Published in Bioinformatics on April 05, 2010
CTCF-mediated functional chromatin interactome in pluripotent cells. Nat Genet (2011) 6.55
Evaluation of algorithm performance in ChIP-seq peak detection. PLoS One (2010) 3.99
ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions. Genome Biol (2011) 2.47
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Integration of regulatory networks by NKX3-1 promotes androgen-dependent prostate cancer survival. Mol Cell Biol (2011) 1.56
Telomerase directly regulates NF-κB-dependent transcription. Nat Cell Biol (2012) 1.53
Picking ChIP-seq peak detectors for analyzing chromatin modification experiments. Nucleic Acids Res (2012) 1.49
AP-2γ regulates oestrogen receptor-mediated long-range chromatin interaction and gene transcription. EMBO J (2011) 1.49
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A transcriptional repressor co-regulatory network governing androgen response in prostate cancers. EMBO J (2012) 1.32
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TET1 is a maintenance DNA demethylase that prevents methylation spreading in differentiated cells. Nucleic Acids Res (2014) 1.19
Ago1 Interacts with RNA polymerase II and binds to the promoters of actively transcribed genes in human cancer cells. PLoS Genet (2013) 1.18
Transcription factor Ebf1 regulates differentiation stage-specific signaling, proliferation, and survival of B cells. Genes Dev (2012) 1.13
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MacroH2A1 regulates the balance between self-renewal and differentiation commitment in embryonic and adult stem cells. Mol Cell Biol (2012) 1.11
Latent regulatory potential of human-specific repetitive elements. Mol Cell (2012) 1.08
Q&A: ChIP-seq technologies and the study of gene regulation. BMC Biol (2010) 1.07
Normalization of ChIP-seq data with control. BMC Bioinformatics (2012) 1.06
Pluripotency-related, valproic acid (VPA)-induced genome-wide histone H3 lysine 9 (H3K9) acetylation patterns in embryonic stem cells. J Biol Chem (2011) 1.05
H3K9 histone acetylation predicts pluripotency and reprogramming capacity of ES cells. Nucleus (2011) 1.04
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A subset of Drosophila Myc sites remain associated with mitotic chromosomes colocalized with insulator proteins. Nat Commun (2013) 0.97
DROMPA: easy-to-handle peak calling and visualization software for the computational analysis and validation of ChIP-seq data. Genes Cells (2013) 0.95
Different promoter affinities account for specificity in MYC-dependent gene regulation. Elife (2016) 0.93
Co-binding by YY1 identifies the transcriptionally active, highly conserved set of CTCF-bound regions in primate genomes. Genome Biol (2013) 0.93
Clustered ChIP-Seq-defined transcription factor binding sites and histone modifications map distinct classes of regulatory elements. BMC Biol (2011) 0.93
Enriched domain detector: a program for detection of wide genomic enrichment domains robust against local variations. Nucleic Acids Res (2014) 0.90
A short survey of computational analysis methods in analysing ChIP-seq data. Hum Genomics (2011) 0.89
Cell-type specificity of ChIP-predicted transcription factor binding sites. BMC Genomics (2012) 0.87
Identification of the transcription factor ZEB1 as a central component of the adipogenic gene regulatory network. Elife (2014) 0.86
HMCan: a method for detecting chromatin modifications in cancer samples using ChIP-seq data. Bioinformatics (2013) 0.86
The Triform algorithm: improved sensitivity and specificity in ChIP-Seq peak finding. BMC Bioinformatics (2012) 0.86
Differential transcript isoform usage pre- and post-zygotic genome activation in zebrafish. BMC Genomics (2013) 0.86
GLUT3 is induced during epithelial-mesenchymal transition and promotes tumor cell proliferation in non-small cell lung cancer. Cancer Metab (2014) 0.85
Is this the right normalization? A diagnostic tool for ChIP-seq normalization. BMC Bioinformatics (2015) 0.81
Human DNA methylomes of neurodegenerative diseases show common epigenomic patterns. Transl Psychiatry (2016) 0.81
PPARG binding landscapes in macrophages suggest a genome-wide contribution of PU.1 to divergent PPARG binding in human and mouse. PLoS One (2012) 0.81
Control of developmentally primed erythroid genes by combinatorial co-repressor actions. Nat Commun (2015) 0.80
A statistical framework for power calculations in ChIP-seq experiments. Bioinformatics (2013) 0.80
Methods for cancer epigenome analysis. Adv Exp Med Biol (2013) 0.80
Chromatin state analysis of the barley epigenome reveals a higher-order structure defined by H3K27me1 and H3K27me3 abundance. Plant J (2015) 0.78
Detecting broad domains and narrow peaks in ChIP-seq data with hiddenDomains. BMC Bioinformatics (2016) 0.78
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Overexpression of the Heterochromatinization Factor BAHD1 in HEK293 Cells Differentially Reshapes the DNA Methylome on Autosomes and X Chromosome. Front Genet (2015) 0.77
A diffusion model for the coordination of DNA replication in Schizosaccharomyces pombe. Sci Rep (2016) 0.77
A computational model for histone mark propagation reproduces the distribution of heterochromatin in different human cell types. PLoS One (2013) 0.77
Features that define the best ChIP-seq peak calling algorithms. Brief Bioinform (2016) 0.76
Computational characterization of modes of transcriptional regulation of nuclear receptor genes. PLoS One (2014) 0.76
Bivalent-like chromatin markers are predictive for transcription start site distribution in human. PLoS One (2012) 0.76
DISMISS: detection of stranded methylation in MeDIP-Seq data. BMC Bioinformatics (2016) 0.75
groHMM: a computational tool for identifying unannotated and cell type-specific transcription units from global run-on sequencing data. BMC Bioinformatics (2015) 0.75
ChIP-BIT: Bayesian inference of target genes using a novel joint probabilistic model of ChIP-seq profiles. Nucleic Acids Res (2015) 0.75
Integrated analysis of hematopoietic differentiation outcomes and molecular characterization reveals unbiased differentiation capacity and minor transcriptional memory in HPC/HSC-iPSCs. Stem Cell Res Ther (2017) 0.75
Identifying peaks in *-seq data using shape information. BMC Bioinformatics (2016) 0.75
Optimizing ChIP-seq peak detectors using visual labels and supervised machine learning. Bioinformatics (2016) 0.75
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell (2008) 28.29
The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells. Nat Genet (2006) 20.76
A global map of p53 transcription-factor binding sites in the human genome. Cell (2006) 20.65
An oestrogen-receptor-alpha-bound human chromatin interactome. Nature (2009) 12.16
Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell (2012) 8.41
Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res (2011) 8.38
Dynamic changes in the human methylome during differentiation. Genome Res (2010) 7.96
Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation. Nat Methods (2005) 7.87
Whole-genome mapping of histone H3 Lys4 and 27 trimethylations reveals distinct genomic compartments in human embryonic stem cells. Cell Stem Cell (2007) 7.05
CTCF-mediated functional chromatin interactome in pluripotent cells. Nat Genet (2011) 6.55
Identification and characterization of enhancers controlling the inflammatory gene expression program in macrophages. Immunity (2010) 6.48
Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells. Nat Genet (2009) 6.39
A large fraction of extragenic RNA pol II transcription sites overlap enhancers. PLoS Biol (2010) 6.01
Whole-genome cartography of estrogen receptor alpha binding sites. PLoS Genet (2007) 5.85
Racial differences in incident heart failure among young adults. N Engl J Med (2009) 5.60
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Global mapping of c-Myc binding sites and target gene networks in human B cells. Proc Natl Acad Sci U S A (2006) 5.27
Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs). Genome Res (2007) 4.99
A common BIM deletion polymorphism mediates intrinsic resistance and inferior responses to tyrosine kinase inhibitors in cancer. Nat Med (2012) 4.90
Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies. Genome Res (2007) 4.59
Multiplex sequencing of paired-end ditags (MS-PET): a strategy for the ultra-high-throughput analysis of transcriptomes and genomes. Nucleic Acids Res (2006) 4.51
Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res (2009) 4.47
Racial differences in the progression from chronic renal insufficiency to end-stage renal disease in the United States. J Am Soc Nephrol (2003) 4.28
Conversion of Bcl-2 from protector to killer by interaction with nuclear orphan receptor Nur77/TR3. Cell (2004) 4.00
Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions. Bioinformatics (2006) 3.94
The sensitivity and specificity of a simple test to distinguish between urge and stress urinary incontinence. Ann Intern Med (2006) 3.93
Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. Genome Res (2007) 3.82
Evolution of the mammalian transcription factor binding repertoire via transposable elements. Genome Res (2008) 3.76
Genomic portrait of resectable hepatocellular carcinomas: implications of RB1 and FGF19 aberrations for patient stratification. Hepatology (2014) 3.31
ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing. Genome Biol (2010) 3.24
Phenotypic predictors of response to simvastatin therapy among African-Americans and Caucasians: the Cholesterol and Pharmacogenetics (CAP) Study. Am J Cardiol (2006) 2.94
Locally produced C5a binds to T cell-expressed C5aR to enhance effector T-cell expansion by limiting antigen-induced apoptosis. Blood (2008) 2.91
Determination of oestrogen-receptor status and ERBB2 status of breast carcinoma: a gene-expression profiling study. Lancet Oncol (2007) 2.90
Endoscopic and surgical treatments for achalasia: a systematic review and meta-analysis. Ann Surg (2009) 2.89
The incidence of end-stage renal disease is increasing faster than the prevalence of chronic renal insufficiency. Ann Intern Med (2004) 2.86
Opera: reconstructing optimal genomic scaffolds with high-throughput paired-end sequences. J Comput Biol (2011) 2.85
An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data. Bioinformatics (2008) 2.85
Jmjd3 contributes to the control of gene expression in LPS-activated macrophages. EMBO J (2009) 2.72
A randomized comparison of total or supracervical hysterectomy: surgical complications and clinical outcomes. Obstet Gynecol (2003) 2.57
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Decay-accelerating factor modulates induction of T cell immunity. J Exp Med (2005) 2.34
Sall4 regulates distinct transcription circuitries in different blastocyst-derived stem cell lineages. Cell Stem Cell (2008) 2.28
CHD7 targets active gene enhancer elements to modulate ES cell-specific gene expression. PLoS Genet (2010) 2.20
Association between marijuana exposure and pulmonary function over 20 years. JAMA (2012) 2.09
Genome-wide mutational signatures of aristolochic acid and its application as a screening tool. Sci Transl Med (2013) 2.07
Hot flushes, coronary heart disease, and hormone therapy in postmenopausal women. Menopause (2009) 2.07
Genome-wide mapping of RELA(p65) binding identifies E2F1 as a transcriptional activator recruited by NF-kappaB upon TLR4 activation. Mol Cell (2007) 2.05
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Effect of postmenopausal hormone therapy on cognitive function: the Heart and Estrogen/progestin Replacement Study. Am J Med (2002) 2.02
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Postmenopausal hormone therapy: does it cause incontinence? Obstet Gynecol (2005) 1.94
Control of hypertension in adults with chronic kidney disease in the United States. Hypertension (2005) 1.92
Oseltamivir ring prophylaxis for containment of 2009 H1N1 influenza outbreaks. N Engl J Med (2010) 1.79
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Absence of signaling into CD4⁺ cells via C3aR and C5aR enables autoinductive TGF-β1 signaling and induction of Foxp3⁺ regulatory T cells. Nat Immunol (2012) 1.74
Predictors of heart failure among women with coronary disease. Circulation (2004) 1.74
Prevalence and risk factors for urinary incontinence in women with type 2 diabetes and impaired fasting glucose: findings from the National Health and Nutrition Examination Survey (NHANES) 2001-2002. Diabetes Care (2006) 1.71
Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes. Genome Res (2011) 1.67
A short Nur77-derived peptide converts Bcl-2 from a protector to a killer. Cancer Cell (2008) 1.66
A genomic survey of positive selection in Burkholderia pseudomallei provides insights into the evolution of accidental virulence. PLoS Pathog (2010) 1.65
The expression of CRM1 is associated with prognosis in human osteosarcoma. Oncol Rep (2009) 1.64
Association of TGFBR2 polymorphism with risk of sudden cardiac arrest in patients with coronary artery disease. Heart Rhythm (2009) 1.59
Decay accelerating factor can control T cell differentiation into IFN-gamma-producing effector cells via regulating local C5a-induced IL-12 production. J Immunol (2007) 1.59
Menopausal symptoms in older women and the effects of treatment with hormone therapy. Obstet Gynecol (2002) 1.57
Common beta-adrenergic receptor polymorphisms are not associated with risk of sudden cardiac death in patients with coronary artery disease. Heart Rhythm (2008) 1.56
Integration of regulatory networks by NKX3-1 promotes androgen-dependent prostate cancer survival. Mol Cell Biol (2011) 1.56
Cellular reprogramming by the conjoint action of ERα, FOXA1, and GATA3 to a ligand-inducible growth state. Mol Syst Biol (2011) 1.55
Telomerase directly regulates NF-κB-dependent transcription. Nat Cell Biol (2012) 1.53
The "costs" of urinary incontinence for women. Obstet Gynecol (2006) 1.52
Using indirect protein-protein interactions for protein complex prediction. J Bioinform Comput Biol (2008) 1.52
Hysterectomy versus expanded medical treatment for abnormal uterine bleeding: clinical outcomes in the medicine or surgery trial. Obstet Gynecol (2004) 1.52
Inherent signals in sequencing-based Chromatin-ImmunoPrecipitation control libraries. PLoS One (2009) 1.49
Clinical significance of postvoid residual volume in older ambulatory women. J Am Geriatr Soc (2011) 1.48
Incarceration, incident hypertension, and access to health care: findings from the coronary artery risk development in young adults (CARDIA) study. Arch Intern Med (2009) 1.47
An eigenfunction method for reconstruction of large-scale and high-contrast objects. IEEE Trans Ultrason Ferroelectr Freq Control (2007) 1.47
IFN-gamma and IL-17 production in experimental autoimmune encephalomyelitis depends on local APC-T cell complement production. J Immunol (2008) 1.45
Lethal-7 is down-regulated by the hepatitis B virus x protein and targets signal transducer and activator of transcription 3. J Hepatol (2010) 1.45
Biomarkers to predict recurrent cardiovascular disease: the Heart and Soul Study. Am J Med (2008) 1.45