Published in Genome Biol on September 17, 2008
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Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions. Genome Res (2011) 3.57
R-loop formation is a distinctive characteristic of unmethylated human CpG island promoters. Mol Cell (2012) 3.56
Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages. Cell (2012) 3.48
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The long noncoding RNA SChLAP1 promotes aggressive prostate cancer and antagonizes the SWI/SNF complex. Nat Genet (2013) 3.39
Genomic determination of the glucocorticoid response reveals unexpected mechanisms of gene regulation. Genome Res (2009) 3.30
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A METTL3-METTL14 complex mediates mammalian nuclear RNA N6-adenosine methylation. Nat Chem Biol (2013) 3.16
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Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids. Plant Cell (2010) 2.92
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Novel Foxo1-dependent transcriptional programs control T(reg) cell function. Nature (2012) 2.77
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Loss of the tumor suppressor BAP1 causes myeloid transformation. Science (2012) 2.69
Genetic analysis of variation in transcription factor binding in yeast. Nature (2010) 2.69
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Recessive mutations in a distal PTF1A enhancer cause isolated pancreatic agenesis. Nat Genet (2013) 2.66
Identifying positioned nucleosomes with epigenetic marks in human from ChIP-Seq. BMC Genomics (2008) 2.66
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Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression. Genome Res (2009) 2.64
Promoter directionality is controlled by U1 snRNP and polyadenylation signals. Nature (2013) 2.63
Revealing long noncoding RNA architecture and functions using domain-specific chromatin isolation by RNA purification. Nat Biotechnol (2014) 2.57
Dual role of FoxA1 in androgen receptor binding to chromatin, androgen signalling and prostate cancer. EMBO J (2011) 2.55
Partitioning heritability of regulatory and cell-type-specific variants across 11 common diseases. Am J Hum Genet (2014) 2.53
Genome-wide analyses of transcription factor GATA3-mediated gene regulation in distinct T cell types. Immunity (2011) 2.53
Dissecting the regulatory architecture of gene expression QTLs. Genome Biol (2012) 2.51
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
Genome-wide mapping of in vivo protein-DNA interactions. Science (2007) 64.92
Global variation in copy number in the human genome. Nature (2006) 57.50
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods (2007) 45.04
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Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature (2001) 21.55
A global map of p53 transcription-factor binding sites in the human genome. Cell (2006) 20.65
Genome-wide analysis of estrogen receptor binding sites. Nat Genet (2006) 18.63
FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription. Cell (2008) 14.18
Model-based analysis of tiling-arrays for ChIP-chip. Proc Natl Acad Sci U S A (2006) 13.68
Model-based analysis of two-color arrays (MA2C). Genome Biol (2007) 7.28
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Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature (2007) 65.18
Genome-wide mapping of in vivo protein-DNA interactions. Science (2007) 64.92
Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol (2011) 53.86
A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science (2002) 42.78
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature (2009) 35.48
Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature (2008) 30.29
In vitro reprogramming of fibroblasts into a pluripotent ES-cell-like state. Nature (2007) 28.24
Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol (2009) 27.17
Mapping and analysis of chromatin state dynamics in nine human cell types. Nature (2011) 24.37
High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci U S A (2010) 22.97
Worldwide human relationships inferred from genome-wide patterns of variation. Science (2008) 22.44
Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci U S A (2009) 20.66
ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res (2008) 20.61
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proc Natl Acad Sci U S A (2002) 20.48
Genome-wide analysis of estrogen receptor binding sites. Nat Genet (2006) 18.63
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Initial genome sequencing and analysis of multiple myeloma. Nature (2011) 17.28
Dissecting direct reprogramming through integrative genomic analysis. Nature (2008) 16.47
Active genes are tri-methylated at K4 of histone H3. Nature (2002) 15.68
Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell (2006) 15.12
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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Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res (2006) 13.32
High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat Methods (2008) 12.56
Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nat Methods (2008) 11.61
The genome sequence of the filamentous fungus Neurospora crassa. Nature (2003) 11.39
Sequencing of 50 human exomes reveals adaptation to high altitude. Science (2010) 11.27
Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet (2008) 11.17
Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature (2004) 11.03
Quality scores and SNP detection in sequencing-by-synthesis systems. Genome Res (2008) 10.49
Widespread parallel evolution in sticklebacks by repeated fixation of Ectodysplasin alleles. Science (2005) 10.46
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science (2010) 9.78
Genome sequence of Aedes aegypti, a major arbovirus vector. Science (2007) 9.19
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Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol (2011) 9.18
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Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat Methods (2010) 9.09
Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2. Nature (2010) 8.87
TreeFam: a curated database of phylogenetic trees of animal gene families. Nucleic Acids Res (2006) 8.83
Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet (2010) 8.75
A high-resolution map of human evolutionary constraint using 29 mammals. Nature (2011) 8.67
The role of microRNA genes in papillary thyroid carcinoma. Proc Natl Acad Sci U S A (2005) 8.60
Integrative analysis of the melanoma transcriptome. Genome Res (2010) 8.46
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Differential chromatin marking of introns and expressed exons by H3K36me3. Nat Genet (2009) 8.11
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Genetic relationship between five psychiatric disorders estimated from genome-wide SNPs. Nat Genet (2013) 8.02
Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells. Nature (2011) 7.43
Charting histone modifications and the functional organization of mammalian genomes. Nat Rev Genet (2010) 7.39
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X chromosomal abnormalities in basal-like human breast cancer. Cancer Cell (2006) 7.17
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Androgen receptor regulates a distinct transcription program in androgen-independent prostate cancer. Cell (2009) 7.09
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ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads. Genome Biol (2009) 6.76
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iPS cells produce viable mice through tetraploid complementation. Nature (2009) 6.51
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Molecular determinants for the tissue specificity of SERMs. Science (2002) 6.20
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Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses. Science (2009) 6.07