Development of an Illumina-based ChIP-exonuclease method provides insight into FoxA1-DNA binding properties

Cooperativity and Rapid Evolution of Cobound Transcription Factors in Closely Related Mammals

(2013) Klara Stefflova et al.   CELL

Comprehensive prediction in 78 human cell lines reveals rigidity and compactness of transcription factor dimers

(2013) A. Jankowski et al.   GENOME RESEARCH

GATA3 acts upstream of FOXA1 in mediating ESR1 binding by shaping enhancer accessibility

(2012) V. Theodorou et al.   GENOME RESEARCH

Genome-wide structure and organization of eukaryotic pre-initiation complexes

(2012) Ho Sung Rhee et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Breast cancer risk–associated SNPs modulate the affinity of chromatin for FOXA1 and alter gene expression

(2012) Richard Cowper-Sal·lari et al.   NATURE GENETICS

ChIP–seq and beyond: new and improved methodologies to detect and characterize protein–DNA interactions

(2012) Terrence S. Furey   NATURE REVIEWS GENETICS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

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

(2011) Ho Sung Rhee et al.   CELL

BigWig and BigBed: enabling browsing of large distributed datasets

(2010) W. J. Kent et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

FOXA1 is a key determinant of estrogen receptor function and endocrine response

(2010) Antoni Hurtado et al.   NATURE GENETICS

Structure of the FoxM1 DNA-recognition domain bound to a promoter sequence

(2010) D. R. Littler et al.   NUCLEIC ACIDS RESEARCH

ChIP-seq: Using high-throughput sequencing to discover protein–DNA interactions

(2009) Dominic Schmidt et al.   METHODS

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

FoxA1 Translates Epigenetic Signatures into Enhancer-Driven Lineage-Specific Transcription

(2008) Mathieu Lupien et al.   CELL

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY