Published in Genome Biol Evol on May 27, 2011
Multiple reference genomes and transcriptomes for Arabidopsis thaliana. Nature (2011) 5.13
Genomic Rearrangements in Arabidopsis Considered as Quantitative Traits. Genetics (2017) 0.78
Chromosome fragile sites in Arabidopsis harbor matrix attachment regions that may be associated with ancestral chromosome rearrangement events. PLoS Genet (2012) 0.76
Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res (2008) 151.16
Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol (2000) 128.08
A map of human genome variation from population-scale sequencing. Nature (2010) 121.13
Accurate whole human genome sequencing using reversible terminator chemistry. Nature (2008) 90.20
ABySS: a parallel assembler for short read sequence data. Genome Res (2009) 43.20
Large-scale copy number polymorphism in the human genome. Science (2004) 34.64
Paired-end mapping reveals extensive structural variation in the human genome. Science (2007) 30.46
Mapping and sequencing of structural variation from eight human genomes. Nature (2008) 30.28
progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One (2010) 24.31
Fine-scale structural variation of the human genome. Nat Genet (2005) 24.31
The evolutionary fate and consequences of duplicate genes. Science (2000) 24.22
Structural variation in the human genome. Nat Rev Genet (2006) 21.40
ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res (2008) 20.61
Assembling millions of short DNA sequences using SSAKE. Bioinformatics (2006) 18.71
BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat Methods (2009) 18.41
Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Res (2009) 15.15
Human genetic variation and its contribution to complex traits. Nat Rev Genet (2009) 12.11
Segmental duplications: organization and impact within the current human genome project assembly. Genome Res (2001) 11.77
Role of transposable elements in heterochromatin and epigenetic control. Nature (2004) 10.51
Sequencing of natural strains of Arabidopsis thaliana with short reads. Genome Res (2008) 8.44
The impact of retrotransposons on human genome evolution. Nat Rev Genet (2009) 8.08
Genomics. Genome project standards in a new era of sequencing. Science (2009) 7.72
Copy number variation in human health, disease, and evolution. Annu Rev Genomics Hum Genet (2009) 7.64
Assembly of large genomes using second-generation sequencing. Genome Res (2010) 5.94
Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps. Genome Biol (2010) 5.79
Naturally occurring genetic variation in Arabidopsis thaliana. Annu Rev Plant Biol (2004) 5.52
Characterization of missing human genome sequences and copy-number polymorphic insertions. Nat Methods (2010) 5.44
Hybrid zones and the genetic architecture of a barrier to gene flow between two sunflower species. Genetics (1999) 4.81
A SNP discovery method to assess variant allele probability from next-generation resequencing data. Genome Res (2009) 4.78
The Human Genome Project: lessons from large-scale biology. Science (2003) 4.69
Structural variation of the human genome. Annu Rev Genomics Hum Genet (2006) 4.25
Segmental duplications and the evolution of the primate genome. Nat Rev Genet (2002) 4.16
AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints. Nucleic Acids Res (2005) 4.13
The 1001 genomes project for Arabidopsis thaliana. Genome Biol (2009) 4.10
Pervasive hitchhiking at coding and regulatory sites in humans. PLoS Genet (2009) 4.02
An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene. Nature (2003) 3.90
Positive selection of a gene family during the emergence of humans and African apes. Nature (2001) 3.68
Attenuation of FLOWERING LOCUS C activity as a mechanism for the evolution of summer-annual flowering behavior in Arabidopsis. Proc Natl Acad Sci U S A (2003) 3.34
DNA Sudoku--harnessing high-throughput sequencing for multiplexed specimen analysis. Genome Res (2009) 3.05
Integrated cytogenetic map of chromosome arm 4S of A. thaliana: structural organization of heterochromatic knob and centromere region. Cell (2000) 3.04
What has natural variation taught us about plant development, physiology, and adaptation? Plant Cell (2009) 2.94
Construction and analysis of a human-chimpanzee comparative clone map. Science (2002) 2.83
Microindel detection in short-read sequence data. Bioinformatics (2010) 2.73
Copy number variation and evolution in humans and chimpanzees. Genome Res (2008) 2.69
Transposable elements, gene creation and genome rearrangement in flowering plants. Curr Opin Genet Dev (2005) 2.62
Population resequencing reveals local adaptation of Arabidopsis lyrata to serpentine soils. Nat Genet (2010) 2.61
A probabilistic approach for SNP discovery in high-throughput human resequencing data. Genome Res (2009) 2.55
Divergent evolution of duplicate genes leads to genetic incompatibilities within A. thaliana. Science (2009) 2.52
Epigenetic regulation of transposable elements in plants. Annu Rev Plant Biol (2009) 2.41
Personal genome sequencing: current approaches and challenges. Genes Dev (2010) 2.38
Comparative genomics of Physcomitrella patens gametophytic transcriptome and Arabidopsis thaliana: implication for land plant evolution. Proc Natl Acad Sci U S A (2003) 2.33
Green genes-comparative genomics of the green branch of life. Cell (2007) 2.30
Population genetic inference from genomic sequence variation. Genome Res (2010) 2.29
Comparing whole genomes using DNA microarrays. Nat Rev Genet (2008) 2.27
Evolving disease resistance genes. Curr Opin Plant Biol (2005) 2.14
Darwinian evolution in the light of genomics. Nucleic Acids Res (2009) 1.92
Comparative genomics in the grass family: molecular characterization of grass genome structure and evolution. Ann Bot (2002) 1.87
Every genome sequence needs a good map. Genome Res (2009) 1.85
Comparison of the genomes of human and mouse lays the foundation of genome zoology. Hum Mol Genet (2003) 1.83
Detecting polymorphic regions in Arabidopsis thaliana with resequencing microarrays. Genome Res (2008) 1.82
Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata. Proc Natl Acad Sci U S A (2011) 1.82
Breakpoint regions and homologous synteny blocks in chromosomes have different evolutionary histories. Genome Res (2009) 1.66
Genome assembly quality: assessment and improvement using the neutral indel model. Genome Res (2010) 1.64
Human, mouse, and rat genome large-scale rearrangements: stability versus speciation. Genome Res (2004) 1.63
Comparative genomics and the study of evolution by natural selection. Mol Ecol (2008) 1.60
Gene-breaking: a new paradigm for human retrotransposon-mediated gene evolution. Genome Res (2005) 1.58
Incremental steps toward incompatibility revealed by Arabidopsis epistatic interactions modulating salicylic acid pathway activation. Proc Natl Acad Sci U S A (2008) 1.51
Using next-generation sequencing for high resolution multiplex analysis of copy number variation from nanogram quantities of DNA from formalin-fixed paraffin-embedded specimens. Nucleic Acids Res (2010) 1.51
An N-ethyl-N-nitrosourea screen for genes involved in variegation in the mouse. Proc Natl Acad Sci U S A (2005) 1.51
Recurrent duplication-driven transposition of DNA during hominoid evolution. Proc Natl Acad Sci U S A (2006) 1.47
The European sea bass Dicentrarchus labrax genome puzzle: comparative BAC-mapping and low coverage shotgun sequencing. BMC Genomics (2010) 1.33
Genome size variation among accessions of Arabidopsis thaliana. Ann Bot (2004) 1.33
Duplication and positive selection among hominin-specific PRAME genes. BMC Genomics (2005) 1.29
Comparative sequence analyses of the major quantitative trait locus phosphorus uptake 1 (Pup1) reveal a complex genetic structure. Plant Biotechnol J (2009) 1.29
A new strategy for genome assembly using short sequence reads and reduced representation libraries. Genome Res (2010) 1.22
Natural variation at Strubbelig Receptor Kinase 3 drives immune-triggered incompatibilities between Arabidopsis thaliana accessions. Nat Genet (2010) 1.22
A genetic defect caused by a triplet repeat expansion in Arabidopsis thaliana. Science (2009) 1.20
Epigenetic interactions between transposons and genes: lessons from plants. Curr Opin Genet Dev (2008) 1.19
Genome sequence comparison of Col and Ler lines reveals the dynamic nature of Arabidopsis chromosomes. Nucleic Acids Res (2009) 1.12
Haplotype structure strongly affects recombination in a maize genetic interval polymorphic for Helitron and retrotransposon insertions. Proc Natl Acad Sci U S A (2009) 1.12
Substantial deletion overlap among divergent Arabidopsis genomes revealed by intersection of short reads and tiling arrays. Genome Biol (2010) 1.08
Whole-genome tiling array analysis of Mycobacterium leprae RNA reveals high expression of pseudogenes and noncoding regions. J Bacteriol (2009) 1.06
Identification and isolation of the FEEBLY gene from tomato by transposon tagging. Mol Gen Genet (1996) 1.03
The xenobiotic beta-aminobutyric acid enhances Arabidopsis thermotolerance. Plant J (2007) 1.02
Sequencing primate genomes: what have we learned? Annu Rev Genomics Hum Genet (2009) 1.00
Selection upon genome architecture: conservation of functional neighborhoods with changing genes. PLoS Comput Biol (2010) 0.97
Rice structural variation: a comparative analysis of structural variation between rice and three of its closest relatives in the genus Oryza. Plant J (2010) 0.97
Ten years of genetics and genomics: what have we achieved and where are we heading? Nat Rev Genet (2010) 0.93
A machine-learning approach to combined evidence validation of genome assemblies. Bioinformatics (2008) 0.91
Targeted resequencing and analysis of the Diamond-Blackfan anemia disease locus RPS19. PLoS One (2009) 0.86
The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science (2007) 11.15
FY is an RNA 3' end-processing factor that interacts with FCA to control the Arabidopsis floral transition. Cell (2003) 3.94
QuantPrime--a flexible tool for reliable high-throughput primer design for quantitative PCR. BMC Bioinformatics (2008) 3.62
PlnTFDB: updated content and new features of the plant transcription factor database. Nucleic Acids Res (2009) 3.12
The Selaginella genome identifies genetic changes associated with the evolution of vascular plants. Science (2011) 3.10
PlnTFDB: an integrative plant transcription factor database. BMC Bioinformatics (2007) 3.01
AtDGK2, a novel diacylglycerol kinase from Arabidopsis thaliana, phosphorylates 1-stearoyl-2-arachidonoyl-sn-glycerol and 1,2-dioleoyl-sn-glycerol and exhibits cold-inducible gene expression. J Biol Chem (2003) 2.13
A quantitative RT-PCR platform for high-throughput expression profiling of 2500 rice transcription factors. Plant Methods (2007) 2.08
A gene regulatory network controlled by the NAC transcription factor ANAC092/AtNAC2/ORE1 during salt-promoted senescence. Plant J (2010) 1.89
JUNGBRUNNEN1, a reactive oxygen species-responsive NAC transcription factor, regulates longevity in Arabidopsis. Plant Cell (2012) 1.75
A growth phenotyping pipeline for Arabidopsis thaliana integrating image analysis and rosette area modeling for robust quantification of genotype effects. New Phytol (2011) 1.69
DOF transcription factor AtDof1.1 (OBP2) is part of a regulatory network controlling glucosinolate biosynthesis in Arabidopsis. Plant J (2006) 1.56
Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol (2010) 1.53
ORS1, an H₂O₂-responsive NAC transcription factor, controls senescence in Arabidopsis thaliana. Mol Plant (2011) 1.50
CIRCADIAN CLOCK-ASSOCIATED 1 regulates ROS homeostasis and oxidative stress responses. Proc Natl Acad Sci U S A (2012) 1.44
The role of bZIP transcription factors in green plant evolution: adaptive features emerging from four founder genes. PLoS One (2008) 1.43
Gene structures and processing of Arabidopsis thaliana HYL1-dependent pri-miRNAs. Nucleic Acids Res (2009) 1.36
Members of the Arabidopsis AtTPK/KCO family form homomeric vacuolar channels in planta. Plant J (2006) 1.33
Generation of superoxide anion in chloroplasts of Arabidopsis thaliana during active photosynthesis: a focus on rapidly induced genes. Plant Mol Biol (2007) 1.32
Vacuolar membrane localization of the Arabidopsis 'two-pore' K+ channel KCO1. Plant J (2002) 1.31
Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice. BMC Genomics (2007) 1.29
The plant multidrug resistance ABC transporter AtMRP5 is involved in guard cell hormonal signalling and water use. Plant J (2003) 1.24
Molecular mechanisms of desiccation tolerance in the resurrection glacial relic Haberlea rhodopensis. Cell Mol Life Sci (2012) 1.17
NAC transcription factor speedy hyponastic growth regulates flooding-induced leaf movement in Arabidopsis. Plant Cell (2013) 1.14
Green transcription factors: a chlamydomonas overview. Genetics (2008) 1.13
Phospholipase C is required for the control of stomatal aperture by ABA. Plant J (2003) 1.13
Salt-responsive ERF1 regulates reactive oxygen species-dependent signaling during the initial response to salt stress in rice. Plant Cell (2013) 1.12
Comprehensive dissection of spatiotemporal metabolic shifts in primary, secondary, and lipid metabolism during developmental senescence in Arabidopsis. Plant Physiol (2013) 1.12
GabiPD: the GABI primary database--a plant integrative 'omics' database. Nucleic Acids Res (2008) 1.12
Arabidopsis onset of leaf death mutants identify a regulatory pathway controlling leaf senescence. Plant J (2002) 1.11
The ATP binding cassette transporter AtMRP5 modulates anion and calcium channel activities in Arabidopsis guard cells. J Biol Chem (2006) 1.11
Ethylene-induced leaf senescence depends on age-related changes and OLD genes in Arabidopsis. J Exp Bot (2005) 1.10
External K+ modulates the activity of the Arabidopsis potassium channel SKOR via an unusual mechanism. Plant J (2006) 1.10
Translatome and metabolome effects triggered by gibberellins during rosette growth in Arabidopsis. J Exp Bot (2012) 1.08
The Arabidopsis onset of leaf death5 mutation of quinolinate synthase affects nicotinamide adenine dinucleotide biosynthesis and causes early ageing. Plant Cell (2008) 1.08
The DOF transcription factor OBP1 is involved in cell cycle regulation in Arabidopsis thaliana. Plant J (2008) 1.08
Diurnal and circadian regulation of putative potassium channels in a leaf moving organ. Plant Physiol (2002) 1.05
Arabidopsis RecQI4A suppresses homologous recombination and modulates DNA damage responses. Plant J (2005) 1.02
Arabidopsis inositol polyphosphate 6-/3-kinase is a nuclear protein that complements a yeast mutant lacking a functional ArgR-Mcm1 transcription complex. Plant Cell (2003) 1.01
Assembly of plant Shaker-like K(out) channels requires two distinct sites of the channel alpha-subunit. Biophys J (2004) 0.99
Arabidopsis NAC transcription factor JUNGBRUNNEN1 affects thermomemory-associated genes and enhances heat stress tolerance in primed and unprimed conditions. Plant Signal Behav (2012) 0.97
ROS homeostasis during development: an evolutionary conserved strategy. Cell Mol Life Sci (2012) 0.97
Auxin flow in anther filaments is critical for pollen grain development through regulating pollen mitosis. Plant Mol Biol (2006) 0.96
Study of early leaf senescence in Arabidopsis thaliana by quantitative proteomics using reciprocal 14N/15N labeling and difference gel electrophoresis. Mol Cell Proteomics (2007) 0.96
Transcription factor AtDOF4;2 affects phenylpropanoid metabolism in Arabidopsis thaliana. New Phytol (2007) 0.96
A unique voltage sensor sensitizes the potassium channel AKT2 to phosphoregulation. J Gen Physiol (2005) 0.96
ORE1 balances leaf senescence against maintenance by antagonizing G2-like-mediated transcription. EMBO Rep (2013) 0.95
Characterization and identification of cis-regulatory elements in Arabidopsis based on single-nucleotide polymorphism information. Plant Physiol (2013) 0.94
Global analysis of the root hair morphogenesis transcriptome reveals new candidate genes involved in root hair formation in barley. J Plant Physiol (2010) 0.94
Assembly and sorting of the tonoplast potassium channel AtTPK1 and its turnover by internalization into the vacuole. Plant Physiol (2011) 0.93
Extensive modulation of the transcription factor transcriptome during somatic embryogenesis in Arabidopsis thaliana. PLoS One (2013) 0.93
An upstream regulator of the 26S proteasome modulates organ size in Arabidopsis thaliana. Plant J (2013) 0.92
At5PTase13 modulates cotyledon vein development through regulating auxin homeostasis. Plant Physiol (2005) 0.92
Expression of human c-reactive protein in different systems and its purification from Leishmania tarentolae. Protein Expr Purif (2011) 0.92
Arabidopsis CPR5 is a senescence-regulatory gene with pleiotropic functions as predicted by the evolutionary theory of senescence. J Exp Bot (2007) 0.91
Orphan transcripts in Arabidopsis thaliana: identification of several hundred previously unrecognized genes. Plant J (2005) 0.91
Salt-triggered expression of the ANAC092-dependent senescence regulon in Arabidopsis thaliana. Plant Signal Behav (2010) 0.91
Rice DUR3 mediates high-affinity urea transport and plays an effective role in improvement of urea acquisition and utilization when expressed in Arabidopsis. New Phytol (2011) 0.91
Enhancement of stress tolerance in transgenic tobacco plants constitutively expressing AtIpk2beta, an inositol polyphosphate 6-/3-kinase from Arabidopsis thaliana. Plant Mol Biol (2007) 0.91
NAC transcription factor ORE1 and senescence-induced BIFUNCTIONAL NUCLEASE1 (BFN1) constitute a regulatory cascade in Arabidopsis. Mol Plant (2013) 0.90
Regulation of photosynthesis and transcription factor expression by leaf shading and re-illumination in Arabidopsis thaliana leaves. J Plant Physiol (2011) 0.89
A role of Arabidopsis inositol polyphosphate kinase, AtIPK2alpha, in pollen germination and root growth. Plant Physiol (2004) 0.89
Action of gibberellins on growth and metabolism of Arabidopsis plants associated with high concentration of carbon dioxide. Plant Physiol (2012) 0.88
Transcription factor OsHsfC1b regulates salt tolerance and development in Oryza sativa ssp. japonica. AoB Plants (2012) 0.88
Expression of ROS-responsive genes and transcription factors after metabolic formation of H(2)O(2) in chloroplasts. Front Plant Sci (2012) 0.87
Overexpression of AtWRKY30 enhances abiotic stress tolerance during early growth stages in Arabidopsis thaliana. Plant Mol Biol (2013) 0.87
Distinct roles of the last transmembrane domain in controlling Arabidopsis K+ channel activity. New Phytol (2009) 0.87
Overproduction of chl B retards senescence through transcriptional reprogramming in Arabidopsis. Plant Cell Physiol (2012) 0.86
Transcription factors relevant to auxin signalling coordinate broad-spectrum metabolic shifts including sulphur metabolism. J Exp Bot (2008) 0.85
Noncanonical translation initiation of the Arabidopsis flowering time and alternative polyadenylation regulator FCA. Plant Cell (2010) 0.85
Different sequence signatures in the upstream regions of plant and animal tRNA genes shape distinct modes of regulation. Nucleic Acids Res (2010) 0.85
Oxidative stress provokes distinct transcriptional responses in the stress-tolerant atr7 and stress-sensitive loh2 Arabidopsis thaliana mutants as revealed by multi-parallel quantitative real-time PCR analysis of ROS marker and antioxidant genes. Plant Physiol Biochem (2012) 0.84
High-throughput protein expression using a combination of ligation-independent cloning (LIC) and infrared fluorescent protein (IFP) detection. PLoS One (2011) 0.84
A highly efficient pipeline for protein expression in Leishmania tarentolae using infrared fluorescence protein as marker. Microb Cell Fact (2010) 0.83
MULTIPASS, a rice R2R3-type MYB transcription factor, regulates adaptive growth by integrating multiple hormonal pathways. Plant J (2013) 0.83
The nuclear proteome of the green alga Chlamydomonas reinhardtii. Proteomics (2011) 0.83
Carbon deprivation-driven transcriptome reprogramming in detached developmentally arresting Arabidopsis inflorescences. Plant Physiol (2012) 0.82
EBE, an AP2/ERF transcription factor highly expressed in proliferating cells, affects shoot architecture in Arabidopsis. Plant Physiol (2013) 0.81
A novel bipartite nuclear localization signal with an atypically long linker in DOF transcription factors. J Plant Physiol (2010) 0.81
The highly charged region of plant beta-type phosphatidylinositol 4-kinase is involved in membrane targeting and phospholipid binding. Plant Mol Biol (2006) 0.81
PageRank-based identification of signaling crosstalk from transcriptomics data: the case of Arabidopsis thaliana. Mol Biosyst (2012) 0.80
Distributed structures underlie gating differences between the kin channel KAT1 and the Kout channel SKOR. Mol Plant (2009) 0.80
The LysM receptor-like kinase LysM RLK1 is required to activate defense and abiotic-stress responses induced by overexpression of fungal chitinases in Arabidopsis plants. Mol Plant (2012) 0.79
Network-based segmentation of biological multivariate time series. PLoS One (2013) 0.79
SALT-RESPONSIVE ERF1 is a negative regulator of grain filling and gibberellin-mediated seedling establishment in rice. Mol Plant (2013) 0.79
Genome-wide identification of regulatory elements and reconstruction of gene regulatory networks of the green alga Chlamydomonas reinhardtii under carbon deprivation. PLoS One (2013) 0.79
Effect of salt stress on genes encoding translation-associated proteins in Arabidopsis thaliana. Plant Signal Behav (2012) 0.78