Published in Annu Rev Plant Biol on January 01, 2011
Genome-wide analysis of DNA methylation and gene expression changes in two Arabidopsis ecotypes and their reciprocal hybrids. Plant Cell (2012) 1.91
Advances in omics and bioinformatics tools for systems analyses of plant functions. Plant Cell Physiol (2011) 1.28
Cytosine methylation and hydroxymethylation mark DNA for elimination in Oxytricha trifallax. Genome Biol (2012) 1.00
Conservation and divergence of transcriptomic and epigenomic variation in maize hybrids. Genome Biol (2013) 0.98
Genetic and epigenetic control of plant heat responses. Front Plant Sci (2015) 0.98
Oral benzo[a]pyrene: understanding pharmacokinetics, detoxication, and consequences--Cyp1 knockout mouse lines as a paradigm. Mol Pharmacol (2013) 0.96
Creating Order from Chaos: Epigenome Dynamics in Plants with Complex Genomes. Plant Cell (2016) 0.92
Genomic basis for light control of plant development. Protein Cell (2012) 0.91
Grafting with rootstocks induces extensive transcriptional re-programming in the shoot apical meristem of grapevine. BMC Plant Biol (2013) 0.91
Histone H2B monoubiquitination facilitates the rapid modulation of gene expression during Arabidopsis photomorphogenesis. PLoS Genet (2012) 0.90
Inference of transcriptional networks in Arabidopsis through conserved noncoding sequence analysis. Plant Cell (2014) 0.85
Plant systems biology: insights, advances and challenges. Planta (2014) 0.83
Unravelling rootstock×scion interactions to improve food security. J Exp Bot (2015) 0.82
Characterization of Chromatin Structure-associated Histone Modifications in Breast Cancer Cells. Genomics Inform (2012) 0.81
The female gametophyte: an emerging model for cell type-specific systems biology in plant development. Front Plant Sci (2015) 0.81
Functional innovations of three chronological mesohexaploid Brassica rapa genomes. BMC Genomics (2014) 0.81
Evaluation of alternative RNA labeling protocols for transcript profiling with Arabidopsis AGRONOMICS1 tiling arrays. Plant Methods (2012) 0.80
Light signaling controls nuclear architecture reorganization during seedling establishment. Proc Natl Acad Sci U S A (2015) 0.80
Identifying microRNAs and transcript targets in Jatropha seeds. PLoS One (2014) 0.80
The Methylome of Soybean Roots during the Compatible Interaction with the Soybean Cyst Nematode. Plant Physiol (2015) 0.80
Bioinformatic analysis of epigenetic and microRNA mediated regulation of drought responsive genes in rice. PLoS One (2012) 0.79
DNA Methylation and Chromatin Regulation during Fleshy Fruit Development and Ripening. Front Plant Sci (2016) 0.77
Complex interplay among DNA modification, noncoding RNA expression and protein-coding RNA expression in Salvia miltiorrhiza chloroplast genome. PLoS One (2014) 0.77
Analysis of the leaf methylomes of parents and their hybrids provides new insight into hybrid vigor in Populus deltoides. BMC Genet (2014) 0.77
Low temperature-induced DNA hypermethylation attenuates expression of RhAG, an AGAMOUS homolog, and increases petal number in rose (Rosa hybrida). BMC Plant Biol (2015) 0.77
Eyes on DNA methylation: current evidence for DNA methylation in ocular development and disease. J Ocul Biol Dis Infor (2012) 0.77
HSI2/VAL1 PHD-like domain promotes H3K27 trimethylation to repress the expression of seed maturation genes and complex transgenes in Arabidopsis seedlings. BMC Plant Biol (2014) 0.76
Molecular mechanisms of epigenetic variation in plants. Int J Mol Sci (2012) 0.76
High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development. Nat Genet (2017) 0.76
Cyst Nematode Parasitism Induces Dynamic Changes in the Root Epigenome. Plant Physiol (2017) 0.75
Hydroxymethylation of DNA: an epigenetic marker. EXCLI J (2014) 0.75
Histone Lysine-to-Methionine Mutations Reduce Histone Methylation and Cause Developmental Pleiotropy. Plant Physiol (2017) 0.75
Response and Tolerance Mechanism of Cotton Gossypium hirsutum L. to Elevated Temperature Stress: A Review. Front Plant Sci (2016) 0.75
Insights into chromatin structure and dynamics in plants. Biology (Basel) (2013) 0.75
Plant Stress Responses and Phenotypic Plasticity in the Epigenomics Era: Perspectives on the Grapevine Scenario, a Model for Perennial Crop Plants. Front Plant Sci (2017) 0.75
PHDs govern plant development. Plant Signal Behav (2015) 0.75
Rosaceae Fruit Development, Ripening and Post-harvest: An Epigenetic Perspective. Front Plant Sci (2017) 0.75
Light-regulated transcriptional networks in higher plants. Nat Rev Genet (2007) 4.82
Coordinated regulation of Arabidopsis thaliana development by light and gibberellins. Nature (2008) 4.71
Analysis of transcription factor HY5 genomic binding sites revealed its hierarchical role in light regulation of development. Plant Cell (2007) 4.13
The COP9 signalosome. Annu Rev Cell Dev Biol (2003) 3.25
COP1 - from plant photomorphogenesis to mammalian tumorigenesis. Trends Cell Biol (2005) 3.01
The COP1-SPA1 interaction defines a critical step in phytochrome A-mediated regulation of HY5 activity. Genes Dev (2003) 2.97
Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids. Plant Cell (2010) 2.92
Phosphate starvation triggers distinct alterations of genome expression in Arabidopsis roots and leaves. Plant Physiol (2003) 2.75
Genome-wide transcription analyses in rice using tiling microarrays. Nat Genet (2005) 2.39
Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and small RNA transcriptomes in maize. Plant Cell (2009) 2.39
COP1 and ELF3 control circadian function and photoperiodic flowering by regulating GI stability. Mol Cell (2008) 2.34
Light regulates COP1-mediated degradation of HFR1, a transcription factor essential for light signaling in Arabidopsis. Plant Cell (2005) 2.31
A molecular framework of light-controlled phytohormone action in Arabidopsis. Curr Biol (2012) 2.02
Structural basis for the specific recognition of methylated histone H3 lysine 4 by the WD-40 protein WDR5. Mol Cell (2006) 2.02
The photomorphogenic repressors COP1 and DET1: 20 years later. Trends Plant Sci (2012) 2.02
Plant hormone signaling lightens up: integrators of light and hormones. Curr Opin Plant Biol (2010) 1.95
An alternative tandem affinity purification strategy applied to Arabidopsis protein complex isolation. Plant J (2005) 1.93
Arabidopsis CULLIN4 Forms an E3 Ubiquitin Ligase with RBX1 and the CDD Complex in Mediating Light Control of Development. Plant Cell (2006) 1.92
Genome-wide analysis of DNA methylation and gene expression changes in two Arabidopsis ecotypes and their reciprocal hybrids. Plant Cell (2012) 1.91
Biochemical characterization of Arabidopsis complexes containing CONSTITUTIVELY PHOTOMORPHOGENIC1 and SUPPRESSOR OF PHYA proteins in light control of plant development. Plant Cell (2008) 1.85
High-resolution mapping of epigenetic modifications of the rice genome uncovers interplay between DNA methylation, histone methylation, and gene expression. Plant Cell (2008) 1.85
Conservation and divergence of light-regulated genome expression patterns during seedling development in rice and Arabidopsis. Plant Cell (2005) 1.84
Organ-specific expression of Arabidopsis genome during development. Plant Physiol (2005) 1.83
The COP9 signalosome interacts physically with SCF COI1 and modulates jasmonate responses. Plant Cell (2003) 1.80
Genome-wide ORFeome cloning and analysis of Arabidopsis transcription factor genes. Plant Physiol (2004) 1.79
Characterization of Arabidopsis and rice DWD proteins and their roles as substrate receptors for CUL4-RING E3 ubiquitin ligases. Plant Cell (2008) 1.77
Global genome expression analysis of rice in response to drought and high-salinity stresses in shoot, flag leaf, and panicle. Plant Mol Biol (2007) 1.76
Interaction of Arabidopsis DET1 with CCA1 and LHY in mediating transcriptional repression in the plant circadian clock. Mol Cell (2011) 1.75
Arabidopsis COP10 forms a complex with DDB1 and DET1 in vivo and enhances the activity of ubiquitin conjugating enzymes. Genes Dev (2004) 1.72
A microarray analysis of the rice transcriptome and its comparison to Arabidopsis. Genome Res (2005) 1.71
Arabidopsis FHY3 defines a key phytochrome A signaling component directly interacting with its homologous partner FAR1. EMBO J (2002) 1.66
Arabidopsis CULLIN4-damaged DNA binding protein 1 interacts with CONSTITUTIVELY PHOTOMORPHOGENIC1-SUPPRESSOR OF PHYA complexes to regulate photomorphogenesis and flowering time. Plant Cell (2010) 1.66
The diverse roles of ubiquitin and the 26S proteasome in the life of plants. Nat Rev Genet (2003) 1.61
Arabidopsis CAND1, an unmodified CUL1-interacting protein, is involved in multiple developmental pathways controlled by ubiquitin/proteasome-mediated protein Degradation. Plant Cell (2004) 1.60
Biochemical evidence for ubiquitin ligase activity of the Arabidopsis COP1 interacting protein 8 (CIP8). Plant J (2002) 1.59
Gibberellins modulate light signaling pathways to prevent Arabidopsis seedling de-etiolation in darkness. Plant J (2007) 1.58
From seed to seed: the role of photoreceptors in Arabidopsis development. Dev Biol (2003) 1.54
An annotation update via cDNA sequence analysis and comprehensive profiling of developmental, hormonal or environmental responsiveness of the Arabidopsis AP2/EREBP transcription factor gene family. Plant Mol Biol (2005) 1.53
Genomic evidence for COP1 as a repressor of light-regulated gene expression and development in Arabidopsis. Plant Cell (2002) 1.52
COP9 signalosome subunit 8 is essential for peripheral T cell homeostasis and antigen receptor-induced entry into the cell cycle from quiescence. Nat Immunol (2007) 1.48
Biochemical insights on degradation of Arabidopsis DELLA proteins gained from a cell-free assay system. Plant Cell (2009) 1.48
Coordinated transcriptional regulation underlying the circadian clock in Arabidopsis. Nat Cell Biol (2011) 1.45
Rice 2020: a call for an international coordinated effort in rice functional genomics. Mol Plant (2008) 1.45
A genome-wide transcription analysis reveals a close correlation of promoter INDEL polymorphism and heterotic gene expression in rice hybrids. Mol Plant (2008) 1.44
Dynamic landscapes of four histone modifications during deetiolation in Arabidopsis. Plant Cell (2009) 1.43
The COP9 signalosome interacts with SCF UFO and participates in Arabidopsis flower development. Plant Cell (2003) 1.43
Arabidopsis FHY3 and HY5 positively mediate induction of COP1 transcription in response to photomorphogenic UV-B light. Plant Cell (2012) 1.41
Global identification and characterization of transcriptionally active regions in the rice genome. PLoS One (2007) 1.41
Role of the MPN subunits in COP9 signalosome assembly and activity, and their regulatory interaction with Arabidopsis Cullin3-based E3 ligases. Plant Cell (2007) 1.40
Arabidopsis has two redundant Cullin3 proteins that are essential for embryo development and that interact with RBX1 and BTB proteins to form multisubunit E3 ubiquitin ligase complexes in vivo. Plant Cell (2005) 1.39
Analysis of the mutational effects of the COP/DET/FUS loci on genome expression profiles reveals their overlapping yet not identical roles in regulating Arabidopsis seedling development. Development (2003) 1.38
A high-density SNP genotyping array for rice biology and molecular breeding. Mol Plant (2013) 1.36
Mammalian DET1 regulates Cul4A activity and forms stable complexes with E2 ubiquitin-conjugating enzymes. Mol Cell Biol (2007) 1.34
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
Dissecting the phytochrome A-dependent signaling network in higher plants. Trends Plant Sci (2003) 1.32
Disruption of phytoene desaturase gene results in albino and dwarf phenotypes in Arabidopsis by impairing chlorophyll, carotenoid, and gibberellin biosynthesis. Cell Res (2007) 1.32
NMPP: a user-customized NimbleGen microarray data processing pipeline. Bioinformatics (2006) 1.30
Arabidopsis COP1/SPA1 complex and FHY1/FHY3 associate with distinct phosphorylated forms of phytochrome A in balancing light signaling. Mol Cell (2008) 1.29
DWA1 and DWA2, two Arabidopsis DWD protein components of CUL4-based E3 ligases, act together as negative regulators in ABA signal transduction. Plant Cell (2010) 1.28
A genome-wide analysis of blue-light regulation of Arabidopsis transcription factor gene expression during seedling development. Plant Physiol (2003) 1.27
Genome-wide binding site analysis of FAR-RED ELONGATED HYPOCOTYL3 reveals its novel function in Arabidopsis development. Plant Cell (2011) 1.27
Arabidopsis CSN5B interacts with VTC1 and modulates ascorbic acid synthesis. Plant Cell (2013) 1.25
Arabidopsis DDB1-CUL4 ASSOCIATED FACTOR1 forms a nuclear E3 ubiquitin ligase with DDB1 and CUL4 that is involved in multiple plant developmental processes. Plant Cell (2008) 1.23
Characterization of the last subunit of the Arabidopsis COP9 signalosome: implications for the overall structure and origin of the complex. Plant Cell (2003) 1.23
Targeted degradation of abscisic acid receptors is mediated by the ubiquitin ligase substrate adaptor DDA1 in Arabidopsis. Plant Cell (2014) 1.23
Arabidopsis transcription factor ELONGATED HYPOCOTYL5 plays a role in the feedback regulation of phytochrome A signaling. Plant Cell (2010) 1.22
The Arabidopsis chaperone J3 regulates the plasma membrane H+-ATPase through interaction with the PKS5 kinase. Plant Cell (2010) 1.18
A rice glutamate receptor-like gene is critical for the division and survival of individual cells in the root apical meristem. Plant Cell (2005) 1.18
F-box protein DOR functions as a novel inhibitory factor for abscisic acid-induced stomatal closure under drought stress in Arabidopsis,. Plant Physiol (2008) 1.18
A tiling microarray expression analysis of rice chromosome 4 suggests a chromosome-level regulation of transcription. Plant Cell (2005) 1.18
Geminiviruses subvert ubiquitination by altering CSN-mediated derubylation of SCF E3 ligase complexes and inhibit jasmonate signaling in Arabidopsis thaliana. Plant Cell (2011) 1.16
Development and application of a set of breeder-friendly SNP markers for genetic analyses and molecular breeding of rice (Oryza sativa L.). Theor Appl Genet (2011) 1.16
ABD1 is an Arabidopsis DCAF substrate receptor for CUL4-DDB1-based E3 ligases that acts as a negative regulator of abscisic acid signaling. Plant Cell (2014) 1.15
Evidence for a physical association of the COP9 signalosome, the proteasome, and specific SCF E3 ligases in vivo. Curr Biol (2003) 1.15
Conversion from CUL4-based COP1-SPA E3 apparatus to UVR8-COP1-SPA complexes underlies a distinct biochemical function of COP1 under UV-B. Proc Natl Acad Sci U S A (2013) 1.13
Phytochrome A mediates rapid red light-induced phosphorylation of Arabidopsis FAR-RED ELONGATED HYPOCOTYL1 in a low fluence response. Plant Cell (2009) 1.12
Major vault protein, in concert with constitutively photomorphogenic 1, negatively regulates c-Jun-mediated activator protein 1 transcription in mammalian cells. Cancer Res (2005) 1.12
The COP9 signalosome: an alternative lid for the 26S proteasome? Trends Cell Biol (2003) 1.11
The Arabidopsis CSN5A and CSN5B subunits are present in distinct COP9 signalosome complexes, and mutations in their JAMM domains exhibit differential dominant negative effects on development. Plant Cell (2004) 1.10
HFR1 sequesters PIF1 to govern the transcriptional network underlying light-initiated seed germination in Arabidopsis. Plant Cell (2013) 1.09
Tiling microarray analysis of rice chromosome 10 to identify the transcriptome and relate its expression to chromosomal architecture. Genome Biol (2005) 1.09
Functional characterization of the Arabidopsis ubiquitin-specific protease gene family reveals specific role and redundancy of individual members in development. Plant J (2008) 1.09
Nematode effector proteins: an emerging paradigm of parasitism. New Phytol (2013) 1.08
Histone modifications and expression of light-regulated genes in Arabidopsis are cooperatively influenced by changing light conditions. Plant Physiol (2008) 1.08
The development of protein microarrays and their applications in DNA-protein and protein-protein interaction analyses of Arabidopsis transcription factors. Mol Plant (2007) 1.05
Global identification of miRNAs and targets in Populus euphratica under salt stress. Plant Mol Biol (2013) 1.00
Analysis of trehalose-6-phosphate synthase (TPS) gene family suggests the formation of TPS complexes in rice. Plant Mol Biol (2011) 0.99
Ethylene-orchestrated circuitry coordinates a seedling's response to soil cover and etiolated growth. Proc Natl Acad Sci U S A (2014) 0.98
Ubiquitin-specific protease16 modulates salt tolerance in Arabidopsis by regulating Na(+)/H(+) antiport activity and serine hydroxymethyltransferase stability. Plant Cell (2012) 0.98
An arabidopsis promoter microarray and its initial usage in the identification of HY5 binding targets in vitro. Plant Mol Biol (2004) 0.98
Conservation and divergence of transcriptomic and epigenomic variation in maize hybrids. Genome Biol (2013) 0.98
The PP6 phosphatase regulates ABI5 phosphorylation and abscisic acid signaling in Arabidopsis. Plant Cell (2013) 0.97
A genome-wide transcriptional activity survey of rice transposable element-related genes. Genome Biol (2007) 0.96
Major emerging problems with minor meloidogyne species. Phytopathology (2013) 0.94
DWA3, an Arabidopsis DWD protein, acts as a negative regulator in ABA signal transduction. Plant Sci (2010) 0.94
Regulation of COP1 nuclear localization by the COP9 signalosome via direct interaction with CSN1. Plant J (2009) 0.93