Published in Proc Natl Acad Sci U S A on October 04, 2010
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An effect of DNA sequence on nucleosome occupancy and removal. Nat Struct Mol Biol (2011) 0.93
Histone H3R2 symmetric dimethylation and histone H3K4 trimethylation are tightly correlated in eukaryotic genomes. Cell Rep (2012) 0.92
Topoisomerases, chromatin and transcription termination. Transcription (2011) 0.91
Transcriptional activation of yeast genes disrupts intragenic nucleosome phasing. Nucleic Acids Res (2012) 0.91
Terminate and make a loop: regulation of transcriptional directionality. Trends Biochem Sci (2014) 0.91
The Roles of the Paf1 Complex and Associated Histone Modifications in Regulating Gene Expression. Genet Res Int (2011) 0.90
Physical properties of naked DNA influence nucleosome positioning and correlate with transcription start and termination sites in yeast. BMC Genomics (2011) 0.89
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A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome Res (2008) 7.89
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Intrinsic histone-DNA interactions and low nucleosome density are important for preferential accessibility of promoter regions in yeast. Mol Cell (2005) 6.17
Nucleosomes unfold completely at a transcriptionally active promoter. Mol Cell (2003) 5.94
Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation. PLoS Biol (2008) 5.88
Distinct modes of regulation by chromatin encoded through nucleosome positioning signals. PLoS Comput Biol (2008) 5.71
Histones are first hyperacetylated and then lose contact with the activated PHO5 promoter. Mol Cell (2003) 5.41
Nucleosome positioning signals in genomic DNA. Genome Res (2007) 4.99
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The anchor-away technique: rapid, conditional establishment of yeast mutant phenotypes. Mol Cell (2008) 3.06
Evidence for distinct mechanisms facilitating transcript elongation through chromatin in vivo. EMBO J (2004) 2.63
A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome. Genome Biol (2009) 2.58
DNAase I, DNAase II and staphylococcal nuclease cut at different, yet symmetrically located, sites in the nucleosome core. Cell (1978) 2.48
Histone acetylation at promoters is differentially affected by specific activators and repressors. Mol Cell Biol (2001) 2.40
A RSC/nucleosome complex determines chromatin architecture and facilitates activator binding. Cell (2010) 2.00
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High-throughput sequencing reveals a simple model of nucleosome energetics. Proc Natl Acad Sci U S A (2010) 1.34
Extensive chromatin fragmentation improves enrichment of protein binding sites in chromatin immunoprecipitation experiments. Nucleic Acids Res (2008) 1.23
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
Model-based analysis of ChIP-Seq (MACS). Genome Biol (2008) 51.63
A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science (2002) 42.78
Genome-wide analysis of estrogen receptor binding sites. Nat Genet (2006) 18.63
Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Nucleic Acids Res (2011) 16.53
Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell (2004) 16.15
Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1. Cell (2005) 14.32
FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription. Cell (2008) 14.18
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Model-based analysis of tiling-arrays for ChIP-chip. Proc Natl Acad Sci U S A (2006) 13.68
WEGO: a web tool for plotting GO annotations. Nucleic Acids Res (2006) 13.06
Targeted recruitment of Set1 histone methylase by elongating Pol II provides a localized mark and memory of recent transcriptional activity. Mol Cell (2003) 11.78
Sequencing of 50 human exomes reveals adaptation to high altitude. Science (2010) 11.27
An epigenetic switch involving NF-kappaB, Lin28, Let-7 MicroRNA, and IL6 links inflammation to cell transformation. Cell (2009) 10.09
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science (2010) 9.78
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res (2012) 9.13
Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2. Nature (2010) 8.87
The genome of the cucumber, Cucumis sativus L. Nat Genet (2009) 8.19
Differential chromatin marking of introns and expressed exons by H3K36me3. Nat Genet (2009) 8.11
An abundance of rare functional variants in 202 drug target genes sequenced in 14,002 people. Science (2012) 7.94
The Genomes of Oryza sativa: a history of duplications. PLoS Biol (2005) 7.67
Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells. Nature (2011) 7.43
Model-based analysis of two-color arrays (MA2C). Genome Biol (2007) 7.28
Androgen receptor regulates a distinct transcription program in androgen-independent prostate cancer. Cell (2009) 7.09
Metformin selectively targets cancer stem cells, and acts together with chemotherapy to block tumor growth and prolong remission. Cancer Res (2009) 6.74
A draft sequence for the genome of the domesticated silkworm (Bombyx mori). Science (2004) 6.62
TREX is a conserved complex coupling transcription with messenger RNA export. Nature (2002) 6.53
Epidemiological serosurvey of hepatitis B in China--declining HBV prevalence due to hepatitis B vaccination. Vaccine (2009) 6.30
Intrinsic histone-DNA interactions and low nucleosome density are important for preferential accessibility of promoter regions in yeast. Mol Cell (2005) 6.17
A hierarchical network of transcription factors governs androgen receptor-dependent prostate cancer growth. Mol Cell (2007) 5.99
Nucleosome dynamics define transcriptional enhancers. Nat Genet (2010) 5.94
A circadian rhythm orchestrated by histone deacetylase 3 controls hepatic lipid metabolism. Science (2011) 5.91
CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res (2007) 5.88
STAT3 activation of miR-21 and miR-181b-1 via PTEN and CYLD are part of the epigenetic switch linking inflammation to cancer. Mol Cell (2010) 5.67
Methylation of H3-lysine 79 is mediated by a new family of HMTases without a SET domain. Curr Biol (2002) 5.53
Chromatin structure analyses identify miRNA promoters. Genes Dev (2008) 5.40
Tsc tumour suppressor proteins antagonize amino-acid-TOR signalling. Nat Cell Biol (2002) 5.37
The oyster genome reveals stress adaptation and complexity of shell formation. Nature (2012) 5.30
A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. Nature (2004) 5.24
High-throughput mapping of the chromatin structure of human promoters. Nat Biotechnol (2007) 5.24
Nucleosome positioning signals in genomic DNA. Genome Res (2007) 4.99
PPARgamma and C/EBP factors orchestrate adipocyte biology via adjacent binding on a genome-wide scale. Genes Dev (2008) 4.83
Eaf3 chromodomain interaction with methylated H3-K36 links histone deacetylation to Pol II elongation. Mol Cell (2005) 4.77
Integrating regulatory motif discovery and genome-wide expression analysis. Proc Natl Acad Sci U S A (2003) 4.74
Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo. Nat Struct Mol Biol (2009) 4.64
A mammalian organelle map by protein correlation profiling. Cell (2006) 4.54
Relationships between p63 binding, DNA sequence, transcription activity, and biological function in human cells. Mol Cell (2006) 4.51
The JAK2/STAT3 signaling pathway is required for growth of CD44⁺CD24⁻ stem cell-like breast cancer cells in human tumors. J Clin Invest (2011) 4.41
RePS: a sequence assembler that masks exact repeats identified from the shotgun data. Genome Res (2002) 4.35
An HNF4α-miRNA inflammatory feedback circuit regulates hepatocellular oncogenesis. Cell (2011) 4.29
CEAS: cis-regulatory element annotation system. Bioinformatics (2009) 4.26
Cistrome: an integrative platform for transcriptional regulation studies. Genome Biol (2011) 4.13
Formation of ArF from LPdAr(F): catalytic conversion of aryl triflates to aryl fluorides. Science (2009) 4.13
Production of offspring from a germline stem cell line derived from neonatal ovaries. Nat Cell Biol (2009) 4.11
Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Res (2008) 4.08
Lysine methylation within the globular domain of histone H3 by Dot1 is important for telomeric silencing and Sir protein association. Genes Dev (2002) 4.07
Evidence for eviction and rapid deposition of histones upon transcriptional elongation by RNA polymerase II. Mol Cell Biol (2004) 4.06
A transcriptional signature and common gene networks link cancer with lipid metabolism and diverse human diseases. Cancer Cell (2010) 4.02
Distinction and relationship between elongation rate and processivity of RNA polymerase II in vivo. Mol Cell (2005) 4.00
Genome-wide location and regulated recruitment of the RSC nucleosome-remodeling complex. Genes Dev (2002) 3.93
An emerging recombinant human enterovirus 71 responsible for the 2008 outbreak of hand foot and mouth disease in Fuyang city of China. Virol J (2010) 3.90
EZH2 oncogenic activity in castration-resistant prostate cancer cells is Polycomb-independent. Science (2012) 3.74
Chromatin marks identify critical cell types for fine mapping complex trait variants. Nat Genet (2012) 3.67
Identifying ChIP-seq enrichment using MACS. Nat Protoc (2012) 3.60
Loss of miR-200 inhibition of Suz12 leads to polycomb-mediated repression required for the formation and maintenance of cancer stem cells. Mol Cell (2010) 3.53
Inducible formation of breast cancer stem cells and their dynamic equilibrium with non-stem cancer cells via IL6 secretion. Proc Natl Acad Sci U S A (2011) 3.42
Tumor cells disseminate early, but immunosurveillance limits metastatic outgrowth, in a mouse model of melanoma. J Clin Invest (2010) 3.41
8q24 prostate, breast, and colon cancer risk loci show tissue-specific long-range interaction with MYC. Proc Natl Acad Sci U S A (2010) 3.37
Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome. Genome Res (2010) 3.34
Decreased serum vitamin D levels in children with asthma are associated with increased corticosteroid use. J Allergy Clin Immunol (2010) 3.22
NONCODE: an integrated knowledge database of non-coding RNAs. Nucleic Acids Res (2005) 3.16
CEAS: cis-regulatory element annotation system. Nucleic Acids Res (2006) 3.15
Ubiquitination of histone H2B by Rad6 is required for efficient Dot1-mediated methylation of histone H3 lysine 79. J Biol Chem (2002) 3.14
A promiscuous intermediate underlies the evolution of LEAFY DNA binding specificity. Science (2014) 3.11
Lysine-79 of histone H3 is hypomethylated at silenced loci in yeast and mammalian cells: a potential mechanism for position-effect variegation. Proc Natl Acad Sci U S A (2003) 3.09
The Rtf1 component of the Paf1 transcriptional elongation complex is required for ubiquitination of histone H2B. J Biol Chem (2003) 3.08
A hidden Markov model for analyzing ChIP-chip experiments on genome tiling arrays and its application to p53 binding sequences. Bioinformatics (2005) 3.06
The FACT complex travels with elongating RNA polymerase II and is important for the fidelity of transcriptional initiation in vivo. Mol Cell Biol (2003) 3.03
New approach for earthquake/tsunami monitoring using dense GPS networks. Sci Rep (2013) 3.03
A nuclear receptor-like pathway regulating multidrug resistance in fungi. Nature (2008) 3.00
The transition between transcriptional initiation and elongation in E. coli is highly variable and often rate limiting. Mol Cell (2006) 2.99
C-H...pi, pi-pi and C-H...Cl interactions in chloro-substituted Schiff bases and 4-chloro-N-[4-(dimethylamino)benzylidene]aniline. Acta Crystallogr C (2004) 2.97
SIRT7 links H3K18 deacetylation to maintenance of oncogenic transformation. Nature (2012) 2.96
Integrative analysis of HIF binding and transactivation reveals its role in maintaining histone methylation homeostasis. Proc Natl Acad Sci U S A (2009) 2.95
Hog1 kinase converts the Sko1-Cyc8-Tup1 repressor complex into an activator that recruits SAGA and SWI/SNF in response to osmotic stress. Mol Cell (2002) 2.93
Close association of RNA polymerase II and many transcription factors with Pol III genes. Proc Natl Acad Sci U S A (2010) 2.90