Published in Plant Physiol on September 22, 2006
Identification and characterization of nucleotide-binding site-leucine-rich repeat genes in the model plant Medicago truncatula. Plant Physiol (2007) 2.01
Genome-wide identification and analysis of MAPK and MAPKK gene families in Brachypodium distachyon. PLoS One (2012) 1.05
Genome Wide Analysis of Nucleotide-Binding Site Disease Resistance Genes in Brachypodium distachyon. Comp Funct Genomics (2012) 1.02
Identification of rhizome-specific genes by genome-wide differential expression analysis in Oryza longistaminata. BMC Plant Biol (2011) 0.99
Ginger and turmeric expressed sequence tags identify signature genes for rhizome identity and development and the biosynthesis of curcuminoids, gingerols and terpenoids. BMC Plant Biol (2013) 0.88
A systems-wide comparison of red rice (Oryza longistaminata) tissues identifies rhizome specific genes and proteins that are targets for cultivated rice improvement. BMC Plant Biol (2014) 0.83
Sequencing of transcriptomes from two Miscanthus species reveals functional specificity in rhizomes, and clarifies evolutionary relationships. BMC Plant Biol (2014) 0.82
Large-scale proteome comparative analysis of developing rhizomes of the ancient vascular plant equisetum hyemale. Front Plant Sci (2012) 0.81
Gibberellin-Stimulation of Rhizome Elongation and Differential GA-Responsive Proteomic Changes in Two Grass Species. Front Plant Sci (2016) 0.81
Transcriptome Analysis of an Insecticide Resistant Housefly Strain: Insights about SNPs and Regulatory Elements in Cytochrome P450 Genes. PLoS One (2016) 0.77
Targeted mapping of quantitative trait locus regions for rhizomatousness in chromosome SBI-01 and analysis of overwintering in a Sorghum bicolor × S. propinquum population. Mol Breed (2012) 0.77
Hormone regulation of rhizome development in tall fescue (Festuca arundinacea) associated with proteomic changes controlling respiratory and amino acid metabolism. Ann Bot (2016) 0.75
De novo Transcriptome Analysis of Miscanthus lutarioriparius Identifies Candidate Genes in Rhizome Development. Front Plant Sci (2017) 0.75
Tissue-specific transcriptomic profiling of Sorghum propinquum using a rice genome array. PLoS One (2013) 0.75
Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res (1998) 106.16
Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res (1998) 96.63
Genomic sequencing. Proc Natl Acad Sci U S A (1984) 92.36
Consed: a graphical tool for sequence finishing. Genome Res (1998) 59.36
Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction. Science (1992) 24.32
Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucleic Acids Res (1999) 13.02
'Green revolution' genes encode mutant gibberellin response modulators. Nature (1999) 8.87
The Arabidopsis GAI gene defines a signaling pathway that negatively regulates gibberellin responses. Genes Dev (1997) 7.30
High throughput fingerprint analysis of large-insert clones. Genome Res (1997) 6.91
The action of ARGONAUTE1 in the miRNA pathway and its regulation by the miRNA pathway are crucial for plant development. Genes Dev (2004) 6.69
Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. Proc Natl Acad Sci U S A (2004) 6.66
The Arabidopsis RGA gene encodes a transcriptional regulator repressing the gibberellin signal transduction pathway. Plant Cell (1998) 5.33
Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing. Proc Natl Acad Sci U S A (2003) 4.62
Control of tillering in rice. Nature (2003) 3.73
Gramene: a resource for comparative grass genomics. Nucleic Acids Res (2002) 3.72
Comparative analysis of QTLs affecting plant height and maturity across the Poaceae, in reference to an interspecific sorghum population. Genetics (1995) 3.60
The major clades of MADS-box genes and their role in the development and evolution of flowering plants. Mol Phylogenet Evol (2003) 3.47
LIPID-TRANSFER PROTEINS IN PLANTS. Annu Rev Plant Physiol Plant Mol Biol (1996) 2.91
HOW GIBBERELLIN REGULATES PLANT GROWTH AND DEVELOPMENT: A Molecular Genetic Analysis of Gibberellin Signaling. Annu Rev Plant Physiol Plant Mol Biol (2001) 2.90
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
The weediness of wild plants: molecular analysis of genes influencing dispersal and persistence of johnsongrass, Sorghum halepense (L.) Pers. Proc Natl Acad Sci U S A (1995) 2.29
QTL clusters reflect character associations in wild and cultivated rice. Theor Appl Genet (2002) 2.01
Expression patterns and mutant phenotype of teosinte branched1 correlate with growth suppression in maize and teosinte. Genetics (2002) 1.98
Purification, characterization, and sequence analysis of a potential virulence factor from Porphyromonas gingivalis, peptidylarginine deiminase. Infect Immun (1999) 1.96
Structure and evolution of cereal genomes. Curr Opin Genet Dev (2003) 1.91
The hormonal regulation of axillary bud growth in Arabidopsis. Plant J (2000) 1.75
Gibberellin-responsive elements in the promoter of a barley high-pI alpha-amylase gene. Plant Cell (1992) 1.59
Genome-wide analysis of the GRAS gene family in rice and Arabidopsis. Plant Mol Biol (2004) 1.58
Convergent evolution of perenniality in rice and sorghum. Proc Natl Acad Sci U S A (2003) 1.55
Alignment of genetic maps and QTLs between inter- and intra-specific sorghum populations. Theor Appl Genet (2006) 1.34
Binding site selection for the plant MADS domain protein AGL15: an in vitro and in vivo study. J Biol Chem (2003) 1.30
Nutritional regulation of ANR1 and other root-expressed MADS-box genes in Arabidopsis thaliana. Planta (2005) 1.24
An improved bacterial colony lysis procedure enables direct DNA hybridisation using short (10, 11 bases) oligonucleotides to cosmids. Nucleic Acids Res (1991) 1.19
Two cis-acting elements necessary and sufficient for gibberellin-upregulated proteinase expression in rice seeds. Plant J (2003) 1.19
A role for the DOF transcription factor BPBF in the regulation of gibberellin-responsive genes in barley aleurone. Plant Physiol (2002) 1.11
Developmental and environmental regulation of two ribosomal protein genes in tobacco. Plant Mol Biol (1994) 1.09
Identification of two essential sequence elements in the nonconsensus type II PatpB-290 plastid promoter by using plastid transcription extracts from cultured tobacco BY-2 cells. Plant Cell (1999) 1.04
One of two tandem Arabidopsis genes homologous to monosaccharide transporters is senescence-associated. Plant Mol Biol (2001) 1.04
The Endoplasmic reticulum-associated maize GL8 protein is a component of the acyl-coenzyme A elongase ivolved in the production of cuticular waxes. Plant Physiol (2002) 1.00
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
Quantitative trait loci controlling phenotypes related to the perennial versus annual habit in wild relatives of maize. Theor Appl Genet (2004) 0.96
Transcription profiling of the early gravitropic response in Arabidopsis using high-density oligonucleotide probe microarrays. Plant Physiol (2002) 0.95
Isolation of MADS-box genes from sweet potato (Ipomoea batatas (L.) Lam.) expressed specifically in vegetative tissues. Plant Cell Physiol (2002) 0.90
Biochemical characterization of elongase activity in corn (Zea mays L.) roots. Phytochemistry (2005) 0.89
Rapid purification of fluorescent dye-labeled products in a 96-well format for high-throughput automated DNA sequencing. Nucleic Acids Res (1995) 0.89
A cathepsin B-like cysteine protease gene from Hordeum vulgare (gene CatB) induced by GA in aleurone cells is under circadian control in leaves. J Exp Bot (2003) 0.88
Silencing of ribosomal protein L3 genes in N. tabacum reveals coordinate expression and significant alterations in plant growth, development and ribosome biogenesis. Plant J (2004) 0.86
Characterization and expression of monosaccharide transporters (osMSTs) in rice. Plant Cell Physiol (2000) 0.85
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
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
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
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
Gene amplification confers glyphosate resistance in Amaranthus palmeri. Proc Natl Acad Sci U S A (2009) 2.23
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
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
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
Genome and gene duplications and gene expression divergence: a view from plants. Ann N Y Acad Sci (2012) 1.25
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
Microcolinearity and genome evolution in the AdhA region of diploid and polyploid cotton (Gossypium). Plant J (2007) 1.17
Sex chromosomes in flowering plants. Am J Bot (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
A nuclear restorer-of-fertility mutation disrupts accumulation of mitochondrial ATP synthase subunit alpha in developing pollen of S male-sterile maize. Genetics (2003) 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
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
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
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
Organization and evolution of resistance gene analogs in peanut. Mol Genet Genomics (2005) 0.94
Emergence of a group 3 coronavirus through recombination. Virology (2010) 0.94
Ancient gene duplicates in Gossypium (cotton) exhibit near-complete expression divergence. Genome Biol Evol (2014) 0.94
A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure. Genome Biol (2011) 0.93
Comparative analysis of QTLs affecting plant height and flowering among closely-related diploid and polyploid genomes. Genome (2002) 0.93
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
Recombination in avian gamma-coronavirus infectious bronchitis virus. Viruses (2011) 0.93
Construction of physical maps for the sex-specific regions of papaya sex chromosomes. BMC Genomics (2012) 0.92
Telomere-centric genome repatterning determines recurring chromosome number reductions during the evolution of eukaryotes. New Phytol (2014) 0.92
Comparative analysis of serine/arginine-rich proteins across 27 eukaryotes: insights into sub-family classification and extent of alternative splicing. PLoS One (2011) 0.92
A phylogenetic analysis of indel dynamics in the cotton genus. Mol Biol Evol (2008) 0.92
A physical map of Brassica oleracea shows complexity of chromosomal changes following recursive paleopolyploidizations. BMC Genomics (2011) 0.92
Rapid divergence and expansion of the X chromosome in papaya. Proc Natl Acad Sci U S A (2012) 0.92
Comparative analysis of peanut NBS-LRR gene clusters suggests evolutionary innovation among duplicated domains and erosion of gene microsynteny. New Phytol (2011) 0.91