Published in Mol Biol Evol on September 01, 2002
Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell (2004) 6.81
Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution. Plant Cell (2004) 6.52
A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome. Genome Res (2003) 5.73
Rapid recent growth and divergence of rice nuclear genomes. Proc Natl Acad Sci U S A (2004) 5.35
The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana. BMC Plant Biol (2004) 3.59
Evidence that rice and other cereals are ancient aneuploids. Plant Cell (2003) 2.62
Buffering of crucial functions by paleologous duplicated genes may contribute cyclicality to angiosperm genome duplication. Proc Natl Acad Sci U S A (2006) 1.87
Adaptive evolution of young gene duplicates in mammals. Genome Res (2009) 1.82
Dynamic evolution of oryza genomes is revealed by comparative genomic analysis of a genus-wide vertical data set. Plant Cell (2008) 1.55
Identification by full-coverage array CGH of human DNA copy number increases relative to chimpanzee and gorilla. Genome Res (2005) 1.51
Extensive concerted evolution of rice paralogs and the road to regaining independence. Genetics (2007) 1.46
Phylogenetic properties of 50 nuclear loci in Medicago (Leguminosae) generated using multiplexed sequence capture and next-generation sequencing. PLoS One (2014) 1.45
Sequencing and comparative analysis of a conserved syntenic segment in the Solanaceae. Genetics (2008) 1.43
Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous-Paleogene boundary. Genome Res (2014) 1.42
Automated SNP detection from a large collection of white spruce expressed sequences: contributing factors and approaches for the categorization of SNPs. BMC Genomics (2006) 1.41
Comparative inference of illegitimate recombination between rice and sorghum duplicated genes produced by polyploidization. Genome Res (2009) 1.35
Consistent patterns of rate asymmetry and gene loss indicate widespread neofunctionalization of yeast genes after whole-genome duplication. Genetics (2006) 1.34
Differential accumulation of retroelements and diversification of NB-LRR disease resistance genes in duplicated regions following polyploidy in the ancestor of soybean. Plant Physiol (2008) 1.34
Sequencing and analysis of 10,967 full-length cDNA clones from Xenopus laevis and Xenopus tropicalis reveals post-tetraploidization transcriptome remodeling. Genome Res (2006) 1.31
Salmo salar and Esox lucius full-length cDNA sequences reveal changes in evolutionary pressures on a post-tetraploidization genome. BMC Genomics (2010) 1.30
Copy number variation shapes genome diversity in Arabidopsis over immediate family generational scales. Genome Biol Evol (2010) 1.29
Mutational decay and age of chloroplast and mitochondrial genomes transferred recently to angiosperm nuclear chromosomes. Plant Physiol (2005) 1.27
Comparative analysis of the small heat shock proteins in three angiosperm genomes identifies new subfamilies and reveals diverse evolutionary patterns. Cell Stress Chaperones (2008) 1.24
Genome wide expression analysis of CBS domain containing proteins in Arabidopsis thaliana (L.) Heynh and Oryza sativa L. reveals their developmental and stress regulation. BMC Genomics (2009) 1.14
Structure and expression analysis of rice paleo duplications. Nucleic Acids Res (2009) 1.13
Homeolog loss and expression changes in natural populations of the recently and repeatedly formed allotetraploid Tragopogon mirus (Asteraceae). BMC Genomics (2010) 1.12
Transcription-related mutations and GC content drive variation in nucleotide substitution rates across the genomes of Arabidopsis thaliana and Arabidopsis lyrata. BMC Evol Biol (2007) 1.02
Genome-wide discovery of DNA polymorphism in Brassica rapa. Mol Genet Genomics (2009) 0.98
Dating and functional characterization of duplicated genes in the apple (Malus domestica Borkh.) by analyzing EST data. BMC Plant Biol (2010) 0.97
Comparative evolution of photosynthetic genes in response to polyploid and nonpolyploid duplication. Plant Physiol (2011) 0.95
Integrated syntenic and phylogenomic analyses reveal an ancient genome duplication in monocots. Plant Cell (2014) 0.94
Genome-wide investigation and transcriptome analysis of the WRKY gene family in Gossypium. Mol Genet Genomics (2014) 0.89
Gene conversion in angiosperm genomes with an emphasis on genes duplicated by polyploidization. Genes (Basel) (2011) 0.89
Maximum-likelihood estimation of rates of recombination within mating-type regions. Genetics (2004) 0.86
High-throughput discovery of mutations in tef semi-dwarfing genes by next-generation sequencing analysis. Genetics (2012) 0.85
Selection for higher gene copy number after different types of plant gene duplications. Genome Biol Evol (2011) 0.82
Locally duplicated ohnologs evolve faster than nonlocally duplicated ohnologs in Arabidopsis and rice. Genome Biol Evol (2013) 0.82
To the beat of a different drum: determinants implicated in the asymmetric sequence divergence of Caenorhabditis elegans paralogs. BMC Evol Biol (2013) 0.81
Functional bias in molecular evolution rate of Arabidopsis thaliana. BMC Evol Biol (2010) 0.81
Organelle DNA accumulation in the recently evolved papaya sex chromosomes. Mol Genet Genomics (2013) 0.79
Local synteny and codon usage contribute to asymmetric sequence divergence of Saccharomyces cerevisiae gene duplicates. BMC Evol Biol (2011) 0.78
Plastid-Nuclear Interaction and Accelerated Coevolution in Plastid Ribosomal Genes in Geraniaceae. Genome Biol Evol (2016) 0.76
Rate heterogeneity in six protein-coding genes from the holoparasite Balanophora (Balanophoraceae) and other taxa of Santalales. Ann Bot (2012) 0.76
Evolutionary Analysis of Sequence Divergence and Diversity of Duplicate Genes in Aspergillus fumigatus. Evol Bioinform Online (2012) 0.76
In Arabidopsis thaliana codon volatility scores reflect GC3 composition rather than selective pressure. BMC Res Notes (2012) 0.75
The phylogeny and evolutionary history of the Lesion Simulating Disease (LSD) gene family in Viridiplantae. Mol Genet Genomics (2015) 0.75
A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet (2005) 20.97
The molecular genetics of crop domestication. Cell (2006) 6.71
The effects of artificial selection on the maize genome. Science (2005) 6.20
The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nat Genet (2011) 4.65
The iPlant Collaborative: Cyberinfrastructure for Plant Biology. Front Plant Sci (2011) 4.16
Data archiving is a good investment. Nature (2011) 3.53
The molecular diversity of adaptive convergence. Science (2012) 3.27
Selection versus demography: a multilocus investigation of the domestication process in maize. Mol Biol Evol (2004) 3.22
Genetic diversity and selection in the maize starch pathway. Proc Natl Acad Sci U S A (2002) 3.20
Molecular population genetics and the search for adaptive evolution in plants. Mol Biol Evol (2004) 2.71
Fast identification and statistical evaluation of segmental homologies in comparative maps. Bioinformatics (2003) 2.68
Multilocus analysis of nucleotide variation of Oryza sativa and its wild relatives: severe bottleneck during domestication of rice. Mol Biol Evol (2007) 2.51
A large-scale screen for artificial selection in maize identifies candidate agronomic loci for domestication and crop improvement. Plant Cell (2005) 2.50
Epigenetic silencing of transposable elements: a trade-off between reduced transposition and deleterious effects on neighboring gene expression. Genome Res (2009) 2.46
Contrasting modes of diversification in the Aux/IAA and ARF gene families. Plant Physiol (2004) 2.41
Plant domestication, a unique opportunity to identify the genetic basis of adaptation. Proc Natl Acad Sci U S A (2007) 2.31
Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus). Proc Natl Acad Sci U S A (2010) 2.30
Patterns of positive selection in the complete NBS-LRR gene family of Arabidopsis thaliana. Genome Res (2002) 2.27
Striking similarities in the genomic distribution of tandemly arrayed genes in Arabidopsis and rice. PLoS Comput Biol (2006) 2.24
Olive domestication and diversification in the Mediterranean Basin. New Phytol (2014) 2.13
Phenex: ontological annotation of phenotypic diversity. PLoS One (2010) 2.13
Molecular and functional diversity of maize. Curr Opin Plant Biol (2006) 2.11
The teleost anatomy ontology: anatomical representation for the genomics age. Syst Biol (2010) 2.07
Evolutionary characters, phenotypes and ontologies: curating data from the systematic biology literature. PLoS One (2010) 1.93
Plant conserved non-coding sequences and paralogue evolution. Trends Genet (2005) 1.91
Extensive gene gain associated with adaptive evolution of poxviruses. Proc Natl Acad Sci U S A (2003) 1.90
Divergence in expression between duplicated genes in Arabidopsis. Mol Biol Evol (2007) 1.83
Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata. Proc Natl Acad Sci U S A (2011) 1.82
Data reuse and the open data citation advantage. PeerJ (2013) 1.79
The Capsella rubella genome and the genomic consequences of rapid mating system evolution. Nat Genet (2013) 1.69
Does recombination shape the distribution and evolution of tandemly arrayed genes (TAGs) in the Arabidopsis thaliana genome? Genome Res (2003) 1.67
Linkage mapping of domestication loci in a large maize teosinte backcross resource. Genetics (2007) 1.66
Gene conversion and the evolution of three leucine-rich repeat gene families in Arabidopsis thaliana. Mol Biol Evol (2005) 1.64
Selection on grain shattering genes and rates of rice domestication. New Phytol (2009) 1.64
Patterns of polymorphism and demographic history in natural populations of Arabidopsis lyrata. PLoS One (2008) 1.63
Patterns of diversity and recombination along chromosome 1 of maize (Zea mays ssp. mays L.). Genetics (2002) 1.60
A computational system to select candidate genes for complex human traits. Bioinformatics (2007) 1.60
Genetic diversity in domesticated soybean (Glycine max) and its wild progenitor (Glycine soja) for simple sequence repeat and single-nucleotide polymorphism loci. New Phytol (2010) 1.57
Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment? BMC Evol Biol (2008) 1.45
A triptych of the evolution of plant transposable elements. Trends Plant Sci (2010) 1.44
Historical divergence and gene flow in the genus Zea. Genetics (2009) 1.43
Genome size and transposable element content as determined by high-throughput sequencing in maize and Zea luxurians. Genome Biol Evol (2011) 1.43
Body-methylated genes in Arabidopsis thaliana are functionally important and evolve slowly. Mol Biol Evol (2011) 1.41
Identification and characterization of aluminum tolerance loci in Arabidopsis (Landsberg erecta x Columbia) by quantitative trait locus mapping. A physiologically simple but genetically complex trait. Plant Physiol (2003) 1.39
500,000 fish phenotypes: The new informatics landscape for evolutionary and developmental biology of the vertebrate skeleton. J Appl Ichthyol (2012) 1.38
Genome-scale phylogenetics: inferring the plant tree of life from 18,896 gene trees. Syst Biol (2010) 1.36
Population and evolutionary dynamics of Helitron transposable elements in Arabidopsis thaliana. Mol Biol Evol (2007) 1.36
Phytome: a platform for plant comparative genomics. Nucleic Acids Res (2006) 1.35
Do genetic recombination and gene density shape the pattern of DNA elimination in rice long terminal repeat retrotransposons? Genome Res (2009) 1.33
Factors that contribute to variation in evolutionary rate among Arabidopsis genes. Mol Biol Evol (2011) 1.31
Gene body methylation is conserved between plant orthologs and is of evolutionary consequence. Proc Natl Acad Sci U S A (2013) 1.28
Testing for effects of recombination rate on nucleotide diversity in natural populations of Arabidopsis lyrata. Genetics (2006) 1.25
Improving quantitative trait loci mapping resolution in experimental crosses by the use of genotypically selected samples. Genetics (2005) 1.25
Selection on amino acid substitutions in Arabidopsis. Mol Biol Evol (2008) 1.23
Timing and rate of speciation in Agave (Agavaceae). Proc Natl Acad Sci U S A (2006) 1.22
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). Genetics (2002) 1.16
A comparative computational analysis of nonautonomous helitron elements between maize and rice. BMC Genomics (2008) 1.15
Demography and weak selection drive patterns of transposable element diversity in natural populations of Arabidopsis lyrata. Proc Natl Acad Sci U S A (2008) 1.13
Variation in mutation dynamics across the maize genome as a function of regional and flanking base composition. Genetics (2005) 1.10
Mapping salinity tolerance during Arabidopsis thaliana germination and seedling growth. PLoS One (2011) 1.10
Evolution of Escherichia coli rifampicin resistance in an antibiotic-free environment during thermal stress. BMC Evol Biol (2013) 1.09
The evolution of transposable elements in natural populations of self-fertilizing Arabidopsis thaliana and its outcrossing relative Arabidopsis lyrata. BMC Evol Biol (2010) 1.08
Uneven distribution of expressed sequence tag loci on maize pachytene chromosomes. Genome Res (2005) 1.06
Transcription-related mutations and GC content drive variation in nucleotide substitution rates across the genomes of Arabidopsis thaliana and Arabidopsis lyrata. BMC Evol Biol (2007) 1.02
The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes. J Biomed Semantics (2013) 1.02
Fine scale genetic structure in the wild ancestor of maize (Zea mays ssp. parviglumis). Mol Ecol (2010) 1.01
Indel-associated mutation rate varies with mating system in flowering plants. Mol Biol Evol (2009) 0.99
Patterns of selection and tissue-specific expression among maize domestication and crop improvement loci. Plant Physiol (2007) 0.97
Lowly expressed genes in Arabidopsis thaliana bear the signature of possible pseudogenization by promoter degradation. Mol Biol Evol (2010) 0.97
Evolutionary radiation of "stone plants" in the genus Argyroderma (Aizoaceae): unraveling the effects of landscape, habitat, and flowering time. Evolution (2006) 0.95
The contribution of transposable elements to expressed coding sequence in Arabidopsis thaliana. J Mol Evol (2009) 0.92
Inferences from the historical distribution of wild and domesticated maize provide ecological and evolutionary insight. PLoS One (2012) 0.91
Retrogenes in rice (Oryza sativa L. ssp. japonica) exhibit correlated expression with their source genes. Genome Biol Evol (2011) 0.90
Tracking the evolution of alternatively spliced exons within the Dscam family. BMC Evol Biol (2006) 0.90
Phylogenetic analysis, genome evolution and the rate of gene gain in the Herpesviridae. Mol Phylogenet Evol (2006) 0.88
Population genetic evidence for rapid changes in intraspecific diversity and allelic cycling of a specialist defense gene in Zea. Genetics (2004) 0.88
Fine mapping a QTL for carbon isotope composition in tomato. Theor Appl Genet (2008) 0.86
Genome size variation in wild and cultivated maize along altitudinal gradients. New Phytol (2013) 0.86
The standing pool of genomic structural variation in a natural population of Mimulus guttatus. Genome Biol Evol (2014) 0.84
Systematic identification of balanced transposition polymorphisms in Saccharomyces cerevisiae. PLoS Genet (2009) 0.81
The reproducibility of adaptation in the light of experimental evolution with whole genome sequencing. Adv Exp Med Biol (2014) 0.81
Compensatory evolution in RNA secondary structures increases substitution rate variation among sites. Mol Biol Evol (2008) 0.81
Recent retrotransposon insertions are methylated and phylogenetically clustered in japonica rice (Oryza sativa spp. japonica). Mol Biol Evol (2012) 0.78
Multiple domestications do not appear monophyletic. Proc Natl Acad Sci U S A (2008) 0.77
A hierarchical model for incomplete alignments in phylogenetic inference. Bioinformatics (2009) 0.76
Spatial scale of local adaptation and population genetic structure in a miniature succulent, Argyroderma pearsonii. New Phytol (2007) 0.75
INVESTIGATING THE IMPORTANCE OF ANATOMICAL HOMOLOGY FOR CROSS-SPECIES PHENOTYPE COMPARISONS USING SEMANTIC SIMILARITY. Pac Symp Biocomput (2016) 0.75