Wellington-bootstrap: differential DNase-seq footprinting identifies cell-type determining transcription factors

DNase Footprint Signatures Are Dictated by Factor Dynamics and DNA Sequence

(2014) Myong-Hee Sung et al.   MOLECULAR CELL

Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape

(2014) Richard I Sherwood et al.   NATURE BIOTECHNOLOGY

Mapping of transcription factor motifs in active chromatin identifies IRF5 as key regulator in classical Hodgkin lymphoma

(2014) Stephan Kreher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification

(2013) Housheng Hansen He et al.   NATURE METHODS

Wellington: a novel method for the accurate identification of digital genomic footprints from DNase-seq data

(2013) Jason Piper et al.   NUCLEIC ACIDS RESEARCH

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics

(2012) Housheng Hansen He et al.   GENOME RESEARCH

Regulation of Neural Stem Cell Differentiation by Transcription Factors HNF4-1 and MAZ-1

(2012) Jiao Wang et al.   MOLECULAR NEUROBIOLOGY

An expansive human regulatory lexicon encoded in transcription factor footprints

(2012) Shane Neph et al.   NATURE

Two distinct auto-regulatory loops operate at the PU.1 locus in B cells and myeloid cells

(2011) M. Leddin et al.   BLOOD

Structure and function of active chromatin and DNase I hypersensitive sites

(2011) Peter N. Cockerill   FEBS Journal

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

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

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

(2010) R. Pique-Regi et al.   GENOME RESEARCH

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

The NIH Roadmap Epigenomics Mapping Consortium

(2010) Bradley E Bernstein et al.   NATURE BIOTECHNOLOGY

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

(2009) Jay R Hesselberth et al.   NATURE METHODS

C/EBPα expression is partially regulated by C/EBPβ in response to DNA damage and C/EBPα-deficient fibroblasts display an impaired G1 checkpoint

(2009) R Ranjan et al.   ONCOGENE

BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources

(2009) Chunlei Wu et al.   GENOME BIOLOGY

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

(2008) Alan P. Boyle et al.   CELL