Genome-wide mapping of in vivo protein-DNA interactions.

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol (2009) 235.12

Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res (2008) 157.44

Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res (2008) 151.16

Accurate whole human genome sequencing using reversible terminator chemistry. Nature (2008) 90.20

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol (2010) 75.21

Model-based analysis of ChIP-Seq (MACS). Genome Biol (2008) 51.63

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc (2012) 35.75

Human DNA methylomes at base resolution show widespread epigenomic differences. Nature (2009) 34.27

Integration of biological networks and gene expression data using Cytoscape. Nat Protoc (2007) 27.10

Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature (2009) 24.41

ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res (2008) 20.61

GREAT improves functional interpretation of cis-regulatory regions. Nat Biotechnol (2010) 16.72

A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol (2011) 16.53

Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell (2008) 16.38

Computation for ChIP-seq and RNA-seq studies. Nat Methods (2009) 16.11

Long noncoding RNA as modular scaffold of histone modification complexes. Science (2010) 15.23

A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet (2014) 14.56

Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat Biotechnol (2012) 14.01

An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat Biotechnol (2008) 13.96

ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet (2009) 13.12

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

Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet (2008) 11.17

Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nat Methods (2009) 10.17

Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nat Biotechnol (2008) 10.10

A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics (2012) 9.97

Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol (2009) 9.59

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. Nucleic Acids Res (2009) 9.42

The case for cloud computing in genome informatics. Genome Biol (2010) 9.20

A census of human transcription factors: function, expression and evolution. Nat Rev Genet (2009) 9.19

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res (2012) 9.13

Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. Nucleic Acids Res (2008) 8.89

Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell (2010) 8.74

A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics (2009) 8.33

Chromatin accessibility pre-determines glucocorticoid receptor binding patterns. Nat Genet (2011) 6.98

UniPROBE: an online database of protein binding microarray data on protein-DNA interactions. Nucleic Acids Res (2008) 6.83

An integrated network of androgen receptor, polycomb, and TMPRSS2-ERG gene fusions in prostate cancer progression. Cancer Cell (2010) 6.76

How to map billions of short reads onto genomes. Nat Biotechnol (2009) 6.59

FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology. Bioinformatics (2008) 6.53

Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data. Nat Rev Genet (2011) 6.52

BAC TransgeneOmics: a high-throughput method for exploration of protein function in mammals. Nat Methods (2008) 6.51

Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. PLoS Biol (2008) 6.30

Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution. Cell (2011) 6.29

Genomic views of distant-acting enhancers. Nature (2009) 6.27

An atlas of combinatorial transcriptional regulation in mouse and man. Cell (2010) 6.24

Next-generation genomics: an integrative approach. Nat Rev Genet (2010) 5.88

Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nat Rev Genet (2011) 5.58

Insights from genomic profiling of transcription factors. Nat Rev Genet (2009) 5.57

Linking disease associations with regulatory information in the human genome. Genome Res (2012) 5.47

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data. Genome Res (2010) 5.40

Bioinformatics challenges of new sequencing technology. Trends Genet (2008) 5.34

Jarid2/Jumonji coordinates control of PRC2 enzymatic activity and target gene occupancy in pluripotent cells. Cell (2009) 5.26

Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions. Genome Biol (2009) 5.23

CNV-seq, a new method to detect copy number variation using high-throughput sequencing. BMC Bioinformatics (2009) 5.14

High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Res (2009) 5.11

The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome. PLoS Genet (2008) 4.91

A cis-regulatory map of the Drosophila genome. Nature (2011) 4.80

F-Seq: a feature density estimator for high-throughput sequence tags. Bioinformatics (2008) 4.77

AlleleSeq: analysis of allele-specific expression and binding in a network framework. Mol Syst Biol (2011) 4.71

ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. Methods (2009) 4.69

Pebble and rock band: heuristic resolution of repeats and scaffolding in the velvet short-read de novo assembler. PLoS One (2009) 4.60

Comparison of next-generation sequencing systems. J Biomed Biotechnol (2012) 4.56

Genome assembly reborn: recent computational challenges. Brief Bioinform (2009) 4.53

Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res (2009) 4.47

Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks. BMC Bioinformatics (2008) 4.41

REST and stress resistance in ageing and Alzheimer's disease. Nature (2014) 4.38

Cistrome: an integrative platform for transcriptional regulation studies. Genome Biol (2011) 4.13

Global analysis of in vivo Foxa2-binding sites in mouse adult liver using massively parallel sequencing. Nucleic Acids Res (2008) 4.08

Comparative epigenomic analysis of murine and human adipogenesis. Cell (2010) 4.08

Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Res (2008) 4.08

Evaluation of algorithm performance in ChIP-seq peak detection. PLoS One (2010) 3.99

Combinatorial binding predicts spatio-temporal cis-regulatory activity. Nature (2009) 3.85

ER-stress-induced transcriptional regulation increases protein synthesis leading to cell death. Nat Cell Biol (2013) 3.84

ORegAnno: an open-access community-driven resource for regulatory annotation. Nucleic Acids Res (2007) 3.80

seqMINER: an integrated ChIP-seq data interpretation platform. Nucleic Acids Res (2010) 3.74

Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors. Genome Biol (2012) 3.61

Identifying ChIP-seq enrichment using MACS. Nat Protoc (2012) 3.60

High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis. Nat Biotechnol (2009) 3.58

Extracting transcription factor targets from ChIP-Seq data. Nucleic Acids Res (2009) 3.58

Sequencing depth and coverage: key considerations in genomic analyses. Nat Rev Genet (2014) 3.52

Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors. Nat Protoc (2009) 3.48

Modeling ChIP sequencing in silico with applications. PLoS Comput Biol (2008) 3.48

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data. BMC Bioinformatics (2010) 3.47

ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genome. PLoS Comput Biol (2008) 3.46

ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments. Bioinformatics (2010) 3.42

On the origin of the beta cell. Genes Dev (2008) 3.34

Application of 'next-generation' sequencing technologies to microbial genetics. Nat Rev Microbiol (2009) 3.30

ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing. Genome Biol (2010) 3.24

Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing. BMC Genomics (2009) 3.22

Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond. Curr Opin Plant Biol (2009) 3.18

A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. Mol Cell (2012) 3.04

Dynamic exchange at regulatory elements during chromatin remodeling underlies assisted loading mechanism. Cell (2011) 3.00

Single-cell systems biology by super-resolution imaging and combinatorial labeling. Nat Methods (2012) 2.98

The androgen receptor fuels prostate cancer by regulating central metabolism and biosynthesis. EMBO J (2011) 2.97

ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells. Proc Natl Acad Sci U S A (2009) 2.96

What would you do if you could sequence everything? Nat Biotechnol (2008) 2.89

Mapping accessible chromatin regions using Sono-Seq. Proc Natl Acad Sci U S A (2009) 2.83

Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data. Nucleic Acids Res (2009) 2.74

Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape. Nat Biotechnol (2014) 2.70

A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments. BMC Genomics (2009) 2.70

Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods (2008) 126.81

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol (2010) 75.21

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09

Model-based analysis of ChIP-Seq (MACS). Genome Biol (2008) 51.63

Worldwide human relationships inferred from genome-wide patterns of variation. Science (2008) 22.44

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

Landscape of transcription in human cells. Nature (2012) 20.18

Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data. Nucleic Acids Res (2005) 17.58

Computation for ChIP-seq and RNA-seq studies. Nat Methods (2009) 16.11

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

Widespread parallel evolution in sticklebacks by repeated fixation of Ectodysplasin alleles. Science (2005) 10.46

The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res (2004) 9.18

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res (2012) 9.13

Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell (2012) 8.41

Signals of recent positive selection in a worldwide sample of human populations. Genome Res (2009) 8.38

Genetic relationship between five psychiatric disorders estimated from genome-wide SNPs. Nat Genet (2013) 8.02

Sequence census methods for functional genomics. Nat Methods (2007) 7.38

Population analysis of large copy number variants and hotspots of human genetic disease. Am J Hum Genet (2009) 6.79

Identification and functional analysis of human transcriptional promoters. Genome Res (2003) 6.23

An abundance of bidirectional promoters in the human genome. Genome Res (2004) 5.90

Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a Pitx1 enhancer. Science (2009) 5.64

The genomic basis of adaptive evolution in threespine sticklebacks. Nature (2012) 5.20

A validated regulatory network for Th17 cell specification. Cell (2012) 4.82

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Res (2012) 4.80

Candidate-gene approaches for studying complex genetic traits: practical considerations. Nat Rev Genet (2002) 4.76

Coding potential of laboratory and clinical strains of human cytomegalovirus. Proc Natl Acad Sci U S A (2003) 4.37

Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions. Genome Res (2007) 4.33

An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol (2012) 4.15

Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver. Genome Res (2009) 4.11

Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Res (2008) 4.08

Ribosomal mutations cause p53-mediated dark skin and pleiotropic effects. Nat Genet (2008) 4.02

Comprehensive analysis of transcriptional promoter structure and function in 1% of the human genome. Genome Res (2005) 3.85

Direct isolation and identification of promoters in the human genome. Genome Res (2005) 3.68

Dynamic DNA methylation across diverse human cell lines and tissues. Genome Res (2013) 3.61

Genome-wide association and meta-analysis of bipolar disorder in individuals of European ancestry. Proc Natl Acad Sci U S A (2009) 3.49

The role of geography in human adaptation. PLoS Genet (2009) 3.41

Defining functional DNA elements in the human genome. Proc Natl Acad Sci U S A (2014) 3.35

Genomic determination of the glucocorticoid response reveals unexpected mechanisms of gene regulation. Genome Res (2009) 3.30

Comparative genomics modeling of the NRSF/REST repressor network: from single conserved sites to genome-wide repertoire. Genome Res (2006) 3.23

Diverse and specific gene expression responses to stresses in cultured human cells. Mol Biol Cell (2004) 3.02

The master sex-determination locus in threespine sticklebacks is on a nascent Y chromosome. Curr Biol (2004) 2.90

High throughput sequencing reveals a complex pattern of dynamic interrelationships among human T cell subsets. Proc Natl Acad Sci U S A (2010) 2.74

Polymorphisms within the C-reactive protein (CRP) promoter region are associated with plasma CRP levels. Am J Hum Genet (2005) 2.71

Susceptibility locus for clinical and subclinical coronary artery disease at chromosome 9p21 in the multi-ethnic ADVANCE study. Hum Mol Genet (2008) 2.71

The role of heat shock transcription factor 1 in the genome-wide regulation of the mammalian heat shock response. Mol Biol Cell (2003) 2.56

Effect of agonal and postmortem factors on gene expression profile: quality control in microarray analyses of postmortem human brain. Biol Psychiatry (2004) 2.53

Widespread plasticity in CTCF occupancy linked to DNA methylation. Genome Res (2012) 2.45

Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation. PLoS Genet (2011) 2.41

Transcription factor binding and modified histones in human bidirectional promoters. Genome Res (2007) 2.40

Dynamic transformations of genome-wide epigenetic marking and transcriptional control establish T cell identity. Cell (2012) 2.38

Systematic changes in gene expression in postmortem human brains associated with tissue pH and terminal medical conditions. Hum Mol Genet (2004) 2.33

Systematic evaluation of factors influencing ChIP-seq fidelity. Nat Methods (2012) 2.31

Evolutionary constraint facilitates interpretation of genetic variation in resequenced human genomes. Genome Res (2010) 2.31

Genomic patterns of homozygosity in worldwide human populations. Am J Hum Genet (2012) 2.30

Selective disruption of lysosomes in HeLa cells triggers apoptosis mediated by cleavage of Bid by multiple papain-like lysosomal cathepsins. J Biol Chem (2003) 2.30

The DNA sequence and biology of human chromosome 19. Nature (2004) 2.29

Quality assessment of the human genome sequence. Nature (2004) 2.29

Generation and annotation of the DNA sequences of human chromosomes 2 and 4. Nature (2005) 2.27

From single-cell to cell-pool transcriptomes: stochasticity in gene expression and RNA splicing. Genome Res (2013) 2.23

Rapid mapping of zebrafish mutations with SNPs and oligonucleotide microarrays. Genome Res (2002) 2.22

The completion of the Mammalian Gene Collection (MGC). Genome Res (2009) 2.21

RNA editing in the human ENCODE RNA-seq data. Genome Res (2012) 2.18

Lack of association between the Trp719Arg polymorphism in kinesin-like protein-6 and coronary artery disease in 19 case-control studies. J Am Coll Cardiol (2010) 2.17

Functional analysis of transcription factor binding sites in human promoters. Genome Biol (2012) 2.12

A role for a neo-sex chromosome in stickleback speciation. Nature (2009) 2.06

Characterizing the admixed African ancestry of African Americans. Genome Biol (2009) 2.01

Effects of sequence variation on differential allelic transcription factor occupancy and gene expression. Genome Res (2012) 1.99

A neurodegeneration-specific gene-expression signature of acutely isolated microglia from an amyotrophic lateral sclerosis mouse model. Cell Rep (2013) 1.92

Lack of replication of thirteen single-nucleotide polymorphisms implicated in Parkinson's disease: a large-scale international study. Lancet Neurol (2006) 1.92

Serum response factor binding sites differ in three human cell types. Genome Res (2007) 1.85

DNA methylation profiling reveals novel biomarkers and important roles for DNA methyltransferases in prostate cancer. Genome Res (2011) 1.85

Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome. Genome Res (2007) 1.82

Behavioral phenotypic variation in autism multiplex families: evidence for a continuous severity gradient. Am J Med Genet (2002) 1.71

Differential DNA methylation with age displays both common and dynamic features across human tissues that are influenced by CpG landscape. Genome Biol (2013) 1.69

The ets-related transcription factor GABP directs bidirectional transcription. PLoS Genet (2007) 1.67

Transposase mediated construction of RNA-seq libraries. Genome Res (2011) 1.66

Circadian patterns of gene expression in the human brain and disruption in major depressive disorder. Proc Natl Acad Sci U S A (2013) 1.63

The DNA sequence and comparative analysis of human chromosome 5. Nature (2004) 1.62

Sample matching by inferred agonal stress in gene expression analyses of the brain. BMC Genomics (2007) 1.54

A genome-wide SNP genotyping array reveals patterns of global and repeated species-pair divergence in sticklebacks. Curr Biol (2011) 1.50

Gene conversion and the evolution of protocadherin gene cluster diversity. Genome Res (2004) 1.42

Sequence features that drive human promoter function and tissue specificity. Genome Res (2010) 1.40

CTCF/cohesin-mediated DNA looping is required for protocadherin α promoter choice. Proc Natl Acad Sci U S A (2012) 1.39

Transcriptional regulation and binding of heat shock factor 1 and heat shock factor 2 to 32 human heat shock genes during thermal stress and differentiation. Cell Stress Chaperones (2004) 1.38

The sequence and analysis of duplication-rich human chromosome 16. Nature (2004) 1.38

Mitochondrial involvement in psychiatric disorders. Ann Med (2008) 1.38

Mitochondrial variants in schizophrenia, bipolar disorder, and major depressive disorder. PLoS One (2009) 1.36

Sequencing and analysis of 10,967 full-length cDNA clones from Xenopus laevis and Xenopus tropicalis reveals post-tetraploidization transcriptome remodeling. Genome Res (2006) 1.31

Sequential use of transcriptional profiling, expression quantitative trait mapping, and gene association implicates MMP20 in human kidney aging. PLoS Genet (2009) 1.30

Coelacanth genome sequence reveals the evolutionary history of vertebrate genes. Genome Res (2004) 1.29

Role of CCCTC binding factor (CTCF) and cohesin in the generation of single-cell diversity of protocadherin-α gene expression. Proc Natl Acad Sci U S A (2012) 1.26

IκB kinase epsilon (IKK(epsilon)) regulates the balance between type I and type II interferon responses. Proc Natl Acad Sci U S A (2011) 1.23