Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements

Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators

(2015) Lauren R. Polstein et al.   GENOME RESEARCH

Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex

(2015) Silvana Konermann et al.   NATURE

Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers

(2015) Isaac B Hilton et al.   NATURE BIOTECHNOLOGY

Functional annotation of native enhancers with a Cas9–histone demethylase fusion

(2015) Nicola A Kearns et al.   NATURE METHODS

Highly efficient Cas9-mediated transcriptional programming

(2015) Alejandro Chavez et al.   NATURE METHODS

A genome-wide analysis of Cas9 binding specificity using ChIP-seq and targeted sequence capture

(2015) Henriette O'Geen et al.   NUCLEIC ACIDS RESEARCH

Reactivation of Developmentally Silenced Globin Genes by Forced Chromatin Looping

(2014) Wulan Deng et al.   CELL

Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation

(2014) Luke A. Gilbert et al.   CELL

Multiplexed and Programmable Regulation of Gene Networks with an Integrated RNA and CRISPR/Cas Toolkit in Human Cells

(2014) Lior Nissim et al.   MOLECULAR CELL

Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells

(2014) Xuebing Wu et al.   NATURE BIOTECHNOLOGY

Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease

(2014) Cem Kuscu et al.   NATURE BIOTECHNOLOGY

Multiplex CRISPR/Cas9-based genome engineering from a single lentiviral vector

(2014) Ami M. Kabadi et al.   NUCLEIC ACIDS RESEARCH

Analysis of an artificial zinc finger epigenetic modulator: widespread binding but limited regulation

(2014) Matthew R. Grimmer et al.   NUCLEIC ACIDS RESEARCH

Comparison of TALE designer transcription factors and the CRISPR/dCas9 in regulation of gene expression by targeting enhancers

(2014) Xuefei Gao et al.   NUCLEIC ACIDS RESEARCH

A CRISPR/Cas9-Based System for Reprogramming Cell Lineage Specification

(2014) Syandan Chakraborty et al.   Stem Cell Reports

CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes

(2013) Luke A. Gilbert et al.   CELL

Targeted DNA demethylation and activation of endogenous genes using programmable TALE-TET1 fusion proteins

(2013) Morgan L Maeder et al.   NATURE BIOTECHNOLOGY

Locus-specific editing of histone modifications at endogenous enhancers

(2013) Eric M Mendenhall et al.   NATURE BIOTECHNOLOGY

RNA-guided gene activation by CRISPR-Cas9–based transcription factors

(2013) Pablo Perez-Pinera et al.   NATURE METHODS

CRISPR RNA–guided activation of endogenous human genes

(2013) Morgan L Maeder et al.   NATURE METHODS

RNA-Guided Human Genome Engineering via Cas9

(2013) P. Mali et al.   SCIENCE

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

Dynamics and Memory of Heterochromatin in Living Cells

(2012) Nathaniel A. Hathaway et al.   CELL

Epigenetic reprogramming of cancer cells via targeted DNA methylation

(2012) Ashley G. Rivenbark et al.   Epigenetics

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity

(2012) M. Jinek et al.   SCIENCE

Comprehensive interrogation of natural TALE DNA-binding modules and transcriptional repressor domains

(2012) Le Cong et al.   Nature Communications

NuRD-mediated deacetylation of H3K27 facilitates recruitment of Polycomb Repressive Complex 2 to direct gene repression

(2011) Nicola Reynolds et al.   EMBO JOURNAL

Transposase mediated construction of RNA-seq libraries

(2011) J. Gertz et al.   GENOME RESEARCH

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

KRAB–Zinc Finger Proteins and KAP1 Can Mediate Long-Range Transcriptional Repression through Heterochromatin Spreading

(2010) Anna C. Groner et al.   PLoS Genetics

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

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

(2008) Alan P. Boyle et al.   CELL

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY