Published in Genome Biol on August 04, 2006
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Chromatin signature of embryonic pluripotency is established during genome activation. Nature (2010) 2.64
Genes for embryo development are packaged in blocks of multivalent chromatin in zebrafish sperm. Genome Res (2011) 1.94
Prdm1- and Sox6-mediated transcriptional repression specifies muscle fibre type in the zebrafish embryo. EMBO Rep (2008) 1.50
Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis. Genome Res (2012) 1.34
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Reproductive and developmental toxicity of dioxin in fish. Mol Cell Endocrinol (2011) 1.05
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Identification of direct T-box target genes in the developing zebrafish mesoderm. Development (2009) 1.02
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Global identification of SMAD2 target genes reveals a role for multiple co-regulatory factors in zebrafish early gastrulas. J Biol Chem (2011) 0.93
Cannabinoid receptor 2 suppresses leukocyte inflammatory migration by modulating the JNK/c-Jun/Alox5 pathway. J Biol Chem (2013) 0.89
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Tiling histone H3 lysine 4 and 27 methylation in zebrafish using high-density microarrays. PLoS One (2010) 0.84
Prdm1a directly activates foxd3 and tfap2a during zebrafish neural crest specification. Development (2013) 0.83
Bcl6a function is required during optic cup formation to prevent p53-dependent apoptosis and colobomata. Hum Mol Genet (2013) 0.81
Tbx6, Mesp-b and Ripply1 regulate the onset of skeletal myogenesis in zebrafish. Development (2015) 0.81
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UXT potentiates angiogenesis by attenuating Notch signaling. Development (2015) 0.77
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DANIO-CODE: Toward an Encyclopedia of DNA Elements in Zebrafish. Zebrafish (2015) 0.75
A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell (2006) 48.80
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Core transcriptional regulatory circuitry in human embryonic stem cells. Cell (2005) 34.93
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Transcriptional regulatory code of a eukaryotic genome. Nature (2004) 27.21
Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature (2006) 25.90
A high-resolution map of active promoters in the human genome. Nature (2005) 24.35
Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature (2001) 21.55
Genomic maps and comparative analysis of histone modifications in human and mouse. Cell (2005) 18.96
Active genes are tri-methylated at K4 of histone H3. Nature (2002) 15.68
Genome-wide map of nucleosome acetylation and methylation in yeast. Cell (2005) 15.08
Chromatin signatures of pluripotent cell lines. Nat Cell Biol (2006) 12.88
Control of pancreas and liver gene expression by HNF transcription factors. Science (2004) 12.05
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The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote. Genes Dev (2004) 7.57
A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells. Proc Natl Acad Sci U S A (2003) 7.30
Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis. Genes Dev (2002) 6.74
Use of chromatin immunoprecipitation to clone novel E2F target promoters. Mol Cell Biol (2001) 5.61
Chd1 chromodomain links histone H3 methylation with SAGA- and SLIK-dependent acetylation. Nature (2005) 5.15
Gene regulatory networks for development. Proc Natl Acad Sci U S A (2005) 4.45
Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray. Genome Biol (2003) 4.24
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Developmental regulation of zebrafish MyoD in wild-type, no tail and spadetail embryos. Development (1996) 3.30
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A homeobox gene essential for zebrafish notochord development. Nature (1995) 2.25
Progress and challenges in profiling the dynamics of chromatin and transcription factor binding with DNA microarrays. Curr Opin Genet Dev (2004) 2.25
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Zebrafish paraxial protocadherin is a downstream target of spadetail involved in morphogenesis of gastrula mesoderm. Development (1998) 1.48
Making waves in cancer research: new models in the zebrafish. Biotechniques (2005) 1.36
Zebrafish as a pharmacological tool: the how, why and when. Curr Opin Pharmacol (2004) 1.35
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A genetic regulatory network for Xenopus mesendoderm formation. Dev Biol (2004) 1.23
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Zebrafish as a genomics research model. Curr Pharm Biotechnol (2004) 1.12
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A mouse homologue of FAST-1 transduces TGF beta superfamily signals and is expressed during early embryogenesis. Mech Dev (1998) 1.04
Zebrafish wnt11: pattern and regulation of the expression by the yolk cell and No tail activity. Mech Dev (1998) 1.01
Transgenes as screening tools to probe and manipulate the zebrafish genome. Dev Dyn (2005) 0.99
Functional interaction of vega2 and goosecoid homeobox genes in zebrafish. Genesis (2000) 0.94
Identifying transcriptional targets. Genome Biol (2004) 0.89
Characterization and expression of a presomitic mesoderm-specific mespo gene in zebrafish. Dev Genes Evol (2003) 0.82
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Control of developmental regulators by Polycomb in human embryonic stem cells. Cell (2006) 28.21
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Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature (2006) 25.90
A chromatin landmark and transcription initiation at most promoters in human cells. Cell (2007) 23.41
An embryonic stem cell-like gene expression signature in poorly differentiated aggressive human tumors. Nat Genet (2008) 17.67
Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell (2008) 16.38
Mesenchymal stem cells within tumour stroma promote breast cancer metastasis. Nature (2007) 15.20
Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Acad Sci U S A (2010) 15.13
Genome-wide map of nucleosome acetylation and methylation in yeast. Cell (2005) 15.08
Mediator and cohesin connect gene expression and chromatin architecture. Nature (2010) 14.34
BET bromodomain inhibition as a therapeutic strategy to target c-Myc. Cell (2011) 14.34
Parkinson's disease patient-derived induced pluripotent stem cells free of viral reprogramming factors. Cell (2009) 13.02
Control of pancreas and liver gene expression by HNF transcription factors. Science (2004) 12.05
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
c-Myc regulates transcriptional pause release. Cell (2010) 11.64
Divergent transcription from active promoters. Science (2008) 11.03
E2F integrates cell cycle progression with DNA repair, replication, and G(2)/M checkpoints. Genes Dev (2002) 10.06
RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo. Nat Genet (2007) 9.56
Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell (2013) 9.55
Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res (2005) 8.69
Selective inhibition of tumor oncogenes by disruption of super-enhancers. Cell (2013) 8.37
Transcriptional amplification in tumor cells with elevated c-Myc. Cell (2012) 8.24
YAP1 increases organ size and expands undifferentiated progenitor cells. Curr Biol (2007) 8.11
Functional genomics reveal that the serine synthesis pathway is essential in breast cancer. Nature (2011) 8.03
Super-enhancers in the control of cell identity and disease. Cell (2013) 7.50
Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding. Science (2010) 7.41
Chromatin immunoprecipitation and microarray-based analysis of protein location. Nat Protoc (2006) 7.29
Densely interconnected transcriptional circuits control cell states in human hematopoiesis. Cell (2011) 7.03
Tissue-specific transcriptional regulation has diverged significantly between human and mouse. Nat Genet (2007) 6.92
NOTCH1 directly regulates c-MYC and activates a feed-forward-loop transcriptional network promoting leukemic cell growth. Proc Natl Acad Sci U S A (2006) 6.80
Computational discovery of gene modules and regulatory networks. Nat Biotechnol (2003) 6.55
Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays. Nat Genet (2004) 6.33
Genome-wide analysis of cAMP-response element binding protein occupancy, phosphorylation, and target gene activation in human tissues. Proc Natl Acad Sci U S A (2005) 6.26
Foxp3 occupancy and regulation of key target genes during T-cell stimulation. Nature (2007) 5.81
Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs. Nat Struct Mol Biol (2011) 5.57
Global and Hox-specific roles for the MLL1 methyltransferase. Proc Natl Acad Sci U S A (2005) 5.53
Human macrophage activation programs induced by bacterial pathogens. Proc Natl Acad Sci U S A (2002) 5.18
Evidence for an instructive mechanism of de novo methylation in cancer cells. Nat Genet (2006) 4.97
Therapeutic silencing of miR-10b inhibits metastasis in a mouse mammary tumor model. Nat Biotechnol (2010) 4.80
The evolutionary landscape of alternative splicing in vertebrate species. Science (2012) 4.78
Tcf3 is an integral component of the core regulatory circuitry of embryonic stem cells. Genes Dev (2008) 4.77
ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. Methods (2009) 4.69
Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo. Genes Dev (2007) 4.59
Chromatin structure and gene expression programs of human embryonic and induced pluripotent stem cells. Cell Stem Cell (2010) 4.59
Wnt signaling promotes reprogramming of somatic cells to pluripotency. Cell Stem Cell (2008) 4.43
Short RNAs are transcribed from repressed polycomb target genes and interact with polycomb repressive complex-2. Mol Cell (2010) 4.36
Exchange of RNA polymerase II initiation and elongation factors during gene expression in vivo. Mol Cell (2002) 4.35
Derivation of pre-X inactivation human embryonic stem cells under physiological oxygen concentrations. Cell (2010) 4.32
Transformation of different human breast epithelial cell types leads to distinct tumor phenotypes. Cancer Cell (2007) 4.30
Insights into hominid evolution from the gorilla genome sequence. Nature (2012) 4.12
Program-specific distribution of a transcription factor dependent on partner transcription factor and MAPK signaling. Cell (2003) 4.12
Insights into host responses against pathogens from transcriptional profiling. Nat Rev Microbiol (2005) 4.11
SetDB1 contributes to repression of genes encoding developmental regulators and maintenance of ES cell state. Genes Dev (2009) 4.09
Species-specific transcription in mice carrying human chromosome 21. Science (2008) 4.03
Activated signal transduction kinases frequently occupy target genes. Science (2006) 4.01
Master transcription factors determine cell-type-specific responses to TGF-β signaling. Cell (2011) 3.94
Genome-wide location and regulated recruitment of the RSC nucleosome-remodeling complex. Genes Dev (2002) 3.93
H2AZ is enriched at polycomb complex target genes in ES cells and is necessary for lineage commitment. Cell (2008) 3.90
A CTCF-independent role for cohesin in tissue-specific transcription. Genome Res (2010) 3.89
Growth-inhibitory and tumor- suppressive functions of p53 depend on its repression of CD44 expression. Cell (2008) 3.75
High-resolution computational models of genome binding events. Nat Biotechnol (2006) 3.74
Global position and recruitment of HATs and HDACs in the yeast genome. Mol Cell (2004) 3.74
Enhancer decommissioning by LSD1 during embryonic stem cell differentiation. Nature (2012) 3.67
Controlling morpholino experiments: don't stop making antisense. Development (2008) 3.63
Revisiting global gene expression analysis. Cell (2012) 3.63
Poised chromatin at the ZEB1 promoter enables breast cancer cell plasticity and enhances tumorigenicity. Cell (2013) 3.61
Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages. Cell (2012) 3.48
The histone methyltransferase SETDB1 is recurrently amplified in melanoma and accelerates its onset. Nature (2011) 3.37
PathBLAST: a tool for alignment of protein interaction networks. Nucleic Acids Res (2004) 3.20
Core transcriptional regulatory circuitry in human hepatocytes. Mol Syst Biol (2006) 3.15
Combining location and expression data for principled discovery of genetic regulatory network models. Pac Symp Biocomput (2002) 3.05
HSF1 drives a transcriptional program distinct from heat shock to support highly malignant human cancers. Cell (2012) 2.94
Transcriptional regulation and its misregulation in disease. Cell (2013) 2.92
Genome-wide maps of histone modifications unwind in vivo chromatin states of the hair follicle lineage. Cell Stem Cell (2011) 2.80
BRACHYURY and CDX2 mediate BMP-induced differentiation of human and mouse pluripotent stem cells into embryonic and extraembryonic lineages. Cell Stem Cell (2011) 2.79
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HIV-1 Tat reprograms immature dendritic cells to express chemoattractants for activated T cells and macrophages. Nat Med (2003) 2.62
Genome-wide analysis of menin binding provides insights into MEN1 tumorigenesis. PLoS Genet (2006) 2.62
Lineage regulators direct BMP and Wnt pathways to cell-specific programs during differentiation and regeneration. Cell (2011) 2.53
CTCF and cohesin: linking gene regulatory elements with their targets. Cell (2013) 2.53
A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data. Bioinformatics (2005) 2.52
Mir-214-dependent regulation of the polycomb protein Ezh2 in skeletal muscle and embryonic stem cells. Mol Cell (2009) 2.47