Published in Nucleic Acids Res on January 09, 2009
Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss. Proc Natl Acad Sci U S A (2011) 2.97
Reconstruction of monocotelydoneous proto-chromosomes reveals faster evolution in plants than in animals. Proc Natl Acad Sci U S A (2009) 1.71
Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution. Genome Res (2010) 1.55
Rice pollen hybrid incompatibility caused by reciprocal gene loss of duplicated genes. Proc Natl Acad Sci U S A (2010) 1.43
Evidence and evolutionary analysis of ancient whole-genome duplication in barley predating the divergence from rice. BMC Evol Biol (2009) 1.19
Gene expression in a paleopolyploid: a transcriptome resource for the ciliate Paramecium tetraurelia. BMC Genomics (2010) 1.12
Structural and functional divergence of a 1-Mb duplicated region in the soybean (Glycine max) genome and comparison to an orthologous region from Phaseolus vulgaris. Plant Cell (2010) 1.09
RNA-seq in grain unveils fate of neo- and paleopolyploidization events in bread wheat (Triticum aestivum L.). Genome Biol (2011) 1.07
Combined meta-genomics analyses unravel candidate genes for the grain dietary fiber content in bread wheat (Triticum aestivum L.). Funct Integr Genomics (2010) 1.01
Organ and cell type-specific complementary expression patterns and regulatory neofunctionalization between duplicated genes in Arabidopsis thaliana. Genome Biol Evol (2011) 1.00
Ancient gene duplicates in Gossypium (cotton) exhibit near-complete expression divergence. Genome Biol Evol (2014) 0.94
Grass microRNA gene paleohistory unveils new insights into gene dosage balance in subgenome partitioning after whole-genome duplication. Plant Cell (2012) 0.92
Identification, nomenclature, and evolutionary relationships of mitogen-activated protein kinase (MAPK) genes in soybean. Evol Bioinform Online (2013) 0.89
ZINC-INDUCED FACILITATOR-LIKE family in plants: lineage-specific expansion in monocotyledons and conserved genomic and expression features among rice (Oryza sativa) paralogs. BMC Plant Biol (2011) 0.83
Genome-Wide Distribution, Organisation and Functional Characterization of Disease Resistance and Defence Response Genes across Rice Species. PLoS One (2015) 0.82
Selection for higher gene copy number after different types of plant gene duplications. Genome Biol Evol (2011) 0.82
Construction of a rice glycoside hydrolase phylogenomic database and identification of targets for biofuel research. Front Plant Sci (2013) 0.82
Comparative structural analysis of Bru1 region homeologs in Saccharum spontaneum and S. officinarum. BMC Genomics (2016) 0.79
The barley UNICULM2 gene resides in a centromeric region and may be associated with signaling and stress responses. Funct Integr Genomics (2012) 0.79
Expression Pattern Similarities Support the Prediction of Orthologs Retaining Common Functions after Gene Duplication Events. Plant Physiol (2016) 0.79
Impacts of Whole-Genome Triplication on MIRNA Evolution in Brassica rapa. Genome Biol Evol (2015) 0.78
Evolution of Gene Duplication in Plants. Plant Physiol (2016) 0.78
Structure, phylogeny, allelic haplotypes and expression of sucrose transporter gene families in Saccharum. BMC Genomics (2016) 0.78
Multiple mechanisms and challenges for the application of allopolyploidy in plants. Int J Mol Sci (2012) 0.77
Hierarchically Aligning 10 Legume Genomes Establishes a Family-Level Genomics Platform. Plant Physiol (2017) 0.75
Diversification of the plant-specific hybrid glycine-rich protein (HyGRP) genes in cereals. Front Plant Sci (2014) 0.75
MYB31/MYB42 Syntelogs Exhibit Divergent Regulation of Phenylpropanoid Genes in Maize, Sorghum and Rice. Sci Rep (2016) 0.75
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31
Basic local alignment search tool. J Mol Biol (1990) 659.07
A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science (2002) 42.78
Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res (2002) 40.03
The evolutionary fate and consequences of duplicate genes. Science (2000) 24.22
The map-based sequence of the rice genome. Nature (2005) 24.17
The Genomes of Oryza sativa: a history of duplications. PLoS Biol (2005) 7.67
Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. Proc Natl Acad Sci U S A (2004) 6.66
Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution. Plant Cell (2004) 6.52
Extensive duplication and reshuffling in the Arabidopsis genome. Plant Cell (2000) 6.16
limmaGUI: a graphical user interface for linear modeling of microarray data. Bioinformatics (2004) 6.04
Duplication of CaMV 35S Promoter Sequences Creates a Strong Enhancer for Plant Genes. Science (1987) 6.00
A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome. Genome Res (2003) 5.73
Duplication and DNA segmental loss in the rice genome: implications for diploidization. New Phytol (2005) 3.65
Identification and characterization of shared duplications between rice and wheat provide new insight into grass genome evolution. Plant Cell (2008) 3.25
Protein-coding genes are epigenetically regulated in Arabidopsis polyploids. Proc Natl Acad Sci U S A (2001) 2.75
Stochastic and epigenetic changes of gene expression in Arabidopsis polyploids. Genetics (2004) 2.62
Evidence that rice and other cereals are ancient aneuploids. Plant Cell (2003) 2.62
Divergence in the spatial pattern of gene expression between human duplicate genes. Genome Res (2003) 2.60
Coexpression of neighboring genes in the genome of Arabidopsis thaliana. Genome Res (2004) 2.52
The sequence of rice chromosomes 11 and 12, rich in disease resistance genes and recent gene duplications. BMC Biol (2005) 2.41
Genome-wide transcription analyses in rice using tiling microarrays. Nat Genet (2005) 2.39
Gene dosage and stochastic effects determine the severity and direction of uniparental ribosomal RNA gene silencing (nucleolar dominance) in Arabidopsis allopolyploids. Proc Natl Acad Sci U S A (1998) 2.25
Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis. Mol Biol Evol (2005) 2.18
Patterns of nucleotide substitution among simultaneously duplicated gene pairs in Arabidopsis thaliana. Mol Biol Evol (2002) 1.97
Transcriptional similarities, dissimilarities, and conservation of cis-elements in duplicated genes of Arabidopsis. Plant Physiol (2004) 1.96
Structure and evolution of cereal genomes. Curr Opin Genet Dev (2003) 1.91
Rapid evolution of expression and regulatory divergences after yeast gene duplication. Proc Natl Acad Sci U S A (2005) 1.88
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
Conservation and divergence of light-regulated genome expression patterns during seedling development in rice and Arabidopsis. Plant Cell (2005) 1.84
Divergence in expression between duplicated genes in Arabidopsis. Mol Biol Evol (2007) 1.83
Identification of the duplicated segments in rice chromosomes 1 and 5 by linkage analysis of cDNA markers of known functions. Theor Appl Genet (1994) 1.63
Composition and structure of the centromeric region of rice chromosome 8. Plant Cell (2004) 1.52
Extensive concerted evolution of rice paralogs and the road to regaining independence. Genetics (2007) 1.46
Gene expression evolves faster in narrowly than in broadly expressed mammalian genes. Mol Biol Evol (2005) 1.44
Transcription factors in rice: a genome-wide comparative analysis between monocots and eudicots. Plant Mol Biol (2005) 1.36
Synteny between Arabidopsis thaliana and rice at the genome level: a tool to identify conservation in the ongoing rice genome sequencing project. Nucleic Acids Res (2002) 1.31
New in silico insight into the synteny between rice (Oryza sativa L.) and maize (Zea mays L.) highlights reshuffling and identifies new duplications in the rice genome. Plant J (2004) 1.23
Characterization of paralogous protein families in rice. BMC Plant Biol (2008) 1.19
Tiling microarray analysis of rice chromosome 10 to identify the transcriptome and relate its expression to chromosomal architecture. Genome Biol (2005) 1.09
Local coexpression domains in the genome of rice show no microsynteny with Arabidopsis domains. Plant Mol Biol (2007) 0.93
Identification and characterization of shared duplications between rice and wheat provide new insight into grass genome evolution. Plant Cell (2008) 3.25
A physical map of the 1-gigabase bread wheat chromosome 3B. Science (2008) 3.21
Molecular basis of evolutionary events that shaped the hardness locus in diploid and polyploid wheat species (Triticum and Aegilops). Plant Cell (2005) 2.40
Genetic architecture of flowering time in maize as inferred from quantitative trait loci meta-analysis and synteny conservation with the rice genome. Genetics (2004) 2.33
Proanthocyanidin-accumulating cells in Arabidopsis testa: regulation of differentiation and role in seed development. Plant Cell (2003) 2.18
Microsatellite-based deletion bin system for the establishment of genetic-physical map relationships in wheat (Triticum aestivum L.). Funct Integr Genomics (2004) 1.93
A worldwide bread wheat core collection arrayed in a 384-well plate. Theor Appl Genet (2007) 1.78
Two cytosolic glutamine synthetase isoforms of maize are specifically involved in the control of grain production. Plant Cell (2006) 1.72
Reconstruction of monocotelydoneous proto-chromosomes reveals faster evolution in plants than in animals. Proc Natl Acad Sci U S A (2009) 1.71
Epigenetic asymmetry of imprinted genes in plant gametes. Nat Genet (2006) 1.68
Palaeogenomics of plants: synteny-based modelling of extinct ancestors. Trends Plant Sci (2010) 1.66
Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution. Genome Res (2010) 1.55
The 'inner circle' of the cereal genomes. Curr Opin Plant Biol (2008) 1.55
SnRK1 (SNF1-related kinase 1) has a central role in sugar and ABA signalling in Arabidopsis thaliana. Plant J (2009) 1.48
Linkage mapping of 1454 new maize candidate gene Loci. Genetics (2005) 1.47
maternally expressed gene1 Is a novel maize endosperm transfer cell-specific gene with a maternal parent-of-origin pattern of expression. Plant Cell (2004) 1.45
An enhanced molecular marker based genetic map of perennial ryegrass (Lolium perenne) reveals comparative relationships with other Poaceae genomes. Genome (2002) 1.32
Types and rates of sequence evolution at the high-molecular-weight glutenin locus in hexaploid wheat and its ancestral genomes. Genetics (2006) 1.31
Wheat syntenome unveils new evidences of contrasted evolutionary plasticity between paleo- and neoduplicated subgenomes. Plant J (2013) 1.26
New insights into the origin of the B genome of hexaploid wheat: evolutionary relationships at the SPA genomic region with the S genome of the diploid relative Aegilops speltoides. BMC Genomics (2008) 1.26
Improved criteria and comparative genomics tool provide new insights into grass paleogenomics. Brief Bioinform (2009) 1.24
The Arabidopsis nuclear DAL gene encodes a chloroplast protein which is required for the maturation of the plastid ribosomal RNAs and is essential for chloroplast differentiation. Plant Mol Biol (2003) 1.20
Bioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oak. BMC Genomics (2010) 1.17
Cross-genome map based dissection of a nitrogen use efficiency ortho-metaQTL in bread wheat unravels concerted cereal genome evolution. Plant J (2011) 1.16
Single-nucleotide polymorphism frequency in a set of selected lines of bread wheat (Triticum aestivum L.). Genome (2006) 1.15
Overexpression of the epidermis-specific homeodomain-leucine zipper IV transcription factor Outer Cell Layer1 in maize identifies target genes involved in lipid metabolism and cuticle biosynthesis. Plant Physiol (2010) 1.11
Genomics in cereals: from genome-wide conserved orthologous set (COS) sequences to candidate genes for trait dissection. Funct Integr Genomics (2009) 1.10
The nuclear localization signal and the C-terminal region of FHY1 are required for transmission of phytochrome A signals. Plant J (2004) 1.09
Association of specific expansins with growth in maize leaves is maintained under environmental, genetic, and developmental sources of variation. Plant Physiol (2006) 1.09
The HD-ZIP IV transcription factor OCL4 is necessary for trichome patterning and anther development in maize. Plant J (2009) 1.07
RNA-seq in grain unveils fate of neo- and paleopolyploidization events in bread wheat (Triticum aestivum L.). Genome Biol (2011) 1.07
Quantitative trait loci (QTL) detection in multicross inbred designs: recovering QTL identical-by-descent status information from marker data. Genetics (2004) 1.07
Transcriptome analysis of Arabidopsis colonized by a plant-growth promoting rhizobacterium reveals a general effect on disease resistance. Plant J (2003) 1.06
empty pericarp4 encodes a mitochondrion-targeted pentatricopeptide repeat protein necessary for seed development and plant growth in maize. Plant Cell (2007) 1.03
Epistatic interactions between Opaque2 transcriptional activator and its target gene CyPPDK1 control kernel trait variation in maize. Plant Physiol (2009) 1.02
Combined meta-genomics analyses unravel candidate genes for the grain dietary fiber content in bread wheat (Triticum aestivum L.). Funct Integr Genomics (2010) 1.01
Nucleotide polymorphism in the wheat transcriptional activator Spa influences its pattern of expression and has pleiotropic effects on grain protein composition, dough viscoelasticity, and grain hardness. Plant Physiol (2009) 1.01
The HEALTHGRAIN wheat diversity screen: effects of genotype and environment on phytochemicals and dietary fiber components. J Agric Food Chem (2010) 1.00
Oryza Tag Line, a phenotypic mutant database for the Genoplante rice insertion line library. Nucleic Acids Res (2007) 1.00
MAIZEWALL. Database and developmental gene expression profiling of cell wall biosynthesis and assembly in maize. Plant Physiol (2006) 1.00
The maize heat shock factor-binding protein paralogs EMP2 and HSBP2 interact non-redundantly with specific heat shock factors. Planta (2005) 0.99
Deciphering the genetics of flowering time by an association study on candidate genes in bread wheat (Triticum aestivum L.). Theor Appl Genet (2011) 0.99
Differential expression of phenylpropanoid and related genes in brown-midrib bm1, bm2, bm3, and bm4 young near-isogenic maize plants. Planta (2007) 0.98
The maize transcription factor myb-related protein-1 is a key regulator of the differentiation of transfer cells. Plant Cell (2009) 0.96
Nucleotide diversity of the ZmPox3 maize peroxidase gene: relationships between a MITE insertion in exon 2 and variation in forage maize digestibility. BMC Genet (2004) 0.95
Analysis of diversity and linkage disequilibrium along chromosome 3B of bread wheat (Triticum aestivum L.). Theor Appl Genet (2009) 0.94
UDP-glucose dehydrogenases of maize: a role in cell wall pentose biosynthesis. Biochem J (2005) 0.94
A hydraulic model is compatible with rapid changes in leaf elongation under fluctuating evaporative demand and soil water status. Plant Physiol (2014) 0.93
High-Quality Draft Genome Sequence of the Xanthomonas translucens pv. cerealis Pathotype Strain CFBP 2541. Genome Announc (2015) 0.93
Grass microRNA gene paleohistory unveils new insights into gene dosage balance in subgenome partitioning after whole-genome duplication. Plant Cell (2012) 0.92
Decoding plant and animal genome plasticity from differential paleo-evolutionary patterns and processes. Genome Biol Evol (2012) 0.92
A joint transcriptomic, proteomic and metabolic analysis of maize endosperm development and starch filling. Plant Biotechnol J (2008) 0.91
Shared subgenome dominance following polyploidization explains grass genome evolutionary plasticity from a seven protochromosome ancestor with 16K protogenes. Genome Biol Evol (2014) 0.91
The ZmASR1 protein influences branched-chain amino acid biosynthesis and maintains kernel yield in maize under water-limited conditions. Plant Physiol (2011) 0.91
Engrailed-ZmOCL1 fusions cause a transient reduction of kernel size in maize. Plant Mol Biol (2005) 0.90
Abscisic acid and stress signals induce Viviparous1 expression in seed and vegetative tissues of maize. Plant Physiol (2007) 0.90
wDBTF: an integrated database resource for studying wheat transcription factor families. BMC Genomics (2010) 0.90
Paleo-evolutionary plasticity of plant disease resistance genes. BMC Genomics (2014) 0.89
Deciphering the genomic structure, function and evolution of carotenogenesis related phytoene synthases in grasses. BMC Genomics (2012) 0.89
Application of a new IBD-based QTL mapping method to common wheat breeding population: analysis of kernel hardness and dough strength. Theor Appl Genet (2005) 0.89
Identification of Glu-B1-1 as a candidate gene for the quantity of high-molecular-weight glutenin in bread wheat (Triticum aestivum L.) by means of an association study. Theor Appl Genet (2005) 0.88
ZmEBE genes show a novel, continuous expression pattern in the central cell before fertilization and in specific domains of the resulting endosperm after fertilization. Plant Mol Biol (2003) 0.88
Maize cytokinin oxidase genes: differential expression and cloning of two new cDNAs. J Exp Bot (2004) 0.88
High level of conservation between genes coding for the GAMYB transcription factor in barley (Hordeum vulgare L.) and bread wheat (Triticum aestivum L.) collections. Theor Appl Genet (2008) 0.87
Effects of genotype and environment on the contents of betaine, choline, and trigonelline in cereal grains. J Agric Food Chem (2012) 0.87
Hydroponics versus field lysimeter studies of urea, ammonium and nitrate uptake by oilseed rape (Brassica napus L.). J Exp Bot (2012) 0.87
Magnesium deficiency in sugar beets alters sugar partitioning and phloem loading in young mature leaves. Planta (2004) 0.86
Fertilization and early seed formation. C R Biol (2008) 0.85
Contrasted microcolinearity and gene evolution within a homoeologous region of wheat and barley species. J Mol Evol (2008) 0.85
Transcriptional and metabolic adjustments in ADP-glucose pyrophosphorylase-deficient bt2 maize kernels. Plant Physiol (2008) 0.85
Comparative cDNA-AFLP analysis of Cd-tolerant and -sensitive genotypes derived from crosses between the Cd hyperaccumulator Arabidopsis halleri and Arabidopsis lyrata ssp. petraea. J Exp Bot (2006) 0.85
Single nucleotide polymorphism, genetic mapping, and expression of genes coding for the DOF wheat prolamin-box binding factor. Funct Integr Genomics (2006) 0.85
QTLs and candidate genes for desiccation and abscisic acid content in maize kernels. BMC Plant Biol (2010) 0.85
Physical mapping in large genomes: accelerating anchoring of BAC contigs to genetic maps through in silico analysis. Funct Integr Genomics (2007) 0.84
Mapping ancestral genomes with massive gene loss: a matrix sandwich problem. Bioinformatics (2011) 0.83