Transcription-factor occupancy at HOT regions quantitatively predicts RNA polymerase recruitment in five human cell lines

A Transcription Factor Collective Defines Cardiac Cell Fate and Reflects Lineage History

(2012) Guillaume Junion et al.   CELL

HOT regions function as patterned developmental enhancers and have a distinct cis-regulatory signature

(2012) E. Z. Kvon et al.   GENES & DEVELOPMENT

Understanding transcriptional regulation by integrative analysis of transcription factor binding data

(2012) C. Cheng et al.   GENOME RESEARCH

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

(2012) J. Wang et al.   GENOME RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development

(2012) Stefan Bonn et al.   NATURE GENETICS

5′ end–centered expression profiling using cap-analysis gene expression and next-generation sequencing

(2012) Hazuki Takahashi et al.   Nature Protocols

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

(2011) Ho Sung Rhee et al.   CELL

A cis-regulatory map of the Drosophila genome

(2011) Nicolas Nègre et al.   NATURE

The transcription factor BATF controls the global regulators of class-switch recombination in both B cells and T cells

(2011) Wataru Ise et al.   NATURE IMMUNOLOGY

An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

(2010) Timothy Ravasi et al.   CELL

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

(2010) M. B. Gerstein et al.   SCIENCE

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

A census of human transcription factors: function, expression and evolution

(2009) Juan M. Vaquerizas et al.   NATURE REVIEWS GENETICS

Cohesin mediates transcriptional insulation by CCCTC-binding factor

(2008) Kerstin S. Wendt et al.   NATURE

Transcription factor Mef2c is required for B cell proliferation and survival after antigen receptor stimulation

(2008) Peter R Wilker et al.   NATURE IMMUNOLOGY

Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data

(2008) Anton Valouev et al.   NATURE METHODS