Sequence and analysis of rice chromosome 4.

The Genomes of Oryza sativa: a history of duplications. PLoS Biol (2005) 7.67

Rapid recent growth and divergence of rice nuclear genomes. Proc Natl Acad Sci U S A (2004) 5.35

Genomewide comparative analysis of alternative splicing in plants. Proc Natl Acad Sci U S A (2006) 4.51

Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice. Genome Res (2004) 4.43

The TIGR Plant Repeat Databases: a collective resource for the identification of repetitive sequences in plants. Nucleic Acids Res (2004) 4.31

Cloning and characterization of microRNAs from rice. Plant Cell (2005) 3.72

Comparative DNA sequence analysis of wheat and rice genomes. Genome Res (2003) 3.63

An overview of gibberellin metabolism enzyme genes and their related mutants in rice. Plant Physiol (2004) 3.32

The use of MPSS for whole-genome transcriptional analysis in Arabidopsis. Genome Res (2004) 3.30

Evolution of DNA sequence nonhomologies among maize inbreds. Plant Cell (2005) 3.17

Evidence that rice and other cereals are ancient aneuploids. Plant Cell (2003) 2.62

Population structure and its effect on haplotype diversity and linkage disequilibrium surrounding the xa5 locus of rice (Oryza sativa L.). Genetics (2003) 2.58

An SNP resource for rice genetics and breeding based on subspecies indica and japonica genome alignments. Genome Res (2004) 2.56

The extent of linkage disequilibrium in rice (Oryza sativa L.). Genetics (2007) 2.56

Fine definition of the pedigree haplotypes of closely related rice cultivars by means of genome-wide discovery of single-nucleotide polymorphisms. BMC Genomics (2010) 2.45

Validation of rice genome sequence by optical mapping. BMC Genomics (2007) 2.44

The Oryza bacterial artificial chromosome library resource: construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus Oryza. Genome Res (2005) 2.23

RNA silencing of single and multiple members in a gene family of rice. Plant Physiol (2005) 2.10

Identification of syn-pimara-7,15-diene synthase reveals functional clustering of terpene synthases involved in rice phytoalexin/allelochemical biosynthesis. Plant Physiol (2004) 2.06

Comparative physical mapping links conservation of microsynteny to chromosome structure and recombination in grasses. Proc Natl Acad Sci U S A (2005) 2.01

Development of genome-wide DNA polymorphism database for map-based cloning of rice genes. Plant Physiol (2004) 1.98

A workshop report on wheat genome sequencing: International Genome Research on Wheat Consortium. Genetics (2004) 1.94

KaPPA-view: a web-based analysis tool for integration of transcript and metabolite data on plant metabolic pathway maps. Plant Physiol (2005) 1.90

Differential methylation of genes and repeats in land plants. Genome Res (2005) 1.77

Global genome expression analysis of rice in response to drought and high-salinity stresses in shoot, flag leaf, and panicle. Plant Mol Biol (2007) 1.76

A microarray analysis of the rice transcriptome and its comparison to Arabidopsis. Genome Res (2005) 1.71

Loss-of-function mutations of the rice GAMYB gene impair alpha-amylase expression in aleurone and flower development. Plant Cell (2003) 1.71

ReAS: Recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun. PLoS Comput Biol (2005) 1.71

Antisense transcripts with rice full-length cDNAs. Genome Biol (2003) 1.69

Locating sequence on FPC maps and selecting a minimal tiling path. Genome Res (2003) 1.67

Identification of miniature inverted-repeat transposable elements (MITEs) and biogenesis of their siRNAs in the Solanaceae: new functional implications for MITEs. Genome Res (2008) 1.63

Sequencing multiple and diverse rice varieties. Connecting whole-genome variation with phenotypes. Plant Physiol (2006) 1.61

Generation and analysis of end sequence database for T-DNA tagging lines in rice. Plant Physiol (2003) 1.56

Genome-wide analysis of CCCH zinc finger family in Arabidopsis and rice. BMC Genomics (2008) 1.55

Composition and structure of the centromeric region of rice chromosome 8. Plant Cell (2004) 1.52

The rice nuclear genome continuously integrates, shuffles, and eliminates the chloroplast genome to cause chloroplast-nuclear DNA flux. Plant Cell (2005) 1.49

Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species. Genome Res (2005) 1.48

Genome-wide comparative phylogenetic analysis of the rice and Arabidopsis Dof gene families. BMC Evol Biol (2003) 1.47

Genome-wide and expression analysis of protein phosphatase 2C in rice and Arabidopsis. BMC Genomics (2008) 1.43

Global identification and characterization of transcriptionally active regions in the rice genome. PLoS One (2007) 1.41

Miniature inverted-repeat transposable elements (MITEs) have been accumulated through amplification bursts and play important roles in gene expression and species diversity in Oryza sativa. Mol Biol Evol (2011) 1.39

Characterization of the maize endosperm transcriptome and its comparison to the rice genome. Genome Res (2004) 1.39

Structure and evolution of the r/b chromosomal regions in rice, maize and sorghum. Genetics (2004) 1.37

The structure of coral allene oxide synthase reveals a catalase adapted for metabolism of a fatty acid hydroperoxide. Proc Natl Acad Sci U S A (2004) 1.33

Comparative DNA sequence analysis of mapped wheat ESTs reveals the complexity of genome relationships between rice and wheat. Funct Integr Genomics (2004) 1.32

The serine/arginine-rich protein family in rice plays important roles in constitutive and alternative splicing of pre-mRNA. Plant Cell (2005) 1.30

Structure-based discovery and description of plant and animal Helitrons. Proc Natl Acad Sci U S A (2009) 1.27

Evolutionary expansion, gene structure, and expression of the rice wall-associated kinase gene family. Plant Physiol (2005) 1.24

Independent losses of function in a polyphenol oxidase in rice: differentiation in grain discoloration between subspecies and the role of positive selection under domestication. Plant Cell (2008) 1.24

A GeneTrek analysis of the maize genome. Proc Natl Acad Sci U S A (2007) 1.23

Generation and evolutionary fate of insertions of organelle DNA in the nuclear genomes of flowering plants. Genome Res (2005) 1.22

Structural features of the rice chromosome 4 centromere. Nucleic Acids Res (2004) 1.21

Identification and characterization of lineage-specific genes within the Poaceae. Plant Physiol (2007) 1.19

Gene enrichment in maize with hypomethylated partial restriction (HMPR) libraries. Genome Res (2005) 1.19

A tiling microarray expression analysis of rice chromosome 4 suggests a chromosome-level regulation of transcription. Plant Cell (2005) 1.18

Organisation and structural evolution of the rice glutathione S-transferase gene family. Mol Genet Genomics (2004) 1.13

Intergenic locations of rice centromeric chromatin. PLoS Biol (2008) 1.13

DNA rearrangement in orthologous orp regions of the maize, rice and sorghum genomes. Genetics (2005) 1.12

Evolutionary dynamics of the DNA-binding domains in putative R2R3-MYB genes identified from rice subspecies indica and japonica genomes. Plant Physiol (2004) 1.11

High potential of a transposon mPing as a marker system in japonica x japonica cross in rice. DNA Res (2009) 1.10

A comparative genomics strategy for targeted discovery of single-nucleotide polymorphisms and conserved-noncoding sequences in orphan crops. Plant Physiol (2006) 1.10

Tiling microarray analysis of rice chromosome 10 to identify the transcriptome and relate its expression to chromosomal architecture. Genome Biol (2005) 1.09

Arabidopsis to rice. Applying knowledge from a weed to enhance our understanding of a crop species. Plant Physiol (2004) 1.08

Distribution of retroelements in centromeres and neocentromeres of maize. Genetics (2003) 1.07

The high diversity of snoRNAs in plants: identification and comparative study of 120 snoRNA genes from Oryza sativa. Nucleic Acids Res (2003) 1.07

Chloroplast DNA insertions into the nuclear genome of rice: the genes, sites and ages of insertion involved. Funct Integr Genomics (2007) 1.05

An-1 encodes a basic helix-loop-helix protein that regulates awn development, grain size, and grain number in rice. Plant Cell (2013) 1.04

Proteomics of the rice cell: systematic identification of the protein populations in subcellular compartments. Mol Genet Genomics (2004) 1.03

Nomenclature for two-component signaling elements of rice. Plant Physiol (2007) 1.03

Rice Annotation Database (RAD): a contig-oriented database for map-based rice genomics. Nucleic Acids Res (2005) 1.02

Chromosomal polymorphism of ribosomal genes in the genus Oryza. Theor Appl Genet (2008) 1.02

Rice as a model for centromere and heterochromatin research. Chromosome Res (2007) 1.01

Tissue culture-induced transpositional activity of mPing is correlated with cytosine methylation in rice. BMC Plant Biol (2009) 1.00

Life sciences and biotechnology in China. Philos Trans R Soc Lond B Biol Sci (2007) 1.00

Significance tests and weighted values for AFLP similarities, based on Arabidopsis in silico AFLP fragment length distributions. Genetics (2004) 0.99

Molecular cloning and expression analysis of the cell-wall invertase gene family in rice (Oryza sativa L.). Plant Cell Rep (2005) 0.98

Antagonistic, overlapping and distinct responses to biotic stress in rice (Oryza sativa) and interactions with abiotic stress. BMC Genomics (2013) 0.96

In-depth sequence analysis of the tomato chromosome 12 centromeric region: identification of a large CAA block and characterization of pericentromere retrotranposons. Chromosoma (2005) 0.96

Structural diversity and differential transcription of the patatin multicopy gene family during potato tuber development. Genetics (2005) 0.95

Rice functional genomics research in China. Philos Trans R Soc Lond B Biol Sci (2007) 0.94

Comparative physical mapping of the apospory-specific genomic region in two apomictic grasses: Pennisetum squamulatum and Cenchrus ciliaris. Genetics (2006) 0.93

Exploring the plant transcriptome through phylogenetic profiling. Plant Physiol (2005) 0.92

Identification and fine mapping of a mutant gene for palealess spikelet in rice. Planta (2004) 0.89

The Rice PIPELINE: a unification tool for plant functional genomics. Nucleic Acids Res (2004) 0.89

Sequence polymorphisms in wild, weedy, and cultivated rice suggest seed-shattering locus sh4 played a minor role in Asian rice domestication. Ecol Evol (2012) 0.87

Genetic and in silico comparative mapping of the polyphenol oxidase gene in bread wheat (Triticum aestivum L.). Funct Integr Genomics (2005) 0.86

Evaluation of monocot and eudicot divergence using the sugarcane transcriptome. Plant Physiol (2004) 0.84

Identification of candidate genes for drought stress tolerance in rice by the integration of a genetic (QTL) map with the rice genome physical map. J Zhejiang Univ Sci B (2005) 0.84

Sources and predictors of resolvable indel polymorphism assessed using rice as a model. Mol Genet Genomics (2004) 0.83

Proteome analysis of rice tissues by two-dimensional electrophoresis: an approach to the investigation of gibberellin regulated proteins. Mol Genet Genomics (2003) 0.83

Preparations of meiotic pachytene chromosomes and extended DNA fibers from cotton suitable for fluorescence in situ hybridization. PLoS One (2012) 0.83

Development of pachytene FISH maps for six maize chromosomes and their integration with other maize maps for insights into genome structure variation. Chromosome Res (2012) 0.82

Microarray and proteomic analysis of brassinosteroid- and gibberellin-regulated gene and protein expression in rice. Genomics Proteomics Bioinformatics (2004) 0.82

Plant biology research comes of age in China. Plant Cell (2006) 0.82

A candidate autonomous version of the wheat MITE Hikkoshi is present in the rice genome. Mol Genet Genomics (2005) 0.82

EMS mutagenesis in mature seed-derived rice calli as a new method for rapidly obtaining TILLING mutant populations. Plant Methods (2014) 0.82

A comprehensive crop genome research project: the Superhybrid Rice Genome Project in China. Philos Trans R Soc Lond B Biol Sci (2007) 0.81

An integrated approach for comparative mapping in rice and barley with special reference to the Rph16 resistance locus. Funct Integr Genomics (2004) 0.80

Gene expression profiling in rice young panicle and vegetative organs and identification of panicle-specific genes through known gene functions. Mol Genet Genomics (2005) 0.80

Two Brassica napus genes encoding NAC transcription factors are involved in response to high-salinity stress. Plant Cell Rep (2012) 0.80

Galaxy: a platform for interactive large-scale genome analysis. Genome Res (2005) 35.75

Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer. Lancet (2005) 29.45

Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature (2004) 24.40

Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science (2002) 24.31

Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification. Nature (2010) 18.63

Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) 18.01

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J Comput Chem (2003) 15.88

Tumor stem cells derived from glioblastomas cultured in bFGF and EGF more closely mirror the phenotype and genotype of primary tumors than do serum-cultured cell lines. Cancer Cell (2006) 15.16

Integrated genomic characterization of endometrial carcinoma. Nature (2013) 14.29

Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science (2011) 14.29

Fever with thrombocytopenia associated with a novel bunyavirus in China. N Engl J Med (2011) 13.18

WEGO: a web tool for plotting GO annotations. Nucleic Acids Res (2006) 13.06

The diverse functions of histone lysine methylation. Nat Rev Mol Cell Biol (2005) 12.70

The developmental transcriptome of Drosophila melanogaster. Nature (2010) 11.85

The somatic genomic landscape of glioblastoma. Cell (2013) 11.73

Oncometabolite 2-hydroxyglutarate is a competitive inhibitor of α-ketoglutarate-dependent dioxygenases. Cancer Cell (2011) 11.44

Trait-associated SNPs are more likely to be eQTLs: annotation to enhance discovery from GWAS. PLoS Genet (2010) 10.75

Histone demethylation by a family of JmjC domain-containing proteins. Nature (2005) 10.36

Role of histone H3 lysine 27 methylation in X inactivation. Science (2003) 9.85

The incidence of co-morbidities related to obesity and overweight: a systematic review and meta-analysis. BMC Public Health (2009) 9.79

Role of histone H2A ubiquitination in Polycomb silencing. Nature (2004) 9.48

Active DNA demethylation: many roads lead to Rome. Nat Rev Mol Cell Biol (2010) 9.35

Structure of dengue virus: implications for flavivirus organization, maturation, and fusion. Cell (2002) 9.13

Complete Khoisan and Bantu genomes from southern Africa. Nature (2010) 9.06

Strong time dependence of the 76-gene prognostic signature for node-negative breast cancer patients in the TRANSBIG multicenter independent validation series. Clin Cancer Res (2007) 8.41

The functions of E(Z)/EZH2-mediated methylation of lysine 27 in histone H3. Curr Opin Genet Dev (2004) 7.89

Effect of PCI on quality of life in patients with stable coronary disease. N Engl J Med (2008) 7.75

MMDB: annotating protein sequences with Entrez's 3D-structure database. Nucleic Acids Res (2006) 7.57

HSV-1 ICP34.5 confers neurovirulence by targeting the Beclin 1 autophagy protein. Cell Host Microbe (2007) 7.34

Consuming fructose-sweetened, not glucose-sweetened, beverages increases visceral adiposity and lipids and decreases insulin sensitivity in overweight/obese humans. J Clin Invest (2009) 7.09

SUZ12 is required for both the histone methyltransferase activity and the silencing function of the EED-EZH2 complex. Mol Cell (2004) 6.90

Probabilistic Boolean Networks: a rule-based uncertainty model for gene regulatory networks. Bioinformatics (2002) 6.90

Association of BRCA1 and BRCA2 mutations with survival, chemotherapy sensitivity, and gene mutator phenotype in patients with ovarian cancer. JAMA (2011) 6.81

The yeast cell-cycle network is robustly designed. Proc Natl Acad Sci U S A (2004) 6.76

The mTOR-regulated phosphoproteome reveals a mechanism of mTORC1-mediated inhibition of growth factor signaling. Science (2011) 6.75

Hydrogen-bonded ferroelectrics based on metal-organic coordination. J Am Chem Soc (2009) 6.69

JmjC-domain-containing proteins and histone demethylation. Nat Rev Genet (2006) 6.65

Dual functions of Tet1 in transcriptional regulation in mouse embryonic stem cells. Nature (2011) 6.48

Role of Bmi-1 and Ring1A in H2A ubiquitylation and Hox gene silencing. Mol Cell (2005) 6.29

Regulation of histone methylation by demethylimination and demethylation. Nat Rev Mol Cell Biol (2007) 6.13

Pten regulates neuronal arborization and social interaction in mice. Neuron (2006) 6.11

A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res (2007) 5.97

SCAN: SNP and copy number annotation. Bioinformatics (2009) 5.96

hDOT1L links histone methylation to leukemogenesis. Cell (2005) 5.83

Structural basis for specific binding of Polycomb chromodomain to histone H3 methylated at Lys 27. Genes Dev (2003) 5.77

Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas. N Engl J Med (2015) 5.71

JHDM2A, a JmjC-containing H3K9 demethylase, facilitates transcription activation by androgen receptor. Cell (2006) 5.54

Methylation of H3-lysine 79 is mediated by a new family of HMTases without a SET domain. Curr Biol (2002) 5.53

The transcriptional repressor JHDM3A demethylates trimethyl histone H3 lysine 9 and lysine 36. Nature (2006) 5.51

New nomenclature for chromatin-modifying enzymes. Cell (2007) 5.34

A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. Nature (2004) 5.24

Tudor, MBT and chromo domains gauge the degree of lysine methylation. EMBO Rep (2006) 5.19

G9a-mediated irreversible epigenetic inactivation of Oct-3/4 during early embryogenesis. Nat Cell Biol (2006) 5.16

Gene expression profiles and molecular markers to predict recurrence of Dukes' B colon cancer. J Clin Oncol (2004) 5.12

Unique physiological and pathogenic features of Leptospira interrogans revealed by whole-genome sequencing. Nature (2003) 5.04

The four-herb Chinese medicine PHY906 reduces chemotherapy-induced gastrointestinal toxicity. Sci Transl Med (2010) 4.78

Supramolecular bola-like ferroelectric: 4-methoxyanilinium tetrafluoroborate-18-crown-6. J Am Chem Soc (2011) 4.73

Genome-wide analysis of PTB-RNA interactions reveals a strategy used by the general splicing repressor to modulate exon inclusion or skipping. Mol Cell (2009) 4.71

Dnmt3a-dependent nonpromoter DNA methylation facilitates transcription of neurogenic genes. Science (2010) 4.60

Recognition of histone H3 lysine-4 methylation by the double tudor domain of JMJD2A. Science (2006) 4.54

Bre1, an E3 ubiquitin ligase required for recruitment and substrate selection of Rad6 at a promoter. Mol Cell (2003) 4.49

Young age at diagnosis correlates with worse prognosis and defines a subset of breast cancers with shared patterns of gene expression. J Clin Oncol (2008) 4.45

Genome-wide analysis of 5-hydroxymethylcytosine distribution reveals its dual function in transcriptional regulation in mouse embryonic stem cells. Genes Dev (2011) 4.45

MMDB: Entrez's 3D-structure database. Nucleic Acids Res (2002) 4.42

Dialysis facility ownership and epoetin dosing in patients receiving hemodialysis. JAMA (2007) 4.40

The zinc finger transcription factor Th-POK regulates CD4 versus CD8 T-cell lineage commitment. Nature (2005) 4.39

Subtypes of breast cancer show preferential site of relapse. Cancer Res (2008) 4.38

A genome-wide approach to identify genetic variants that contribute to etoposide-induced cytotoxicity. Proc Natl Acad Sci U S A (2007) 4.35

Diisopropylammonium chloride: a ferroelectric organic salt with a high phase transition temperature and practical utilization level of spontaneous polarization. Adv Mater (2011) 4.30

Nanog and Oct4 associate with unique transcriptional repression complexes in embryonic stem cells. Nat Cell Biol (2008) 4.30

Abnormal spine morphology and enhanced LTP in LIMK-1 knockout mice. Neuron (2002) 4.18

Concern Calmodulin kinase II and arrhythmias in a mouse model of cardiac hypertrophy. Circulation (2002) 4.16

Purification and functional characterization of SET8, a nucleosomal histone H4-lysine 20-specific methyltransferase. Curr Biol (2002) 4.12

Replication-dependent loss of 5-hydroxymethylcytosine in mouse preimplantation embryos. Science (2011) 4.12

Gene expression signatures for predicting prognosis of squamous cell and adenocarcinomas of the lung. Cancer Res (2006) 4.11

Human mesenchymal stem cells inhibit differentiation and function of monocyte-derived dendritic cells. Blood (2005) 4.10

Mechanisms and functions of Tet protein-mediated 5-methylcytosine oxidation. Genes Dev (2011) 4.09

Lysine methylation within the globular domain of histone H3 by Dot1 is important for telomeric silencing and Sir protein association. Genes Dev (2002) 4.07

Casq2 deletion causes sarcoplasmic reticulum volume increase, premature Ca2+ release, and catecholaminergic polymorphic ventricular tachycardia. J Clin Invest (2006) 4.06

iPS cells can support full-term development of tetraploid blastocyst-complemented embryos. Cell Stem Cell (2009) 4.04

Meta-analysis of genome-wide association studies identifies common variants associated with blood pressure variation in east Asians. Nat Genet (2011) 4.04

On the use of general control samples for genome-wide association studies: genetic matching highlights causal variants. Am J Hum Genet (2008) 3.95

Probing cellular protein complexes using single-molecule pull-down. Nature (2011) 3.92

Lung metastasis genes couple breast tumor size and metastatic spread. Proc Natl Acad Sci U S A (2007) 3.92

Parkin mediates nonclassical, proteasomal-independent ubiquitination of synphilin-1: implications for Lewy body formation. J Neurosci (2005) 3.92

Stargazin modulates AMPA receptor gating and trafficking by distinct domains. Nature (2005) 3.88

Epigenetic-mediated dysfunction of the bone morphogenetic protein pathway inhibits differentiation of glioblastoma-initiating cells. Cancer Cell (2008) 3.87

Structure of the immature dengue virus at low pH primes proteolytic maturation. Science (2008) 3.86

Genome-wide translocation sequencing reveals mechanisms of chromosome breaks and rearrangements in B cells. Cell (2011) 3.81

The H3K36 demethylase Jhdm1b/Kdm2b regulates cell proliferation and senescence through p15(Ink4b). Nat Struct Mol Biol (2008) 3.80

The retinoblastoma binding protein RBP2 is an H3K4 demethylase. Cell (2007) 3.79

Cortical and trabecular bone mineral loss from the spine and hip in long-duration spaceflight. J Bone Miner Res (2004) 3.77

Hierarchical recruitment of polycomb group silencing complexes. Mol Cell (2004) 3.73

Preferential occupancy of histone variant H2AZ at inactive promoters influences local histone modifications and chromatin remodeling. Proc Natl Acad Sci U S A (2005) 3.72

Variation in virulence among clades of Escherichia coli O157:H7 associated with disease outbreaks. Proc Natl Acad Sci U S A (2008) 3.69

PLU-1 is an H3K4 demethylase involved in transcriptional repression and breast cancer cell proliferation. Mol Cell (2007) 3.68

Imaging of amyloid beta in Alzheimer's disease with 18F-BAY94-9172, a novel PET tracer: proof of mechanism. Lancet Neurol (2008) 3.67

Conformational changes of the flavivirus E glycoprotein. Structure (2004) 3.66

Association of plasma clusterin concentration with severity, pathology, and progression in Alzheimer disease. Arch Gen Psychiatry (2010) 3.64

Shell-isolated nanoparticle-enhanced Raman spectroscopy. Nature (2010) 3.64