Published in Genome Res on March 01, 2011
Epigenome characterization at single base-pair resolution. Proc Natl Acad Sci U S A (2011) 2.22
Genome-wide nucleosome positioning during embryonic stem cell development. Nat Struct Mol Biol (2012) 1.80
DANPOS: dynamic analysis of nucleosome position and occupancy by sequencing. Genome Res (2012) 1.65
Swi/Snf chromatin remodeling/tumor suppressor complex establishes nucleosome occupancy at target promoters. Proc Natl Acad Sci U S A (2013) 1.60
High-resolution mapping of chromatin packaging in mouse embryonic stem cells and sperm. Dev Cell (2014) 1.44
Insights into Nucleosome Organization in Mouse Embryonic Stem Cells through Chemical Mapping. Cell (2016) 1.41
Nucleosome-free region dominates histone acetylation in targeting SWR1 to promoters for H2A.Z replacement. Cell (2013) 1.35
Heat shock reduces stalled RNA polymerase II and nucleosome turnover genome-wide. Genes Dev (2011) 1.26
Remodelers organize cellular chromatin by counteracting intrinsic histone-DNA sequence preferences in a class-specific manner. Mol Cell Biol (2011) 1.19
Nucleosome positioning: bringing order to the eukaryotic genome. Trends Cell Biol (2012) 1.06
Two distinct promoter architectures centered on dynamic nucleosomes control ribosomal protein gene transcription. Genes Dev (2014) 1.05
MACE: model based analysis of ChIP-exo. Nucleic Acids Res (2014) 0.99
The budding yeast Centromere DNA Element II wraps a stable Cse4 hemisome in either orientation in vivo. Elife (2014) 0.95
The prenucleosome, a stable conformational isomer of the nucleosome. Genes Dev (2015) 0.94
RSC-dependent constructive and destructive interference between opposing arrays of phased nucleosomes in yeast. Genome Res (2014) 0.93
Stabilization of the promoter nucleosomes in nucleosome-free regions by the yeast Cyc8-Tup1 corepressor. Genome Res (2012) 0.93
Standardized collection of MNase-seq experiments enables unbiased dataset comparisons. BMC Mol Biol (2012) 0.92
Differential nuclease sensitivity profiling of chromatin reveals biochemical footprints coupled to gene expression and functional DNA elements in maize. Plant Cell (2014) 0.91
The Pioneer Transcription Factor FoxA Maintains an Accessible Nucleosome Configuration at Enhancers for Tissue-Specific Gene Activation. Mol Cell (2016) 0.90
MPE-seq, a new method for the genome-wide analysis of chromatin structure. Proc Natl Acad Sci U S A (2015) 0.89
Proximity of H2A.Z containing nucleosome to the transcription start site influences gene expression levels in the mammalian liver and brain. Nucleic Acids Res (2012) 0.88
MNase titration reveals differences between nucleosome occupancy and chromatin accessibility. Nat Commun (2016) 0.86
Uncoupling transcription from covalent histone modification. PLoS Genet (2014) 0.86
Genome-wide profiling of nucleosome sensitivity and chromatin accessibility in Drosophila melanogaster. Nucleic Acids Res (2015) 0.84
Genome-wide prediction of nucleosome occupancy in maize reveals plant chromatin structural features at genes and other elements at multiple scales. Plant Physiol (2013) 0.84
Nucleosome architecture throughout the cell cycle. Sci Rep (2016) 0.82
A conserved function for the H2A.Z C terminus. J Biol Chem (2012) 0.81
Epigenomics and the structure of the living genome. Genome Res (2015) 0.80
MNase-Sensitive Complexes in Yeast: Nucleosomes and Non-histone Barriers. Mol Cell (2017) 0.80
Dynamic nucleosome organization at hox promoters during zebrafish embryogenesis. PLoS One (2013) 0.79
Constitutive turnover of histone H2A.Z at yeast promoters requires the preinitiation complex. Elife (2016) 0.79
Yeast high mobility group protein HMO1 stabilizes chromatin and is evicted during repair of DNA double strand breaks. Nucleic Acids Res (2015) 0.78
Topoisomerase II regulates yeast genes with singular chromatin architectures. Nucleic Acids Res (2013) 0.77
Uncovering the functional constraints underlying the genomic organization of the odorant-binding protein genes. Genome Biol Evol (2013) 0.77
Nucleosome fragility is associated with future transcriptional response to developmental cues and stress in C. elegans. Genome Res (2016) 0.76
A matter of access. Nucleosome disassembly from gene promoters is the central goal of transcriptional activators. Transcription (2014) 0.76
Enhancer regions show high histone H3.3 turnover that changes during differentiation. Elife (2016) 0.76
Understanding nucleosome dynamics and their links to gene expression and DNA replication. Nat Rev Mol Cell Biol (2017) 0.76
Prenucleosomes and Active Chromatin. Cold Spring Harb Symp Quant Biol (2016) 0.75
Dissecting relative contributions of cis- and trans-determinants to nucleosome distribution by comparing Tetrahymena macronuclear and micronuclear chromatin. Nucleic Acids Res (2016) 0.75
Widespread changes in nucleosome accessibility without changes in nucleosome occupancy during a rapid transcriptional induction. Genes Dev (2017) 0.75
Molecular mechanisms that distinguish TFIID housekeeping from regulatable SAGA promoters. EMBO J (2016) 0.75
H4K44 Acetylation Facilitates Chromatin Accessibility during Meiosis. Cell Rep (2015) 0.75
CAM: A quality control pipeline for MNase-seq data. PLoS One (2017) 0.75
Genome-wide Mapping of the Nucleosome Landscape by Micrococcal Nuclease and Chemical Mapping. Trends Genet (2017) 0.75
Genome-wide chromatin mapping with size resolution reveals a dynamic sub-nucleosomal landscape in Arabidopsis. PLoS Genet (2017) 0.75
The transcriptional landscape of the yeast genome defined by RNA sequencing. Science (2008) 48.99
Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature (1997) 44.55
Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell (2000) 36.09
Genome-scale identification of nucleosome positions in S. cerevisiae. Science (2005) 15.04
A high-resolution atlas of nucleosome occupancy in yeast. Nat Genet (2007) 12.21
The DNA-encoded nucleosome organization of a eukaryotic genome. Nature (2008) 11.41
Remodeling of yeast genome expression in response to environmental changes. Mol Biol Cell (2001) 9.63
Alteration of nucleosome structure as a mechanism of transcriptional regulation. Annu Rev Biochem (1998) 8.86
Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome. Nature (2007) 8.68
Nucleosome organization in the Drosophila genome. Nature (2008) 8.65
A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome Res (2008) 7.89
H3.3/H2A.Z double variant-containing nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions. Nat Genet (2009) 5.82
Distinct modes of regulation by chromatin encoded through nucleosome positioning signals. PLoS Comput Biol (2008) 5.71
Action of micrococcal nuclease on chromatin and the location of histone H1. J Mol Biol (1977) 5.61
Rapid spontaneous accessibility of nucleosomal DNA. Nat Struct Mol Biol (2004) 5.00
Nucleosome stability mediated by histone variants H3.3 and H2A.Z. Genes Dev (2007) 4.19
Two strategies for gene regulation by promoter nucleosomes. Genome Res (2008) 4.19
High-resolution nucleosome mapping reveals transcription-dependent promoter packaging. Genome Res (2009) 3.99
The logic of chromatin architecture and remodelling at promoters. Nature (2009) 3.63
Genome-wide analysis of the biology of stress responses through heat shock transcription factor. Mol Cell Biol (2004) 3.61
The yeast Mediator complex and its regulation. Trends Biochem Sci (2005) 2.15
Mediator complexes and eukaryotic transcription regulation: an overview. Biochimie (2007) 1.60
Stress-dependent dynamics of global chromatin remodeling in yeast: dual role for SWI/SNF in the heat shock stress response. Mol Cell Biol (2008) 1.54
Blurring of high-resolution data shows that the effect of intrinsic nucleosome occupancy on transcription factor binding is mostly regional, not local. PLoS Comput Biol (2010) 0.94
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 sequence of the Brown Norway rat yields insights into mammalian evolution. Nature (2004) 24.40
Genome-wide analysis of estrogen receptor binding sites. Nat Genet (2006) 18.63
Evolutionary and biomedical insights from the rhesus macaque genome. Science (2007) 16.21
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
The Atlas genome assembly system. Genome Res (2004) 9.78
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
Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution. Genome Res (2005) 8.38
The genome of the cucumber, Cucumis sativus L. Nat Genet (2009) 8.19
Model-based analysis of two-color arrays (MA2C). Genome Biol (2007) 7.28
Performance comparison of exome DNA sequencing technologies. Nat Biotechnol (2011) 7.11
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
The DNA sequence of the human X chromosome. Nature (2005) 6.97
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
Performance comparison of whole-genome sequencing platforms. Nat Biotechnol (2011) 5.79
BSMAP: whole genome bisulfite sequence MAPping program. BMC Bioinformatics (2009) 5.67
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
High-precision, whole-genome sequencing of laboratory strains facilitates genetic studies. PLoS Genet (2008) 4.86
Dnmt3a is essential for hematopoietic stem cell differentiation. Nat Genet (2011) 4.85
A G protein-coupled receptor is a plasma membrane receptor for the plant hormone abscisic acid. Science (2007) 4.61
RSeQC: quality control of RNA-seq experiments. Bioinformatics (2012) 4.31
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
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
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
Simultaneous generation and germline transmission of multiple gene mutations in rat using CRISPR-Cas systems. Nat Biotechnol (2013) 3.65
Regulation of hypoxia-inducible factor 2alpha signaling by the stress-responsive deacetylase sirtuin 1. Science (2009) 3.64
Molecular phenotyping of human ovarian cancer stem cells unravels the mechanisms for repair and chemoresistance. Cell Cycle (2009) 3.60
Patient-specific induced pluripotent stem cells as a model for familial dilated cardiomyopathy. Sci Transl Med (2012) 3.53
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
The Felodipine Event Reduction (FEVER) Study: a randomized long-term placebo-controlled trial in Chinese hypertensive patients. J Hypertens (2005) 3.27
TLR-4 signaling promotes tumor growth and paclitaxel chemoresistance in ovarian cancer. Cancer Res (2006) 3.21
CEAS: cis-regulatory element annotation system. Nucleic Acids Res (2006) 3.15
optix drives the repeated convergent evolution of butterfly wing pattern mimicry. Science (2011) 2.99
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
Prolonged diabetes reversal after intraportal xenotransplantation of wild-type porcine islets in immunosuppressed nonhuman primates. Nat Med (2006) 2.83
Huntington toxicity in yeast model depends on polyglutamine aggregation mediated by a prion-like protein Rnq1. J Cell Biol (2002) 2.76
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
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
Exome capture reveals ZNF423 and CEP164 mutations, linking renal ciliopathies to DNA damage response signaling. Cell (2012) 2.54
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
Mutations in U4atac snRNA, a component of the minor spliceosome, in the developmental disorder MOPD I. Science (2011) 2.47
A drinking water crisis in Lake Taihu, China: linkage to climatic variability and lake management. Environ Manage (2010) 2.45
Hyperglycemia-induced apoptosis in mouse myocardium: mitochondrial cytochrome C-mediated caspase-3 activation pathway. Diabetes (2002) 2.44
Early use of noninvasive positive pressure ventilation for acute lung injury: a multicenter randomized controlled trial. Crit Care Med (2012) 2.43
Fission yeast Scm3: A CENP-A receptor required for integrity of subkinetochore chromatin. Mol Cell (2009) 2.41
GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis. Nucleic Acids Res (2008) 2.35
Molecular architecture of the kinetochore-microtubule attachment site is conserved between point and regional centromeres. J Cell Biol (2008) 2.34
Genetic association of FOXO1A and FOXO3A with longevity trait in Han Chinese populations. Hum Mol Genet (2009) 2.34
Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing. BMC Genomics (2005) 2.34
Hemorrhagic fever caused by a novel Bunyavirus in China: pathogenesis and correlates of fatal outcome. Clin Infect Dis (2011) 2.34
Parallel processing in two transmitter microenvironments at the cone photoreceptor synapse. Neuron (2006) 2.34
Role of hydrogen sulfide in the development of atherosclerotic lesions in apolipoprotein E knockout mice. Arterioscler Thromb Vasc Biol (2008) 2.29
Molecular analysis of kinetochore architecture in fission yeast. EMBO J (2005) 2.29
NSD2 links dimethylation of histone H3 at lysine 36 to oncogenic programming. Mol Cell (2011) 2.27
ElliPro: a new structure-based tool for the prediction of antibody epitopes. BMC Bioinformatics (2008) 2.26
A phase II trial of Xeloda and oxaliplatin (XELOX) neo-adjuvant chemotherapy followed by surgery for advanced gastric cancer patients with para-aortic lymph node metastasis. Cancer Chemother Pharmacol (2014) 2.26
Derepression of ethylene-stabilized transcription factors (EIN3/EIL1) mediates jasmonate and ethylene signaling synergy in Arabidopsis. Proc Natl Acad Sci U S A (2011) 2.25
Extracellular signal-regulated kinase 2 is necessary for mesoderm differentiation. Proc Natl Acad Sci U S A (2003) 2.25
The Drosophila melanogaster transcriptome by paired-end RNA sequencing. Genome Res (2010) 2.25
Identification of drought-induced microRNAs in rice. Biochem Biophys Res Commun (2007) 2.24
The ecology, genetic diversity, and phylogeny of Huaiyangshan virus in China. J Virol (2011) 2.23
Oxysterols direct immune cell migration via EBI2. Nature (2011) 2.19
Ventricular fibrosis suggested by cardiovascular magnetic resonance in adults with repaired tetralogy of fallot and its relationship to adverse markers of clinical outcome. Circulation (2006) 2.18
Prognostic value of coronary CT angiography and calcium score for major adverse cardiac events in outpatients. JACC Cardiovasc Imaging (2012) 2.17
Conserved developmental transcriptomes in evolutionarily divergent species. Genome Biol (2010) 2.16
An oligonucleotide microarray for microRNA expression analysis based on labeling RNA with quantum dot and nanogold probe. Nucleic Acids Res (2005) 2.15
Hemorrhagic fever caused by a novel tick-borne Bunyavirus in Huaiyangshan, China. Zhonghua Liu Xing Bing Xue Za Zhi (2011) 2.15
The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome. Nat Biotechnol (2012) 2.14
The cytochrome P450scc system opens an alternate pathway of vitamin D3 metabolism. FEBS J (2005) 2.12
EuPathDB: a portal to eukaryotic pathogen databases. Nucleic Acids Res (2009) 2.11
Erk5 null mice display multiple extraembryonic vascular and embryonic cardiovascular defects. Proc Natl Acad Sci U S A (2002) 2.11
Foxa2 and H2A.Z mediate nucleosome depletion during embryonic stem cell differentiation. Cell (2012) 2.02