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An extended transcriptional network for pluripotency of embryonic stem cells. Cell (2008) 14.64

FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription. Cell (2008) 14.18

An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat Biotechnol (2008) 13.96

Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nat Biotechnol (2008) 10.10

A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome Res (2008) 7.89

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

The 8q24 cancer risk variant rs6983267 shows long-range interaction with MYC in colorectal cancer. Nat Genet (2009) 6.99

EZH1 mediates methylation on histone H3 lysine 27 and complements EZH2 in maintaining stem cell identity and executing pluripotency. Mol Cell (2008) 6.86

Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. PLoS Biol (2008) 6.30

Modeling non-uniformity in short-read rates in RNA-Seq data. Genome Biol (2010) 6.10

MADS: a new and improved method for analysis of differential alternative splicing by exon-tiling microarrays. RNA (2008) 5.78

H3K79 methylation profiles define murine and human MLL-AF4 leukemias. Cancer Cell (2008) 5.23

PPARgamma and C/EBP factors orchestrate adipocyte biology via adjacent binding on a genome-wide scale. Genes Dev (2008) 4.83

Cistrome: an integrative platform for transcriptional regulation studies. Genome Biol (2011) 4.13

Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Res (2008) 4.08

Evaluation of algorithm performance in ChIP-seq peak detection. PLoS One (2010) 3.99

Jumonji modulates polycomb activity and self-renewal versus differentiation of stem cells. Cell (2009) 3.75

Function of C/EBPdelta in a regulatory circuit that discriminates between transient and persistent TLR4-induced signals. Nat Immunol (2009) 3.60

ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genome. PLoS Comput Biol (2008) 3.46

Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments. Nucleic Acids Res (2010) 3.36

A comprehensive map of insulator elements for the Drosophila genome. PLoS Genet (2010) 3.25

The transcriptional foundation of pluripotency. Development (2009) 3.21

Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements). Methods (2009) 3.16

NELF and GAGA factor are linked to promoter-proximal pausing at many genes in Drosophila. Mol Cell Biol (2008) 3.11

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

Transcriptional silencing of {gamma}-globin by BCL11A involves long-range interactions and cooperation with SOX6. Genes Dev (2010) 2.93

Linking cell cycle to histone modifications: SBF and H2B monoubiquitination machinery and cell-cycle regulation of H3K79 dimethylation. Mol Cell (2009) 2.91

Transcriptional dysregulation in NIPBL and cohesin mutant human cells. PLoS Biol (2009) 2.89

A canonical promoter organization of the transcription machinery and its regulators in the Saccharomyces genome. Genome Res (2009) 2.89

Breast cancer risk-associated SNPs modulate the affinity of chromatin for FOXA1 and alter gene expression. Nat Genet (2012) 2.86

Exon arrays provide accurate assessments of gene expression. Genome Biol (2007) 2.86

Cross-hybridization modeling on Affymetrix exon arrays. Bioinformatics (2008) 2.54

Regulation of ERBB2 by oestrogen receptor-PAX2 determines response to tamoxifen. Nature (2008) 2.51

Ringo--an R/Bioconductor package for analyzing ChIP-chip readouts. BMC Bioinformatics (2007) 2.50

DNA methylation profile of tissue-dependent and differentially methylated regions (T-DMRs) in mouse promoter regions demonstrating tissue-specific gene expression. Genome Res (2008) 2.48

Tilescope: online analysis pipeline for high-density tiling microarray data. Genome Biol (2007) 2.48

Consolidation of the cancer genome into domains of repressive chromatin by long-range epigenetic silencing (LRES) reduces transcriptional plasticity. Nat Cell Biol (2010) 2.38

TIF1gamma controls erythroid cell fate by regulating transcription elongation. Cell (2010) 2.33

Systematic evaluation of factors influencing ChIP-seq fidelity. Nat Methods (2012) 2.31

Cutting edge: developmental stage-specific recruitment of cohesin to CTCF sites throughout immunoglobulin loci during B lymphocyte development. J Immunol (2009) 2.20

Unique ERalpha cistromes control cell type-specific gene regulation. Mol Endocrinol (2008) 2.19

A wave of nascent transcription on activated human genes. Proc Natl Acad Sci U S A (2009) 2.18

FOXC2 controls formation and maturation of lymphatic collecting vessels through cooperation with NFATc1. J Cell Biol (2009) 2.17

A hierarchical Bayesian model for comparing transcriptomes at the individual transcript isoform level. Nucleic Acids Res (2009) 2.12

Accurate genome-scale percentage DNA methylation estimates from microarray data. Biostatistics (2010) 2.11

Normalization and experimental design for ChIP-chip data. BMC Bioinformatics (2007) 2.08

A systems approach reveals regulatory circuitry for Arabidopsis trichome initiation by the GL3 and GL1 selectors. PLoS Genet (2009) 2.07

Retracted The noncoding RNA Mistral activates Hoxa6 and Hoxa7 expression and stem cell differentiation by recruiting MLL1 to chromatin. Mol Cell (2011) 2.07

Interaction of transcriptional regulators with specific nucleosomes across the Saccharomyces genome. Mol Cell (2009) 2.06

Genomic study of replication initiation in human chromosomes reveals the influence of transcription regulation and chromatin structure on origin selection. Mol Biol Cell (2009) 1.94

Growth factor stimulation induces a distinct ER(alpha) cistrome underlying breast cancer endocrine resistance. Genes Dev (2010) 1.92

Epigenetic switch involved in activation of pioneer factor FOXA1-dependent enhancers. Genome Res (2011) 1.92

Cell-type selective chromatin remodeling defines the active subset of FOXA1-bound enhancers. Genome Res (2009) 1.89

Definition of a FoxA1 Cistrome that is crucial for G1 to S-phase cell-cycle transit in castration-resistant prostate cancer. Cancer Res (2011) 1.89

Differential roles of Sall4 isoforms in embryonic stem cell pluripotency. Mol Cell Biol (2010) 1.88

Systems biology of innate immunity. Immunol Rev (2009) 1.87

ETV1 directs androgen metabolism and confers aggressive prostate cancer in targeted mice and patients. Genes Dev (2013) 1.87

ChIP-chip versus ChIP-seq: lessons for experimental design and data analysis. BMC Genomics (2011) 1.80

Chromatin immunoprecipitation on microarray analysis of Smad2/3 binding sites reveals roles of ETS1 and TFAP2A in transforming growth factor beta signaling. Mol Cell Biol (2008) 1.77

Evaluation of affinity-based genome-wide DNA methylation data: effects of CpG density, amplification bias, and copy number variation. Genome Res (2010) 1.77

Significance analysis and statistical dissection of variably methylated regions. Biostatistics (2011) 1.74

Human LSD2/KDM1b/AOF1 regulates gene transcription by modulating intragenic H3K4me2 methylation. Mol Cell (2010) 1.73

COUP-TFII acts downstream of Wnt/beta-catenin signal to silence PPARgamma gene expression and repress adipogenesis. Proc Natl Acad Sci U S A (2009) 1.67

A comprehensive view of nuclear receptor cancer cistromes. Cancer Res (2011) 1.64

Prevalence of transcription promoters within archaeal operons and coding sequences. Mol Syst Biol (2009) 1.62

Palindromic gene amplification--an evolutionarily conserved role for DNA inverted repeats in the genome. Nat Rev Cancer (2009) 1.62

Neurons show distinctive DNA methylation profile and higher interindividual variations compared with non-neurons. Genome Res (2011) 1.61

Elucidation of the ELK1 target gene network reveals a role in the coordinate regulation of core components of the gene regulation machinery. Genome Res (2009) 1.60

Genome-wide identification of targets of the drosha-pasha/DGCR8 complex. RNA (2009) 1.59

Regulation of the Drosophila Enhancer of split and invected-engrailed gene complexes by sister chromatid cohesion proteins. PLoS One (2009) 1.58

Dynamic PER repression mechanisms in the Drosophila circadian clock: from on-DNA to off-DNA. Genes Dev (2010) 1.57

A role for microRNAs in the Drosophila circadian clock. Genes Dev (2009) 1.56

A single-sample microarray normalization method to facilitate personalized-medicine workflows. Genomics (2012) 1.55

ChIPping away at gene regulation. EMBO Rep (2008) 1.54

Diverse splicing patterns of exonized Alu elements in human tissues. PLoS Genet (2008) 1.52

H3K27me3 profiling of the endosperm implies exclusion of polycomb group protein targeting by DNA methylation. PLoS Genet (2010) 1.51

Identification of an OCT4 and SRY regulatory module using integrated computational and experimental genomics approaches. Genome Res (2007) 1.50

Drosophila CLOCK target gene characterization: implications for circadian tissue-specific gene expression. Genes Dev (2011) 1.49

Repitools: an R package for the analysis of enrichment-based epigenomic data. Bioinformatics (2010) 1.45

Gene expression profiling of human breast tissue samples using SAGE-Seq. Genome Res (2010) 1.41

A blind deconvolution approach to high-resolution mapping of transcription factor binding sites from ChIP-seq data. Genome Biol (2009) 1.39

Genomic collaboration of estrogen receptor alpha and extracellular signal-regulated kinase 2 in regulating gene and proliferation programs. Mol Cell Biol (2010) 1.38

Genome-wide control of RNA polymerase II activity by cohesin. PLoS Genet (2013) 1.38

Nucleosome depletion at yeast terminators is not intrinsic and can occur by a transcriptional mechanism linked to 3'-end formation. Proc Natl Acad Sci U S A (2010) 1.37

Genome-wide profiling of the core clock protein BMAL1 targets reveals a strict relationship with metabolism. Mol Cell Biol (2010) 1.35

Profiling of promoter occupancy by PPARalpha in human hepatoma cells via ChIP-chip analysis. Nucleic Acids Res (2010) 1.34

TLS/FUS (translocated in liposarcoma/fused in sarcoma) regulates target gene transcription via single-stranded DNA response elements. Proc Natl Acad Sci U S A (2012) 1.33

AGRONOMICS1: a new resource for Arabidopsis transcriptome profiling. Plant Physiol (2009) 1.33

Setdb1 histone methyltransferase regulates mood-related behaviors and expression of the NMDA receptor subunit NR2B. J Neurosci (2010) 1.33

TCF4 and CDX2, major transcription factors for intestinal function, converge on the same cis-regulatory regions. Proc Natl Acad Sci U S A (2010) 1.32

CMARRT: a tool for the analysis of ChIP-chip data from tiling arrays by incorporating the correlation structure. Pac Symp Biocomput (2008) 1.31

Statistical approaches for the analysis of DNA methylation microarray data. Hum Genet (2011) 1.31

Cohesin selectively binds and regulates genes with paused RNA polymerase. Curr Biol (2011) 1.30

Coactivator function defines the active estrogen receptor alpha cistrome. Mol Cell Biol (2009) 1.29

Nuclear receptors and chromatin remodeling machinery. Mol Cell Endocrinol (2007) 1.28

The genome landscape of ERalpha- and ERbeta-binding DNA regions. Proc Natl Acad Sci U S A (2008) 1.27

Preferential binding of HIF-1 to transcriptionally active loci determines cell-type specific response to hypoxia. Genome Biol (2009) 1.27

Cohesin and polycomb proteins functionally interact to control transcription at silenced and active genes. PLoS Genet (2013) 1.25

A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics (2003) 82.89

Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res (1999) 49.21

Genome-wide location and function of DNA binding proteins. Science (2000) 31.25

Transcriptional regulatory code of a eukaryotic genome. Nature (2004) 27.21

Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature (2001) 21.55

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

Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat Genet (2001) 13.05

Segmental duplications: organization and impact within the current human genome project assembly. Genome Res (2001) 11.77

TileMap: create chromosomal map of tiling array hybridizations. Bioinformatics (2005) 5.68

Absolute mRNA concentrations from sequence-specific calibration of oligonucleotide arrays. Nucleic Acids Res (2003) 5.13

A hidden Markov model for analyzing ChIP-chip experiments on genome tiling arrays and its application to p53 binding sequences. Bioinformatics (2005) 3.06

Multiple testing methods for ChIP-Chip high density oligonucleotide array data. J Comput Biol (2006) 2.08

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

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

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

Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet (2010) 8.75

The role of microRNA genes in papillary thyroid carcinoma. Proc Natl Acad Sci U S A (2005) 8.60

Differential chromatin marking of introns and expressed exons by H3K36me3. Nat Genet (2009) 8.11

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

X chromosomal abnormalities in basal-like human breast cancer. Cancer Cell (2006) 7.17

Androgen receptor regulates a distinct transcription program in androgen-independent prostate cancer. Cell (2009) 7.09

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol (2010) 7.00

PlasmoDB: a functional genomic database for malaria parasites. Nucleic Acids Res (2008) 6.73

iPS cells produce viable mice through tetraploid complementation. Nature (2009) 6.51

Molecular determinants for the tissue specificity of SERMs. Science (2002) 6.20

Origin and diversity of novel avian influenza A H7N9 viruses causing human infection: phylogenetic, structural, and coalescent analyses. Lancet (2013) 6.10

Pioneer transcription factors: establishing competence for gene expression. Genes Dev (2011) 6.01

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

Differential oestrogen receptor binding is associated with clinical outcome in breast cancer. Nature (2012) 5.84

BSMAP: whole genome bisulfite sequence MAPping program. BMC Bioinformatics (2009) 5.67

Chromatin structure analyses identify miRNA promoters. Genes Dev (2008) 5.40

Spatial and temporal recruitment of androgen receptor and its coactivators involves chromosomal looping and polymerase tracking. Mol Cell (2005) 5.38

High-throughput mapping of the chromatin structure of human promoters. Nat Biotechnol (2007) 5.24

FOXA1 is a key determinant of estrogen receptor function and endocrine response. Nat Genet (2010) 5.22

Evidence that ternary complex (eIF2-GTP-tRNA(i)(Met))-deficient preinitiation complexes are core constituents of mammalian stress granules. Mol Biol Cell (2002) 5.20

Automated gating of flow cytometry data via robust model-based clustering. Cytometry A (2008) 5.10

Bone marrow edema and its relation to progression of knee osteoarthritis. Ann Intern Med (2003) 4.98

Formation of the androgen receptor transcription complex. Mol Cell (2002) 4.93

Cardiovascular risk and events in 17 low-, middle-, and high-income countries. N Engl J Med (2014) 4.88

Association of urinary sodium and potassium excretion with blood pressure. N Engl J Med (2014) 4.86

Dnmt3a is essential for hematopoietic stem cell differentiation. Nat Genet (2011) 4.85

PPARgamma and C/EBP factors orchestrate adipocyte biology via adjacent binding on a genome-wide scale. Genes Dev (2008) 4.83

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 G protein-coupled receptor is a plasma membrane receptor for the plant hormone abscisic acid. Science (2007) 4.61

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

RSeQC: quality control of RNA-seq experiments. Bioinformatics (2012) 4.31

CEAS: cis-regulatory element annotation system. Bioinformatics (2009) 4.26

Productivity is a poor predictor of plant species richness. Science (2011) 4.21

A novel influenza A (H1N1) vaccine in various age groups. N Engl J Med (2009) 4.20

Cistrome: an integrative platform for transcriptional regulation studies. Genome Biol (2011) 4.13

Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Res (2008) 4.08

A broadly implementable research course in phage discovery and genomics for first-year undergraduate students. MBio (2014) 3.93

A CTCF-independent role for cohesin in tissue-specific transcription. Genome Res (2010) 3.89

TriTrypDB: a functional genomic resource for the Trypanosomatidae. Nucleic Acids Res (2009) 3.79

EZH2 oncogenic activity in castration-resistant prostate cancer cells is Polycomb-independent. Science (2012) 3.74

Receptor-like cytoplasmic kinases integrate signaling from multiple plant immune receptors and are targeted by a Pseudomonas syringae effector. Cell Host Microbe (2010) 3.73

Chromatin marks identify critical cell types for fine mapping complex trait variants. Nat Genet (2012) 3.67

Simultaneous generation and germline transmission of multiple gene mutations in rat using CRISPR-Cas systems. Nat Biotechnol (2013) 3.65

Estrogen-dependent signaling in a molecularly distinct subclass of aggressive prostate cancer. J Natl Cancer Inst (2008) 3.55

Meta-analysis of traditional Chinese patent medicine for ischemic stroke. Stroke (2007) 3.46

High tumor incidence and activation of the PI3K/AKT pathway in transgenic mice define AIB1 as an oncogene. Cancer Cell (2004) 3.46

Common variants on 9q22.33 and 14q13.3 predispose to thyroid cancer in European populations. Nat Genet (2009) 3.46

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

p63 regulates an adhesion programme and cell survival in epithelial cells. Nat Cell Biol (2006) 3.37

Critical assessment of automated flow cytometry data analysis techniques. Nat Methods (2013) 3.30

The Felodipine Event Reduction (FEVER) Study: a randomized long-term placebo-controlled trial in Chinese hypertensive patients. J Hypertens (2005) 3.27

CEAS: cis-regulatory element annotation system. Nucleic Acids Res (2006) 3.15

A hidden Markov model for analyzing ChIP-chip experiments on genome tiling arrays and its application to p53 binding sequences. Bioinformatics (2005) 3.06

Analysis of the human endogenous coregulator complexome. Cell (2011) 2.97