PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls

Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

1995 • 93,704 citations

The Human Genome Browser at UCSC

2002 • 9,920 citations

A Direct Approach to False Discovery Rates

2002 • 5,455 citations

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

2007 • 5,117 citations

SOAP: short oligonucleotide alignment program

2008 • 3,006 citations

Genome-Wide Mapping of in Vivo Protein-DNA Interactions

2007 • 2,764 citations

Mapping short DNA sequencing reads and calling variants using mapping quality scores

2008 • 2,646 citations

The positive false discovery rate: a Bayesian interpretation and the q-value

2003 • 2,137 citations

Genome-Wide Location and Function of DNA Binding Proteins

2000 • 1,720 citations

Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing

2007 • 1,389 citations

Paired-End Mapping Reveals Extensive Structural Variation in the Human Genome

2007 • 1,150 citations

A Global Map of p53 Transcription-Factor Binding Sites in the Human Genome

2006 • 1,137 citations

Mapping and sequencing of structural variation from eight human genomes

2008 • 1,132 citations

Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF

2001 • 1,101 citations

Unbiased Mapping of Transcription Factor Binding Sites along Human Chromosomes 21 and 22 Points to Widespread Regulation of Noncoding RNAs

2004 • 1,079 citations

FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin

2006 • 899 citations

Mapping of transcription factor binding regions in mammalian cells by ChIP: Comparison of array- and sequencing-based technologies

2007 • 196 citations

ChIP-chip: A genomic approach for identifying transcription factor binding sites

2002 • 176 citations

An analysis of the feasibility of short read sequencing

2005 • 126 citations

Mapping DNA-protein interactions in large genomes by sequence tag analysis of genomic enrichment

2004 • 104 citations

Modeling ChIP Sequencing In Silico with Applications

2008 • 101 citations

Tilescope: online analysis pipeline for high-density tiling microarray data

2007 • 50 citations

Assessing the need for sequence-based normalization in tiling microarray experiments

2007 • 40 citations

Chipper: discovering transcription-factor targets from chromatin immunoprecipitation microarrays using variance stabilization.

2005 • 39 citations