Published in Genome Res on October 29, 2008
The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets. Bioinformatics (2009) 10.30
Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver. Genome Res (2009) 4.11
g:Profiler--a web server for functional interpretation of gene lists (2011 update). Nucleic Acids Res (2011) 3.94
Epigenetic mechanisms that underpin metabolic and cardiovascular diseases. Nat Rev Endocrinol (2009) 3.25
Redefining CpG islands using hidden Markov models. Biostatistics (2010) 2.03
DNA methylation status predicts cell type-specific enhancer activity. EMBO J (2011) 1.98
Tissue-specific dysregulation of DNA methylation in aging. Aging Cell (2010) 1.90
Identification and systematic annotation of tissue-specific differentially methylated regions using the Illumina 450k array. Epigenetics Chromatin (2013) 1.62
Genome-wide survey reveals dynamic widespread tissue-specific changes in DNA methylation during development. BMC Genomics (2011) 1.56
A pipeline for the quantitative analysis of CG dinucleotide methylation using mass spectrometry. Bioinformatics (2009) 1.42
QDMR: a quantitative method for identification of differentially methylated regions by entropy. Nucleic Acids Res (2011) 1.37
A species-generalized probabilistic model-based definition of CpG islands. Mamm Genome (2009) 1.36
Genomic landscape of developing male germ cells. Birth Defects Res C Embryo Today (2009) 1.00
Characterization of tissue-specific differential DNA methylation suggests distinct modes of positive and negative gene expression regulation. BMC Genomics (2015) 0.95
Emerging patterns of epigenomic variation. Trends Genet (2011) 0.95
Functional O-GlcNAc modifications: implications in molecular regulation and pathophysiology. Crit Rev Biochem Mol Biol (2014) 0.94
Single-stranded noncoding RNAs mediate local epigenetic alterations at gene promoters in rat cell lines. J Biol Chem (2011) 0.92
Regulation of IGF2 transcript and protein expression by altered methylation in breast cancer. J Cancer Res Clin Oncol (2010) 0.91
Genetic modifiers of carcinogen DNA adducts in target lung and peripheral blood mononuclear cells. Carcinogenesis (2010) 0.91
Limitation of immune tolerance-inducing thymic epithelial cell development by Spi-B-mediated negative feedback regulation. J Exp Med (2014) 0.90
Oocyte-specific linker histone H1foo is an epigenomic modulator that decondenses chromatin and impairs pluripotency. Epigenetics (2012) 0.86
Comparative DNA methylome analysis of endometrial carcinoma reveals complex and distinct deregulation of cancer promoters and enhancers. BMC Genomics (2014) 0.86
Epigenetic switching by the metabolism-sensing factors in the generation of orexin neurons from mouse embryonic stem cells. J Biol Chem (2013) 0.85
Cross-tissue comparisons of leptin and adiponectin: DNA methylation profiles. Adipocyte (2014) 0.84
DNA methylation status of NKX2-5, GATA4 and HAND1 in patients with tetralogy of fallot. BMC Med Genomics (2013) 0.83
swDMR: A Sliding Window Approach to Identify Differentially Methylated Regions Based on Whole Genome Bisulfite Sequencing. PLoS One (2015) 0.83
Association of promoter methylation statuses of congenital heart defect candidate genes with Tetralogy of Fallot. J Transl Med (2014) 0.83
DNA methylation: conducting the orchestra from exposure to phenotype? Clin Epigenetics (2016) 0.81
Revealing the transcriptome landscape of mouse spermatogonial cells by tiling microarray. Methods Mol Biol (2012) 0.81
Diabetes Induces Aberrant DNA Methylation in the Proximal Tubules of the Kidney. J Am Soc Nephrol (2015) 0.81
DNA methylation profile dynamics of tissue-dependent and differentially methylated regions during mouse brain development. BMC Genomics (2013) 0.80
DNA methylation status of nuclear-encoded mitochondrial genes underlies the tissue-dependent mitochondrial functions. BMC Genomics (2010) 0.80
DNA methylation profiles provide a viable index for porcine pluripotent stem cells. Genesis (2013) 0.80
Potential mechanisms of aberrant DNA hypomethylation on the x chromosome in uterine leiomyomas. J Reprod Dev (2013) 0.80
DNA methylation profile of Aire-deficient mouse medullary thymic epithelial cells. BMC Immunol (2012) 0.79
Genome-wide DNA methylation analyses in the brain reveal four differentially methylated regions between humans and non-human primates. BMC Evol Biol (2012) 0.79
Sequence and expression analysis of gaps in human chromosome 20. Nucleic Acids Res (2012) 0.79
Bridging sequence diversity and tissue-specific expression by DNA methylation in genes of the mouse prolactin superfamily. Mamm Genome (2011) 0.78
Epigenetic regulation of sox30 is associated with testis development in mice. PLoS One (2014) 0.78
Identification of embryonic precursor cells that differentiate into thymic epithelial cells expressing autoimmune regulator. J Exp Med (2016) 0.78
High-resolution genome-wide DNA methylation maps of mouse primary female dermal fibroblasts and keratinocytes. Epigenetics Chromatin (2014) 0.77
Ultra-Deep Bisulfite Sequencing to Detect Specific DNA Methylation Patterns of Minor Cell Types in Heterogeneous Cell Populations: An Example of the Pituitary Tissue. PLoS One (2016) 0.77
Regulation of maintenance DNA methylation via histone ubiquitylation. J Biochem (2015) 0.77
Nucleosomes are enriched at the boundaries of hypomethylated regions (HMRs) in mouse dermal fibroblasts and keratinocytes. Epigenetics Chromatin (2014) 0.77
CpG methylation changes within the IL2RA promoter in type 1 diabetes of childhood onset. PLoS One (2013) 0.76
Influence of relative NK-DC abundance on placentation and its relation to epigenetic programming in the offspring. Cell Death Dis (2014) 0.76
Cell-Specific Polymorphism and Hormonal Regulation of DNA Methylation in Scavenger Receptor Class B, Type I. DNA Cell Biol (2016) 0.76
Intraindividual dynamics of transcriptome and genome-wide stability of DNA methylation. Sci Rep (2016) 0.75
Putative Epimutagens in Maternal Peripheral and Cord Blood Samples Identified Using Human Induced Pluripotent Stem Cells. Biomed Res Int (2015) 0.75
The promoter of the oocyte-specific gene, Oog1, functions in both male and female meiotic germ cells in transgenic mice. PLoS One (2013) 0.75
DNA methylation profiling of the fibrinogen gene landscape in human cells and during mouse and zebrafish development. PLoS One (2013) 0.75
Identification of uterine leiomyoma-specific marker genes based on DNA methylation and their clinical application. Sci Rep (2016) 0.75
Establishment of DNA methylation patterns of the Fibrillin1 (FBN1) gene in porcine embryos and tissues. J Reprod Dev (2017) 0.75
DNA methylation signature of long noncoding RNA genes during human pre-implantation embryonic development. Oncotarget (2017) 0.75
Origin of a rapidly evolving homeostatic control system programming testis function. J Endocrinol (2017) 0.75
Genome-Wide Epigenetic Characterization of Tissues from Three Germ Layers Isolated from Sheep Fetuses. Front Genet (2017) 0.75
Hydroxylation of methylated DNA by TET1 in chondrocyte differentiation of C3H10T1/2 cells. Biochem Biophys Rep (2015) 0.75
Bioconductor: open software development for computational biology and bioinformatics. Genome Biol (2004) 143.19
High-resolution profiling of histone methylations in the human genome. Cell (2007) 85.74
EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet (2000) 69.26
From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res (2006) 44.35
TM4: a free, open-source system for microarray data management and analysis. Biotechniques (2003) 38.02
Galaxy: a platform for interactive large-scale genome analysis. Genome Res (2005) 35.75
Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell (2008) 32.65
Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature (2008) 30.29
Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature (2008) 26.78
Large-scale analysis of the human and mouse transcriptomes. Proc Natl Acad Sci U S A (2002) 25.47
CpG islands in vertebrate genomes. J Mol Biol (1987) 23.16
Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet (2007) 20.22
DNA methylation profiling of human chromosomes 6, 20 and 22. Nat Genet (2006) 18.08
DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists. Nucleic Acids Res (2007) 17.46
Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet (2005) 15.37
Model-based analysis of tiling-arrays for ChIP-chip. Proc Natl Acad Sci U S A (2006) 13.68
The UCSC genome browser database: update 2007. Nucleic Acids Res (2006) 13.04
Control of pancreas and liver gene expression by HNF transcription factors. Science (2004) 12.05
An overview of Ensembl. Genome Res (2004) 10.35
COBRA: a sensitive and quantitative DNA methylation assay. Nucleic Acids Res (1997) 9.94
DNA methylation and the frequency of CpG in animal DNA. Nucleic Acids Res (1980) 9.34
The non-coding Air RNA is required for silencing autosomal imprinted genes. Nature (2002) 7.37
g:Profiler--a web-based toolset for functional profiling of gene lists from large-scale experiments. Nucleic Acids Res (2007) 6.44
Comparative isoschizomer profiling of cytosine methylation: the HELP assay. Genome Res (2006) 5.99
BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing. Bioinformatics (2005) 5.95
A fraction of the mouse genome that is derived from islands of nonmethylated, CpG-rich DNA. Cell (1985) 5.63
Evidence for an instructive mechanism of de novo methylation in cancer cells. Nat Genet (2006) 4.97
MIRA-assisted microarray analysis, a new technology for the determination of DNA methylation patterns, identifies frequent methylation of homeodomain-containing genes in lung cancer cells. Cancer Res (2006) 3.66
A genome-wide screen for normally methylated human CpG islands that can identify novel imprinted genes. Genome Res (2002) 3.50
Orphan nuclear receptors: from gene to function. Endocr Rev (1999) 3.29
Detection and interpretation of altered methylation patterns in cancer cells. Nat Rev Cancer (2005) 3.27
Tissue-specific DNA methylation in a cluster of rabbit beta-like globin genes. Proc Natl Acad Sci U S A (1980) 2.74
Epigenetic control of mouse Oct-4 gene expression in embryonic stem cells and trophoblast stem cells. J Biol Chem (2004) 2.63
Epigenetic marks by DNA methylation specific to stem, germ and somatic cells in mice. Genes Cells (2002) 2.52
Epigenome analyses using BAC microarrays identify evolutionary conservation of tissue-specific methylation of SHANK3. Nat Genet (2005) 2.51
Epigenetic regulation of Nanog gene in embryonic stem and trophoblast stem cells. Genes Cells (2007) 2.51
Comprehensive DNA methylation profiling in a human cancer genome identifies novel epigenetic targets. Carcinogenesis (2006) 2.45
Abnormal CpG island methylation occurs during in vitro differentiation of human embryonic stem cells. Hum Mol Genet (2006) 2.27
Liver-enriched transcription factors in liver function and development. Part I: the hepatocyte nuclear factor network and liver-specific gene expression. Pharmacol Rev (2002) 2.02
DNA methylation and cancer. Oncogene (2002) 1.98
DNA methylation profiles of CpG islands for cellular differentiation and development in mammals. Cytogenet Genome Res (2004) 1.98
The MAPPER database: a multi-genome catalog of putative transcription factor binding sites. Nucleic Acids Res (2005) 1.80
Modulation of hepatic gene expression by hepatocyte nuclear factor 1. Science (1997) 1.79
Principles of hepatic organic anion transporter regulation during cholestasis, inflammation and liver regeneration. Biochim Biophys Acta (2006) 1.57
Genome-wide analysis reveals strong correlation between CpG islands with nearby transcription start sites of genes and their tissue specificity. Gene (2005) 1.57
Genome-wide profiling of promoter methylation in human. Oncogene (2006) 1.55
Genome-wide and locus-specific DNA hypomethylation in G9a deficient mouse embryonic stem cells. Genes Cells (2007) 1.52
Non-coding RNA directed DNA demethylation of Sphk1 CpG island. Biochem Biophys Res Commun (2004) 1.39
RNA-mediated gene silencing. Cell Mol Life Sci (2003) 1.35
Cell type-specific methylation profiles occurring disproportionately in CpG-less regions that delineate developmental similarity. Genes Cells (2007) 1.29
Regulatory network of lipid-sensing nuclear receptors: roles for CAR, PXR, LXR, and FXR. Arch Biochem Biophys (2005) 1.27
CpG island of rat sphingosine kinase-1 gene: tissue-dependent DNA methylation status and multiple alternative first exons. Genomics (2001) 1.27
DNA methylation-mediated control of Sry gene expression in mouse gonadal development. J Biol Chem (2004) 1.24
Preference of DNA methyltransferases for CpG islands in mouse embryonic stem cells. Genome Res (2004) 1.20
New insights into the regulation of methyl group and homocysteine metabolism. J Nutr (2007) 1.14
xMAN: extreme MApping of OligoNucleotides. BMC Genomics (2008) 1.06
DNA methylation regulates placental lactogen I gene expression. Endocrinology (2001) 1.06
Analysis of CpG islands of trophoblast giant cells by restriction landmark genomic scanning. Dev Genet (1998) 1.04
Applying whole-genome studies of epigenetic regulation to study human disease. Cytogenet Genome Res (2006) 1.01
Localizing hotspots of antisense transcription. Nucleic Acids Res (2007) 0.99
Two novel RXR alpha isoforms from mouse testis. Biochem Biophys Res Commun (1996) 0.85
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
Model-based analysis of tiling-arrays for ChIP-chip. Proc Natl Acad Sci U S A (2006) 13.68
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
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
MassBank: a public repository for sharing mass spectral data for life sciences. J Mass Spectrom (2010) 6.16
Origin and diversity of novel avian influenza A H7N9 viruses causing human infection: phylogenetic, structural, and coalescent analyses. Lancet (2013) 6.10
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
BSMAP: whole genome bisulfite sequence MAPping program. BMC Bioinformatics (2009) 5.67
Chromatin structure analyses identify miRNA promoters. Genes Dev (2008) 5.40
High-throughput mapping of the chromatin structure of human promoters. Nat Biotechnol (2007) 5.24
Chemotherapy-resistant human AML stem cells home to and engraft within the bone-marrow endosteal region. Nat Biotechnol (2007) 5.21
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
Bone marrow edema and its relation to progression of knee osteoarthritis. Ann Intern Med (2003) 4.98
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
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
PGC7/Stella protects against DNA demethylation in early embryogenesis. Nat Cell Biol (2006) 3.54
Meta-analysis of traditional Chinese patent medicine for ischemic stroke. Stroke (2007) 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
T cell self-reactivity forms a cytokine milieu for spontaneous development of IL-17+ Th cells that cause autoimmune arthritis. J Exp Med (2007) 3.29
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
Induction of cell cycle entry eliminates human leukemia stem cells in a mouse model of AML. Nat Biotechnol (2010) 3.13
A hidden Markov model for analyzing ChIP-chip experiments on genome tiling arrays and its application to p53 binding sequences. Bioinformatics (2005) 3.06
Analysis of the human endogenous coregulator complexome. Cell (2011) 2.97
SIRT7 links H3K18 deacetylation to maintenance of oncogenic transformation. Nature (2012) 2.96
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
CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model. Nucleic Acids Res (2013) 2.88
Crystal structure of a stable dimer reveals the molecular basis of serpin polymerization. Nature (2008) 2.88
Right ventricular function in adults with repaired tetralogy of Fallot assessed with cardiovascular magnetic resonance imaging: detrimental role of right ventricular outflow aneurysms or akinesia and adverse right-to-left ventricular interaction. J Am Coll Cardiol (2002) 2.87
Androgen receptor gene expression in prostate cancer is directly suppressed by the androgen receptor through recruitment of lysine-specific demethylase 1. Cancer Cell (2011) 2.86
Differentiation-specific histone modifications reveal dynamic chromatin interactions and partners for the intestinal transcription factor CDX2. Dev Cell (2010) 2.84
Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer. Nat Struct Mol Biol (2013) 2.84
Eukaryotic regulatory element conservation analysis and identification using comparative genomics. Genome Res (2004) 2.84
Prolonged diabetes reversal after intraportal xenotransplantation of wild-type porcine islets in immunosuppressed nonhuman primates. Nat Med (2006) 2.83
A role for fungal {beta}-glucans and their receptor Dectin-1 in the induction of autoimmune arthritis in genetically susceptible mice. J Exp Med (2005) 2.80
Evolutionarily conserved multisubunit RBL2/p130 and E2F4 protein complex represses human cell cycle-dependent genes in quiescence. Mol Cell (2007) 2.74
Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq. Genome Res (2010) 2.73
The PSA(-/lo) prostate cancer cell population harbors self-renewing long-term tumor-propagating cells that resist castration. Cell Stem Cell (2012) 2.69
A C. elegans model of nicotine-dependent behavior: regulation by TRP-family channels. Cell (2006) 2.68
Identifying positioned nucleosomes with epigenetic marks in human from ChIP-Seq. BMC Genomics (2008) 2.66
Chromatin signature of embryonic pluripotency is established during genome activation. Nature (2010) 2.64
Epigenetic control of mouse Oct-4 gene expression in embryonic stem cells and trophoblast stem cells. J Biol Chem (2004) 2.63
Genome-wide genetic changes during modern breeding of maize. Nat Genet (2012) 2.60
A complete sequence of the T. tengcongensis genome. Genome Res (2002) 2.60
A new Mycobacterium species causing diffuse lepromatous leprosy. Am J Clin Pathol (2008) 2.59
Activation of the imprinted Dlk1-Dio3 region correlates with pluripotency levels of mouse stem cells. J Biol Chem (2010) 2.59
Epigenetic marks by DNA methylation specific to stem, germ and somatic cells in mice. Genes Cells (2002) 2.52