Published in Genome Biol on March 16, 2012
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Combinatorial assembly of developmental stage-specific enhancers controls gene expression programs during human erythropoiesis. Dev Cell (2012) 1.63
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Dynamics of MBD2 deposition across methylated DNA regions during malignant transformation of human mammary epithelial cells. Nucleic Acids Res (2015) 0.80
Accounting for immunoprecipitation efficiencies in the statistical analysis of ChIP-seq data. BMC Bioinformatics (2013) 0.80
EIN2-dependent regulation of acetylation of histone H3K14 and non-canonical histone H3K23 in ethylene signalling. Nat Commun (2016) 0.80
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Identifying differential transcription factor binding in ChIP-seq. Front Genet (2015) 0.79
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DNA methylation and chromatin organization in insects: insights from the Ant Camponotus floridanus. Genome Biol Evol (2015) 0.78
An Alternative Approach to ChIP-Seq Normalization Enables Detection of Genome-Wide Changes in Histone H3 Lysine 27 Trimethylation upon EZH2 Inhibition. PLoS One (2016) 0.78
Cross Talk Between GH-Regulated Transcription Factors HNF6 and CUX2 in Adult Mouse Liver. Mol Endocrinol (2015) 0.77
Selective coregulator function and restriction of steroid receptor chromatin occupancy by Hic-5. Mol Endocrinol (2015) 0.76
Identifying TF-MiRNA Regulatory Relationships Using Multiple Features. PLoS One (2015) 0.76
Glucocorticoid receptor ChIP-sequencing of subcutaneous fat reveals modulation of inflammatory pathways. Obesity (Silver Spring) (2015) 0.76
MEF2C protects bone marrow B-lymphoid progenitors during stress haematopoiesis. Nat Commun (2016) 0.76
Chromatin module inference on cellular trajectories identifies key transition points and poised epigenetic states in diverse developmental processes. Genome Res (2017) 0.76
A ChIP-Seq Data Analysis Pipeline Based on Bioconductor Packages. Genomics Inform (2017) 0.75
Distinct Roles of Brd2 and Brd4 in Potentiating the Transcriptional Program for Th17 Cell Differentiation. Mol Cell (2017) 0.75
Transcriptome-wide N (6) -methyladenosine methylome profiling of porcine muscle and adipose tissues reveals a potential mechanism for transcriptional regulation and differential methylation pattern. BMC Genomics (2017) 0.75
H2A monoubiquitination in Arabidopsis thaliana is generally independent of LHP1 and PRC2 activity. Genome Biol (2017) 0.75
Nonparametric Tests for Differential Histone Enrichment with ChIP-Seq Data. Cancer Inform (2015) 0.75
Myotonic dystrophy type 1 patient-derived iPSCs for the investigation of CTG repeat instability. Sci Rep (2017) 0.75
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Differential peak calling of ChIP-seq signals with replicates with THOR. Nucleic Acids Res (2016) 0.75
Systematic identification of gene family regulators in mouse and human embryonic stem cells. Nucleic Acids Res (2016) 0.75
Lkb1 inactivation drives lung cancer lineage switching governed by Polycomb Repressive Complex 2. Nat Commun (2017) 0.75
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Developmental alterations in Huntington's disease neural cells and pharmacological rescue in cells and mice. Nat Neurosci (2017) 0.75
Nuclear PKC-θ facilitates rapid transcriptional responses in human memory CD4+ T cells through p65 and H2B phosphorylation. J Cell Sci (2016) 0.75
YY1 Haploinsufficiency Causes an Intellectual Disability Syndrome Featuring Transcriptional and Chromatin Dysfunction. Am J Hum Genet (2017) 0.75
Identifying therapeutic targets by combining transcriptional data with ordinal clinical measurements. Nat Commun (2017) 0.75
Epimetheus - a multi-profile normalizer for epigenomic sequencing data. BMC Bioinformatics (2017) 0.75
Chromatin immunoprecipitation and an open chromatin assay in zebrafish erythrocytes. Methods Cell Biol (2016) 0.75
Use antibiotics in cell culture with caution: genome-wide identification of antibiotic-induced changes in gene expression and regulation. Sci Rep (2017) 0.75
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Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Acad Sci U S A (2010) 15.13
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An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat Biotechnol (2008) 13.96
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Unlocking the secrets of the genome. Nature (2009) 11.80
c-Myc regulates transcriptional pause release. Cell (2010) 11.64
PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat Biotechnol (2009) 11.28
Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat Biotechnol (2010) 9.84
TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity. Nature (2011) 8.31
Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding. Science (2010) 7.41
Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature (2010) 6.87
A Myc network accounts for similarities between embryonic stem and cancer cell transcription programs. Cell (2010) 6.00
Whole-genome cartography of estrogen receptor alpha binding sites. PLoS Genet (2007) 5.85
A cis-regulatory map of the Drosophila genome. Nature (2011) 4.80
Self-renewal of teratocarcinoma and embryonic stem cells. Oncogene (2004) 4.40
Discovering hematopoietic mechanisms through genome-wide analysis of GATA factor chromatin occupancy. Mol Cell (2009) 3.96
Insights into GATA-1-mediated gene activation versus repression via genome-wide chromatin occupancy analysis. Mol Cell (2009) 3.05
PHF8 mediates histone H4 lysine 20 demethylation events involved in cell cycle progression. Nature (2010) 2.91
An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data. Bioinformatics (2008) 2.85
Genome-wide analysis reveals novel molecular features of mouse recombination hotspots. Nature (2011) 2.61
Role for Dpy-30 in ES cell-fate specification by regulation of H3K4 methylation within bivalent domains. Cell (2011) 2.30
Genomic mapping of RNA polymerase II reveals sites of co-transcriptional regulation in human cells. Genome Biol (2005) 2.11
Comparative study on ChIP-seq data: normalization and binding pattern characterization. Bioinformatics (2009) 2.02
Nutrition, epigenetics, and developmental plasticity: implications for understanding human disease. Annu Rev Nutr (2010) 1.97
Unbiased, genome-wide in vivo mapping of transcriptional regulatory elements reveals sex differences in chromatin structure associated with sex-specific liver gene expression. Mol Cell Biol (2010) 1.45
Histone modification patterns and epigenetic codes. Biochim Biophys Acta (2009) 1.45
Automating dChip: toward reproducible sharing of microarray data analysis. BMC Bioinformatics (2008) 1.44
Dynamic, sex-differential STAT5 and BCL6 binding to sex-biased, growth hormone-regulated genes in adult mouse liver. Mol Cell Biol (2011) 1.36
Expression profile of CREB knockdown in myeloid leukemia cells. BMC Cancer (2008) 1.01
Prediction of Polycomb target genes in mouse embryonic stem cells. Genomics (2010) 0.94
Epigenetic domains found in mouse embryonic stem cells via a hidden Markov model. BMC Bioinformatics (2010) 0.89
An extended transcriptional network for pluripotency of embryonic stem cells. Cell (2008) 14.64
A protein interaction network for pluripotency of embryonic stem cells. Nature (2006) 9.63
Endogenous oncogenic K-ras(G12D) stimulates proliferation and widespread neoplastic and developmental defects. Cancer Cell (2004) 8.16
Prostaglandin E2 regulates vertebrate haematopoietic stem cell homeostasis. Nature (2007) 7.55
Tet1 and Tet2 regulate 5-hydroxymethylcytosine production and cell lineage specification in mouse embryonic stem cells. Cell Stem Cell (2011) 7.41
EZH1 mediates methylation on histone H3 lysine 27 and complements EZH2 in maintaining stem cell identity and executing pluripotency. Mol Cell (2008) 6.86
Human fetal hemoglobin expression is regulated by the developmental stage-specific repressor BCL11A. Science (2008) 6.66
A Myc network accounts for similarities between embryonic stem and cancer cell transcription programs. Cell (2010) 6.00
Toward improving Caenorhabditis elegans phenome mapping with an ORFeome-based RNAi library. Genome Res (2004) 5.81
A critical role for eosinophils in allergic airways remodeling. Science (2004) 5.53
Genome-wide association study shows BCL11A associated with persistent fetal hemoglobin and amelioration of the phenotype of beta-thalassemia. Proc Natl Acad Sci U S A (2008) 5.27
Peroxisomes are signaling platforms for antiviral innate immunity. Cell (2010) 5.24
Targeted deletion of a high-affinity GATA-binding site in the GATA-1 promoter leads to selective loss of the eosinophil lineage in vivo. J Exp Med (2002) 5.07
Developmental origin of a bipotential myocardial and smooth muscle cell precursor in the mammalian heart. Cell (2006) 5.03
Transcriptional regulation of erythropoiesis: an affair involving multiple partners. Oncogene (2002) 4.80
Gfi-1 restricts proliferation and preserves functional integrity of haematopoietic stem cells. Nature (2004) 4.68
The SWI/SNF complex--chromatin and cancer. Nat Rev Cancer (2004) 4.59
DNA polymorphisms at the BCL11A, HBS1L-MYB, and beta-globin loci associate with fetal hemoglobin levels and pain crises in sickle cell disease. Proc Natl Acad Sci U S A (2008) 4.46
A genome-wide RNAi screen identifies a new transcriptional module required for self-renewal. Genes Dev (2009) 4.23
The placenta is a niche for hematopoietic stem cells. Dev Cell (2005) 3.83
Rb regulates interactions between hematopoietic stem cells and their bone marrow microenvironment. Cell (2007) 3.82
Essential role for the peroxiredoxin Prdx1 in erythrocyte antioxidant defence and tumour suppression. Nature (2003) 3.77
Jumonji modulates polycomb activity and self-renewal versus differentiation of stem cells. Cell (2009) 3.75
Expression of CD41 marks the initiation of definitive hematopoiesis in the mouse embryo. Blood (2002) 3.59
Developmental and species-divergent globin switching are driven by BCL11A. Nature (2009) 3.49
Haematopoietic stem cells retain long-term repopulating activity and multipotency in the absence of stem-cell leukaemia SCL/tal-1 gene. Nature (2003) 3.25
Intrinsic requirement for zinc finger transcription factor Gfi-1 in neutrophil differentiation. Immunity (2003) 3.17
The emergence of hematopoietic stem cells is initiated in the placental vasculature in the absence of circulation. Cell Stem Cell (2008) 3.09
DNA methyltransferase 1 is essential for and uniquely regulates hematopoietic stem and progenitor cells. Cell Stem Cell (2009) 3.08
Insights into GATA-1-mediated gene activation versus repression via genome-wide chromatin occupancy analysis. Mol Cell (2009) 3.05
Polycomb group proteins Ezh2 and Rnf2 direct genomic contraction and imprinted repression in early mouse embryos. Dev Cell (2008) 2.96
GATA-2 plays two functionally distinct roles during the ontogeny of hematopoietic stem cells. J Exp Med (2004) 2.94
Transcriptional silencing of {gamma}-globin by BCL11A involves long-range interactions and cooperation with SOX6. Genes Dev (2010) 2.93
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Conditional mouse osteosarcoma, dependent on p53 loss and potentiated by loss of Rb, mimics the human disease. Genes Dev (2008) 2.74
The journey of developing hematopoietic stem cells. Development (2006) 2.71
An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level. Science (2013) 2.71
ADAR1 is essential for the maintenance of hematopoiesis and suppression of interferon signaling. Nat Immunol (2008) 2.70
Fine-mapping at three loci known to affect fetal hemoglobin levels explains additional genetic variation. Nat Genet (2010) 2.63
Epigenetic regulation of hematopoietic differentiation by Gfi-1 and Gfi-1b is mediated by the cofactors CoREST and LSD1. Mol Cell (2007) 2.62
Early asymmetry of gene transcription in embryonic human left and right cerebral cortex. Science (2005) 2.56
Tel/Etv6 is an essential and selective regulator of adult hematopoietic stem cell survival. Genes Dev (2004) 2.56
Highly penetrant, rapid tumorigenesis through conditional inversion of the tumor suppressor gene Snf5. Cancer Cell (2002) 2.51
Haploinsufficiency of GATA-2 perturbs adult hematopoietic stem-cell homeostasis. Blood (2005) 2.47
Developmental stage-selective effect of somatically mutated leukemogenic transcription factor GATA1. Nat Genet (2005) 2.44
Schizosaccharomyces pombe genome-wide nucleosome mapping reveals positioning mechanisms distinct from those of Saccharomyces cerevisiae. Nat Struct Mol Biol (2010) 2.40
The zinc finger transcription factor Gfi1, implicated in lymphomagenesis, is required for inner ear hair cell differentiation and survival. Development (2003) 2.38
PRC1 and Suv39h specify parental asymmetry at constitutive heterochromatin in early mouse embryos. Nat Genet (2008) 2.37
Correction of sickle cell disease in adult mice by interference with fetal hemoglobin silencing. Science (2011) 2.36
TIF1gamma controls erythroid cell fate by regulating transcription elongation. Cell (2010) 2.33
A functional element necessary for fetal hemoglobin silencing. N Engl J Med (2011) 2.25
MicroRNA-21 promotes fibrosis of the kidney by silencing metabolic pathways. Sci Transl Med (2012) 2.20
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Sex-dependent liver gene expression is extensive and largely dependent upon signal transducer and activator of transcription 5b (STAT5b): STAT5b-dependent activation of male genes and repression of female genes revealed by microarray analysis. Mol Endocrinol (2006) 2.17
Exome sequencing identifies GATA1 mutations resulting in Diamond-Blackfan anemia. J Clin Invest (2012) 2.15
Identification of distinct molecular phenotypes in acute megakaryoblastic leukemia by gene expression profiling. Proc Natl Acad Sci U S A (2006) 2.08
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Polycomb repressive complex 2 regulates normal development of the mouse heart. Circ Res (2011) 2.05
miR-125b-2 is a potential oncomiR on human chromosome 21 in megakaryoblastic leukemia. Genes Dev (2010) 2.05
MicroRNA-21 limits in vivo immune response-mediated activation of the IL-12/IFN-gamma pathway, Th1 polarization, and the severity of delayed-type hypersensitivity. J Immunol (2011) 2.00
Coregulator-dependent facilitation of chromatin occupancy by GATA-1. Proc Natl Acad Sci U S A (2004) 1.99
The zinc-finger proto-oncogene Gfi-1b is essential for development of the erythroid and megakaryocytic lineages. Genes Dev (2002) 1.99
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GATA-1 as a regulator of mast cell differentiation revealed by the phenotype of the GATA-1low mouse mutant. J Exp Med (2003) 1.96
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ETV1 directs androgen metabolism and confers aggressive prostate cancer in targeted mice and patients. Genes Dev (2013) 1.87
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Human LSD2/KDM1b/AOF1 regulates gene transcription by modulating intragenic H3K4me2 methylation. Mol Cell (2010) 1.73
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PRC2 directly methylates GATA4 and represses its transcriptional activity. Genes Dev (2012) 1.66
The zebrafish moonshine gene encodes transcriptional intermediary factor 1gamma, an essential regulator of hematopoiesis. PLoS Biol (2004) 1.64
Gonadal differentiation, sex determination and normal Sry expression in mice require direct interaction between transcription partners GATA4 and FOG2. Development (2002) 1.64
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Coregulation of GATA factors by the Friend of GATA (FOG) family of multitype zinc finger proteins. Semin Cell Dev Biol (2004) 1.59
Reawakening fetal hemoglobin: prospects for new therapies for the β-globin disorders. Blood (2012) 1.58
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Broadly heterogeneous activation of the master regulator for sporulation in Bacillus subtilis. Proc Natl Acad Sci U S A (2010) 1.56
MicroRNA-15a and -16-1 act via MYB to elevate fetal hemoglobin expression in human trisomy 13. Proc Natl Acad Sci U S A (2011) 1.54
ETV6-NTRK3 fusion oncogene initiates breast cancer from committed mammary progenitors via activation of AP1 complex. Cancer Cell (2007) 1.53
Polycomb repressive complex 2 is required for MLL-AF9 leukemia. Proc Natl Acad Sci U S A (2012) 1.52