Published in Genome Biol on April 15, 2010
A double take on bivalent promoters. Genes Dev (2013) 2.79
The Pan-Cancer analysis of pseudogene expression reveals biologically and clinically relevant tumour subtypes. Nat Commun (2014) 2.48
Polycomb repressive complex 2 controls the embryo-to-seedling phase transition. PLoS Genet (2011) 1.79
The stem cell niche: lessons from the Drosophila testis. Development (2011) 1.67
Dynamic regulation of alternative splicing and chromatin structure in Drosophila gonads revealed by RNA-seq. Cell Res (2010) 1.64
Protein identification using customized protein sequence databases derived from RNA-Seq data. J Proteome Res (2011) 1.62
Reprogramming of Yersinia from virulent to persistent mode revealed by complex in vivo RNA-seq analysis. PLoS Pathog (2015) 1.53
mRNA and Small RNA Transcriptomes Reveal Insights into Dynamic Homoeolog Regulation of Allopolyploid Heterosis in Nascent Hexaploid Wheat. Plant Cell (2014) 1.33
Poised RNA polymerase II changes over developmental time and prepares genes for future expression. Cell Rep (2012) 1.25
EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era. Nucleic Acids Res (2012) 1.17
Genome-wide chromatin occupancy analysis reveals a role for ASH2 in transcriptional pausing. Nucleic Acids Res (2011) 1.08
Sequential changes at differentiation gene promoters as they become active in a stem cell lineage. Development (2011) 1.05
H2B monoubiquitylation is a 5'-enriched active transcription mark and correlates with exon-intron structure in human cells. Genome Res (2012) 1.02
The transcriptome profile of the mosquito Culex quinquefasciatus following permethrin selection. PLoS One (2012) 0.90
Epigenetic regulation of germ cell differentiation. Curr Opin Cell Biol (2010) 0.87
The Drosophila BCL6 homolog Ken and Barbie promotes somatic stem cell self-renewal in the testis niche. Dev Biol (2012) 0.87
Histone demethylase dUTX antagonizes JAK-STAT signaling to maintain proper gene expression and architecture of the Drosophila testis niche. Development (2013) 0.86
Transcription termination between polo and snap, two closely spaced tandem genes of D. melanogaster. Transcription (2012) 0.86
chroGPS, a global chromatin positioning system for the functional analysis and visualization of the epigenome. Nucleic Acids Res (2013) 0.84
Recruiting polycomb to chromatin. Int J Biochem Cell Biol (2015) 0.83
Genome-wide and cell-specific epigenetic analysis challenges the role of polycomb in Drosophila spermatogenesis. PLoS Genet (2013) 0.81
The histone demethylase dKDM5/LID interacts with the SIN3 histone deacetylase complex and shares functional similarities with SIN3. Epigenetics Chromatin (2016) 0.80
Genome-wide identification of chromatin transitional regions reveals diverse mechanisms defining the boundary of facultative heterochromatin. PLoS One (2013) 0.80
Transcriptional regulation during Drosophila spermatogenesis. Spermatogenesis (2012) 0.78
Disruption of Methionine Metabolism in Drosophila melanogaster Impacts Histone Methylation and Results in Loss of Viability. G3 (Bethesda) (2015) 0.78
Arpeggio: harmonic compression of ChIP-seq data reveals protein-chromatin interaction signatures. Nucleic Acids Res (2013) 0.77
Chromatin Immunoprecipitation (ChIP) using Drosophila tissue. J Vis Exp (2012) 0.76
Functional Interaction between HEXIM and Hedgehog Signaling during Drosophila Wing Development. PLoS One (2016) 0.75
The Transcriptional Corepressor SIN3 Directly Regulates Genes Involved in Methionine Catabolism and Affects Histone Methylation, Linking Epigenetics and Metabolism. J Biol Chem (2016) 0.75
Enhancer of polycomb coordinates multiple signaling pathways to promote both cyst and germline stem cell differentiation in the Drosophila adult testis. PLoS Genet (2017) 0.75
Comparative analysis and modeling of the severity of steatohepatitis in DDC-treated mouse strains. PLoS One (2014) 0.75
Integrative analysis with ChIP-seq advances the limits of transcript quantification from RNA-seq. Genome Res (2016) 0.75
Temporal Gene Expression Profiles of Pre Blood-Fed Adult Females Immediately Following Eclosion in the Southern House Mosquito Culex Quinquefasciatus. Int J Biol Sci (2015) 0.75
Polycomb group gene E(z) is required for spermatogonial dedifferentiation in Drosophila adult testis. J Mol Biol (2017) 0.75
The antenna transcriptome changes in mosquito Anopheles sinensis, pre- and post- blood meal. PLoS One (2017) 0.75
Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods (2008) 126.81
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
RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet (2009) 58.77
A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell (2006) 48.80
A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science (2008) 29.99
Control of developmental regulators by Polycomb in human embryonic stem cells. Cell (2006) 28.21
Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature (2006) 25.90
Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science (2002) 24.31
A chromatin landmark and transcription initiation at most promoters in human cells. Cell (2007) 23.41
Dynamic regulation of nucleosome positioning in the human genome. Cell (2008) 15.60
Stem cells, the molecular circuitry of pluripotency and nuclear reprogramming. Cell (2008) 14.17
The Polycomb group protein EZH2 directly controls DNA methylation. Nature (2005) 13.67
Histone methyltransferase activity of a Drosophila Polycomb group repressor complex. Cell (2002) 13.05
Epigenetic regulation of cellular memory by the Polycomb and Trithorax group proteins. Annu Rev Genet (2004) 11.31
Global mapping of H3K4me3 and H3K27me3 reveals specificity and plasticity in lineage fate determination of differentiating CD4+ T cells. Immunity (2009) 9.73
RNA polymerase is poised for activation across the genome. Nat Genet (2007) 9.57
RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo. Nat Genet (2007) 9.56
Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation. Cell Stem Cell (2009) 8.62
Whole-genome analysis of histone H3 lysine 4 and lysine 27 methylation in human embryonic stem cells. Cell Stem Cell (2007) 8.59
A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics (2009) 8.33
Whole-genome mapping of histone H3 Lys4 and 27 trimethylations reveals distinct genomic compartments in human embryonic stem cells. Cell Stem Cell (2007) 7.05
Ring1-mediated ubiquitination of H2A restrains poised RNA polymerase II at bivalent genes in mouse ES cells. Nat Cell Biol (2007) 6.30
Epigenetic codes for heterochromatin formation and silencing: rounding up the usual suspects. Cell (2002) 6.25
Polycomb/Trithorax response elements and epigenetic memory of cell identity. Development (2007) 4.80
Genome-wide approaches to studying chromatin modifications. Nat Rev Genet (2008) 4.28
DNA methylation in Drosophila melanogaster. Nature (2000) 3.46
Male and female Drosophila germline stem cells: two versions of immortality. Science (2007) 3.31
Functional anatomy of polycomb and trithorax chromatin landscapes in Drosophila embryos. PLoS Biol (2009) 3.24
Long-range chromosomal interactions regulate the timing of the transition between poised and active gene expression. EMBO J (2007) 2.99
PcG proteins, DNA methylation, and gene repression by chromatin looping. PLoS Biol (2008) 2.85
A hierarchy of H3K4me3 and H3K27me3 acquisition in spatial gene regulation in Xenopus embryos. Dev Cell (2009) 2.84
Molecular control of pluripotency. Curr Opin Genet Dev (2006) 2.75
bag-of-marbles: a Drosophila gene required to initiate both male and female gametogenesis. Genes Dev (1990) 2.71
DNA sequence requirements for generating paused polymerase at the start of hsp70. Genes Dev (1992) 2.63
Zfh-1 controls somatic stem cell self-renewal in the Drosophila testis and nonautonomously influences germline stem cell self-renewal. Cell Stem Cell (2008) 2.62
Genomic location analysis by ChIP-Seq. J Cell Biochem (2009) 2.44
The histone methyltransferases Trithorax and Ash1 prevent transcriptional silencing by Polycomb group proteins. EMBO Rep (2004) 2.36
Testis-specific TAF homologs collaborate to control a tissue-specific transcription program. Development (2004) 2.35
Characterization of human epigenomes. Curr Opin Genet Dev (2009) 2.17
Alternative epigenetic chromatin states of polycomb target genes. PLoS Genet (2010) 2.15
Tissue-specific TAFs counteract Polycomb to turn on terminal differentiation. Science (2005) 2.13
Structural basis of transcription: mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA. Mol Cell (2009) 2.00
Differential H3K4 methylation identifies developmentally poised hematopoietic genes. Dev Cell (2008) 1.89
bag-of-marbles and benign gonial cell neoplasm act in the germline to restrict proliferation during Drosophila spermatogenesis. Development (1997) 1.86
ASH1, a Drosophila trithorax group protein, is required for methylation of lysine 4 residues on histone H3. Proc Natl Acad Sci U S A (2003) 1.84
Immediate mediators of the inflammatory response are poised for gene activation through RNA polymerase II stalling. Proc Natl Acad Sci U S A (2009) 1.83
Genetic control of cell proliferation and differentiation in Drosophila spermatogenesis. Semin Cell Dev Biol (1998) 1.68
Dynamic regulation of alternative splicing and chromatin structure in Drosophila gonads revealed by RNA-seq. Cell Res (2010) 1.64
Searching chromatin for stem cell identity. Cell (2006) 1.40
Novel regulators revealed by profiling Drosophila testis stem cells within their niche. Dev Biol (2006) 1.37
Drosophila proteins related to vertebrate DNA (5-cytosine) methyltransferases. Proc Natl Acad Sci U S A (1999) 1.30
RNA polymerase II elongation complexes paused after the synthesis of 15- or 35-base transcripts have different structures. Mol Cell Biol (1991) 1.29
The active migration of Drosophila primordial germ cells. Development (1995) 1.26
Germ cells are forever. Cell (2008) 1.18
The putative Drosophila methyltransferase gene dDnmt2 is contained in a transposon-like element and is expressed specifically in ovaries. Mech Dev (2000) 1.15
Bmi1 cooperates with Dnmt1-associated protein 1 in gene silencing. Biochem Biophys Res Commun (2006) 1.14
Downstream DNA selectively affects a paused conformation of human RNA polymerase II. J Mol Biol (2004) 1.08
Sequence-specific termination by T7 RNA polymerase requires formation of paused conformation prior to the point of RNA release. Genes Cells (2001) 0.88
The curious case of bivalent marks. Dev Cell (2009) 0.87
Stem cells: what can we learn from flies? Fly (Austin) (2011) 0.86
Paused Pol II captures enhancer activity and acts as a potent insulator. Genes Dev (2009) 0.85
Quiet and poised: "silent" genes accumulate transcription machinery. PLoS Biol (2010) 0.77
High-resolution profiling of histone methylations in the human genome. Cell (2007) 85.74
Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet (2008) 18.28
Dynamic regulation of nucleosome positioning in the human genome. Cell (2008) 15.60
Global mapping of H3K4me3 and H3K27me3 reveals specificity and plasticity in lineage fate determination of differentiating CD4+ T cells. Immunity (2009) 9.73
Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. Nucleic Acids Res (2008) 8.89
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 clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics (2009) 8.33
Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains. Genome Res (2008) 7.41
Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping. Genes Dev (2005) 7.21
The microRNA miR-34a inhibits prostate cancer stem cells and metastasis by directly repressing CD44. Nat Med (2011) 6.85
c-Myc is a universal amplifier of expressed genes in lymphocytes and embryonic stem cells. Cell (2012) 6.49
Dual functions of Tet1 in transcriptional regulation in mouse embryonic stem cells. Nature (2011) 6.48
BMP4 initiates human embryonic stem cell differentiation to trophoblast. Nat Biotechnol (2002) 6.20
The genomic landscape of histone modifications in human T cells. Proc Natl Acad Sci U S A (2006) 6.09
Nucleosome dynamics define transcriptional enhancers. Nat Genet (2010) 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
PTEN tumor suppressor regulates p53 protein levels and activity through phosphatase-dependent and -independent mechanisms. Cancer Cell (2003) 5.13
dbCAN: a web resource for automated carbohydrate-active enzyme annotation. Nucleic Acids Res (2012) 4.91
Gene expression patterns in human embryonic stem cells and human pluripotent germ cell tumors. Proc Natl Acad Sci U S A (2003) 4.67
Genome-wide analysis of 5-hydroxymethylcytosine distribution reveals its dual function in transcriptional regulation in mouse embryonic stem cells. Genes Dev (2011) 4.45
Genome-wide approaches to studying chromatin modifications. Nat Rev Genet (2008) 4.28
An embryonic stem cell chromatin remodeling complex, esBAF, is an essential component of the core pluripotency transcriptional network. Proc Natl Acad Sci U S A (2009) 4.07
The novel marker, DOG1, is expressed ubiquitously in gastrointestinal stromal tumors irrespective of KIT or PDGFRA mutation status. Am J Pathol (2004) 3.84
The metabolic profile of tumors depends on both the responsible genetic lesion and tissue type. Cell Metab (2012) 3.81
Dynamic reprogramming of the kinome in response to targeted MEK inhibition in triple-negative breast cancer. Cell (2012) 3.77
Directed neural differentiation of human embryonic stem cells via an obligated primitive anterior stage. Stem Cells (2007) 3.71
A chemical probe selectively inhibits G9a and GLP methyltransferase activity in cells. Nat Chem Biol (2011) 3.60
Multigait soft robot. Proc Natl Acad Sci U S A (2011) 3.57
Hybrid DNA virus in Chinese patients with seronegative hepatitis discovered by deep sequencing. Proc Natl Acad Sci U S A (2013) 3.35
Gene expression patterns of human colon tops and basal crypts and BMP antagonists as intestinal stem cell niche factors. Proc Natl Acad Sci U S A (2007) 3.20
Topoisomerase inhibitors unsilence the dormant allele of Ube3a in neurons. Nature (2011) 3.19
Decoding global gene expression programs in liver cancer by noninvasive imaging. Nat Biotechnol (2007) 3.17
Molecular and epidemiologic trends of caliciviruses associated with outbreaks of acute gastroenteritis in the United States, 2000-2004. J Infect Dis (2005) 3.16
[GSDS: a gene structure display server]. Yi Chuan (2007) 3.02
Ultrafast dynamics of solute-solvent complexation observed at thermal equilibrium in real time. Science (2005) 2.88
IL-1 family members and STAT activators induce cytokine production by Th2, Th17, and Th1 cells. Proc Natl Acad Sci U S A (2009) 2.83
Brief communication: American ginseng reduces warfarin's effect in healthy patients: a randomized, controlled Trial. Ann Intern Med (2004) 2.83
Novel Foxo1-dependent transcriptional programs control T(reg) cell function. Nature (2012) 2.77
PBAF chromatin-remodeling complex requires a novel specificity subunit, BAF200, to regulate expression of selective interferon-responsive genes. Genes Dev (2005) 2.70
The PSA(-/lo) prostate cancer cell population harbors self-renewing long-term tumor-propagating cells that resist castration. Cell Stem Cell (2012) 2.69
High-resolution genome-wide mapping of histone modifications. Nat Biotechnol (2004) 2.69
Genome-wide prediction of conserved and nonconserved enhancers by histone acetylation patterns. Genome Res (2006) 2.67
Detection of single nucleotide variations in expressed exons of the human genome using RNA-Seq. Nucleic Acids Res (2009) 2.61
Cholangiocarcinomas can originate from hepatocytes in mice. J Clin Invest (2012) 2.56
Distinct pathways of genomic progression to benign and malignant tumors of the liver. Proc Natl Acad Sci U S A (2007) 2.56
Genome-wide analyses of transcription factor GATA3-mediated gene regulation in distinct T cell types. Immunity (2011) 2.53
Follicular T-helper cell recruitment governed by bystander B cells and ICOS-driven motility. Nature (2013) 2.52
Increased lipogenesis, induced by AKT-mTORC1-RPS6 signaling, promotes development of human hepatocellular carcinoma. Gastroenterology (2010) 2.48
Genomic location analysis by ChIP-Seq. J Cell Biochem (2009) 2.44
GATA3 controls Foxp3⁺ regulatory T cell fate during inflammation in mice. J Clin Invest (2011) 2.43
Reciprocal regulation of CD4/CD8 expression by SWI/SNF-like BAF complexes. Nature (2002) 2.41
The transcription factor GATA3 actively represses RUNX3 protein-regulated production of interferon-gamma. Immunity (2010) 2.38
Organic cation transporters are determinants of oxaliplatin cytotoxicity. Cancer Res (2006) 2.37
Testis-specific TAF homologs collaborate to control a tissue-specific transcription program. Development (2004) 2.35
Priming for T helper type 2 differentiation by interleukin 2-mediated induction of interleukin 4 receptor alpha-chain expression. Nat Immunol (2008) 2.31
Chromatin poises miRNA- and protein-coding genes for expression. Genome Res (2009) 2.28
Expression of a functionally active gp91phox-containing neutrophil-type NAD(P)H oxidase in smooth muscle cells from human resistance arteries: regulation by angiotensin II. Circ Res (2002) 2.27
c-Jun N-terminal kinases mediate reactivation of Akt and cardiomyocyte survival after hypoxic injury in vitro and in vivo. Circ Res (2005) 2.23
Single ion-channel recordings using glass nanopore membranes. J Am Chem Soc (2007) 2.22
H2A.Z facilitates access of active and repressive complexes to chromatin in embryonic stem cell self-renewal and differentiation. Cell Stem Cell (2012) 2.20