An integrated encyclopedia of DNA elements in the human genome

Model-based Analysis of ChIP-Seq (MACS)

2008 • 15,719 citations

Chromatin Modifications and Their Function

2007 • 10,144 citations

A map of human genome variation from population-scale sequencing

2010 • 7,765 citations

Initial sequencing and comparative analysis of the mouse genome

2002 • 6,971 citations

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

2007 • 5,117 citations

Landscape of transcription in human cells

2012 • 4,929 citations

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

2012 • 4,722 citations

GENCODE: The reference human genome annotation for The ENCODE Project

2012 • 4,557 citations

Human DNA methylomes at base resolution show widespread epigenomic differences

2009 • 4,388 citations

GREAT improves functional interpretation of cis-regulatory regions

2010 • 4,233 citations

Potential etiologic and functional implications of genome-wide association loci for human diseases and traits

2009 • 4,036 citations

The Role of Chromatin during Transcription

2007 • 3,396 citations

Mapping and analysis of chromatin state dynamics in nine human cell types

2011 • 2,880 citations

The Transcriptional Coactivators p300 and CBP Are Histone Acetyltransferases

1996 • 2,873 citations

Evolution at Two Levels in Humans and Chimpanzees

1975 • 2,796 citations

The accessible chromatin landscape of the human genome

2012 • 2,663 citations

Annotation of functional variation in personal genomes using RegulomeDB

2012 • 2,538 citations

Genome-scale DNA methylation maps of pluripotent and differentiated cells

2008 • 2,432 citations

RNA Maps Reveal New RNA Classes and a Possible Function for Pervasive Transcription

2007 • 2,414 citations

The ENCODE (ENCyclopedia Of DNA Elements) Project

2004 • 2,327 citations

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

2012 • 1,867 citations

An oestrogen-receptor-α-bound human chromatin interactome

2009 • 1,675 citations

Architecture of the human regulatory network derived from ENCODE data

2012 • 1,468 citations

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

2011 • 1,457 citations

The long-range interaction landscape of gene promoters

2012 • 1,429 citations

Distribution and intensity of constraint in mammalian genomic sequence

2005 • 1,350 citations

Dynamic Regulation of Nucleosome Positioning in the Human Genome

2008 • 1,325 citations

NUCLEASE HYPERSENSITIVE SITES IN CHROMATIN

1988 • 1,233 citations

SETDB1: a novel KAP-1-associated histone H3, lysine 9-specific methyltransferase that contributes to HP1-mediated silencing of euchromatic genes by KRAB zinc-finger proteins

2002 • 1,207 citations

Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation

2012 • 1,199 citations

Chromosome Conformation Capture Carbon Copy (5C): A massively parallel solution for mapping interactions between genomic elements

2006 • 1,176 citations

A high-resolution map of human evolutionary constraint using 29 mammals

2011 • 1,140 citations

Charting histone modifications and the functional organization of mammalian genomes

2010 • 1,086 citations

Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells

2009 • 1,056 citations

Measuring reproducibility of high-throughput experiments

2011 • 1,018 citations

An expansive human regulatory lexicon encoded in transcription factor footprints

2012 • 790 citations

Linking disease associations with regulatory information in the human genome

2012 • 710 citations

Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding

2010 • 709 citations

Determinants of nucleosome organization in primary human cells

2011 • 656 citations

9p21 DNA variants associated with coronary artery disease impair interferon-γ signalling response

2011 • 609 citations

Unsupervised pattern discovery in human chromatin structure through genomic segmentation

2012 • 577 citations

Global mapping of protein-DNA interactions in vivo by digital genomic footprinting

2009 • 574 citations

Novel Crohn Disease Locus Identified by Genome-Wide Association Maps to a Gene Desert on 5p13.1 and Modulates Expression of PTGER4

2007 • 564 citations

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

2010 • 551 citations

Tissue-specific transcriptional regulation has diverged significantly between human and mouse

2007 • 520 citations

Complete Khoisan and Bantu genomes from southern Africa

2010 • 502 citations

Mammalian RNA polymerase II core promoters: insights from genome-wide studies

2007 • 498 citations

Unsupervised pattern discovery in human chromatin structure through genomic segmentation

2013 • 477 citations

Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs

2012 • 452 citations

The Insulator Binding Protein CTCF Positions 20 Nucleosomes around Its Binding Sites across the Human Genome

2008 • 381 citations

Divergence of Transcription Factor Binding Sites Across Related Yeast Species

2007 • 341 citations

AlleleSeq: analysis of allele‐specific expression and binding in a network framework

2011 • 328 citations

The GENCODE pseudogene resource

2012 • 319 citations

High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells

2010 • 314 citations

Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters

2011 • 298 citations

Statistical distributions of nucleosomes: nonrandom locations by a stochastic mechanism

1988 • 291 citations

Modeling gene expression using chromatin features in various cellular contexts

2012 • 270 citations

Gene Regulation in the Third Dimension

2008 • 265 citations

Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors

2012 • 265 citations

Raising the estimate of functional human sequences: Figure 1.

2007 • 237 citations

The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding

2011 • 225 citations

Predictive chromatin signatures in the mammalian genome

2009 • 214 citations

Local DNA Topography Correlates with Functional Noncoding Regions of the Human Genome

2009 • 208 citations

Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements

2012 • 187 citations

Understanding transcriptional regulation by integrative analysis of transcription factor binding data

2012 • 177 citations

Quantitative Models of the Mechanisms That Control Genome-Wide Patterns of Transcription Factor Binding during Early Drosophila Development

2011 • 174 citations

Functional analysis of transcription factor binding sites in human promoters

2012 • 168 citations

Discovery and Annotation of Functional Chromatin Signatures in the Human Genome

2009 • 168 citations

ZNF274 Recruits the Histone Methyltransferase SETDB1 to the 3′ Ends of ZNF Genes

2010 • 164 citations

What fraction of the human genome is functional?

2011 • 151 citations

Reciprocal intronic and exonic histone modification regions in humans

2010 • 124 citations

Personal and population genomics of human regulatory variation

2012 • 112 citations

Cell type-specific binding patterns reveal that TCF7L2 can be tethered to the genome by association with GATA3

2012 • 112 citations

Analysis of variation at transcription factor binding sites in Drosophila and humans

2012 • 103 citations

Widely distributed noncoding purifying selection in the human genome

2007 • 97 citations

The Share of Human Genomic DNA under Selection Estimated from Human-Mouse Genomic Alignments

2003 • 64 citations

Subsampling methods for genomic inference

2010 • 61 citations

Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome

2012 • 55 citations

Chromatin remodeling as a guide to transcriptional regulatory networks in mammals

2003 • 38 citations

Primary sequence and epigenetic determinants of in vivo occupancy of genomic DNA by GATA1

2009 • 28 citations