Measurement of differential chromatin interactions with absolute quantification of architecture (AQuA-HiChIP)

Histone hyperacetylation disrupts core gene regulatory architecture in rhabdomyosarcoma

(2019) Berkley E. Gryder et al.   NATURE GENETICS

The dTAG system for immediate and target-specific protein degradation

(2018) Behnam Nabet et al.   Nature Chemical Biology

MEK inhibition induces MYOG and remodels super-enhancers in RAS-driven rhabdomyosarcoma

(2018) Marielle E. Yohe et al.   Science Translational Medicine

HiCcompare: an R-package for joint normalization and comparison of HI-C datasets

(2018) John C. Stansfield et al.   BMC BIOINFORMATICS

Trac-looping measures genome structure and chromatin accessibility

(2018) Binbin Lai et al.   NATURE METHODS

Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements

(2017) Maxwell R Mumbach et al.   NATURE GENETICS

PAX3–FOXO1 Establishes Myogenic Super Enhancers and Confers BET Bromodomain Vulnerability

(2017) Berkley E. Gryder et al.   Cancer Discovery

Smarca4 ATPase mutations disrupt direct eviction of PRC1 from chromatin

(2016) Benjamin Z Stanton et al.   NATURE GENETICS

HiChIP: efficient and sensitive analysis of protein-directed genome architecture

(2016) Maxwell R Mumbach et al.   NATURE METHODS

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom

(2016) Neva C. Durand et al.   Cell Systems

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Quantitative ChIP-Seq Normalization Reveals Global Modulation of the Epigenome

(2014) David A. Orlando et al.   Cell Reports

ENCODE Project Writes Eulogy for Junk DNA

(2012) E. Pennisi   SCIENCE

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

An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

An auxin-based degron system for the rapid depletion of proteins in nonplant cells

(2009) Kohei Nishimura et al.   NATURE METHODS

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

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