Published in Proc Natl Acad Sci U S A on June 06, 2011
Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nat Genet (2011) 6.59
Multiple reference genomes and transcriptomes for Arabidopsis thaliana. Nature (2011) 5.13
A map of rice genome variation reveals the origin of cultivated rice. Nature (2012) 4.92
Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm. Nat Genet (2011) 4.19
Genome-wide genetic changes during modern breeding of maize. Nat Genet (2012) 2.60
Natural variation in Arabidopsis: from molecular genetics to ecological genomics. Plant Physiol (2011) 2.06
Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden. Nat Genet (2013) 1.96
1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana. Cell (2016) 1.87
Plant mitochondrial genome evolution can be explained by DNA repair mechanisms. Genome Biol Evol (2013) 1.60
A haplotype map of genomic variations and genome-wide association studies of agronomic traits in foxtail millet (Setaria italica). Nat Genet (2013) 1.58
Phylogenetic properties of 50 nuclear loci in Medicago (Leguminosae) generated using multiplexed sequence capture and next-generation sequencing. PLoS One (2014) 1.45
Successful Recovery of Nuclear Protein-Coding Genes from Small Insects in Museums Using Illumina Sequencing. PLoS One (2015) 1.42
Heterosis of Arabidopsis hybrids between C24 and Col is associated with increased photosynthesis capacity. Proc Natl Acad Sci U S A (2012) 1.24
Transposon variants and their effects on gene expression in Arabidopsis. PLoS Genet (2013) 1.17
Analysis of Arabidopsis genome-wide variations before and after meiosis and meiotic recombination by resequencing Landsberg erecta and all four products of a single meiosis. Genome Res (2011) 1.15
Epigenetic and epigenomic variation in Arabidopsis thaliana. Trends Plant Sci (2012) 1.15
The genomic landscape of meiotic crossovers and gene conversions in Arabidopsis thaliana. Elife (2013) 1.12
A field guide to whole-genome sequencing, assembly and annotation. Evol Appl (2014) 1.12
User guide for mapping-by-sequencing in Arabidopsis. Genome Biol (2013) 1.10
Different gene families in Arabidopsis thaliana transposed in different epochs and at different frequencies throughout the rosids. Plant Cell (2011) 1.08
Dynamic expression of imprinted genes associates with maternally controlled nutrient allocation during maize endosperm development. Plant Cell (2013) 1.07
Century-scale methylome stability in a recently diverged Arabidopsis thaliana lineage. PLoS Genet (2015) 1.05
Great majority of recombination events in Arabidopsis are gene conversion events. Proc Natl Acad Sci U S A (2012) 1.05
The high polyphenol content of grapevine cultivar tannat berries is conferred primarily by genes that are not shared with the reference genome. Plant Cell (2013) 1.04
Epigenetic Changes in Hybrids. Plant Physiol (2015) 1.04
Remarkably Divergent Regions Punctuate the Genome Assembly of the Caenorhabditis elegans Hawaiian Strain CB4856. Genetics (2015) 1.04
Functional test of Brassica self-incompatibility modifiers in Arabidopsis thaliana. Proc Natl Acad Sci U S A (2011) 1.01
Natural CMT2 variation is associated with genome-wide methylation changes and temperature seasonality. PLoS Genet (2014) 1.00
LOCAS--a low coverage assembly tool for resequencing projects. PLoS One (2011) 0.99
Inheritance of Trans Chromosomal Methylation patterns from Arabidopsis F1 hybrids. Proc Natl Acad Sci U S A (2014) 0.99
Genome-wide identification of CCA1 targets uncovers an expanded clock network in Arabidopsis. Proc Natl Acad Sci U S A (2015) 0.97
Genetic anchoring of whole-genome shotgun assemblies. Front Genet (2014) 0.96
GBshape: a genome browser database for DNA shape annotations. Nucleic Acids Res (2014) 0.95
Characterization and identification of cis-regulatory elements in Arabidopsis based on single-nucleotide polymorphism information. Plant Physiol (2013) 0.94
Ancestral repeats have shaped epigenome and genome composition for millions of years in Arabidopsis thaliana. Nat Commun (2014) 0.92
AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references. Bioinformatics (2014) 0.91
Accurate indel prediction using paired-end short reads. BMC Genomics (2013) 0.91
A Journey Through a Leaf: Phenomics Analysis of Leaf Growth in Arabidopsis thaliana. Arabidopsis Book (2015) 0.90
Orchidstra: an integrated orchid functional genomics database. Plant Cell Physiol (2013) 0.89
Variation of presence/absence genes among Arabidopsis populations. BMC Evol Biol (2012) 0.89
Inferring short tandem repeat variation from paired-end short reads. Nucleic Acids Res (2013) 0.89
Chromosome-level assembly of Arabidopsis thaliana Ler reveals the extent of translocation and inversion polymorphisms. Proc Natl Acad Sci U S A (2016) 0.89
Intraspecific sequence variation and differential expression in starch synthase genes of Arabidopsis thaliana. BMC Res Notes (2013) 0.88
Extensive cis-regulatory variation robust to environmental perturbation in Arabidopsis. Plant Cell (2014) 0.88
Natural variation of H3K27me3 distribution between two Arabidopsis accessions and its association with flanking transposable elements. Genome Biol (2012) 0.87
Deep investigation of Arabidopsis thaliana junk DNA reveals a continuum between repetitive elements and genomic dark matter. PLoS One (2014) 0.87
Whole genome sequencing of the black grouse (Tetrao tetrix): reference guided assembly suggests faster-Z and MHC evolution. BMC Genomics (2014) 0.86
The Arabidopsis thaliana mobilome and its impact at the species level. Elife (2016) 0.86
Identifying and classifying trait linked polymorphisms in non-reference species by walking coloured de bruijn graphs. PLoS One (2013) 0.86
Metabolic fingerprinting of Arabidopsis thaliana accessions. Front Plant Sci (2015) 0.85
Improving the Annotation of Arabidopsis lyrata Using RNA-Seq Data. PLoS One (2015) 0.84
Detection of genomic variations and DNA polymorphisms and impact on analysis of meiotic recombination and genetic mapping. Proc Natl Acad Sci U S A (2014) 0.84
Jitterbug: somatic and germline transposon insertion detection at single-nucleotide resolution. BMC Genomics (2015) 0.84
Patchwork sequencing of tomato San Marzano and Vesuviano varieties highlights genome-wide variations. BMC Genomics (2014) 0.84
Analysis of natural and induced variation in tomato glandular trichome flavonoids identifies a gene not present in the reference genome. Plant Cell (2014) 0.83
Methylation interactions in Arabidopsis hybrids require RNA-directed DNA methylation and are influenced by genetic variation. Proc Natl Acad Sci U S A (2016) 0.81
Structure and Function of Centromeric and Pericentromeric Heterochromatin in Arabidopsis thaliana. Front Plant Sci (2015) 0.80
Building two indica rice reference genomes with PacBio long-read and Illumina paired-end sequencing data. Sci Data (2016) 0.80
Hybrid mimics and hybrid vigor in Arabidopsis. Proc Natl Acad Sci U S A (2015) 0.79
Effector-Triggered Immune Response in Arabidopsis thaliana Is a Quantitative Trait. Genetics (2016) 0.79
Natural variation in cross-talk between glucosinolates and onset of flowering in Arabidopsis. Front Plant Sci (2015) 0.79
SHEAR: sample heterogeneity estimation and assembly by reference. BMC Genomics (2014) 0.78
The pangenome of an agronomically important crop plant Brassica oleracea. Nat Commun (2016) 0.78
The Quantitative Basis of the Arabidopsis Innate Immune System to Endemic Pathogens Depends on Pathogen Genetics. PLoS Genet (2016) 0.78
Arabidopsis thaliana DM2h (R8) within the Landsberg RPP1-like Resistance Locus Underlies Three Different Cases of EDS1-Conditioned Autoimmunity. PLoS Genet (2016) 0.78
Genomic variation in Arabidopsis: tools and insights from next-generation sequencing. Chromosome Res (2014) 0.78
Genomics: endless variation most beautiful. Nature (2011) 0.78
Tailoring high-density oligonucleotide arrays for transcript profiling of different Arabidopsis thaliana accessions using a sequence-based approach. Plant Cell Rep (2017) 0.77
Epiallelic variation in Arabidopsis thaliana. Cold Spring Harb Symp Quant Biol (2012) 0.77
Two low coverage bird genomes and a comparison of reference-guided versus de novo genome assemblies. PLoS One (2014) 0.77
A comparison of the molecular organization of genomic regions associated with resistance to common bacterial blight in two Phaseolus vulgaris genotypes. Front Plant Sci (2013) 0.77
TOPOISOMERASE 6B is involved in chromatin remodelling associated with control of carbon partitioning into secondary metabolites and cell walls, and epidermal morphogenesis in Arabidopsis. J Exp Bot (2014) 0.77
Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation. Elife (2016) 0.76
HyDA-Vista: towards optimal guided selection of k-mer size for sequence assembly. BMC Genomics (2014) 0.76
Quantitative Genetics Identifies Cryptic Genetic Variation Involved in the Paternal Regulation of Seed Development. PLoS Genet (2016) 0.75
Comparative mapping of the wild perennial Glycine latifolia and soybean (G. max) reveals extensive chromosome rearrangements in the genus Glycine. PLoS One (2014) 0.75
A De Novo Genome Sequence Assembly of the Arabidopsis thaliana Accession Niederzenz-1 Displays Presence/Absence Variation and Strong Synteny. PLoS One (2016) 0.75
Re-Evaluation of Reportedly Metal Tolerant Arabidopsis thaliana Accessions. PLoS One (2016) 0.75
DRUMS: Disk Repository with Update Management and Select option for high throughput sequencing data. BMC Bioinformatics (2014) 0.75
Linkage illuminates a complex genome. Nat Biotechnol (2011) 0.75
Exploiting the great potential of Sequence Capture data by a new tool, SUPER-CAP. DNA Res (2016) 0.75
Extracting genotype information of Arabidopsis thaliana recombinant inbred lines from transcript profiles established with high-density oligonucleotide arrays. Plant Cell Rep (2017) 0.75
Genomic localization of AtRE1 and AtRE2, copia-type retrotransposons, in natural variants of Arabidopsis thaliana. Mol Genet Genomics (2014) 0.75
Basic local alignment search tool. J Mol Biol (1990) 659.07
Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res (2008) 157.44
Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res (2008) 151.16
Accurate whole human genome sequencing using reversible terminator chemistry. Nature (2008) 90.20
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature (2000) 70.33
Versatile and open software for comparing large genomes. Genome Biol (2004) 49.45
Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat Genet (2008) 43.63
ABySS: a parallel assembler for short read sequence data. Genome Res (2009) 43.20
Paired-end mapping reveals extensive structural variation in the human genome. Science (2007) 30.46
Fine-scale structural variation of the human genome. Nat Genet (2005) 24.31
High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci U S A (2010) 22.97
PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Res (2007) 19.07
The sequence and de novo assembly of the giant panda genome. Nature (2009) 15.76
Short read fragment assembly of bacterial genomes. Genome Res (2007) 15.40
High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat Methods (2008) 12.56
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
Sequencing of natural strains of Arabidopsis thaliana with short reads. Genome Res (2008) 8.44
The genome of the cucumber, Cucumis sativus L. Nat Genet (2009) 8.19
A first-generation haplotype map of maize. Science (2009) 6.82
Comparative genome assembly. Brief Bioinform (2004) 5.81
Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PLoS Biol (2010) 5.39
Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library. Nat Biotechnol (2009) 5.13
Hierarchical scaffolding with Bambus. Genome Res (2004) 4.95
The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nat Genet (2011) 4.65
Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome. Genome Res (2010) 4.22
PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. Genome Biol (2009) 4.18
Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content. PLoS Genet (2009) 3.88
The characterization of twenty sequenced human genomes. PLoS Genet (2010) 3.72
MoDIL: detecting small indels from clone-end sequencing with mixtures of distributions. Nat Methods (2009) 3.15
A robust framework for detecting structural variations in a genome. Bioinformatics (2008) 3.03
Uniparental expression of PolIV-dependent siRNAs in developing endosperm of Arabidopsis. Nature (2009) 3.01
Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery. Bioinformatics (2010) 2.90
Simultaneous alignment of short reads against multiple genomes. Genome Biol (2009) 2.79
Selective epigenetic control of retrotransposition in Arabidopsis. Nature (2009) 2.41
Detecting polymorphic regions in Arabidopsis thaliana with resequencing microarrays. Genome Res (2008) 1.82
At-TAX: a whole genome tiling array resource for developmental expression analysis and transcript identification in Arabidopsis thaliana. Genome Biol (2008) 1.62
A new strategy for genome assembly using short sequence reads and reduced representation libraries. Genome Res (2010) 1.22
Identification of a spontaneous frame shift mutation in a nonreference Arabidopsis accession using whole genome sequencing. Plant Physiol (2010) 1.22
Comprehensive analysis of Arabidopsis expression level polymorphisms with simple inheritance. Mol Syst Biol (2009) 1.09
Shotguns and SNPs: how fast and cheap sequencing is revolutionizing plant biology. Plant J (2010) 1.01
Goodbye to 'one by one' genetics. Genome Biol (2001) 0.82
Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science (2003) 39.19
A gene expression map of Arabidopsis thaliana development. Nat Genet (2005) 17.39
DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics (2009) 14.83
Control of leaf morphogenesis by microRNAs. Nature (2003) 11.36
Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature (2010) 10.66
Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana. Science (2007) 9.85
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science (2010) 9.78
A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome. Science (2002) 9.59
Target mimicry provides a new mechanism for regulation of microRNA activity. Nat Genet (2007) 9.48
Optimal spliced alignments of short sequence reads. Bioinformatics (2008) 9.45
The zebrafish reference genome sequence and its relationship to the human genome. Nature (2013) 8.52
Specific effects of microRNAs on the plant transcriptome. Dev Cell (2005) 8.48
Sequencing of natural strains of Arabidopsis thaliana with short reads. Genome Res (2008) 8.44
Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA. Science (2005) 8.14
Criteria for annotation of plant MicroRNAs. Plant Cell (2008) 7.49
Highly specific gene silencing by artificial microRNAs in Arabidopsis. Plant Cell (2006) 7.06
Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nat Genet (2011) 6.59
MetaSim: a sequencing simulator for genomics and metagenomics. PLoS One (2008) 6.54
Integration of spatial and temporal information during floral induction in Arabidopsis. Science (2005) 6.24
Whole-genome shotgun assembly and comparison of human genome assemblies. Proc Natl Acad Sci U S A (2004) 6.08
Large-scale identification of single-feature polymorphisms in complex genomes. Genome Res (2003) 6.04
Recombination and linkage disequilibrium in Arabidopsis thaliana. Nat Genet (2007) 5.69
The sequential action of miR156 and miR172 regulates developmental timing in Arabidopsis. Cell (2009) 5.52
The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana. Science (2010) 5.19
The extent of linkage disequilibrium in Arabidopsis thaliana. Nat Genet (2002) 4.96
miR156-regulated SPL transcription factors define an endogenous flowering pathway in Arabidopsis thaliana. Cell (2009) 4.95
Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. Proc Natl Acad Sci U S A (2009) 4.65
Who ate whom? Adaptive Helicobacter genomic changes that accompanied a host jump from early humans to large felines. PLoS Genet (2006) 4.65
The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nat Genet (2011) 4.65
Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome. PLoS One (2008) 4.54
Autoimmune response as a mechanism for a Dobzhansky-Muller-type incompatibility syndrome in plants. PLoS Biol (2007) 4.30
Specificity prediction of adenylation domains in nonribosomal peptide synthetases (NRPS) using transductive support vector machines (TSVMs). Nucleic Acids Res (2005) 4.15
OSLay: optimal syntenic layout of unfinished assemblies. Bioinformatics (2007) 4.10
SHOREmap: simultaneous mapping and mutation identification by deep sequencing. Nat Methods (2009) 4.01
A predator unmasked: life cycle of Bdellovibrio bacteriovorus from a genomic perspective. Science (2004) 3.87
Antagonistic regulation of PIN phosphorylation by PP2A and PINOID directs auxin flux. Cell (2007) 3.84
Spontaneous epigenetic variation in the Arabidopsis thaliana methylome. Nature (2011) 3.66
Dissection of floral induction pathways using global expression analysis. Development (2003) 3.43
The genome of Tetranychus urticae reveals herbivorous pest adaptations. Nature (2011) 3.29
Next-generation genetics in plants. Nature (2008) 3.27
Targeted mutagenesis in the model plant Nicotiana benthamiana using Cas9 RNA-guided endonuclease. Nat Biotechnol (2013) 3.20
Comprehensive interaction map of the Arabidopsis MADS Box transcription factors. Plant Cell (2005) 3.12
Insights into genome plasticity and pathogenicity of the plant pathogenic bacterium Xanthomonas campestris pv. vesicatoria revealed by the complete genome sequence. J Bacteriol (2005) 3.12
The scale of population structure in Arabidopsis thaliana. PLoS Genet (2010) 3.12
A promiscuous intermediate underlies the evolution of LEAFY DNA binding specificity. Science (2014) 3.11
The PHYTOCHROME C photoreceptor gene mediates natural variation in flowering and growth responses of Arabidopsis thaliana. Nat Genet (2006) 3.11
Control of jasmonate biosynthesis and senescence by miR319 targets. PLoS Biol (2008) 3.09
Transcriptional control of gene expression by microRNAs. Cell (2010) 3.05
Gene silencing in plants using artificial microRNAs and other small RNAs. Plant J (2008) 3.03
Export of FT protein from phloem companion cells is sufficient for floral induction in Arabidopsis. Curr Biol (2007) 3.00
Evolution of metal hyperaccumulation required cis-regulatory changes and triplication of HMA4. Nature (2008) 3.00
Inactivation of p53 and Pten promotes invasive bladder cancer. Genes Dev (2009) 2.99
A thermosensory pathway controlling flowering time in Arabidopsis thaliana. Nat Genet (2003) 2.95
Sequence and expression differences underlie functional specialization of Arabidopsis microRNAs miR159 and miR319. Dev Cell (2007) 2.90
Dual effects of miR156-targeted SPL genes and CYP78A5/KLUH on plastochron length and organ size in Arabidopsis thaliana. Plant Cell (2008) 2.87
Move on up, it's time for change--mobile signals controlling photoperiod-dependent flowering. Genes Dev (2007) 2.82
Epigenetic antagonism between polycomb and SWI/SNF complexes during oncogenic transformation. Cancer Cell (2010) 2.80
Transgenic plants expressing two Bacillus thuringiensis toxins delay insect resistance evolution. Nat Biotechnol (2003) 2.80
Simultaneous alignment of short reads against multiple genomes. Genome Biol (2009) 2.79
Dual roles of the nuclear cap-binding complex and SERRATE in pre-mRNA splicing and microRNA processing in Arabidopsis thaliana. Proc Natl Acad Sci U S A (2008) 2.74
Diversity of flowering responses in wild Arabidopsis thaliana strains. PLoS Genet (2005) 2.74
Launching eLife, Part 1. Elife (2012) 2.72
Potent induction of Arabidopsis thaliana flowering by elevated growth temperature. PLoS Genet (2006) 2.69
Acidobacteria form a coherent but highly diverse group within the bacterial domain: evidence from environmental genomics. Mol Microbiol (2003) 2.65
Hybrid necrosis: autoimmunity as a potential gene-flow barrier in plant species. Nat Rev Genet (2007) 2.55
Identification of the pollen determinant of S-RNase-mediated self-incompatibility. Nature (2004) 2.53
Text similarity: an alternative way to search MEDLINE. Bioinformatics (2006) 2.53
Quantitative trait locus mapping and DNA array hybridization identify an FLM deletion as a cause for natural flowering-time variation. Proc Natl Acad Sci U S A (2005) 2.47