STAT3 acts through pre-existing nucleosome-depleted regions bound by FOS during an epigenetic switch linking inflammation to cancer

NF-κB and STAT3 signaling pathways collaboratively link inflammation to cancer

(2013) Yihui Fan et al.   Protein & Cell

Genome-wide analysis of STAT3 binding in vivo predicts effectors of the anti-inflammatory response in macrophages

(2012) A. P. Hutchins et al.   BLOOD

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

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

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

PeakAnalyzer: Genome-wide annotation of chromatin binding and modification loci

(2010) Mali Salmon-Divon et al.   BMC BIOINFORMATICS

A Transcriptional Signature and Common Gene Networks Link Cancer with Lipid Metabolism and Diverse Human Diseases

(2010) Heather A. Hirsch et al.   CANCER CELL

NF-κB and STAT3 – key players in liver inflammation and cancer

(2010) Guobin He et al.   CELL RESEARCH

STAT3 Activation of miR-21 and miR-181b-1 via PTEN and CYLD Are Part of the Epigenetic Switch Linking Inflammation to Cancer

(2010) Dimitrios Iliopoulos et al.   MOLECULAR CELL

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

Signal Transducer and Activator of Transcription-3, Inflammation, and Cancer

(2009) Bharat B. Aggarwal et al.   Annals of the New York Academy of Sciences

An Epigenetic Switch Involving NF-κB, Lin28, Let-7 MicroRNA, and IL6 Links Inflammation to Cell Transformation

(2009) Dimitrios Iliopoulos et al.   CELL

STAT3 as a Central Regulator of Tumor Metastases

(2009) Eswaran Devarajan et al.   CURRENT MOLECULAR MEDICINE

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY