article • BMC Evolutionary Biology, December 2015, Springer Science + Business Media

    Professor Santiago F Elena

  20. Viral Strain-Specific Differential Alterations in Arabidopsis Developmental Patterns

    Article • Molecular Plant-Microbe Interactions, December 2015, Scientific Societies

    Professor Santiago F Elena

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

    Article • Annual Review of Virology, November 2015, Annual Reviews

    Professor Santiago F Elena

  22. Virus Satellites Drive Viral Evolution and Ecology

    Article • PLoS Genetics, October 2015, PLOS

    Professor Santiago F Elena

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

    Article • Philosophical Transactions of the Royal Society B Biological Sciences, July 2015, Royal Society Publishing

    Professor Santiago F Elena

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

    Article • Scientific Reports, June 2015, Nature

    Professor Santiago F Elena

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

    Article • Virus Evolution, March 2015, Oxford University Press (OUP)

    Professor Santiago F Elena

  26. Temporal Dynamics of Intrahost Molecular Evolution for a Plant RNA Virus

    Article • Molecular Biology and Evolution, February 2015, Oxford University Press (OUP)

    Professor Santiago F Elena

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

    Article • Virology, February 2015, Elsevier

    Professor Santiago F Elena

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

    Article • Current Opinion in Virology, February 2015, Elsevier

    Professor Santiago F Elena

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

    Article • Scientific Reports, January 2015, Nature

    Professor Santiago F Elena

  30. Molecular evolution ofPepino mosaic virusduring long-term passaging in different hosts and its impact on virus virulence

    Article • Annals of Applied Biology, January 2015, Wiley

    Professor Santiago F Elena, BeataB Hasiów-Jaroszewska

  31. BrazilianPotato virus Yisolates identified as members of a new clade facilitate the reconstruction of evolutionary traits within this species

    Article • Plant Pathology, January 2015, Wiley

    Professor Santiago F Elena

  32. Tracking the Population Dynamics of Plant Virus Escape Mutants

    Article • January 2015, Springer Science + Business Media

    Professor Santiago F Elena

  33. Testing the Independent Action Hypothesis of Plant Pathogen Mode of Action: A Simple and Powerful New Approach

    Article • Phytopathology, January 2015, Scientific Societies

    Professor Santiago F Elena

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

    Article • BMC Systems Biology, November 2014, Springer Science + Business Media

    Professor Santiago F Elena

  35. The games plant viruses play

    Article • Current Opinion in Virology, October 2014, Elsevier

    Professor Santiago F Elena

  36. Viroids: Survivors from the RNA World?

    Article • Annual Review of Microbiology, September 2014, Annual Reviews

    Professor Santiago F Elena

  37. Experimental Virus Evolution Reveals a Role of Plant Microtubule Dynamics and TORTIFOLIA1/SPIRAL2 in RNA Trafficking

    Article • PLoS ONE, August 2014, PLOS

    Professor Santiago F Elena

  38. EXPERIMENTAL EVOLUTION OF AN EMERGING PLANT VIRUS IN HOST GENOTYPES THAT DIFFER IN THEIR SUSCEPTIBILITY TO INFECTION

    Article • Evolution, July 2014, Wiley

    Professor Santiago F Elena, Dr Sergi Valverde

  39. The rugged adaptive landscape of an emerging plant RNA virus

    Article • June 2014, Cold Spring Harbor Laboratory Press

    Professor Santiago F Elena

  40. A putative antiviral role of plant cytidine deaminases

    Article • May 2014, Cold Spring Harbor Laboratory Press

    Professor Santiago F Elena, Dr Ana Grande-Perez

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

    Article • Scientific Reports, April 2014, Springer Science + Business Media

    Professor Santiago F Elena

  42. Within-Host Spatiotemporal Dynamics of Plant Virus Infection at the Cellular Level

    Article • PLoS Genetics, February 2014, PLOS

    Professor Santiago F Elena

  43. Faculty Opinions recommendation of Variation in RNA virus mutation rates across host cells.

    Article • February 2014, F1000Research

    Professor Santiago F Elena

  44. Relocation of the NIb Gene in the Tobacco Etch Potyvirus Genome

    Article • Journal of Virology, January 2014, ASM Journals

    Professor Santiago F Elena

  45. Evolution and Emergence of Plant Viruses

    Article • January 2014, Elsevier

    Professor Santiago F Elena

  46. Estimation of the in vivo recombination rate for a plant RNA virus

    Article • Journal of General Virology, December 2013, Society for General Microbiology

    Professor Santiago F Elena

  47. Faculty Opinions recommendation of Mutational and fitness landscapes of an RNA virus revealed through population sequencing.

    Article • December 2013, F1000Research

    Professor Santiago F Elena

  48. Faculty Opinions recommendation of Environment determines epistatic patterns for a ssDNA virus.

    Article • December 2013, F1000Research

    Professor Santiago F Elena

  49. Molecular Evolution of Viral Multifunctional Proteins: The Case of Potyvirus HC-Pro

    Article • Journal of Molecular Evolution, November 2013, Springer Science + Business Media

    Professor Santiago F Elena

  50. Intra-specific variability and biological relevance of P3N-PIPO protein length in potyviruses

    Article • BMC Evolutionary Biology, November 2013, Springer Science + Business Media

    Professor Santiago F Elena

  51. Genetic Diversity and Potential Vectors and Reservoirs of Cucurbit aphid-borne yellows virus in Southeastern Spain

    Article • Phytopathology, November 2013, Scientific Societies

    Professor Santiago F Elena, Dr Pedro Gomez Lopez

  52. Faculty Opinions recommendation of Molecular evolution in court: analysis of a large hepatitis C virus outbreak from an evolving source.

    Article • October 2013, F1000Research

    Professor Santiago F Elena

  53. Experimental Evolution of Pseudogenization and Gene Loss in a Plant RNA Virus

    Article • Molecular Biology and Evolution, October 2013, Oxford University Press (OUP)

    Professor Santiago F Elena

  54. Plant RNA virus fitness predictability: contribution of genetic and environmental factors

    Article • Plant Pathology, August 2013, Wiley

    Professor Santiago F Elena

  55. Fate of Artificial MicroRNA-Mediated Resistance to Plant Viruses in Mixed Infections

    Article • Phytopathology, August 2013, Scientific Societies

    Professor Santiago F Elena

  56. Effects of the Number of Genome Segments on Primary and Systemic Infections with a Multipartite Plant RNA Virus

    Article • Journal of Virology, July 2013, ASM Journals

    Professor Santiago F Elena

  57. Natural selection fails to optimize mutation rates for long-term adaptation on rugged fitness landscapes

    Article • July 2013, ACM (Association for Computing Machinery)

    Professor Santiago F Elena, Dr. Charles Ofria, Dusan Misevic

  58. Emergence and Phylodynamics of Citrus tristeza virus in Sicily, Italy

    Article • PLoS ONE, June 2013, PLOS

    Professor Santiago F Elena

  59. Faculty Opinions recommendation of The environment affects epistatic interactions to alter the topology of an empirical fitness landscape.

    Article • May 2013, F1000Research

    Professor Santiago F Elena

  60. Model-Selection-Based Approach for Calculating Cellular Multiplicity of Infection during Virus Colonization of Multi-Cellular Hosts

    Article • PLoS ONE, May 2013, PLOS

    Professor Santiago F Elena

  61. Improving the Effectiveness of Artificial MicroRNA (amiR)-Mediated Resistance against Turnip Mosaic Virus by Combining Two amiRs or by Targeting Highly Conserved Viral Genomic Regions

    Article • Journal of Virology, May 2013, ASM Journals

    Professor Santiago F Elena

  62. Complex dynamics of defective interfering baculoviruses during serial passage in insect cells

    Article • Journal of Biological Physics, March 2013, Springer Science + Business Media

    Professor Santiago F Elena, G Pijlman

  63. Faculty Opinions recommendation of A virus responds instantly to the presence of the vector on the host and forms transmission morphs.

    Article • January 2013, F1000Research

    Professor Santiago F Elena

  64. Genotypic but not phenotypic historical contingency revealed by viral experimental evolution

    Article • BMC Evolutionary Biology, January 2013, Springer Science + Business Media

    Professor Santiago F Elena, Gui laf

  65. Computational design of host transcription-factors sets whose misregulation mimics the transcriptomic effect of viral infections

    Article • Scientific Reports, December 2012, Springer Science + Business Media

    Professor Santiago F Elena

  66. Towards an integrated molecular model of plant–virus interactions

    Article • Current Opinion in Virology, December 2012, Elsevier

    Professor Santiago F Elena

  67. Faculty Opinions recommendation of Codon usage determines the mutational robustness, evolutionary capacity, and virulence of an RNA virus.

    Article • November 2012, F1000Research

    Professor Santiago F Elena

  68. Faculty Opinions recommendation of Genomic analysis of a key innovation in an experimental Escherichia coli population.

    Article • October 2012, F1000Research

    Professor Santiago F Elena

  69. RNA virus genetic robustness: possible causes and some consequences

    Article • Current Opinion in Virology, October 2012, Elsevier

    Professor Santiago F Elena

  70. Dynamics of the Establishment of Systemic Potyvirus Infection: Independent yet Cumulative Action of Primary Infection Sites

    Article • Journal of Virology, September 2012, ASM Journals

    Professor Santiago F Elena

  71. Computational design of genomic transcriptional networks with adaptation to varying environments

    Article • Proceedings of the National Academy of Sciences, August 2012, Proceedings of the National Academy of Sciences

    Professor Santiago F Elena

  72. Molecular evolution and phylogeography of potato virus Y based on the CP gene

    Article • Journal of General Virology, July 2012, Society for General Microbiology

    Professor Santiago F Elena

  73. Epistasis between mutations is host-dependent for an RNA virus

    Article • Proceedings of the Royal Society B Biological Sciences, July 2012, Royal Society Publishing

    Professor Santiago F Elena

  74. A Meta-Analysis Reveals the Commonalities and Differences in Arabidopsis thaliana Response to Different Viral Pathogens

    Article • PLoS ONE, July 2012, PLOS

    Professor Santiago F Elena

  75. Effects of Potyvirus Effective Population Size in Inoculated Leaves on Viral Accumulation and the Onset of Symptoms

    Article • Journal of Virology, June 2012, ASM Journals

    Professor Santiago F Elena

  76. Phylodynamics of Pepino mosaic virus in Spain

    Article • European Journal of Plant Pathology, June 2012, Springer Science + Business Media

    Professor Santiago F Elena

  77. Fine-Tuning Tomato Agronomic Properties by Computational Genome Redesign

    Article • PLoS Computational Biology, June 2012, PLOS

    Professor Santiago F Elena

  78. Phylogeography and Molecular Evolution of Potato virus Y

    Article • PLoS ONE, May 2012, PLOS

    Professor Santiago F Elena

  79. Ultradeep Sequencing Analysis of Population Dynamics of Virus Escape Mutants in RNAi-Mediated Resistant Plants

    Article • Molecular Biology and Evolution, May 2012, Oxford University Press (OUP)

    Professor Santiago F Elena

  80. Faculty Opinions recommendation of Modelling the evolutionary dynamics of viruses within their hosts: a case study using high-throughput sequencing.

    Article • April 2012, F1000Research

    Professor Santiago F Elena

  81. Magnitude and sign epistasis among deleterious mutations in a positive-sense plant RNA virus

    Article • Heredity, April 2012, Nature

    Professor Santiago F Elena

  82. Faculty Opinions recommendation of Mutational robustness of an RNA virus influences sensitivity to lethal mutagenesis.

    Article • February 2012, F1000Research

    Professor Santiago F Elena

  83. Luria-Delbruck Estimation of Turnip Mosaic Virus Mutation Rate In Vivo

    Article • Journal of Virology, January 2012, ASM Journals

    Professor Santiago F Elena

  84. Transcript Profiling of Different Arabidopsis thaliana Ecotypes in Response to Tobacco etch potyvirus Infection

    Article • Frontiers in Microbiology, January 2012, Frontiers

    Professor Santiago F Elena

  85. Multihost Experimental Evolution of a Plant RNA Virus Reveals Local Adaptation and Host-Specific Mutations

    Article • Molecular Biology and Evolution, December 2011, Oxford University Press (OUP)

    Professor Santiago F Elena

  86. The Core/E1 domain of hepatitis C virus genotype 4a in Egypt does not contain viral mutations or strains specific for hepatocellular carcinoma

    Article • Journal of Clinical Virology, December 2011, Elsevier

    Professor Santiago F Elena

  87. Effect of Host Species on the Distribution of Mutational Fitness Effects for an RNA Virus

    Article • PLoS Genetics, November 2011, PLOS

    Professor Santiago F Elena

  88. Faculty Opinions recommendation of The length of adaptive walks is insensitive to starting fitness in Aspergillus nidulans.

    Article • November 2011, F1000Research

    Professor Santiago F Elena

  89. Measuring Selection Coefficients Below 10−3: Method, Questions, and Prospects

    Article • Genetics, October 2011, Genetics Society of America

    Professor Santiago F Elena

  90. The causes of epistasis

    Article • Proceedings of the Royal Society B Biological Sciences, October 2011, Royal Society Publishing

    Professor Santiago F Elena

  91. Advances in Plant Virus Evolution: Translating Evolutionary Insights into Better Disease Management

    Article • Phytopathology, October 2011, Scientific Societies

    Professor Santiago F Elena

  92. THE CAUSES OF EPISTASIS IN GENETIC NETWORKS

    Article • Evolution, September 2011, Wiley

    Professor Santiago F Elena

  93. Quasispecies Spatial Models for RNA Viruses with Different Replication Modes and Infection Strategies

    Article • PLoS ONE, September 2011, PLOS

    Professor Santiago F Elena

  94. Dynamics of alternative modes of RNA replication for positive-sense RNA viruses

    Article • Journal of The Royal Society Interface, September 2011, Royal Society Publishing

    Professor Santiago F Elena

  95. Faculty Opinions recommendation of Epistasis between beneficial mutations and the phenotype-to-fitness Map for a ssDNA virus.

    Article • August 2011, F1000Research

    Professor Santiago F Elena

  96. A systems biology approach to the evolution of plant–virus interactions

    Article • Current Opinion in Plant Biology, August 2011, Elsevier

    Professor Santiago F Elena

  97. Faculty Opinions recommendation of Bacteria-phage coevolution and the emergence of generalist pathogens.

    Article • July 2011, F1000Research

    Professor Santiago F Elena

  98. Tempo and Mode of Plant RNA Virus Escape from RNA Interference-Mediated Resistance

    Article • Journal of Virology, July 2011, ASM Journals

    Professor Santiago F Elena

  99. One Is Enough: In Vivo Effective Population Size Is Dose-Dependent for a Plant RNA Virus

    Article • PLoS Pathogens, July 2011, PLOS

    Professor Santiago F Elena

  100. Tridimensional model structure and patterns of molecular evolution of Pepino mosaic virus TGBp3 protein

    Article • Virology Journal, June 2011, Springer Science + Business Media

    Professor Santiago F Elena

  101. Faculty Opinions recommendation of Beyond the consensus: dissecting within-host viral population diversity of foot-and-mouth disease virus by using next-generation genome sequencing.

    Article • April 2011, F1000Research

    Professor Santiago F Elena

  102. Faculty Opinions recommendation of Reciprocal gene loss following experimental whole-genome duplication causes reproductive isolation in yeast.

    Article • April 2011, F1000Research

    Professor Santiago F Elena

  103. Dynamics of a Plant RNA Virus Intracellular Accumulation: Stamping Machine vs. Geometric Replication

    Article • Genetics, April 2011, Genetics Society of America

    Professor Santiago F Elena

  104. Differences in Accumulation and Virulence Determine the Outcome of Competition during Tobacco etch virus Coinfection

    Article • PLoS ONE, March 2011, PLOS

    Professor Santiago F Elena

  105. The Evolutionary Genetics of Emerging Plant RNA Viruses

    Article • Molecular Plant-Microbe Interactions, March 2011, Scientific Societies

    Professor Santiago F Elena

  106. Virus Infection Suppresses Nicotiana benthamiana Adaptive Phenotypic Plasticity

    Article • PLoS ONE, February 2011, PLOS

    Professor Santiago F Elena

  107. Structural Discrimination of Robustness in Transcriptional Feedforward Loops for Pattern Formation

    Article • PLoS ONE, February 2011, PLOS

    Professor Santiago F Elena

  108. Faculty Opinions recommendation of Mutation of HIV-1 genomes in a clinical population treated with the mutagenic nucleoside KP1461.

    Article • February 2011, F1000Research

    Professor Santiago F Elena

  109. Dynamics of Molecular Evolution and Phylogeography of Barley yellow dwarf virus-PAV

    Article • PLoS ONE, February 2011, PLOS

    Professor Santiago F Elena

  110. Population differentiation and selective constraints in Pelargonium line pattern virus

    Article • Virus Research, January 2011, Elsevier

    Professor Santiago F Elena

  111. Error threshold in RNA quasispecies models with complementation

    Article • Journal of Theoretical Biology, August 2010, Elsevier

    Professor Santiago F Elena

  112. Network design meets in silico evolutionary biology

    Article • Biochimie, July 2010, Elsevier

    Professor Santiago F Elena

  113. Optimal viral strategies for bypassing RNA silencing

    Article • Journal of The Royal Society Interface, June 2010, Royal Society Publishing

    Professor Santiago F Elena

  114. Simple genomes, complex interactions: Epistasis in RNA virus

    Article • Chaos An Interdisciplinary Journal of Nonlinear Science, June 2010, American Institute of Physics

    Professor Santiago F Elena

  115. Adaptation of tobacco etch potyvirus to a susceptible ecotype of Arabidopsis thaliana capacitates it for systemic infection of resistant ecotypes

    Article • Philosophical Transactions of the Royal Society B Biological Sciences, May 2010, Royal Society Publishing

    Professor Santiago F Elena

  116. New experimental and theoretical approaches towards the understanding of the emergence of viral infections

    Article • Philosophical Transactions of the Royal Society B Biological Sciences, May 2010, Royal Society Publishing

    Professor Santiago F Elena

  117. The Rate and Spectrum of Spontaneous Mutations in a Plant RNA Virus

    Article • Genetics, May 2010, Genetics Society of America

    Professor Santiago F Elena

  118. Robust dynamical pattern formation from a multifunctional minimal genetic circuit

    Article • BMC Systems Biology, April 2010, Springer Science + Business Media

    Professor Santiago F Elena

  119. HC-Pro hypo- and hypersuppressor mutants: differences in viral siRNA accumulation in vivo and siRNA binding activity in vitro

    Article • Archives of Virology, November 2009, Springer Science + Business Media

    Professor Santiago F Elena

  120. Compensatory Molecular Evolution of HC-Pro, an RNA-Silencing Suppressor from a Plant RNA Virus

    Article • Molecular Biology and Evolution, November 2009, Oxford University Press (OUP)

    Professor Santiago F Elena

  121. Replication Mode and Landscape Topology Differentially Affect RNA Virus Mutational Load and Robustness

    Article • Journal of Virology, September 2009, ASM Journals

    Professor Santiago F Elena

  122. Mixed Infections of Pepino Mosaic Virus Strains Modulate the Evolutionary Dynamics of this Emergent Virus

    Article • Journal of Virology, September 2009, ASM Journals

    Professor Santiago F Elena

  123. Evolutionary Constraints to Viroid Evolution

    Article • Viruses, September 2009, MDPI AG

    Professor Santiago F Elena

  124. Application of game theory to the interaction between plant viruses during mixed infections

    Article • Journal of General Virology, July 2009, Society for General Microbiology

    Professor Santiago F Elena

  125. Contribution of recombination and selection to molecular evolution of Citrus tristeza virus

    Article • Journal of General Virology, June 2009, Society for General Microbiology

    Professor Santiago F Elena

  126. Effect of citrus hosts on the generation, maintenance and evolutionary fate of genetic variability of citrus exocortis viroid

    Article • Journal of General Virology, April 2009, Society for General Microbiology

    Professor Santiago F Elena

  127. The Evolution of Viruses in Multi-Host Fitness Landscapes

    Article • The Open Virology Journal, April 2009, Bentham Science Publishers

    Professor Santiago F Elena

  128. Extremely High Mutation Rate of a Hammerhead Viroid

    Article • Science, March 2009, American Association for the Advancement of Science

    Professor Santiago F Elena

  129. Molecular Evolution of a Viral Non-Coding Sequence under the Selective Pressure of amiRNA-Mediated Silencing

    Article • PLoS Pathogens, February 2009, PLOS

    Professor Santiago F Elena

  130. Upper-limit mutation rate estimation for a plant RNA virus

    Article • Biology Letters, February 2009, Royal Society Publishing

    Professor Santiago F Elena

  131. Reverse-engineering the Arabidopsis thaliana transcriptional network under changing environmental conditions

    Article • Genome Biology, January 2009, Springer Science + Business Media

    Professor Santiago F Elena

  132. The pleiotropic cost of host-specialization in Tobacco etch potyvirus

    Article • Infection Genetics and Evolution, December 2008, Elsevier

    Professor Santiago F Elena

  133. Natural Selection Fails to Optimize Mutation Rates for Long-Term Adaptation on Rugged Fitness Landscapes

    Article • PLoS Computational Biology, September 2008, PLOS

    Professor Santiago F Elena

  134. From Hypo- to Hypersuppression: Effect of Amino Acid Substitutions on the RNA-Silencing Suppressor Activity of the Tobacco etch potyvirus HC-Pro

    Article • Genetics, September 2008, Genetics Society of America

    Professor Santiago F Elena

  135. Changes in the gene expression profile of Arabidopsis thaliana after infection with Tobacco etch virus

    Article • Virology Journal, August 2008, Springer Science + Business Media

    Professor Santiago F Elena

  136. The promiscuous evolutionary history of the family Bromoviridae

    Article • Journal of General Virology, July 2008, Society for General Microbiology

    Professor Santiago F Elena

  137. Virus Adaptation by Manipulation of Host's Gene Expression

    Article • PLoS ONE, June 2008, PLOS

    Professor Santiago F Elena

  138. Genetic diversity of the movement and coat protein genes of South American isolates of Prunus necrotic ringspot virus

    Article • Archives of Virology, March 2008, Springer Science + Business Media

    Professor Santiago F Elena

  139. Experimental evolution of plant RNA viruses

    Article • Heredity, February 2008, Springer Science + Business Media

    Professor Santiago F Elena

  140. Simple quasispecies models for the survival-of-the-flattest effect: The role of space

    Article • Journal of Theoretical Biology, February 2008, Elsevier

    Professor Santiago F Elena

  141. The effect of genetic robustness on evolvability in digital organisms

    Article • BMC Evolutionary Biology, January 2008, Springer Science + Business Media

    Professor Santiago F Elena

  142. Structure and Evolution of Viroids

    Article • January 2008, Elsevier

    Professor Santiago F Elena

  143. Contributors

    Article • January 2008, Elsevier

    Professor Santiago F Elena

  144. Low genetic variability in the coat and movement proteins of American plum line pattern virus isolates from different geographic origins

    Article • Archives of Virology, December 2007, Springer Science + Business Media

    Professor Santiago F Elena

  145. Virus Evolution: Insights from an Experimental Approach

    Article • Annual Review of Ecology Evolution and Systematics, December 2007, Annual Reviews

    Professor Santiago F Elena

  146. Distribution of Fitness and Virulence Effects Caused by Single-Nucleotide Substitutions in Tobacco Etch Virus

    Article • Journal of Virology, September 2007, ASM Journals

    Professor Santiago F Elena

  147. Distributions of epistasis in microbes fit predictions from a fitness landscape model

    Article • Nature Genetics, March 2007, Springer Science + Business Media

    Professor Santiago F Elena

  148. Fitness Declines in Tobacco Etch Virus upon Serial Bottleneck Transfers

    Article • Journal of Virology, March 2007, ASM Journals

    Professor Santiago F Elena

  149. EFFECTS OF POPULATION SIZE AND MUTATION RATE ON THE EVOLUTION OF MUTATIONAL ROBUSTNESS

    Article • Evolution, March 2007, Wiley

    Professor Santiago F Elena

  150. The evolution of sex: empirical insights into the roles of epistasis and drift

    Article • Nature Reviews Genetics, February 2007, Springer Science + Business Media

    Professor Santiago F Elena

  151. A real-time RT-PCR assay for quantifying the fitness of tobacco etch virus in competition experiments

    Article • Journal of Virological Methods, February 2007, Elsevier

    Professor Santiago F Elena

  152. Analysis of epistatic interactions and fitness landscapes using a new geometric approach

    Article • BMC Evolutionary Biology, January 2007, Springer Science + Business Media

    Professor Santiago F Elena

  153. Epistasis correlates to genomic complexity

    Article • Proceedings of the National Academy of Sciences, September 2006, Proceedings of the National Academy of Sciences

    Professor Santiago F Elena

  154. Insights into the Selective Pressures Restricting Pelargonium Flower Break Virus Genome Variability: Evidence for Host Adaptation

    Article • Journal of Virology, August 2006, ASM Journals

    Professor Santiago F Elena

  155. In Silico Predicted Robustness of Viroid RNA Secondary Structures. II. Interaction between Mutation Pairs

    Article • Molecular Biology and Evolution, August 2006, Oxford University Press (OUP)

    Professor Santiago F Elena

  156. Adaptive Covariation between the Coat and Movement Proteins of Prunus Necrotic Ringspot Virus

    Article • Journal of Virology, June 2006, ASM Journals

    Professor Santiago F Elena

  157. Viroids: an Ariadne's thread into the RNA labyrinth

    Article • EMBO Reports, June 2006, EMBO

    Professor Santiago F Elena

  158. In Silico Predicted Robustness of Viroids RNA Secondary Structures. I. The Effect of Single Mutations

    Article • Molecular Biology and Evolution, May 2006, Oxford University Press (OUP)

    Professor Santiago F Elena

  159. Mechanisms of genetic robustness in RNA viruses

    Article • EMBO Reports, February 2006, EMBO

    Professor Santiago F Elena

  160. The Fittest versus the Flattest: Experimental Confirmation of the Quasispecies Effect with Subviral Pathogens

    Article • PLoS Pathogens, January 2006, PLOS

    Professor Santiago F Elena

  161. Molecular Evolution of the Plant Virus Family Bromoviridae Based on RNA3-Encoded Proteins

    Article • Journal of Molecular Evolution, October 2005, Springer Science + Business Media

    Professor Santiago F Elena

  162. Evolutionary relationships among members of the Bromoviridae deduced from whole proteome analysis

    Article • Archives of Virology, September 2005, Springer Science + Business Media

    Professor Santiago F Elena

  163. Adaptive Value of High Mutation Rates of RNA Viruses: Separating Causes from Consequences

    Article • Journal of Virology, September 2005, ASM Journals

    Professor Santiago F Elena

  164. RNA viruses as complex adaptive systems

    Article • Biosystems, July 2005, Elsevier

    Professor Santiago F Elena

  165. Epistasis and the Adaptability of an RNA Virus

    Article • Genetics, May 2005, Genetics Society of America

    Professor Santiago F Elena

  166. Parasites and mutational load: an experimental test of a pluralistic theory for the evolution of sex

    Article • Proceedings of the Royal Society B Biological Sciences, February 2005, Royal Society Publishing

    Professor Santiago F Elena

  167. Mode of selection and experimental evolution of antiviral drugs resistance in vesicular stomatitis virus

    Article • Infection Genetics and Evolution, January 2005, Elsevier

    Professor Santiago F Elena

  168. The contribution of epistasis to the architecture of fitness in an RNA virus

    Article • Proceedings of the National Academy of Sciences, October 2004, Proceedings of the National Academy of Sciences

    Professor Santiago F Elena

  169. NATURAL SELECTION AND THE ORGAN-SPECIFIC DIFFERENTIATION OF HIV-1 V3 HYPERVARIABLE REGION

    Article • Evolution, June 2004, Wiley

    Professor Santiago F Elena

  170. The distribution of fitness effects caused by single-nucleotide substitutions in an RNA virus

    Article • Proceedings of the National Academy of Sciences, May 2004, Proceedings of the National Academy of Sciences

    Professor Santiago F Elena

  171. NATURAL SELECTION AND THE ORGAN-SPECIFIC DIFFERENTIATION OF HIV-1 V3 HYPERVARIABLE REGION

    Article • Evolution, January 2004, The Society for the Study of Evolution

    Professor Santiago F Elena

  172. EVOLUTION: Climb Every Mountain?

    Article • Science, December 2003, American Association for the Advancement of Science

    Professor Santiago F Elena

  173. PERSPECTIVE: EVOLUTION AND DETECTION OF GENETIC ROBUSTNESS

    Article • Evolution, September 2003, Wiley

    Professor Santiago F Elena

  174. Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation

    Article • Nature Reviews Genetics, June 2003, Springer Science + Business Media

    Professor Santiago F Elena

  175. Coinfection and superinfection in RNA virus populations: a selection–mutation model

    Article • Mathematical Biosciences, June 2003, Elsevier

    Professor Santiago F Elena

  176. Intraclonal variation in RNA viruses: generation, maintenance and consequences

    Article • Biological Journal of the Linnean Society, May 2003, Oxford University Press (OUP)

    Professor Santiago F Elena

  177. Evolution of RNA virus in spatially structured heterogeneous environments

    Article • Journal of Evolutionary Biology, April 2003, Wiley

    Professor Santiago F Elena

  178. PERSPECTIVE:EVOLUTION AND DETECTION OF GENETIC ROBUSTNESS

    Article • Evolution, January 2003, The Society for the Study of Evolution

    Professor Santiago F Elena

  179. Article • Journal of Biology, January 2003, Springer Science + Business Media

    Professor Santiago F Elena

  180. r- and K-selection in experimental populations of vesicular stomatitis virus

    Article • Infection Genetics and Evolution, December 2002, Elsevier

    Professor Santiago F Elena

  181. A Sliding Window-Based Method to Detect Selective Constraints in Protein-Coding Genes and Its Application to RNA Viruses

    Article • Journal of Molecular Evolution, November 2002, Springer Science + Business Media

    Professor Santiago F Elena

  182. Differential effects of vertical and horizontal transmission in the fitness of an RNA virus: A reanalysis

    Article • Infection Genetics and Evolution, July 2002, Elsevier

    Professor Santiago F Elena

  183. GroEL buffers against deleterious mutations

    Article • Nature, May 2002, Springer Science + Business Media

    Professor Santiago F Elena

  184. Article • Antonie van Leeuwenhoek, January 2002, Springer Science + Business Media

    Professor Santiago F Elena

  185. Multiple infection dynamics has pronounced effects on the fitness of RNA viruses

    Article • Journal of Evolutionary Biology, December 2001, Wiley

    Professor Santiago F Elena

  186. Evolutionary history conditions the timing of transmission in vesicular stomatitis virus

    Article • Infection Genetics and Evolution, December 2001, Elsevier

    Professor Santiago F Elena

  187. EPISTASIS BETWEEN NEW MUTATIONS AND GENETIC BACKGROUND AND A TEST OF GENETIC CANALIZATION

    Article • Evolution, September 2001, Wiley

    Professor Santiago F Elena

  188. Phylogenetic Analysis of Viroid and Viroid-Like Satellite RNAs from Plants: A Reassessment

    Article • Journal of Molecular Evolution, August 2001, Springer Science + Business Media

    Professor Santiago F Elena, Marcos de la Pena

  189. Transmission bottlenecks and the evolution of fitness in rapidly evolving RNA viruses

    Article • Infection Genetics and Evolution, July 2001, Elsevier

    Professor Santiago F Elena

  190. EPISTASIS BETWEEN NEW MUTATIONS AND GENETIC BACKGROUND AND A TEST OF GENETIC CANALIZATION

    Article • Evolution, January 2001, The Society for the Study of Evolution

    Professor Santiago F Elena

  191. The evolution of RNA viruses: A population genetics view

    Article • Proceedings of the National Academy of Sciences, June 2000, Proceedings of the National Academy of Sciences

    Professor Santiago F Elena

  192. Diminishing Returns of Population Size in the Rate of RNA Virus Adaptation

    Article • Journal of Virology, April 2000, ASM Journals

    Professor Santiago F Elena

  193. EFFECT OF DELETERIOUS MUTATION-ACCUMULATION ON THE FITNESS OF RNA BACTERIOPHAGE MS2

    Article • Evolution, April 2000, Wiley

    Professor Santiago F Elena, Marcos de la Pena

  194. The Two Faces of Mutation: Extinction and Adaptation in RNA Viruses

    Article • IUBMB Life, January 2000, Taylor & Francis

    Professor Santiago F Elena

  195. EFFECT OF DELETERIOUS MUTATION-ACCUMULATION ON THE FITNESS OF RNA BACTERIOPHAGE MS2

    Article • Evolution, January 2000, The Society for the Study of Evolution

    Professor Santiago F Elena, Marcos de la Pena

  196. The Two Faces of Mutation: Extinction and Adaptation in RNA Viruses

    Article • IUBMB Life, January 2000, Wiley

    Professor Santiago F Elena

  197. Little Evidence for Synergism Among Deleterious Mutations in a Nonsegmented RNA Virus

    Article • Journal of Molecular Evolution, November 1999, Springer Science + Business Media

    Professor Santiago F Elena

  198. Rate of deleterious mutation and the distribution of its effects on fitness in vesicular stomatitis virus

    Article • Journal of Evolutionary Biology, November 1999, Wiley

    Professor Santiago F Elena

  199. Clonal Interference and the Evolution of RNA Viruses

    Article • Science, September 1999, American Association for the Advancement of Science

    Professor Santiago F Elena

  200. Effect of population patchiness and migration rates on the adaptation and divergence of vesicular stomatitis virus quasispecies populations

    Article • Journal of General Virology, August 1999, Society for General Microbiology

    Professor Santiago F Elena

  201. Evolutionary Dynamics of Fitness Recovery from the Debilitating Effects of Muller's Ratchet

    Article • Evolution, April 1998, JSTOR

    Professor Santiago F Elena

  202. Distribution of fitness effects caused by random insertion mutations in Escherichia coli

    Article • January 1998, Springer Science + Business Media

    Professor Santiago F Elena

  203. Article • Genetica, January 1998, Springer Science + Business Media

    Professor Santiago F Elena

  204. Test of synergistic interactions among deleterious mutations in bacteria

    Article • Nature, November 1997, Springer Science + Business Media

    Professor Santiago F Elena

  205. Long-Term Experimental Evolution in Escherichia coli. VII. Mechanisms Maintaining Genetic Variability Within Populations

    Article • Evolution, August 1997, JSTOR

    Professor Santiago F Elena

  206. Frequency-Dependent Selection in a Mammalian RNA Virus

    Article • Evolution, June 1997, JSTOR

    Professor Santiago F Elena

  207. Is group selection a factor modulating the virulence of RNA viruses?

    Article • Genetics Research, June 1997, Hindawi Publishing Corporation

    Professor Santiago F Elena

  208. Mechanisms of Punctuated Evolution

    Article • Science, December 1996, American Association for the Advancement of Science

    Professor Santiago F Elena

  209. Response: Mechanisms of Punctuated Evolution

    Article • Science, December 1996, American Association for the Advancement of Science

    Professor Santiago F Elena

  210. Repeated transfer of small RNA virus populations leading to balanced fitness with infrequent stochastic drift

    Article • MGG Molecular & General Genetics, October 1996, Springer Science + Business Media

    Professor Santiago F Elena

  211. Punctuated Evolution Caused by Selection of Rare Beneficial Mutations

    Article • Science, June 1996, American Association for the Advancement of Science

    Professor Santiago F Elena

  212. Repeated transfer of small RNA virus populations leading to balanced fitness with infrequent stochastic drift

    Article • MGG Molecular & General Genetics, January 1996, Springer Science + Business Media

    Professor Santiago F Elena

  213. Exponential increases of RNA virus fitness during large population transmissions.

    Article • Proceedings of the National Academy of Sciences, June 1995, Proceedings of the National Academy of Sciences

    Professor Santiago F Elena

  214. The red queen reigns in the kingdom of RNA viruses.

    Article • Proceedings of the National Academy of Sciences, May 1994, Proceedings of the National Academy of Sciences

    Professor Santiago F Elena

  215. Pear Blister Canker Viroid is a Member of the Apple Scar Skin Subgroup (apscaviroids) and also has Sequence Homology with Viroids from other Subgroups

    Article • Journal of General Virology, October 1992, Society for General Microbiology

    Professor Santiago F Elena

  216. Does the VP1 gene of foot-and-mouth disease virus behave as a molecular clock?

    Article • Journal of Molecular Evolution, September 1992, Springer Science + Business Media

    Professor Santiago F Elena

  217. The strands of both polarities of a small circular RNA from carnation self-cleave in vitro through alternative double- and single-hammerhead structures

    Article • Nucleic Acids Research, January 1992, Oxford University Press (OUP)

    Professor Santiago F Elena

  218. Phylogeny of viroids, viroidlike satellite RNAs, and the viroidlike domain of hepatitis delta virus RNA.

    Article • Proceedings of the National Academy of Sciences, July 1991, Proceedings of the National Academy of Sciences

    Professor Santiago F Elena

  219. High genetic stability in natural populations of the plant RNA virus tobacco mild green mosaic virus

    Article • Journal of Molecular Evolution, April 1991, Springer Science + Business Media

    Professor Santiago F Elena

  220. Faculty of 1000 evaluation for Single-Cell Analysis of RNA Virus Infection Identifies Multiple Genetically Diverse Viral Genomes within Single Infectious Units.

    Article • Faculty of 1000, Ltd.

    Professor Santiago F Elena