Comprehensive off-target analysis of dCas9-SAM-mediated HIV reactivation via long noncoding RNA and mRNA profiling

Target Specificity of Cas9 Nuclease via DNA Rearrangement Regulated by the REC2 Domain

(2018) Keewon Sung et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

CRISPR GENOME SURGERY IN THE RETINA IN LIGHT OF OFF-TARGETING

(2018) Galaxy Y. Cho et al.   RETINA-THE JOURNAL OF RETINAL AND VITREOUS DISEASES

Re-engineered RNA-Guided FokI-Nucleases for Improved Genome Editing in Human Cells

(2017) Steven Havlicek et al.   MOLECULAR THERAPY

In Vivo Excision of HIV-1 Provirus by saCas9 and Multiplex Single-Guide RNAs in Animal Models

(2017) Chaoran Yin et al.   MOLECULAR THERAPY

An analysis of possible off target effects following CAS9/CRISPR targeted deletions of neuropeptide gene enhancers from the mouse genome

(2017) Elizabeth Anne Hay et al.   NEUROPEPTIDES

Targeted gene knock-in by homology-directed genome editing using Cas9 ribonucleoprotein and AAV donor delivery

(2017) Thomas Gaj et al.   NUCLEIC ACIDS RESEARCH

Genomic targeting of epigenetic probes using a chemically tailored Cas9 system

(2017) Glen P. Liszczak et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-throughput biochemical profiling reveals sequence determinants of dCas9 off-target binding and unbinding

(2017) Evan A. Boyle et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Linking deregulation of non-coding RNA to the core pathophysiology of Alzheimer’s disease: An integrative review

(2017) Mark J. Millan   PROGRESS IN NEUROBIOLOGY

HIV Latency: Should We Shock or Lock?

(2017) Gilles Darcis et al.   TRENDS IN IMMUNOLOGY

sgRNA Scorer 2.0: A Species-Independent Model To Predict CRISPR/Cas9 Activity

(2017) Raj Chari et al.   ACS Synthetic Biology

Functional screening of guide RNAs targeting the regulatory and structural HIV-1 viral genome for a cure of AIDS

(2016) Chaoran Yin et al.   AIDS

Long noncoding RNAs in prostate cancer: overview and clinical implications

(2016) FelixY Feng et al.   ASIAN JOURNAL OF ANDROLOGY

CRISPR-DO for genome-wide CRISPR design and optimization

(2016) Jian Ma et al.   BIOINFORMATICS

xHMMER3x2: Utilizing HMMER3’s speed and HMMER2’s sensitivity and specificity in the glocal alignment mode for improved large-scale protein domain annotation

(2016) Choon-Kong Yap et al.   Biology Direct

Trimming of sequence reads alters RNA-Seq gene expression estimates

(2016) Claire R. Williams et al.   BMC BIOINFORMATICS

Inheritable Silencing of Endogenous Genes by Hit-and-Run Targeted Epigenetic Editing

(2016) Angelo Amabile et al.   CELL

Editing DNA Methylation in the Mammalian Genome

(2016) X. Shawn Liu et al.   CELL

Targeted Epigenetic Remodeling of Endogenous Loci by CRISPR/Cas9-Based Transcriptional Activators Directly Converts Fibroblasts to Neuronal Cells

(2016) Joshua B. Black et al.   Cell Stem Cell

Excision of HIV-1 DNA by gene editing: a proof-of-concept in vivo study

(2016) R Kaminski et al.   GENE THERAPY

Genome-wide target specificities of CRISPR-Cas9 nucleases revealed by multiplex Digenome-seq

(2016) Daesik Kim et al.   GENOME RESEARCH

Methods for Optimizing CRISPR-Cas9 Genome Editing Specificity

(2016) Josh Tycko et al.   MOLECULAR CELL

Potent and Targeted Activation of Latent HIV-1 Using the CRISPR/dCas9 Activator Complex

(2016) Sheena M Saayman et al.   MOLECULAR THERAPY

CRISPR-mediated Activation of Latent HIV-1 Expression

(2016) Prajit Limsirichai et al.   MOLECULAR THERAPY

Specific Reactivation of Latent HIV-1 by dCas9-SunTag-VP64-mediated Guide RNA Targeting the HIV-1 Promoter

(2016) Haiyan Ji et al.   MOLECULAR THERAPY

High-fidelity CRISPR–Cas9 nucleases with no detectable genome-wide off-target effects

(2016) Benjamin P. Kleinstiver et al.   NATURE

Genome-wide analysis reveals specificities of Cpf1 endonucleases in human cells

(2016) Daesik Kim et al.   NATURE BIOTECHNOLOGY

Editing the epigenome: technologies for programmable transcription and epigenetic modulation

(2016) Pratiksha I Thakore et al.   NATURE METHODS

Comparison of Cas9 activators in multiple species

(2016) Alejandro Chavez et al.   NATURE METHODS

Non-coding RNAs as drug targets

(2016) Masayuki Matsui et al.   NATURE REVIEWS DRUG DISCOVERY

Defining and improving the genome-wide specificities of CRISPR–Cas9 nucleases

(2016) Shengdar Q. Tsai et al.   NATURE REVIEWS GENETICS

Epigenome Editing: State of the Art, Concepts, and Perspectives

(2016) Goran Kungulovski et al.   TRENDS IN GENETICS

GUIDE-Seq to Detect Genome-wide Double-Stranded Breaks in Plants

(2016) Lina Shi et al.   TRENDS IN PLANT SCIENCE

The lncRNA landscape of breast cancer reveals a role for DSCAM-AS1 in breast cancer progression

(2016) Yashar S. Niknafs et al.   Nature Communications

lncRNA profiling in early-stage chronic lymphocytic leukemia identifies transcriptional fingerprints with relevance in clinical outcome

(2016) D Ronchetti et al.   Blood Cancer Journal

Achieving Plant CRISPR Targeting that Limits Off-Target Effects

(2016) Jeffrey D. Wolt et al.   Plant Genome

Reprogrammable CRISPR/Cas9-based system for inducing site-specific DNA methylation

(2016) James I. McDonald et al.   Biology Open

Targeted HIV-1 Latency Reversal Using CRISPR/Cas9-Derived Transcriptional Activator Systems

(2016) Julia K. Bialek et al.   PLoS One

Elimination of HIV-1 Genomes from Human T-lymphoid Cells by CRISPR/Cas9 Gene Editing

(2016) Rafal Kaminski et al.   Scientific Reports

Negative Feedback Regulation of HIV-1 by Gene Editing Strategy

(2016) Rafal Kaminski et al.   Scientific Reports

Comprehensive evaluation of AmpliSeq transcriptome, a novel targeted whole transcriptome RNA sequencing methodology for global gene expression analysis

(2015) Wenli Li et al.   BMC GENOMICS

The therapeutic application of CRISPR/Cas9 technologies for HIV

(2015) Sheena Saayman et al.   EXPERT OPINION ON BIOLOGICAL THERAPY

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

TCF4 gene polymorphism is associated with cognition in patients with schizophrenia and healthy controls

(2015) Li Hui et al.   JOURNAL OF PSYCHIATRIC RESEARCH

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

(2015) Silvana Konermann et al.   NATURE

In vivo genome editing using Staphylococcus aureus Cas9

(2015) F. Ann Ran et al.   NATURE

Unbiased detection of off-target cleavage by CRISPR-Cas9 and TALENs using integrase-defective lentiviral vectors

(2015) Xiaoling Wang et al.   NATURE BIOTECHNOLOGY

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

(2015) Isaac B Hilton et al.   NATURE BIOTECHNOLOGY

Highly efficient Cas9-mediated transcriptional programming

(2015) Alejandro Chavez et al.   NATURE METHODS

Digenome-seq: genome-wide profiling of CRISPR-Cas9 off-target effects in human cells

(2015) Daesik Kim et al.   NATURE METHODS

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

(2015) Pratiksha I Thakore et al.   NATURE METHODS

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Specific induction of endogenous viral restriction factors using CRISPR/Cas-derived transcriptional activators

(2015) Hal P. Bogerd et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome editing at the crossroads of delivery, specificity, and fidelity

(2015) Ignazio Maggio et al.   TRENDS IN BIOTECHNOLOGY

Genome-editing tools for stem cell biology

(2015) E A Vasileva et al.   Cell Death & Disease

Somatic CRISPR/Cas9-mediated tumour suppressor disruption enables versatile brain tumour modelling

(2015) Marc Zuckermann et al.   Nature Communications

CRISPR/gRNA-directed synergistic activation mediator (SAM) induces specific, persistent and robust reactivation of the HIV-1 latent reservoirs

(2015) Yonggang Zhang et al.   Scientific Reports

Application of CRISPR/Cas9 for biomedical discoveries

(2015) Sean M. Riordan et al.   Cell and Bioscience

Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases

(2014) S. Bae et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Low Incidence of Off-Target Mutations in Individual CRISPR-Cas9 and TALEN Targeted Human Stem Cell Clones Detected by Whole-Genome Sequencing

(2014) Adrian Veres et al.   Cell Stem Cell

Whole-Genome Sequencing Analysis Reveals High Specificity of CRISPR/Cas9 and TALEN-Based Genome Editing in Human iPSCs

(2014) Cory Smith et al.   Cell Stem Cell

CRISPR-Cas systems for editing, regulating and targeting genomes

(2014) Jeffry D Sander 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

GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases

(2014) Shengdar Q Tsai et al.   NATURE BIOTECHNOLOGY

Genome-wide detection of DNA double-stranded breaks induced by engineered nucleases

(2014) Richard L Frock et al.   NATURE BIOTECHNOLOGY

RNA-directed gene editing specifically eradicates latent and prevents new HIV-1 infection

(2014) W. Hu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Targeted and genome-wide sequencing reveal single nucleotide variations impacting specificity of Cas9 in human stem cells

(2014) Luhan Yang et al.   Nature Communications

Modularized CRISPR/dCas9 Effector Toolkit for Target-Specific Gene Regulation

(2014) Michael Agne et al.   ACS Synthetic Biology

COSMID: A Web-based Tool for Identifying and Validating CRISPR/Cas Off-target Sites

(2014) Thomas J Cradick et al.   Molecular Therapy-Nucleic Acids

Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression

(2013) Lei S. Qi et al.   CELL

Double Nicking by RNA-Guided CRISPR Cas9 for Enhanced Genome Editing Specificity

(2013) F. Ann Ran et al.   CELL

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

(2013) Luke A. Gilbert et al.   CELL

Multiplexed activation of endogenous genes by CRISPR-on, an RNA-guided transcriptional activator system

(2013) Albert W Cheng et al.   CELL RESEARCH

Review: Alternative Splicing (AS) of Genes As An Approach for Generating Protein Complexity

(2013) Bishakha Roy et al.   CURRENT GENOMICS

Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases

(2013) S. W. Cho et al.   GENOME RESEARCH

DNA targeting specificity of RNA-guided Cas9 nucleases

(2013) Patrick D Hsu et al.   NATURE BIOTECHNOLOGY

High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity

(2013) Vikram Pattanayak et al.   NATURE BIOTECHNOLOGY

High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells

(2013) Yanfang Fu 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

RNA-programmed genome editing in human cells

(2013) Martin Jinek et al.   eLife

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

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

(2012) M. Jinek et al.   SCIENCE

Epigenetic Regulation by Long Noncoding RNAs

(2012) J. T. Lee   SCIENCE

Transcript amplification from single bacterium for transcriptome analysis

(2011) Y. Kang et al.   GENOME RESEARCH

Differential Inhibition of Human Immunodeficiency Virus Type 1 in Peripheral Blood Mononuclear Cells and TZM-bl Cells by Endotoxin-Mediated Chemokine and Gamma Interferon Production

(2010) Anthony R. Geonnotti et al.   AIDS RESEARCH AND HUMAN RETROVIRUSES

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Analysis and design of RNA sequencing experiments for identifying isoform regulation

(2010) Yarden Katz et al.   NATURE METHODS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Post-transcriptional processing generates a diversity of 5′-modified long and short RNAs

(2009)   NATURE

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Expression of a noncoding RNA is elevated in Alzheimer's disease and drives rapid feed-forward regulation of β-secretase

(2008) Mohammad Ali Faghihi et al.   NATURE MEDICINE