Published in Nat Protoc on December 16, 2010
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Proteomics-based identification of low-abundance signaling and regulatory protein complexes in native plant tissues. Nat Protoc (2012) 0.91
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Global SUMO Proteome Responses Guide Gene Regulation, mRNA Biogenesis, and Plant Stress Responses. Front Plant Sci (2012) 0.89
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Unleashing the potential of the root hair cell as a single plant cell type model in root systems biology. Front Plant Sci (2013) 0.86
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Site-specific biotinylation of purified proteins using BirA. Methods Mol Biol (2015) 0.86
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Temporally and spatially restricted gene expression profiling. Curr Genomics (2014) 0.83
Signaling networks in palate development. Wiley Interdiscip Rev Syst Biol Med (2014) 0.83
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DNA demethylation is initiated in the central cells of Arabidopsis and rice. Proc Natl Acad Sci U S A (2016) 0.81
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'Memory and molecular turnover,' 30 years after inception. Epigenetics Chromatin (2014) 0.79
New tangles in the auxin signaling web. F1000Prime Rep (2015) 0.79
Myogenic conversion and transcriptional profiling of embryonic blastomeres in Caenorhabditis elegans. Methods (2011) 0.79
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The influence of DNA sequence on epigenome-induced pathologies. Epigenetics Chromatin (2012) 0.77
Technologies for systems-level analysis of specific cell types in plants. Plant Sci (2012) 0.77
Optimized Methods for the Isolation of Arabidopsis Female Central Cells and Their Nuclei. Mol Cells (2016) 0.77
Improved DNase-seq protocol facilitates high resolution mapping of DNase I hypersensitive sites in roots in Arabidopsis thaliana. Plant Methods (2015) 0.77
Plant chromatin warms up in Madrid: meeting summary of the 3rd European Workshop on Plant Chromatin 2013, Madrid, Spain. Epigenetics (2014) 0.77
Affinity-based isolation of tagged nuclei from Drosophila tissues for gene expression analysis. J Vis Exp (2014) 0.77
Nascent RNA sequencing reveals distinct features in plant transcription. Proc Natl Acad Sci U S A (2016) 0.77
pENCODE: a plant encyclopedia of DNA elements. Annu Rev Genet (2014) 0.77
Getting Down to Specifics: Profiling Gene Expression and Protein-DNA Interactions in a Cell Type-Specific Manner. Adv Genet (2015) 0.77
Emerging roles of long non-coding RNA in root developmental plasticity and regulation of phosphate homeostasis. Front Plant Sci (2015) 0.76
Chromatin remodeling during in vivo neural stem cells differentiating to neurons in early Drosophila embryos. Cell Death Differ (2016) 0.76
MOBE-ChIP: a large-scale chromatin immunoprecipitation assay for cell type-specific studies. Plant J (2015) 0.76
Chromatin remodeling during the in vivo glial differentiation in early Drosophila embryos. Sci Rep (2016) 0.76
Complementarity of medium-throughput in situ RNA hybridization and tissue-specific transcriptomics: case study of Arabidopsis seed development kinetics. Sci Rep (2016) 0.75
Decipher the Molecular Response of Plant Single Cell Types to Environmental Stresses. Biomed Res Int (2016) 0.75
BES1 regulates the localization of the brassinosteroid receptor BRL3 within the provascular tissue of the Arabidopsis primary root. J Exp Bot (2016) 0.75
Interspecies Gene Transfer as a Method for Understanding the Genetic Basis for Evolutionary Change: Progress, Pitfalls, and Prospects. Front Plant Sci (2015) 0.75
Integrating Large-Scale Data and RNA Technology to Protect Crops from Fungal Pathogens. Front Plant Sci (2016) 0.75
Epigenetic memory and cell fate reprogramming in plants. Regeneration (Oxf) (2017) 0.75
Editing the Neuronal Genome: a CRISPR View of Chromatin Regulation in Neuronal Development, Function, and Plasticity. Yale J Biol Med (2016) 0.75
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Epigenetic dysregulation of brainstem nuclei in the pathogenesis of Alzheimer's disease: looking in the correct place at the right time? Cell Mol Life Sci (2016) 0.75
Making Plants Break a Sweat: the Structure, Function, and Evolution of Plant Salt Glands. Front Plant Sci (2017) 0.75
cgChIP: a cell type- and gene-specific method for chromatin analysis. Methods Mol Biol (2014) 0.75
Cell-type specific cis-regulatory networks: insights from Hox transcription factors. Fly (Austin) (2012) 0.75
Applying the INTACT method to purify endosperm nuclei and to generate parental-specific epigenome profiles. Nat Protoc (2017) 0.75
Adipocyte nuclei captured from VAT and SAT. BMC Obes (2016) 0.75
Recent advances in functional assays of transcriptional enhancers. Genomics (2015) 0.75
Plants: a tool box of cell-based assays. Nat Methods (2016) 0.75
Biochemical isolation of myonuclei employed to define changes to the myonuclear proteome that occur with aging. Aging Cell (2017) 0.75
Rapid flow cytometric analysis of the cell cycle in intact plant tissues. Science (1983) 10.84
A gene expression map of the Arabidopsis root. Science (2003) 9.95
A translational profiling approach for the molecular characterization of CNS cell types. Cell (2008) 8.69
Chromosomal clustering of muscle-expressed genes in Caenorhabditis elegans. Nature (2002) 8.32
Genome-scale profiling of histone H3.3 replacement patterns. Nat Genet (2005) 7.22
A minimal peptide substrate in biotin holoenzyme synthetase-catalyzed biotinylation. Protein Sci (1999) 6.05
Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks. Nature (2008) 4.20
Strong, constitutive expression of the Arabidopsis ACT2/ACT8 actin subclass in vegetative tissues. Plant J (1996) 4.08
The homeobox gene GLABRA2 is required for position-dependent cell differentiation in the root epidermis of Arabidopsis thaliana. Development (1996) 3.59
Profiling histone modification patterns in plants using genomic tiling microarrays. Nat Methods (2005) 3.28
Cell-specific nitrogen responses mediate developmental plasticity. Proc Natl Acad Sci U S A (2008) 3.17
Profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis. Proc Natl Acad Sci U S A (2009) 2.77
Cell type-specific expression profiling in plants via cell sorting of protoplasts from fluorescent reporter lines. Nat Methods (2005) 2.62
A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies. Nat Genet (2009) 2.53
Atlas of gene expression in the developing kidney at microanatomic resolution. Dev Cell (2008) 2.44
Identification of genes expressed in C. elegans touch receptor neurons. Nature (2002) 2.39
A simple method for gene expression and chromatin profiling of individual cell types within a tissue. Dev Cell (2010) 2.24
TU-tagging: cell type-specific RNA isolation from intact complex tissues. Nat Methods (2009) 1.90
A domain unique to plant RanGAP is responsible for its targeting to the plant nuclear rim. Proc Natl Acad Sci U S A (2001) 1.72
Global characterization of cell-specific gene expression through fluorescence-activated sorting of nuclei. Plant Physiol (2008) 1.44
The ancient subclasses of Arabidopsis Actin Depolymerizing Factor genes exhibit novel and differential expression. Plant J (2007) 1.42
Comparison of the contributions of the nuclear and cytoplasmic compartments to global gene expression in human cells. BMC Genomics (2007) 1.30
The nuclear pore protein AtTPR is required for RNA homeostasis, flowering time, and auxin signaling. Plant Physiol (2007) 1.26
Directed differentiation of pluripotent stem cells: from developmental biology to therapeutic applications. Cold Spring Harb Symp Quant Biol (2009) 1.25
A review of gene expression profiling of human embryonic stem cell lines and their differentiated progeny. Curr Stem Cell Res Ther (2009) 1.12
Gene expression profiling of embryonic stem cells leads to greater understanding of pluripotency and early developmental events. Biol Reprod (2004) 1.10
Going green: plants' alternative way to position the Ran gradient. J Microsc (2008) 0.94
SIFT: Predicting amino acid changes that affect protein function. Nucleic Acids Res (2003) 52.26
Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc (2009) 38.62
Accounting for human polymorphisms predicted to affect protein function. Genome Res (2002) 14.10
Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science (2010) 12.39
Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat Genet (2006) 11.88
Unlocking the secrets of the genome. Nature (2009) 11.80
Predicting the effects of amino acid substitutions on protein function. Annu Rev Genomics Hum Genet (2006) 9.80
The histone variant H3.3 marks active chromatin by replication-independent nucleosome assembly. Mol Cell (2002) 9.80
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science (2010) 9.78
The epigenetic progenitor origin of human cancer. Nat Rev Genet (2006) 9.65
Genome-scale profiling of histone H3.3 replacement patterns. Nat Genet (2005) 7.22
Histone H3.3 is enriched in covalent modifications associated with active chromatin. Proc Natl Acad Sci U S A (2004) 4.88
Genome-wide kinetics of nucleosome turnover determined by metabolic labeling of histones. Science (2010) 4.72
Centromeric nucleosomes induce positive DNA supercoils. Cell (2009) 4.57
DNA demethylation in the Arabidopsis genome. Proc Natl Acad Sci U S A (2007) 4.55
SIFT web server: predicting effects of amino acid substitutions on proteins. Nucleic Acids Res (2012) 4.45
Histone variants--ancient wrap artists of the epigenome. Nat Rev Mol Cell Biol (2010) 4.45
Large-scale discovery of induced point mutations with high-throughput TILLING. Genome Res (2003) 4.39
Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks. Nature (2008) 4.20
Histone replacement marks the boundaries of cis-regulatory domains. Science (2007) 4.06
Spectrum of chemically induced mutations from a large-scale reverse-genetic screen in Arabidopsis. Genetics (2003) 3.70
Sequencing of a rice centromere uncovers active genes. Nat Genet (2004) 3.66
CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primer) PCR primer design. Nucleic Acids Res (2003) 3.55
DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes. Curr Biol (2005) 3.54
Phylogenomics of the nucleosome. Nat Struct Biol (2003) 3.52
DNA demethylation by DNA repair. Trends Genet (2009) 3.49
Genome-wide profiling of DNA methylation reveals transposon targets of CHROMOMETHYLASE3. Curr Biol (2002) 3.37
Extensive demethylation of repetitive elements during seed development underlies gene imprinting. Science (2009) 3.33
A comprehensive map of insulator elements for the Drosophila genome. PLoS Genet (2010) 3.25
Tetrameric structure of centromeric nucleosomes in interphase Drosophila cells. PLoS Biol (2007) 3.25
Histone H3 variants specify modes of chromatin assembly. Proc Natl Acad Sci U S A (2002) 3.06
Centromeric localization and adaptive evolution of an Arabidopsis histone H3 variant. Plant Cell (2002) 2.72
Regulation of nucleosome dynamics by histone modifications. Nat Struct Mol Biol (2013) 2.71
Spreading of silent chromatin: inaction at a distance. Nat Rev Genet (2006) 2.64
Discovery of induced point mutations in maize genes by TILLING. BMC Plant Biol (2004) 2.57
Major evolutionary transitions in centromere complexity. Cell (2009) 2.49
Discovery of chemically induced mutations in rice by TILLING. BMC Plant Biol (2007) 2.46
Efficient discovery of DNA polymorphisms in natural populations by Ecotilling. Plant J (2004) 2.45
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Epigenome characterization at single base-pair resolution. Proc Natl Acad Sci U S A (2011) 2.22
Conflict begets complexity: the evolution of centromeres. Curr Opin Genet Dev (2002) 2.14
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TILLING to detect induced mutations in soybean. BMC Plant Biol (2008) 2.13
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A protocol for TILLING and Ecotilling in plants and animals. Nat Protoc (2006) 2.09
Chromatin immunoprecipitation reveals that the 180-bp satellite repeat is the key functional DNA element of Arabidopsis thaliana centromeres. Genetics (2003) 2.05
Maize centromeres: organization and functional adaptation in the genetic background of oat. Plant Cell (2004) 2.01
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Adaptive evolution of centromere proteins in plants and animals. J Biol (2004) 1.90
A unified phylogeny-based nomenclature for histone variants. Epigenetics Chromatin (2012) 1.82
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High-throughput TILLING for functional genomics. Methods Mol Biol (2003) 1.70
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Epigenetic consequences of nucleosome dynamics. Cell (2002) 1.60
Doxorubicin enhances nucleosome turnover around promoters. Curr Biol (2013) 1.58
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Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis. Genome Biol (2005) 1.55
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ISWI and CHD chromatin remodelers bind promoters but act in gene bodies. PLoS Genet (2013) 1.25
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