Published in Science on October 22, 2004
A haplotype map of the human genome. Nature (2005) 105.70
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
An integrated encyclopedia of DNA elements in the human genome. Nature (2012) 64.73
The diploid genome sequence of an individual human. PLoS Biol (2007) 44.80
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res (2005) 44.08
Integrative genomics viewer. Nat Biotechnol (2011) 42.83
Galaxy: a platform for interactive large-scale genome analysis. Genome Res (2005) 35.75
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
Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform (2012) 23.58
Landscape of transcription in human cells. Nature (2012) 20.18
Ensembl 2007. Nucleic Acids Res (2006) 20.10
Distribution and intensity of constraint in mammalian genomic sequence. Genome Res (2005) 18.85
DNA methylation profiling of human chromosomes 6, 20 and 22. Nat Genet (2006) 18.08
Genome-wide associations of gene expression variation in humans. PLoS Genet (2005) 17.27
Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell (2007) 16.66
The UCSC Genome Browser database: update 2010. Nucleic Acids Res (2009) 16.58
A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol (2011) 16.53
The UCSC Genome Browser database: update 2011. Nucleic Acids Res (2010) 16.24
GENCODE: producing a reference annotation for ENCODE. Genome Biol (2006) 15.08
Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res (2006) 13.32
The UCSC genome browser database: update 2007. Nucleic Acids Res (2006) 13.04
Unlocking the secrets of the genome. Nature (2009) 11.80
Ensembl 2006. Nucleic Acids Res (2006) 11.66
The UCSC Genome Browser Database: update 2006. Nucleic Acids Res (2006) 11.05
Most rare missense alleles are deleterious in humans: implications for complex disease and association studies. Am J Hum Genet (2007) 10.92
The UCSC Genome Browser Database: update 2009. Nucleic Acids Res (2008) 10.31
SNPdetector: a software tool for sensitive and accurate SNP detection. PLoS Comput Biol (2005) 10.04
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res (2012) 9.13
Identifying a high fraction of the human genome to be under selective constraint using GERP++. PLoS Comput Biol (2010) 8.69
Dindel: accurate indel calls from short-read data. Genome Res (2010) 8.62
FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Res (2006) 7.72
The vertebrate genome annotation (Vega) database. Nucleic Acids Res (2007) 7.53
AceView: a comprehensive cDNA-supported gene and transcripts annotation. Genome Biol (2006) 7.52
Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms. Am J Hum Genet (2008) 7.36
Concept, design and implementation of a cardiovascular gene-centric 50 k SNP array for large-scale genomic association studies. PLoS One (2008) 7.16
Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences. Genome Res (2005) 7.09
The Vertebrate Genome Annotation (Vega) database. Nucleic Acids Res (2005) 7.06
EGASP: the human ENCODE Genome Annotation Assessment Project. Genome Biol (2006) 7.06
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res (2007) 7.05
Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human genome. Genome Res (2006) 6.54
ENCODE data in the UCSC Genome Browser: year 5 update. Nucleic Acids Res (2012) 6.29
9p21 DNA variants associated with coronary artery disease impair interferon-γ signalling response. Nature (2011) 6.25
DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays. Nat Methods (2006) 6.25
JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. Nucleic Acids Res (2013) 6.12
ENCODE whole-genome data in the UCSC Genome Browser. Nucleic Acids Res (2009) 5.98
A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res (2007) 5.97
Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). Genome Res (2005) 5.71
The landscape of histone modifications across 1% of the human genome in five human cell lines. Genome Res (2007) 5.67
Efficient storage of high throughput DNA sequencing data using reference-based compression. Genome Res (2011) 5.60
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
Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Genome Res (2005) 5.22
Spatial preferences of microRNA targets in 3' untranslated regions. BMC Genomics (2007) 4.99
Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs). Genome Res (2007) 4.99
Statistical evaluation of alternative models of human evolution. Proc Natl Acad Sci U S A (2007) 4.88
HIV integration site selection: analysis by massively parallel pyrosequencing reveals association with epigenetic modifications. Genome Res (2007) 4.72
Hardy-Weinberg equilibrium testing of biological ascertainment for Mendelian randomization studies. Am J Epidemiol (2009) 4.70
High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells. Genome Res (2010) 4.69
Initial sequence and comparative analysis of the cat genome. Genome Res (2007) 4.67
Influence of child abuse on adult depression: moderation by the corticotropin-releasing hormone receptor gene. Arch Gen Psychiatry (2008) 4.65
A large-scale evaluation of computational protein function prediction. Nat Methods (2013) 4.61
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
An initial strategy for the systematic identification of functional elements in the human genome by low-redundancy comparative sequencing. Proc Natl Acad Sci U S A (2005) 4.38
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
A new generation of JASPAR, the open-access repository for transcription factor binding site profiles. Nucleic Acids Res (2006) 4.32
An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol (2012) 4.15
Epidermal barrier formation and recovery in skin disorders. J Clin Invest (2006) 4.14
Thousands of human mobile element fragments undergo strong purifying selection near developmental genes. Proc Natl Acad Sci U S A (2007) 4.11
ENCODE whole-genome data in the UCSC Genome Browser: update 2012. Nucleic Acids Res (2011) 4.00
The implications of alternative splicing in the ENCODE protein complement. Proc Natl Acad Sci U S A (2007) 3.93
Tandem chimerism as a means to increase protein complexity in the human genome. Genome Res (2005) 3.89
Comprehensive analysis of transcriptional promoter structure and function in 1% of the human genome. Genome Res (2005) 3.85
Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. Genome Res (2007) 3.82
Recent developments in genomewide association scans: a workshop summary and review. Am J Hum Genet (2005) 3.76
Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biol (2008) 3.73
Direct isolation and identification of promoters in the human genome. Genome Res (2005) 3.68
Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors. Genome Biol (2012) 3.61
The ENCODE Project at UC Santa Cruz. Nucleic Acids Res (2006) 3.57
Sequencing depth and coverage: key considerations in genomic analyses. Nat Rev Genet (2014) 3.52
ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genome. PLoS Comput Biol (2008) 3.46
Defining functional DNA elements in the human genome. Proc Natl Acad Sci U S A (2014) 3.35
Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome. Genome Biol (2008) 3.34
Forces shaping the fastest evolving regions in the human genome. PLoS Genet (2006) 3.32
Power to detect risk alleles using genome-wide tag SNP panels. PLoS Genet (2007) 3.29
The UCSC genome browser and associated tools. Brief Bioinform (2012) 3.29
NCBI Epigenomics: a new public resource for exploring epigenomic data sets. Nucleic Acids Res (2010) 3.27
Predictive chromatin signatures in the mammalian genome. Hum Mol Genet (2009) 3.25
Selection of target sites for mobile DNA integration in the human genome. PLoS Comput Biol (2006) 3.21
Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions. Cell (2015) 3.10
Genomic screening with RNAi: results and challenges. Annu Rev Biochem (2010) 3.08
On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE. Genome Biol Evol (2013) 3.00
Transcriptional silencing of {gamma}-globin by BCL11A involves long-range interactions and cooperation with SOX6. Genes Dev (2010) 2.93
Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability. Nucleic Acids Res (2005) 2.89
REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila. Nucleic Acids Res (2010) 2.84
Pan-S replication patterns and chromosomal domains defined by genome-tiling arrays of ENCODE genomic areas. Genome Res (2007) 2.82
A benchmark for RNA-seq quantification pipelines. Genome Biol (2016) 2.78
Genome-wide studies highlight indirect links between human replication origins and gene regulation. Proc Natl Acad Sci U S A (2008) 2.77
Improving gene annotation using peptide mass spectrometry. Genome Res (2006) 2.69
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
An integrated encyclopedia of DNA elements in the human genome. Nature (2012) 64.73
The ENCODE Project at UC Santa Cruz. Nucleic Acids Res (2006) 3.57