Published in Genome Res on February 04, 2011
Genome-wide maps of histone modifications unwind in vivo chromatin states of the hair follicle lineage. Cell Stem Cell (2011) 2.80
Modeling gene expression using chromatin features in various cellular contexts. Genome Biol (2012) 2.76
Genomic and epigenetic insights into the molecular bases of heterosis. Nat Rev Genet (2013) 1.87
Genome-wide identification of regulatory DNA elements and protein-binding footprints using signatures of open chromatin in Arabidopsis. Plant Cell (2012) 1.38
N6-methyldeoxyadenosine marks active transcription start sites in chlamydomonas. Cell (2015) 1.28
The Fusarium graminearum histone H3 K27 methyltransferase KMT6 regulates development and expression of secondary metabolite gene clusters. PLoS Genet (2013) 1.11
DNA methylation and transcriptional noise. Epigenetics Chromatin (2013) 1.09
Plants Release Precursors of Histone Deacetylase Inhibitors to Suppress Growth of Competitors. Plant Cell (2015) 1.06
Cis- and trans-regulatory divergence between progenitor species determines gene-expression novelty in Arabidopsis allopolyploids. Nat Commun (2012) 1.03
Proteomic divergence in Arabidopsis autopolyploids and allopolyploids and their progenitors. Heredity (Edinb) (2011) 1.03
Tissue-specific expression of FLOWERING LOCUS T in Arabidopsis is maintained independently of polycomb group protein repression. Plant Cell (2011) 0.99
Genomic distribution of maize facultative heterochromatin marked by trimethylation of H3K27. Plant Cell (2013) 0.98
The role of small RNAs in wide hybridisation and allopolyploidisation between Brassica rapa and Brassica nigra. BMC Plant Biol (2014) 0.97
Convergence of auxin and gibberellin signaling on the regulation of the GATA transcription factors GNC and GNL in Arabidopsis thaliana. Proc Natl Acad Sci U S A (2013) 0.94
Data integration through proximity-based networks provides biological principles of organization across scales. Plant Cell (2013) 0.93
HMGA proteins as modulators of chromatin structure during transcriptional activation. Front Cell Dev Biol (2014) 0.92
Genome-wide analysis of histone modifications: H3K4me2, H3K4me3, H3K9ac, and H3K27ac in Oryza sativa L. Japonica. Mol Plant (2013) 0.91
Epigenetic modifications are associated with inter-species gene expression variation in primates. Genome Biol (2014) 0.90
Analysis of the epigenetic status of telomeres by using ChIP-seq data. Nucleic Acids Res (2012) 0.88
Modeling the relationship of epigenetic modifications to transcription factor binding. Nucleic Acids Res (2015) 0.86
Environmental heterogeneity and phenotypic divergence: can heritable epigenetic variation aid speciation? Genet Res Int (2012) 0.84
Genome-wide mapping reveals conservation of promoter DNA methylation following chicken domestication. Sci Rep (2015) 0.81
Histone methylation analysis and pathway predictions in chickens after MDV infection. PLoS One (2012) 0.81
Predicting the probability of H3K4me3 occupation at a base pair from the genome sequence context. Bioinformatics (2013) 0.81
Developmental silencing of the AtTERT gene is associated with increased H3K27me3 loading and maintenance of its euchromatic environment. J Exp Bot (2012) 0.80
Genomic change, retrotransposon mobilization and extensive cytosine methylation alteration in Brassica napus introgressions from two intertribal hybridizations. PLoS One (2013) 0.80
Interrogation of allelic chromatin states in human cells by high-density ChIP-genotyping. Epigenetics (2014) 0.79
Genetic and Epigenetic Alterations of Brassica nigra Introgression Lines from Somatic Hybridization: A Resource for Cauliflower Improvement. Front Plant Sci (2016) 0.78
AtmiRNET: a web-based resource for reconstructing regulatory networks of Arabidopsis microRNAs. Database (Oxford) (2015) 0.77
A cotton miRNA is involved in regulation of plant response to salt stress. Sci Rep (2016) 0.77
A systemic identification approach for primary transcription start site of Arabidopsis miRNAs from multidimensional omics data. Funct Integr Genomics (2016) 0.77
Genome-wide mapping of histone H3 lysine 4 trimethylation in Eucalyptus grandis developing xylem. BMC Plant Biol (2015) 0.76
Histone modifications facilitate the coexpression of bidirectional promoters in rice. BMC Genomics (2016) 0.76
DNA methylation reactivates GAD1 expression in cancer by preventing CTCF-mediated polycomb repressive complex 2 recruitment. Oncogene (2015) 0.76
Functional divergence of GhCFE5 homoeologs revealed in cotton fiber and Arabidopsis root cell development. Plant Cell Rep (2016) 0.76
The transposable element environment of human genes is associated with histone and expression changes in cancer. BMC Genomics (2016) 0.75
DNA context represents transcription regulation of the gene in mouse embryonic stem cells. Sci Rep (2016) 0.75
Intron-Mediated Enhancement: A Tool for Heterologous Gene Expression in Plants? Front Plant Sci (2017) 0.75
Genome-wide analyses of four major histone modifications in Arabidopsis hybrids at the germinating seed stage. BMC Genomics (2017) 0.75
Increasing phosphatidylinositol (4,5) bisphosphate biosynthesis affects plant nuclear lipids and nuclear functions. Plant Physiol Biochem (2012) 0.75
Histone Modifications Define Expression Bias of Homoeologous Genomes in Allotetraploid Cotton. Plant Physiol (2016) 0.75
Distinct patterns of the histone marks associated with recruitment of the methionine chain-elongation pathway from leucine biosynthesis. J Exp Bot (2014) 0.75
Regulation of transcription by the Arabidopsis UVR8 photoreceptor involves a specific histone modification. Plant Mol Biol (2016) 0.75
Abnormal epigenetic regulation of the gene expression levels of Wnt2b and Wnt7b: Implications for neural tube defects. Mol Med Rep (2015) 0.75
The Second Subunit of DNA Polymerase Delta Is Required for Genomic Stability and Epigenetic Regulation. Plant Physiol (2016) 0.75
Correlation Between Expression of Recombinant Proteins and Abundance of H3K4Me3 on the Enhancer of Human Cytomegalovirus Major Immediate-Early Promoter. Mol Biotechnol (2017) 0.75
High-resolution profiling of histone methylations in the human genome. Cell (2007) 85.74
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature (2007) 65.18
Translating the histone code. Science (2001) 56.77
A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell (2006) 48.80
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
The role of chromatin during transcription. Cell (2007) 26.48
The complex language of chromatin regulation during transcription. Nature (2007) 16.97
Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis. Cell (2006) 15.24
FLOWERING LOCUS C encodes a novel MADS domain protein that acts as a repressor of flowering. Plant Cell (1999) 12.64
Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat Genet (2006) 11.88
Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive genes. Cell (2009) 8.69
Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation. Cell Stem Cell (2009) 8.62
A histone H3 methyltransferase controls DNA methylation in Neurospora crassa. Nature (2001) 8.27
Distinctive chromatin in human sperm packages genes for embryo development. Nature (2009) 6.18
Nucleosomes unfold completely at a transcriptionally active promoter. Mol Cell (2003) 5.94
H3.3/H2A.Z double variant-containing nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions. Nat Genet (2009) 5.82
Histones are first hyperacetylated and then lose contact with the activated PHO5 promoter. Mol Cell (2003) 5.41
Functional annotation of the Arabidopsis genome using controlled vocabularies. Plant Physiol (2004) 5.17
Preprocessing of oligonucleotide array data. Nat Biotechnol (2004) 4.70
Whole-genome analysis of histone H3 lysine 27 trimethylation in Arabidopsis. PLoS Biol (2007) 4.30
Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks. Nature (2008) 4.20
Genetic and epigenetic mechanisms for gene expression and phenotypic variation in plant polyploids. Annu Rev Plant Biol (2007) 4.07
Histone acetyltransferase complexes stabilize swi/snf binding to promoter nucleosomes. Cell (2001) 3.54
Altered circadian rhythms regulate growth vigour in hybrids and allopolyploids. Nature (2008) 2.95
A concerted DNA methylation/histone methylation switch regulates rRNA gene dosage control and nucleolar dominance. Mol Cell (2004) 2.92
Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana. Genome Biol (2009) 2.86
An efficient chromatin immunoprecipitation (ChIP) protocol for studying histone modifications in Arabidopsis plants. Nat Protoc (2008) 2.35
Blocking histone deacetylation in Arabidopsis induces pleiotropic effects on plant gene regulation and development. Proc Natl Acad Sci U S A (2001) 2.05
The epigenetic landscape of plants. Science (2008) 1.78
Epigenetic regulation and the variability of gene expression. Nat Genet (2008) 1.67
Genic and global functions for Paf1C in chromatin modification and gene expression in Arabidopsis. PLoS Genet (2008) 1.63
Reversible histone acetylation and deacetylation mediate genome-wide, promoter-dependent and locus-specific changes in gene expression during plant development. Genetics (2004) 1.59
Methylation of histone H3 mediates the association of the NuA3 histone acetyltransferase with chromatin. Mol Cell Biol (2006) 1.58
Roles of dynamic and reversible histone acetylation in plant development and polyploidy. Biochim Biophys Acta (2007) 1.58
Pluripotent versus totipotent plant stem cells: dependence versus autonomy? Trends Plant Sci (2007) 1.55
A genome-wide analysis in Saccharomyces cerevisiae demonstrates the influence of chromatin modifiers on transcription. Nat Genet (2007) 1.53
Duplicate genes increase expression diversity in closely related species and allopolyploids. Proc Natl Acad Sci U S A (2009) 1.52
Nonadditive regulation of FRI and FLC loci mediates flowering-time variation in Arabidopsis allopolyploids. Genetics (2006) 1.49
Genome-wide profiling of histone H3 lysine 9 acetylation and dimethylation in Arabidopsis reveals correlation between multiple histone marks and gene expression. Plant Mol Biol (2010) 1.33
RNAi of met1 reduces DNA methylation and induces genome-specific changes in gene expression and centromeric small RNA accumulation in Arabidopsis allopolyploids. Genetics (2008) 1.17
Control of Arabidopsis apical-basal embryo polarity by antagonistic transcription factors. Nature (2010) 1.16
External factors accelerate expression divergence between duplicate genes. Trends Genet (2007) 1.14
Role of duplicate genes in genetic robustness against null mutations. Nature (2003) 7.81
Human polymorphism at microRNAs and microRNA target sites. Proc Natl Acad Sci U S A (2007) 4.87
Comparative analysis of the receptor-like kinase family in Arabidopsis and rice. Plant Cell (2004) 4.59
Dating the monocot-dicot divergence and the origin of core eudicots using whole chloroplast genomes. J Mol Evol (2004) 4.08
Genomewide nonadditive gene regulation in Arabidopsis allotetraploids. Genetics (2005) 3.78
Mammalian housekeeping genes evolve more slowly than tissue-specific genes. Mol Biol Evol (2003) 3.33
Chromosome-wide SNPs reveal an ancient origin for Plasmodium falciparum. Nature (2002) 3.23
Uncovering small RNA-mediated responses to phosphate deficiency in Arabidopsis by deep sequencing. Plant Physiol (2009) 2.98
Altered circadian rhythms regulate growth vigour in hybrids and allopolyploids. Nature (2008) 2.95
A concerted DNA methylation/histone methylation switch regulates rRNA gene dosage control and nucleolar dominance. Mol Cell (2004) 2.92
Evolution of genome size in Brassicaceae. Ann Bot (2005) 2.91
The K(A)/K(S) ratio test for assessing the protein-coding potential of genomic regions: an empirical and simulation study. Genome Res (2002) 2.84
Extent of gene duplication in the genomes of Drosophila, nematode, and yeast. Mol Biol Evol (2002) 2.73
A large number of novel coding small open reading frames in the intergenic regions of the Arabidopsis thaliana genome are transcribed and/or under purifying selection. Genome Res (2007) 2.72
Simultaneous amino acid substitutions at antigenic sites drive influenza A hemagglutinin evolution. Proc Natl Acad Sci U S A (2007) 2.67
Stochastic and epigenetic changes of gene expression in Arabidopsis polyploids. Genetics (2004) 2.62
Divergence in the spatial pattern of gene expression between human duplicate genes. Genome Res (2003) 2.60
Reorganization of adjacent gene relationships in yeast genomes by whole-genome duplication and gene deletion. Mol Biol Evol (2006) 2.55
Strong male-driven evolution of DNA sequences in humans and apes. Nature (2002) 2.53
Duplicate genes increase gene expression diversity within and between species. Nat Genet (2004) 2.40
Slow molecular clocks in Old World monkeys, apes, and humans. Mol Biol Evol (2002) 2.20
Low nucleotide diversity in chimpanzees and bonobos. Genetics (2003) 2.16
Toward sequencing cotton (Gossypium) genomes. Plant Physiol (2007) 2.16
Small RNAs serve as a genetic buffer against genomic shock in Arabidopsis interspecific hybrids and allopolyploids. Proc Natl Acad Sci U S A (2009) 2.08
Different evolutionary patterns between young duplicate genes in the human genome. Genome Biol (2003) 1.92
Gene essentiality, gene duplicability and protein connectivity in human and mouse. Trends Genet (2007) 1.89
Comparative methods for the analysis of gene-expression evolution: an example using yeast functional genomic data. Mol Biol Evol (2004) 1.88
MicroRNA regulation of human protein protein interaction network. RNA (2007) 1.82
Statistical methods for identifying yeast cell cycle transcription factors. Proc Natl Acad Sci U S A (2005) 1.81
Concern Protein under-wrapping causes dosage sensitivity and decreases gene duplicability. PLoS Genet (2007) 1.80
Evolution of the yeast protein interaction network. Proc Natl Acad Sci U S A (2003) 1.78
Patterns of segmental duplication in the human genome. Mol Biol Evol (2004) 1.76
Molecular evolution meets the genomics revolution. Nat Genet (2003) 1.76
Organismal complexity, protein complexity, and gene duplicability. Proc Natl Acad Sci U S A (2003) 1.67
Natural selection on cis and trans regulation in yeasts. Genome Res (2010) 1.65
Gene expression changes and early events in cotton fibre development. Ann Bot (2007) 1.64
Human SNPs reveal no evidence of frequent positive selection. Mol Biol Evol (2005) 1.63
Larger genetic differences within africans than between Africans and Eurasians. Genetics (2002) 1.62
Evolution and expression of homeologous loci in Tragopogon miscellus (Asteraceae), a recent and reciprocally formed allopolyploid. Genetics (2006) 1.61
Signalling pathway for RKIP and Let-7 regulates and predicts metastatic breast cancer. EMBO J (2011) 1.60
Reversible histone acetylation and deacetylation mediate genome-wide, promoter-dependent and locus-specific changes in gene expression during plant development. Genetics (2004) 1.59
Lowly expressed human microRNA genes evolve rapidly. Mol Biol Evol (2009) 1.58
Multidimensional scaling for large genomic data sets. BMC Bioinformatics (2008) 1.54
Genetic control of developmental changes induced by disruption of Arabidopsis histone deacetylase 1 (AtHD1) expression. Genetics (2003) 1.52
Duplicate genes increase expression diversity in closely related species and allopolyploids. Proc Natl Acad Sci U S A (2009) 1.52
MYBS: a comprehensive web server for mining transcription factor binding sites in yeast. Nucleic Acids Res (2007) 1.50
Nonadditive regulation of FRI and FLC loci mediates flowering-time variation in Arabidopsis allopolyploids. Genetics (2006) 1.49
Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle. BMC Bioinformatics (2006) 1.47
RNA landscape of evolution for optimal exon and intron discrimination. Proc Natl Acad Sci U S A (2008) 1.45
Transcription factor families have much higher expansion rates in plants than in animals. Plant Physiol (2005) 1.44
Genomic and expression plasticity of polyploidy. Curr Opin Plant Biol (2009) 1.44
Gene expression evolves faster in narrowly than in broadly expressed mammalian genes. Mol Biol Evol (2005) 1.44
Quantitative characterization of the transcriptional regulatory network in the yeast cell cycle. Bioinformatics (2004) 1.43
Nucleotide variation and haplotype diversity in a 10-kb noncoding region in three continental human populations. Genetics (2006) 1.42
Rate of protein evolution versus fitness effect of gene deletion. Mol Biol Evol (2003) 1.41
DNA replication timing and selection shape the landscape of nucleotide variation in cancer genomes. Nat Commun (2012) 1.40
Signatures of domain shuffling in the human genome. Genome Res (2002) 1.39
Protein function, connectivity, and duplicability in yeast. Mol Biol Evol (2005) 1.39
Patterns of expansion and expression divergence in the plant polygalacturonase gene family. Genome Biol (2006) 1.36
The chicken frizzle feather is due to an α-keratin (KRT75) mutation that causes a defective rachis. PLoS Genet (2012) 1.36
Developmental and gene expression analyses of a cotton naked seed mutant. Planta (2005) 1.34
Human-specific insertions and deletions inferred from mammalian genome sequences. Genome Res (2006) 1.34
Sensitivity of 70-mer oligonucleotides and cDNAs for microarray analysis of gene expression in Arabidopsis and its related species. Plant Biotechnol J (2004) 1.32
Alternatively and constitutively spliced exons are subject to different evolutionary forces. Mol Biol Evol (2005) 1.31
Comment on "Chromosomal speciation and molecular divergence-accelerated evolution in rearranged chromosomes". Science (2003) 1.30
CpG island density and its correlations with genomic features in mammalian genomes. Genome Biol (2008) 1.30
Nucleotide diversity in gorillas. Genetics (2004) 1.28
Genome-wide analysis reveals rapid and dynamic changes in miRNA and siRNA sequence and expression during ovule and fiber development in allotetraploid cotton (Gossypium hirsutum L.). Genome Biol (2009) 1.26
Systematic identification of yeast cell cycle transcription factors using multiple data sources. BMC Bioinformatics (2008) 1.25
Role of positive selection in the retention of duplicate genes in mammalian genomes. Proc Natl Acad Sci U S A (2006) 1.24
Proportion of solvent-exposed amino acids in a protein and rate of protein evolution. Mol Biol Evol (2007) 1.23
Evolutionary diversification of DNA methyltransferases in eukaryotic genomes. Mol Biol Evol (2005) 1.23
Features and trend of loss of promoter-associated CpG islands in the human and mouse genomes. Mol Biol Evol (2007) 1.23
Expression evolution in yeast genes of single-input modules is mainly due to changes in trans-acting factors. Genome Res (2007) 1.21
News and views: the chimpanzee and us. Nature (2005) 1.21
Natural variation in nucleolar dominance reveals the relationship between nucleolus organizer chromatin topology and rRNA gene transcription in Arabidopsis. Proc Natl Acad Sci U S A (2003) 1.21
Human TRIM71 and its nematode homologue are targets of let-7 microRNA and its zebrafish orthologue is essential for development. Mol Biol Evol (2007) 1.20
Characterizing regulatory and functional differentiation between maize mesophyll and bundle sheath cells by transcriptomic analysis. Plant Physiol (2012) 1.18
RNAi of met1 reduces DNA methylation and induces genome-specific changes in gene expression and centromeric small RNA accumulation in Arabidopsis allopolyploids. Genetics (2008) 1.17
Intragenic spatial patterns of codon usage bias in prokaryotic and eukaryotic genomes. Genetics (2004) 1.17
Prediction of splice sites with dependency graphs and their expanded bayesian networks. Bioinformatics (2004) 1.17
Ploidy and Hybridity Effects on Growth Vigor and Gene Expression in Arabidopsis thaliana Hybrids and Their Parents. G3 (Bethesda) (2012) 1.17
Human adaptive evolution at Myostatin (GDF8), a regulator of muscle growth. Am J Hum Genet (2006) 1.16
Origins, lineage-specific expansions, and multiple losses of tyrosine kinases in eukaryotes. Mol Biol Evol (2004) 1.16
Maternal siRNAs as regulators of parental genome imbalance and gene expression in endosperm of Arabidopsis seeds. Proc Natl Acad Sci U S A (2012) 1.16
cis- and trans-Regulation of miR163 and target genes confers natural variation of secondary metabolites in two Arabidopsis species and their allopolyploids. Plant Cell (2011) 1.15
Evolution of the hominoid semenogelin genes, the major proteins of ejaculated semen. J Mol Evol (2003) 1.14
External factors accelerate expression divergence between duplicate genes. Trends Genet (2007) 1.14
Effects of GC content and mutational pressure on the lengths of exons and coding sequences. J Mol Evol (2003) 1.13
A new measure of the robustness of biochemical networks. Bioinformatics (2005) 1.13
How strong is the mutagenicity of recombination in mammals? Mol Biol Evol (2004) 1.13
The spatial distribution of cis regulatory elements in yeast promoters and its implications for transcriptional regulation. BMC Genomics (2010) 1.12
Identifying gene regulatory modules of heat shock response in yeast. BMC Genomics (2008) 1.12
Spotted cotton oligonucleotide microarrays for gene expression analysis. BMC Genomics (2007) 1.12
Evidence from opsin genes rejects nocturnality in ancestral primates. Proc Natl Acad Sci U S A (2005) 1.11
Whole genome transcriptome polymorphisms in Arabidopsis thaliana. Genome Biol (2008) 1.09
A study of the phylogeny of Brassica rapa, B. nigra, Raphanus sativus, and their related genera using noncoding regions of chloroplast DNA. Mol Phylogenet Evol (2002) 1.09
Identifying regulatory targets of cell cycle transcription factors using gene expression and ChIP-chip data. BMC Bioinformatics (2007) 1.09
Big roles for small RNAs in polyploidy, hybrid vigor, and hybrid incompatibility. Curr Opin Plant Biol (2012) 1.08