Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA

Measuring reproducibility of high-throughput experiments

(2011) Qunhua Li et al.   Annals of Applied Statistics

Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity

(2011) L. Song et al.   GENOME RESEARCH

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

(2011)   PLOS BIOLOGY

ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions

(2011) Naim U Rashid et al.   GENOME BIOLOGY

Nucleosome landscape and control of transcription in the human malaria parasite

(2010) N. Ponts et al.   GENOME RESEARCH

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

(2010) A. P. Boyle et al.   GENOME RESEARCH

Allele-specific and heritable chromatin signatures in humans

(2010) E. Birney et al.   HUMAN MOLECULAR GENETICS

A map of open chromatin in human pancreatic islets

(2010) Kyle J Gaulton et al.   NATURE GENETICS

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

(2010) Antoni Hurtado et al.   NATURE GENETICS

An assessment of histone-modification antibody quality

(2010) Thea A Egelhofer et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The UCSC Genome Browser database: update 2011

(2010) P. A. Fujita et al.   NUCLEIC ACIDS RESEARCH

TagDust--a program to eliminate artifacts from next generation sequencing data

(2009) T. Lassmann et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Improved ChIP-chip analysis by a mixture model approach

(2009) Wei Sun et al.   BMC BIOINFORMATICS

Cell-type selective chromatin remodeling defines the active subset of FOXA1-bound enhancers

(2009) J. Eeckhoute et al.   GENOME RESEARCH

Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements)

(2009) Paul G. Giresi et al.   METHODS

Tissue- and Expression Level-Specific Chromatin Looping at Maize b1 Epialleles

(2009) M. Louwers et al.   PLANT CELL

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

F-Seq: a feature density estimator for high-throughput sequence tags

(2008) A. P. Boyle et al.   BIOINFORMATICS

High-Resolution Mapping and Characterization of Open Chromatin across the Genome

(2008) Alan P. Boyle et al.   CELL

Analyzing real-time PCR data by the comparative CT method

(2008) Thomas D Schmittgen et al.   Nature Protocols

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY