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List of works by Brandon S Gaut

A comparative computational analysis of nonautonomous helitron elements between maize and rice

scientific article

A convergent outcome: small genomes in mangroves

scientific article published in January 2018

A large-scale screen for artificial selection in maize identifies candidate agronomic loci for domestication and crop improvement.

scientific article

A role for palindromic structures in the cis-region of maize Sirevirus LTRs in transposable element evolution and host epigenetic response.

scientific article published on 2 December 2015

A triptych of the evolution of plant transposable elements

scientific article published on 11 June 2010

A unified mixed-model method for association mapping that accounts for multiple levels of relatedness

scientific article published on February 2006

A weak effect of background selection on trinucleotide microsatellites in maize

scientific article published on 24 October 2007

Adaptive Mutations in RNA Polymerase and the Transcriptional Terminator Rho Have Similar Effects on Escherichia coli Gene Expression.

scientific article published on 9 August 2017

Adaptive selection of mitochondrial complex I subunits during primate radiation

scientific article published on 7 July 2006

Arabidopsis thaliana as a model for the genetics of local adaptation ⬇️

scientific article published on January 27, 2012

Body-Methylated Genes in Arabidopsis thaliana Are Functionally Important and Evolve Slowly ⬇️

scientific article published on August 2, 2011

CG Methylation Covaries with Differential Gene Expression between Leaf and Floral Bud Tissues of Brachypodium distachyon

scientific article

CHH Methylation Islands: A Nonconserved Feature of Grass Genomes That Is Positively Associated with Transposable Elements but Negatively Associated with Gene-Body Methylation

scientific article published on 01 August 2021

Considerations and complications of mapping small RNA high-throughput data to transposable elements

scientific article

Correction: Patterns of Polymorphism and Demographic History in Natural Populations of Arabidopsis lyrata

scientific article published on 18 August 2010

Deleterious Variants in Asian Rice and the Potential Cost of Domestication

scientific article published on 12 January 2017

Demography and its effects on genomic variation in crop domestication

scientific article published on 30 July 2018

Demography and weak selection drive patterns of transposable element diversity in natural populations of Arabidopsis lyrata

scholarly article

Different tradeoffs result from alternate genetic adaptations to a common environment

scientific article

Divergence with gene flow is driven by local adaptation to temperature and soil phosphorus concentration in teosinte subspecies (Zea mays parviglumis and Zea mays mexicana)

scientific article published on 07 June 2019

Do genetic recombination and gene density shape the pattern of DNA elimination in rice long terminal repeat retrotransposons?

scientific article published on 29 September 2009

Does recombination shape the distribution and evolution of tandemly arrayed genes (TAGs) in the Arabidopsis thaliana genome?

scientific article

Epigenetic silencing of transposable elements: a trade-off between reduced transposition and deleterious effects on neighboring gene expression

scientific article published on 28 May 2009

Epigenetics and plant genome evolution

scientific article published on 25 December 2013

EvoChromo: towards a synthesis of chromatin biology and evolution

scientific article published on 26 September 2019

Evolution Is an Experiment: Assessing Parallelism in Crop Domestication and Experimental Evolution: (Nei Lecture, SMBE 2014, Puerto Rico).

scientific article published on 26 May 2015

Evolution of Escherichia coli rifampicin resistance in an antibiotic-free environment during thermal stress

scientific article

Evolutionary genomics of grape (Vitis vinifera ssp. vinifera) domestication

scientific article

Evolutionary genomics of structural variation in Asian rice (Oryza sativa) domestication

scientific article published on 18 July 2020

Evolutionary patterns of genic DNA methylation vary across land plants.

scientific article published on 25 January 2016

Evolutionary radiation of "stone plants" in the genus Argyroderma (Aizoaceae): unraveling the effects of landscape, habitat, and flowering time

scientific article published in January 2006

Extensive gene gain associated with adaptive evolution of poxviruses

scientific article

Factors that Contribute to Variation in Evolutionary Rate among Arabidopsis Genes ⬇️

scientific article published on March 9, 2011

Fine scale genetic structure in the wild ancestor of maize (Zea mays ssp. parviglumis).

scientific article

First-Step Mutations during Adaptation Restore the Expression of Hundreds of Genes

scientific article published on 24 October 2015

Gene body methylation is conserved between plant orthologs and is of evolutionary consequence ⬇️

scientific article published on January 14, 2013

Gene capture by transposable elements leads to epigenetic conflict in maize

scientific article published on 07 November 2020

Gene conversion and the evolution of three leucine-rich repeat gene families in Arabidopsis thaliana

scientific article

Genetic Mutations that Drive Evolutionary Rescue to Lethal Temperature in Escherichia coli

scientific article published on 12 August 2020

Genetic diversity and selection in the maize starch pathway

scientific article

Genetic diversity in domesticated soybean (Glycine max) and its wild progenitor (Glycine soja) for simple sequence repeat and single-nucleotide polymorphism loci

scientific article published on 6 July 2010

Genome size and transposable element content as determined by high-throughput sequencing in maize and Zea luxurians

scientific article published on 4 February 2011

Genome size variation in wild and cultivated maize along altitudinal gradients.

scientific article

Genomic evidence for recurrent genetic admixture during the domestication of Mediterranean olive trees (Olea europaea L.).

scientific article published on 26 October 2020

Genomics and the Contrasting Dynamics of Annual and Perennial Domestication

scientific article

HapSolo: an optimization approach for removing secondary haplotigs during diploid genome assembly and scaffolding

scientific article published on 06 January 2021

Historical divergence and gene flow in the genus Zea

scientific article (publication date: April 2009)

How Single Molecule Real-Time Sequencing and Haplotype Phasing Have Enabled Reference-Grade Diploid Genome Assembly of Wine Grapes

scientific article published on 17 May 2017

Indel-associated mutation rate varies with mating system in flowering plants

scientific article

Inferences from the historical distribution of wild and domesticated maize provide ecological and evolutionary insight

scientific article

Insights into the domestication of avocado and potential genetic contributors to heterodichogamy

scientific article published in 2022

Large chromosomal variants drive adaptation in sunflowers

scientific article published on 01 July 2020

LineUp: statistical detection of chromosomal homology with application to plant comparative genomics

scientific article

Linkage mapping of domestication loci in a large maize teosinte backcross resource

scientific article

Living with Two Genomes: Grafting and Its Implications for Plant Genome-to-Genome Interactions, Phenotypic Variation, and Evolution

scientific article published on 19 August 2019

Loss of gene body methylation in Eutrema salsugineum is associated with reduced gene expression

article

Lowly expressed genes in Arabidopsis thaliana bear the signature of possible pseudogenization by promoter degradation ⬇️

scientific article published on November 8, 2010

Maize HapMap2 identifies extant variation from a genome in flux.

scientific article

Maize transposable elements contribute to long non-coding RNAs that are regulatory hubs for abiotic stress response

scientific article published on 15 November 2019

Mapping Salinity Tolerance during Arabidopsis thaliana Germination and Seedling Growth ⬇️

scientific article published on August 12, 2011

Mechanistic and evolutionary questions about epigenetic conflicts between transposable elements and their plant hosts.

scientific article published on 4 March 2016

Modeling Interactions between Transposable Elements and the Plant Epigenetic Response: A Surprising Reliance on Element Retention.

scientific article published in March 2018

Molecular and functional diversity of maize

scientific article

Molecular population genetics and the search for adaptive evolution in plants

scientific article

Multilocus analysis of nucleotide variation of Oryza sativa and its wild relatives: severe bottleneck during domestication of rice

scientific article published on 11 January 2007

Multiple domestications do not appear monophyletic

scholarly article

Multiple introductions and population structure during the rapid expansion of the invasive Sahara mustard (Brassica tournefortii) ⬇️

scientific article published on 28 June 2019

Olive domestication and diversification in the Mediterranean Basin

scientific article published on 24 November 2014

Panzea: a database and resource for molecular and functional diversity in the maize genome

scientific article

Patterns of diversity and recombination along chromosome 1 of maize (Zea mays ssp. mays L.).

scientific article

Patterns of nucleotide substitution among simultaneously duplicated gene pairs in Arabidopsis thaliana

scientific article published in September 2002

Patterns of polymorphism and demographic history in natural populations of Arabidopsis lyrata

scientific article

Patterns of positive selection in the complete NBS-LRR gene family of Arabidopsis thaliana.

scientific article published on September 2002

Patterns of selection and tissue-specific expression among maize domestication and crop improvement loci

scientific article

Phylogenetic Hypotheses for the Monocotyledons Constructed from rbcL Sequence Data

article

Phylogenetic Shifts in Gene Body Methylation Correlate with Gene Expression and Reflect Trait Conservation

scientific article published on 01 January 2020

Phylogenetic analysis, genome evolution and the rate of gene gain in the Herpesviridae

scientific article published on 29 November 2006

Phylogenetics of Seed Plants: An Analysis of Nucleotide Sequences from the Plastid Gene rbcL

article

Plant conserved non-coding sequences and paralogue evolution

scientific article

Plant domestication, a unique opportunity to identify the genetic basis of adaptation

scholarly article

Population and evolutionary dynamics of Helitron transposable elements in Arabidopsis thaliana

scientific article published on 21 September 2007

Population genetic evidence for rapid changes in intraspecific diversity and allelic cycling of a specialist defense gene in Zea.

scientific article

Population genetics of duplicated disease-defense genes, hm1 and hm2, in maize (Zea mays ssp. mays L.) and its wild ancestor (Zea mays ssp. parviglumis).

scientific article

Recent retrotransposon insertions are methylated and phylogenetically clustered in japonica rice (Oryza sativa spp. japonica).

scientific article

Receptor-Like Genes in the Major Resistance Locus of Lettuce Are Subject to Divergent Selection

article

Recombination: an underappreciated factor in the evolution of plant genomes

scientific article published on January 2007

Retrogenes in rice (Oryza sativa L. ssp. japonica) exhibit correlated expression with their source genes

scientific article published on 31 October 2011

Sahara mustard as a major threat to desert biodiversity in the southwest United States and the need to integrate contemporary methods to understand its biology

scientific article published on 20 November 2020

Seasonal Changes in a Maize-Based Polyculture of Central Mexico Reshape the Co-occurrence Networks of Soil Bacterial Communities

scientific article published on 18 December 2017

Selection on amino acid substitutions in Arabidopsis

scientific article

Selection on grain shattering genes and rates of rice domestication

scientific article published on 5 August 2009

Selection on major components of angiosperm genomes

scientific article

Selection versus demography: a multilocus investigation of the domestication process in maize

scientific article published on 10 March 2004

Spatial scale of local adaptation and population genetic structure in a miniature succulent, Argyroderma pearsonii

scientific article

Striking similarities in the genomic distribution of tandemly arrayed genes in Arabidopsis and rice

scientific article

Testing for effects of recombination rate on nucleotide diversity in natural populations of Arabidopsis lyrata.

scientific article

The Arabidopsis lyrata genome sequence and the basis of rapid genome size change

scientific article

The Capsella rubella genome and the genomic consequences of rapid mating system evolution

scientific article

The Evolutionary Dynamics of Orthologs That Shift in Gene Body Methylation between Arabidopsis Species

scientific article

The complex domestication history of the common bean

scientific article published in July 2014

The contribution of transposable elements to expressed coding sequence in Arabidopsis thaliana

scientific article published on 3 January 2009

The effects of artificial selection on the maize genome

scientific article

The evolution of transposable elements in natural populations of self-fertilizing Arabidopsis thaliana and its outcrossing relative Arabidopsis lyrata

scientific article published on 12 January 2010

The evolutionary genomics of species’ responses to climate change

scientific article published on 09 August 2021

The genetic basis of sex determination in grapes

scientific article published on 09 June 2020

The genome-wide dynamics of purging during selfing in maize

scientific article published on 02 September 2019

The genomic diversification of grapevine clones

scientific article published on 12 December 2019

The jury may be out, but it is important that it deliberates: a response to Besnard and Rubio de Casas about olive domestication

scientific article published on 24 November 2015

The lowdown on linkage disequilibrium.

scientific article

The molecular diversity of adaptive convergence.

scientific article

The molecular genetics of crop domestication

scientific article

The phenotypic signature of adaptation to thermal stress in Escherichia coli

scientific article published on 2 September 2015

The population genetics of structural variants in grapevine domestication

scientific article published on 09 September 2019

The reproducibility of adaptation in the light of experimental evolution with whole genome sequencing

scientific article published on 01 January 2014

Three groups of transposable elements with contrasting copy number dynamics and host responses in the maize (Zea mays ssp. mays) genome.

scientific article

Timing and rate of speciation in Agave (Agavaceae)

scientific article (publication date: 13 June 2006)

Transcription-related mutations and GC content drive variation in nucleotide substitution rates across the genomes of Arabidopsis thaliana and Arabidopsis lyrata

scientific article

Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata

scientific article

Uneven distribution of expressed sequence tag loci on maize pachytene chromosomes

scientific article

Using Genomes and Evolutionary Analyses to Screen for Host-Specificity and Positive Selection in the Plant Pathogen Xylella fastidiosa

scientific article published in 2022

Variation in mutation dynamics across the maize genome as a function of regional and flanking base composition

scientific article

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