Published in Nucleic Acids Res on May 17, 2011
The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell (2013) 3.27
Patterns of population epigenomic diversity. Nature (2013) 2.70
Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting. Elife (2014) 1.52
Aberration in DNA methylation in B-cell lymphomas has a complex origin and increases with disease severity. PLoS Genet (2013) 1.50
Methylome evolution in plants. Genome Biol (2016) 1.39
CHH islands: de novo DNA methylation in near-gene chromatin regulation in maize. Genome Res (2012) 1.36
Epialleles in plant evolution. Genome Biol (2012) 1.30
Spreading of heterochromatin is limited to specific families of maize retrotransposons. PLoS Genet (2012) 1.25
RNA polymerase V-dependent small RNAs in Arabidopsis originate from small, intergenic loci including most SINE repeats. Epigenetics (2012) 1.19
Transposon variants and their effects on gene expression in Arabidopsis. PLoS Genet (2013) 1.17
Epigenetic and epigenomic variation in Arabidopsis thaliana. Trends Plant Sci (2012) 1.15
Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements. Elife (2015) 1.07
Extensive natural epigenetic variation at a de novo originated gene. PLoS Genet (2013) 1.07
Low relative humidity triggers RNA-directed de novo DNA methylation and suppression of genes controlling stomatal development. J Exp Bot (2012) 1.05
Conservation and divergence of transcriptomic and epigenomic variation in maize hybrids. Genome Biol (2013) 0.98
Divergent DNA methylation patterns associated with gene expression in rice cultivars with contrasting drought and salinity stress response. Sci Rep (2015) 0.93
Creating Order from Chaos: Epigenome Dynamics in Plants with Complex Genomes. Plant Cell (2016) 0.92
Ancestral repeats have shaped epigenome and genome composition for millions of years in Arabidopsis thaliana. Nat Commun (2014) 0.92
A Comparative Epigenomic Analysis of Polyploidy-Derived Genes in Soybean and Common Bean. Plant Physiol (2015) 0.90
Composition and expression of conserved microRNA genes in diploid cotton (Gossypium) species. Genome Biol Evol (2013) 0.89
Whole genome comparative analysis of transposable elements provides new insight into mechanisms of their inactivation in fungal genomes. BMC Genomics (2015) 0.89
Divergence of gene body DNA methylation and evolution of plant duplicate genes. PLoS One (2014) 0.86
The Arabidopsis thaliana mobilome and its impact at the species level. Elife (2016) 0.86
DNA DAMAGE BINDING PROTEIN 2 (DDB2) Shapes the DNA Methylation Landscape. Plant Cell (2016) 0.84
TE-Tracker: systematic identification of transposition events through whole-genome resequencing. BMC Bioinformatics (2014) 0.83
Transposable Element Insertion and Epigenetic Modification Cause the Multiallelic Variation in the Expression of FAE1 in Sinapis alba. Plant Cell (2014) 0.83
Identification, characterization and distribution of transposable elements in the flax (Linum usitatissimum L.) genome. BMC Genomics (2012) 0.82
Covering your bases: inheritance of DNA methylation in plant genomes. Mol Plant (2013) 0.81
Stemming epigenetics in marine stramenopiles. Curr Genomics (2011) 0.80
Chromatin resetting mechanisms preventing transgenerational inheritance of epigenetic states. Front Plant Sci (2015) 0.79
Epigenetic dynamics: role of epimarks and underlying machinery in plants exposed to abiotic stress. Int J Genomics (2014) 0.78
DNA methylation profiles of diverse Brachypodium distachyon align with underlying genetic diversity. Genome Res (2016) 0.77
Epiallelic variation in Arabidopsis thaliana. Cold Spring Harb Symp Quant Biol (2012) 0.77
The Tnt1 retrotransposon escapes silencing in tobacco, its natural host. PLoS One (2012) 0.75
Structural Diversity of a Novel LTR Retrotransposon, RTPOSON, in the Genus Oryza. Evol Bioinform Online (2016) 0.75
The SUMO E3 Ligase-Like Proteins PIAL1 and PIAL2 Interact with MOM1 and Form a Novel Complex Required for Transcriptional Silencing. Plant Cell (2016) 0.75
Comprehensive repeatome annotation reveals strong potential impact of repetitive elements on tomato ripening. BMC Genomics (2016) 0.75
The DNA methylation level against the background of the genome size and t-heterochromatin content in some species of the genus Secale L. PeerJ (2017) 0.75
Mutations in the promoter, intron and CDS of two FAD2 generate multiple alleles modulating linoleic acid level in yellow mustard. Sci Rep (2017) 0.75
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature (2000) 70.33
Profile hidden Markov models. Bioinformatics (1998) 56.04
Versatile and open software for comparing large genomes. Genome Biol (2004) 49.45
Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res (1999) 49.21
Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell (2008) 32.65
Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature (2008) 26.78
Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet (2010) 15.70
Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat Genet (2006) 11.88
Role of transposable elements in heterochromatin and epigenetic control. Nature (2004) 10.51
Transposable elements and the epigenetic regulation of the genome. Nat Rev Genet (2007) 7.14
Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor. BMC Bioinformatics (2006) 5.50
DNA demethylation in the Arabidopsis genome. Proc Natl Acad Sci U S A (2007) 4.55
Finding the fifth base: genome-wide sequencing of cytosine methylation. Genome Res (2009) 4.16
CENSOR--a program for identification and elimination of repetitive elements from DNA sequences. Comput Chem (1996) 4.09
MaskerAid: a performance enhancement to RepeatMasker. Bioinformatics (2000) 3.66
A local alignment tool for very long DNA sequences. Comput Appl Biosci (1995) 3.58
mreps: Efficient and flexible detection of tandem repeats in DNA. Nucleic Acids Res (2003) 3.27
The age of Alu subfamilies. J Mol Evol (1996) 2.85
A structural-maintenance-of-chromosomes hinge domain-containing protein is required for RNA-directed DNA methylation. Nat Genet (2008) 2.74
Genome-wide association of histone H3 lysine nine methylation with CHG DNA methylation in Arabidopsis thaliana. PLoS One (2008) 2.69
Epigenetic silencing of transposable elements: a trade-off between reduced transposition and deleterious effects on neighboring gene expression. Genome Res (2009) 2.46
Tandem repeats upstream of the Arabidopsis endogene SDC recruit non-CG DNA methylation and initiate siRNA spreading. Genes Dev (2008) 2.16
Heritable epigenetic mutation of a transposon-flanked Arabidopsis gene due to lack of the chromatin-remodeling factor DDM1. EMBO J (2007) 2.05
An Arabidopsis jmjC domain protein protects transcribed genes from DNA methylation at CHG sites. EMBO J (2009) 2.00
Computational and analytical framework for small RNA profiling by high-throughput sequencing. RNA (2009) 1.97
A stepwise pathway for biogenesis of 24-nt secondary siRNAs and spreading of DNA methylation. EMBO J (2008) 1.93
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
Detection of new transposable element families in Drosophila melanogaster and Anopheles gambiae genomes. J Mol Evol (2003) 1.78
Improved detection and annotation of transposable elements in sequenced genomes using multiple reference sequence sets. Genomics (2008) 1.45
Give-and-take: interactions between DNA transposons and their host plant genomes. Curr Opin Genet Dev (2007) 1.43
Repeat elements and the Arabidopsis DNA methylation landscape. Heredity (Edinb) (2010) 1.25
Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) 18.01
The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science (2007) 11.15
Role of transposable elements in heterochromatin and epigenetic control. Nature (2004) 10.51
The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism. Science (2004) 9.97
Genome sequence of Aedes aegypti, a major arbovirus vector. Science (2007) 9.19
Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita. Nat Biotechnol (2008) 5.19
Understanding mechanisms of novel gene expression in polyploids. Trends Genet (2003) 4.90
Assessing the impact of transgenerational epigenetic variation on complex traits. PLoS Genet (2009) 4.57
Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features. Proc Natl Acad Sci U S A (2006) 4.52
Reinforcement of silencing at transposons and highly repeated sequences requires the concerted action of two distinct RNA polymerases IV in Arabidopsis. Genes Dev (2005) 4.50
Dependence of heterochromatic histone H3 methylation patterns on the Arabidopsis gene DDM1. Science (2002) 4.49
The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization. Science (2007) 4.43
A role for RNAi in the selective correction of DNA methylation defects. Science (2009) 4.30
Epigenetic natural variation in Arabidopsis thaliana. PLoS Biol (2007) 4.29
The Ectocarpus genome and the independent evolution of multicellularity in brown algae. Nature (2010) 3.60
The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation. Proc Natl Acad Sci U S A (2007) 3.58
Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea. PLoS Genet (2011) 3.52
Genome expansion and gene loss in powdery mildew fungi reveal tradeoffs in extreme parasitism. Science (2010) 3.35
Genomic footprints of a cryptic plastid endosymbiosis in diatoms. Science (2009) 3.31
Profiling histone modification patterns in plants using genomic tiling microarrays. Nat Methods (2005) 3.28
Integrative epigenomic mapping defines four main chromatin states in Arabidopsis. EMBO J (2011) 3.16
Mapping the epigenetic basis of complex traits. Science (2014) 3.13
Epigenome dynamics: a quantitative genetics perspective. Nat Rev Genet (2008) 3.13
Arabidopsis TFL2/LHP1 specifically associates with genes marked by trimethylation of histone H3 lysine 27. PLoS Genet (2007) 3.11
Versatile gene-specific sequence tags for Arabidopsis functional genomics: transcript profiling and reverse genetics applications. Genome Res (2004) 3.02
Retracted RNAi-dependent and independent control of LINE1 accumulation and mobility in mouse embryonic stem cells. PLoS Genet (2013) 2.91
Obligate biotrophy features unraveled by the genomic analysis of rust fungi. Proc Natl Acad Sci U S A (2011) 2.84
Genome-wide studies highlight indirect links between human replication origins and gene regulation. Proc Natl Acad Sci U S A (2008) 2.77
A holistic approach to marine eco-systems biology. PLoS Biol (2011) 2.71
Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis. Nature (2010) 2.61
Fruit-specific RNAi-mediated suppression of DET1 enhances carotenoid and flavonoid content in tomatoes. Nat Biotechnol (2005) 2.41
A stress surveillance system based on calcium and nitric oxide in marine diatoms. PLoS Biol (2006) 2.40
Whole-cell response of the pennate diatom Phaeodactylum tricornutum to iron starvation. Proc Natl Acad Sci U S A (2008) 2.26
A model for carbohydrate metabolism in the diatom Phaeodactylum tricornutum deduced from comparative whole genome analysis. PLoS One (2008) 2.17
Concern Misregulation of AUXIN RESPONSE FACTOR 8 underlies the developmental abnormalities caused by three distinct viral silencing suppressors in Arabidopsis. PLoS Pathog (2011) 2.12
Considering transposable element diversification in de novo annotation approaches. PLoS One (2011) 2.11
Profiling DNA methylation patterns using genomic tiling microarrays. Nat Methods (2005) 2.10
Evolution and metabolic significance of the urea cycle in photosynthetic diatoms. Nature (2011) 2.06
Molecular toolbox for studying diatom biology in Phaeodactylum tricornutum. Gene (2007) 2.05
Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations. Nat Commun (2011) 2.03
Highly dynamic and sex-specific expression of microRNAs during early ES cell differentiation. PLoS Genet (2009) 1.96
Recurrent insertion and duplication generate networks of transposable element sequences in the Drosophila melanogaster genome. Genome Biol (2006) 1.81
Polycomb repressive complex 2 controls the embryo-to-seedling phase transition. PLoS Genet (2011) 1.79
Manipulation of light signal transduction as a means of modifying fruit nutritional quality in tomato. Proc Natl Acad Sci U S A (2004) 1.70
Variation in crossing-over rates across chromosome 4 of Arabidopsis thaliana reveals the presence of meiotic recombination "hot spots". Genome Res (2005) 1.70
The Capsella rubella genome and the genomic consequences of rapid mating system evolution. Nat Genet (2013) 1.69
Gene silencing in the marine diatom Phaeodactylum tricornutum. Nucleic Acids Res (2009) 1.67
Discovering and detecting transposable elements in genome sequences. Brief Bioinform (2007) 1.63
Chloroplast genomes of the diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana: comparison with other plastid genomes of the red lineage. Mol Genet Genomics (2007) 1.52
A diatom gene regulating nitric-oxide signaling and susceptibility to diatom-derived aldehydes. Curr Biol (2008) 1.48
Changes in 5S rDNA chromatin organization and transcription during heterochromatin establishment in Arabidopsis. Plant Cell (2003) 1.48
The photomorphogenesis regulator DET1 binds the amino-terminal tail of histone H2B in a nucleosome context. Curr Biol (2002) 1.46
Improved detection and annotation of transposable elements in sequenced genomes using multiple reference sequence sets. Genomics (2008) 1.45
An atypical member of the light-harvesting complex stress-related protein family modulates diatom responses to light. Proc Natl Acad Sci U S A (2010) 1.42
The INO80 protein controls homologous recombination in Arabidopsis thaliana. Mol Cell (2004) 1.41
Reconstructing de novo silencing of an active plant retrotransposon. Nat Genet (2013) 1.40
Comparative genomics of the pennate diatom Phaeodactylum tricornutum. Plant Physiol (2005) 1.39
The wheat powdery mildew genome shows the unique evolution of an obligate biotroph. Nat Genet (2013) 1.38
Genome properties of the diatom Phaeodactylum tricornutum. Plant Physiol (2002) 1.38
Epigenomic mapping in Arabidopsis using tiling microarrays. Chromosome Res (2005) 1.35
An ecological and evolutionary context for integrated nitrogen metabolism and related signaling pathways in marine diatoms. Curr Opin Plant Biol (2006) 1.33
A model of segmental duplication formation in Drosophila melanogaster. Genome Res (2007) 1.30
Epialleles in plant evolution. Genome Biol (2012) 1.30
Hyperosmotic priming of Arabidopsis seedlings establishes a long-term somatic memory accompanied by specific changes of the epigenome. Genome Biol (2013) 1.30
CUL4 associates with DDB1 and DET1 and its downregulation affects diverse aspects of development in Arabidopsis thaliana. Plant J (2006) 1.29
Wheat syntenome unveils new evidences of contrasted evolutionary plasticity between paleo- and neoduplicated subgenomes. Plant J (2013) 1.26
Epigenetic variation creates potential for evolution of plant phenotypic plasticity. New Phytol (2012) 1.24
NERD, a plant-specific GW protein, defines an additional RNAi-dependent chromatin-based pathway in Arabidopsis. Mol Cell (2012) 1.24
The development of an Arabidopsis model system for genome-wide analysis of polyploidy effects. Biol J Linn Soc Lond (2004) 1.22
Chromatin indexing in Arabidopsis: an epigenomic tale of tails and more. Trends Genet (2009) 1.22
Genome-wide epigenetic perturbation jump-starts patterns of heritable variation found in nature. Genetics (2011) 1.21
Evolutionary origins and functions of the carotenoid biosynthetic pathway in marine diatoms. PLoS One (2008) 1.21
Formation of plant metabolic gene clusters within dynamic chromosomal regions. Proc Natl Acad Sci U S A (2011) 1.18
Diatom PtCPF1 is a new cryptochrome/photolyase family member with DNA repair and transcription regulation activity. EMBO Rep (2009) 1.15
The Diatom EST Database. Nucleic Acids Res (2005) 1.14
Integrative transcript and metabolite analysis of nutritionally enhanced DE-ETIOLATED1 downregulated tomato fruit. Plant Cell (2010) 1.13
Genome-wide analysis of the diatom cell cycle unveils a novel type of cyclins involved in environmental signaling. Genome Biol (2010) 1.12
Iron utilization in marine cyanobacteria and eukaryotic algae. Front Microbiol (2012) 1.11
Features of the Arabidopsis recombination landscape resulting from the combined loss of sequence variation and DNA methylation. Proc Natl Acad Sci U S A (2012) 1.10
Update of the Diatom EST Database: a new tool for digital transcriptomics. Nucleic Acids Res (2008) 1.10
Promoter DNA hypermethylation and gene repression in undifferentiated Arabidopsis cells. PLoS One (2008) 1.09
Nuclear retention of the transcription factor NLP7 orchestrates the early response to nitrate in plants. Nat Commun (2013) 1.09
A modified Gateway cloning strategy for overexpressing tagged proteins in plants. Plant Methods (2008) 1.09
Localization of putative carbonic anhydrases in two marine diatoms, Phaeodactylum tricornutum and Thalassiosira pseudonana. Photosynth Res (2011) 1.09
LTR retrotransposons in rice (Oryza sativa, L.): recent burst amplifications followed by rapid DNA loss. BMC Genomics (2007) 1.07
Detection of transposable elements by their compositional bias. BMC Bioinformatics (2004) 1.07
Extensive natural epigenetic variation at a de novo originated gene. PLoS Genet (2013) 1.07
AUREOCHROME1a-mediated induction of the diatom-specific cyclin dsCYC2 controls the onset of cell division in diatoms (Phaeodactylum tricornutum). Plant Cell (2013) 1.05
Arabidopsis epigenetics: when RNA meets chromatin. Curr Opin Plant Biol (2005) 1.05
TriAnnot: A Versatile and High Performance Pipeline for the Automated Annotation of Plant Genomes. Front Plant Sci (2012) 1.04
Characterization of two members of the cryptochrome/photolyase family from Ostreococcus tauri provides insights into the origin and evolution of cryptochromes. Plant Cell Environ (2010) 1.04