Published in Ann N Y Acad Sci on January 18, 2012
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The high polyphenol content of grapevine cultivar tannat berries is conferred primarily by genes that are not shared with the reference genome. Plant Cell (2013) 1.04
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Shared subgenome dominance following polyploidization explains grass genome evolutionary plasticity from a seven protochromosome ancestor with 16K protogenes. Genome Biol Evol (2014) 0.91
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Sugarcane genome sequencing by methylation filtration provides tools for genomic research in the genus Saccharum. Plant J (2014) 0.87
Homoeologous duplicated regions are involved in quantitative resistance of Brassica napus to stem canker. BMC Genomics (2014) 0.87
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Genome-wide analysis reveals diverged patterns of codon bias, gene expression, and rates of sequence evolution in picea gene families. Genome Biol Evol (2015) 0.86
Gene regulatory variation mediates flowering responses to vernalization along an altitudinal gradient in Arabidopsis. Plant Physiol (2014) 0.85
Functional evolution of phosphatidylethanolamine binding proteins in soybean and Arabidopsis. Plant Cell (2015) 0.85
The pattern of Phosphate transporter 1 genes evolutionary divergence in Glycine max L. BMC Plant Biol (2013) 0.84
Combining phylogenetic and syntenic analyses for understanding the evolution of TCP ECE genes in eudicots. PLoS One (2013) 0.82
Locally duplicated ohnologs evolve faster than nonlocally duplicated ohnologs in Arabidopsis and rice. Genome Biol Evol (2013) 0.82
Differential gene expression and alternative splicing between diploid and tetraploid watermelon. J Exp Bot (2014) 0.81
Comparative genomic and transcriptomic analysis of tandemly and segmentally duplicated genes in rice. PLoS One (2013) 0.81
Dissecting a hidden gene duplication: the Arabidopsis thaliana SEC10 locus. PLoS One (2014) 0.81
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Faster evolving Drosophila paralogs lose expression rate and ubiquity and accumulate more non-synonymous SNPs. Biol Direct (2014) 0.79
Genome-wide analysis of PHOSPHOLIPID:DIACYLGLYCEROL ACYLTRANSFERASE (PDAT) genes in plants reveals the eudicot-wide PDAT gene expansion and altered selective pressures acting on the core eudicot PDAT paralogs. Plant Physiol (2015) 0.79
Genome-Wide Identification of Jatropha curcas Aquaporin Genes and the Comparative Analysis Provides Insights into the Gene Family Expansion and Evolution in Hevea brasiliensis. Front Plant Sci (2016) 0.79
A tandem array of CBF/DREB1 genes is located in a major freezing tolerance QTL region on Medicago truncatula chromosome 6. BMC Genomics (2013) 0.78
Did androgen-binding protein paralogs undergo neo- and/or Subfunctionalization as the Abp gene region expanded in the mouse genome? PLoS One (2014) 0.78
Impacts of Whole-Genome Triplication on MIRNA Evolution in Brassica rapa. Genome Biol Evol (2015) 0.78
The Phenotypic Plasticity of Duplicated Genes in Saccharomyces cerevisiae and the Origin of Adaptations. G3 (Bethesda) (2016) 0.77
Circadian rhythms of sense and antisense transcription in sugarcane, a highly polyploid crop. PLoS One (2013) 0.77
Genome-wide identification and comparative analysis of the cation proton antiporters family in pear and four other Rosaceae species. Mol Genet Genomics (2016) 0.77
Large-Scale Gene Relocations following an Ancient Genome Triplication Associated with the Diversification of Core Eudicots. PLoS One (2016) 0.75
Survey of the rubber tree genome reveals a high number of cysteine protease-encoding genes homologous to Arabidopsis SAG12. PLoS One (2017) 0.75
Identification and characterization of large DNA deletions affecting oil quality traits in soybean seeds through transcriptome sequencing analysis. Theor Appl Genet (2016) 0.75
Comparative genomic analysis of duplicated homoeologous regions involved in the resistance of Brassica napus to stem canker. Front Plant Sci (2015) 0.75
Genome expression balance in a triploid trihybrid vertebrate. Genome Biol Evol (2017) 0.75
Comparative Transcriptomic Analysis of Two Brassica napus Near-Isogenic Lines Reveals a Network of Genes That Influences Seed Oil Accumulation. Front Plant Sci (2016) 0.75
Comparative analyses of ubiquitin-like ATG8 and cysteine protease ATG4 autophagy genes in the plant lineage and cross-kingdom processing of ATG8 by ATG4. Autophagy (2016) 0.75
The Evolutionary Relationship between Alternative Splicing and Gene Duplication. Front Genet (2017) 0.75
Evolution of intrinsic disorder in eukaryotic proteins. Cell Mol Life Sci (2017) 0.75
The Sorghum bicolor genome and the diversification of grasses. Nature (2009) 14.62
Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature (2003) 10.65
The genome of the mesopolyploid crop species Brassica rapa. Nat Genet (2011) 8.23
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The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature (2008) 5.54
Synteny and collinearity in plant genomes. Science (2008) 5.26
Polyploidy and angiosperm diversification. Am J Bot (2009) 4.41
Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps. Genome Res (2008) 4.02
Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature (2012) 4.00
Physical and genetic structure of the maize genome reflects its complex evolutionary history. PLoS Genet (2007) 3.66
Evolutionary genetics of genome merger and doubling in plants. Annu Rev Genet (2008) 3.45
MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res (2012) 3.02
Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar, and grape: CoGe with rosids. Plant Physiol (2008) 2.91
A 3347-locus genetic recombination map of sequence-tagged sites reveals features of genome organization, transmission and evolution of cotton (Gossypium). Genetics (2004) 2.84
A primitive Y chromosome in papaya marks incipient sex chromosome evolution. Nature (2004) 2.81
Rate variation among nuclear genes and the age of polyploidy in Gossypium. Mol Biol Evol (2003) 2.64
An SNP resource for rice genetics and breeding based on subspecies indica and japonica genome alignments. Genome Res (2004) 2.56
A high-density genetic recombination map of sequence-tagged sites for sorghum, as a framework for comparative structural and evolutionary genomics of tropical grains and grasses. Genetics (2003) 2.40
A global assembly of cotton ESTs. Genome Res (2006) 2.18
Toward sequencing cotton (Gossypium) genomes. Plant Physiol (2007) 2.16
Genetic, physical, and informatics resources for maize. On the road to an integrated map. Plant Physiol (2002) 2.13
Comparative physical mapping links conservation of microsynteny to chromosome structure and recombination in grasses. Proc Natl Acad Sci U S A (2005) 2.01
Comparative analysis between homoeologous genome segments of Brassica napus and its progenitor species reveals extensive sequence-level divergence. Plant Cell (2009) 2.01
Angiosperm genome comparisons reveal early polyploidy in the monocot lineage. Proc Natl Acad Sci U S A (2009) 1.94
Integration of Cot analysis, DNA cloning, and high-throughput sequencing facilitates genome characterization and gene discovery. Genome Res (2002) 1.94
Chromosome evolution in eukaryotes: a multi-kingdom perspective. Trends Genet (2005) 1.93
PGDD: a database of gene and genome duplication in plants. Nucleic Acids Res (2012) 1.90
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
Meta-analysis of polyploid cotton QTL shows unequal contributions of subgenomes to a complex network of genes and gene clusters implicated in lint fiber development. Genetics (2007) 1.84
The repetitive landscape of the chicken genome. Genome Res (2004) 1.72
QUBIC: a qualitative biclustering algorithm for analyses of gene expression data. Nucleic Acids Res (2009) 1.69
Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.). Genome Biol (2013) 1.59
Comparative population genetics of the panicoid grasses: sequence polymorphism, linkage disequilibrium and selection in a diverse sample of sorghum bicolor. Genetics (2004) 1.58
Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea. Genome Biol (2014) 1.56
Insights from the comparison of plant genome sequences. Annu Rev Plant Biol (2010) 1.47
Extensive concerted evolution of rice paralogs and the road to regaining independence. Genetics (2007) 1.46
A detailed look at 7 million years of genome evolution in a 439 kb contiguous sequence at the barley Hv-eIF4E locus: recombination, rearrangements and repeats. Plant J (2005) 1.45
Azospirillum genomes reveal transition of bacteria from aquatic to terrestrial environments. PLoS Genet (2011) 1.45
Draft genome sequence of the mulberry tree Morus notabilis. Nat Commun (2013) 1.38
SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data. BMC Genomics (2014) 1.36
Comparative inference of illegitimate recombination between rice and sorghum duplicated genes produced by polyploidization. Genome Res (2009) 1.35
Chromosomal location and gene paucity of the male specific region on papaya Y chromosome. Mol Genet Genomics (2007) 1.35
Sequencing papaya X and Yh chromosomes reveals molecular basis of incipient sex chromosome evolution. Proc Natl Acad Sci U S A (2012) 1.35
Microcollinearity between autopolyploid sugarcane and diploid sorghum genomes. BMC Genomics (2010) 1.32
A draft physical map of a D-genome cotton species (Gossypium raimondii). BMC Genomics (2010) 1.32
High-density linkage mapping revealed suppression of recombination at the sex determination locus in papaya. Genetics (2004) 1.31
Equilibrium processes cannot explain high levels of short- and medium-range linkage disequilibrium in the domesticated grass Sorghum bicolor. Genetics (2005) 1.30
Incongruent patterns of local and global genome size evolution in cotton. Genome Res (2004) 1.30
Genetic mapping and comparative analysis of seven mutants related to seed fiber development in cotton. Theor Appl Genet (2005) 1.29
Low X/Y divergence in four pairs of papaya sex-linked genes. Plant J (2007) 1.28
Comparative genomic analysis of C4 photosynthetic pathway evolution in grasses. Genome Biol (2009) 1.27
A comparative phylogenetic approach for dating whole genome duplication events. Bioinformatics (2004) 1.23
Seventy million years of concerted evolution of a homoeologous chromosome pair, in parallel, in major Poaceae lineages. Plant Cell (2011) 1.23
Domestication and plant genomes. Curr Opin Plant Biol (2009) 1.22
Modes of gene duplication contribute differently to genetic novelty and redundancy, but show parallels across divergent angiosperms. PLoS One (2011) 1.20
Challenges of detecting directional selection after a bottleneck: lessons from Sorghum bicolor. Genetics (2006) 1.18
Sex chromosomes in flowering plants. Am J Bot (2007) 1.17
Microcolinearity and genome evolution in the AdhA region of diploid and polyploid cotton (Gossypium). Plant J (2007) 1.17
Comparative genomics of Gossypium and Arabidopsis: unraveling the consequences of both ancient and recent polyploidy. Genome Res (2005) 1.16
Chromosome structural changes in diploid and tetraploid A genomes of Gossypium. Genome (2006) 1.14
Efficient capture of unique sequences from eukaryotic genomes. Trends Genet (2002) 1.12
SSR-based genetic maps of Miscanthus sinensis and M. sacchariflorus, and their comparison to sorghum. Theor Appl Genet (2012) 1.12
Screening synteny blocks in pairwise genome comparisons through integer programming. BMC Bioinformatics (2011) 1.11
A physical map of the papaya genome with integrated genetic map and genome sequence. BMC Genomics (2009) 1.08
Molecular dissection of interspecific variation between Gossypium hirsutum and Gossypium barbadense (cotton) by a backcross-self approach: I. Fiber elongation. Theor Appl Genet (2005) 1.05
EST derived PCR-based markers for functional gene homologues in cotton. Genome (2004) 1.03
Complexity of genome evolution by segmental rearrangement in Brassica rapa revealed by sequence-level analysis. BMC Genomics (2009) 1.02
A whole-genome DNA marker map for cotton based on the D-genome sequence of Gossypium raimondii L. G3 (Bethesda) (2013) 1.02
Functional classification, genomic organization, putatively cis-acting regulatory elements, and relationship to quantitative trait loci, of sorghum genes with rhizome-enriched expression. Plant Physiol (2006) 1.01
Genetic mapping of a cross between Gossypium hirsutum (cotton) and the Hawaiian endemic, Gossypium tomentosum. Theor Appl Genet (2005) 1.00
Building the sugarcane genome for biotechnology and identifying evolutionary trends. BMC Genomics (2014) 1.00
Molecular dissection of phenotypic variation between Gossypium hirsutum and Gossypium barbadense (cotton) by a backcross-self approach: III. Fiber length. Theor Appl Genet (2005) 0.99
Sorghum expressed sequence tags identify signature genes for drought, pathogenesis, and skotomorphogenesis from a milestone set of 16,801 unique transcripts. Plant Physiol (2005) 0.98
Molecular dissection of interspecific variation between Gossypium hirsutum and G. barbadense (cotton) by a backcross-self approach: II. Fiber fineness. Theor Appl Genet (2005) 0.98
Restriction landmark genome scanning method using isoschizomers (MspI/HpaII) for DNA methylation analysis. Electrophoresis (2006) 0.97
Gene body methylation shows distinct patterns associated with different gene origins and duplication modes and has a heterogeneous relationship with gene expression in Oryza sativa (rice). New Phytol (2013) 0.96
Matita, a new retroelement from peanut: characterization and evolutionary context in the light of the Arachis A-B genome divergence. Mol Genet Genomics (2011) 0.96
QTL alleles for improved fiber quality from a wild Hawaiian cotton, Gossypium tomentosum. Theor Appl Genet (2011) 0.95
Function relaxation followed by diversifying selection after whole-genome duplication in flowering plants. Plant Physiol (2013) 0.95
Comparative genomics of grasses promises a bountiful harvest. Plant Physiol (2009) 0.95
Organization and evolution of resistance gene analogs in peanut. Mol Genet Genomics (2005) 0.94
Ancient gene duplicates in Gossypium (cotton) exhibit near-complete expression divergence. Genome Biol Evol (2014) 0.94
Emergence of a group 3 coronavirus through recombination. Virology (2010) 0.94
Molecular biogeographic study of recently described B- and A-genome Arachis species, also providing new insights into the origins of cultivated peanut. Genome (2009) 0.93
Comparative analysis of QTLs affecting plant height and flowering among closely-related diploid and polyploid genomes. Genome (2002) 0.93