Published in Nat Genet on October 24, 2010
A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One (2011) 15.19
Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nat Genet (2011) 6.59
Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nat Commun (2011) 5.41
A map of rice genome variation reveals the origin of cultivated rice. Nature (2012) 4.92
Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nat Biotechnol (2011) 4.84
Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. Rice (N Y) (2013) 4.27
Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm. Nat Genet (2011) 4.19
Next-generation phenotyping: requirements and strategies for enhancing our understanding of genotype-phenotype relationships and its relevance to crop improvement. Theor Appl Genet (2013) 2.75
Crop genomics: advances and applications. Nat Rev Genet (2011) 2.72
A mixed-model approach for genome-wide association studies of correlated traits in structured populations. Nat Genet (2012) 2.69
Evolution of crop species: genetics of domestication and diversification. Nat Rev Genet (2013) 2.59
The 3,000 rice genomes project. Gigascience (2014) 2.57
Population genomic and genome-wide association studies of agroclimatic traits in sorghum. Proc Natl Acad Sci U S A (2012) 2.40
Genetic architecture of aluminum tolerance in rice (Oryza sativa) determined through genome-wide association analysis and QTL mapping. PLoS Genet (2011) 2.34
Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics. Plant Cell Physiol (2013) 2.28
Genome-wide SNP detection, validation, and development of an 8K SNP array for apple. PLoS One (2012) 2.26
Genome-wide association study dissects the genetic architecture of oil biosynthesis in maize kernels. Nat Genet (2012) 2.25
A next-generation sequencing method for genotyping-by-sequencing of highly heterozygous autotetraploid potato. PLoS One (2013) 2.22
Natural variation in Arabidopsis: from molecular genetics to ecological genomics. Plant Physiol (2011) 2.06
Genome-wide patterns of genetic variation in sweet and grain sorghum (Sorghum bicolor). Genome Biol (2011) 2.02
Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ). Plant J (2013) 2.02
Genome-wide association studies in plants: the missing heritability is in the field. Genome Biol (2011) 1.93
Gains in QTL detection using an ultra-high density SNP map based on population sequencing relative to traditional RFLP/SSR markers. PLoS One (2011) 1.84
NGS technologies for analyzing germplasm diversity in genebanks. Brief Funct Genomics (2012) 1.76
Genome-wide association mapping identifies a new arsenate reductase enzyme critical for limiting arsenic accumulation in plants. PLoS Biol (2014) 1.74
A genome-wide association study of seed protein and oil content in soybean. BMC Genomics (2014) 1.73
High-throughput SNP discovery and genotyping for constructing a saturated linkage map of chickpea (Cicer arietinum L.). DNA Res (2012) 1.66
Two evolutionary histories in the genome of rice: the roles of domestication genes. PLoS Genet (2011) 1.63
Genome-wide association mapping of root traits in a japonica rice panel. PLoS One (2013) 1.58
A haplotype map of genomic variations and genome-wide association studies of agronomic traits in foxtail millet (Setaria italica). Nat Genet (2013) 1.58
Genetic control of seed shattering in rice by the APETALA2 transcription factor shattering abortion1. Plant Cell (2012) 1.56
Investigating natural variation in Drosophila courtship song by the evolve and resequence approach. Genetics (2012) 1.55
Finding our way through phenotypes. PLoS Biol (2015) 1.53
High-density SNP-based genetic map development and linkage disequilibrium assessment in Brassica napus L. BMC Genomics (2013) 1.51
Multi-parent advanced generation inter-cross (MAGIC) populations in rice: progress and potential for genetics research and breeding. Rice (N Y) (2013) 1.50
Single-nucleotide polymorphism discovery by high-throughput sequencing in sorghum. BMC Genomics (2011) 1.48
Dissecting yield-associated loci in super hybrid rice by resequencing recombinant inbred lines and improving parental genome sequences. Proc Natl Acad Sci U S A (2013) 1.48
SNP Discovery through Next-Generation Sequencing and Its Applications. Int J Plant Genomics (2012) 1.46
Whole-genome nucleotide diversity, recombination, and linkage disequilibrium in the model legume Medicago truncatula. Proc Natl Acad Sci U S A (2011) 1.46
Harvesting the promising fruits of genomics: applying genome sequencing technologies to crop breeding. PLoS Biol (2014) 1.42
Quantifying effects of environmental and geographical factors on patterns of genetic differentiation. Mol Ecol (2011) 1.42
Genome-wide haplotype changes produced by artificial selection during modern rice breeding in Japan. PLoS One (2012) 1.42
SNP-based analysis of genetic diversity reveals important alleles associated with seed size in rice. BMC Plant Biol (2016) 1.42
Genome wide association mapping of grain arsenic, copper, molybdenum and zinc in rice (Oryza sativa L.) grown at four international field sites. PLoS One (2014) 1.42
Discovery of genome-wide DNA polymorphisms in a landrace cultivar of Japonica rice by whole-genome sequencing. Plant Cell Physiol (2011) 1.41
Genome-wide association study dissects the genetic architecture of seed weight and seed quality in rapeseed (Brassica napus L.). DNA Res (2014) 1.34
The nature of confounding in genome-wide association studies. Nat Rev Genet (2012) 1.32
SNP markers and their impact on plant breeding. Int J Plant Genomics (2012) 1.32
Genomic analysis of hybrid rice varieties reveals numerous superior alleles that contribute to heterosis. Nat Commun (2015) 1.32
Unraveling the complex trait of harvest index with association mapping in rice (Oryza sativa L.). PLoS One (2012) 1.30
Genome-wide association mapping of salinity tolerance in rice (Oryza sativa). DNA Res (2015) 1.30
Application of genotyping-by-sequencing on semiconductor sequencing platforms: a comparison of genetic and reference-based marker ordering in barley. PLoS One (2013) 1.30
A genome-wide, fine-scale map of natural pigmentation variation in Drosophila melanogaster. PLoS Genet (2013) 1.29
Sequence-based genotyping for marker discovery and co-dominant scoring in germplasm and populations. PLoS One (2012) 1.28
Advances in omics and bioinformatics tools for systems analyses of plant functions. Plant Cell Physiol (2011) 1.28
Combining high-throughput phenotyping and genome-wide association studies to reveal natural genetic variation in rice. Nat Commun (2014) 1.26
Genic and nongenic contributions to natural variation of quantitative traits in maize. Genome Res (2012) 1.26
Open access resources for genome-wide association mapping in rice. Nat Commun (2016) 1.26
Genome-wide association mapping of quantitative resistance to sudden death syndrome in soybean. BMC Genomics (2014) 1.26
Can genomics boost productivity of orphan crops? Nat Biotechnol (2012) 1.24
Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica. Genome Biol (2014) 1.24
Improving the accuracy of whole genome prediction for complex traits using the results of genome wide association studies. PLoS One (2014) 1.20
Copy number polymorphism in plant genomes. Theor Appl Genet (2013) 1.20
Genome wide association studies using a new nonparametric model reveal the genetic architecture of 17 agronomic traits in an enlarged maize association panel. PLoS Genet (2014) 1.19
Novel genomic approaches unravel genetic architecture of complex traits in apple. BMC Genomics (2013) 1.18
Genome-wide association studies identify heavy metal ATPase3 as the primary determinant of natural variation in leaf cadmium in Arabidopsis thaliana. PLoS Genet (2012) 1.16
High-throughput novel microsatellite marker of faba bean via next generation sequencing. BMC Genomics (2012) 1.15
Advanced phenotyping and phenotype data analysis for the study of plant growth and development. Front Plant Sci (2015) 1.13
RiceVarMap: a comprehensive database of rice genomic variations. Nucleic Acids Res (2014) 1.13
Evolution and association analysis of Ghd7 in rice. PLoS One (2012) 1.12
Genome wide allele frequency fingerprints (GWAFFs) of populations via genotyping by sequencing. PLoS One (2013) 1.11
Whole genome sequencing of elite rice cultivars as a comprehensive information resource for marker assisted selection. PLoS One (2015) 1.10
A combined linkage and regional association mapping validation and fine mapping of two major pleiotropic QTLs for seed weight and silique length in rapeseed (Brassica napus L.). BMC Plant Biol (2014) 1.10
Application of genomic tools in plant breeding. Curr Genomics (2012) 1.09
Getting to the roots of it: Genetic and hormonal control of root architecture. Front Plant Sci (2013) 1.08
Genome-Wide Association in Tomato Reveals 44 Candidate Loci for Fruit Metabolic Traits. Plant Physiol (2014) 1.08
Metabolic variation between japonica and indica rice cultivars as revealed by non-targeted metabolomics. Sci Rep (2014) 1.08
Genome-wide association study for flowering time, maturity dates and plant height in early maturing soybean (Glycine max) germplasm. BMC Genomics (2015) 1.07
Genome-wide association mapping for yield and other agronomic traits in an elite breeding population of tropical rice (Oryza sativa). PLoS One (2015) 1.06
Genome-wide association study identifies candidate genes that affect plant height in Chinese elite maize (Zea mays L.) inbred lines. PLoS One (2011) 1.06
The acid phosphatase-encoding gene GmACP1 contributes to soybean tolerance to low-phosphorus stress. PLoS Genet (2014) 1.05
Prevalence of single nucleotide polymorphism among 27 diverse alfalfa genotypes as assessed by transcriptome sequencing. BMC Genomics (2012) 1.05
The BIG Data Center: from deposition to integration to translation. Nucleic Acids Res (2016) 1.04
Genetic analysis of the metabolome exemplified using a rice population. Proc Natl Acad Sci U S A (2013) 1.04
De novo genome assembly of the economically important weed horseweed using integrated data from multiple sequencing platforms. Plant Physiol (2014) 1.02
OsSPL13 controls grain size in cultivated rice. Nat Genet (2016) 1.02
Population structure and domestication revealed by high-depth resequencing of Korean cultivated and wild soybean genomes. DNA Res (2013) 1.02
Genome-wide SNP discovery from transcriptome of four common carp strains. PLoS One (2012) 1.02
Recovering power in association mapping panels with variable levels of linkage disequilibrium. Genetics (2014) 1.02
Genetic structure, linkage disequilibrium and association mapping of Verticillium wilt resistance in elite cotton (Gossypium hirsutum L.) germplasm population. PLoS One (2014) 1.02
Evolutionary biology for the 21st century. PLoS Biol (2013) 1.01
Vitis phylogenomics: hybridization intensities from a SNP array outperform genotype calls. PLoS One (2013) 1.01
Quantitative Trait Locus (QTL) meta-analysis and comparative genomics for candidate gene prediction in perennial ryegrass (Lolium perenne L.). BMC Genet (2012) 1.01
Genome-wide analysis of ZmDREB genes and their association with natural variation in drought tolerance at seedling stage of Zea mays L. PLoS Genet (2013) 1.01
Association mapping for important agronomic traits in core collection of rice (Oryza sativa L.) with SSR markers. PLoS One (2014) 0.99
Emerging Genomic Tools for Legume Breeding: Current Status and Future Prospects. Front Plant Sci (2016) 0.99
Genetic diversity and association mapping of seed vigor in rice (Oryza sativa L.). Planta (2014) 0.98
Large scale germplasm screening for identification of novel rice blast resistance sources. Front Plant Sci (2014) 0.98
Employing genome-wide SNP discovery and genotyping strategy to extrapolate the natural allelic diversity and domestication patterns in chickpea. Front Plant Sci (2015) 0.98
Unlocking Triticeae genomics to sustainably feed the future. Plant Cell Physiol (2013) 0.98
Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature (2007) 144.95
Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics (2004) 125.23
Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet (2006) 115.71
A haplotype map of the human genome. Nature (2005) 105.70
A second generation human haplotype map of over 3.1 million SNPs. Nature (2007) 85.39
Evolutionary relationship of DNA sequences in finite populations. Genetics (1983) 40.67
The map-based sequence of the rice genome. Nature (2005) 24.17
A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet (2005) 20.97
Missing value estimation methods for DNA microarrays. Bioinformatics (2001) 20.84
Genetic mapping in human disease. Science (2008) 15.12
Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature (2010) 10.66
The pattern of polymorphism in Arabidopsis thaliana. PLoS Biol (2005) 10.13
Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana. Science (2007) 9.85
The genetic architecture of maize flowering time. Science (2009) 9.27
Mixed linear model approach adapted for genome-wide association studies. Nat Genet (2010) 8.47
Genetic properties of the maize nested association mapping population. Science (2009) 7.78
A first-generation haplotype map of maize. Science (2009) 6.82
High-throughput genotyping by whole-genome resequencing. Genome Res (2009) 5.74
Deletion in a gene associated with grain size increased yields during rice domestication. Nat Genet (2008) 5.57
GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein. Theor Appl Genet (2006) 5.51
Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. Proc Natl Acad Sci U S A (2009) 4.65
Association mapping: critical considerations shift from genotyping to experimental design. Plant Cell (2009) 4.59
The 1001 genomes project for Arabidopsis thaliana. Genome Biol (2009) 4.10
Genome-wide patterns of nucleotide polymorphism in domesticated rice. PLoS Genet (2007) 3.83
Next-generation genetics in plants. Nature (2008) 3.27
Caught red-handed: Rc encodes a basic helix-loop-helix protein conditioning red pericarp in rice. Plant Cell (2006) 2.82
The extent of linkage disequilibrium in rice (Oryza sativa L.). Genetics (2007) 2.56
Multilocus analysis of nucleotide variation of Oryza sativa and its wild relatives: severe bottleneck during domestication of rice. Mol Biol Evol (2007) 2.51
Fire and flood management of coastal swamp enabled first rice paddy cultivation in east China. Nature (2007) 2.36
The amylose content in rice endosperm is related to the post-transcriptional regulation of the waxy gene. Plant J (1995) 2.29
Allelic diversities in rice starch biosynthesis lead to a diverse array of rice eating and cooking qualities. Proc Natl Acad Sci U S A (2009) 2.19
Inferring missing genotypes in large SNP panels using fast nearest-neighbor searches over sliding windows. Bioinformatics (2007) 2.17
OsMADS51 is a short-day flowering promoter that functions upstream of Ehd1, OsMADS14, and Hd3a. Plant Physiol (2007) 1.59
Genetic structure and differentiation of Oryza sativa L. in China revealed by microsatellites. Theor Appl Genet (2009) 1.53
Allelic diversification at the C (OsC1) locus of wild and cultivated rice: nucleotide changes associated with phenotypes. Genetics (2004) 1.50
Rice 2020: a call for an international coordinated effort in rice functional genomics. Mol Plant (2008) 1.45
Genome-wide analysis of transposon insertion polymorphisms reveals intraspecific variation in cultivated rice. Plant Physiol (2008) 1.37
Map-based cloning of the ALK gene, which controls the gelatinization temperature of rice. Sci China C Life Sci (2003) 1.21
Model-based analysis of ChIP-Seq (MACS). Genome Biol (2008) 51.63
A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science (2002) 42.78
The NIH Human Microbiome Project. Genome Res (2009) 24.61
A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet (2005) 20.97
Genome-wide analysis of estrogen receptor binding sites. Nat Genet (2006) 18.63
A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One (2011) 15.19
TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics (2007) 14.95
Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1. Cell (2005) 14.32
FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription. Cell (2008) 14.18
Model-based analysis of tiling-arrays for ChIP-chip. Proc Natl Acad Sci U S A (2006) 13.68
MET amplification occurs with or without T790M mutations in EGFR mutant lung tumors with acquired resistance to gefitinib or erlotinib. Proc Natl Acad Sci U S A (2007) 11.85
Circulating mutant DNA to assess tumor dynamics. Nat Med (2007) 10.33
Identification and characterization of a novel and specific inhibitor of the ataxia-telangiectasia mutated kinase ATM. Cancer Res (2004) 9.70
Conversion of embryonic stem cells into neuroectodermal precursors in adherent monoculture. Nat Biotechnol (2003) 9.41
The genetic architecture of maize flowering time. Science (2009) 9.27
The role of microRNA genes in papillary thyroid carcinoma. Proc Natl Acad Sci U S A (2005) 8.60
Mixed linear model approach adapted for genome-wide association studies. Nat Genet (2010) 8.47
The genetic landscape of the childhood cancer medulloblastoma. Science (2010) 8.34
Genetic properties of the maize nested association mapping population. Science (2009) 7.78
Model-based analysis of two-color arrays (MA2C). Genome Biol (2007) 7.28
Androgen receptor regulates a distinct transcription program in androgen-independent prostate cancer. Cell (2009) 7.09
Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol (2010) 7.00
A first-generation haplotype map of maize. Science (2009) 6.82
PlasmoDB: a functional genomic database for malaria parasites. Nucleic Acids Res (2008) 6.73
iPS cells produce viable mice through tetraploid complementation. Nature (2009) 6.51
Origin and diversity of novel avian influenza A H7N9 viruses causing human infection: phylogenetic, structural, and coalescent analyses. Lancet (2013) 6.10
A hierarchical network of transcription factors governs androgen receptor-dependent prostate cancer growth. Mol Cell (2007) 5.99
Detection and quantification of mutations in the plasma of patients with colorectal tumors. Proc Natl Acad Sci U S A (2005) 5.91
Structure of linkage disequilibrium in plants. Annu Rev Plant Biol (2003) 5.87
Structure of the human dopamine D3 receptor in complex with a D2/D3 selective antagonist. Science (2010) 5.86
High-throughput genotyping by whole-genome resequencing. Genome Res (2009) 5.74
BSMAP: whole genome bisulfite sequence MAPping program. BMC Bioinformatics (2009) 5.67
Cytokinin oxidase regulates rice grain production. Science (2005) 5.60
GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein. Theor Appl Genet (2006) 5.51
Physical activity and weight gain prevention. JAMA (2010) 5.27
Evidence that ternary complex (eIF2-GTP-tRNA(i)(Met))-deficient preinitiation complexes are core constituents of mammalian stress granules. Mol Biol Cell (2002) 5.20
Genome-wide association study of leaf architecture in the maize nested association mapping population. Nat Genet (2011) 5.16
Rice domestication by reducing shattering. Science (2006) 5.11
Bone marrow edema and its relation to progression of knee osteoarthritis. Ann Intern Med (2003) 4.98
A map of rice genome variation reveals the origin of cultivated rice. Nature (2012) 4.92
Genetic design and statistical power of nested association mapping in maize. Genetics (2008) 4.92
Optimization of dosing for EGFR-mutant non-small cell lung cancer with evolutionary cancer modeling. Sci Transl Med (2011) 4.91
Cardiovascular risk and events in 17 low-, middle-, and high-income countries. N Engl J Med (2014) 4.88
Association of urinary sodium and potassium excretion with blood pressure. N Engl J Med (2014) 4.86
Dnmt3a is essential for hematopoietic stem cell differentiation. Nat Genet (2011) 4.85
Analysis of Longitudinal Data with Semiparametric Estimation of Covariance Function. J Am Stat Assoc (2007) 4.68
Growth and differentiation of mouse tracheal epithelial cells: selection of a proliferative population. Am J Physiol Lung Cell Mol Physiol (2002) 4.68
A G protein-coupled receptor is a plasma membrane receptor for the plant hormone abscisic acid. Science (2007) 4.61
Association mapping: critical considerations shift from genotyping to experimental design. Plant Cell (2009) 4.59
Gramene: a growing plant comparative genomics resource. Nucleic Acids Res (2007) 4.59
Maize association population: a high-resolution platform for quantitative trait locus dissection. Plant J (2005) 4.59
Sequence and analysis of rice chromosome 4. Nature (2002) 4.39
RSeQC: quality control of RNA-seq experiments. Bioinformatics (2012) 4.31
CO/FT regulatory module controls timing of flowering and seasonal growth cessation in trees. Science (2006) 4.26
The Rice Annotation Project Database (RAP-DB): 2008 update. Nucleic Acids Res (2007) 4.23
Productivity is a poor predictor of plant species richness. Science (2011) 4.21
Five-year outcomes of the China National Free Antiretroviral Treatment Program. Ann Intern Med (2009) 4.21
BEAMing: single-molecule PCR on microparticles in water-in-oil emulsions. Nat Methods (2006) 4.21
A novel influenza A (H1N1) vaccine in various age groups. N Engl J Med (2009) 4.20
Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm. Nat Genet (2011) 4.19