Annotation of functional variation in personal genomes using RegulomeDB

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

2009 • 20,860 citations

An integrated encyclopedia of DNA elements in the human genome

2012 • 16,874 citations

Model-based Analysis of ChIP-Seq (MACS)

2008 • 15,719 citations

Finding the missing heritability of complex diseases

2009 • 8,030 citations

A map of human genome variation from population-scale sequencing

2010 • 7,765 citations

A haplotype map of the human genome

2005 • 5,856 citations

Table S2: Trans-factors and trinucleotide repeat instability Trans-factor

2010 • 5,471 citations

GENCODE: The reference human genome annotation for The ENCODE Project

2012 • 4,557 citations

A second generation human haplotype map of over 3.1 million SNPs

2007 • 4,436 citations

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

2009 • 4,036 citations

TRANSFAC(R) and its module TRANSCompel(R): transcriptional gene regulation in eukaryotes

2005 • 2,172 citations

HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants

2011 • 2,130 citations

Understanding mechanisms underlying human gene expression variation with RNA sequencing

2010 • 1,303 citations

Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes

2012 • 1,242 citations

Human Genome Sequencing Using Unchained Base Reads on Self-Assembling DNA Nanoarrays

2009 • 1,207 citations

Population genomics of human gene expression

2007 • 1,146 citations

VISTA Enhancer Browser--a database of tissue-specific human enhancers

2006 • 1,053 citations

Discovery and characterization of chromatin states for systematic annotation of the human genome

2010 • 1,037 citations

Diversity and Complexity in DNA Recognition by Transcription Factors

2009 • 982 citations

Mapping the Genetic Architecture of Gene Expression in Human Liver

2008 • 935 citations

Design and analysis of ChIP-seq experiments for DNA-binding proteins

2008 • 909 citations

Densely Interconnected Transcriptional Circuits Control Cell States in Human Hematopoiesis

2011 • 900 citations

Transcriptome genetics using second generation sequencing in a Caucasian population

2010 • 826 citations

Abundant Quantitative Trait Loci Exist for DNA Methylation and Gene Expression in Human Brain

2010 • 777 citations

Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution

2011 • 750 citations

Common Regulatory Variation Impacts Gene Expression in a Cell Type–Dependent Manner

2009 • 738 citations

Linking disease associations with regulatory information in the human genome

2012 • 710 citations

JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update

2007 • 687 citations

Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities

2006 • 680 citations

DNase I sensitivity QTLs are a major determinant of human expression variation

2012 • 654 citations

Variation in Homeodomain DNA Binding Revealed by High-Resolution Analysis of Sequence Preferences

2008 • 618 citations

Genetics and Beyond – The Transcriptome of Human Monocytes and Disease Susceptibility

2010 • 590 citations

Variation in Transcription Factor Binding Among Humans

2010 • 568 citations

High-Resolution Mapping of Expression-QTLs Yields Insight into Human Gene Regulation

2008 • 561 citations

Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo

2010 • 552 citations

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

2010 • 551 citations

A survey of genetic human cortical gene expression

2007 • 473 citations

Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities

2010 • 432 citations

UniPROBE: an online database of protein binding microarray data on protein-DNA interactions

2008 • 369 citations

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

2011 • 328 citations

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

2010 • 314 citations

Association of a functional variant downstream of TNFAIP3 with systemic lupus erythematosus

2011 • 268 citations

Inhibition of calpains improves memory and synaptic transmission in a mouse model of Alzheimer disease

2008 • 203 citations

Differentiation-Specific Histone Modifications Reveal Dynamic Chromatin Interactions and Partners for the Intestinal Transcription Factor CDX2

2010 • 202 citations

DNA Specificity Determinants Associate with Distinct Transcription Factor Functions

2009 • 183 citations

Genome-Wide Promoter Analysis of the SOX4 Transcriptional Network in Prostate Cancer Cells

2009 • 179 citations

Regulation of nucleosome landscape and transcription factor targeting at tissue-specific enhancers by BRG1

2011 • 177 citations

Differential genomic targeting of the transcription factor TAL1 in alternate haematopoietic lineages

2010 • 136 citations

Efficient and accurate P-value computation for Position Weight Matrices

2007 • 126 citations

GABP controls a critical transcription regulatory module that is essential for maintenance and differentiation of hematopoietic stem/progenitor cells

2010 • 79 citations

Genome-Wide Profiling of H3K56 Acetylation and Transcription Factor Binding Sites in Human Adipocytes

2011 • 55 citations

Cooperative transcription factor associations discovered using regulatory variation

2011 • 53 citations