Published in Nat Biotechnol on December 11, 2011
A map of rice genome variation reveals the origin of cultivated rice. Nature (2012) 4.92
Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. Rice (N Y) (2013) 4.27
Characterization of polyploid wheat genomic diversity using a high-density 90,000 single nucleotide polymorphism array. Plant Biotechnol J (2014) 4.02
Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars. Proc Natl Acad Sci U S A (2013) 3.48
Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nat Biotechnol (2013) 3.41
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
SLAF-seq: an efficient method of large-scale de novo SNP discovery and genotyping using high-throughput sequencing. PLoS One (2013) 2.36
The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions. Nat Genet (2012) 2.33
How important are transposons for plant evolution? Nat Rev Genet (2013) 2.00
The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine. Elife (2013) 1.84
Parallel domestication of the Shattering1 genes in cereals. Nat Genet (2012) 1.75
High-throughput SNP discovery and genotyping for constructing a saturated linkage map of chickpea (Cicer arietinum L.). DNA Res (2012) 1.66
Whole-genome sequencing reveals untapped genetic potential in Africa's indigenous cereal crop sorghum. Nat Commun (2013) 1.60
Genome-wide association mapping of root traits in a japonica rice panel. PLoS One (2013) 1.58
Accuracy of Genomic Selection in a Rice Synthetic Population Developed for Recurrent Selection Breeding. PLoS One (2015) 1.49
Structural variants in the soybean genome localize to clusters of biotic stress-response genes. Plant Physiol (2012) 1.48
SNP Discovery through Next-Generation Sequencing and Its Applications. Int J Plant Genomics (2012) 1.46
Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing. BMC Genomics (2013) 1.46
SNP-based analysis of genetic diversity reveals important alleles associated with seed size in rice. BMC Plant Biol (2016) 1.42
Quantifying population genetic differentiation from next-generation sequencing data. Genetics (2013) 1.41
Genome sequencing of the high oil crop sesame provides insight into oil biosynthesis. Genome Biol (2014) 1.38
SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data. BMC Genomics (2014) 1.36
Genome sequence of the date palm Phoenix dactylifera L. Nat Commun (2013) 1.35
A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity. Nat Genet (2013) 1.34
Genomic analysis of hybrid rice varieties reveals numerous superior alleles that contribute to heterosis. Nat Commun (2015) 1.32
Open access resources for genome-wide association mapping in rice. Nat Commun (2016) 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
Copy number polymorphism in plant genomes. Theor Appl Genet (2013) 1.20
Dynamic nucleotide-binding site and leucine-rich repeat-encoding genes in the grass family. Plant Physiol (2012) 1.16
A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes. Genome Biol (2015) 1.14
LABA1, a Domestication Gene Associated with Long, Barbed Awns in Wild Rice. Plant Cell (2015) 1.14
Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation. Genome Res (2013) 1.12
Advances in genome editing technology and its promising application in evolutionary and ecological studies. Gigascience (2014) 1.11
Construction of pseudomolecule sequences of the aus rice cultivar Kasalath for comparative genomics of Asian cultivated rice. DNA Res (2014) 1.11
Whole genome sequencing of elite rice cultivars as a comprehensive information resource for marker assisted selection. PLoS One (2015) 1.10
Genome-wide association studies using single nucleotide polymorphism markers developed by re-sequencing of the genomes of cultivated tomato. DNA Res (2013) 1.09
Whole genome resequencing in tomato reveals variation associated with introgression and breeding events. BMC Genomics (2013) 1.09
Survey of genome sequences in a wild sweet potato, Ipomoea trifida (H. B. K.) G. Don. DNA Res (2015) 1.08
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
The Tyrosine Aminomutase TAM1 Is Required for β-Tyrosine Biosynthesis in Rice. Plant Cell (2015) 1.06
Whole-Genome Resequencing Reveals Extensive Natural Variation in the Model Green Alga Chlamydomonas reinhardtii. Plant Cell (2015) 1.04
The BIG Data Center: from deposition to integration to translation. Nucleic Acids Res (2016) 1.04
Population structure and domestication revealed by high-depth resequencing of Korean cultivated and wild soybean genomes. DNA Res (2013) 1.02
Identification of Pyrus single nucleotide polymorphisms (SNPs) and evaluation for genetic mapping in European pear and interspecific Pyrus hybrids. PLoS One (2013) 1.02
Rapid diversification of five Oryza AA genomes associated with rice adaptation. Proc Natl Acad Sci U S A (2014) 1.01
cnvHiTSeq: integrative models for high-resolution copy number variation detection and genotyping using population sequencing data. Genome Biol (2012) 0.98
Structural variations in plant genomes. Brief Funct Genomics (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
Genome-wide DNA polymorphisms in two cultivars of mei (Prunus mume sieb. et zucc.). BMC Genet (2013) 0.98
Identification of candidate genes for drought tolerance by whole-genome resequencing in maize. BMC Plant Biol (2014) 0.97
Analysis of elite variety tag SNPs reveals an important allele in upland rice. Nat Commun (2013) 0.97
Efficient imputation of missing markers in low-coverage genotyping-by-sequencing data from multiparental crosses. Genetics (2014) 0.96
Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments. Nat Biotechnol (2017) 0.96
Single nucleotide polymorphisms generated by genotyping by sequencing to characterize genome-wide diversity, linkage disequilibrium, and selective sweeps in cultivated watermelon. BMC Genomics (2014) 0.95
Reference-free detection of isolated SNPs. Nucleic Acids Res (2014) 0.95
Bioenergy grass feedstock: current options and prospects for trait improvement using emerging genetic, genomic, and systems biology toolkits. Biotechnol Biofuels (2012) 0.94
An integrated framework for discovery and genotyping of genomic variants from high-throughput sequencing experiments. Nucleic Acids Res (2014) 0.94
Genomic regions involved in yield potential detected by genome-wide association analysis in Japanese high-yielding rice cultivars. BMC Genomics (2014) 0.94
Comparative population genomics reveals the domestication history of the peach, Prunus persica, and human influences on perennial fruit crops. Genome Biol (2014) 0.94
Dicer-like 3 produces transposable element-associated 24-nt siRNAs that control agricultural traits in rice. Proc Natl Acad Sci U S A (2014) 0.94
Allele mining and enhanced genetic recombination for rice breeding. Rice (N Y) (2015) 0.92
Single-copy gene based 50 K SNP chip for genetic studies and molecular breeding in rice. Sci Rep (2015) 0.92
The organelle genomes of Hassawi rice (Oryza sativa L.) and its hybrid in saudi arabia: genome variation, rearrangement, and origins. PLoS One (2012) 0.91
STV11 encodes a sulphotransferase and confers durable resistance to rice stripe virus. Nat Commun (2014) 0.91
Key applications of plant metabolic engineering. PLoS Biol (2014) 0.91
RiceWiki: a wiki-based database for community curation of rice genes. Nucleic Acids Res (2013) 0.91
Identification and characterization of transcript polymorphisms in soybean lines varying in oil composition and content. BMC Genomics (2014) 0.90
The Rice Genome Knowledgebase (RGKbase): an annotation database for rice comparative genomics and evolutionary biology. Nucleic Acids Res (2012) 0.90
Genetic control of inflorescence architecture during rice domestication. Nat Commun (2013) 0.90
Genome-wide characterization of nonreference transposons reveals evolutionary propensities of transposons in soybean. Plant Cell (2012) 0.90
Identifying the genome-wide sequence variations and developing new molecular markers for genetics research by re-sequencing a Landrace cultivar of foxtail millet. PLoS One (2013) 0.90
Decreased Nucleotide and Expression Diversity and Modified Coexpression Patterns Characterize Domestication in the Common Bean. Plant Cell (2014) 0.89
Quantitative trait locus mapping of deep rooting by linkage and association analysis in rice. J Exp Bot (2015) 0.89
Effect of quantitative trait loci for seed shattering on abscission layer formation in Asian wild rice Oryza rufipogon. Breed Sci (2014) 0.88
Heterogeneity in the entire genome for three genotypes of peach [Prunus persica (L.) Batsch] as distinguished from sequence analysis of genomic variants. BMC Genomics (2013) 0.88
Construction of a high-density integrated genetic linkage map of rubber tree (Hevea brasiliensis) using genotyping-by-sequencing (GBS). Front Plant Sci (2015) 0.87
The Sequences of 1,504 Mutants in the Model Rice Variety Kitaake Facilitate Rapid Functional Genomic Studies. Plant Cell (2017) 0.86
Detecting SNPs underlying domestication-related traits in soybean. BMC Plant Biol (2014) 0.86
Genome-wide copy number variations in Oryza sativa L. BMC Genomics (2013) 0.86
The plasticity of NBS resistance genes in sorghum is driven by multiple evolutionary processes. BMC Plant Biol (2014) 0.86
Scanning and Filling: Ultra-Dense SNP Genotyping Combining Genotyping-By-Sequencing, SNP Array and Whole-Genome Resequencing Data. PLoS One (2015) 0.86
Potential Uses of Wild Germplasms of Grain Legumes for Crop Improvement. Int J Mol Sci (2017) 0.86
Natural insertions in rice commonly form tandem duplications indicative of patch-mediated double-strand break induction and repair. Proc Natl Acad Sci U S A (2014) 0.85
Identification of genome-wide single nucleotide polymorphisms in allopolyploid crop Brassica napus. BMC Genomics (2013) 0.85
Quantitative trait locus mapping and candidate gene analysis for plant architecture traits using whole genome re-sequencing in rice. Mol Cells (2014) 0.84
Genetic analysis of inflorescence and plant height components in sorghum (Panicoidae) and comparative genetics with rice (Oryzoidae). BMC Plant Biol (2015) 0.84
Genome re-sequencing suggested a weedy rice origin from domesticated indica-japonica hybridization: a case study from southern China. Planta (2014) 0.84
Epigenetic Mutation of RAV6 Affects Leaf Angle and Seed Size in Rice. Plant Physiol (2015) 0.83
Information Commons for Rice (IC4R). Nucleic Acids Res (2015) 0.83
Genome-wide survey on genomic variation, expression divergence, and evolution in two contrasting rice genotypes under high salinity stress. Genome Biol Evol (2013) 0.83
Subgenome parallel selection is associated with morphotype diversification and convergent crop domestication in Brassica rapa and Brassica oleracea. Nat Genet (2016) 0.83
Candidate loci involved in domestication and improvement detected by a published 90K wheat SNP array. Sci Rep (2017) 0.83
Application of resequencing to rice genomics, functional genomics and evolutionary analysis. Rice (N Y) (2014) 0.82
Whole genome re-sequencing reveals genome-wide variations among parental lines of 16 mapping populations in chickpea (Cicer arietinum L.). BMC Plant Biol (2016) 0.82
Recent trends and perspectives of molecular markers against fungal diseases in wheat. Front Microbiol (2015) 0.82
Genome-wide resequencing of KRICE_CORE reveals their potential for future breeding, as well as functional and evolutionary studies in the post-genomic era. BMC Genomics (2016) 0.82
TASUKE: a web-based visualization program for large-scale resequencing data. Bioinformatics (2013) 0.82
Sequence and expression analyses of KIX domain proteins suggest their importance in seed development and determination of seed size in rice, and genome stability in Arabidopsis. Mol Genet Genomics (2013) 0.82
Basic local alignment search tool. J Mol Biol (1990) 659.07
The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol (1987) 266.90
MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol (2007) 168.76
BLAT--the BLAST-like alignment tool. Genome Res (2002) 126.78
Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics (2004) 125.23
Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics (1989) 73.50
SOAP: short oligonucleotide alignment program. Bioinformatics (2008) 68.13
On the number of segregating sites in genetical models without recombination. Theor Popul Biol (1975) 60.96
The diploid genome sequence of an Asian individual. Nature (2008) 46.29
De novo assembly of human genomes with massively parallel short read sequencing. Genome Res (2009) 45.91
Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat Genet (2008) 43.63
Evolutionary relationship of DNA sequences in finite populations. Genetics (1983) 40.67
SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics (2009) 39.47
Population structure and eigenanalysis. PLoS Genet (2006) 37.21
Genome-wide association studies for common diseases and complex traits. Nat Rev Genet (2005) 33.96
Paired-end mapping reveals extensive structural variation in the human genome. Science (2007) 30.46
InterProScan--an integration platform for the signature-recognition methods in InterPro. Bioinformatics (2001) 28.35
Fine-scale structural variation of the human genome. Nat Genet (2005) 24.31
The map-based sequence of the rice genome. Nature (2005) 24.17
A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science (2002) 21.26
SNP detection for massively parallel whole-genome resequencing. Genome Res (2009) 15.96
Linkage disequilibrium in finite populations. Theor Appl Genet (1968) 12.55
Sequencing of 50 human exomes reveals adaptation to high altitude. Science (2010) 11.27
Estimation of individual admixture: analytical and study design considerations. Genet Epidemiol (2005) 11.00
Synthetic maps of human gene frequencies in Europeans. Science (1978) 10.35
Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana. Science (2007) 9.85
Estimation of levels of gene flow from DNA sequence data. Genetics (1992) 9.82
Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet (2010) 8.75
Seed banks and molecular maps: unlocking genetic potential from the wild. Science (1997) 8.64
Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science (2009) 7.64
The genetics of inbreeding depression. Nat Rev Genet (2009) 7.13
The effects of artificial selection on the maize genome. Science (2005) 6.20
Intraspecific violation of genetic colinearity and its implications in maize. Proc Natl Acad Sci U S A (2002) 5.85
Genetic structure and diversity in Oryza sativa L. Genetics (2005) 5.74
Whole-genome resequencing reveals loci under selection during chicken domestication. Nature (2010) 5.48
Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources. BMC Bioinformatics (2006) 5.23
Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nat Genet (2010) 5.20
Rice domestication by reducing shattering. Science (2006) 5.11
Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. Proc Natl Acad Sci U S A (2009) 4.65
Phylogeography of Asian wild rice, Oryza rufipogon, reveals multiple independent domestications of cultivated rice, Oryza sativa. Proc Natl Acad Sci U S A (2006) 4.43
The Rice Annotation Project Database (RAP-DB): 2008 update. Nucleic Acids Res (2007) 4.23
The domestication process and domestication rate in rice: spikelet bases from the Lower Yangtze. Science (2009) 3.98
Genome-wide patterns of nucleotide polymorphism in domesticated rice. PLoS Genet (2007) 3.83
Phylogenetic analysis using PHYLIP. Methods Mol Biol (2000) 3.27
Selection versus demography: a multilocus investigation of the domestication process in maize. Mol Biol Evol (2004) 3.22
Isozymes and classification of Asian rice varieties. Theor Appl Genet (1987) 2.92
New insights into the history of rice domestication. Trends Genet (2007) 2.88
Caught red-handed: Rc encodes a basic helix-loop-helix protein conditioning red pericarp in rice. Plant Cell (2006) 2.82
Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx). Science (2009) 2.68
Allelic variation and heterosis in maize: how do two halves make more than a whole? Genome Res (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
A large-scale screen for artificial selection in maize identifies candidate agronomic loci for domestication and crop improvement. Plant Cell (2005) 2.50
Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly. Nat Biotechnol (2011) 2.45
Control of a key transition from prostrate to erect growth in rice domestication. Nat Genet (2008) 2.42
Phylogenetic relationships among A-genome species of the genus Oryza revealed by intron sequences of four nuclear genes. New Phytol (2005) 2.25
Genetic control of rice plant architecture under domestication. Nat Genet (2008) 2.17
Genetics and phylogenetics of rice domestication. Curr Opin Genet Dev (2007) 1.65
Two evolutionary histories in the genome of rice: the roles of domestication genes. PLoS Genet (2011) 1.63
Transcript profiling reveals diverse roles of auxin-responsive genes during reproductive development and abiotic stress in rice. FEBS J (2009) 1.57
The evolution of nuclear auxin signalling. BMC Evol Biol (2009) 1.27
Genomic screening for artificial selection during domestication and improvement in maize. Ann Bot (2007) 1.09
A second generation human haplotype map of over 3.1 million SNPs. Nature (2007) 85.39
SOAP: short oligonucleotide alignment program. Bioinformatics (2008) 68.13
The diploid genome sequence of an Asian individual. Nature (2008) 46.29
De novo assembly of human genomes with massively parallel short read sequencing. Genome Res (2009) 45.91
A human gut microbial gene catalogue established by metagenomic sequencing. Nature (2010) 43.63
A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science (2002) 42.78
SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics (2009) 39.47
Enterotypes of the human gut microbiome. Nature (2011) 24.36
SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience (2012) 20.89
Characterization of microRNAs in serum: a novel class of biomarkers for diagnosis of cancer and other diseases. Cell Res (2008) 20.59
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proc Natl Acad Sci U S A (2002) 20.48
The genome sequence of the malaria mosquito Anopheles gambiae. Science (2002) 20.36
International network of cancer genome projects. Nature (2010) 20.35
Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) 18.01
Genome-wide detection and characterization of positive selection in human populations. Nature (2007) 17.27
Evolutionary and biomedical insights from the rhesus macaque genome. Science (2007) 16.21
SNP detection for massively parallel whole-genome resequencing. Genome Res (2009) 15.96
The sequence and de novo assembly of the giant panda genome. Nature (2009) 15.76
WEGO: a web tool for plotting GO annotations. Nucleic Acids Res (2006) 13.06
Mapping copy number variation by population-scale genome sequencing. Nature (2011) 12.55
A systematic survey of loss-of-function variants in human protein-coding genes. Science (2012) 12.25
A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature (2012) 11.68
Sequencing of 50 human exomes reveals adaptation to high altitude. Science (2010) 11.27
Bayes empirical bayes inference of amino acid sites under positive selection. Mol Biol Evol (2005) 11.26
Natural selection on protein-coding genes in the human genome. Nature (2005) 10.84
A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome. Science (2002) 9.59
Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios. Science (2003) 9.20
The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing. PLoS One (2007) 9.17
Assessing the evolutionary impact of amino acid mutations in the human genome. PLoS Genet (2008) 8.92
TreeFam: a curated database of phylogenetic trees of animal gene families. Nucleic Acids Res (2006) 8.83
Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol Biol Evol (2005) 8.74
Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution. Genome Res (2005) 8.38
Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res (2011) 8.38
The genome of the mesopolyploid crop species Brassica rapa. Nat Genet (2011) 8.23
The genome of the cucumber, Cucumis sativus L. Nat Genet (2009) 8.19
Prostate-specific deletion of the murine Pten tumor suppressor gene leads to metastatic prostate cancer. Cancer Cell (2003) 8.11
An abundance of rare functional variants in 202 drug target genes sequenced in 14,002 people. Science (2012) 7.94
Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics (2004) 7.79