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List of works by Santiago F. Elena

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

article

A meta-analysis reveals the commonalities and differences in Arabidopsis thaliana response to different viral pathogens

scientific article

A putative antiviral role of plant cytidine deaminases

scientific article published on 3 May 2017

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

scientific article published on 7 November 2006

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

scientific article published on 30 March 2011

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

scientific article published on June 2010

Adaptation of turnip mosaic potyvirus to a specific niche reduces its genetic and environmental robustness

scientific article published on 20 May 2020

Adaptive covariation between the coat and movement proteins of prunus necrotic ringspot virus

scientific article

Adaptive value of high mutation rates of RNA viruses: separating causes from consequences

scientific article

Advances in plant virus evolution: translating evolutionary insights into better disease management

scientific article published in October 2011

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

scientific article

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

article

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

scientific article published on 7 August 2008

Clonal interference and the evolution of RNA viruses.

scientific article published on September 1999

Coinfection and superinfection in RNA virus populations: a selection-mutation model

scientific article published in June 2003

Compensatory molecular evolution of HC-Pro, an RNA-silencing suppressor from a plant RNA virus

scientific article published on 11 November 2009

Computational design of genomic transcriptional networks with adaptation to varying environments

scientific article

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

scientific article published on 19 December 2012

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

scientific article published on 4 March 2009

DVGfinder: A Metasearch Tool for Identifying Defective Viral Genomes in RNA-Seq Data ⬇️

scientific article published on 23 May 2022

Differences in accumulation and virulence determine the outcome of competition during Tobacco etch virus coinfection

scientific article

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

article

Diminishing returns of population size in the rate of RNA virus adaptation

scientific article published on April 2000

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

scientific article

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

1998 scientific article

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

scientific article published on 7 December 2015

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

scientific article published on 18 March 2007

Dynamics of a plant RNA virus intracellular accumulation: stamping machine vs. geometric replication

scientific article published on 21 April 2011

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

scientific article published on 7 September 2011

Dynamics of molecular evolution and phylogeography of Barley yellow dwarf virus-PAV.

scientific article

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

scientific article published on September 19, 2012

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

scientific article published on 01 September 2001

EVOLUTIONARY DYNAMICS OF FITNESS RECOVERY FROM THE DEBILITATING EFFECTS OF MULLER'S RATCHET.

scientific article

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

scientific article published on 29 April 2009

Effect of host species on the distribution of mutational fitness effects for an RNA virus

scientific article

Effect of host species on the topography of fitness landscape for a plant RNA virus.

scientific article published on 31 August 2016

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

scientific article published on June 27, 2012

Effects of population size and mutation rate on the evolution of mutational robustness

scientific article published on March 2007

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

scientific article published in August 2016

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

scientific article

Endosymbiotic bacteria: groEL buffers against deleterious mutations

scientific article (publication date: 23 May 2002)

Environmental stress and the effects of mutation

scientific article

Epistasis and the adaptability of an RNA virus

scientific article published on 6 May 2005

Epistasis correlates to genomic complexity

scholarly article

Error threshold in RNA quasispecies models with complementation

article

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

scientific article published on August 2015

Evolution of RNA virus in spatially structured heterogeneous environments

scientific article published in May 2003

Evolution. Climb every mountain?

scientific article published in December 2003

Evolutionary Constraints to Viroid Evolution ⬇️

scientific article published on September 2, 2009

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

article

Evolutionary history conditions the timing of transmission in vesicular stomatitis virus

scientific article published in December 2001

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

scientific article published on 20 September 2005

Evolutionary transitions during RNA virus experimental evolution

scientific article

Experimental evolution of plant RNA viruses

scientific article published on 06 February 2008

Exponential increases of RNA virus fitness during large population transmissions

scientific article

Extremely high mutation rate of a hammerhead viroid

scientific article

FREQUENCY-DEPENDENT SELECTION IN A MAMMALIAN RNA VIRUS.

scientific article published in June 1997

Faculty of 1000 evaluation for A virus responds instantly to the presence of the vector on the host and forms transmission morphs

article

Faculty of 1000 evaluation for Bacteria-phage coevolution and the emergence of generalist pathogens

Faculty of 1000 evaluation for Beyond the consensus: dissecting within-host viral population diversity of foot-and-mouth disease virus by using next-generation genome sequencing

Faculty of 1000 evaluation for Codon usage determines the mutational robustness, evolutionary capacity, and virulence of an RNA virus

Faculty of 1000 evaluation for Epistasis between beneficial mutations and the phenotype-to-fitness Map for a ssDNA virus

Faculty of 1000 evaluation for Genomic analysis of a key innovation in an experimental Escherichia coli population

article

Faculty of 1000 evaluation for Modelling the evolutionary dynamics of viruses within their hosts: a case study using high-throughput sequencing

Faculty of 1000 evaluation for Molecular evolution in court: analysis of a large hepatitis C virus outbreak from an evolving source

article published in 2013

Faculty of 1000 evaluation for Mutation of HIV-1 genomes in a clinical population treated with the mutagenic nucleoside KP1461

article

Faculty of 1000 evaluation for Mutational robustness of an RNA virus influences sensitivity to lethal mutagenesis

Faculty of 1000 evaluation for Reciprocal gene loss following experimental whole-genome duplication causes reproductive isolation in yeast

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

Faculty of 1000 evaluation for The environment affects epistatic interactions to alter the topology of an empirical fitness landscape

Faculty of 1000 evaluation for The length of adaptive walks is insensitive to starting fitness in Aspergillus nidulans

Faculty of 1000 evaluation for Variation in RNA Virus Mutation Rates across Host Cells

Fine-tuning tomato agronomic properties by computational genome redesign

scientific article

Fitness declines in Tobacco etch virus upon serial bottleneck transfers

scientific article published on 7 March 2007

Frequency-Dependent Selection in a Mammalian RNA Virus

From hypo- to hypersuppression: effect of amino acid substitutions on the RNA-silencing suppressor activity of the Tobacco etch potyvirus HC-Pro

scientific article published on 9 September 2008

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

scientific article

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

scientific article

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

scientific article published on 29 November 2009

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

article

Host-virus evolutionary dynamics with specialist and generalist infection strategies: Bifurcations, bistability, and chaos

scientific article published on 01 May 2020

In silico predicted robustness of viroid RNA secondary structures. II. Interaction between mutation pairs

scientific article published on 10 August 2006

In silico predicted robustness of viroids RNA secondary structures. I. The effect of single mutations

scientific article published on 5 May 2006

Innate immune pathways act synergistically to constrain RNA virus evolution in Drosophila melanogaster

scientific article published on 10 March 2022

Insights into the selective pressures restricting Pelargonium flower break virus genome variability: Evidence for host adaptation.

scientific article published in August 2006

Intraclonal variation in RNA viruses: generation, maintenance and consequences

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

scientific article published on 01 June 1997

LONG-TERM EXPERIMENTAL EVOLUTION IN ESCHERICHIA COLI. VII. MECHANISMS MAINTAINING GENETIC VARIABILITY WITHIN POPULATIONS.

scientific article published in August 1997

Little evidence for synergism among deleterious mutations in a nonsegmented RNA virus

scientific article published in November 1999

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

scholarly article by Santiago F. Elena & Richard E. Lenski published August 1997 in Evolution

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

scientific article published on 17 December 2007

Luria-delbruck estimation of turnip mosaic virus mutation rate in vivo

scientific article published on 11 January 2012

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

scientific article published on 11 April 2012

Measuring selection coefficients below 10(-3): method, questions, and prospects

scientific article published on 31 October 2011

Mechanisms of genetic robustness in RNA viruses

scientific article

Microbial genetics: Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation

scientific article

Mixed infections of Pepino mosaic virus strains modulate the evolutionary dynamics of this emergent virus

scientific article published on 16 September 2009

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

scientific article published in January 2005

Modeling multipartite virus evolution: the genome formula facilitates rapid adaptation to heterogeneous environments†

scientific article published on 01 January 2020

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

scientific article

Molecular evolution of a viral non-coding sequence under the selective pressure of amiRNA-mediated silencing

scientific article published on 27 February 2009

Molecular evolution of the plant virus family Bromoviridae based on RNA3-encoded proteins

scientific article

Multihost experimental evolution of a plant RNA virus reveals local adaptation and host-specific mutations

scientific article published on 22 December 2011

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

article

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

scientific article

Network design meets in silico evolutionary biology

scientific article published on 23 April 2010

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

scientific article published on June 2010

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

scientific article published in May 2017

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

scientific article published on July 7, 2011

Optimal viral strategies for bypassing RNA silencing

scientific article published on 23 June 2010

PERSPECTIVE:EVOLUTION AND DETECTION OF GENETIC ROBUSTNESS

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

scientific article published in February 2005

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

scientific article

Phase transitions in virology

Phylogeography and molecular evolution of potato virus Y.

scientific article

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

scientific article published on 01 February 2021

Population differentiation and selective constraints in Pelargonium line pattern virus

scientific article

Punctuated evolution caused by selection of rare beneficial mutations.

scientific article published on June 1996

Quasispecies spatial models for RNA viruses with different replication modes and infection strategies

scientific article

RNA virus genetic robustness: possible causes and some consequences ⬇️

scientific article published on July 19, 2012

RNA viruses as complex adaptive systems

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

scientific article published on October 1996

Replication mode and landscape topology differentially affect RNA virus mutational load and robustness

scientific article published on 23 September 2009

Response: Mechanisms of Punctuated Evolution

scientific article published in Science

Restrictions to RNA virus adaptation: an experimental approach

scientific article

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

scientific article published on 15 September 2009

Robust dynamical pattern formation from a multifunctional minimal genetic circuit

scientific article

Role of host genetic diversity for susceptibility-to-infection in the evolution of virulence of a plant virus

scientific article published on 01 July 2019

Simple genomes, complex interactions: epistasis in RNA virus

scientific article published on June 2010

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

scientific article

Structural discrimination of robustness in transcriptional feedforward loops for pattern formation.

scientific article

Tempo and mode of plant RNA virus escape from RNA interference-mediated resistance

scientific article

Test of synergistic interactions among deleterious mutations in bacteria ⬇️

scientific article published on November 27, 1997

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

scientific article published on 17 September 2011

The causes of epistasis

scientific article

The causes of epistasis in genetic networks

scientific article published on 20 September 2011

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

scholarly article

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

scientific article

The effect of genetic robustness on evolvability in digital organisms

scientific article

The evolution of RNA viruses: A population genetics view

scientific article

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

scientific article published on February 2007

The evolutionary genetics of emerging plant RNA viruses

scientific article published on March 2011

The fittest versus the flattest: experimental confirmation of the quasispecies effect with subviral pathogens.

scientific article

The games plant viruses play

scientific article published on 24 July 2014

The pleiotropic cost of host-specialization in Tobacco etch potyvirus

scientific article published on 14 August 2008

The promiscuous evolutionary history of the family Bromoviridae

scientific article published on 01 July 2008

The rate and spectrum of spontaneous mutations in a plant RNA virus

scientific article published on 3 May 2010

The red queen reigns in the kingdom of RNA viruses

scientific article

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

scientific article published on December 1992

The two faces of mutation: extinction and adaptation in RNA viruses

scientific article

The utility of fitness landscapes and big data for predicting evolution

scientific article published on 20 August 2018

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

scientific article published on 09 January 2019

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

scientific article published on 7 June 2017

Towards an integrated molecular model of plant-virus interactions

scientific article published on 25 September 2012

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

scientific article

Transmission modes affect the population structure of potato virus Y in potato

scientific article published on 23 June 2020

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

scientific article

Ultradeep sequencing analysis of population dynamics of virus escape mutants in RNAi-mediated resistant plants

scientific article published on 15 May 2012

Upper-limit mutation rate estimation for a plant RNA virus

scientific article published on 25 February 2009

Viroids: an Ariadne's thread into the RNA labyrinth

scientific article

Virus Evolution: Insights from an Experimental Approach

scientific article published in 2007

Virus Infection Suppresses Nicotiana benthamiana Adaptive Phenotypic Plasticity ⬇️

scientific article published on February 17, 2011

Virus adaptation by manipulation of host's gene expression

scientific article

Why are viral genomes so fragile? The bottleneck hypothesis

scientific article published in 2021

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

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

scientific article published on 10 July 2017

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

scientific article published in December 2002

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