Published in Genome Res on February 07, 2008
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
Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat Biotechnol (2010) 9.84
Androgen receptor regulates a distinct transcription program in androgen-independent prostate cancer. Cell (2009) 7.09
Insights from genomic profiling of transcription factors. Nat Rev Genet (2009) 5.57
Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks. BMC Bioinformatics (2008) 4.41
ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data. BMC Bioinformatics (2010) 3.47
Advantages and limitations of current network inference methods. Nat Rev Microbiol (2010) 2.97
Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression. Genome Res (2009) 2.64
Systematic evaluation of factors influencing ChIP-seq fidelity. Nat Methods (2012) 2.31
Genome-wide tissue-specific farnesoid X receptor binding in mouse liver and intestine. Hepatology (2010) 2.10
A systems approach reveals regulatory circuitry for Arabidopsis trichome initiation by the GL3 and GL1 selectors. PLoS Genet (2009) 2.07
E2F in vivo binding specificity: comparison of consensus versus nonconsensus binding sites. Genome Res (2008) 2.07
Chromatin immunoprecipitation (ChIP) of plant transcription factors followed by sequencing (ChIP-SEQ) or hybridization to whole genome arrays (ChIP-CHIP). Nat Protoc (2010) 1.85
ChIP-chip versus ChIP-seq: lessons for experimental design and data analysis. BMC Genomics (2011) 1.80
Evaluation of affinity-based genome-wide DNA methylation data: effects of CpG density, amplification bias, and copy number variation. Genome Res (2010) 1.77
The histone demethylase UTX enables RB-dependent cell fate control. Genes Dev (2010) 1.62
W-ChIPeaks: a comprehensive web application tool for processing ChIP-chip and ChIP-seq data. Bioinformatics (2010) 1.57
Discovery and verification of functional single nucleotide polymorphisms in regulatory genomic regions: current and developing technologies. Mutat Res (2008) 1.56
Promoter DNA methylation patterns of differentiated cells are largely programmed at the progenitor stage. Mol Biol Cell (2010) 1.49
A large-scale identification of direct targets of the tomato MADS box transcription factor RIPENING INHIBITOR reveals the regulation of fruit ripening. Plant Cell (2013) 1.41
Activation-induced cytidine deaminase induces reproducible DNA breaks at many non-Ig Loci in activated B cells. Mol Cell (2011) 1.39
Genome-wide control of RNA polymerase II activity by cohesin. PLoS Genet (2013) 1.38
Genome-wide profiling of the core clock protein BMAL1 targets reveals a strict relationship with metabolism. Mol Cell Biol (2010) 1.35
Nuclear translocated Ehrlichia chaffeensis ankyrin protein interacts with a specific adenine-rich motif of host promoter and intronic Alu elements. Infect Immun (2009) 1.32
A data integration approach to mapping OCT4 gene regulatory networks operative in embryonic stem cells and embryonal carcinoma cells. PLoS One (2010) 1.31
CLEAN: CLustering Enrichment ANalysis. BMC Bioinformatics (2009) 1.29
Coactivator function defines the active estrogen receptor alpha cistrome. Mol Cell Biol (2009) 1.29
Genome-wide binding site analysis of FAR-RED ELONGATED HYPOCOTYL3 reveals its novel function in Arabidopsis development. Plant Cell (2011) 1.27
Histone H3 lysine 27 methylation asymmetry on developmentally-regulated promoters distinguish the first two lineages in mouse preimplantation embryos. PLoS One (2010) 1.27
Cohesin and polycomb proteins functionally interact to control transcription at silenced and active genes. PLoS Genet (2013) 1.25
ChIP on Chip: surprising results are often artifacts. BMC Genomics (2010) 1.24
Using ChIP-chip and ChIP-seq to study the regulation of gene expression: genome-wide localization studies reveal widespread regulation of transcription elongation. Methods (2009) 1.23
Optimization of experimental design parameters for high-throughput chromatin immunoprecipitation studies. Nucleic Acids Res (2008) 1.12
JAMIE: joint analysis of multiple ChIP-chip experiments. Bioinformatics (2010) 1.12
Genome-wide binding analysis of the transcription activator ideal plant architecture1 reveals a complex network regulating rice plant architecture. Plant Cell (2013) 1.10
Fast genomic muChIP-chip from 1,000 cells. Genome Biol (2009) 1.09
MM-ChIP enables integrative analysis of cross-platform and between-laboratory ChIP-chip or ChIP-seq data. Genome Biol (2011) 1.07
Using ChIP-seq technology to identify targets of zinc finger transcription factors. Methods Mol Biol (2010) 1.06
Comprehensive genomic screens identify a role for PLZF-RARalpha as a positive regulator of cell proliferation via direct regulation of c-MYC. Blood (2009) 1.06
Common fragile sites are characterized by histone hypoacetylation. Hum Mol Genet (2009) 1.02
Chromatin environment of histone variant H3.3 revealed by quantitative imaging and genome-scale chromatin and DNA immunoprecipitation. Mol Biol Cell (2010) 1.01
A functional analysis of the CREB signaling pathway using HaloCHIP-chip and high throughput reporter assays. BMC Genomics (2009) 0.98
Analysis of epigenetic alterations to chromatin during development. Genesis (2009) 0.98
PMeS: prediction of methylation sites based on enhanced feature encoding scheme. PLoS One (2012) 0.97
Developmental features of DNA methylation during activation of the embryonic zebrafish genome. Genome Biol (2012) 0.95
Correlation between DNase I hypersensitive site distribution and gene expression in HeLa S3 cells. PLoS One (2012) 0.94
Adaptive variation regulates the expression of the human SGK1 gene in response to stress. PLoS Genet (2009) 0.93
A comprehensive and universal method for assessing the performance of differential gene expression analyses. PLoS One (2010) 0.88
Screening of potential diagnostic markers and therapeutic targets against colorectal cancer. Onco Targets Ther (2015) 0.88
Improved ChIP-chip analysis by a mixture model approach. BMC Bioinformatics (2009) 0.85
Tiling histone H3 lysine 4 and 27 methylation in zebrafish using high-density microarrays. PLoS One (2010) 0.84
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
LTR: Linear Cross-Platform Integration of Microarray Data. Cancer Inform (2010) 0.81
Human Transcriptome and Chromatin Modifications: An ENCODE Perspective. Genomics Inform (2013) 0.81
Utilizing gene pair orientations for HMM-based analysis of promoter array ChIP-chip data. Bioinformatics (2009) 0.81
Discriminating between lysine sumoylation and lysine acetylation using mRMR feature selection and analysis. PLoS One (2014) 0.80
Interindividual variation in epigenomic phenomena in humans. Mamm Genome (2009) 0.79
OccuPeak: ChIP-Seq peak calling based on internal background modelling. PLoS One (2014) 0.78
Quantized correlation coefficient for measuring reproducibility of ChIP-chip data. BMC Bioinformatics (2010) 0.77
Profiling of promoter occupancy by the SND1 transcriptional coactivator identifies downstream glycerolipid metabolic genes involved in TNFα response in human hepatoma cells. Nucleic Acids Res (2015) 0.77
Identification of thyroid hormone receptor binding sites in developing mouse cerebellum. BMC Genomics (2013) 0.76
Comments on sequence normalization of tiling array expression. Bioinformatics (2009) 0.76
Double error shrinkage method for identifying protein binding sites observed by tiling arrays with limited replication. Bioinformatics (2009) 0.76
Sandcastle: software for revealing latent information in multiple experimental ChIP-chip datasets via a novel normalisation procedure. Sci Rep (2015) 0.76
Detection of target ssDNA using a microfabricated Hall magnetometer with correlated optical readout. J Biomed Biotechnol (2012) 0.75
Location, location, (ChIP-)location! Mapping chromatin landscapes one immunoprecipitation at a time. J Cell Biochem (2009) 0.75
Statistical metrics for quality assessment of high-density tiling array data. Biometrics (2009) 0.75
Group normalization for genomic data. PLoS One (2012) 0.75
Protein post-translational modifications: In silico prediction tools and molecular modeling. Comput Struct Biotechnol J (2017) 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
BLAT--the BLAST-like alignment tool. Genome Res (2002) 126.78
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
Genome-wide mapping of in vivo protein-DNA interactions. Science (2007) 64.92
Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res (1999) 49.21
The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol (2006) 30.90
Control of developmental regulators by Polycomb in human embryonic stem cells. Cell (2006) 28.21
A high-resolution map of active promoters in the human genome. Nature (2005) 24.35
Genome-wide analysis of estrogen receptor binding sites. Nat Genet (2006) 18.63
Repbase update: a database and an electronic journal of repetitive elements. Trends Genet (2000) 16.94
Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell (2004) 16.15
Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat Biotechnol (2001) 14.57
Model-based analysis of tiling-arrays for ChIP-chip. Proc Natl Acad Sci U S A (2006) 13.68
Segmental duplications: organization and impact within the current human genome project assembly. Genome Res (2001) 11.77
Multiple-laboratory comparison of microarray platforms. Nat Methods (2005) 11.74
Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset. Genome Biol (2005) 8.32
Model-based analysis of two-color arrays (MA2C). Genome Biol (2007) 7.28
Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human genome. Genome Res (2006) 6.54
Genome-wide analysis of protein-DNA interactions. Annu Rev Genomics Hum Genet (2006) 6.47
Performance comparison of one-color and two-color platforms within the MicroArray Quality Control (MAQC) project. Nat Biotechnol (2006) 5.92
Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies. Genome Res (2007) 4.59
Relationships between p63 binding, DNA sequence, transcription activity, and biological function in human cells. Mol Cell (2006) 4.51
Comprehensive analysis of transcriptional promoter structure and function in 1% of the human genome. Genome Res (2005) 3.85
Genome-wide analysis of KAP1 binding suggests autoregulation of KRAB-ZNFs. PLoS Genet (2007) 3.75
Statistics for ChIP-chip and DNase hypersensitivity experiments on NimbleGen arrays. Methods Enzymol (2006) 3.53
Hybridization interactions between probesets in short oligo microarrays lead to spurious correlations. BMC Bioinformatics (2006) 3.44
Comparison of sample preparation methods for ChIP-chip assays. Biotechniques (2006) 2.89
Tilescope: online analysis pipeline for high-density tiling microarray data. Genome Biol (2007) 2.48
Progress and challenges in profiling the dynamics of chromatin and transcription factor binding with DNA microarrays. Curr Opin Genet Dev (2004) 2.25
Development and validation of a T7 based linear amplification for genomic DNA. BMC Genomics (2003) 2.23
Assessing the need for sequence-based normalization in tiling microarray experiments. Bioinformatics (2007) 2.08
High-throughput mapping of origins of replication in human cells. EMBO Rep (2007) 1.75
High-throughput methods of regulatory element discovery. Biotechniques (2006) 1.22
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
Genome-wide mapping of in vivo protein-DNA interactions. Science (2007) 64.92
RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet (2009) 58.77
Model-based analysis of ChIP-Seq (MACS). Genome Biol (2008) 51.63
The transcriptional landscape of the yeast genome defined by RNA sequencing. Science (2008) 48.99
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods (2007) 45.04
Transcriptional regulatory networks in Saccharomyces cerevisiae. Science (2002) 43.52
A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science (2002) 42.78
Functional profiling of the Saccharomyces cerevisiae genome. Nature (2002) 36.10
Human DNA methylomes at base resolution show widespread epigenomic differences. Nature (2009) 34.27
Targeted capture and massively parallel sequencing of 12 human exomes. Nature (2009) 33.96
Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet (2007) 32.41
Paired-end mapping reveals extensive structural variation in the human genome. Science (2007) 30.46
Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell (2007) 30.22
Transcriptional regulatory code of a eukaryotic genome. Nature (2004) 27.21
STAR: ultrafast universal RNA-seq aligner. Bioinformatics (2012) 25.21
Population genomics of human gene expression. Nat Genet (2007) 24.49
Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature (2009) 24.41
A high-resolution map of active promoters in the human genome. Nature (2005) 24.35
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature (2006) 24.29
Worldwide human relationships inferred from genome-wide patterns of variation. Science (2008) 22.44
A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat Biotechnol (2008) 21.72
An integrated semiconductor device enabling non-optical genome sequencing. Nature (2011) 20.85
A global map of p53 transcription-factor binding sites in the human genome. Cell (2006) 20.65
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proc Natl Acad Sci U S A (2002) 20.48
International network of cancer genome projects. Nature (2010) 20.35
Landscape of transcription in human cells. Nature (2012) 20.18
GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res (2012) 19.19
Genomic maps and comparative analysis of histone modifications in human and mouse. Cell (2005) 18.96
Genome-wide analysis of estrogen receptor binding sites. Nat Genet (2006) 18.63
RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science (2007) 18.59
ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature (2009) 18.38
Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature (2012) 18.23
Global identification of human transcribed sequences with genome tiling arrays. Science (2004) 17.85
Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data. Nucleic Acids Res (2005) 17.58
The accessible chromatin landscape of the human genome. Nature (2012) 16.86
Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science (2005) 16.82
Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell (2007) 16.66
Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell (2004) 16.15
High-resolution mapping and characterization of open chromatin across the genome. Cell (2008) 15.93
Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics (2010) 15.90
A map of the interactome network of the metazoan C. elegans. Science (2004) 15.60
The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res (2012) 15.41
Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Res (2009) 15.15
Ensembl 2011. Nucleic Acids Res (2010) 14.68