Published in Genome Biol on January 01, 2007
Model-based analysis of ChIP-Seq (MACS). Genome Biol (2008) 51.63
Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature (2009) 24.41
An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat Biotechnol (2008) 13.96
Differential chromatin marking of introns and expressed exons by H3K36me3. Nat Genet (2009) 8.11
Modeling non-uniformity in short-read rates in RNA-Seq data. Genome Biol (2010) 6.10
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
Drosophila ORC localizes to open chromatin and marks sites of cohesin complex loading. Genome Res (2009) 2.66
Chromatin signature of embryonic pluripotency is established during genome activation. Nature (2010) 2.64
An epigenetic signature for monoallelic olfactory receptor expression. Cell (2011) 2.56
Broad chromosomal domains of histone modification patterns in C. elegans. Genome Res (2010) 2.36
Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs. Genome Res (2007) 2.16
ChIP-chip versus ChIP-seq: lessons for experimental design and data analysis. BMC Genomics (2011) 1.80
Significance analysis and statistical dissection of variably methylated regions. Biostatistics (2011) 1.74
Caenorhabditis elegans chromosome arms are anchored to the nuclear membrane via discontinuous association with LEM-2. Genome Biol (2010) 1.69
Identification and characterization of Hoxa9 binding sites in hematopoietic cells. Blood (2011) 1.63
Impact of an exercise intervention on DNA methylation in skeletal muscle from first-degree relatives of patients with type 2 diabetes. Diabetes (2012) 1.54
Condensin controls recruitment of RNA polymerase II to achieve nematode X-chromosome dosage compensation. Elife (2013) 1.51
A study of the relationships between oligonucleotide properties and hybridization signal intensities from NimbleGen microarray datasets. Nucleic Acids Res (2008) 1.47
Gene expression profiling of human breast tissue samples using SAGE-Seq. Genome Res (2010) 1.41
Activation-induced cytidine deaminase induces reproducible DNA breaks at many non-Ig Loci in activated B cells. Mol Cell (2011) 1.39
A blind deconvolution approach to high-resolution mapping of transcription factor binding sites from ChIP-seq data. Genome Biol (2009) 1.39
Gene-body hypermethylation of ATM in peripheral blood DNA of bilateral breast cancer patients. Hum Mol Genet (2009) 1.33
Statistical approaches for the analysis of DNA methylation microarray data. Hum Genet (2011) 1.31
A data integration approach to mapping OCT4 gene regulatory networks operative in embryonic stem cells and embryonal carcinoma cells. PLoS One (2010) 1.31
PU.1 and C/EBP(alpha) synergistically program distinct response to NF-kappaB activation through establishing monocyte specific enhancers. Proc Natl Acad Sci U S A (2011) 1.30
Chromatin organization in sperm may be the major functional consequence of base composition variation in the human genome. PLoS Genet (2011) 1.27
Lamin A/C-promoter interactions specify chromatin state-dependent transcription outcomes. Genome Res (2013) 1.23
The SKP1-Cul1-F-box and leucine-rich repeat protein 4 (SCF-FbxL4) ubiquitin ligase regulates lysine demethylase 4A (KDM4A)/Jumonji domain-containing 2A (JMJD2A) protein. J Biol Chem (2011) 1.22
Developmental control of gene copy number by repression of replication initiation and fork progression. Genome Res (2011) 1.20
Chromosome-biased binding and gene regulation by the Caenorhabditis elegans DRM complex. PLoS Genet (2011) 1.20
Getting started in tiling microarray analysis. PLoS Comput Biol (2007) 1.20
Pre-replication complex proteins assemble at regions of low nucleosome occupancy within the Chinese hamster dihydrofolate reductase initiation zone. Nucleic Acids Res (2010) 1.13
CBX3 regulates efficient RNA processing genome-wide. Genome Res (2012) 1.10
Role for the nuclear receptor-binding SET domain protein 1 (NSD1) methyltransferase in coordinating lysine 36 methylation at histone 3 with RNA polymerase II function. Proc Natl Acad Sci U S A (2010) 1.09
Dynamic changes in nucleosome occupancy are not predictive of gene expression dynamics but are linked to transcription and chromatin regulators. Mol Cell Biol (2012) 1.08
An extended set of PRDM1/BLIMP1 target genes links binding motif type to dynamic repression. Nucleic Acids Res (2010) 1.07
MM-ChIP enables integrative analysis of cross-platform and between-laboratory ChIP-chip or ChIP-seq data. Genome Biol (2011) 1.07
Association of reading disabilities with regions marked by acetylated H3 histones in KIAA0319. Am J Med Genet B Neuropsychiatr Genet (2010) 1.05
Integrative analysis of gene amplification in Drosophila follicle cells: parameters of origin activation and repression. Genes Dev (2011) 1.02
Caenorhabditis elegans dosage compensation regulates histone H4 chromatin state on X chromosomes. Mol Cell Biol (2012) 1.02
Multiplatform single-sample estimates of transcriptional activation. Proc Natl Acad Sci U S A (2013) 1.00
The level of origin firing inversely affects the rate of replication fork progression. J Cell Biol (2013) 1.00
Probe signal correction for differential methylation hybridization experiments. BMC Bioinformatics (2008) 0.99
Waved aCGH: to smooth or not to smooth. Nucleic Acids Res (2010) 0.93
Systems analysis of ATF3 in stress response and cancer reveals opposing effects on pro-apoptotic genes in p53 pathway. PLoS One (2011) 0.90
Dynamic loading and redistribution of the Mcm2-7 helicase complex through the cell cycle. EMBO J (2015) 0.89
An evaluation of two-channel ChIP-on-chip and DNA methylation microarray normalization strategies. BMC Genomics (2012) 0.87
Euchromatic subdomains in rice centromeres are associated with genes and transcription. Plant Cell (2011) 0.86
Defining heterochromatin in C. elegans through genome-wide analysis of the heterochromatin protein 1 homolog HPL-2. Genome Res (2014) 0.85
Improved ChIP-chip analysis by a mixture model approach. BMC Bioinformatics (2009) 0.85
Genome-wide analysis links emerin to neuromuscular junction activity in Caenorhabditis elegans. Genome Biol (2014) 0.85
Tiling array data analysis: a multiscale approach using wavelets. BMC Bioinformatics (2011) 0.84
Comparison of sequence-dependent tiling array normalization approaches. BMC Bioinformatics (2009) 0.82
A Method to Study the Epigenetic Chromatin States of Rare Hematopoietic Stem and Progenitor Cells; MiniChIP-Chip. Biol Proced Online (2010) 0.80
Targeted chromatin profiling reveals novel enhancers in Ig H and Ig L chain Loci. J Immunol (2013) 0.80
Characterizing the interplay between multiple levels of organization within bacterial sigma factor regulatory networks. Nat Commun (2013) 0.79
Analysis of biological features associated with meiotic recombination hot and cold spots in Saccharomyces cerevisiae. PLoS One (2011) 0.79
Epigenetic change detection and pattern recognition via Bayesian hierarchical hidden Markov models. Stat Med (2012) 0.79
Current trends in the development and application of molecular technologies for cancer epigenetics. World J Gastroenterol (2013) 0.78
ChIP-Chip: algorithms for calling binding sites. Methods Mol Biol (2009) 0.78
Genome-wide measurement of protein-DNA binding dynamics using competition ChIP. Nat Protoc (2013) 0.78
Dynamic estrogen receptor interactomes control estrogen-responsive trefoil Factor (TFF) locus cell-specific activities. Mol Cell Biol (2014) 0.77
Double error shrinkage method for identifying protein binding sites observed by tiling arrays with limited replication. Bioinformatics (2009) 0.76
Identification of thyroid hormone receptor binding sites in developing mouse cerebellum. BMC Genomics (2013) 0.76
Conserved forkhead dimerization motif controls DNA replication timing and spatial organization of chromosomes in S. cerevisiae. Proc Natl Acad Sci U S A (2017) 0.75
Detection of epigenetic changes using ANOVA with spatially varying coefficients. Stat Appl Genet Mol Biol (2013) 0.75
Sensitive and accurate identification of protein-DNA binding events in ChIP-chip assays using higher order derivative analysis. Nucleic Acids Res (2010) 0.75
Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics (2003) 100.88
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics (2003) 82.89
Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res (2002) 40.03
Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet (2007) 32.41
A high-resolution map of active promoters in the human genome. Nature (2005) 24.35
Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science (2005) 16.82
Genome-scale identification of nucleosome positions in S. cerevisiae. Science (2005) 15.04
Model-based analysis of tiling-arrays for ChIP-chip. Proc Natl Acad Sci U S A (2006) 13.68
Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects. Nucleic Acids Res (2001) 12.92
Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays. Nat Methods (2006) 8.52
Feature extraction and normalization algorithms for high-density oligonucleotide gene expression array data. J Cell Biochem Suppl (2001) 8.50
Robust estimators for expression analysis. Bioinformatics (2002) 8.30
High-throughput mapping of the chromatin structure of human promoters. Nat Biotechnol (2007) 5.24
DPY-27:a chromosome condensation protein homolog that regulates C. elegans dosage compensation through association with the X chromosome. Cell (1994) 4.74
Genome-wide mapping of the cohesin complex in the yeast Saccharomyces cerevisiae. PLoS Biol (2004) 4.03
ChIPOTle: a user-friendly tool for the analysis of ChIP-chip data. Genome Biol (2005) 3.83
Microarray-based DNA methylation profiling: technology and applications. Nucleic Acids Res (2006) 3.73
X chromosome repression by localization of the C. elegans dosage compensation machinery to sites of transcription initiation. Nat Genet (2007) 3.14
Profound effect of normalization on detection of differentially expressed genes in oligonucleotide microarray data analysis. Genome Biol (2002) 2.64
Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome. Genome Res (2006) 1.95
A new approach to intensity-dependent normalization of two-channel microarrays. Biostatistics (2006) 1.86
SDC-3 coordinates the assembly of a dosage compensation complex on the nematode X chromosome. Development (1997) 1.76
How to find an opening (or lots of them). Nat Methods (2006) 1.19
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
Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature (2009) 24.41
Genome-wide analysis of estrogen receptor binding sites. Nat Genet (2006) 18.63
Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature (2012) 18.23
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
Tackling the widespread and critical impact of batch effects in high-throughput data. Nat Rev Genet (2010) 11.82
Bayesian haplotype inference for multiple linked single-nucleotide polymorphisms. Am J Hum Genet (2001) 10.48
An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments. Nat Biotechnol (2002) 10.23
Partition-ligation-expectation-maximization algorithm for haplotype inference with single-nucleotide polymorphisms. Am J Hum Genet (2002) 10.12
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
Methylation of histone H3 Lys 4 in coding regions of active genes. Proc Natl Acad Sci U S A (2002) 7.67
Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells. Nature (2011) 7.43
The CREB coactivator TORC2 is a key regulator of fasting glucose metabolism. Nature (2005) 7.14
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
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
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
Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157. Nucleic Acids Res (2002) 4.92
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 sva package for removing batch effects and other unwanted variation in high-throughput experiments. Bioinformatics (2012) 4.48
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
Bayesian inference of epistatic interactions in case-control studies. Nat Genet (2007) 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
Frequent switching of Polycomb repressive marks and DNA hypermethylation in the PC3 prostate cancer cell line. Proc Natl Acad Sci U S A (2008) 4.20
A novel influenza A (H1N1) vaccine in various age groups. N Engl J Med (2009) 4.20
The Spo0A regulon of Bacillus subtilis. Mol Microbiol (2003) 4.19
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
Candidate exome capture identifies mutation of SDCCAG8 as the cause of a retinal-renal ciliopathy. Nat Genet (2010) 3.99
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
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
Using VAAST to identify an X-linked disorder resulting in lethality in male infants due to N-terminal acetyltransferase deficiency. Am J Hum Genet (2011) 3.43
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
The program of gene transcription for a single differentiating cell type during sporulation in Bacillus subtilis. PLoS Biol (2004) 3.33
The Felodipine Event Reduction (FEVER) Study: a randomized long-term placebo-controlled trial in Chinese hypertensive patients. J Hypertens (2005) 3.27
Genomic sequence is highly predictive of local nucleosome depletion. PLoS Comput Biol (2007) 3.24
NONCODE: an integrated knowledge database of non-coding RNAs. Nucleic Acids Res (2005) 3.16
CEAS: cis-regulatory element annotation system. Nucleic Acids Res (2006) 3.15
X chromosome repression by localization of the C. elegans dosage compensation machinery to sites of transcription initiation. Nat Genet (2007) 3.14
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
Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids. Plant Cell (2010) 2.92
Homeobox gene methylation in lung cancer studied by genome-wide analysis with a microarray-based methylated CpG island recovery assay. Proc Natl Acad Sci U S A (2007) 2.91
Topological structure analysis of the protein-protein interaction network in budding yeast. Nucleic Acids Res (2003) 2.90
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