Published in BMC Genomics on December 18, 2009
Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo. EMBO J (2010) 4.78
Evaluation of algorithm performance in ChIP-seq peak detection. PLoS One (2010) 3.99
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Identifying ChIP-seq enrichment using MACS. Nat Protoc (2012) 3.60
ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions. Nat Rev Genet (2012) 3.23
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
HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data. BMC Bioinformatics (2010) 2.41
Systematic evaluation of factors influencing ChIP-seq fidelity. Nat Methods (2012) 2.31
Genome-wide analysis of simultaneous GATA1/2, RUNX1, FLI1, and SCL binding in megakaryocytes identifies hematopoietic regulators. Dev Cell (2011) 2.30
An integrated ChIP-seq analysis platform with customizable workflows. BMC Bioinformatics (2011) 1.92
High-resolution genome-wide mapping of the primary structure of chromatin. Cell (2011) 1.89
ChIP-chip versus ChIP-seq: lessons for experimental design and data analysis. BMC Genomics (2011) 1.80
Picking ChIP-seq peak detectors for analyzing chromatin modification experiments. Nucleic Acids Res (2012) 1.49
Shape-based peak identification for ChIP-Seq. BMC Bioinformatics (2011) 1.38
A manually curated ChIP-seq benchmark demonstrates room for improvement in current peak-finder programs. Nucleic Acids Res (2010) 1.35
Discovering homotypic binding events at high spatial resolution. Bioinformatics (2010) 1.33
Genome-wide binding site analysis of FAR-RED ELONGATED HYPOCOTYL3 reveals its novel function in Arabidopsis development. Plant Cell (2011) 1.27
De novo detection of differentially bound regions for ChIP-seq data using peaks and windows: controlling error rates correctly. Nucleic Acids Res (2014) 1.23
Efficiently identifying genome-wide changes with next-generation sequencing data. Nucleic Acids Res (2011) 1.14
Comprehensive meta-analysis of Signal Transducers and Activators of Transcription (STAT) genomic binding patterns discerns cell-specific cis-regulatory modules. BMC Genomics (2013) 1.12
DIME: R-package for identifying differential ChIP-seq based on an ensemble of mixture models. Bioinformatics (2011) 1.10
An integrated pipeline for the genome-wide analysis of transcription factor binding sites from ChIP-Seq. PLoS One (2011) 1.08
Q&A: ChIP-seq technologies and the study of gene regulation. BMC Biol (2010) 1.07
DROMPA: easy-to-handle peak calling and visualization software for the computational analysis and validation of ChIP-seq data. Genes Cells (2013) 0.95
VDA, a method of choosing a better algorithm with fewer validations. PLoS One (2011) 0.94
Neural crest deletion of Dlx3 leads to major dentin defects through down-regulation of Dspp. J Biol Chem (2012) 0.93
Combining multiple ChIP-seq peak detection systems using combinatorial fusion. BMC Genomics (2012) 0.92
ChIP-PED enhances the analysis of ChIP-seq and ChIP-chip data. Bioinformatics (2013) 0.89
Genome-wide identification of binding sites for NAC and YABBY transcription factors and co-regulated genes during soybean seedling development by ChIP-Seq and RNA-Seq. BMC Genomics (2013) 0.88
A novel statistical method for quantitative comparison of multiple ChIP-seq datasets. Bioinformatics (2015) 0.87
The Triform algorithm: improved sensitivity and specificity in ChIP-Seq peak finding. BMC Bioinformatics (2012) 0.86
WaveSeq: a novel data-driven method of detecting histone modification enrichments using wavelets. PLoS One (2012) 0.85
Processing and analyzing ChIP-seq data: from short reads to regulatory interactions. Brief Funct Genomics (2010) 0.84
Protein-DNA binding in high-resolution. Crit Rev Biochem Mol Biol (2015) 0.83
Statistical Issues in the Analysis of ChIP-Seq and RNA-Seq Data. Genes (Basel) (2010) 0.83
Differential principal component analysis of ChIP-seq. Proc Natl Acad Sci U S A (2013) 0.83
Pinpointing transcription factor binding sites from ChIP-seq data with SeqSite. BMC Syst Biol (2011) 0.82
A strand specific high resolution normalization method for chip-sequencing data employing multiple experimental control measurements. Algorithms Mol Biol (2012) 0.82
PolyaPeak: detecting transcription factor binding sites from ChIP-seq using peak shape information. PLoS One (2014) 0.81
A co-localization model of paired ChIP-seq data using a large ENCODE data set enables comparison of multiple samples. Nucleic Acids Res (2012) 0.80
Saturation analysis of ChIP-seq data for reproducible identification of binding peaks. Genome Res (2015) 0.80
Improving ChIP-seq peak-calling for functional co-regulator binding by integrating multiple sources of biological information. BMC Genomics (2012) 0.78
OccuPeak: ChIP-Seq peak calling based on internal background modelling. PLoS One (2014) 0.78
Optimized detection of transcription factor-binding sites in ChIP-seq experiments. Nucleic Acids Res (2011) 0.77
De novo prediction of cis-regulatory elements and modules through integrative analysis of a large number of ChIP datasets. BMC Genomics (2014) 0.77
D-peaks: a visual tool to display ChIP-seq peaks along the genome. Transcription (2012) 0.76
An improved ChIP-seq peak detection system for simultaneously identifying post-translational modified transcription factors by combinatorial fusion, using SUMOylation as an example. BMC Genomics (2014) 0.76
Features that define the best ChIP-seq peak calling algorithms. Brief Bioinform (2016) 0.76
NEXT-peak: a normal-exponential two-peak model for peak-calling in ChIP-seq data. BMC Genomics (2013) 0.76
Discovering cooperative relationships of chromatin modifications in human T cells based on a proposed closeness measure. PLoS One (2010) 0.76
NF-Y Binding Site Architecture Defines a C-Fos Targeted Promoter Class. PLoS One (2016) 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
SOAP: short oligonucleotide alignment program. Bioinformatics (2008) 68.13
Genome-wide mapping of in vivo protein-DNA interactions. Science (2007) 64.92
Alternative isoform regulation in human tissue transcriptomes. Nature (2008) 52.76
Model-based analysis of ChIP-Seq (MACS). Genome Biol (2008) 51.63
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods (2007) 45.04
Whole-genome re-sequencing. Curr Opin Genet Dev (2006) 35.24
Next-generation DNA sequencing. Nat Biotechnol (2008) 34.95
Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell (2008) 28.29
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
Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nat Methods (2008) 11.61
PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat Biotechnol (2009) 11.28
Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Res (2008) 10.18
Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nat Biotechnol (2008) 10.10
Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. Nucleic Acids Res (2008) 8.89
Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains. Genome Res (2008) 7.41
FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology. Bioinformatics (2008) 6.53
Transcriptional noise and the fidelity of initiation by RNA polymerase II. Nat Struct Mol Biol (2007) 6.53
Genome-wide analysis of protein-DNA interactions. Annu Rev Genomics Hum Genet (2006) 6.47
Insights from genomic profiling of transcription factors. Nat Rev Genet (2009) 5.57
ChIP-Seq of ERalpha and RNA polymerase II defines genes differentially responding to ligands. EMBO J (2009) 5.36
Genome-wide profiling of PPARgamma:RXR and RNA polymerase II occupancy reveals temporal activation of distinct metabolic pathways and changes in RXR dimer composition during adipogenesis. Genes Dev (2008) 4.93
Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies. Genome Res (2007) 4.59
Modeling ChIP sequencing in silico with applications. PLoS Comput Biol (2008) 3.48
Comparative genomics modeling of the NRSF/REST repressor network: from single conserved sites to genome-wide repertoire. Genome Res (2006) 3.23
Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing. BMC Genomics (2009) 3.22
GeneTrack--a genomic data processing and visualization framework. Bioinformatics (2008) 2.51
Genomic location analysis by ChIP-Seq. J Cell Biochem (2009) 2.44
Priming for T helper type 2 differentiation by interleukin 2-mediated induction of interleukin 4 receptor alpha-chain expression. Nat Immunol (2008) 2.31
The transcriptional program controlled by the stem cell leukemia gene Scl/Tal1 during early embryonic hematopoietic development. Blood (2009) 1.97
ChIPping away at gene regulation. EMBO Rep (2008) 1.54
Analysis of the life cycle of stat6. Continuous cycling of STAT6 is required for IL-4 signaling. J Biol Chem (2002) 1.28
Copy number variation and selection during reprogramming to pluripotency. Nature (2011) 8.24
Tet1 and Tet2 regulate 5-hydroxymethylcytosine production and cell lineage specification in mouse embryonic stem cells. Cell Stem Cell (2011) 7.41
Exosomes with immune modulatory features are present in human breast milk. J Immunol (2007) 3.47
High-resolution DNA analysis of human embryonic stem cell lines reveals culture-induced copy number changes and loss of heterozygosity. Nat Biotechnol (2010) 3.21
Dysregulation of lipid and amino acid metabolism precedes islet autoimmunity in children who later progress to type 1 diabetes. J Exp Med (2008) 2.79
GOlorize: a Cytoscape plug-in for network visualization with Gene Ontology-based layout and coloring. Bioinformatics (2006) 2.37
Genomic views of STAT function in CD4+ T helper cell differentiation. Nat Rev Immunol (2011) 2.09
Individualized systems medicine strategy to tailor treatments for patients with chemorefractory acute myeloid leukemia. Cancer Discov (2013) 1.93
Gene expression profiling during differentiation of human monocytes to macrophages or dendritic cells. J Leukoc Biol (2007) 1.90
Difference in gene expression between human fetal liver and adult bone marrow mesenchymal stem cells. Haematologica (2005) 1.90
Gene expression signatures of seven individual human embryonic stem cell lines. Stem Cells (2005) 1.86
Comparison of software packages for detecting differential expression in RNA-seq studies. Brief Bioinform (2013) 1.71
Timing of infant feeding in relation to childhood asthma and allergic diseases. J Allergy Clin Immunol (2012) 1.62
Improving missing value estimation in microarray data with gene ontology. Bioinformatics (2005) 1.57
Systematic construction of gene coexpression networks with applications to human T helper cell differentiation process. Bioinformatics (2007) 1.54
Integrating probe-level expression changes across generations of Affymetrix arrays. Nucleic Acids Res (2005) 1.42
Genetic variants and their interactions in the prediction of increased pre-clinical carotid atherosclerosis: the cardiovascular risk in young Finns study. PLoS Genet (2010) 1.39
Genetic and epigenetic stability of human pluripotent stem cells. Nat Rev Genet (2012) 1.38
Early target genes of IL-12 and STAT4 signaling in th cells. J Immunol (2004) 1.31
Genome-wide profiling of interleukin-4 and STAT6 transcription factor regulation of human Th2 cell programming. Immunity (2010) 1.28
Global chromatin state analysis reveals lineage-specific enhancers during the initiation of human T helper 1 and T helper 2 cell polarization. Immunity (2013) 1.27
Quantitative subcellular proteome and secretome profiling of influenza A virus-infected human primary macrophages. PLoS Pathog (2011) 1.22
Alignment of LC-MS images, with applications to biomarker discovery and protein identification. Proteomics (2008) 1.22
Genome-wide identification of novel genes involved in early Th1 and Th2 cell differentiation. J Immunol (2007) 1.21
Identification of novel IL-4/Stat6-regulated genes in T lymphocytes. J Immunol (2003) 1.20
Differential expression of IFN regulatory factor 4 gene in human monocyte-derived dendritic cells and macrophages. J Immunol (2005) 1.15
Identification of genes involved in the initiation of human Th1 or Th2 cell commitment. Eur J Immunol (2005) 1.12
Probe-level estimation improves the detection of differential splicing in Affymetrix exon array studies. Genome Biol (2009) 1.10
Association analysis of common variants of STAT6, GATA3, and STAT4 to asthma and high serum IgE phenotypes. J Allergy Clin Immunol (2005) 1.08
PARP-14, a member of the B aggressive lymphoma family, transduces survival signals in primary B cells. Blood (2009) 1.08
Th1 response and cytotoxicity genes are down-regulated in cutaneous T-cell lymphoma. Clin Cancer Res (2006) 1.05
Genoscape: a Cytoscape plug-in to automate the retrieval and integration of gene expression data and molecular networks. Bioinformatics (2009) 1.02
Identification of novel genes regulated by IL-12, IL-4, or TGF-beta during the early polarization of CD4+ lymphocytes. J Immunol (2003) 1.02
Gene expression profiling of immune-competent human cells exposed to engineered zinc oxide or titanium dioxide nanoparticles. PLoS One (2013) 1.02
Capturing cell-fate decisions from the molecular signatures of a receptor-dependent signaling response. Mol Syst Biol (2007) 1.02
RNA-binding protein L1TD1 interacts with LIN28 via RNA and is required for human embryonic stem cell self-renewal and cancer cell proliferation. Stem Cells (2012) 1.01
Autoimmune regulator induced changes in the gene expression profile of human monocyte-dendritic cell-lineage. Mol Immunol (2004) 1.01
Probabilistic analysis of probe reliability in differential gene expression studies with short oligonucleotide arrays. IEEE/ACM Trans Comput Biol Bioinform (2010) 1.01
A comparative evaluation of software for the analysis of liquid chromatography-tandem mass spectrometry data from isotope coded affinity tag experiments. Proteomics (2005) 1.00
Quality classification of tandem mass spectrometry data. Bioinformatics (2005) 1.00
Target inhibition networks: predicting selective combinations of druggable targets to block cancer survival pathways. PLoS Comput Biol (2013) 1.00
Identification of early gene expression changes during human Th17 cell differentiation. Blood (2012) 0.99
CD73 participates in cellular multiresistance program and protects against TRAIL-induced apoptosis. J Immunol (2008) 0.99
Genome-wide comparison of two RNA-stabilizing reagents for transcriptional profiling of peripheral blood. Transl Res (2012) 0.98
A statistical score for assessing the quality of multiple sequence alignments. BMC Bioinformatics (2006) 0.98
Global phospholipidomics analysis reveals selective pulmonary peroxidation profiles upon inhalation of single-walled carbon nanotubes. ACS Nano (2011) 0.97
Transcriptional and epigenetic regulation of T-helper lineage specification. Immunol Rev (2014) 0.97
Unique gene expression signature by human embryonic stem cells cultured under serum-free conditions correlates with their enhanced and prolonged growth in an undifferentiated stage. Stem Cells (2005) 0.97
Quantitative proteomics reveals GIMAP family proteins 1 and 4 to be differentially regulated during human T helper cell differentiation. Mol Cell Proteomics (2008) 0.97
Distinct sets of developmentally regulated genes that are expressed by human oocytes and human embryonic stem cells. Fertil Steril (2006) 0.96
Missing value imputation improves clustering and interpretation of gene expression microarray data. BMC Bioinformatics (2008) 0.96
An insight into molecular mechanisms of human T helper cell differentiation. Ann Med (2008) 0.96
Expression of human pim family genes is selectively up-regulated by cytokines promoting T helper type 1, but not T helper type 2, cell differentiation. Immunology (2005) 0.95
Making sense of large-scale kinase inhibitor bioactivity data sets: a comparative and integrative analysis. J Chem Inf Model (2014) 0.95
Optimized detection of differential expression in global profiling experiments: case studies in clinical transcriptomic and quantitative proteomic datasets. Brief Bioinform (2009) 0.95
Reactive oxygen species deficiency induces autoimmunity with type 1 interferon signature. Antioxid Redox Signal (2014) 0.94
PRELI is a mitochondrial regulator of human primary T-helper cell apoptosis, STAT6, and Th2-cell differentiation. Blood (2008) 0.94
Activating transcription factor 3 is a positive regulator of human IFNG gene expression. J Immunol (2010) 0.94
Obatoclax, saliphenylhalamide, and gemcitabine inhibit influenza a virus infection. J Biol Chem (2012) 0.94
SATB1 dictates expression of multiple genes including IL-5 involved in human T helper cell differentiation. Blood (2010) 0.93
Reproducibility-optimized test statistic for ranking genes in microarray studies. IEEE/ACM Trans Comput Biol Bioinform (2008) 0.93
Toward more realistic drug-target interaction predictions. Brief Bioinform (2014) 0.92
New separation-free assay technique for SNPs using two-photon excitation fluorometry. Nucleic Acids Res (2004) 0.92
GIMAP Proteins in T-Lymphocytes. J Signal Transduct (2010) 0.92
Improved statistical modeling of tumor growth and treatment effect in preclinical animal studies with highly heterogeneous responses in vivo. Clin Cancer Res (2012) 0.92
Early suppression of immune response pathways characterizes children with prediabetes in genome-wide gene expression profiling. J Autoimmun (2010) 0.91
IL-12 up-regulates T-bet independently of IFN-gamma in human CD4+ T cells. Eur J Immunol (2005) 0.91
High-throughput karyotyping of human pluripotent stem cells. Stem Cell Res (2012) 0.90
Enrichment of nucleofected primary human CD4+ T cells: a novel and efficient method for studying gene function and role in human primary T helper cell differentiation. J Immunol Methods (2006) 0.90
An update on clinical proteomics in Alzheimer's research. J Neurochem (2009) 0.90
Model-based prediction of sequence alignment quality. Bioinformatics (2008) 0.89
A mutant collagen XIII alters intestinal expression of immune response genes and predisposes transgenic mice to develop B-cell lymphomas. Cancer Res (2008) 0.88
Filtering strategies for improving protein identification in high-throughput MS/MS studies. Proteomics (2009) 0.88
Quantitative maps of genetic interactions in yeast - comparative evaluation and integrative analysis. BMC Syst Biol (2011) 0.87
A fully scalable online pre-processing algorithm for short oligonucleotide microarray atlases. Nucleic Acids Res (2013) 0.87
Quantitative proteomics analysis of the nuclear fraction of human CD4+ cells in the early phases of IL-4-induced Th2 differentiation. Mol Cell Proteomics (2010) 0.87