RAD: a web application to identify region associated differentially expressed genes

Co-targeting RNA Polymerases IV and V Promotes Efficient De Novo DNA Methylation in Arabidopsis

(2019) Javier Gallego-Bartolomé et al.   CELL

BART: a transcription factor prediction tool with query gene sets or epigenomic profiles

(2018) Zhenjia Wang et al.   BIOINFORMATICS

TFAP2C regulates transcription in human naive pluripotency by opening enhancers

(2018) William A. Pastor et al.   NATURE CELL BIOLOGY

A DNA methylation reader complex that enhances gene transcription

(2018) C. Jake Harris et al.   SCIENCE

Transcriptional enhancers: from properties to genome-wide predictions

(2014) Daria Shlyueva et al.   NATURE REVIEWS GENETICS

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Target analysis by integration of transcriptome and ChIP-seq data with BETA

(2013) Su Wang et al.   Nature Protocols

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Dynamic Regulation of Nucleosome Positioning in the Human Genome

(2008) Dustin E. Schones et al.   CELL

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

(2008) Alan P. Boyle et al.   CELL

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

(2008) Shawn J. Cokus et al.   NATURE