HDAC inhibitors cause site-specific chromatin remodeling at PU.1-bound enhancers in K562 cells

HDAC inhibitors still need a home run, despite recent approval

(2015) Malini Guha   NATURE REVIEWS DRUG DISCOVERY

Acute promyelocytic leukemia: where did we start, where are we now and the future

(2015) C C Coombs et al.   Blood Cancer Journal

New and emerging HDAC inhibitors for cancer treatment

(2014) Alison C. West et al.   JOURNAL OF CLINICAL INVESTIGATION

Comprehensive molecular characterization of urothelial bladder carcinoma

(2014)   NATURE

Histone deacetylases and their inhibitors in cancer, neurological diseases and immune disorders

(2014) Katrina J. Falkenberg et al.   NATURE REVIEWS DRUG DISCOVERY

The hematopoietic regulator TAL1 is required for chromatin looping between the β-globin LCR and human γ-globin genes to activate transcription

(2014) Won Ju Yun et al.   NUCLEIC ACIDS RESEARCH

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

MEME-ChIP: motif analysis of large DNA datasets

(2011) Philip Machanick et al.   BIOINFORMATICS

Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions

(2011) Gabriel E. Zentner et al.   GENOME RESEARCH

Pluripotency-related, Valproic Acid (VPA)-induced Genome-wide Histone H3 Lysine 9 (H3K9) Acetylation Patterns in Embryonic Stem Cells

(2011) Hadas Hezroni et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo

(2010) Gong-Hong Wei et al.   EMBO JOURNAL

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

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

Identification and Characterization of Enhancers Controlling the Inflammatory Gene Expression Program in Macrophages

(2010) Serena Ghisletti et al.   IMMUNITY

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

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Polycomb group protein-mediated repression of transcription

(2010) Lluís Morey et al.   TRENDS IN BIOCHEMICAL SCIENCES

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Genome-wide Mapping of HATs and HDACs Reveals Distinct Functions in Active and Inactive Genes

(2009) Zhibin Wang et al.   CELL

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